All Stories

  1. Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data

    Article • PLoS Computational Biology, September 2020, PLOS

    Professor Gary D Bader

  2. Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data

    Article • F1000Research, March 2019, Faculty of 1000, Ltd.

    Dr Alexander Pico, Professor Gary D Bader, Javier Diaz

  3. Point-and-click sharing of single-cell data.

    Article • F1000Research, September 2018, Faculty of 1000, Ltd.

    Professor Gary D Bader, Brendan Innes

  4. The Cytoscape Automation app article collection

    Article • F1000Research, June 2018, Faculty of 1000, Ltd.

    Dr Barry Demchak, Professor Gary D Bader

  5. AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations

    Article • F1000Research, July 2016, Faculty of 1000, Ltd.

    Professor Gary D Bader, Ruth Isserlin

  6. author networks

    Article • F1000Research, August 2015, Faculty of 1000, Ltd.

    Professor Gary D Bader, Dr Alison M Buchan, Ruth Isserlin

  7. NetMatchStar: an enhanced Cytoscape network querying app

    Article • F1000Research, August 2015, Faculty of 1000, Ltd.

    Professor Gary D Bader, Ph.D. Vincenzo VB Bonnici, Fabio Rinnone, Prof Alfredo Ferro

  8. Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes

    Article • F1000Research, January 2015, Faculty of 1000, Ltd.

    Professor Gary D Bader

  9. Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy

    Article • Molecular BioSystems, January 2015, Royal Society of Chemistry

    Professor Gary D Bader, Associate Professor Dajana Vuckovic

  10. Faculty Opinions recommendation of VarWalker: personalized mutation network analysis of putative cancer genes from next-generation sequencing data.

    Article • September 2014, F1000Research

    Professor Gary D Bader

  11. Biological Network Exploration with Cytoscape 3

    Article • Current Protocols in Bioinformatics, September 2014, Wiley

    Professor Gary D Bader, Dr Barry Demchak

  12. GeneMANIA: Fast gene network construction and function prediction for Cytoscape

    Article • F1000Research, July 2014, Faculty of 1000, Ltd.

    Professor Gary D Bader

  13. Enrichment Map – a Cytoscape app to visualize and explore OMICs pathway enrichment results

    Article • F1000Research, July 2014, Faculty of 1000, Ltd.

    Professor Gary D Bader, Ruth Isserlin

  14. The Cytoscape app article collection

    Article • F1000Research, July 2014, Faculty of 1000, Ltd.

    Professor Gary D Bader, Dr Alexander Pico, David Welker, Dr Barry Demchak

  15. Quiescent Sox2+ Cells Drive Hierarchical Growth and Relapse in Sonic Hedgehog Subgroup Medulloblastoma

    Article • Cancer Cell, July 2014, Elsevier

    Professor Gary D Bader

  16. Highlights of B/D‐HPP and HPP Resource Pillar Workshops at 12th Annual HUPO World Congress of Proteomics

    Article • PROTEOMICS, April 2014, Wiley

    Professor Gary D Bader

  17. Prediction and Experimental Characterization of nsSNPs Altering Human PDZ-Binding Motifs

    Article • PLoS ONE, April 2014, PLOS

    Professor Gary D Bader

  18. Coordinate MicroRNA-Mediated Regulation of Protein Complexes in Prostate Cancer

    Article • PLoS ONE, December 2013, PLOS

    Professor Gary D Bader

  19. Erratum: Comprehensive identification of mutational cancer driver genes across 12 tumor types

    Article • Scientific Reports, October 2013, Springer Science + Business Media

    Professor Gary D Bader

  20. The mutational landscape of phosphorylation signaling in cancer

    Article • Scientific Reports, October 2013, Springer Science + Business Media

    Professor Gary D Bader

  21. Comprehensive identification of mutational cancer driver genes across 12 tumor types

    Article • Scientific Reports, October 2013, Springer Science + Business Media

    Professor Gary D Bader

  22. Using Biological Pathway Data with Paxtools

    Article • PLoS Computational Biology, September 2013, PLOS

    Professor Gary D Bader

  23. Computational approaches to identify functional genetic variants in cancer genomes

    Article • Nature Chemical Biology, July 2013, Springer Science + Business Media

    Professor Gary D Bader

  24. 2035 EPIGENETIC REGULATION OF GENE EXPRESSION PATTERNS IN HUMAN TESTIS XENOTRANSPLANTS AFTER TREATMENT WITH CYCLOPHOSPHAMIDE

    Article • The Journal of Urology, April 2013, Wolters Kluwer Health

    Professor Gary D Bader

  25. Faculty Opinions recommendation of Structure-based prediction of protein-protein interactions on a genome-wide scale.

