diff --git a/papers/_posts/2008-01-01-sample-align-d--a-high-performance-multiple-sequence-alignment-system-using-phylogenetic-sampling-and-domain-decomposition.md b/papers/_posts/2008-01-01-sample-align-d--a-high-performance-multiple-sequence-alignment-system-using-phylogenetic-sampling-and-domain-decomposition.md index 01a2740e..fe7b0e6d 100644 --- a/papers/_posts/2008-01-01-sample-align-d--a-high-performance-multiple-sequence-alignment-system-using-phylogenetic-sampling-and-domain-decomposition.md +++ b/papers/_posts/2008-01-01-sample-align-d--a-high-performance-multiple-sequence-alignment-system-using-phylogenetic-sampling-and-domain-decomposition.md @@ -1,10 +1,10 @@ --- layout: paper title: "Sample-align-d: A high performance multiple sequence alignment system using phylogenetic sampling and domain decomposition" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2008-01-01-sample-align-d--a-high-performance-multiple-sequence-alignment-system-using-phylogenetic-sampling-and-domain-decomposition authors: "Saeed, Fahad; Khokhar, Ashfaq; " year: "2008" -journal: IEEE +journal: "IEEE 2008 IEEE International Symposium on Parallel and Distributed Processing" volume: issue: pages: 1-9 diff --git a/papers/_posts/2009-01-01-a-domain-decomposition-strategy-for-alignment-of-multiple-biological-sequences-on-multiprocessor-platforms.md b/papers/_posts/2009-01-01-a-domain-decomposition-strategy-for-alignment-of-multiple-biological-sequences-on-multiprocessor-platforms.md index a2d2b595..5516fbd5 100644 --- a/papers/_posts/2009-01-01-a-domain-decomposition-strategy-for-alignment-of-multiple-biological-sequences-on-multiprocessor-platforms.md +++ b/papers/_posts/2009-01-01-a-domain-decomposition-strategy-for-alignment-of-multiple-biological-sequences-on-multiprocessor-platforms.md @@ -1,10 +1,10 @@ --- layout: paper title: "A domain decomposition strategy for alignment of multiple biological sequences on multiprocessor platforms" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2009-01-01-a-domain-decomposition-strategy-for-alignment-of-multiple-biological-sequences-on-multiprocessor-platforms authors: "Saeed, Fahad; Khokhar, Ashfaq; " year: "2009" -journal: Academic Press +journal: "Academic Press Journal of Parallel and Distributed Computing" volume: 69 issue: pages: 666-677 diff --git a/papers/_posts/2009-01-01-an-overview-of-multiple-sequence-alignment-systems.md b/papers/_posts/2009-01-01-an-overview-of-multiple-sequence-alignment-systems.md index 481edf49..f19406a5 100644 --- a/papers/_posts/2009-01-01-an-overview-of-multiple-sequence-alignment-systems.md +++ b/papers/_posts/2009-01-01-an-overview-of-multiple-sequence-alignment-systems.md @@ -1,7 +1,7 @@ --- layout: paper title: "An Overview of Multiple Sequence Alignment Systems" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2009-01-01-an-overview-of-multiple-sequence-alignment-systems authors: "Saeed, Fahad; Khokhar, Ashfaq; " year: "2009" journal: diff --git a/papers/_posts/2009-01-01-multiple-sequence-alignment-system-for-pyrosequencing-reads.md b/papers/_posts/2009-01-01-multiple-sequence-alignment-system-for-pyrosequencing-reads.md index 534e1531..999aac99 100644 --- a/papers/_posts/2009-01-01-multiple-sequence-alignment-system-for-pyrosequencing-reads.md +++ b/papers/_posts/2009-01-01-multiple-sequence-alignment-system-for-pyrosequencing-reads.md @@ -1,10 +1,10 @@ --- layout: paper title: "Multiple sequence alignment system for pyrosequencing reads" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2009-01-01-multiple-sequence-alignment-system-for-pyrosequencing-reads authors: "Saeed, Fahad; Khokhar, Ashfaq; Zagordi, Osvaldo; Beerenwinkel, Niko; " year: "2009" -journal: Springer Berlin Heidelberg +journal: "Springer Berlin Heidelberg Bioinformatics and Computational Biology: First International Conference, BICoB 2009, New Orleans, LA, USA, April 8-10, 2009. Proceedings" volume: issue: pages: 362-375 diff --git a/papers/_posts/2009-01-01-pyro-align--sample-align-based-multiple-alignment-system-for-pyrosequencing-reads-of-large-number.md b/papers/_posts/2009-01-01-pyro-align--sample-align-based-multiple-alignment-system-for-pyrosequencing-reads-of-large-number.md index 54d5eedb..1549031d 100644 --- a/papers/_posts/2009-01-01-pyro-align--sample-align-based-multiple-alignment-system-for-pyrosequencing-reads-of-large-number.md +++ b/papers/_posts/2009-01-01-pyro-align--sample-align-based-multiple-alignment-system-for-pyrosequencing-reads-of-large-number.md @@ -1,7 +1,7 @@ --- layout: paper title: "Pyro-align: Sample-align based multiple alignment system for pyrosequencing reads of large number" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2009-01-01-pyro-align--sample-align-based-multiple-alignment-system-for-pyrosequencing-reads-of-large-number authors: "Saeed, Fahad; " year: "2009" journal: diff --git a/papers/_posts/2010-01-01-a-graph-theoretic-framework-for-efficient-computation-of-hmm-based-motif-finder.md b/papers/_posts/2010-01-01-a-graph-theoretic-framework-for-efficient-computation-of-hmm-based-motif-finder.md index 6415eb7c..c0dc26da 100644 --- a/papers/_posts/2010-01-01-a-graph-theoretic-framework-for-efficient-computation-of-hmm-based-motif-finder.md +++ b/papers/_posts/2010-01-01-a-graph-theoretic-framework-for-efficient-computation-of-hmm-based-motif-finder.md @@ -1,7 +1,7 @@ --- layout: paper title: "A graph-theoretic framework for efficient computation of HMM based motif finder" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2010-01-01-a-graph-theoretic-framework-for-efficient-computation-of-hmm-based-motif-finder authors: "Saeed, Fahad; Burger, Lukas; Khokhar, Ashfaq; Zavolan, Mihaela; " year: "2010" journal: diff --git a/papers/_posts/2010-01-01-high-performance-computational-biology-algorithms.md b/papers/_posts/2010-01-01-high-performance-computational-biology-algorithms.md index d46868a1..766722e8 100644 --- a/papers/_posts/2010-01-01-high-performance-computational-biology-algorithms.md +++ b/papers/_posts/2010-01-01-high-performance-computational-biology-algorithms.md @@ -1,10 +1,10 @@ --- layout: paper title: "High performance computational biology algorithms" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2010-01-01-high-performance-computational-biology-algorithms authors: "Saeed, Fahad; " year: "2010" -journal: University of Illinois at Chicago +journal: "University of Illinois at Chicago" volume: issue: pages: diff --git a/papers/_posts/2010-01-01-parallel-algorithm-for-center-star-sequence-and-alignments-with-applications-to-short-reads.md b/papers/_posts/2010-01-01-parallel-algorithm-for-center-star-sequence-and-alignments-with-applications-to-short-reads.md index d0c7ba97..db549dac 100644 --- a/papers/_posts/2010-01-01-parallel-algorithm-for-center-star-sequence-and-alignments-with-applications-to-short-reads.md +++ b/papers/_posts/2010-01-01-parallel-algorithm-for-center-star-sequence-and-alignments-with-applications-to-short-reads.md @@ -1,7 +1,7 @@ --- layout: paper title: "Parallel Algorithm for Center Star Sequence and Alignments with Applications to Short Reads" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2010-01-01-parallel-algorithm-for-center-star-sequence-and-alignments-with-applications-to-short-reads authors: "Saeed, Fahad; Khokhar, Ashfaq; " year: "2010" journal: diff --git "a/papers/_posts/2011-01-01-large\342\200\220scale-itraq\342\200\220based-quantification-of-phosphorylation-changes-during-vasopressin-signaling.md" "b/papers/_posts/2011-01-01-large\342\200\220scale-itraq\342\200\220based-quantification-of-phosphorylation-changes-during-vasopressin-signaling.md" index c2cfbaaa..4b11a4e5 100644 --- "a/papers/_posts/2011-01-01-large\342\200\220scale-itraq\342\200\220based-quantification-of-phosphorylation-changes-during-vasopressin-signaling.md" +++ "b/papers/_posts/2011-01-01-large\342\200\220scale-itraq\342\200\220based-quantification-of-phosphorylation-changes-during-vasopressin-signaling.md" @@ -1,10 +1,10 @@ --- layout: paper title: "Large‐scale iTRAQ‐based quantification of phosphorylation changes during vasopressin signaling" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2011-01-01-large‐scale-itraq‐based-quantification-of-phosphorylation-changes-during-vasopressin-signaling authors: "Hoffert, Jason; Pisitkun, T; Saeed, F; Song, J; Knepper, M; " year: "2011" -journal: Federation of American Societies for Experimental Biology +journal: "Federation of American Societies for Experimental Biology" volume: issue: pages: diff --git "a/papers/_posts/2011-01-01-mapping\342\200\220based-temporal-pattern-mining-algorithm-mtpma-identifies-unique-clusters-of-phosphopeptides-regulated-by-vasopressin-in-collecting-duct.md" "b/papers/_posts/2011-01-01-mapping\342\200\220based-temporal-pattern-mining-algorithm-mtpma-identifies-unique-clusters-of-phosphopeptides-regulated-by-vasopressin-in-collecting-duct.md" index 988eb113..39c0b7fe 100644 --- "a/papers/_posts/2011-01-01-mapping\342\200\220based-temporal-pattern-mining-algorithm-mtpma-identifies-unique-clusters-of-phosphopeptides-regulated-by-vasopressin-in-collecting-duct.md" +++ "b/papers/_posts/2011-01-01-mapping\342\200\220based-temporal-pattern-mining-algorithm-mtpma-identifies-unique-clusters-of-phosphopeptides-regulated-by-vasopressin-in-collecting-duct.md" @@ -1,10 +1,10 @@ --- layout: paper title: "Mapping‐based temporal pattern mining algorithm (MTPMA) identifies unique clusters of phosphopeptides regulated by vasopressin in collecting duct" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2011-01-01-mapping‐based-temporal-pattern-mining-algorithm-mtpma-identifies-unique-clusters-of-phosphopeptides-regulated-by-vasopressin-in-collecting-duct authors: "Saeed, Fahad; Hoffert, Jason; Pisitkun, Trairak; Knepper, Mark; " year: "2011" -journal: Federation of American Societies for Experimental Biology +journal: "Federation of American Societies for Experimental Biology" volume: issue: pages: diff --git a/papers/_posts/2011-01-01-mining-temporal-patterns-from-itraq-mass-spectrometry-lc-ms-ms-data.md b/papers/_posts/2011-01-01-mining-temporal-patterns-from-itraq-mass-spectrometry-lc-ms-ms-data.md index 7aeff582..eae3d086 100644 --- a/papers/_posts/2011-01-01-mining-temporal-patterns-from-itraq-mass-spectrometry-lc-ms-ms-data.md +++ b/papers/_posts/2011-01-01-mining-temporal-patterns-from-itraq-mass-spectrometry-lc-ms-ms-data.md @@ -1,7 +1,7 @@ --- layout: paper title: "Mining temporal patterns from iTRAQ mass spectrometry (LC-MS/MS) data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2011-01-01-mining-temporal-patterns-from-itraq-mass-spectrometry-lc-ms-ms-data authors: "Saeed, Fahad; Pisitkun, Trairak; Knepper, Mark A; Hoffert, Jason D; " year: "2011" journal: diff --git a/papers/_posts/2012-01-01-a-high-performance-multiple-sequence-alignment-system-for-pyrosequencing-reads-from-multiple-reference-genomes.md b/papers/_posts/2012-01-01-a-high-performance-multiple-sequence-alignment-system-for-pyrosequencing-reads-from-multiple-reference-genomes.md index 4b64f474..11a17bac 100644 --- a/papers/_posts/2012-01-01-a-high-performance-multiple-sequence-alignment-system-for-pyrosequencing-reads-from-multiple-reference-genomes.md +++ b/papers/_posts/2012-01-01-a-high-performance-multiple-sequence-alignment-system-for-pyrosequencing-reads-from-multiple-reference-genomes.md @@ -1,10 +1,10 @@ --- layout: paper title: "A high performance multiple sequence alignment system for pyrosequencing reads from multiple reference genomes" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2012-01-01-a-high-performance-multiple-sequence-alignment-system-for-pyrosequencing-reads-from-multiple-reference-genomes authors: "Saeed, Fahad; Perez-Rathke, Alan; Gwarnicki, Jaroslaw; Berger-Wolf, Tanya; Khokhar, Ashfaq; " year: "2012" -journal: Academic Press +journal: "Academic Press Journal of parallel and distributed computing" volume: 72 issue: pages: 83-93 diff --git a/papers/_posts/2012-01-01-an-efficient-algorithm-for-clustering-of-large-scale-mass-spectrometry-data.md b/papers/_posts/2012-01-01-an-efficient-algorithm-for-clustering-of-large-scale-mass-spectrometry-data.md index 7624488b..50f00b58 100644 --- a/papers/_posts/2012-01-01-an-efficient-algorithm-for-clustering-of-large-scale-mass-spectrometry-data.md +++ b/papers/_posts/2012-01-01-an-efficient-algorithm-for-clustering-of-large-scale-mass-spectrometry-data.md @@ -1,10 +1,10 @@ --- layout: paper title: "An efficient algorithm for clustering of large-scale mass spectrometry data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2012-01-01-an-efficient-algorithm-for-clustering-of-large-scale-mass-spectrometry-data authors: "Saeed, Fahad; Pisitkun, Trairak; Knepper, Mark A; Hoffert, Jason D; " year: "2012" -journal: IEEE +journal: "IEEE 2012 IEEE International Conference on Bioinformatics and Biomedicine" volume: issue: pages: 1-4 diff --git a/papers/_posts/2012-01-01-an-efficient-dynamic-programming-algorithm-for-phosphorylation-site-assignment-of-large-scale-mass-spectrometry-data.md b/papers/_posts/2012-01-01-an-efficient-dynamic-programming-algorithm-for-phosphorylation-site-assignment-of-large-scale-mass-spectrometry-data.md index 0da8c57f..276bf135 100644 --- a/papers/_posts/2012-01-01-an-efficient-dynamic-programming-algorithm-for-phosphorylation-site-assignment-of-large-scale-mass-spectrometry-data.md +++ b/papers/_posts/2012-01-01-an-efficient-dynamic-programming-algorithm-for-phosphorylation-site-assignment-of-large-scale-mass-spectrometry-data.md @@ -1,10 +1,10 @@ --- layout: paper title: "An efficient dynamic programming algorithm for phosphorylation site assignment of large-scale mass spectrometry data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2012-01-01-an-efficient-dynamic-programming-algorithm-for-phosphorylation-site-assignment-of-large-scale-mass-spectrometry-data authors: "Saeed, Fahad; Pisitkun, Trairak; Hoffert, Jason D; Wang, Guanghui; Gucek, Marjan; Knepper, Mark A; " year: "2012" -journal: IEEE +journal: "IEEE 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops" volume: issue: pages: 618-625 diff --git a/papers/_posts/2012-01-01-cp-hos--a-program-to-calculate-and-visualize-evolutionarily-conserved-functional-phosphorylation-sites.md b/papers/_posts/2012-01-01-cp-hos--a-program-to-calculate-and-visualize-evolutionarily-conserved-functional-phosphorylation-sites.md index afd7a228..70272138 100644 --- a/papers/_posts/2012-01-01-cp-hos--a-program-to-calculate-and-visualize-evolutionarily-conserved-functional-phosphorylation-sites.md +++ b/papers/_posts/2012-01-01-cp-hos--a-program-to-calculate-and-visualize-evolutionarily-conserved-functional-phosphorylation-sites.md @@ -1,7 +1,7 @@ --- layout: paper title: "CP hos: a program to calculate and visualize evolutionarily conserved functional phosphorylation sites" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2012-01-01-cp-hos--a-program-to-calculate-and-visualize-evolutionarily-conserved-functional-phosphorylation-sites authors: "Zhao, Boyang; Pisitkun, Trairak; Hoffert, Jason D; Knepper, Mark A; Saeed, Fahad; " year: "2012" journal: diff --git a/papers/_posts/2012-01-01-dynamics-of-the-g-protein-coupled-vasopressin-v2-receptor-signaling-network-revealed-by-quantitative-phosphoproteomics.md b/papers/_posts/2012-01-01-dynamics-of-the-g-protein-coupled-vasopressin-v2-receptor-signaling-network-revealed-by-quantitative-phosphoproteomics.md index b75c88aa..3f2e98f7 100644 --- a/papers/_posts/2012-01-01-dynamics-of-the-g-protein-coupled-vasopressin-v2-receptor-signaling-network-revealed-by-quantitative-phosphoproteomics.md +++ b/papers/_posts/2012-01-01-dynamics-of-the-g-protein-coupled-vasopressin-v2-receptor-signaling-network-revealed-by-quantitative-phosphoproteomics.md @@ -1,10 +1,10 @@ --- layout: paper title: "Dynamics of the G protein-coupled vasopressin V2 receptor signaling network revealed by quantitative phosphoproteomics" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2012-01-01-dynamics-of-the-g-protein-coupled-vasopressin-v2-receptor-signaling-network-revealed-by-quantitative-phosphoproteomics authors: "Hoffert, Jason D; Pisitkun, Trairak; Saeed, Fahad; Song, Jae H; Chou, Chung-Lin; Knepper, Mark A; " year: "2012" -journal: Elsevier +journal: "Elsevier Molecular & cellular proteomics" volume: 11 issue: pages: diff --git a/papers/_posts/2012-01-01-high-performance-phosphorylation-site-assignment-algorithm-for-mass-spectrometry-data-using-multicore-systems.md b/papers/_posts/2012-01-01-high-performance-phosphorylation-site-assignment-algorithm-for-mass-spectrometry-data-using-multicore-systems.md index 385a7751..2da974a5 100644 --- a/papers/_posts/2012-01-01-high-performance-phosphorylation-site-assignment-algorithm-for-mass-spectrometry-data-using-multicore-systems.md +++ b/papers/_posts/2012-01-01-high-performance-phosphorylation-site-assignment-algorithm-for-mass-spectrometry-data-using-multicore-systems.md @@ -1,7 +1,7 @@ --- layout: paper title: "High performance phosphorylation site assignment algorithm for mass