All Stories

  1. Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies
  2. The germline genetic component of drug sensitivity in cancer cell lines
  3. Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting
  4. In silico prioritization of transporter-drug relationships from drug sensitivity screens
  5. How to find the right drug for each patient? Advances and challenges in pharmacogenomics
  6. A microfluidics platform for combinatorial drug screening on cancer biopsies
  7. Benchmark and integration of resources for the estimation of human transcription factor activities
  8. Linking drug target and pathway activation for effective therapy using multi-task learning
  9. Alternative models for sharing confidential biomedical data
  10. Analysis of the human kinome and phosphatome reveals diseased signaling networks induced by overexpression
  11. Pathway-based dissection of the genomic heterogeneity of cancer hallmarks’ acquisition with SLAPenrich
  12. Genomic, Proteomic and Phenotypic Heterogeneity in HeLa Cells across Laboratories: Implications for Reproducibility of Research Results
  13. Kinetic modelling of quantitative proteome data predicts metabolic reprogramming of liver cancer
  14. CELLector: Genomics Guided Selection of Cancer in vitro Models
  15. Whither systems medicine?
  16. Rapid proteotyping reveals cancer biology and drug response determinants in the NCI-60 cells
  17. Open Community Challenge Reveals Molecular Network Modules with Key Roles in Diseases
  18. Modelling cell-cell interactions from spatial molecular data with spatial variance component analysis
  19. A functional landscape of chronic kidney disease entities from public transcriptomic data
  20. NADH Shuttling Couples Cytosolic Reductive Carboxylation of Glutamine with Glycolysis in Cells with Mitochondrial Dysfunction
  21. Perturbation-response genes reveal signaling footprints in cancer gene expression
  22. A systematic atlas of chaperome deregulation topologies across the human cancer landscape
  23. Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells
  24. Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells
  25. Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer
  26. Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting
  27. Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines
  28. GDSCTools for mining pharmacogenomic interactions in cancer
  29. A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines
  30. A cancer pharmacogenomic screen powering crowd-sourced advancement of drug combination prediction
  31. Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer
  32. A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology
  33. Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells
  34. Logic Modeling in Quantitative Systems Pharmacology
  35. Gli1 + Mesenchymal Stromal Cells Are a Key Driver of Bone Marrow Fibrosis and an Important Cellular Therapeutic Target
  36. Transcription factor activities enhance markers of drug response in cancer
  37. Drug resistance mechanisms in colorectal cancer dissected with cell type-specific dynamic logic models
  38. Mechanism-based biomarker discovery
  39. A Systematic Atlas of Chaperome Deregulation Topologies Across the Human Cancer Landscape
  40. Benchmarking substrate-based kinase activity inference using phosphoproteomic data
  41. Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations
  42. Data-driven reverse engineering of signaling pathways using ensembles of dynamic models
  43. Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast
  44. System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects
  45. caspo: a toolbox for automated reasoning on the response of logical signaling networks families
  46. Stem cell-like transcriptional reprogramming mediates metastatic resistance to mTOR inhibition
  47. Dissecting cancer resistance to therapies with cell-type-specific dynamic logic models
  48. Rapid identification of optimal drug combinations for personalized cancer therapy using microfluidics
  49. Chromosomal rearrangements are commonly post-transcriptionally attenuated in cancer
  50. Efficient randomization of biological networks while preserving functional characterization of individual nodes
  51. OmniPath: guidelines and gateway for literature-curated signaling pathway resources
  52. Looking beyond the cancer cell for effective drug combinations
  53. Benchmarking substrate-based kinase activity inference using phosphoproteomic data
  54. A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia
  55. Population-level characterization of pathway alterations with SLAPenrich dissects heterogeneity of cancer hallmark acquisition
  56. Efficient randomization of biological networks while preserving functional characterization of individual nodes
  57. Phosphoproteomics-based Profiling of Kinase Activities in Cancer Cells
  58. Perturbation-response genes reveal signaling footprints in cancer gene expression
  59. Crowdsourcing biomedical research: leveraging communities as innovation engines
  60. Transcriptional response networks for elucidating mechanisms of action of multitargeted agents
  61. A Landscape of Pharmacogenomic Interactions in Cancer
  62. Systematic analysis of transcriptional and post-transcriptional regulation of metabolism in yeast
  63. Logical Modeling and Dynamical Analysis of Cellular Networks
  64. System-wide quantitative proteomics of the metabolic syndrome in mice: genotypic and dietary effects
  65. A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin
  66. DREAMTools: a Python package for scoring collaborative challenges
  67. Integrated transcriptomic and proteomic analysis identifies protein kinase CK2 as a key signaling node in an inflammatory cytokine network in ovarian cancer cells
  68. Inferring causal molecular networks: empirical assessment through a community-based effort
  69. Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A
  70. The orchestra of lipid-transfer proteins at the crossroads between metabolism and signaling
  71. Modeling Signaling Networks to Advance New Cancer Therapies
  72. Pharmacogenomic agreement between two cancer cell line data sets
  73. Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies
  74. DREAMTools: a Python package for scoring collaborative challenges
