pcdslab · Prof-S · Jul 5, 2024 · Jul 5, 2024 · Jul 5, 2024
diff --git a/...quence-alignment-system-using-phylogenetic-sampling-and-domain-decomposition.md b/...quence-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/...y-for-alignment-of-multiple-biological-sequences-on-multiprocessor-platforms.md b/...y-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
@@ -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/...posts/2009-01-01-multiple-sequence-alignment-system-for-pyrosequencing-reads.md b/...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/...ign-based-multiple-alignment-system-for-pyrosequencing-reads-of-large-number.md b/...ign-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/...raph-theoretic-framework-for-efficient-computation-of-hmm-based-motif-finder.md b/...raph-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
@@ -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/...thm-for-center-star-sequence-and-alignments-with-applications-to-short-reads.md b/...thm-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/...based-quantification-of-phosphorylation-changes-during-vasopressin-signaling.md b/...based-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/...ique-clusters-of-phosphopeptides-regulated-by-vasopressin-in-collecting-duct.md b/...ique-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/...11-01-01-mining-temporal-patterns-from-itraq-mass-spectrometry-lc-ms-ms-data.md b/...11-01-01-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/...ce-alignment-system-for-pyrosequencing-reads-from-multiple-reference-genomes.md b/...ce-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/...-an-efficient-algorithm-for-clustering-of-large-scale-mass-spectrometry-data.md b/...-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/...hm-for-phosphorylation-site-assignment-of-large-scale-mass-spectrometry-data.md b/...hm-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/...late-and-visualize-evolutionarily-conserved-functional-phosphorylation-sites.md b/...late-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/...sin-v2-receptor-signaling-network-revealed-by-quantitative-phosphoproteomics.md b/...sin-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/...site-assignment-algorithm-for-mass-spectrometry-data-using-multicore-systems.md b/...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/...-01-01-identifying-protein-kinase-target-preferences-using-mass-spectrometry.md b/...-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/...1-nhlbi-abdesigner--an-online-tool-for-design-of-peptide-directed-antibodies.md b/...1-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/...phoproteomics-in-nuclei-of-vasopressin-sensitive-renal-collecting-duct-cells.md b/...phoproteomics-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/...phoproteomics-in-nuclei-of-vasopressin-sensitive-renal-collecting-duct-cells.md b/...phoproteomics-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/...ce-gui-for-phosphorylation-site-assignment-of-protein-mass-spectrometry-data.md b/...ce-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/...of-large-scale-protein-mass-spectrometry-data-using-multi-core-architectures.md b/...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/...ernational-conference-on-bioinformatics-and-computational-biology-bicob-2013.md b/...ernational-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/...ccurate-phosphorylation-site-assignment-algorithm-for-mass-spectrometry-data.md b/...ccurate-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/...f-lives-and-translation-rates-in-vasopressin-sensitive-collecting-duct-cells.md b/...f-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/...adhesion-and-transcriptional-regulation-in-the-vasopressin-signaling-network.md b/...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/...ernational-conference-on-bioinformatics-and-computational-biology-bicob-2014.md b/...ernational-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
@@ -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/...ctrometry-data-using-restricted-search-space-and-intelligent-random-sampling.md b/...ctrometry-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/...-parallelism-to-cluster-mass-spectrometry-data-using-multicore-architectures.md b/...-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/...rnational-conference-on-bioinformatics-and-computational-biology-bicob-2014..md b/...rnational-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/...receptor-antagonist-satavaptan-on-protein-phosphorylation-in-collecting-duct.md b/...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/...for-an-exact-match-short-read-aligner-using-burrows-wheeler-aligner-on-fpgas.md b/...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: