All Stories

  1. Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data
  2. Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data
  3. Point-and-click sharing of single-cell data.
  4. The Cytoscape Automation app article collection
  5. AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations
  6. author networks
  7. NetMatchStar: an enhanced Cytoscape network querying app
  8. Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes
  9. Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy
  10. Faculty Opinions recommendation of VarWalker: personalized mutation network analysis of putative cancer genes from next-generation sequencing data.
  11. Biological Network Exploration with Cytoscape 3
  12. GeneMANIA: Fast gene network construction and function prediction for Cytoscape
  13. Enrichment Map – a Cytoscape app to visualize and explore OMICs pathway enrichment results
  14. The Cytoscape app article collection
  15. Quiescent Sox2+ Cells Drive Hierarchical Growth and Relapse in Sonic Hedgehog Subgroup Medulloblastoma
  16. Highlights of B/D‐HPP and HPP Resource Pillar Workshops at 12th Annual HUPO World Congress of Proteomics
  17. Prediction and Experimental Characterization of nsSNPs Altering Human PDZ-Binding Motifs
  18. Coordinate MicroRNA-Mediated Regulation of Protein Complexes in Prostate Cancer
  19. Erratum: Comprehensive identification of mutational cancer driver genes across 12 tumor types
  20. The mutational landscape of phosphorylation signaling in cancer
  21. Comprehensive identification of mutational cancer driver genes across 12 tumor types
  22. Using Biological Pathway Data with Paxtools
  23. Computational approaches to identify functional genetic variants in cancer genomes
  24. 2035 EPIGENETIC REGULATION OF GENE EXPRESSION PATTERNS IN HUMAN TESTIS XENOTRANSPLANTS AFTER TREATMENT WITH CYCLOPHOSPHAMIDE
  25. Faculty Opinions recommendation of Structure-based prediction of protein-protein interactions on a genome-wide scale.
  26. Metabolic Adaptation to Chronic Inhibition of Mitochondrial Protein Synthesis in Acute Myeloid Leukemia Cells
  27. Predicting PDZ domain mediated protein interactions from structure
  28. Integrative pathway dissection of molecular mechanisms of moxLDL-induced vascular smooth muscle phenotype transformation
  29. Chemogenomic Profiling
  30. The Biology/Disease-driven Human Proteome Project (B/D-HPP): Enabling Protein Research for the Life Sciences Community
  31. Chromatin is an ancient innovation conserved between Archaea and Eukarya
  32. Attenuation of miR-126 Activity Expands HSC In Vivo without Exhaustion
  33. Faculty Opinions recommendation of Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells.
  34. A travel guide to Cytoscape plugins
  35. A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals
  36. Multiple Genetic Interaction Experiments Provide Complementary Information Useful for Gene Function Prediction
  37. Faculty Opinions recommendation of Mutual exclusivity analysis identifies oncogenic network modules.
  38. Domain‐mediated protein interaction prediction: From genome to network
  39. Phosphorylation sites of higher stoichiometry are more conserved
  40. Mapping the Hsp90 Genetic Interaction Network in Candida albicans Reveals Environmental Contingency and Rewired Circuitry
  41. Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study
  42. Faculty Opinions recommendation of Toward an understanding of the protein interaction network of the human liver.
  43. Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)
  44. clusterMaker: a multi-algorithm clustering plugin for Cytoscape
  45. Faculty Opinions recommendation of Believe it or not: how much can we rely on published data on potential drug targets?
  46. Faculty Opinions recommendation of Predicting selective drug targets in cancer through metabolic networks.
  47. Compound Prioritization Methods Increase Rates of Chemical Probe Discovery in Model Organisms
  48. Faculty Opinions recommendation of Testing the ortholog conjecture with comparative functional genomic data from mammals.
  49. Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma
  50. PSICQUIC and PSISCORE: accessing and scoring molecular interactions
  51. Faculty Opinions recommendation of Quantitative epistasis analysis and pathway inference from genetic interaction data.
  52. Faculty Opinions recommendation of NOA: a novel Network Ontology Analysis method.
  53. WordCloud: a Cytoscape plugin to create a visual semantic summary of networks
  54. Faculty Opinions recommendation of Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome.
  55. Protein Complexes are Central in the Yeast Genetic Landscape
  56. Faculty Opinions recommendation of Measuring the evolutionary rewiring of biological networks.
  57. Too many roads not taken
  58. Visualizing Gene-Set Enrichment Results Using the Cytoscape Plug-in Enrichment Map
  59. Displaying Chemical Information on a Biological Network Using Cytoscape
  60. Bringing order to protein disorder through comparative genomics and genetic interactions
  61. Functional complexes between YAP2 and ZO-2 are PDZ domain-dependent, and regulate YAP2 nuclear localization and signalling
  62. Faculty Opinions recommendation of STITCH: interaction networks of chemicals and proteins.
  63. An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology
  64. Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
  65. Quantitative analysis of fitness and genetic interactions in yeast on a genome scale
  66. Faculty Opinions recommendation of A comprehensive molecular interaction map of the budding yeast cell cycle.
  67. Dynamic interaction networks in a hierarchically organized tissue
  68. Faculty Opinions recommendation of Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line.
  69. Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps
  70. Faculty Opinions recommendation of A global protein kinase and phosphatase interaction network in yeast.
  71. Faculty Opinions recommendation of Modeling synthetic lethality.
  72. Faculty Opinions recommendation of Reverse engineering a signaling network using alternative inputs.
  73. A predictive model for drug bioaccumulation and bioactivity in Caenorhabditis elegans
  74. Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps
  75. Coevolution of PDZ domain–ligand interactions analyzed by high-throughput phage display and deep sequencing
  76. Bayesian Modeling of the Yeast SH3 Domain Interactome Predicts Spatiotemporal Dynamics of Endocytosis Proteins
  77. How to visually interpret biological data using networks
  78. A Specificity Map for the PDZ Domain Family
  79. Exploring Biological Networks with Cytoscape Software
  80. Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions
  81. Integration of biological networks and gene expression data using Cytoscape
  82. Computational Prediction of Protein–Protein Interactions
  83. The minimum information required for reporting a molecular interaction experiment (MIMIx)
  84. Germ-line DNA copy number variation frequencies in a large North American population
  85. From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research
  86. Computational prediction of cancer-gene function
  87. BioPAX– biological pathway data exchange format
  88. Protein Interaction Databases
  89. Pathway information for systems biology
  90. Computational Prediction of Protein-Protein Interactions
  91. The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data
  92. Playing tag with the yeast proteome
  93. Functional genomics and proteomics: charting a multidimensional map of the yeast cell
  94. Functional genomics of intracellular peptide recognition domains with combinatorial biology methods
  95. Peptide Recognition Module Networks: Combining Phage Display with Two-Hybrid Analysis to Define Protein-Protein Interactions
  96. Analyzing yeast protein–protein interaction data obtained from different sources
  97. Bioinformatics: Interaction Databases
  98. Approaches to Analyze Protein Interactions
  99. Interaction Databases
  100. Interaction Databases