  75. A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions
  76. Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data
  77. Designing Experiments to Discriminate Families of Logic Models
  78. Learning Boolean logic models of signaling networks with ASP
  79. Prediction of human population responses to toxic compounds by a collaborative competition
  80. Empirical inference of circuitry and plasticity in a kinase signaling network
  81. A single-cell model of PIP3 dynamics using chemical dimerization
  82. Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach
  83. Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients
  84. BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology
  85. Cooperative development of logical modelling standards and tools with CoLoMoTo
  86. Identification of drug-specific pathways based on gene expression data: application to drug induced lung injury
  87. Integrative approaches for signalling and metabolic networks
  88. Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast
  89. A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models
  90. Fast randomization of large genomic datasets while preserving alteration counts
  91. Signaling networks in MS: A systems-based approach to developing new pharmacological therapies
  92. Cyrface: An interface from Cytoscape to R that provides a user interface to R packages
  93. A community effort to assess and improve drug sensitivity prediction algorithms
  94. A Rapidly Reversible Chemical Dimerizer System to Study Lipid Signaling in Living Cells
  95. A Rapidly Reversible Chemical Dimerizer System to Study Lipid Signaling in Living Cells
  96. PIP3 Induces the Recycling of Receptor Tyrosine Kinases
  97. Dynamic transcription factor activity and networks during ErbB2 breast oncogenesis and targeted therapy
  98. Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach
  99. MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics
  100. BioServices: a common Python package to access biological Web Services programmatically
  101. Cyrface: An interface from Cytoscape to R that provides a user interface to R packages
  102. Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming
  103. Machine Learning Prediction of Cancer Cell Sensitivity to Drugs Based on Genomic and Chemical Properties
  104. Transcriptional data: a new gateway to drug repositioning?
  105. Critical assessment of automated flow cytometry data analysis techniques
  106. Evaluation of methods for modeling transcription factor sequence specificity
  107. Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models
  108. Path2Models: large-scale generation of computational models from biochemical pathway maps
  109. SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
  110. Modeling Signaling Networks with Different Formalisms: A Preview
  111. Network based elucidation of drug response: from modulators to targets
  112. CySBGN: A Cytoscape plug-in to integrate SBGN maps
  113. Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors
  114. Non Linear Programming (NLP) Formulation for Quantitative Modeling of Protein Signal Transduction Pathways
  115. DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data
  116. Construction of Cell Type-Specific Logic Models of Signaling Networks Using CellNOpt
  117. Mapping the human phosphatome on growth pathways
  118. State–time spectrum of signal transduction logic models
  119. Integrating literature-constrained and data-driven inference of signalling networks
  120. Systematic identification of genomic markers of drug sensitivity in cancer cells
  121. Cancer develops, progresses and responds to therapies through restricted perturbation of the protein–protein interaction network
  122. Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data
  123. CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms
  124. Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks
  125. Revisiting the Training of Logic Models of Protein Signaling Networks with ASP
  126. Modeling Signaling Networks Using High-throughput Phospho-proteomics
  127. Crowdsourcing Network Inference: The DREAM Predictive Signaling Network Challenge
  128. Comparing Signaling Networks between Normal and Transformed Hepatocytes Using Discrete Logical Models
  129. Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli
  130. Setting the Standards for Signal Transduction Research
  131. Retroactivity as a Criterion to Define Modules in Signaling Networks
  132. Construction of signaling pathways and identification of drug effects on the liver cancer cell HepG2
  133. Networks Inferred from Biochemical Data Reveal Profound Differences in Toll-like Receptor and Inflammatory Signaling between Normal and Transformed Hepatocytes
  134. Logic-Based Models for the Analysis of Cell Signaling Networks
  135. Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges
  136. Cellular Regulatory Networks
  137. Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data
  138. Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction
  139. A multipathway phosphoproteomic signaling network model of idiosyncratic drug- and inflammatory cytokine-induced toxicity in human hepatocytes
  140. The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data
  141. Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling
  142. Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling
  143. Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules
  144. Multistability of signal transduction motifs
  145. Flexible informatics for linking experimental data to mathematical models via DataRail
  146. A Logical Model Provides Insights into T Cell Receptor Signaling
  147. Systems biology—An engineering perspective
  148. Dissecting the puzzle of life: modularization of signal transduction networks
  149. A Logical Model Provides Insights into T-cell Receptor Signaling
  150. Using chemical reaction network theory to discard a kinetic mechanism hypothesis
  151. Modular analysis of signal transduction networks - How engineering tools can be applied to the analysis of cellular machinery
  152. Reduction of mathematical models of signal transduction networks: simulation-based approach applied to EGF receptor signalling
  153. High-Throughput Protein-Based Technologies and Computational Models for Drug Development, Efficacy, and Toxicity