    Article • March 2013, F1000Research

    Professor Gary D Bader

  26. Metabolic Adaptation to Chronic Inhibition of Mitochondrial Protein Synthesis in Acute Myeloid Leukemia Cells

    Article • PLoS ONE, March 2013, PLOS

    Professor Gary D Bader

  27. Predicting PDZ domain mediated protein interactions from structure

    Article • BMC Bioinformatics, January 2013, Springer Science + Business Media

    Professor Gary D Bader

  28. Integrative pathway dissection of molecular mechanisms of moxLDL-induced vascular smooth muscle phenotype transformation

    Article • BMC Cardiovascular Disorders, January 2013, Springer Science + Business Media

    Professor Gary D Bader

  29. Chemogenomic Profiling

    Article • January 2013, Elsevier

    Professor Gary D Bader, Professor Corey Nislow

  30. The Biology/Disease-driven Human Proteome Project (B/D-HPP): Enabling Protein Research for the Life Sciences Community

    Article • Journal of Proteome Research, December 2012, American Chemical Society (ACS)

    Professor Gary D Bader

  31. Chromatin is an ancient innovation conserved between Archaea and Eukarya

    Article • eLife, December 2012, eLife

    Professor Gary D Bader, Professor Corey Nislow

  32. Attenuation of miR-126 Activity Expands HSC In Vivo without Exhaustion

    Article • Cell Stem Cell, December 2012, Elsevier

    Professor Gary D Bader

  33. Faculty Opinions recommendation of Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells.

    Article • November 2012, F1000Research

    Professor Gary D Bader

  34. A travel guide to Cytoscape plugins

    Article • Nature Chemical Biology, November 2012, Springer Science + Business Media

    Professor Gary D Bader, Dr Alexander Pico

  35. A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals

    Article • Stem Cells, July 2012, Oxford University Press (OUP)

    Professor Gary D Bader

  36. Multiple Genetic Interaction Experiments Provide Complementary Information Useful for Gene Function Prediction

    Article • PLoS Computational Biology, June 2012, PLOS

    Professor Gary D Bader

  37. Faculty Opinions recommendation of Mutual exclusivity analysis identifies oncogenic network modules.

    Article • May 2012, F1000Research

    Professor Gary D Bader

  38. Domain‐mediated protein interaction prediction: From genome to network

    Article • FEBS Letters, May 2012, Wiley

    Professor Gary D Bader

  39. Phosphorylation sites of higher stoichiometry are more conserved

    Article • Nature Chemical Biology, March 2012, Springer Science + Business Media

    Professor Gary D Bader

  40. Mapping the Hsp90 Genetic Interaction Network in Candida albicans Reveals Environmental Contingency and Rewired Circuitry

    Article • PLoS Genetics, March 2012, PLOS

    Professor Gary D Bader

  41. Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study

    Article • BMC Systems Biology, January 2012, Springer Science + Business Media

    Professor Gary D Bader

  42. Faculty Opinions recommendation of Toward an understanding of the protein interaction network of the human liver.

    Article • December 2011, F1000Research

    Professor Gary D Bader

  43. Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)

    Article • Standards in Genomic Sciences, November 2011, Springer Science + Business Media

    Professor Gary D Bader

  44. clusterMaker: a multi-algorithm clustering plugin for Cytoscape

    Article • BMC Bioinformatics, November 2011, Springer Science + Business Media

    Professor Gary D Bader

  45. Faculty Opinions recommendation of Believe it or not: how much can we rely on published data on potential drug targets?

