Julio Saez-Rodriguez

Julio Saez-Rodriguez

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Julio Saez-Rodriguez

Publications by authors named "Julio Saez-Rodriguez"

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Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis.

Cell Rep 2019 Oct;29(1):202-211.e6

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany; Division of Computational Genomics and Systems Genetics, German Cancer Research Center, 69120 Heidelberg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.08.077DOI Listing
October 2019

Transfer of regulatory knowledge from human to mouse for functional genomic analysis.

Biochim Biophys Acta Gene Regul Mech 2019 Sep 13:194431. Epub 2019 Sep 13.

Institute of Computational Biomedicine, Heidelberg University, Faculty of Medicine, Bioquant - Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, Pauwelsstrasse 19, 52074 Aachen, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.bbagrm.2019.194431DOI Listing
September 2019

Signatures of cell death and proliferation in perturbation transcriptomics data-from confounding factor to effective prediction.

Nucleic Acids Res 2019 Sep 25. Epub 2019 Sep 25.

RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 52074 Aachen, Germany.

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http://dx.doi.org/10.1093/nar/gkz805DOI Listing
September 2019

Benchmark and integration of resources for the estimation of human transcription factor activities.

Genome Res 2019 08 24;29(8):1363-1375. Epub 2019 Jul 24.

European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, CB10 1SD Cambridge, United Kingdom.

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http://dx.doi.org/10.1101/gr.240663.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6673718PMC
August 2019

Big science and big data in nephrology.

Kidney Int 2019 Jun 5;95(6):1326-1337. Epub 2019 Mar 5.

RWTH Aachen, Department of Nephrology and Clinical Immunology, Aachen, Germany; Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.kint.2018.11.048DOI Listing
June 2019

Author Correction: Linking drug target and pathway activation for effective therapy using multi-task learning.

Sci Rep 2019 May 3;9(1):7106. Epub 2019 May 3.

RWTH Aachen University, Faculty of Medicine, Joint Research Center for Computational Biomedicine, Aachen, Germany.

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http://www.nature.com/articles/s41598-019-43503-0
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http://dx.doi.org/10.1038/s41598-019-43503-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499772PMC
May 2019

The proteome microenvironment determines the protective effect of preconditioning in cisplatin-induced acute kidney injury.

Kidney Int 2019 02 3;95(2):333-349. Epub 2018 Dec 3.

Department II of Internal Medicine, University of Cologne, Cologne, Germany; Center for Molecular Medicine, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Cologne, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.kint.2018.08.037DOI Listing
February 2019

Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury.

Front Genet 2018 20;9:527. Epub 2018 Nov 20.

Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands.

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http://dx.doi.org/10.3389/fgene.2018.00527DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6255978PMC
November 2018

Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells.

Methods Mol Biol 2018 ;1711:103-132

Joint Research Center for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, MTZ Pauwelsstrasse 19, D-52074, Aachen, Germany.

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http://dx.doi.org/10.1007/978-1-4939-7493-1_6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6126574PMC
October 2018

Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data.

PLoS Comput Biol 2018 10 29;14(10):e1006538. Epub 2018 Oct 29.

Université de Nantes, Centrale Nantes, CNRS, Laboratoire des Sciences du Numérique de Nantes (LS2N UMR 6004), F-44000, Nantes, France.

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http://dx.doi.org/10.1371/journal.pcbi.1006538DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6224120PMC
October 2018

Prioritization of Transporter-Drug Relationships From Drug Sensitivity Screens.

Front Pharmacol 2018 7;9:1011. Epub 2018 Sep 7.

CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.

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http://dx.doi.org/10.3389/fphar.2018.01011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6137680PMC
September 2018

The germline genetic component of drug sensitivity in cancer cell lines.

Nat Commun 2018 08 23;9(1):3385. Epub 2018 Aug 23.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://www.nature.com/articles/s41467-018-05811-3
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http://dx.doi.org/10.1038/s41467-018-05811-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6107640PMC
August 2018

A microfluidics platform for combinatorial drug screening on cancer biopsies.

Nat Commun 2018 06 22;9(1):2434. Epub 2018 Jun 22.

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117, Heidelberg, Germany.

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http://dx.doi.org/10.1038/s41467-018-04919-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015045PMC
June 2018

Alternative models for sharing confidential biomedical data.