spectrometry data using multicore systems" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2012-01-01-high-performance-phosphorylation-site-assignment-algorithm-for-mass-spectrometry-data-using-multicore-systems authors: "Saeed, Fahad; Hoffert, Jason; Pisitkun, Trairak; Knepper, Mark; " year: "2012" journal: diff --git a/papers/_posts/2012-01-01-identifying-protein-kinase-target-preferences-using-mass-spectrometry.md b/papers/_posts/2012-01-01-identifying-protein-kinase-target-preferences-using-mass-spectrometry.md index 60d8c971..8bebb191 100644 --- a/papers/_posts/2012-01-01-identifying-protein-kinase-target-preferences-using-mass-spectrometry.md +++ b/papers/_posts/2012-01-01-identifying-protein-kinase-target-preferences-using-mass-spectrometry.md @@ -1,10 +1,10 @@ --- layout: paper title: "Identifying protein kinase target preferences using mass spectrometry" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2012-01-01-identifying-protein-kinase-target-preferences-using-mass-spectrometry authors: "Douglass, Jacqueline; Gunaratne, Ruwan; Bradford, Davis; Saeed, Fahad; Hoffert, Jason D; Steinbach, Peter J; Knepper, Mark A; Pisitkun, Trairak; " year: "2012" -journal: American Physiological Society Bethesda, MD +journal: "American Physiological Society Bethesda, MD American Journal of Physiology-Cell Physiology" volume: 303 issue: pages: C715-C727 diff --git a/papers/_posts/2012-01-01-nhlbi-abdesigner--an-online-tool-for-design-of-peptide-directed-antibodies.md b/papers/_posts/2012-01-01-nhlbi-abdesigner--an-online-tool-for-design-of-peptide-directed-antibodies.md index 16131ea6..b82fd401 100644 --- a/papers/_posts/2012-01-01-nhlbi-abdesigner--an-online-tool-for-design-of-peptide-directed-antibodies.md +++ b/papers/_posts/2012-01-01-nhlbi-abdesigner--an-online-tool-for-design-of-peptide-directed-antibodies.md @@ -1,10 +1,10 @@ --- layout: paper title: "NHLBI-AbDesigner: an online tool for design of peptide-directed antibodies" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2012-01-01-nhlbi-abdesigner--an-online-tool-for-design-of-peptide-directed-antibodies authors: "Pisitkun, Trairak; Hoffert, Jason D; Saeed, Fahad; Knepper, Mark A; " year: "2012" -journal: American Physiological Society Bethesda, MD +journal: "American Physiological Society Bethesda, MD American Journal of Physiology-Cell Physiology" volume: 302 issue: pages: C154-C164 diff --git a/papers/_posts/2012-01-01-proteomic-and-metabolomic-approaches-to-cell-physiology-and-pathophysiology--quantitative-phosphoproteomics-in-nuclei-of-vasopressin-sensitive-renal-collecting-duct-cells.md b/papers/_posts/2012-01-01-proteomic-and-metabolomic-approaches-to-cell-physiology-and-pathophysiology--quantitative-phosphoproteomics-in-nuclei-of-vasopressin-sensitive-renal-collecting-duct-cells.md index f0cb8598..a5efb1d9 100644 --- a/papers/_posts/2012-01-01-proteomic-and-metabolomic-approaches-to-cell-physiology-and-pathophysiology--quantitative-phosphoproteomics-in-nuclei-of-vasopressin-sensitive-renal-collecting-duct-cells.md +++ b/papers/_posts/2012-01-01-proteomic-and-metabolomic-approaches-to-cell-physiology-and-pathophysiology--quantitative-phosphoproteomics-in-nuclei-of-vasopressin-sensitive-renal-collecting-duct-cells.md @@ -1,10 +1,10 @@ --- layout: paper title: "Proteomic and Metabolomic Approaches to Cell Physiology and Pathophysiology: Quantitative phosphoproteomics in nuclei of vasopressin-sensitive renal collecting duct cells" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2012-01-01-proteomic-and-metabolomic-approaches-to-cell-physiology-and-pathophysiology--quantitative-phosphoproteomics-in-nuclei-of-vasopressin-sensitive-renal-collecting-duct-cells authors: "Bolger, Steven J; Hurtado, Patricia A Gonzales; Hoffert, Jason D; Saeed, Fahad; Pisitkun, Trairak; Knepper, Mark A; " year: "2012" -journal: American Physiological Society +journal: "American Physiological Society American Journal of Physiology-Cell Physiology" volume: 303 issue: pages: C1006 diff --git a/papers/_posts/2012-01-01-quantitative-phosphoproteomics-in-nuclei-of-vasopressin-sensitive-renal-collecting-duct-cells.md b/papers/_posts/2012-01-01-quantitative-phosphoproteomics-in-nuclei-of-vasopressin-sensitive-renal-collecting-duct-cells.md index bd666277..b4d0bc71 100644 --- a/papers/_posts/2012-01-01-quantitative-phosphoproteomics-in-nuclei-of-vasopressin-sensitive-renal-collecting-duct-cells.md +++ b/papers/_posts/2012-01-01-quantitative-phosphoproteomics-in-nuclei-of-vasopressin-sensitive-renal-collecting-duct-cells.md @@ -1,10 +1,10 @@ --- layout: paper title: "Quantitative phosphoproteomics in nuclei of vasopressin-sensitive renal collecting duct cells" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2012-01-01-quantitative-phosphoproteomics-in-nuclei-of-vasopressin-sensitive-renal-collecting-duct-cells authors: "Bolger, Steven J; Hurtado, Patricia A Gonzales; Hoffert, Jason D; Saeed, Fahad; Pisitkun, Trairak; Knepper, Mark A; " year: "2012" -journal: American Physiological Society Bethesda, MD +journal: "American Physiological Society Bethesda, MD American Journal of Physiology-Cell Physiology" volume: 303 issue: pages: C1006-C1020 diff --git a/papers/_posts/2013-01-01-a-graphical-user-interface-gui-for-phosphorylation-site-assignment-of-protein-mass-spectrometry-data.md b/papers/_posts/2013-01-01-a-graphical-user-interface-gui-for-phosphorylation-site-assignment-of-protein-mass-spectrometry-data.md index 109cc0ef..2ea794fa 100644 --- a/papers/_posts/2013-01-01-a-graphical-user-interface-gui-for-phosphorylation-site-assignment-of-protein-mass-spectrometry-data.md +++ b/papers/_posts/2013-01-01-a-graphical-user-interface-gui-for-phosphorylation-site-assignment-of-protein-mass-spectrometry-data.md @@ -1,7 +1,7 @@ --- layout: paper title: "A Graphical User Interface (GUI) for Phosphorylation Site Assignment of Protein Mass Spectrometry Data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2013-01-01-a-graphical-user-interface-gui-for-phosphorylation-site-assignment-of-protein-mass-spectrometry-data authors: "Saeed, Fahad; " year: "2013" journal: diff --git a/papers/_posts/2013-01-01-a-high-performance-algorithm-for-clustering-of-large-scale-protein-mass-spectrometry-data-using-multi-core-architectures.md b/papers/_posts/2013-01-01-a-high-performance-algorithm-for-clustering-of-large-scale-protein-mass-spectrometry-data-using-multi-core-architectures.md index 0142c9e7..12a5e026 100644 --- a/papers/_posts/2013-01-01-a-high-performance-algorithm-for-clustering-of-large-scale-protein-mass-spectrometry-data-using-multi-core-architectures.md +++ b/papers/_posts/2013-01-01-a-high-performance-algorithm-for-clustering-of-large-scale-protein-mass-spectrometry-data-using-multi-core-architectures.md @@ -1,7 +1,7 @@ --- layout: paper title: "A high performance algorithm for clustering of large-scale protein mass spectrometry data using multi-core architectures" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2013-01-01-a-high-performance-algorithm-for-clustering-of-large-scale-protein-mass-spectrometry-data-using-multi-core-architectures authors: "Saeed, Fahad; Hoffert, Jason D; Knepper, Mark A; " year: "2013" journal: diff --git a/papers/_posts/2013-01-01-foreword-to-the-special-issue-on-selected-papers-from-the-5th-international-conference-on-bioinformatics-and-computational-biology-bicob-2013.md b/papers/_posts/2013-01-01-foreword-to-the-special-issue-on-selected-papers-from-the-5th-international-conference-on-bioinformatics-and-computational-biology-bicob-2013.md index 7de7a2cd..466c6c9b 100644 --- a/papers/_posts/2013-01-01-foreword-to-the-special-issue-on-selected-papers-from-the-5th-international-conference-on-bioinformatics-and-computational-biology-bicob-2013.md +++ b/papers/_posts/2013-01-01-foreword-to-the-special-issue-on-selected-papers-from-the-5th-international-conference-on-bioinformatics-and-computational-biology-bicob-2013.md @@ -1,10 +1,10 @@ --- layout: paper title: "Foreword to the special issue on selected papers from the 5th International Conference on Bioinformatics and Computational Biology (BICoB 2013)" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2013-01-01-foreword-to-the-special-issue-on-selected-papers-from-the-5th-international-conference-on-bioinformatics-and-computational-biology-bicob-2013 authors: "Dasgupta, Bhaskar; Al-Mubaid, Hisham; Saeed, Fahad; " year: "2013" -journal: Imperial College Press +journal: "Imperial College Press Journal of Bioinformatics and Computational Biology" volume: 11 issue: pages: 1302002 diff --git a/papers/_posts/2013-01-01-phossa--fast-and-accurate-phosphorylation-site-assignment-algorithm-for-mass-spectrometry-data.md b/papers/_posts/2013-01-01-phossa--fast-and-accurate-phosphorylation-site-assignment-algorithm-for-mass-spectrometry-data.md index 3b6824ae..ad85aaae 100644 --- a/papers/_posts/2013-01-01-phossa--fast-and-accurate-phosphorylation-site-assignment-algorithm-for-mass-spectrometry-data.md +++ b/papers/_posts/2013-01-01-phossa--fast-and-accurate-phosphorylation-site-assignment-algorithm-for-mass-spectrometry-data.md @@ -1,10 +1,10 @@ --- layout: paper title: "PhosSA: Fast and accurate phosphorylation site assignment algorithm for mass spectrometry data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2013-01-01-phossa--fast-and-accurate-phosphorylation-site-assignment-algorithm-for-mass-spectrometry-data authors: "Saeed, Fahad; Pisitkun, Trairak; Hoffert, Jason D; Rashidian, Sara; Wang, Guanghui; Gucek, Marjan; Knepper, Mark A; " year: "2013" -journal: BioMed Central +journal: "BioMed Central Proteome science" volume: 11 issue: pages: 1-15 diff --git a/papers/_posts/2013-01-01-proteome-wide-measurement-of-protein-half-lives-and-translation-rates-in-vasopressin-sensitive-collecting-duct-cells.md b/papers/_posts/2013-01-01-proteome-wide-measurement-of-protein-half-lives-and-translation-rates-in-vasopressin-sensitive-collecting-duct-cells.md index 24847bbe..b5aa6dc1 100644 --- a/papers/_posts/2013-01-01-proteome-wide-measurement-of-protein-half-lives-and-translation-rates-in-vasopressin-sensitive-collecting-duct-cells.md +++ b/papers/_posts/2013-01-01-proteome-wide-measurement-of-protein-half-lives-and-translation-rates-in-vasopressin-sensitive-collecting-duct-cells.md @@ -1,10 +1,10 @@ --- layout: paper title: "Proteome-wide measurement of protein half-lives and translation rates in vasopressin-sensitive collecting duct cells" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2013-01-01-proteome-wide-measurement-of-protein-half-lives-and-translation-rates-in-vasopressin-sensitive-collecting-duct-cells authors: "Sandoval, Pablo C; Slentz, Dane H; Pisitkun, Trairak; Saeed, Fahad; Hoffert, Jason D; Knepper, Mark A; " year: "2013" -journal: LWW +journal: "LWW Journal of the American Society of Nephrology" volume: 24 issue: pages: 1793-1805 diff --git "a/papers/_posts/2013-01-01-quantitative-phosphoproteomics-implicates-clusters-of-proteins-involved-in-cell\342\200\220cell-adhesion-and-transcriptional-regulation-in-the-vasopressin-signaling-network.md" "b/papers/_posts/2013-01-01-quantitative-phosphoproteomics-implicates-clusters-of-proteins-involved-in-cell\342\200\220cell-adhesion-and-transcriptional-regulation-in-the-vasopressin-signaling-network.md" index d734901e..b23bf795 100644 --- "a/papers/_posts/2013-01-01-quantitative-phosphoproteomics-implicates-clusters-of-proteins-involved-in-cell\342\200\220cell-adhesion-and-transcriptional-regulation-in-the-vasopressin-signaling-network.md" +++ "b/papers/_posts/2013-01-01-quantitative-phosphoproteomics-implicates-clusters-of-proteins-involved-in-cell\342\200\220cell-adhesion-and-transcriptional-regulation-in-the-vasopressin-signaling-network.md" @@ -1,10 +1,10 @@ --- layout: paper title: "Quantitative phosphoproteomics implicates clusters of proteins involved in cell‐cell adhesion and transcriptional regulation in the vasopressin signaling network" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2013-01-01-quantitative-phosphoproteomics-implicates-clusters-of-proteins-involved-in-cell‐cell-adhesion-and-transcriptional-regulation-in-the-vasopressin-signaling-network authors: "Bolger, Steven J; Hurtado, Patricia A Gonzales; Hoffert, Jason D; Saeed, Fahad; Pisitkun, Trairak; Knepper, Mark A; " year: "2013" -journal: The Federation of American Societies for Experimental Biology +journal: "The Federation of American Societies for Experimental Biology" volume: issue: pages: diff --git a/papers/_posts/2014-01-01-6th-international-conference-on-bioinformatics-and-computational-biology-bicob-2014.md b/papers/_posts/2014-01-01-6th-international-conference-on-bioinformatics-and-computational-biology-bicob-2014.md index ee05178f..59affad7 100644 --- a/papers/_posts/2014-01-01-6th-international-conference-on-bioinformatics-and-computational-biology-bicob-2014.md +++ b/papers/_posts/2014-01-01-6th-international-conference-on-bioinformatics-and-computational-biology-bicob-2014.md @@ -1,7 +1,7 @@ --- layout: paper title: "6th International Conference on Bioinformatics and Computational Biology (BICoB 2014)" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2014-01-01-6th-international-conference-on-bioinformatics-and-computational-biology-bicob-2014 authors: "Saeed, Fahad; DasGupta, B; " year: "2014" journal: diff --git a/papers/_posts/2014-01-01-a-knowledge-base-of-vasopressin-actions-in-the-kidney.md b/papers/_posts/2014-01-01-a-knowledge-base-of-vasopressin-actions-in-the-kidney.md index 4dfe5eb9..375b1d62 100644 --- a/papers/_posts/2014-01-01-a-knowledge-base-of-vasopressin-actions-in-the-kidney.md +++ b/papers/_posts/2014-01-01-a-knowledge-base-of-vasopressin-actions-in-the-kidney.md @@ -1,10 +1,10 @@ --- layout: paper title: "A knowledge base of vasopressin actions in the kidney" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2014-01-01-a-knowledge-base-of-vasopressin-actions-in-the-kidney authors: "Sanghi, Akshay; Zaringhalam, Matthew; Corcoran, Callan C; Saeed, Fahad; Hoffert, Jason D; Sandoval, Pablo; Pisitkun, Trairak; Knepper, Mark A; " year: "2014" -journal: American Physiological Society Bethesda, MD +journal: "American Physiological Society Bethesda, MD American Journal of Physiology-Renal Physiology" volume: 307 issue: pages: F747-F755 diff --git a/papers/_posts/2014-01-01-cams-rs--clustering-algorithm-for-large-scale-mass-spectrometry-data-using-restricted-search-space-and-intelligent-random-sampling.md b/papers/_posts/2014-01-01-cams-rs--clustering-algorithm-for-large-scale-mass-spectrometry-data-using-restricted-search-space-and-intelligent-random-sampling.md index 78700f68..5a8b1bb9 100644 --- a/papers/_posts/2014-01-01-cams-rs--clustering-algorithm-for-large-scale-mass-spectrometry-data-using-restricted-search-space-and-intelligent-random-sampling.md +++ b/papers/_posts/2014-01-01-cams-rs--clustering-algorithm-for-large-scale-mass-spectrometry-data-using-restricted-search-space-and-intelligent-random-sampling.md @@ -1,10 +1,10 @@ --- layout: paper title: "Cams-rs: clustering algorithm for large-scale mass spectrometry data using restricted search space and intelligent random sampling" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2014-01-01-cams-rs--clustering-algorithm-for-large-scale-mass-spectrometry-data-using-restricted-search-space-and-intelligent-random-sampling authors: "Saeed, Fahad; Hoffert, Jason D; Knepper, Mark A; " year: "2014" -journal: IEEE Computer Society Press +journal: "IEEE Computer Society Press IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)" volume: 11 issue: pages: 128-141 diff --git a/papers/_posts/2014-01-01-exploiting-thread-level-and-instruction-level-parallelism-to-cluster-mass-spectrometry-data-using-multicore-architectures.md b/papers/_posts/2014-01-01-exploiting-thread-level-and-instruction-level-parallelism-to-cluster-mass-spectrometry-data-using-multicore-architectures.md index 59e2d530..8b04df08 100644 --- a/papers/_posts/2014-01-01-exploiting-thread-level-and-instruction-level-parallelism-to-cluster-mass-spectrometry-data-using-multicore-architectures.md +++ b/papers/_posts/2014-01-01-exploiting-thread-level-and-instruction-level-parallelism-to-cluster-mass-spectrometry-data-using-multicore-architectures.md @@ -1,10 +1,10 @@ --- layout: paper title: "Exploiting thread-level and instruction-level parallelism to cluster mass spectrometry data using multicore architectures" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2014-01-01-exploiting-thread-level-and-instruction-level-parallelism-to-cluster-mass-spectrometry-data-using-multicore-architectures authors: "Saeed, Fahad; Hoffert, Jason D; Pisitkun, Trairak; Knepper, Mark A; " year: "2014" -journal: Springer Vienna +journal: "Springer Vienna Network Modeling Analysis in Health Informatics and Bioinformatics" volume: 3 issue: pages: 1-19 diff --git a/papers/_posts/2014-01-01-foreword-to-the-special-issue-on-selected-papers-from-the-6th-international-conference-on-bioinformatics-and-computational-biology-bicob-2014..md