All Stories

  1. Using Published Pathway Figures in Enrichment Analysis and Machine Learning

    Article • July 2023, Cold Spring Harbor Laboratory Press

    Dr Alexander Pico

  2. NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange

    Article • October 2022, Cold Spring Harbor Laboratory Press

    Dr Alexander Pico

  3. Introducing R as a smart version of calculators enables beginners to explore it on their own

    Article • F1000Research, June 2022, Faculty of 1000, Ltd.

    Dr Alexander Pico

  4. Introducing R as a smart version of calculators enables beginners to explore it on their own

    Article • F1000Research, August 2021, Faculty of 1000, Ltd.

    Dr Alexander Pico

  5. scNetViz: from single cells to networks using Cytoscape

    Article • F1000Research, June 2021, Faculty of 1000, Ltd.

    Dr Alexander Pico

  6. The Dynamic Platelet Transcriptome in Obesity and Weight Loss

    Article • Arteriosclerosis Thrombosis and Vascular Biology, December 2020, Wolters Kluwer Health

    Dr Alexander Pico

  7. Comprehensive Metabolic Phenotyping Refines Cardiovascular Risk in Young Adults

    Article • Circulation, October 2020, Wolters Kluwer Health

    Dr Alexander Pico

  8. Metabolic Architecture of Acute Exercise Response in Middle-Aged Adults in the Community

    Article • Circulation, September 2020, Wolters Kluwer Health

    Dr Alexander Pico

  9. 25 Years of Pathway Figures

    Article • May 2020, Cold Spring Harbor Laboratory Press

    Dr Alexander Pico

  10. RCy3: Network biology using Cytoscape from within R

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

    Dr Alexander Pico

  11. RCy3: Network biology using Cytoscape from within R

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

    Dr Alexander Pico

  12. RCy3: Network biology using Cytoscape from within R

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

    Dr Alexander Pico, Julia Gustavsen, Ruth Isserlin, Shraddha Pai

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

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

    Dr Alexander Pico

  14. RCy3: Network Biology using Cytoscape from within R

    Article • October 2019, Cold Spring Harbor Laboratory Press

    Dr Alexander Pico, Dr Barry Demchak

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

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

    Dr Alexander Pico

  16. pathwayPCA: an R package for integrative pathway analysis with modern PCA methodology and gene selection

    Article • April 2019, Cold Spring Harbor Laboratory Press

    Dr Alexander Pico

  17. 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

  18. Identifier Mapping in Cytoscape

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

    Dr Alexander Pico

  19. Identifying Genes in Published Pathway Figure Images

    Article • July 2018, Cold Spring Harbor Laboratory Press

    Dr Alexander Pico

  20. Identifier Mapping in Cytoscape: idmapper

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

    Dr Alexander Pico

  21. Research synergy and drug development: Bright stars in neighboring constellations

    Article • Heliyon, November 2017, Elsevier

    Dr Alexander Pico

  22. PSFC: a Pathway Signal Flow Calculator App for Cytoscape

    Article • F1000Research, April 2017, Faculty of 1000, Ltd.

    Dr Alexander Pico

  23. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

    Article • PLoS Computational Biology, June 2016, PLOS

    Professor Chris Evelo, Dr Alexander Pico

  24. Reactome from a WikiPathways Perspective

    Article • PLoS Computational Biology, May 2016, PLOS

    Dr Alexander Pico, Professor Chris Evelo

  25. CyAnimator: Simple Animations of Cytoscape Networks

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

    Dr Alexander Pico

  26. Longer genotypically-estimated leukocyte telomere length is associated with increased adult glioma risk

    Article • Oncotarget, December 2015, Impact Journals, LLC

    Dr Alexander Pico

  27. A community-created database of biological knowledge, freely available and easy to reuse

    Article • Nucleic Acids Research, October 2015, Oxford University Press (OUP)