Nat Biotechnol 2018 05;36(5):391-392

RWTH Aachen University, Faculty of Medicine, Germany.

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http://dx.doi.org/10.1038/nbt.4128DOI Listing
May 2018

Linking drug target and pathway activation for effective therapy using multi-task learning.

Sci Rep 2018 05 29;8(1):8322. Epub 2018 May 29.

RWTH Aachen University, Faculty of Medicine, Joint Research Center for Computational Biomedicine, Aachen, Germany.

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http://dx.doi.org/10.1038/s41598-018-25947-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5974390PMC
May 2018

GDSCTools for mining pharmacogenomic interactions in cancer.

Bioinformatics 2018 04;34(7):1226-1228

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/btx744DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031019PMC
April 2018

Pathway-based dissection of the genomic heterogeneity of cancer hallmarks' acquisition with SLAPenrich.

Sci Rep 2018 04 30;8(1):6713. Epub 2018 Apr 30.

European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1038/s41598-018-25076-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5928049PMC
April 2018

Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer.

Cancer Res 2018 02 11;78(3):769-780. Epub 2017 Dec 11.

European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-1679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6522379PMC
February 2018

NADH Shuttling Couples Cytosolic Reductive Carboxylation of Glutamine with Glycolysis in Cells with Mitochondrial Dysfunction.

Mol Cell 2018 02;69(4):581-593.e7

Medical Research Council Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.01.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5823973PMC
February 2018

Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells.

Metab Eng 2018 01 27;45:149-157. Epub 2017 Nov 27.

RWTH Aachen University, Faculty of Medicine, Joint Research Center for Computational Biomedicine, Aachen, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.ymben.2017.11.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5805855PMC
January 2018

A systematic atlas of chaperome deregulation topologies across the human cancer landscape.

PLoS Comput Biol 2018 01 2;14(1):e1005890. Epub 2018 Jan 2.

Joint Research Center for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Aachen, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1005890DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5766242PMC
January 2018

Perturbation-response genes reveal signaling footprints in cancer gene expression.

Nat Commun 2018 01 2;9(1):20. Epub 2018 Jan 2.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1038/s41467-017-02391-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5750219PMC
January 2018

Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines.

Cell Syst 2017 12 6;5(6):604-619.e7. Epub 2017 Dec 6.

Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2017.11.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5747350PMC
December 2017

A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology.

PLoS One 2017 15;12(8):e0182186. Epub 2017 Aug 15.

BioProcess Engineering Group. IIM-CSIC, Spanish National Research Council. C/Eduardo Cabello, 6. E-36208 Vigo, Spain.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0182186PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5557587PMC
October 2017

Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer.

Cell Syst 2017 10 11;5(4):386-398.e4. Epub 2017 Oct 11.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2017.08.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5660600PMC
October 2017

Mechanism-based biomarker discovery.

Drug Discov Today 2017 08 27;22(8):1209-1215. Epub 2017 Apr 27.

National Technical University of Athens, Athens, Greece; ProtATonce Ltd, Athens, Greece. Electronic address:

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http://dx.doi.org/10.1016/j.drudis.2017.04.013DOI Listing
August 2017

Logic Modeling in Quantitative Systems Pharmacology.

CPT Pharmacometrics Syst Pharmacol 2017 08 29;6(8):499-511. Epub 2017 Jul 29.

RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine, Aachen, Germany.

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http://dx.doi.org/10.1002/psp4.12225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5572374PMC
August 2017

Benchmarking substrate-based kinase activity inference using phosphoproteomic data.

Bioinformatics 2017 Jun;33(12):1845-1851

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.

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http://dx.doi.org/10.1093/bioinformatics/btx082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870625PMC
June 2017

Drug Resistance Mechanisms in Colorectal Cancer Dissected with Cell Type-Specific Dynamic Logic Models.

Cancer Res 2017 06 5;77(12):3364-3375. Epub 2017 Apr 5.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-0078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6433282PMC
June 2017

System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects.

J Proteome Res 2017 02 10;16(2):831-841. Epub 2017 Jan 10.

Department of Biology, Institute of Molecular Systems Biology, ETH Zürich , Zürich 8093, Switzerland.