b/papers/_posts/2014-01-01-foreword-to-the-special-issue-on-selected-papers-from-the-6th-international-conference-on-bioinformatics-and-computational-biology-bicob-2014..md index af8f2a53..18bc8bf9 100644 --- a/papers/_posts/2014-01-01-foreword-to-the-special-issue-on-selected-papers-from-the-6th-international-conference-on-bioinformatics-and-computational-biology-bicob-2014..md +++ b/papers/_posts/2014-01-01-foreword-to-the-special-issue-on-selected-papers-from-the-6th-international-conference-on-bioinformatics-and-computational-biology-bicob-2014..md @@ -1,7 +1,7 @@ --- layout: paper title: "Foreword to the special issue on selected papers from the 6th International Conference on Bioinformatics and Computational Biology (BICoB 2014)." -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2014-01-01-foreword-to-the-special-issue-on-selected-papers-from-the-6th-international-conference-on-bioinformatics-and-computational-biology-bicob-2014. authors: "Saeed, Fahad; Al-Mubaid, Hisham; Dasgupta, Bhaskar; " year: "2014" journal: diff --git a/papers/_posts/2014-01-01-global-analysis-of-the-effects-of-the-v2-receptor-antagonist-satavaptan-on-protein-phosphorylation-in-collecting-duct.md b/papers/_posts/2014-01-01-global-analysis-of-the-effects-of-the-v2-receptor-antagonist-satavaptan-on-protein-phosphorylation-in-collecting-duct.md index eb2865de..51c9694e 100644 --- a/papers/_posts/2014-01-01-global-analysis-of-the-effects-of-the-v2-receptor-antagonist-satavaptan-on-protein-phosphorylation-in-collecting-duct.md +++ b/papers/_posts/2014-01-01-global-analysis-of-the-effects-of-the-v2-receptor-antagonist-satavaptan-on-protein-phosphorylation-in-collecting-duct.md @@ -1,10 +1,10 @@ --- layout: paper title: "Global analysis of the effects of the V2 receptor antagonist satavaptan on protein phosphorylation in collecting duct" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2014-01-01-global-analysis-of-the-effects-of-the-v2-receptor-antagonist-satavaptan-on-protein-phosphorylation-in-collecting-duct authors: "Hoffert, Jason D; Pisitkun, Trairak; Saeed, Fahad; Wilson, Justin L; Knepper, Mark A; " year: "2014" -journal: American Physiological Society Bethesda, MD +journal: "American Physiological Society Bethesda, MD American Journal of Physiology-Renal Physiology" volume: 306 issue: pages: 410-421 diff --git a/papers/_posts/2015-01-01-a-high-performance-architecture-for-an-exact-match-short-read-aligner-using-burrows-wheeler-aligner-on-fpgas.md b/papers/_posts/2015-01-01-a-high-performance-architecture-for-an-exact-match-short-read-aligner-using-burrows-wheeler-aligner-on-fpgas.md index 543d0421..91f460d9 100644 --- a/papers/_posts/2015-01-01-a-high-performance-architecture-for-an-exact-match-short-read-aligner-using-burrows-wheeler-aligner-on-fpgas.md +++ b/papers/_posts/2015-01-01-a-high-performance-architecture-for-an-exact-match-short-read-aligner-using-burrows-wheeler-aligner-on-fpgas.md @@ -1,7 +1,7 @@ --- layout: paper title: "A High Performance Architecture for an Exact Match Short-Read Aligner Using Burrows-Wheeler Aligner on FPGAs" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2015-01-01-a-high-performance-architecture-for-an-exact-match-short-read-aligner-using-burrows-wheeler-aligner-on-fpgas authors: "Qader, Dana Abdul; " year: "2015" journal: diff --git a/papers/_posts/2015-01-01-a-parallel-algorithm-for-compression-of-big-next-generation-sequencing-datasets.md b/papers/_posts/2015-01-01-a-parallel-algorithm-for-compression-of-big-next-generation-sequencing-datasets.md index e28c6814..2a15dfa0 100644 --- a/papers/_posts/2015-01-01-a-parallel-algorithm-for-compression-of-big-next-generation-sequencing-datasets.md +++ b/papers/_posts/2015-01-01-a-parallel-algorithm-for-compression-of-big-next-generation-sequencing-datasets.md @@ -1,10 +1,10 @@ --- layout: paper title: "A parallel algorithm for compression of big next-generation sequencing datasets" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2015-01-01-a-parallel-algorithm-for-compression-of-big-next-generation-sequencing-datasets authors: "Pérez, Sandino Vargas; Saeed, Fahad; " year: "2015" -journal: IEEE +journal: "IEEE 2015 IEEE Trustcom/BigDataSE/ISPA" volume: 3 issue: pages: 196-201 diff --git a/papers/_posts/2015-01-01-autophagic-degradation-of-aquaporin-2-is-an-early-event-in-hypokalemia-induced-nephrogenic-diabetes-insipidus.md b/papers/_posts/2015-01-01-autophagic-degradation-of-aquaporin-2-is-an-early-event-in-hypokalemia-induced-nephrogenic-diabetes-insipidus.md index 55c76d31..94b6e4e6 100644 --- a/papers/_posts/2015-01-01-autophagic-degradation-of-aquaporin-2-is-an-early-event-in-hypokalemia-induced-nephrogenic-diabetes-insipidus.md +++ b/papers/_posts/2015-01-01-autophagic-degradation-of-aquaporin-2-is-an-early-event-in-hypokalemia-induced-nephrogenic-diabetes-insipidus.md @@ -1,10 +1,10 @@ --- layout: paper title: "Autophagic degradation of aquaporin-2 is an early event in hypokalemia-induced nephrogenic diabetes insipidus" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2015-01-01-autophagic-degradation-of-aquaporin-2-is-an-early-event-in-hypokalemia-induced-nephrogenic-diabetes-insipidus authors: "Khositseth, Sookkasem; Uawithya, Panapat; Somparn, Poorichaya; Charngkaew, Komgrid; Thippamom, Nattakan; Hoffert, Jason D; Saeed, Fahad; Michael Payne, D; Chen, Shu-Hui; Fenton, Robert A; " year: "2015" -journal: Nature Publishing Group UK London +journal: "Nature Publishing Group UK London Scientific reports" volume: 5 issue: pages: 18311 diff --git a/papers/_posts/2015-01-01-big-data-proteogenomics-and-high-performance-computing--challenges-and-opportunities.md b/papers/_posts/2015-01-01-big-data-proteogenomics-and-high-performance-computing--challenges-and-opportunities.md index a9a7c12b..5a92cc72 100644 --- a/papers/_posts/2015-01-01-big-data-proteogenomics-and-high-performance-computing--challenges-and-opportunities.md +++ b/papers/_posts/2015-01-01-big-data-proteogenomics-and-high-performance-computing--challenges-and-opportunities.md @@ -1,10 +1,10 @@ --- layout: paper title: "Big data proteogenomics and high performance computing: Challenges and opportunities" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2015-01-01-big-data-proteogenomics-and-high-performance-computing--challenges-and-opportunities authors: "Saeed, Fahad; " year: "2015" -journal: IEEE +journal: "IEEE 2015 IEEE Global Conference on Signal and Information Processing (GlobalSIP)" volume: issue: pages: 141-145 diff --git a/papers/_posts/2015-01-01-design-and-implementation-of-network-transfer-protocol-for-big-genomic-data.md b/papers/_posts/2015-01-01-design-and-implementation-of-network-transfer-protocol-for-big-genomic-data.md index e12af616..66eece31 100644 --- a/papers/_posts/2015-01-01-design-and-implementation-of-network-transfer-protocol-for-big-genomic-data.md +++ b/papers/_posts/2015-01-01-design-and-implementation-of-network-transfer-protocol-for-big-genomic-data.md @@ -1,15 +1,15 @@ --- layout: paper title: "Design and implementation of network transfer protocol for big genomic data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2015-01-01-design-and-implementation-of-network-transfer-protocol-for-big-genomic-data authors: "Aledhari, Mohammed; Saeed, Fahad; " year: "2015" -journal: IEEE +journal: "IEEE 2015 IEEE International Congress on Big Data" volume: issue: pages: 281-288 is_published: True -image: /assets/images/papers/ieee.png +image: /assets/images/papers/biorxiv.png projects: [] tags: [] diff --git a/papers/_posts/2015-01-01-on-the-sampling-of-big-mass-spectrometry-data.md b/papers/_posts/2015-01-01-on-the-sampling-of-big-mass-spectrometry-data.md index b7b7e3d7..cee6867c 100644 --- a/papers/_posts/2015-01-01-on-the-sampling-of-big-mass-spectrometry-data.md +++ b/papers/_posts/2015-01-01-on-the-sampling-of-big-mass-spectrometry-data.md @@ -1,7 +1,7 @@ --- layout: paper title: "On the sampling of big mass spectrometry data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2015-01-01-on-the-sampling-of-big-mass-spectrometry-data authors: "Awan, Muaaz Gul; Saeed, Fahad; " year: "2015" journal: diff --git a/papers/_posts/2016-01-01-a-parallel-peptide-indexer-and-decoy-generator-for-crux-tide-using-openmp.md b/papers/_posts/2016-01-01-a-parallel-peptide-indexer-and-decoy-generator-for-crux-tide-using-openmp.md index 450f5a4f..b9fe9e87 100644 --- a/papers/_posts/2016-01-01-a-parallel-peptide-indexer-and-decoy-generator-for-crux-tide-using-openmp.md +++ b/papers/_posts/2016-01-01-a-parallel-peptide-indexer-and-decoy-generator-for-crux-tide-using-openmp.md @@ -1,10 +1,10 @@ --- layout: paper title: "A Parallel Peptide Indexer and Decoy Generator for Crux Tide using OpenMP" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2016-01-01-a-parallel-peptide-indexer-and-decoy-generator-for-crux-tide-using-openmp authors: "Maabreh, Majdi; Gupta, Ajay; Saeed, Fahad; " year: "2016" -journal: IEEE +journal: "IEEE 2016 International Conference on High Performance Computing Simulation (HPCS)" volume: issue: pages: 411-418 diff --git a/papers/_posts/2016-01-01-a-variable-length-network-encoding-protocol-for-big-genomic-data.md b/papers/_posts/2016-01-01-a-variable-length-network-encoding-protocol-for-big-genomic-data.md index f41c8a4b..c4a0d7c4 100644 --- a/papers/_posts/2016-01-01-a-variable-length-network-encoding-protocol-for-big-genomic-data.md +++ b/papers/_posts/2016-01-01-a-variable-length-network-encoding-protocol-for-big-genomic-data.md @@ -1,10 +1,10 @@ --- layout: paper title: "A variable-length network encoding protocol for big genomic data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2016-01-01-a-variable-length-network-encoding-protocol-for-big-genomic-data authors: "Aledhari, Mohammed; Hefeida, Mohamed S; Saeed, Fahad; " year: "2016" -journal: Springer International Publishing +journal: "Springer International Publishing Wired/Wireless Internet Communications: 14th IFIP WG 6.2 International Conference, WWIC 2016, Thessaloniki, Greece, May 25-27, 2016, Proceedings 14" volume: issue: pages: 212-224 diff --git a/papers/_posts/2016-01-01-data-aware-communication-for-energy-harvesting-sensor-networks.md b/papers/_posts/2016-01-01-data-aware-communication-for-energy-harvesting-sensor-networks.md index ccd34996..50a02b4e 100644 --- a/papers/_posts/2016-01-01-data-aware-communication-for-energy-harvesting-sensor-networks.md +++ b/papers/_posts/2016-01-01-data-aware-communication-for-energy-harvesting-sensor-networks.md @@ -1,10 +1,10 @@ --- layout: paper title: "Data Aware Communication for Energy Harvesting Sensor Networks" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2016-01-01-data-aware-communication-for-energy-harvesting-sensor-networks authors: "Hefeida, Mohamed S; Saeed, Fahad; " year: "2016" -journal: Springer International Publishing +journal: "Springer International Publishing Wired/Wireless Internet Communications: 14th IFIP WG 6.2 International Conference, WWIC 2016, Thessaloniki, Greece, May 25-27, 2016, Proceedings 14" volume: issue: pages: 121-132 diff --git a/papers/_posts/2016-01-01-gpu-arraysort--a-parallel,-in-place-algorithm-for-sorting-large-number-of-arrays.md b/papers/_posts/2016-01-01-gpu-arraysort--a-parallel,-in-place-algorithm-for-sorting-large-number-of-arrays.md index a14bb621..ca1c54ce 100644 --- a/papers/_posts/2016-01-01-gpu-arraysort--a-parallel,-in-place-algorithm-for-sorting-large-number-of-arrays.md +++ b/papers/_posts/2016-01-01-gpu-arraysort--a-parallel,-in-place-algorithm-for-sorting-large-number-of-arrays.md @@ -1,7 +1,7 @@ --- layout: paper title: "GPU-ArraySort: A parallel, in-place algorithm for sorting large number of arrays" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2016-01-01-gpu-arraysort--a-parallel,-in-place-algorithm-for-sorting-large-number-of-arrays authors: "Awan, Muaaz; Saeed, Fahad; " year: "2016" journal: diff --git a/papers/_posts/2016-01-01-introduction-to-the-selected-papers-from-the-7th-international-conference-on-bioinformatics-and-computational-biology-bicob-2015.md b/papers/_posts/2016-01-01-introduction-to-the-selected-papers-from-the-7th-international-conference-on-bioinformatics-and-computational-biology-bicob-2015.md index 632e509a..743b4d53 100644 --- a/papers/_posts/2016-01-01-introduction-to-the-selected-papers-from-the-7th-international-conference-on-bioinformatics-and-computational-biology-bicob-2015.md +++ b/papers/_posts/2016-01-01-introduction-to-the-selected-papers-from-the-7th-international-conference-on-bioinformatics-and-computational-biology-bicob-2015.md @@ -1,10 +1,10 @@ --- layout: paper title: "Introduction to the selected papers from the 7th International Conference on Bioinformatics and Computational Biology (BICoB 2015)" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2016-01-01-introduction-to-the-selected-papers-from-the-7th-international-conference-on-bioinformatics-and-computational-biology-bicob-2015 authors: "Saeed, Fahad; Haspel, Nurit; Al-Mubaid, Hisham; " year: "2016" -journal: World Scientific Publishing Company +journal: "World Scientific Publishing Company Journal of Bioinformatics and Computational Biology" volume: 14 issue: pages: 1602002 diff --git a/papers/_posts/2016-01-01-ms-reduce--an-ultrafast-technique-for-reduction-of-big-mass-spectrometry-data-for-high-throughput-processing.md b/papers/_posts/2016-01-01-ms-reduce--an-ultrafast-technique-for-reduction-of-big-mass-spectrometry-data-for-high-throughput-processing.md index c9b4c839..83bb714c 100644 --- a/papers/_posts/2016-01-01-ms-reduce--an-ultrafast-technique-for-reduction-of-big-mass-spectrometry-data-for-high-throughput-processing.md +++ b/papers/_posts/2016-01-01-ms-reduce--an-ultrafast-technique-for-reduction-of-big-mass-spectrometry-data-for-high-throughput-processing.md @@ -1,10 +1,10 @@ --- layout: paper title: "MS-REDUCE: an ultrafast technique for reduction of big mass spectrometry data for high-throughput processing" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2016-01-01-ms-reduce--an-ultrafast-technique-for-reduction-of-big-mass-spectrometry-data-for-high-throughput-processing authors: "Awan, Muaaz Gul; Saeed, Fahad; " year: "2016" -journal: Oxford University Press +journal: "Oxford University Press Bioinformatics" volume: 32 issue: pages: 1518-1526 diff --git a/papers/_posts/2016-01-01-reductive-analytics-on-big-ms-data-leads-to-tremendous-reduction-in-time-for-peptide-deduction.md b/papers/_posts/2016-01-01-reductive-analytics-on-big-ms-data-leads-to-tremendous-reduction-in-time-for-peptide-deduction.md index 0b1d1645..df169834 100644 --- a/papers/_posts/2016-01-01-reductive-analytics-on-big-ms-data-leads-to-tremendous-reduction-in-time-for-peptide-deduction.md +++ b/papers/_posts/2016-01-01-reductive-analytics-on-big-ms-data-leads-to-tremendous-reduction-in-time-for-peptide-deduction.md @@ -1,10 +1,10 @@ --- layout: paper title: "Reductive Analytics on Big MS Data leads to tremendous reduction in time for peptide deduction" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2016-01-01-reductive-analytics-on-big-ms-data-leads-to-tremendous-reduction-in-time-for-peptide-deduction authors: "Awan, Muaaz Gul; Saeed, Fahad; " year: "2016" -journal: Cold Spring Harbor Laboratory +journal: "Cold Spring Harbor Laboratory bioRxiv" volume: issue: pages: 73064 diff --git a/papers/_posts/2016-01-01-selected-papers-from-bicob2015.md b/papers/_posts/2016-01-01-selected-papers-from-bicob2015.md index 9367b80d..6263effb 100644 --- a/papers/_posts/2016-01-01-selected-papers-from-bicob2015.md +++ b/papers/_posts/2016-01-01-selected-papers-from-bicob2015.md @@ -1,10 +1,10 @@ --- layout: paper title: "Selected Papers from BICoB2015" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2016-01-01-selected-papers-from-bicob2015 authors: "BICoB; " year: "2016" -journal: World Scientific +journal: "World Scientific" volume: issue: pages: diff --git a/papers/_posts/2016-01-01-systems-level-analysis-reveals-selective-regulation-of-aqp2-gene-expression-by-vasopressin.md b/papers/_posts/2016-01-01-systems-level-analysis-reveals-selective-regulation-of-aqp2-gene-expression-by-vasopressin.md index 2af19b01..4f28e83a 100644 --- a/papers/_posts/2016-01-01-systems-level-analysis-reveals-selective-regulation-of-aqp2-gene-expression-by-vasopressin.md +++ b/papers/_posts/2016-01-01-systems-level-analysis-reveals-selective-regulation-of-aqp2-gene-expression-by-vasopressin.md @@ -1,10 +1,10 @@ --- layout: paper title: "Systems-level analysis reveals selective regulation of Aqp2 gene expression by vasopressin" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2016-01-01-systems-level-analysis-reveals-selective-regulation-of-aqp2-gene-expression-by-vasopressin authors: "Sandoval, Pablo C; Claxton, J’Neka S; Lee, Jae Wook; Saeed, Fahad; Hoffert, Jason D; Knepper, Mark A; " year: "2016" -journal: Nature Publishing Group UK London +journal: "Nature Publishing Group UK London Scientific reports" volume: 6 issue: pages: 34863 diff --git a/papers/_posts/2017-01-01-a-hybrid-mpi-openmp-strategy-to-speedup-the-compression-of-big-next-generation-sequencing-datasets.md