    Dr Alexander Pico, Professor Chris Evelo

  28. From Scientific Discovery to Cures: Bright Stars within a Galaxy

    Article • Cell, September 2015, Elsevier

    Dr Alexander Pico

  29. PSFC: a Pathway Signal Flow Calculator App for Cytoscape

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

    Dr Alexander Pico, G J

  30. CyAnimator: Simple Animations of Cytoscape Networks

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

    Dr Alexander Pico

  31. setsApp for Cytoscape: Set operations for Cytoscape Nodes and Edges

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

    Dr Alexander Pico

  32. Glioma Groups Based on 1p/19q, IDH, and TERT Promoter Mutations in Tumors

    Article • New England Journal of Medicine, June 2015, New England Journal of Medicine (NEJM/MMS)

    Dr Alexander Pico

  33. PathVisio 3: An Extendable Pathway Analysis Toolbox

    Article • PLoS Computational Biology, February 2015, PLOS

    Dr Alexander Pico, Professor Chris Evelo

  34. Affinity purification–mass spectrometry and network analysis to understand protein-protein interactions

    Article • Nature Protocols, October 2014, Springer Science + Business Media

    Dr Alexander Pico

  35. WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization

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

    Professor Chris Evelo, Dr Alexander Pico

  36. 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

  37. setsApp: Set operations for Cytoscape Nodes and Edges

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

    Dr Alexander Pico

  38. BridgeDb app: unifying identifier mapping services for Cytoscape

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

    Dr Alexander Pico

  39. Easily import and use WikiPathways biological pathways in the common network biology tool Cytoscape

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

    Dr Alexander Pico, Professor Chris Evelo

  40. enhancedGraphics: a Cytoscape app for enhanced node graphics

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

    Dr Alexander Pico

  41. Variants near TERT and TERC influencing telomere length are associated with high-grade glioma risk

    Article • Nature Genetics, June 2014, Nature

    Dr Alexander Pico

  42. NOA: a cytoscape plugin for network ontology analysis

    Article • Bioinformatics, June 2013, Oxford University Press (OUP)

    Dr Alexander Pico

  43. Genetic variants in telomerase-related genes are associated with an older age at diagnosis in glioma patients: evidence for distinct pathways of gliomagenesis

    Article • Neuro-Oncology, June 2013, Oxford University Press (OUP)

    Dr Alexander Pico

  44. Cytoscape App Store

    Article • Bioinformatics, April 2013, Oxford University Press (OUP)

    Dr Alexander Pico

  45. Inherited variant on chromosome 11q23 increases susceptibility to IDH-mutated but not IDH-normal gliomas regardless of grade or histology

    Article • Neuro-Oncology, January 2013, Oxford University Press (OUP)

    Dr Alexander Pico

  46. Analysis of 60 Reported Glioma Risk SNPs Replicates Published GWAS Findings but Fails to Replicate Associations From Published Candidate-Gene Studies

    Article • Genetic Epidemiology, December 2012, Wiley

    Dr Alexander Pico

  47. A travel guide to Cytoscape plugins

    Article • Nature Methods, November 2012, Springer Science + Business Media

    Professor Gary D Bader, Dr Alexander Pico

  48. Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage

    Article • Cell, September 2012, Elsevier

    Dr Alexander Pico

  49. A low-frequency variant at 8q24.21 is strongly associated with risk of oligodendroglial tumors and astrocytomas with IDH1 or IDH2 mutation

    Article • Nature Genetics, August 2012, Springer Science + Business Media

    Dr Alexander Pico

  50. GO-Elite: a flexible solution for pathway and ontology over-representation

    Article • Bioinformatics, June 2012, Oxford University Press (OUP)

    Professor Chris Evelo, Dr Alexander Pico

  51. Mosaic: making biological sense of complex networks

    Article • Bioinformatics, May 2012, Oxford University Press (OUP)

    Dr Alexander Pico

  52. Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

    Article • Nature Biotechnology, April 2012, Springer Science + Business Media

    Dr Alexander Pico

  53. WikiPathways: building research communities on biological pathways

    Article • Nucleic Acids Research, November 2011, Oxford University Press (OUP)