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http://dx.doi.org/10.1021/acs.jproteome.6b00815DOI Listing
February 2017

Data-driven reverse engineering of signaling pathways using ensembles of dynamic models.

PLoS Comput Biol 2017 02 6;13(2):e1005379. Epub 2017 Feb 6.

Bioprocess Engineering Group, Spanish National Research Council, IIM-CSIC, Vigo, Spain.

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http://dx.doi.org/10.1371/journal.pcbi.1005379DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319798PMC
February 2017

Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.

PLoS Comput Biol 2017 01 10;13(1):e1005297. Epub 2017 Jan 10.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1005297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224888PMC
January 2017

Efficient randomization of biological networks while preserving functional characterization of individual nodes.

BMC Bioinformatics 2016 Dec 20;17(1):542. Epub 2016 Dec 20.

European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1186/s12859-016-1402-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5168876PMC
December 2016

Looking beyond the cancer cell for effective drug combinations.

Genome Med 2016 11 25;8(1):125. Epub 2016 Nov 25.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1186/s13073-016-0379-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5124246PMC
November 2016

OmniPath: guidelines and gateway for literature-curated signaling pathway resources.

Nat Methods 2016 11;13(12):966-967

European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK.

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http://www.nature.com/articles/nmeth.4077
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http://dx.doi.org/10.1038/nmeth.4077DOI Listing
November 2016

Modeling Signaling Networks to Advance New Cancer Therapies.

Annu Rev Biomed Eng 2015 14;17:143-63. Epub 2015 Aug 14.

Signalling Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom; email:

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http://dx.doi.org/10.1146/annurev-bioeng-071813-104927DOI Listing
September 2016

Transcriptional response networks for elucidating mechanisms of action of multitargeted agents.

Drug Discov Today 2016 07 12;21(7):1063-75. Epub 2016 Mar 12.

Institute for Molecular Medicine Finland (FIMM), Biomedicum Helsinki 2U, Tukholmankatu 8, University of Helsinki, Helsinki 00014, Finland; Department of Mathematics and Statistics, Quantum, University of Turku, Turku 20014, Finland.

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http://dx.doi.org/10.1016/j.drudis.2016.03.001DOI Listing
July 2016

DREAMTools: a Python package for scoring collaborative challenges.

F1000Res 2015 9;4:1030. Epub 2015 Oct 9.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI),Wellcome Trust Genome Campus, Cambridge, UK; RWTH Aachen University Medical Hospital, Joint Research Centre for Computational Biomedicine (JRCCOMBINE), Aachen, Germany.

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http://dx.doi.org/10.12688/f1000research.7118.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4837986PMC
May 2016

The orchestra of lipid-transfer proteins at the crossroads between metabolism and signaling.

Prog Lipid Res 2016 Jan 1;61:30-9. Epub 2015 Dec 1.

European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany; European Molecular Biology Laboratory (EMBL), Molecular Medicine Partnership Unit (MMPU), Meyerhofstrasse 1, D-69117 Heidelberg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.plipres.2015.10.004DOI Listing
January 2016

Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies.

BMC Bioinformatics 2015 Oct 28;16:345. Epub 2015 Oct 28.

Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, 39106, Germany.

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http://dx.doi.org/10.1186/s12859-015-0733-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4625540PMC
October 2015

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.

Bioinformatics 2015 Sep 21;31(18):2999-3007. Epub 2015 May 21.

Bioprocess Engineering Group, Spanish National Research Council, IIM-CSIC, C/Eduardo Cabello 6, 36208 Vigo, Spain, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal and European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btv314DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4565031PMC
September 2015

Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data.

Nat Commun 2015 Sep 10;6:8033. Epub 2015 Sep 10.

European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1038/ncomms9033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4579397PMC
September 2015

Designing Experiments to Discriminate Families of Logic Models.

Front Bioeng Biotechnol 2015 4;3:131. Epub 2015 Sep 4.

IRCCyN UMR CNRS 6597, École Centrale de Nantes , Nantes , France.

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http://dx.doi.org/10.3389/fbioe.2015.00131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560026PMC
September 2015

Identification of drug-specific pathways based on gene expression data: application to drug induced lung injury.

Integr Biol (Camb) 2015 Aug;7(8):904-20

Office of Clinical Pharmacology, Office of Translational Science, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA.