b/papers/_posts/2017-01-01-a-hybrid-mpi-openmp-strategy-to-speedup-the-compression-of-big-next-generation-sequencing-datasets.md index 8ce376bc..b7d5c9f5 100644 --- a/papers/_posts/2017-01-01-a-hybrid-mpi-openmp-strategy-to-speedup-the-compression-of-big-next-generation-sequencing-datasets.md +++ b/papers/_posts/2017-01-01-a-hybrid-mpi-openmp-strategy-to-speedup-the-compression-of-big-next-generation-sequencing-datasets.md @@ -1,7 +1,7 @@ --- layout: paper title: "A Hybrid MPI-OpenMP Strategy to Speedup the Compression of Big Next-Generation Sequencing Datasets" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2017-01-01-a-hybrid-mpi-openmp-strategy-to-speedup-the-compression-of-big-next-generation-sequencing-datasets authors: "Vargas-Perez, Sandino; Saeed, Fahad; " year: "2017" journal: diff --git a/papers/_posts/2017-01-01-a-new-cryptography-algorithm-to-protect-cloud-based-healthcare-services.md b/papers/_posts/2017-01-01-a-new-cryptography-algorithm-to-protect-cloud-based-healthcare-services.md index 3b703c10..fa7dff45 100644 --- a/papers/_posts/2017-01-01-a-new-cryptography-algorithm-to-protect-cloud-based-healthcare-services.md +++ b/papers/_posts/2017-01-01-a-new-cryptography-algorithm-to-protect-cloud-based-healthcare-services.md @@ -1,10 +1,10 @@ --- layout: paper title: "A new cryptography algorithm to protect cloud-based healthcare services" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2017-01-01-a-new-cryptography-algorithm-to-protect-cloud-based-healthcare-services authors: "Aledhari, Mohammed; Marhoon, Ali; Hamad, Ali; Saeed, Fahad; " year: "2017" -journal: IEEE +journal: "IEEE 2017 IEEE/ACM International Conference on Connected Health: Applications, Systems and Engineering Technologies (CHASE)" volume: issue: pages: 37-43 diff --git a/papers/_posts/2017-01-01-an-out-of-core-gpu-based-dimensionality-reduction-algorithm-for-big-mass-spectrometry-data-and-its-application-in-bottom-up-proteomics.md b/papers/_posts/2017-01-01-an-out-of-core-gpu-based-dimensionality-reduction-algorithm-for-big-mass-spectrometry-data-and-its-application-in-bottom-up-proteomics.md index e4ed6bc1..2fc1f4c5 100644 --- a/papers/_posts/2017-01-01-an-out-of-core-gpu-based-dimensionality-reduction-algorithm-for-big-mass-spectrometry-data-and-its-application-in-bottom-up-proteomics.md +++ b/papers/_posts/2017-01-01-an-out-of-core-gpu-based-dimensionality-reduction-algorithm-for-big-mass-spectrometry-data-and-its-application-in-bottom-up-proteomics.md @@ -1,7 +1,7 @@ --- layout: paper title: "An out-of-core gpu based dimensionality reduction algorithm for big mass spectrometry data and its application in bottom-up proteomics" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2017-01-01-an-out-of-core-gpu-based-dimensionality-reduction-algorithm-for-big-mass-spectrometry-data-and-its-application-in-bottom-up-proteomics authors: "Awan, Muaaz Gul; Saeed, Fahad; " year: "2017" journal: diff --git a/papers/_posts/2017-01-01-gpu-pcc--a-gpu-based-technique-to-compute-pairwise-pearson's-correlation-coefficients-for-big-fmri-data.md b/papers/_posts/2017-01-01-gpu-pcc--a-gpu-based-technique-to-compute-pairwise-pearson's-correlation-coefficients-for-big-fmri-data.md index 79b98426..7e1e0600 100644 --- a/papers/_posts/2017-01-01-gpu-pcc--a-gpu-based-technique-to-compute-pairwise-pearson's-correlation-coefficients-for-big-fmri-data.md +++ b/papers/_posts/2017-01-01-gpu-pcc--a-gpu-based-technique-to-compute-pairwise-pearson's-correlation-coefficients-for-big-fmri-data.md @@ -1,7 +1,7 @@ --- layout: paper title: "GPU-PCC: A GPU Based Technique to Compute Pairwise Pearson's Correlation Coefficients for Big fMRI Data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2017-01-01-gpu-pcc--a-gpu-based-technique-to-compute-pairwise-pearson's-correlation-coefficients-for-big-fmri-data authors: "Eslami, Taban; Awan, Muaaz Gul; Saeed, Fahad; " year: "2017" journal: diff --git a/papers/_posts/2017-01-01-power-efficient-and-highly-scalable-parallel-graph-sampling-using-fpgas.md b/papers/_posts/2017-01-01-power-efficient-and-highly-scalable-parallel-graph-sampling-using-fpgas.md index 90cf1c32..dadecf54 100644 --- a/papers/_posts/2017-01-01-power-efficient-and-highly-scalable-parallel-graph-sampling-using-fpgas.md +++ b/papers/_posts/2017-01-01-power-efficient-and-highly-scalable-parallel-graph-sampling-using-fpgas.md @@ -1,7 +1,7 @@ --- layout: paper title: "Power-Efficient and Highly Scalable Parallel Graph Sampling using FPGAs" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2017-01-01-power-efficient-and-highly-scalable-parallel-graph-sampling-using-fpgas authors: "Tariq, Usman; Cheema, Umer; Saeed, Fahad; " year: "2017" journal: diff --git a/papers/_posts/2017-01-01-scalable-data-structure-to-compress-next-generation-sequencing-files-and-its-application-to-compressive-genomics.md b/papers/_posts/2017-01-01-scalable-data-structure-to-compress-next-generation-sequencing-files-and-its-application-to-compressive-genomics.md index 27c6971d..d123b351 100644 --- a/papers/_posts/2017-01-01-scalable-data-structure-to-compress-next-generation-sequencing-files-and-its-application-to-compressive-genomics.md +++ b/papers/_posts/2017-01-01-scalable-data-structure-to-compress-next-generation-sequencing-files-and-its-application-to-compressive-genomics.md @@ -1,10 +1,10 @@ --- layout: paper title: "Scalable data structure to compress next-generation sequencing files and its application to compressive genomics" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2017-01-01-scalable-data-structure-to-compress-next-generation-sequencing-files-and-its-application-to-compressive-genomics authors: "Pérez, Sandino Vargas; Saeed, Fahad; " year: "2017" -journal: IEEE +journal: "IEEE 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)" volume: issue: pages: 1923-1928 diff --git a/papers/_posts/2018-01-01-a-deep-learning-based-data-minimization-algorithm-for-fast-and-secure-transfer-of-big-genomic-datasets.md b/papers/_posts/2018-01-01-a-deep-learning-based-data-minimization-algorithm-for-fast-and-secure-transfer-of-big-genomic-datasets.md index 68ba5cc6..5e3bd269 100644 --- a/papers/_posts/2018-01-01-a-deep-learning-based-data-minimization-algorithm-for-fast-and-secure-transfer-of-big-genomic-datasets.md +++ b/papers/_posts/2018-01-01-a-deep-learning-based-data-minimization-algorithm-for-fast-and-secure-transfer-of-big-genomic-datasets.md @@ -1,10 +1,10 @@ --- layout: paper title: "A deep learning-based data minimization algorithm for fast and secure transfer of big genomic datasets" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2018-01-01-a-deep-learning-based-data-minimization-algorithm-for-fast-and-secure-transfer-of-big-genomic-datasets authors: "Aledhari, Mohammed; Di Pierro, Marianne; Hefeida, Mohamed; Saeed, Fahad; " year: "2018" -journal: IEEE +journal: "IEEE IEEE Transactions on Big Data" volume: 7 issue: pages: 271-284 diff --git a/papers/_posts/2018-01-01-a-fourier-based-data-minimization-algorithm-for-fast-and-secure-transfer-of-big-genomic-datasets.md b/papers/_posts/2018-01-01-a-fourier-based-data-minimization-algorithm-for-fast-and-secure-transfer-of-big-genomic-datasets.md index 0a658cf8..0922f789 100644 --- a/papers/_posts/2018-01-01-a-fourier-based-data-minimization-algorithm-for-fast-and-secure-transfer-of-big-genomic-datasets.md +++ b/papers/_posts/2018-01-01-a-fourier-based-data-minimization-algorithm-for-fast-and-secure-transfer-of-big-genomic-datasets.md @@ -1,7 +1,7 @@ --- layout: paper title: "A Fourier-Based Data Minimization Algorithm for Fast and Secure Transfer of Big Genomic Datasets" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2018-01-01-a-fourier-based-data-minimization-algorithm-for-fast-and-secure-transfer-of-big-genomic-datasets authors: "Aledhari, Mohammed; Pierro, Marianne Di; Saeed, Fahad; " year: "2018" journal: diff --git "a/papers/_posts/2018-01-01-fast-gpu-pcc--a-gpu-based-technique-to-compute-pairwise-pearson\342\200\231s-correlation-coefficients-for-time-series-data---an-fmri-study.md" "b/papers/_posts/2018-01-01-fast-gpu-pcc--a-gpu-based-technique-to-compute-pairwise-pearson\342\200\231s-correlation-coefficients-for-time-series-data---an-fmri-study.md" index c4175857..2307bbf1 100644 --- "a/papers/_posts/2018-01-01-fast-gpu-pcc--a-gpu-based-technique-to-compute-pairwise-pearson\342\200\231s-correlation-coefficients-for-time-series-data---an-fmri-study.md" +++ "b/papers/_posts/2018-01-01-fast-gpu-pcc--a-gpu-based-technique-to-compute-pairwise-pearson\342\200\231s-correlation-coefficients-for-time-series-data---an-fmri-study.md" @@ -1,10 +1,10 @@ --- layout: paper title: "Fast-GPU-PCC: A GPU-Based Technique to Compute Pairwise Pearson’s Correlation Coefficients for Time Series Data - An fMRI Study" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2018-01-01-fast-gpu-pcc--a-gpu-based-technique-to-compute-pairwise-pearson’s-correlation-coefficients-for-time-series-data---an-fmri-study authors: "Eslami, Taban; Saeed, Fahad; " year: "2018" -journal: MDPI +journal: "MDPI High-Throughput Journal" volume: issue: pages: diff --git a/papers/_posts/2018-01-01-gpu-daemon--gpu-algorithm-design,-data-management-&-optimization-template-for-array-based-big-omics-data.md b/papers/_posts/2018-01-01-gpu-daemon--gpu-algorithm-design,-data-management-&-optimization-template-for-array-based-big-omics-data.md index 59e2885c..cec8b34a 100644 --- a/papers/_posts/2018-01-01-gpu-daemon--gpu-algorithm-design,-data-management-&-optimization-template-for-array-based-big-omics-data.md +++ b/papers/_posts/2018-01-01-gpu-daemon--gpu-algorithm-design,-data-management-&-optimization-template-for-array-based-big-omics-data.md @@ -1,10 +1,10 @@ --- layout: paper title: "GPU-DAEMON: GPU algorithm design, data management & optimization template for array based big omics data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2018-01-01-gpu-daemon--gpu-algorithm-design,-data-management-&-optimization-template-for-array-based-big-omics-data authors: "Awan, Muaaz Gul; Eslami, Taban; Saeed, Fahad; " year: "2018" -journal: Pergamon +journal: "Pergamon Computers in biology and medicine" volume: 101 issue: pages: 163-173 diff --git "a/papers/_posts/2018-01-01-mass\342\200\220simulator--a-highly-configurable-simulator-for-generating-ms-ms-datasets-for-benchmarking-of-proteomics-algorithms.md" "b/papers/_posts/2018-01-01-mass\342\200\220simulator--a-highly-configurable-simulator-for-generating-ms-ms-datasets-for-benchmarking-of-proteomics-algorithms.md" index 7dc9e2c9..c908c295 100644 --- "a/papers/_posts/2018-01-01-mass\342\200\220simulator--a-highly-configurable-simulator-for-generating-ms-ms-datasets-for-benchmarking-of-proteomics-algorithms.md" +++ "b/papers/_posts/2018-01-01-mass\342\200\220simulator--a-highly-configurable-simulator-for-generating-ms-ms-datasets-for-benchmarking-of-proteomics-algorithms.md" @@ -1,10 +1,10 @@ --- layout: paper title: "MaSS‐Simulator: A Highly Configurable Simulator for Generating MS/MS Datasets for Benchmarking of Proteomics Algorithms" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2018-01-01-mass‐simulator--a-highly-configurable-simulator-for-generating-ms-ms-datasets-for-benchmarking-of-proteomics-algorithms authors: "Awan, Muaaz Gul; Saeed, Fahad; " year: "2018" -journal: Wiley +journal: "Wiley PROTEOMICS" volume: issue: pages: diff --git a/papers/_posts/2018-01-01-parallel-sampling-pipeline-for-indefinite-stream-of-heterogeneous-graphs-using-opencl-for-fpgas.md b/papers/_posts/2018-01-01-parallel-sampling-pipeline-for-indefinite-stream-of-heterogeneous-graphs-using-opencl-for-fpgas.md index bdeb9d55..bdee5d8f 100644 --- a/papers/_posts/2018-01-01-parallel-sampling-pipeline-for-indefinite-stream-of-heterogeneous-graphs-using-opencl-for-fpgas.md +++ b/papers/_posts/2018-01-01-parallel-sampling-pipeline-for-indefinite-stream-of-heterogeneous-graphs-using-opencl-for-fpgas.md @@ -1,10 +1,10 @@ --- layout: paper title: "Parallel sampling-pipeline for indefinite stream of heterogeneous graphs using OpenCL for FPGAs" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2018-01-01-parallel-sampling-pipeline-for-indefinite-stream-of-heterogeneous-graphs-using-opencl-for-fpgas authors: "Tariq, Muhammad Usman; Saeed, Fahad; " year: "2018" -journal: IEEE +journal: "IEEE 2018 IEEE International Conference on Big Data (Big Data)" volume: issue: pages: 4752-4761 diff --git a/papers/_posts/2018-01-01-similarity-based-classification-of-adhd-using-singular-value-decomposition.md b/papers/_posts/2018-01-01-similarity-based-classification-of-adhd-using-singular-value-decomposition.md index 034e0e00..aeef0127 100644 --- a/papers/_posts/2018-01-01-similarity-based-classification-of-adhd-using-singular-value-decomposition.md +++ b/papers/_posts/2018-01-01-similarity-based-classification-of-adhd-using-singular-value-decomposition.md @@ -1,7 +1,7 @@ --- layout: paper title: "Similarity based classification of ADHD using Singular Value Decomposition" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2018-01-01-similarity-based-classification-of-adhd-using-singular-value-decomposition authors: "Eslami, Taban; Saeed, Fahad; " year: "2018" journal: diff --git a/papers/_posts/2018-01-01-towards-quantifying-psychiatric-diagnosis-using-machine-learning-algorithms-and-big-fmri-data.md b/papers/_posts/2018-01-01-towards-quantifying-psychiatric-diagnosis-using-machine-learning-algorithms-and-big-fmri-data.md index 4bd7048b..881dc36b 100644 --- a/papers/_posts/2018-01-01-towards-quantifying-psychiatric-diagnosis-using-machine-learning-algorithms-and-big-fmri-data.md +++ b/papers/_posts/2018-01-01-towards-quantifying-psychiatric-diagnosis-using-machine-learning-algorithms-and-big-fmri-data.md @@ -1,10 +1,10 @@ --- layout: paper title: "Towards quantifying psychiatric diagnosis using machine learning algorithms and big fMRI data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2018-01-01-towards-quantifying-psychiatric-diagnosis-using-machine-learning-algorithms-and-big-fmri-data authors: "Saeed, Fahad; " year: "2018" -journal: BMC +journal: "BMC BMC Big Data Analytics" volume: 3 issue: pages: 7 diff --git a/papers/_posts/2019-01-01-2019-ieee-international-conference-on-bioinformatics-and-biomedicine-bibm.md b/papers/_posts/2019-01-01-2019-ieee-international-conference-on-bioinformatics-and-biomedicine-bibm.md index a3beee39..e9b3484d 100644 --- a/papers/_posts/2019-01-01-2019-ieee-international-conference-on-bioinformatics-and-biomedicine-bibm.md +++ b/papers/_posts/2019-01-01-2019-ieee-international-conference-on-bioinformatics-and-biomedicine-bibm.md @@ -1,7 +1,7 @@ --- layout: paper title: "2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2019-01-01-2019-ieee-international-conference-on-bioinformatics-and-biomedicine-bibm authors: "Haseeb, Muhammad; Saeed, Fahad; " year: "2019" journal: diff --git a/papers/_posts/2019-01-01-asd-diagnet--a-hybrid-learning-approach-for-detection-of-autism-spectrum-disorder-using-fmri-data.md b/papers/_posts/2019-01-01-asd-diagnet--a-hybrid-learning-approach-for-detection-of-autism-spectrum-disorder-using-fmri-data.md new file mode 100644 index 00000000..81d25287 --- /dev/null +++ b/papers/_posts/2019-01-01-asd-diagnet--a-hybrid-learning-approach-for-detection-of-autism-spectrum-disorder-using-fmri-data.md @@ -0,0 +1,40 @@ +--- +layout: paper +title: "ASD-DiagNet: A hybrid learning approach for detection of Autism Spectrum Disorder using fMRI data" +nickname: 2019-01-01-asd-diagnet--a-hybrid-learning-approach-for-detection-of-autism-spectrum-disorder-using-fmri-data +authors: "Eslami, Taban; Mirjalili, Vahid; Fong, Alvis; Laird, Angela; Saeed, Fahad; " +year: "2019" +journal: "Frontiers Frontiers in Neuroinformatics" +volume: 13 +issue: +pages: 70 +is_published: True +image: /assets/images/papers/biorxiv.png +projects: [] +tags: [] + +# Text +fulltext: +pdf: +pdflink: +pmcid: +preprint: +supplement: + +# Links +doi: "10.3389/fninf.2019.00070/full" +pmid: + +# Data and code +github: [] +neurovault: +openneuro: [] +figshare: +figshare_names: +osf: +--- +{% include JB/setup %} + +# Abstract + +Heterogeneous mental disorders such as Autism Spectrum Disorder (ASD) are notoriously difficult to diagnose, especially in children. The current psychiatric diagnostic process is based purely on the behavioral observation of symptomology (DSM-5/ICD-10) and may be prone to misdiagnosis. In order to move the field toward more quantitative diagnosis, we need advanced and scalable machine learning infrastructure that will allow us to identify reliable biomarkers of mental health disorders. In this paper, we propose a framework called ASD-DiagNet for classifying subjects with ASD from healthy subjects by using only fMRI data. We designed and implemented a joint learning procedure using an autoencoder and a single layer perceptron (SLP) which results in improved quality of extracted features and optimized parameters for the model. Further, we designed and implemented a data augmentation strategy, based