    Article • October 2011, F1000Research

    Professor Gary D Bader

  46. Faculty Opinions recommendation of Predicting selective drug targets in cancer through metabolic networks.

    Article • October 2011, F1000Research

    Professor Gary D Bader

  47. Compound Prioritization Methods Increase Rates of Chemical Probe Discovery in Model Organisms

    Article • Chemistry & Biology, October 2011, Elsevier

    Professor Gary D Bader, Professor Corey Nislow

  48. Faculty Opinions recommendation of Testing the ortholog conjecture with comparative functional genomic data from mammals.

    Article • August 2011, F1000Research

    Professor Gary D Bader

  49. Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma

    Article • Cancer Cell, August 2011, Elsevier

    Professor Gary D Bader

  50. PSICQUIC and PSISCORE: accessing and scoring molecular interactions

    Article • Nature Chemical Biology, June 2011, Springer Science + Business Media

    Sylvie RICARD-BLUM, Professor Gary D Bader, Mr Rafael C Jimenez

  51. Faculty Opinions recommendation of Quantitative epistasis analysis and pathway inference from genetic interaction data.

    Article • June 2011, F1000Research

    Professor Gary D Bader

  52. Faculty Opinions recommendation of NOA: a novel Network Ontology Analysis method.

    Article • May 2011, F1000Research

    Professor Gary D Bader

  53. WordCloud: a Cytoscape plugin to create a visual semantic summary of networks

    Article • Source Code for Biology and Medicine, April 2011, Springer Science + Business Media

    Professor Gary D Bader

  54. Faculty Opinions recommendation of Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome.

    Article • March 2011, F1000Research

    Professor Gary D Bader

  55. Protein Complexes are Central in the Yeast Genetic Landscape

    Article • PLoS Computational Biology, February 2011, PLOS

    Professor Gary D Bader

  56. Faculty Opinions recommendation of Measuring the evolutionary rewiring of biological networks.

    Article • February 2011, F1000Research

    Professor Gary D Bader

  57. Bringing order to protein disorder through comparative genomics and genetic interactions

    Article • Genome Biology, February 2011, Springer Science + Business Media

    Professor Gary D Bader

  58. Too many roads not taken

    Article • Nature, February 2011, Springer Science + Business Media

    Professor Gary D Bader

  59. Visualizing Gene-Set Enrichment Results Using the Cytoscape Plug-in Enrichment Map

    Article • January 2011, Springer Science + Business Media

    Professor Gary D Bader

  60. Displaying Chemical Information on a Biological Network Using Cytoscape

    Article • January 2011, Springer Science + Business Media

    Professor Gary D Bader, Professor Corey Nislow

  61. Functional complexes between YAP2 and ZO-2 are PDZ domain-dependent, and regulate YAP2 nuclear localization and signalling

    Article • Biochemical Journal, December 2010, Portland Press Ltd.

    Professor Gary D Bader

  62. Faculty Opinions recommendation of STITCH: interaction networks of chemicals and proteins.

    Article • December 2010, F1000Research

    Professor Gary D Bader

  63. An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology

    Article • BMC Bioinformatics, November 2010, Springer Science + Business Media

    Professor Gary D Bader

  64. Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

    Article • PLoS ONE, November 2010, PLOS

    Professor Gary D Bader

  65. Quantitative analysis of fitness and genetic interactions in yeast on a genome scale

    Article • Nature Chemical Biology, November 2010, Springer Science + Business Media