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http://xlink.rsc.org/?DOI=C4IB00294F
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http://dx.doi.org/10.1039/c4ib00294fDOI Listing
August 2015

Integrative approaches for signalling and metabolic networks.

Integr Biol (Camb) 2015 Aug;7(8):844-5

Laboratory of Computational Systems Biotechnology (LCSB), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1039/c5ib90030aDOI Listing
August 2015

A single-cell model of PIP3 dynamics using chemical dimerization.

Bioorg Med Chem 2015 Jun 7;23(12):2868-76. Epub 2015 May 7.

European Molecular Biology Laboratory, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Electronic address:

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http://dx.doi.org/10.1016/j.bmc.2015.04.074DOI Listing
June 2015

Empirical inference of circuitry and plasticity in a kinase signaling network.

Proc Natl Acad Sci U S A 2015 Jun 9;112(25):7719-24. Epub 2015 Jun 9.

Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, United Kingdom;

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http://www.pnas.org/content/112/25/7719.full.pdf
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http://www.pnas.org/lookup/doi/10.1073/pnas.1423344112
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http://dx.doi.org/10.1073/pnas.1423344112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4485132PMC
June 2015

Cooperative development of logical modelling standards and tools with CoLoMoTo.

Bioinformatics 2015 Apr 25;31(7):1154-9. Epub 2015 Jan 25.

Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv013DOI Listing
April 2015

Signaling networks in MS: a systems-based approach to developing new pharmacological therapies.

Mult Scler 2015 Feb 11;21(2):138-46. Epub 2014 Aug 11.

Institute Biomedical Research August Pi Sunyer (IDIBAPS) - Hospital Clinic of Barcelona, Spain/Personal Biomedicine ZAO, and A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Russia

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http://dx.doi.org/10.1177/1352458514543339DOI Listing
February 2015

A community computational challenge to predict the activity of pairs of compounds.

Nat Biotechnol 2014 Dec 17;32(12):1213-22. Epub 2014 Nov 17.

1] Department of Systems Biology, Columbia University, New York, New York, USA. [2] Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA. [3] Department of Biomedical Informatics, Columbia University, New York, New York, USA. [4] Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA. [5] Institute for Cancer Genetics, Columbia University, New York, New York, USA. [6] Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York, USA.

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http://dx.doi.org/10.1038/nbt.3052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4399794PMC
December 2014

Fast randomization of large genomic datasets while preserving alteration counts.

Bioinformatics 2014 Sep;30(17):i617-23

Fondazione Bruno Kessler, I-38100 Povo (Trento), Italy, European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, UK, Wellcome Trust Sanger Institute, Cambridge CB10 1SD, UK and Universitat Pompeu Fabra, Barcelona 08003, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btu474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147926PMC
September 2014

A rapidly reversible chemical dimerizer system to study lipid signaling in living cells.

Angew Chem Int Ed Engl 2014 Jun 19;53(26):6720-3. Epub 2014 May 19.

Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany).

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http://dx.doi.org/10.1002/anie.201402294DOI Listing
June 2014

PIP₃ induces the recycling of receptor tyrosine kinases.

Sci Signal 2014 Jan 14;7(308):ra5. Epub 2014 Jan 14.

1Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1126/scisignal.2004532DOI Listing
January 2014

Modeling signaling networks with different formalisms: a preview.

Methods Mol Biol 2013 ;1021:89-105

EMBL Outstation-European Bioinformatics Institute, Cambridge, UK.

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http://dx.doi.org/10.1007/978-1-62703-450-0_5DOI Listing
December 2013

BioServices: a common Python package to access biological Web Services programmatically.

Bioinformatics 2013 Dec 23;29(24):3241-2. Epub 2013 Sep 23.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense 5230, Denmark, Translational Research Laboratory, Breast Cancer Unit, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), Gran via 199, L'Hospitalet del Llobregat, Barcelona 08908, Catalonia, Spain and Biomedical Research Institute of Girona, Girona 17007, Catalonia, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btt547DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3842755PMC
December 2013

Network based elucidation of drug response: from modulators to targets.

BMC Syst Biol 2013 Dec 13;7:139. Epub 2013 Dec 13.

Telethon Institute of Genetics and Medicine, Naples, Italy.

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http://dx.doi.org/10.1186/1752-0509-7-139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3878740PMC
December 2013