PubRank

Julio Saez-Rodriguez

Author PubWeight™ 75.94‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 2012 15.91
2 Towards a rigorous assessment of systems biology models: the DREAM3 challenges. PLoS One 2010 4.94
3 Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst Biol 2007 4.52
4 A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinformatics 2006 3.55
5 Evaluation of methods for modeling transcription factor sequence specificity. Nat Biotechnol 2013 2.34
6 Logic-based models for the analysis of cell signaling networks. Biochemistry 2010 2.21
7 The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Comput Biol 2009 1.88
8 Crowdsourcing network inference: the DREAM predictive signaling network challenge. Sci Signal 2011 1.83
9 Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data. PLoS Comput Biol 2009 1.80
10 Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. BMC Syst Biol 2009 1.78
11 Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes. Mol Cell Proteomics 2010 1.77
12 Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling. PLoS Comput Biol 2009 1.69
13 CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. BMC Syst Biol 2012 1.60
14 Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli. PLoS Comput Biol 2011 1.53
15 A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks. BMC Bioinformatics 2006 1.53
16 Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties. PLoS One 2013 1.50
17 Transcriptional data: a new gateway to drug repositioning? Drug Discov Today 2012 1.40
18 Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst Biol 2013 1.29
19 Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. BMC Syst Biol 2012 1.28
20 SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst Biol 2013 1.20
21 Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. BMC Syst Biol 2014 1.06
22 DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data. Bioinformatics 2012 1.04
23 Integrating literature-constrained and data-driven inference of signalling networks. Bioinformatics 2012 1.03
24 Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinformatics 2013 1.02
25 State-time spectrum of signal transduction logic models. Phys Biol 2012 1.02
26 Dynamics of proximal signaling events after TCR/CD8-mediated induction of proliferation or apoptosis in mature CD8+ T cells. J Immunol 2008 1.02
27 Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models. Mol Biosyst 2013 0.98
28 CySBGN: a Cytoscape plug-in to integrate SBGN maps. BMC Bioinformatics 2013 0.94
29 Modeling signaling networks using high-throughput phospho-proteomics. Adv Exp Med Biol 2012 0.92
30 Prediction of human population responses to toxic compounds by a collaborative competition. Nat Biotechnol 2015 0.88
31 A rapidly reversible chemical dimerizer system to study lipid signaling in living cells. Angew Chem Int Ed Engl 2014 0.87
32 MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. BMC Bioinformatics 2014 0.86
33 Mapping the human phosphatome on growth pathways. Mol Syst Biol 2012 0.85
34 Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors. Genome Biol 2013 0.85
35 A multipathway phosphoproteomic signaling network model of idiosyncratic drug- and inflammatory cytokine-induced toxicity in human hepatocytes. Conf Proc IEEE Eng Med Biol Soc 2009 0.85
36 BioServices: a common Python package to access biological Web Services programmatically. Bioinformatics 2013 0.84
37 Network based elucidation of drug response: from modulators to targets. BMC Syst Biol 2013 0.83
38 Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways. PLoS One 2012 0.82
39 PIP₃ induces the recycling of receptor tyrosine kinases. Sci Signal 2014 0.81
40 Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network. Integr Biol (Camb) 2012 0.80
41 Identification of drug-specific pathways based on gene expression data: application to drug induced lung injury. Integr Biol (Camb) 2015 0.80
42 Modeling signaling networks with different formalisms: a preview. Methods Mol Biol 2013 0.79
43 Corrigendum: Fumarate is an epigenetic modifier that elicits epithelial-to-mesenchymal transition. Nature 2016 0.77
44 Construction of cell type-specific logic models of signaling networks using CellNOpt. Methods Mol Biol 2013 0.75
45 Benchmarking substrate-based kinase activity inference using phosphoproteomic data. Bioinformatics 2017 0.75
46 Integrative approaches for signalling and metabolic networks. Integr Biol (Camb) 2015 0.75
47 Erratum: Prediction of human population responses to toxic compounds by a collaborative competition. Nat Biotechnol 2015 0.75
48 Construction of signaling pathways and identification of drug effects on the liver cancer cell HepG2. Conf Proc IEEE Eng Med Biol Soc 2010 0.75