on linear interpolation on available feature vectors, that allows us to produce synthetic datasets needed for training of machine learning models. The proposed approach is evaluated on a public dataset provided by Autism Brain Imaging Data Exchange including 1, 035 subjects coming from 17 different brain imaging centers. Our machine learning model outperforms other state of the art methods from 10 imaging centers with increase in classification accuracy up to 28% with maximum accuracy of 82%. The machine learning technique presented in this paper, in addition to yielding better quality, gives enormous advantages in terms of execution time (40 min vs. 7 h on other methods). The implemented code is available as GPL license … diff --git a/papers/_posts/2019-01-01-auto-asd-network--a-technique-based-on-deep-learning-and-support-vector-machines-for-diagnosing-autism-spectrum-disorder-using-fmri-data.md b/papers/_posts/2019-01-01-auto-asd-network--a-technique-based-on-deep-learning-and-support-vector-machines-for-diagnosing-autism-spectrum-disorder-using-fmri-data.md index 4e72c11b..b9172998 100644 --- a/papers/_posts/2019-01-01-auto-asd-network--a-technique-based-on-deep-learning-and-support-vector-machines-for-diagnosing-autism-spectrum-disorder-using-fmri-data.md +++ b/papers/_posts/2019-01-01-auto-asd-network--a-technique-based-on-deep-learning-and-support-vector-machines-for-diagnosing-autism-spectrum-disorder-using-fmri-data.md @@ -1,7 +1,7 @@ --- layout: paper title: "Auto-ASD-Network: A technique based on Deep Learning and Support Vector Machines for diagnosing Autism Spectrum Disorder using fMRI data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2019-01-01-auto-asd-network--a-technique-based-on-deep-learning-and-support-vector-machines-for-diagnosing-autism-spectrum-disorder-using-fmri-data authors: "Eslami, Taban; Saeed, Fahad; " year: "2019" journal: diff --git a/papers/_posts/2019-01-01-efficient-shared-peak-counting-in-database-peptide-search-using-compact-data-structure-for-fragment-ion-index.md b/papers/_posts/2019-01-01-efficient-shared-peak-counting-in-database-peptide-search-using-compact-data-structure-for-fragment-ion-index.md index eb9e028c..0ae39611 100644 --- a/papers/_posts/2019-01-01-efficient-shared-peak-counting-in-database-peptide-search-using-compact-data-structure-for-fragment-ion-index.md +++ b/papers/_posts/2019-01-01-efficient-shared-peak-counting-in-database-peptide-search-using-compact-data-structure-for-fragment-ion-index.md @@ -1,10 +1,10 @@ --- layout: paper title: "Efficient shared peak counting in database peptide search using compact data structure for fragment-ion index" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2019-01-01-efficient-shared-peak-counting-in-database-peptide-search-using-compact-data-structure-for-fragment-ion-index authors: "Haseeb, Muhammad; Saeed, Fahad; " year: "2019" -journal: IEEE +journal: "IEEE 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)" volume: issue: pages: 275-278 diff --git a/papers/_posts/2019-01-01-gpu-dfc--a-gpu-based-parallel-algorithm-for-computing-dynamic-functional-connectivity-of-big-fmri-data.md b/papers/_posts/2019-01-01-gpu-dfc--a-gpu-based-parallel-algorithm-for-computing-dynamic-functional-connectivity-of-big-fmri-data.md index b83ed8da..6f87e5c9 100644 --- a/papers/_posts/2019-01-01-gpu-dfc--a-gpu-based-parallel-algorithm-for-computing-dynamic-functional-connectivity-of-big-fmri-data.md +++ b/papers/_posts/2019-01-01-gpu-dfc--a-gpu-based-parallel-algorithm-for-computing-dynamic-functional-connectivity-of-big-fmri-data.md @@ -1,7 +1,7 @@ --- layout: paper title: "GPU-DFC: A GPU-based parallel algorithm for computing dynamic-functional connectivity of big fMRI data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2019-01-01-gpu-dfc--a-gpu-based-parallel-algorithm-for-computing-dynamic-functional-connectivity-of-big-fmri-data authors: "Eslami, Taban; Saeed, Fahad; " year: "2019" journal: diff --git a/papers/_posts/2019-01-01-gpu-sfft--a-gpu-based-parallel-algorithm-for-computing-the-sparse-fast-fourier-transform-sfft-of-k-sparse-signals.md b/papers/_posts/2019-01-01-gpu-sfft--a-gpu-based-parallel-algorithm-for-computing-the-sparse-fast-fourier-transform-sfft-of-k-sparse-signals.md index 0c772a44..28213dba 100644 --- a/papers/_posts/2019-01-01-gpu-sfft--a-gpu-based-parallel-algorithm-for-computing-the-sparse-fast-fourier-transform-sfft-of-k-sparse-signals.md +++ b/papers/_posts/2019-01-01-gpu-sfft--a-gpu-based-parallel-algorithm-for-computing-the-sparse-fast-fourier-transform-sfft-of-k-sparse-signals.md @@ -1,10 +1,10 @@ --- layout: paper title: "GPU-SFFT: A GPU based parallel algorithm for computing the Sparse Fast Fourier Transform (SFFT) of k-sparse signals" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2019-01-01-gpu-sfft--a-gpu-based-parallel-algorithm-for-computing-the-sparse-fast-fourier-transform-sfft-of-k-sparse-signals authors: "Artiles, Oswaldo; Saeed, Fahad; " year: "2019" -journal: IEEE +journal: "IEEE 2019 IEEE International Conference on Big Data (Big Data)" volume: issue: pages: 3303-3311 diff --git a/papers/_posts/2019-01-01-high-performance-reductive-strategies-for-big-data-from-lc-ms-ms-proteomics.md b/papers/_posts/2019-01-01-high-performance-reductive-strategies-for-big-data-from-lc-ms-ms-proteomics.md index b6a3a41e..1d944f45 100644 --- a/papers/_posts/2019-01-01-high-performance-reductive-strategies-for-big-data-from-lc-ms-ms-proteomics.md +++ b/papers/_posts/2019-01-01-high-performance-reductive-strategies-for-big-data-from-lc-ms-ms-proteomics.md @@ -1,10 +1,10 @@ --- layout: paper title: "High-Performance Reductive Strategies for Big Data from LC-MS/MS Proteomics" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2019-01-01-high-performance-reductive-strategies-for-big-data-from-lc-ms-ms-proteomics authors: "Awan, Muaaz Gul; " year: "2019" -journal: Western Michigan University +journal: "Western Michigan University" volume: issue: pages: diff --git a/papers/_posts/2019-01-01-lbe--a-computational-load-balancing-algorithm-for-speeding-up-parallel-peptide-search-in-mass-spectrometry-based-proteomics.md b/papers/_posts/2019-01-01-lbe--a-computational-load-balancing-algorithm-for-speeding-up-parallel-peptide-search-in-mass-spectrometry-based-proteomics.md index 6609e47b..6f476100 100644 --- a/papers/_posts/2019-01-01-lbe--a-computational-load-balancing-algorithm-for-speeding-up-parallel-peptide-search-in-mass-spectrometry-based-proteomics.md +++ b/papers/_posts/2019-01-01-lbe--a-computational-load-balancing-algorithm-for-speeding-up-parallel-peptide-search-in-mass-spectrometry-based-proteomics.md @@ -1,7 +1,7 @@ --- layout: paper title: "LBE: A Computational Load Balancing Algorithm for Speeding up Parallel Peptide Search in Mass-Spectrometry based Proteomics" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2019-01-01-lbe--a-computational-load-balancing-algorithm-for-speeding-up-parallel-peptide-search-in-mass-spectrometry-based-proteomics authors: "Haseeb, Muhammad; Afzali, Fatima; Saeed, Fahad; " year: "2019" journal: diff --git "a/papers/_posts/2019-01-01-ngs\342\200\220integrator--a-tool-for-combining-information-from-multiple-genome\342\200\220wide-ngs-data-tracks-using-minimum-bayes-factors.md" "b/papers/_posts/2019-01-01-ngs\342\200\220integrator--a-tool-for-combining-information-from-multiple-genome\342\200\220wide-ngs-data-tracks-using-minimum-bayes-factors.md" index 87e2044f..abd879ac 100644 --- "a/papers/_posts/2019-01-01-ngs\342\200\220integrator--a-tool-for-combining-information-from-multiple-genome\342\200\220wide-ngs-data-tracks-using-minimum-bayes-factors.md" +++ "b/papers/_posts/2019-01-01-ngs\342\200\220integrator--a-tool-for-combining-information-from-multiple-genome\342\200\220wide-ngs-data-tracks-using-minimum-bayes-factors.md" @@ -1,10 +1,10 @@ --- layout: paper title: "NGS‐Integrator: A Tool for Combining Information from Multiple Genome‐Wide NGS Data Tracks Using Minimum Bayes Factors" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2019-01-01-ngs‐integrator--a-tool-for-combining-information-from-multiple-genome‐wide-ngs-data-tracks-using-minimum-bayes-factors authors: "Jung, Hyun Jun; Wen, Bronte; Chen, Lihe; Saeed, Fahad; Knepper, Mark A; " year: "2019" -journal: The Federation of American Societies for Experimental Biology +journal: "The Federation of American Societies for Experimental Biology The FASEB Journal" volume: 33 issue: pages: 637.2-637.2 diff --git a/papers/_posts/2019-01-01-optimized-cnn-based-diagnosis-system-to-detect-the-pneumonia-from-chest-radiographs.md b/papers/_posts/2019-01-01-optimized-cnn-based-diagnosis-system-to-detect-the-pneumonia-from-chest-radiographs.md index 0a335699..3a4fdcc2 100644 --- a/papers/_posts/2019-01-01-optimized-cnn-based-diagnosis-system-to-detect-the-pneumonia-from-chest-radiographs.md +++ b/papers/_posts/2019-01-01-optimized-cnn-based-diagnosis-system-to-detect-the-pneumonia-from-chest-radiographs.md @@ -1,10 +1,10 @@ --- layout: paper title: "Optimized CNN-based diagnosis system to detect the pneumonia from chest radiographs" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2019-01-01-optimized-cnn-based-diagnosis-system-to-detect-the-pneumonia-from-chest-radiographs authors: "Aledhari, Mohammed; Joji, Shelby; Hefeida, Mohamed; Saeed, Fahad; " year: "2019" -journal: IEEE +journal: "IEEE 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)" volume: issue: pages: 2405-2412 diff --git a/papers/_posts/2019-01-01-slm-transform--a-method-for-memory-efficient-indexing-of-spectra-for-database-search-in-lc-ms-ms-proteomics.md b/papers/_posts/2019-01-01-slm-transform--a-method-for-memory-efficient-indexing-of-spectra-for-database-search-in-lc-ms-ms-proteomics.md index db945b39..8fbb2290 100644 --- a/papers/_posts/2019-01-01-slm-transform--a-method-for-memory-efficient-indexing-of-spectra-for-database-search-in-lc-ms-ms-proteomics.md +++ b/papers/_posts/2019-01-01-slm-transform--a-method-for-memory-efficient-indexing-of-spectra-for-database-search-in-lc-ms-ms-proteomics.md @@ -1,10 +1,10 @@ --- layout: paper title: "Slm-transform: A method for memory-efficient indexing of spectra for database search in lc-ms/ms proteomics" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2019-01-01-slm-transform--a-method-for-memory-efficient-indexing-of-spectra-for-database-search-in-lc-ms-ms-proteomics authors: "Haseeb, Muhammad; Awan, Muaaz G; Cadigan, Alexander S; Saeed, Fahad; " year: "2019" -journal: Cold Spring Harbor Laboratory +journal: "Cold Spring Harbor Laboratory bioRxiv" volume: issue: pages: 531681 diff --git a/papers/_posts/2020-01-01-federated-learning--a-survey-on-enabling-technologies,-protocols,-and-applications.md b/papers/_posts/2020-01-01-federated-learning--a-survey-on-enabling-technologies,-protocols,-and-applications.md index 969fb014..67f152a3 100644 --- a/papers/_posts/2020-01-01-federated-learning--a-survey-on-enabling-technologies,-protocols,-and-applications.md +++ b/papers/_posts/2020-01-01-federated-learning--a-survey-on-enabling-technologies,-protocols,-and-applications.md @@ -1,10 +1,10 @@ --- layout: paper title: "Federated learning: A survey on enabling technologies, protocols, and applications" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2020-01-01-federated-learning--a-survey-on-enabling-technologies,-protocols,-and-applications authors: "Aledhari, Mohammed; Razzak, Rehma; Parizi, Reza M; Saeed, Fahad; " year: "2020" -journal: IEEE +journal: "IEEE IEEE Access" volume: 8 issue: pages: 140699-140725 diff --git a/papers/_posts/2020-01-01-high-performance-and-machine-learning-algorithms-for-brain-fmri-data.md b/papers/_posts/2020-01-01-high-performance-and-machine-learning-algorithms-for-brain-fmri-data.md index b9db4910..ae17b4e7 100644 --- a/papers/_posts/2020-01-01-high-performance-and-machine-learning-algorithms-for-brain-fmri-data.md +++ b/papers/_posts/2020-01-01-high-performance-and-machine-learning-algorithms-for-brain-fmri-data.md @@ -1,10 +1,10 @@ --- layout: paper title: "High Performance and Machine Learning Algorithms for Brain fMRI Data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2020-01-01-high-performance-and-machine-learning-algorithms-for-brain-fmri-data authors: "Eslami, Taban; " year: "2020" -journal: Western Michigan University +journal: "Western Michigan University" volume: issue: pages: diff --git a/papers/_posts/2020-01-01-methods-and-systems-for-compressing-data.md b/papers/_posts/2020-01-01-methods-and-systems-for-compressing-data.md index 4b1a1fda..096e4215 100644 --- a/papers/_posts/2020-01-01-methods-and-systems-for-compressing-data.md +++ b/papers/_posts/2020-01-01-methods-and-systems-for-compressing-data.md @@ -1,10 +1,10 @@ --- layout: paper title: "Methods and systems for compressing data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2020-01-01-methods-and-systems-for-compressing-data authors: "Saeed, Fahad; Haseeb, Muhammad; " year: "2020" -journal: US Patent 10,810,180 +journal: "US Patent 10,810,180" volume: issue: pages: diff --git "a/papers/_posts/2020-01-01-ngs-integrator--an-efficient-tool-for-combining-multiple-ngs-data-tracks-using-minimum-bayes\342\200\231-factors.md" "b/papers/_posts/2020-01-01-ngs-integrator--an-efficient-tool-for-combining-multiple-ngs-data-tracks-using-minimum-bayes\342\200\231-factors.md" index ddef6a08..c1b33481 100644 --- "a/papers/_posts/2020-01-01-ngs-integrator--an-efficient-tool-for-combining-multiple-ngs-data-tracks-using-minimum-bayes\342\200\231-factors.md" +++ "b/papers/_posts/2020-01-01-ngs-integrator--an-efficient-tool-for-combining-multiple-ngs-data-tracks-using-minimum-bayes\342\200\231-factors.md" @@ -1,10 +1,10 @@ --- layout: paper title: "NGS-Integrator: An efficient tool for combining multiple NGS data tracks using minimum Bayes’ factors" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2020-01-01-ngs-integrator--an-efficient-tool-for-combining-multiple-ngs-data-tracks-using-minimum-bayes’-factors authors: "Wen, Bronte; Jung, Hyun Jun; Chen, Lihe; Saeed, Fahad; Knepper, Mark A; " year: "2020" -journal: BioMed Central +journal: "BioMed Central BMC genomics" volume: 21 issue: pages: 1-7 diff --git a/papers/_posts/2021-01-01-a-multi-factorial-assessment-of-functional-human-autistic-spectrum-brain-network-analysis.md b/papers/_posts/2021-01-01-a-multi-factorial-assessment-of-functional-human-autistic-spectrum-brain-network-analysis.md index b43de7dc..7d0939b2 100644 --- a/papers/_posts/2021-01-01-a-multi-factorial-assessment-of-functional-human-autistic-spectrum-brain-network-analysis.md +++ b/papers/_posts/2021-01-01-a-multi-factorial-assessment-of-functional-human-autistic-spectrum-brain-network-analysis.md @@ -1,10 +1,10 @@ --- layout: paper title: "A Multi-Factorial Assessment of Functional Human Autistic Spectrum Brain Network Analysis" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2021-01-01-a-multi-factorial-assessment-of-functional-human-autistic-spectrum-brain-network-analysis authors: "Artiles, Oswaldo; Saeed, Fahad; " year: "2021" -journal: IEEE +journal: "IEEE 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)" volume: issue: pages: 3526-3531 diff --git a/papers/_posts/2021-01-01-asd-saenet--a-sparse-autoencoder,-and-deep-neural-network-model-for-detecting-autism-spectrum-disorder-asd-using-fmri-data.md b/papers/_posts/2021-01-01-asd-saenet--a-sparse-autoencoder,-and-deep-neural-network-model-for-detecting-autism-spectrum-disorder-asd-using-fmri-data.md index 96d850da..13278dcf 100644 --- a/papers/_posts/2021-01-01-asd-saenet--a-sparse-autoencoder,-and-deep-neural-network-model-for-detecting-autism-spectrum-disorder-asd-using-fmri-data.md +++ b/papers/_posts/2021-01-01-asd-saenet--a-sparse-autoencoder,-and-deep-neural-network-model-for-detecting-autism-spectrum-disorder-asd-using-fmri-data.md @@ -1,10 +1,10 @@ --- layout: paper title: "ASD-SAENet: a sparse autoencoder, and deep-neural network model for detecting autism spectrum disorder (ASD) using fMRI data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2021-01-01-asd-saenet--a-sparse-autoencoder,-and-deep-neural-network-model-for-detecting-autism-spectrum-disorder-asd-using-fmri-data authors: "Almuqhim, Fahad; Saeed, Fahad; " year: "2021" -journal: Frontiers Media SA +journal: "Frontiers Media SA Frontiers in Computational Neuroscience" volume: 15 issue: pages: 654315 diff --git a/papers/_posts/2021-01-01-benchmarking-mass-spectrometry-based-proteomics-algorithms-using-a-simulated-database.md b/papers/_posts/2021-01-01-benchmarking-mass-spectrometry-based-proteomics-algorithms-using-a-simulated-database.md index f93ebd7f..240afe4b 100644 --- a/papers/_posts/2021-01-01-benchmarking-mass-spectrometry-based-proteomics-algorithms-using-a-simulated-database.md +++ b/papers/_posts/2021-01-01-benchmarking-mass-spectrometry-based-proteomics-algorithms-using-a-simulated-database.md @@ -1,10 +1,10 @@ --- layout: paper title: "Benchmarking mass spectrometry based proteomics algorithms using a simulated database" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2021-01-01-benchmarking-mass-spectrometry-based-proteomics-algorithms-using-a-simulated-database authors: "Awan, Muaaz Gul; Awan, Abdullah Gul; Saeed, Fahad; " year: "2021" -journal: Springer Vienna Vienna +journal: "Springer Vienna Vienna Network Modeling Analysis in Health Informatics and Bioinformatics" volume: 10 issue: pages: 23 diff --git a/papers/_posts/2021-01-01-communication-avoiding-micro-architecture-to-compute-xcorr-scores-for-peptide-identification.md b/papers/_posts/2021-01-01-communication-avoiding-micro-architecture-to-compute-xcorr-scores-for-peptide-identification.md index e4f23cb0..34ea210d 100644 --- a/papers/_posts/2021-01-01-communication-avoiding-micro-architecture-to-compute-xcorr-scores-for-peptide-identification.md +++ b/papers/_posts/2021-01-01-communication-avoiding-micro-architecture-to-compute-xcorr-scores-for-peptide-identification.md @@ -1,10 +1,10 @@ --- layout: paper title: "Communication-avoiding micro-architecture to compute Xcorr scores for peptide identification" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2021-01-01-communication-avoiding-micro-architecture-to-compute-xcorr-scores-for-peptide-identification authors: "Kumar, Sumesh; Saeed, Fahad; " year: "2021" -journal: IEEE +journal: "IEEE 2021 31st International Conference on Field-Programmable Logic and Applications (FPL)" volume: issue: pages: 99-103 diff --git a/papers/_posts/2021-01-01-deepcovidnet--deep-convolutional-neural-network-for-covid-19-detection-from-chest-radiographic-images.md b/papers/_posts/2021-01-01-deepcovidnet--deep-convolutional-neural-network-for-covid-19-detection-from-chest-radiographic-images.md index b8f69f54..6ec40d77 100644 --- a/papers/_posts/2021-01-01-deepcovidnet--deep-convolutional-neural-network-for-covid-19-detection-from-chest-radiographic-images.md +++ b/papers/_posts/2021-01-01-deepcovidnet--deep-convolutional-neural-network-for-covid-19-detection-from-chest-radiographic-images.md @@ -1,10 +1,10 @@ --- layout: paper title: "DeepCOVIDNet: Deep Convolutional Neural Network for COVID-19 Detection from Chest Radiographic Images" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2021-01-01-deepcovidnet--deep-convolutional-neural-network-for-covid-19-detection-from-chest-radiographic-images authors: "Ahmed, Khandaker Mamun; Eslami, Taban; Saeed, Fahad; Amini, M Hadi; " year: "2021" -journal: IEEE +journal: "IEEE 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)" volume: issue: pages: 1703-1710 diff --git a/papers/_posts/2021-01-01-explainable-and-scalable-machine-learning-algorithms-for-detection-of-autism-spectrum-disorder-using-fmri-data.md b/papers/_posts/2021-01-01-explainable-and-scalable-machine-learning-algorithms-for-detection-of-autism-spectrum-disorder-using-fmri-data.md index 2beed741..2f006c52 100644 --- a/papers/_posts/2021-01-01-explainable-and-scalable-machine-learning-algorithms-for-detection-of-autism-spectrum-disorder-using-fmri-data.md +++ b/papers/_posts/2021-01-01-explainable-and-scalable-machine-learning-algorithms-for-detection-of-autism-spectrum-disorder-using-fmri-data.md @@ -1,10 +1,10 @@ --- layout: paper title: "Explainable and scalable machine learning algorithms for detection of autism spectrum disorder using fMRI data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2021-01-01-explainable-and-scalable-machine-learning-algorithms-for-detection-of-autism-spectrum-disorder-using-fmri-data authors: "Eslami, Taban; Raiker, Joseph S; Saeed, Fahad; " year: "2021" -journal: Academic Press +journal: "Academic Press Neural Engineering Techniques for Autism Spectrum Disorder" volume: issue: pages: 39-54 diff --git a/papers/_posts/2021-01-01-graph-theoretic-approach-for-the-analysis-of-comprehensive-mass-spectrometry-ms-ms-data-of-dissolved-organic-matter.md b/papers/_posts/2021-01-01-graph-theoretic-approach-for-the-analysis-of-comprehensive-mass-spectrometry-ms-ms-data-of-dissolved-organic-matter.md index 0c9367ea..a583b78a 100644 --- a/papers/_posts/2021-01-01-graph-theoretic-approach-for-the-analysis-of-comprehensive-mass-spectrometry-ms-ms-data-of-dissolved-organic-matter.md +++ b/papers/_posts/2021-01-01-graph-theoretic-approach-for-the-analysis-of-comprehensive-mass-spectrometry-ms-ms-data-of-dissolved-organic-matter.md @@ -1,10 +1,10 @@ --- layout: paper title: "Graph Theoretic Approach for the Analysis of Comprehensive Mass-Spectrometry (MS/MS) Data of Dissolved Organic Matter" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2021-01-01-graph-theoretic-approach-for-the-analysis-of-comprehensive-mass-spectrometry-ms-ms-data-of-dissolved-organic-matter authors: "Tariq, Muhammad Usman; Leyvay, Dennys; Limaz, Francisco Alberto Fernandez; Saeed, Fahad; " year: "2021" -journal: IEEE +journal: "IEEE 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)" volume: issue: pages: 3742-3746 diff --git a/papers/_posts/2021-01-01-hicops--high-performance-computing-framework-for-tera-scale-database-search-of-mass-spectrometry-based-omics-data.md b/papers/_posts/2021-01-01-hicops--high-performance-computing-framework-for-tera-scale-database-search-of-mass-spectrometry-based-omics-data.md index e5695b43..680ca7a2 100644 --- a/papers/_posts/2021-01-01-hicops--high-performance-computing-framework-for-tera-scale-database-search-of-mass-spectrometry-based-omics-data.md +++ b/papers/_posts/2021-01-01-hicops--high-performance-computing-framework-for-tera-scale-database-search-of-mass-spectrometry-based-omics-data.md @@ -1,7 +1,7 @@ --- layout: paper title: "HiCOPS: High Performance Computing Framework for Tera-Scale Database Search of Mass Spectrometry based Omics Data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2021-01-01-hicops--high-performance-computing-framework-for-tera-scale-database-search-of-mass-spectrometry-based-omics-data authors: "Haseeb, Muhammad; Saeed, Fahad; " year: "2021" journal: diff --git a/papers/_posts/2021-01-01-high-performance-computing-framework-for-tera-scale-database-search-of-mass-spectrometry-data.md b/papers/_posts/2021-01-01-high-performance-computing-framework-for-tera-scale-database-search-of-mass-spectrometry-data.md index e35aa107..2c20c89d 100644 --- a/papers/_posts/2021-01-01-high-performance-computing-framework-for-tera-scale-database-search-of-mass-spectrometry-data.md +++ b/papers/_posts/2021-01-01-high-performance-computing-framework-for-tera-scale-database-search-of-mass-spectrometry-data.md @@ -1,10 +1,10 @@ --- layout: paper title: "High performance computing framework for tera-scale database search of mass spectrometry data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2021-01-01-high-performance-computing-framework-for-tera-scale-database-search-of-mass-spectrometry-data authors: "Haseeb, Muhammad; Saeed, Fahad; " year: "2021" -journal: Nature Publishing Group +journal: "Nature Publishing Group Nature computational science" volume: 1 issue: pages: 550-561 diff --git a/papers/_posts/2021-01-01-machine-learning-methods-for-diagnosing-autism-spectrum-disorder-and-attention-deficit-hyperactivity-disorder-using-functional-and-structural-mri--a-survey.md b/papers/_posts/2021-01-01-machine-learning-methods-for-diagnosing-autism-spectrum-disorder-and-attention-deficit-hyperactivity-disorder-using-functional-and-structural-mri--a-survey.md index 5decfe48..725d1148 100644 --- a/papers/_posts/2021-01-01-machine-learning-methods-for-diagnosing-autism-spectrum-disorder-and-attention-deficit-hyperactivity-disorder-using-functional-and-structural-mri--a-survey.md +++ b/papers/_posts/2021-01-01-machine-learning-methods-for-diagnosing-autism-spectrum-disorder-and-attention-deficit-hyperactivity-disorder-using-functional-and-structural-mri--a-survey.md @@ -1,10 +1,10 @@ --- layout: paper title: "Machine Learning methods for diagnosing Autism Spectrum Disorder and Attention-deficit/Hyperactivity Disorder using functional and structural MRI: A Survey" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2021-01-01-machine-learning-methods-for-diagnosing-autism-spectrum-disorder-and-attention-deficit-hyperactivity-disorder-using-functional-and-structural-mri--a-survey authors: "Eslami, Taban; Almuqhim, Fahad; Raiker, Joseph S; Saeed, Fahad; " year: "2021" -journal: Frontiers +journal: "Frontiers Frontiers in Neuroinformatics" volume: 14 issue: pages: 62 diff --git a/papers/_posts/2021-01-01-methods-for-proteogenomics-data-analysis,-challenges,-and-scalability-bottlenecks--a-survey.md b/papers/_posts/2021-01-01-methods-for-proteogenomics-data-analysis,-challenges,-and-scalability-bottlenecks--a-survey.md index 6b22448c..dff638ba 100644 --- a/papers/_posts/2021-01-01-methods-for-proteogenomics-data-analysis,-challenges,-and-scalability-bottlenecks--a-survey.md +++ b/papers/_posts/2021-01-01-methods-for-proteogenomics-data-analysis,-challenges,-and-scalability-bottlenecks--a-survey.md @@ -1,10 +1,10 @@ --- layout: paper title: "Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2021-01-01-methods-for-proteogenomics-data-analysis,-challenges,-and-scalability-bottlenecks--a-survey authors: "Tariq, Muhammad Usman; Haseeb, Muhammad; Aledhari, Mohammed; Razzak, Rehma; Parizi, Reza M; Saeed, Fahad; " year: "2021" -journal: IEEE +journal: "IEEE IEEE Access" volume: issue: pages: diff --git a/papers/_posts/2021-01-01-neural-engineering-techniques-for-autism-spectrum-disorder--volume-1--imaging-and-signal-analysis.md b/papers/_posts/2021-01-01-neural-engineering-techniques-for-autism-spectrum-disorder--volume-1--imaging-and-signal-analysis.md index b5d96ea7..76cb2200 100644 --- a/papers/_posts/2021-01-01-neural-engineering-techniques-for-autism-spectrum-disorder--volume-1--imaging-and-signal-analysis.md +++ b/papers/_posts/2021-01-01-neural-engineering-techniques-for-autism-spectrum-disorder--volume-1--imaging-and-signal-analysis.md @@ -1,10 +1,10 @@ --- layout: paper title: "Neural Engineering Techniques for Autism Spectrum Disorder: Volume 1: Imaging and Signal Analysis" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2021-01-01-neural-engineering-techniques-for-autism-spectrum-disorder--volume-1--imaging-and-signal-analysis authors: "El-Baz, Ayman S; Suri, Jasjit S; " year: "2021" -journal: Academic Press +journal: "Academic Press" volume: issue: pages: diff --git a/papers/_posts/2021-01-01-real-time-peptide-identification-from-high-throughput-mass-spectrometry-data.md b/papers/_posts/2021-01-01-real-time-peptide-identification-from-high-throughput-mass-spectrometry-data.md index 7f242766..74decea2 100644 --- a/papers/_posts/2021-01-01-real-time-peptide-identification-from-high-throughput-mass-spectrometry-data.md +++ b/papers/_posts/2021-01-01-real-time-peptide-identification-from-high-throughput-mass-spectrometry-data.md @@ -1,7 +1,7 @@ --- layout: paper title: "Real-time peptide identification from high-throughput mass-spectrometry data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2021-01-01-real-time-peptide-identification-from-high-throughput-mass-spectrometry-data authors: "Kumar, Sumesh; Saeed, Fahad; " year: "2021" journal: diff --git a/papers/_posts/2021-01-01-search-feasibility-in-distributed-ms-proteomics-big-data.md b/papers/_posts/2021-01-01-search-feasibility-in-distributed-ms-proteomics-big-data.md index 67b032d8..58c90820 100644 --- a/papers/_posts/2021-01-01-search-feasibility-in-distributed-ms-proteomics-big-data.md +++ b/papers/_posts/2021-01-01-search-feasibility-in-distributed-ms-proteomics-big-data.md @@ -1,7 +1,7 @@ --- layout: paper title: "Search feasibility in distributed MS-proteomics big data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2021-01-01-search-feasibility-in-distributed-ms-proteomics-big-data authors: "Mohammad, Umair; Saeed, Fahad; " year: "2021" journal: diff --git a/papers/_posts/2021-01-01-simulation-testbed-for-evaluating-distributed-querying-and-searching-of-mass-spectrometry-big-data-in-a-network-based-infrastructure.md b/papers/_posts/2021-01-01-simulation-testbed-for-evaluating-distributed-querying-and-searching-of-mass-spectrometry-big-data-in-a-network-based-infrastructure.md index 095ae5fe..75765f94 100644 --- a/papers/_posts/2021-01-01-simulation-testbed-for-evaluating-distributed-querying-and-searching-of-mass-spectrometry-big-data-in-a-network-based-infrastructure.md +++ b/papers/_posts/2021-01-01-simulation-testbed-for-evaluating-distributed-querying-and-searching-of-mass-spectrometry-big-data-in-a-network-based-infrastructure.md @@ -1,10 +1,10 @@ --- layout: paper title: "Simulation Testbed for Evaluating Distributed Querying and Searching of Mass Spectrometry Big Data in a Network-based Infrastructure" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2021-01-01-simulation-testbed-for-evaluating-distributed-querying-and-searching-of-mass-spectrometry-big-data-in-a-network-based-infrastructure authors: "Mohammad, Umair; Saeed, Fahad; " year: "2021" -journal: IEEE +journal: "IEEE 2021 IEEE Seventh International Conference on Big Data Computing Service and Applications (BigDataService)" volume: issue: pages: 137-142 diff --git a/papers/_posts/2021-01-01-source-data--high-performance-computing-framework-for-tera-scale-database-search-of-mass-spectrometry-data.md b/papers/_posts/2021-01-01-source-data--high-performance-computing-framework-for-tera-scale-database-search-of-mass-spectrometry-data.md index 896a5724..7aa24208 100644 --- a/papers/_posts/2021-01-01-source-data--high-performance-computing-framework-for-tera-scale-database-search-of-mass-spectrometry-data.md +++ b/papers/_posts/2021-01-01-source-data--high-performance-computing-framework-for-tera-scale-database-search-of-mass-spectrometry-data.md @@ -1,7 +1,7 @@ --- layout: paper title: "Source data: high performance computing framework for tera-scale database search of mass spectrometry data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2021-01-01-source-data--high-performance-computing-framework-for-tera-scale-database-search-of-mass-spectrometry-data authors: "Haseeb, Muhammad; Saeed, Fahad; " year: "2021" journal: diff --git a/papers/_posts/2021-01-01-specollate--deep-cross-modal-similarity-network-for-mass-spectrometry-data-based-peptide-deductions.md b/papers/_posts/2021-01-01-specollate--deep-cross-modal-similarity-network-for-mass-spectrometry-data-based-peptide-deductions.md index 16a73135..ed7c02fd 100644 --- a/papers/_posts/2021-01-01-specollate--deep-cross-modal-similarity-network-for-mass-spectrometry-data-based-peptide-deductions.md +++ b/papers/_posts/2021-01-01-specollate--deep-cross-modal-similarity-network-for-mass-spectrometry-data-based-peptide-deductions.md @@ -1,10 +1,10 @@ --- layout: paper title: "SpeCollate: Deep cross-modal similarity network for mass spectrometry data based peptide deductions" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2021-01-01-specollate--deep-cross-modal-similarity-network-for-mass-spectrometry-data-based-peptide-deductions authors: "Tariq, Muhammad Usman; Saeed, Fahad; " year: "2021" -journal: Public Library of Science San Francisco, CA USA +journal: "Public Library of Science San Francisco, CA USA PloS one" volume: 16 issue: pages: e0259349 diff --git a/papers/_posts/2021-01-01-turbobc--a-memory-efficient-and-scalable-gpu-based-betweenness-centrality-algorithm-in-the-language-of-linear-algebra.md b/papers/_posts/2021-01-01-turbobc--a-memory-efficient-and-scalable-gpu-based-betweenness-centrality-algorithm-in-the-language-of-linear-algebra.md index f0e29fe4..1075940d 100644 --- a/papers/_posts/2021-01-01-turbobc--a-memory-efficient-and-scalable-gpu-based-betweenness-centrality-algorithm-in-the-language-of-linear-algebra.md +++ b/papers/_posts/2021-01-01-turbobc--a-memory-efficient-and-scalable-gpu-based-betweenness-centrality-algorithm-in-the-language-of-linear-algebra.md @@ -1,7 +1,7 @@ --- layout: paper title: "TurboBC: A Memory Efficient and Scalable GPU Based Betweenness Centrality Algorithm in the Language of Linear Algebra" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2021-01-01-turbobc--a-memory-efficient-and-scalable-gpu-based-betweenness-centrality-algorithm-in-the-language-of-linear-algebra authors: "Artiles, Oswaldo; Saeed, Fahad; " year: "2021" journal: diff --git a/papers/_posts/2021-01-01-turbobfs--gpu-based-breadth-first-search-bfs-algorithms-in-the-language-of-linear-algebra.md b/papers/_posts/2021-01-01-turbobfs--gpu-based-breadth-first-search-bfs-algorithms-in-the-language-of-linear-algebra.md index 346cd3eb..26eb11a8 100644 --- a/papers/_posts/2021-01-01-turbobfs--gpu-based-breadth-first-search-bfs-algorithms-in-the-language-of-linear-algebra.md +++ b/papers/_posts/2021-01-01-turbobfs--gpu-based-breadth-first-search-bfs-algorithms-in-the-language-of-linear-algebra.md @@ -1,10 +1,10 @@ --- layout: paper title: "TurboBFS: GPU Based Breadth-First Search (BFS) Algorithms in the Language of Linear Algebra" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2021-01-01-turbobfs--gpu-based-breadth-first-search-bfs-algorithms-in-the-language-of-linear-algebra authors: "Artiles, Oswaldo; Saeed, Fahad; " year: "2021" -journal: IEEE +journal: "IEEE 2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)" volume: issue: pages: 520-528 diff --git a/papers/_posts/2022-01-01-a-easy-to-use-generalized-template-to-support-development-of-gpu-algorithms.md b/papers/_posts/2022-01-01-a-easy-to-use-generalized-template-to-support-development-of-gpu-algorithms.md index 581dc309..741d3810 100644 --- a/papers/_posts/2022-01-01-a-easy-to-use-generalized-template-to-support-development-of-gpu-algorithms.md +++ b/papers/_posts/2022-01-01-a-easy-to-use-generalized-template-to-support-development-of-gpu-algorithms.md @@ -1,10 +1,10 @@ --- layout: paper title: "A Easy to Use Generalized Template to Support Development of GPU Algorithms" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-a-easy-to-use-generalized-template-to-support-development-of-gpu-algorithms authors: "Saeed, Fahad; Haseeb, Muhammad; " year: "2022" -journal: Springer +journal: "Springer High-Performance Algorithms for Mass Spectrometry-Based Omics" volume: issue: pages: 77-87 diff --git a/papers/_posts/2022-01-01-biomedical-iot--enabling-technologies,-architectural-elements,-challenges,-and-future-directions.md b/papers/_posts/2022-01-01-biomedical-iot--enabling-technologies,-architectural-elements,-challenges,-and-future-directions.md index 768c037c..f6ef0628 100644 --- a/papers/_posts/2022-01-01-biomedical-iot--enabling-technologies,-architectural-elements,-challenges,-and-future-directions.md +++ b/papers/_posts/2022-01-01-biomedical-iot--enabling-technologies,-architectural-elements,-challenges,-and-future-directions.md @@ -1,10 +1,10 @@ --- layout: paper title: "Biomedical IoT: Enabling Technologies, Architectural Elements, Challenges, and Future Directions" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-biomedical-iot--enabling-technologies,-architectural-elements,-challenges,-and-future-directions authors: "Aledhari, Mohammed; Razzak, Rehma; Qolomany, Basheer; Al-Fuqaha, Ala; Saeed, Fahad; " year: "2022" -journal: IEEE +journal: "IEEE IEEE Access" volume: 10 issue: pages: 31306-31339 diff --git a/papers/_posts/2022-01-01-classification-of-autism-spectrum-disorder-using-rs-fmri-data-and-graph-convolutional-networks.md b/papers/_posts/2022-01-01-classification-of-autism-spectrum-disorder-using-rs-fmri-data-and-graph-convolutional-networks.md index dab23207..6e9af0ca 100644 --- a/papers/_posts/2022-01-01-classification-of-autism-spectrum-disorder-using-rs-fmri-data-and-graph-convolutional-networks.md +++ b/papers/_posts/2022-01-01-classification-of-autism-spectrum-disorder-using-rs-fmri-data-and-graph-convolutional-networks.md @@ -1,10 +1,10 @@ --- layout: paper title: "Classification of Autism Spectrum Disorder Using rs-fMRI data and Graph Convolutional Networks" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-classification-of-autism-spectrum-disorder-using-rs-fmri-data-and-graph-convolutional-networks authors: "Yang, Tianren; Al-Duailij, Mai A; Bozdag, Serdar; Saeed, Fahad; " year: "2022" -journal: IEEE +journal: "IEEE 2022 IEEE International Conference on Big Data (Big Data)" volume: issue: pages: 3131-3138 diff --git a/papers/_posts/2022-01-01-communication-lower-bounds-for-distributed-memory-computations-for-mass-spectrometry-based-omics-data.md b/papers/_posts/2022-01-01-communication-lower-bounds-for-distributed-memory-computations-for-mass-spectrometry-based-omics-data.md index 784fa672..f6d34fbc 100644 --- a/papers/_posts/2022-01-01-communication-lower-bounds-for-distributed-memory-computations-for-mass-spectrometry-based-omics-data.md +++ b/papers/_posts/2022-01-01-communication-lower-bounds-for-distributed-memory-computations-for-mass-spectrometry-based-omics-data.md @@ -1,10 +1,10 @@ --- layout: paper title: "Communication lower-bounds for distributed-memory computations for mass spectrometry based omics data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-communication-lower-bounds-for-distributed-memory-computations-for-mass-spectrometry-based-omics-data authors: "Saeed, Fahad; Haseeb, Muhammad; Iyengar, SS; " year: "2022" -journal: Academic Press +journal: "Academic Press Journal of Parallel and Distributed Computing" volume: 161 issue: pages: 37-47 diff --git a/papers/_posts/2022-01-01-computational-cpu-gpu-template-for-pre-processing-of-floating-point-ms-data.md b/papers/_posts/2022-01-01-computational-cpu-gpu-template-for-pre-processing-of-floating-point-ms-data.md index febff147..7e0d924d 100644 --- a/papers/_posts/2022-01-01-computational-cpu-gpu-template-for-pre-processing-of-floating-point-ms-data.md +++ b/papers/_posts/2022-01-01-computational-cpu-gpu-template-for-pre-processing-of-floating-point-ms-data.md @@ -1,10 +1,10 @@ --- layout: paper title: "Computational CPU-GPU Template for Pre-processing of Floating-Point MS Data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-computational-cpu-gpu-template-for-pre-processing-of-floating-point-ms-data authors: "Saeed, Fahad; Haseeb, Muhammad; " year: "2022" -journal: Springer +journal: "Springer High-Performance Algorithms for Mass Spectrometry-Based Omics" volume: issue: pages: 89-97 diff --git a/papers/_posts/2022-01-01-existing-hpc-methods-and-the-communication-lower-bounds-for-distributed-memory-computations-for-mass-spectrometry-based-omics-data.md b/papers/_posts/2022-01-01-existing-hpc-methods-and-the-communication-lower-bounds-for-distributed-memory-computations-for-mass-spectrometry-based-omics-data.md index 5bd80f95..806d5471 100644 --- a/papers/_posts/2022-01-01-existing-hpc-methods-and-the-communication-lower-bounds-for-distributed-memory-computations-for-mass-spectrometry-based-omics-data.md +++ b/papers/_posts/2022-01-01-existing-hpc-methods-and-the-communication-lower-bounds-for-distributed-memory-computations-for-mass-spectrometry-based-omics-data.md @@ -1,10 +1,10 @@ --- layout: paper title: "Existing HPC Methods and the Communication Lower Bounds for Distributed-Memory Computations for Mass Spectrometry-Based Omics Data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-existing-hpc-methods-and-the-communication-lower-bounds-for-distributed-memory-computations-for-mass-spectrometry-based-omics-data authors: "Saeed, Fahad; Haseeb, Muhammad; " year: "2022" -journal: Springer +journal: "Springer High-Performance Algorithms for Mass Spectrometry-Based Omics" volume: issue: pages: 21-35 diff --git a/papers/_posts/2022-01-01-fast-spectral-pre-processing-for-big-ms-data.md b/papers/_posts/2022-01-01-fast-spectral-pre-processing-for-big-ms-data.md index 3b23e9be..1a4a3cf7 100644 --- a/papers/_posts/2022-01-01-fast-spectral-pre-processing-for-big-ms-data.md +++ b/papers/_posts/2022-01-01-fast-spectral-pre-processing-for-big-ms-data.md @@ -1,10 +1,10 @@ --- layout: paper title: "Fast Spectral Pre-processing for Big MS Data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-fast-spectral-pre-processing-for-big-ms-data authors: "Saeed, Fahad; Haseeb, Muhammad; " year: "2022" -journal: Springer +journal: "Springer High-Performance Algorithms for Mass Spectrometry-Based Omics" volume: issue: pages: 57-75 diff --git a/papers/_posts/2022-01-01-g-msr--a-gpu-based-dimensionality-reduction-algorithm.md b/papers/_posts/2022-01-01-g-msr--a-gpu-based-dimensionality-reduction-algorithm.md index b2ea2205..9705cf5d 100644 --- a/papers/_posts/2022-01-01-g-msr--a-gpu-based-dimensionality-reduction-algorithm.md +++ b/papers/_posts/2022-01-01-g-msr--a-gpu-based-dimensionality-reduction-algorithm.md @@ -1,10 +1,10 @@ --- layout: paper title: "G-MSR: A GPU-Based Dimensionality Reduction Algorithm" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-g-msr--a-gpu-based-dimensionality-reduction-algorithm authors: "Saeed, Fahad; Haseeb, Muhammad; " year: "2022" -journal: Springer +journal: "Springer High-Performance Algorithms for Mass Spectrometry-Based Omics" volume: issue: pages: 99-110 diff --git a/papers/_posts/2022-01-01-high-performance-algorithms-for-mass-spectrometry-based-omics.md b/papers/_posts/2022-01-01-high-performance-algorithms-for-mass-spectrometry-based-omics.md index 09563798..77ddad96 100644 --- a/papers/_posts/2022-01-01-high-performance-algorithms-for-mass-spectrometry-based-omics.md +++ b/papers/_posts/2022-01-01-high-performance-algorithms-for-mass-spectrometry-based-omics.md @@ -1,10 +1,10 @@ --- layout: paper title: "High-Performance Algorithms for Mass Spectrometry-Based Omics" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-high-performance-algorithms-for-mass-spectrometry-based-omics authors: "Saeed, Fahad; Haseeb, Muhammad; " year: "2022" -journal: Springer +journal: "Springer" volume: issue: pages: diff --git a/papers/_posts/2022-01-01-high-performance-computing-strategy-using-distributed-memory-supercomputers.md b/papers/_posts/2022-01-01-high-performance-computing-strategy-using-distributed-memory-supercomputers.md index be65ddc5..33448fc0 100644 --- a/papers/_posts/2022-01-01-high-performance-computing-strategy-using-distributed-memory-supercomputers.md +++ b/papers/_posts/2022-01-01-high-performance-computing-strategy-using-distributed-memory-supercomputers.md @@ -1,10 +1,10 @@ --- layout: paper title: "High-Performance Computing Strategy Using Distributed-Memory Supercomputers" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-high-performance-computing-strategy-using-distributed-memory-supercomputers authors: "Saeed, Fahad; Haseeb, Muhammad; " year: "2022" -journal: Springer +journal: "Springer High-Performance Algorithms for Mass Spectrometry-Based Omics" volume: issue: pages: 37-56 diff --git a/papers/_posts/2022-01-01-introduction-to-mass-spectrometry-data.md b/papers/_posts/2022-01-01-introduction-to-mass-spectrometry-data.md index 0220ef07..a6c049b6 100644 --- a/papers/_posts/2022-01-01-introduction-to-mass-spectrometry-data.md +++ b/papers/_posts/2022-01-01-introduction-to-mass-spectrometry-data.md @@ -1,10 +1,10 @@ --- layout: paper title: "Introduction to Mass Spectrometry Data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-introduction-to-mass-spectrometry-data authors: "Saeed, Fahad; Haseeb, Muhammad; " year: "2022" -journal: Springer +journal: "Springer High-Performance Algorithms for Mass Spectrometry-Based Omics" volume: issue: pages: 7-19 diff --git a/papers/_posts/2022-01-01-machine-learning-and-the-future-of-hpc-for-ms-based-omics.md b/papers/_posts/2022-01-01-machine-learning-and-the-future-of-hpc-for-ms-based-omics.md index 1837ce93..0bf20d15 100644 --- a/papers/_posts/2022-01-01-machine-learning-and-the-future-of-hpc-for-ms-based-omics.md +++ b/papers/_posts/2022-01-01-machine-learning-and-the-future-of-hpc-for-ms-based-omics.md @@ -1,10 +1,10 @@ --- layout: paper title: "Machine-Learning and the Future of HPC for MS-Based Omics" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-machine-learning-and-the-future-of-hpc-for-ms-based-omics authors: "Saeed, Fahad; Haseeb, Muhammad; " year: "2022" -journal: Springer +journal: "Springer High-Performance Algorithms for Mass Spectrometry-Based Omics" volume: issue: pages: 125-129 diff --git a/papers/_posts/2022-01-01-molecular-level-characterization-of-dom-along-a-freshwater-to-estuarine-coastal-gradient-in-the-florida-everglades.md b/papers/_posts/2022-01-01-molecular-level-characterization-of-dom-along-a-freshwater-to-estuarine-coastal-gradient-in-the-florida-everglades.md index d4a4a6c2..b590fbc8 100644 --- a/papers/_posts/2022-01-01-molecular-level-characterization-of-dom-along-a-freshwater-to-estuarine-coastal-gradient-in-the-florida-everglades.md +++ b/papers/_posts/2022-01-01-molecular-level-characterization-of-dom-along-a-freshwater-to-estuarine-coastal-gradient-in-the-florida-everglades.md @@ -1,10 +1,10 @@ --- layout: paper title: "Molecular level characterization of DOM along a freshwater-to-estuarine coastal gradient in the Florida Everglades" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-molecular-level-characterization-of-dom-along-a-freshwater-to-estuarine-coastal-gradient-in-the-florida-everglades authors: "Leyva, Dennys; Jaffé, Rudolf; Courson, Jessica; Kominoski, John S; Tariq, Muhammad Usman; Saeed, Fahad; Fernandez-Lima, Francisco; " year: "2022" -journal: Springer International Publishing Cham +journal: "Springer International Publishing Cham Aquatic Sciences" volume: 84 issue: pages: 63 diff --git a/papers/_posts/2022-01-01-need-for-high-performance-computing-for-ms-based-omics-data-analysis.md b/papers/_posts/2022-01-01-need-for-high-performance-computing-for-ms-based-omics-data-analysis.md index cfa8d5c2..e610b741 100644 --- a/papers/_posts/2022-01-01-need-for-high-performance-computing-for-ms-based-omics-data-analysis.md +++ b/papers/_posts/2022-01-01-need-for-high-performance-computing-for-ms-based-omics-data-analysis.md @@ -1,10 +1,10 @@ --- layout: paper title: "Need for High-Performance Computing for MS-Based Omics Data Analysis" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-need-for-high-performance-computing-for-ms-based-omics-data-analysis authors: "Saeed, Fahad; Haseeb, Muhammad; " year: "2022" -journal: Springer +journal: "Springer High-Performance Algorithms for Mass Spectrometry-Based Omics" volume: issue: pages: 1-5 diff --git a/papers/_posts/2022-01-01-re-configurable-hardware-for-computational-proteomics.md b/papers/_posts/2022-01-01-re-configurable-hardware-for-computational-proteomics.md index ec61434d..278e287a 100644 --- a/papers/_posts/2022-01-01-re-configurable-hardware-for-computational-proteomics.md +++ b/papers/_posts/2022-01-01-re-configurable-hardware-for-computational-proteomics.md @@ -1,10 +1,10 @@ --- layout: paper title: "Re-configurable Hardware for Computational Proteomics" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-re-configurable-hardware-for-computational-proteomics authors: "Saeed, Fahad; Haseeb, Muhammad; Kumar, Sumesh; " year: "2022" -journal: Springer +journal: "Springer High-Performance Algorithms for Mass Spectrometry-Based Omics" volume: issue: pages: 111-124 diff --git a/papers/_posts/2022-01-01-spertl--epileptic-seizure-prediction-using-eeg-with-resnets-and-transfer-learning.md b/papers/_posts/2022-01-01-spertl--epileptic-seizure-prediction-using-eeg-with-resnets-and-transfer-learning.md index 7c0be004..6fd2a058 100644 --- a/papers/_posts/2022-01-01-spertl--epileptic-seizure-prediction-using-eeg-with-resnets-and-transfer-learning.md +++ b/papers/_posts/2022-01-01-spertl--epileptic-seizure-prediction-using-eeg-with-resnets-and-transfer-learning.md @@ -1,10 +1,10 @@ --- layout: paper title: "SPERTL: Epileptic Seizure Prediction using EEG with ResNets and Transfer Learning" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-spertl--epileptic-seizure-prediction-using-eeg-with-resnets-and-transfer-learning authors: "Mohammad, Umair; Saeed, Fahad; " year: "2022" -journal: IEEE +journal: "IEEE 2022 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI)" volume: issue: pages: 1-5 diff --git a/papers/_posts/2022-01-01-systems-and-methods-for-diagnosing-autism-spectrum-disorder-using-fmri-data.md b/papers/_posts/2022-01-01-systems-and-methods-for-diagnosing-autism-spectrum-disorder-using-fmri-data.md index 1dc23067..972bced2 100644 --- a/papers/_posts/2022-01-01-systems-and-methods-for-diagnosing-autism-spectrum-disorder-using-fmri-data.md +++ b/papers/_posts/2022-01-01-systems-and-methods-for-diagnosing-autism-spectrum-disorder-using-fmri-data.md @@ -1,10 +1,10 @@ --- layout: paper title: "Systems And Methods For Diagnosing Autism Spectrum Disorder Using fMRI Data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-systems-and-methods-for-diagnosing-autism-spectrum-disorder-using-fmri-data authors: "Saeed, Fahad; Almuqhim, Fahad; " year: "2022" -journal: US Patent 11,379,981 +journal: "US Patent 11,379,981" volume: issue: pages: diff --git a/papers/_posts/2022-01-01-systems-and-methods-for-measuring-similarity-between-mass-spectra-and-peptides.md b/papers/_posts/2022-01-01-systems-and-methods-for-measuring-similarity-between-mass-spectra-and-peptides.md index d1706289..a579d359 100644 --- a/papers/_posts/2022-01-01-systems-and-methods-for-measuring-similarity-between-mass-spectra-and-peptides.md +++ b/papers/_posts/2022-01-01-systems-and-methods-for-measuring-similarity-between-mass-spectra-and-peptides.md @@ -1,10 +1,10 @@ --- layout: paper title: "Systems and methods for measuring similarity between mass spectra and peptides" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-systems-and-methods-for-measuring-similarity-between-mass-spectra-and-peptides authors: "Saeed, Fahad; Tariq, Muhammad Usman; " year: "2022" -journal: US Patent 11,251,031 +journal: "US Patent 11,251,031" volume: issue: pages: diff --git a/papers/_posts/2022-01-01-systems-and-methods-for-peptide-identification.md b/papers/_posts/2022-01-01-systems-and-methods-for-peptide-identification.md index f239fb87..6c42f372 100644 --- a/papers/_posts/2022-01-01-systems-and-methods-for-peptide-identification.md +++ b/papers/_posts/2022-01-01-systems-and-methods-for-peptide-identification.md @@ -1,10 +1,10 @@ --- layout: paper title: "Systems and methods