    Dr Alexander Pico, Professor Chris Evelo

  54. Human Heart Development Pathways

    Article • Nature Precedings, October 2011, Springer Science + Business Media

    Dr Alexander Pico

  55. WikiPathways: Community Curation of Biological Pathways

    Article • Nature Precedings, December 2010, Springer Science + Business Media

    Dr Alexander Pico

  56. Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

    Article • Nature Biotechnology, December 2010, Springer Science + Business Media

    Dr Alexander Pico

  57. BridgeDb: standardized access to gene, protein and metabolite identifier mapping services

    Article • Nature Precedings, October 2010, Springer Science + Business Media

    Dr Alexander Pico

  58. The BioPAX community standard for pathway data sharing

    Article • Nature Biotechnology, September 2010, Springer Science + Business Media

    Dr Alexander Pico

  59. Finding the Right Questions: Exploratory Pathway Analysis to Enhance Biological Discovery in Large Datasets

    Article • PLoS Biology, August 2010, PLOS

    Dr Alexander Pico, Professor Chris Evelo

  60. Structure of the Human BK Channel Ca2+-Activation Apparatus at 3.0 A Resolution

    Article • Science, May 2010, American Association for the Advancement of Science

    Dr Alexander Pico

  61. Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation

    Article • Proceedings of the National Academy of Sciences, May 2010, Proceedings of the National Academy of Sciences

    Dr Alexander Pico

  62. The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

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

    Professor Chris Evelo, Dr Alexander Pico

  63. Alternative Splicing in the Differentiation of Human Embryonic Stem Cells into Cardiac Precursors

    Article • PLoS Computational Biology, November 2009, PLOS

    Dr Alexander Pico

  64. Mining Biological Pathways Using WikiPathways Web Services

    Article • PLoS ONE, July 2009, PLOS

    Dr Alexander Pico, Professor Chris Evelo

  65. Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility

    Article • Nature Genetics, July 2009, Nature

    Dr Alexander Pico

  66. SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system

    Article • Nucleic Acids Research, January 2009, Oxford University Press (OUP)

    Dr Alexander Pico

  67. The public road to high-quality curated biological pathways

    Article • Drug Discovery Today, October 2008, Elsevier

    Professor Chris Evelo, Dr Alexander Pico

  68. WikiPathways: Pathway Editing for the People

    Article • PLoS Biology, July 2008, PLOS

    Dr Alexander Pico, Professor Chris Evelo

  69. Pathway Analysis of Single-Nucleotide Polymorphisms Potentially Associated with Glioblastoma Multiforme Susceptibility Using Random Forests

    Article • Cancer Epidemiology Biomarkers & Prevention, June 2008, American Association for Cancer Research (AACR)

    Dr Alexander Pico

  70. An Introduction to Pathway Analysis with GenMAPP

    Article • NCI Nature Pathway Interaction Database, April 2008, Springer Science + Business Media

    Dr Alexander Pico

  71. Presenting and exploring biological pathways with PathVisio

    Article • BMC Bioinformatics, January 2008, Springer Science + Business Media

    Dr Alexander Pico, Professor Chris Evelo

  72. 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

  73. GenMAPP 2: new features and resources for pathway analysis

    Article • BMC Bioinformatics, January 2007, Springer Science + Business Media

    Dr Alexander Pico

  74. Structure of the RCK Domain from the E. coli K+ Channel and Demonstration of Its Presence in the Human BK Channel

    Article • Neuron, March 2001, Elsevier

    Dr Alexander Pico

  75. Local cortical injections of glutamate and noradrenaline alter high-frequency (245Hz) neuronal activity in rat cortex

    Article • Neurocomputing, June 1999, Elsevier

    Dr Alexander Pico

  76. Crystal Structure of Hck in Complex with a Src Family–Selective Tyrosine Kinase Inhibitor

    Article • Molecular Cell, May 1999, Elsevier

    Dr Alexander Pico

  77. Intramolecular Regulatory Interactions in the Src Family Kinase Hck Probed by Mutagenesis of a Conserved Tryptophan Residue

    Article • Journal of Biological Chemistry, November 1998, American Society for Biochemistry & Molecular Biology (ASBMB)

    Dr Alexander Pico

  78. Sol-Gel Synthesis of the Strontium-Copper Oxycarbonate Superconductor Sr2CuO2(CO3)1−x(BO3)x

    Article • MRS Proceedings, January 1996, Springer Science + Business Media

    Dr Alexander Pico