    Professor Gary D Bader

  66. Faculty Opinions recommendation of A comprehensive molecular interaction map of the budding yeast cell cycle.

    Article • October 2010, F1000Research

    Professor Gary D Bader

  67. Dynamic interaction networks in a hierarchically organized tissue

    Article • Molecular Systems Biology, October 2010, EMBO

    Professor Gary D Bader

  68. Faculty Opinions recommendation of Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line.

    Article • September 2010, F1000Research

    Professor Gary D Bader

  69. Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps

    Article • PROTEOMICS - CLINICAL APPLICATIONS, September 2010, Wiley

    Professor Gary D Bader

  70. Faculty Opinions recommendation of A global protein kinase and phosphatase interaction network in yeast.

    Article • August 2010, F1000Research

    Professor Gary D Bader

  71. Faculty Opinions recommendation of Modeling synthetic lethality.

    Article • August 2010, F1000Research

    Professor Gary D Bader

  72. Faculty Opinions recommendation of Reverse engineering a signaling network using alternative inputs.

    Article • July 2010, F1000Research

    Professor Gary D Bader

  73. A predictive model for drug bioaccumulation and bioactivity in Caenorhabditis elegans

    Article • Nature Chemical Biology, May 2010, Springer Science + Business Media

    Professor Gary D Bader, Professor Corey Nislow

  74. Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps

    Article • PROTEOMICS, March 2010, Wiley

    Professor Gary D Bader

  75. Coevolution of PDZ domain–ligand interactions analyzed by high-throughput phage display and deep sequencing

    Article • Molecular BioSystems, January 2010, Royal Society of Chemistry

    Professor Gary D Bader

  76. Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins

    Article • PLoS Biology, October 2009, PLOS

    Professor Gary D Bader

  77. How to visually interpret biological data using networks

    Article • Nature Biotechnology, October 2009, Springer Science + Business Media

    Professor Gary D Bader

  78. A Specificity Map for the PDZ Domain Family

    Article • PLoS Biology, September 2008, PLOS

    Professor Gary D Bader

  79. Exploring Biological Networks with Cytoscape Software

    Article • Current Protocols in Bioinformatics, September 2008, Wiley

    Professor Gary D Bader

  80. Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions

    Article • BMC Biology, October 2007, Springer Science + Business Media

    Professor Gary D Bader

  81. Integration of biological networks and gene expression data using Cytoscape

    Article • Nature Protocols, September 2007, Springer Science + Business Media

    Professor Gary D Bader, Dr Alexander Pico

  82. Computational Prediction of Protein–Protein Interactions

    Article • Molecular Biotechnology, August 2007, Springer Science + Business Media

    Professor Gary D Bader

  83. The minimum information required for reporting a molecular interaction experiment (MIMIx)

    Article • Nature Biotechnology, August 2007, Springer Science + Business Media

    Professor Gary D Bader, Dr Lyle Burgoon, Dr. Peter Uetz

  84. Germ-line DNA copy number variation frequencies in a large North American population

    Article • Human Genetics, July 2007, Springer Science + Business Media

    Professor Gary D Bader

  85. From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research

    Article • PLoS Computational Biology, February 2007, PLOS

    Professor Gary D Bader

  86. Computational prediction of cancer-gene function

    Article • Nature Reviews Drug Discovery, December 2006, Springer Science + Business Media

    Professor Gary D Bader

  87. BioPAX– biological pathway data exchange format

    Article • September 2005, Wiley

    Professor Gary D Bader

  88. Protein Interaction Databases

    Article • May 2005, Wiley

    Professor Gary D Bader

  89. Pathway information for systems biology

    Article • FEBS Letters, February 2005, Wiley

    Professor Gary D Bader

  90. Computational Prediction of Protein-Protein Interactions

    Article • January 2005, Springer Science + Business Media

    Professor Gary D Bader

  91. The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data

    Article • Nature Biotechnology, January 2004, Springer Science + Business Media

    Professor Gary D Bader

  92. Playing tag with the yeast proteome

    Article • Nature Biotechnology, November 2003, Springer Science + Business Media

    Professor Gary D Bader

  93. Functional genomics and proteomics: charting a multidimensional map of the yeast cell

    Article • Trends in Cell Biology, July 2003, Elsevier

    Professor Gary D Bader

  94. Functional genomics of intracellular peptide recognition domains with combinatorial biology methods

    Article • Current Opinion in Chemical Biology, February 2003, Elsevier

    Professor Gary D Bader

  95. Peptide Recognition Module Networks: Combining Phage Display with Two-Hybrid Analysis to Define Protein-Protein Interactions

    Article • January 2003, Elsevier

    Professor Gary D Bader

  96. Analyzing yeast protein–protein interaction data obtained from different sources

    Article • Nature Biotechnology, October 2002, Springer Science + Business Media

    Professor Gary D Bader

  97. Bioinformatics: Interaction Databases

    Article • February 2002, Wiley

    Professor Gary D Bader

  98. Approaches to Analyze Protein Interactions

    Article • The Scientific World JOURNAL, January 2002, Hindawi Publishing Corporation

    Professor Gary D Bader

  99. Interaction Databases

    Article • May 2001, Wiley

    Professor Gary D Bader

  100. Interaction Databases

    Article • April 2001, Wiley

    Professor Gary D Bader