for peptide identification" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-systems-and-methods-for-peptide-identification authors: "Saeed, Fahad; Haseeb, Muhammad; " year: "2022" -journal: US Patent 11,309,061 +journal: "US Patent 11,309,061" volume: issue: pages: diff --git a/papers/_posts/2022-01-01-unsupervised-structural-classification-of-dissolved-organic-matter-based-on-fragmentation-pathways.md b/papers/_posts/2022-01-01-unsupervised-structural-classification-of-dissolved-organic-matter-based-on-fragmentation-pathways.md index fcc54e65..1e9d41ec 100644 --- a/papers/_posts/2022-01-01-unsupervised-structural-classification-of-dissolved-organic-matter-based-on-fragmentation-pathways.md +++ b/papers/_posts/2022-01-01-unsupervised-structural-classification-of-dissolved-organic-matter-based-on-fragmentation-pathways.md @@ -1,10 +1,10 @@ --- layout: paper title: "Unsupervised structural classification of dissolved organic matter based on fragmentation pathways" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2022-01-01-unsupervised-structural-classification-of-dissolved-organic-matter-based-on-fragmentation-pathways authors: "Leyva, Dennys; Tariq, Muhammad Usman; Jaffé, Rudolf; Saeed, Fahad; Lima, Francisco Fernandez; " year: "2022" -journal: American Chemical Society +journal: "American Chemical Society Environmental Science & Technology" volume: 56 issue: pages: 1458-1468 diff --git a/papers/_posts/2023-01-01-22nd-ieee-international-workshop-on-high-performance-computational-biology-hicomb-2023.md b/papers/_posts/2023-01-01-22nd-ieee-international-workshop-on-high-performance-computational-biology-hicomb-2023.md index b7f1c73d..5d69d0a6 100644 --- a/papers/_posts/2023-01-01-22nd-ieee-international-workshop-on-high-performance-computational-biology-hicomb-2023.md +++ b/papers/_posts/2023-01-01-22nd-ieee-international-workshop-on-high-performance-computational-biology-hicomb-2023.md @@ -1,7 +1,7 @@ --- layout: paper title: "22nd IEEE International Workshop on High Performance Computational Biology (HiCOMB 2023)" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2023-01-01-22nd-ieee-international-workshop-on-high-performance-computational-biology-hicomb-2023 authors: "de Melo, Alba Cristina MA; Kalyanaraman, Ananth; Saeed, Fahad; Bozdag, Serdar; Ahmed, Zeeshan; Alser, Mohammed; Awan, Muaaz Gul; Baur, Brittany; Bhowmick, Sanjukta; Bose, Banabithi; " year: "2023" journal: diff --git a/papers/_posts/2023-01-01-asd-grestm--deep-learning-framework-for-asd-classification-using-gramian-angular-field.md b/papers/_posts/2023-01-01-asd-grestm--deep-learning-framework-for-asd-classification-using-gramian-angular-field.md index c50464ae..a7f2922e 100644 --- a/papers/_posts/2023-01-01-asd-grestm--deep-learning-framework-for-asd-classification-using-gramian-angular-field.md +++ b/papers/_posts/2023-01-01-asd-grestm--deep-learning-framework-for-asd-classification-using-gramian-angular-field.md @@ -1,10 +1,10 @@ --- layout: paper title: "ASD-GResTM: Deep Learning Framework for ASD classification using Gramian Angular Field" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2023-01-01-asd-grestm--deep-learning-framework-for-asd-classification-using-gramian-angular-field authors: "Almuqhim, Fahad; Saeed, Fahad; " year: "2023" -journal: IEEE +journal: "IEEE 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)" volume: issue: pages: 2837-2843 diff --git a/papers/_posts/2023-01-01-confounding-effects-on-the-performance-of-machine-learning-analysis-of-static-functional-connectivity-computed-from-rs-fmri-multi-site-data.md b/papers/_posts/2023-01-01-confounding-effects-on-the-performance-of-machine-learning-analysis-of-static-functional-connectivity-computed-from-rs-fmri-multi-site-data.md index de29d78f..a9135c9f 100644 --- a/papers/_posts/2023-01-01-confounding-effects-on-the-performance-of-machine-learning-analysis-of-static-functional-connectivity-computed-from-rs-fmri-multi-site-data.md +++ b/papers/_posts/2023-01-01-confounding-effects-on-the-performance-of-machine-learning-analysis-of-static-functional-connectivity-computed-from-rs-fmri-multi-site-data.md @@ -1,10 +1,10 @@ --- layout: paper title: "Confounding Effects on the Performance of Machine Learning Analysis of Static Functional Connectivity Computed from rs-fMRI Multi-site Data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2023-01-01-confounding-effects-on-the-performance-of-machine-learning-analysis-of-static-functional-connectivity-computed-from-rs-fmri-multi-site-data authors: "Artiles, Oswaldo; Al Masry, Zeina; Saeed, Fahad; " year: "2023" -journal: Springer US New York +journal: "Springer US New York Neuroinformatics" volume: 21 issue: pages: 651-668 diff --git a/papers/_posts/2023-01-01-description-of-dissolved-organic-matter-transformational-networks-at-the-molecular-level.md b/papers/_posts/2023-01-01-description-of-dissolved-organic-matter-transformational-networks-at-the-molecular-level.md index f728aa6e..f64177dc 100644 --- a/papers/_posts/2023-01-01-description-of-dissolved-organic-matter-transformational-networks-at-the-molecular-level.md +++ b/papers/_posts/2023-01-01-description-of-dissolved-organic-matter-transformational-networks-at-the-molecular-level.md @@ -1,10 +1,10 @@ --- layout: paper title: "Description of Dissolved Organic Matter Transformational Networks at the Molecular Level" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2023-01-01-description-of-dissolved-organic-matter-transformational-networks-at-the-molecular-level authors: "Leyva, Dennys; Usman Tariq, Muhammad; Jaffé, Rudolf; Saeed, Fahad; Fernandez-Lima, Francisco; " year: "2023" -journal: American Chemical Society +journal: "American Chemical Society Environmental Science & Technology" volume: 57 issue: pages: 2672-2681 diff --git a/papers/_posts/2023-01-01-energy-efficient-ai-ml-based-continuous-monitoring-at-the-edge--ecg-and-eeg-case-study.md b/papers/_posts/2023-01-01-energy-efficient-ai-ml-based-continuous-monitoring-at-the-edge--ecg-and-eeg-case-study.md index 030b6309..57c09579 100644 --- a/papers/_posts/2023-01-01-energy-efficient-ai-ml-based-continuous-monitoring-at-the-edge--ecg-and-eeg-case-study.md +++ b/papers/_posts/2023-01-01-energy-efficient-ai-ml-based-continuous-monitoring-at-the-edge--ecg-and-eeg-case-study.md @@ -1,10 +1,10 @@ --- layout: paper title: "Energy Efficient AI/ML based Continuous Monitoring at the Edge: ECG and EEG Case Study" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2023-01-01-energy-efficient-ai-ml-based-continuous-monitoring-at-the-edge--ecg-and-eeg-case-study authors: "Mohammad, Umair; Saeed, Fahad; " year: "2023" -journal: IEEE +journal: "IEEE 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)" volume: issue: pages: 3313-3320 diff --git a/papers/_posts/2023-01-01-gpu-acceleration-of-the-distributed-memory-database-peptide-search-of-mass-spectrometry-data.md b/papers/_posts/2023-01-01-gpu-acceleration-of-the-distributed-memory-database-peptide-search-of-mass-spectrometry-data.md index ecb48ed1..d804d1d4 100644 --- a/papers/_posts/2023-01-01-gpu-acceleration-of-the-distributed-memory-database-peptide-search-of-mass-spectrometry-data.md +++ b/papers/_posts/2023-01-01-gpu-acceleration-of-the-distributed-memory-database-peptide-search-of-mass-spectrometry-data.md @@ -1,10 +1,10 @@ --- layout: paper title: "GPU-acceleration of the distributed-memory database peptide search of mass spectrometry data" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2023-01-01-gpu-acceleration-of-the-distributed-memory-database-peptide-search-of-mass-spectrometry-data authors: "Haseeb, Muhammad; Saeed, Fahad; " year: "2023" -journal: Nature Publishing Group UK London +journal: "Nature Publishing Group UK London Scientific Reports" volume: 13 issue: pages: 18713 diff --git a/papers/_posts/2023-01-01-high-performance-computing-algorithms-for-accelerating-peptide-identification-from-mass-spectrometry-data-using-heterogeneous-supercomputers.md b/papers/_posts/2023-01-01-high-performance-computing-algorithms-for-accelerating-peptide-identification-from-mass-spectrometry-data-using-heterogeneous-supercomputers.md index 4e4f471c..e0da548d 100644 --- a/papers/_posts/2023-01-01-high-performance-computing-algorithms-for-accelerating-peptide-identification-from-mass-spectrometry-data-using-heterogeneous-supercomputers.md +++ b/papers/_posts/2023-01-01-high-performance-computing-algorithms-for-accelerating-peptide-identification-from-mass-spectrometry-data-using-heterogeneous-supercomputers.md @@ -1,7 +1,7 @@ --- layout: paper title: "High Performance Computing Algorithms for Accelerating Peptide Identification from Mass-Spectrometry Data Using Heterogeneous Supercomputers" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2023-01-01-high-performance-computing-algorithms-for-accelerating-peptide-identification-from-mass-spectrometry-data-using-heterogeneous-supercomputers authors: "Haseeb, Muhammad; Saeed, Fahad; " year: "2023" journal: diff --git "a/papers/_posts/2023-01-01-ppad--a-deep-learning-architecture-to-predict-progression-of-alzheimer\342\200\231s-disease.md" "b/papers/_posts/2023-01-01-ppad--a-deep-learning-architecture-to-predict-progression-of-alzheimer\342\200\231s-disease.md" index 3974e9fc..ee8be0ee 100644 --- "a/papers/_posts/2023-01-01-ppad--a-deep-learning-architecture-to-predict-progression-of-alzheimer\342\200\231s-disease.md" +++ "b/papers/_posts/2023-01-01-ppad--a-deep-learning-architecture-to-predict-progression-of-alzheimer\342\200\231s-disease.md" @@ -1,10 +1,10 @@ --- layout: paper title: "PPAD: a deep learning architecture to predict progression of Alzheimer’s disease" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2023-01-01-ppad--a-deep-learning-architecture-to-predict-progression-of-alzheimer’s-disease authors: "Al Olaimat, Mohammad; Martinez, Jared; Saeed, Fahad; Bozdag, Serdar; Alzheimer’s Disease Neuroimaging Initiative; " year: "2023" -journal: Oxford University Press +journal: "Oxford University Press Bioinformatics" volume: 39 issue: pages: i149-i157 diff --git "a/papers/_posts/2023-01-01-pvtad--alzheimer\342\200\231s-disease-diagnosis-using-pyramid-vision-transformer-applied-to-white-matter-of-t1-weighted-structural-mri-data.md" "b/papers/_posts/2023-01-01-pvtad--alzheimer\342\200\231s-disease-diagnosis-using-pyramid-vision-transformer-applied-to-white-matter-of-t1-weighted-structural-mri-data.md" index 218e7ecc..b7f4be1f 100644 --- "a/papers/_posts/2023-01-01-pvtad--alzheimer\342\200\231s-disease-diagnosis-using-pyramid-vision-transformer-applied-to-white-matter-of-t1-weighted-structural-mri-data.md" +++ "b/papers/_posts/2023-01-01-pvtad--alzheimer\342\200\231s-disease-diagnosis-using-pyramid-vision-transformer-applied-to-white-matter-of-t1-weighted-structural-mri-data.md" @@ -1,10 +1,10 @@ --- layout: paper title: "PVTAD: ALZHEIMER’S DISEASE DIAGNOSIS USING PYRAMID VISION TRANSFORMER APPLIED TO WHITE MATTER OF T1-WEIGHTED STRUCTURAL MRI DATA" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2023-01-01-pvtad--alzheimer’s-disease-diagnosis-using-pyramid-vision-transformer-applied-to-white-matter-of-t1-weighted-structural-mri-data authors: "Aghdam, Maryam Akhavan; Bozdag, Serdar; Saeed, Fahad; Alzheimer’s Disease Neuroimaging Initiative; " year: "2023" -journal: Cold Spring Harbor Laboratory Preprints +journal: "Cold Spring Harbor Laboratory Preprints bioRxiv" volume: issue: pages: diff --git a/papers/_posts/2023-01-01-q-casa-invited-speakers-quantum-centric-supercomputing-strategies-for-neuroscience-problems--challenges-and-progress.md b/papers/_posts/2023-01-01-q-casa-invited-speakers-quantum-centric-supercomputing-strategies-for-neuroscience-problems--challenges-and-progress.md index 9fa69415..f82a4e85 100644 --- a/papers/_posts/2023-01-01-q-casa-invited-speakers-quantum-centric-supercomputing-strategies-for-neuroscience-problems--challenges-and-progress.md +++ b/papers/_posts/2023-01-01-q-casa-invited-speakers-quantum-centric-supercomputing-strategies-for-neuroscience-problems--challenges-and-progress.md @@ -1,10 +1,10 @@ --- layout: paper title: "Q-CASA Invited Speakers Quantum-Centric Supercomputing Strategies for Neuroscience problems: Challenges and Progress" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2023-01-01-q-casa-invited-speakers-quantum-centric-supercomputing-strategies-for-neuroscience-problems--challenges-and-progress authors: "Loredo, Robert; Saeed, Fahad; " year: "2023" -journal: IEEE +journal: "IEEE 2023 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)" volume: issue: pages: 499-499 diff --git a/papers/_posts/2023-01-01-statistical-and-machine-learning-analysis-of-the-human-brain-functional-network-in-a-multi-site-resting-state-functional-mri-database-framework.md b/papers/_posts/2023-01-01-statistical-and-machine-learning-analysis-of-the-human-brain-functional-network-in-a-multi-site-resting-state-functional-mri-database-framework.md index 4424d7f0..6b8b1a60 100644 --- a/papers/_posts/2023-01-01-statistical-and-machine-learning-analysis-of-the-human-brain-functional-network-in-a-multi-site-resting-state-functional-mri-database-framework.md +++ b/papers/_posts/2023-01-01-statistical-and-machine-learning-analysis-of-the-human-brain-functional-network-in-a-multi-site-resting-state-functional-mri-database-framework.md @@ -1,7 +1,7 @@ --- layout: paper title: "Statistical and Machine Learning Analysis of the Human Brain Functional Network in a Multi-Site Resting-State Functional MRI Database Framework" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2023-01-01-statistical-and-machine-learning-analysis-of-the-human-brain-functional-network-in-a-multi-site-resting-state-functional-mri-database-framework authors: "Artiles, Oswaldo; Saeed, Fahad; " year: "2023" journal: diff --git a/papers/_posts/2023-01-01-systems-and-methods-for-matching-mass-spectrometry-data-with-a-peptide-database.md b/papers/_posts/2023-01-01-systems-and-methods-for-matching-mass-spectrometry-data-with-a-peptide-database.md index 0f01eba3..7c29c82d 100644 --- a/papers/_posts/2023-01-01-systems-and-methods-for-matching-mass-spectrometry-data-with-a-peptide-database.md +++ b/papers/_posts/2023-01-01-systems-and-methods-for-matching-mass-spectrometry-data-with-a-peptide-database.md @@ -1,10 +1,10 @@ --- layout: paper title: "Systems and methods for matching mass spectrometry data with a peptide database" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2023-01-01-systems-and-methods-for-matching-mass-spectrometry-data-with-a-peptide-database authors: "Kumar, Sumesh; Saeed, Fahad; " year: "2023" -journal: US Patent 11,842,799 +journal: "US Patent 11,842,799" volume: issue: pages: diff --git a/papers/_posts/2024-01-01-communication-evaluation-of-a-wireless-4-channel-wearable-eeg-for-brain-computer-interface-bci-and-healthcare-applications.md b/papers/_posts/2024-01-01-communication-evaluation-of-a-wireless-4-channel-wearable-eeg-for-brain-computer-interface-bci-and-healthcare-applications.md index 559c0799..513cde22 100644 --- a/papers/_posts/2024-01-01-communication-evaluation-of-a-wireless-4-channel-wearable-eeg-for-brain-computer-interface-bci-and-healthcare-applications.md +++ b/papers/_posts/2024-01-01-communication-evaluation-of-a-wireless-4-channel-wearable-eeg-for-brain-computer-interface-bci-and-healthcare-applications.md @@ -1,10 +1,10 @@ --- layout: paper title: "Communication Evaluation of a Wireless 4-Channel Wearable EEG for Brain-Computer Interface (BCI) and Healthcare Applications" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2024-01-01-communication-evaluation-of-a-wireless-4-channel-wearable-eeg-for-brain-computer-interface-bci-and-healthcare-applications authors: "Bhattarai, Abhishek; Mohammad, Umair; Saeed, Fahad; " year: "2024" -journal: IEEE +journal: "IEEE SoutheastCon 2024" volume: issue: pages: 902-903 diff --git a/papers/_posts/2024-01-01-heterogeneity-aware-distributed-machine-learning-at-the-wireless-edge-for-health-iot-applications--an-eeg-data-case-study.md b/papers/_posts/2024-01-01-heterogeneity-aware-distributed-machine-learning-at-the-wireless-edge-for-health-iot-applications--an-eeg-data-case-study.md index 9913d4bf..75da6ac6 100644 --- a/papers/_posts/2024-01-01-heterogeneity-aware-distributed-machine-learning-at-the-wireless-edge-for-health-iot-applications--an-eeg-data-case-study.md +++ b/papers/_posts/2024-01-01-heterogeneity-aware-distributed-machine-learning-at-the-wireless-edge-for-health-iot-applications--an-eeg-data-case-study.md @@ -1,10 +1,10 @@ --- layout: paper title: "Heterogeneity Aware Distributed Machine Learning at the Wireless Edge for Health IoT Applications: An EEG Data Case Study" -nickname: 2024-04-16-bottenhorn-salo-diva +nickname: 2024-01-01-heterogeneity-aware-distributed-machine-learning-at-the-wireless-edge-for-health-iot-applications--an-eeg-data-case-study authors: "Mohammad, Umair; Saeed, Fahad; " year: "2024" -journal: Springer +journal: "Springer Distributed Machine Learning and Computing: Theory and Applications" volume: issue: pages: 33-70