Publications by authors named "Julio Saez-Rodriguez"

100Publications

The tissue proteome in the multi-omic landscape of kidney disease.

Nat Rev Nephrol 2020 Oct 7. Epub 2020 Oct 7.

Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, and Heidelberg University Hospital, Bioquant, Heidelberg, Germany.

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http://dx.doi.org/10.1038/s41581-020-00348-5DOI Listing
October 2020

Big Data Approaches in Heart Failure Research.

Curr Heart Fail Rep 2020 Oct;17(5):213-224

Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany.

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http://dx.doi.org/10.1007/s11897-020-00469-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7496059PMC
October 2020

Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics.

Cell Syst 2020 Aug 24;11(2):186-195.e9. Epub 2020 Jul 24.

Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, 52074 Aachen, Germany; European Molecular Biology Laboratory-The European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK; Institute for Computational Biomedicine, Heidelberg University Hospital and Heidelberg University, Faculty of Medicine, Bioquant Heidelberg, Hedelberg 69120, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2020.06.013DOI Listing
August 2020

Footprint-based functional analysis of multiomic data.

Curr Opin Syst Biol 2019 Jun;15:82-90

Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.coisb.2019.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7357600PMC
June 2019

The Global Phosphorylation Landscape of SARS-CoV-2 Infection.

Cell 2020 08 28;182(3):685-712.e19. Epub 2020 Jun 28.

QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2020.06.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7321036PMC
August 2020

Converting networks to predictive logic models from perturbation signalling data with CellNOpt.

Bioinformatics 2020 Aug;36(16):4523-4524

Faculty of Medicine, Heidelberg University, Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuant 69120 Heidelberg, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btaa561DOI Listing
August 2020

Stratification and prediction of drug synergy based on target functional similarity.

NPJ Syst Biol Appl 2020 06 2;6(1):16. Epub 2020 Jun 2.

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

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http://dx.doi.org/10.1038/s41540-020-0136-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7265486PMC
June 2020

CELLector: Genomics-Guided Selection of Cancer In Vitro Models.

Cell Syst 2020 May;10(5):424-432.e6

Open Targets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK; Human Technopole, 20157, Milano, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2020.04.007DOI Listing
May 2020

Personalized signaling models for personalized treatments.

Mol Syst Biol 2020 01;16(1):e9042

Institute of Pathology, Charité - Universitätsmedizin Berlin, Berlin, Germany.

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http://dx.doi.org/10.15252/msb.20199042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6951359PMC
January 2020

Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data.

Genome Biol 2020 02 12;21(1):36. Epub 2020 Feb 12.

Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany.

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http://dx.doi.org/10.1186/s13059-020-1949-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7017576PMC
February 2020

A Functional Landscape of CKD Entities From Public Transcriptomic Data.

Kidney Int Rep 2020 Feb 13;5(2):211-224. Epub 2019 Nov 13.

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

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http://dx.doi.org/10.1016/j.ekir.2019.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7000845PMC
February 2020

Quantitative Systems Toxicology Modeling To Address Key Safety Questions in Drug Development: A Focus of the TransQST Consortium.

Chem Res Toxicol 2020 01 7;33(1):7-9. Epub 2020 Jan 7.

Drug Metabolism Pharmacokinetics and Bioanalysis , AbbVie Deutschland GmbH & Co. KG , D-67008 Ludwigshafen , Germany.

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http://dx.doi.org/10.1021/acs.chemrestox.9b00499DOI Listing
January 2020

Bringing data from curated pathway resources to Cytoscape with OmniPath.

Bioinformatics 2020 04;36(8):2632-2633

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

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http://dx.doi.org/10.1093/bioinformatics/btz968DOI Listing
April 2020

Metabolic rewiring of the hypertensive kidney.

Sci Signal 2019 12 10;12(611). Epub 2019 Dec 10.

Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA 92122, USA.

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http://dx.doi.org/10.1126/scisignal.aax9760DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7273358PMC
December 2019

The authors reply.

Kidney Int 2019 12;96(6):1422-1423

RWTH Aachen University, 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.2019.09.011DOI Listing
December 2019

From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL.

NPJ Syst Biol Appl 2019 11;5:40. Epub 2019 Nov 11.

Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany.

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http://dx.doi.org/10.1038/s41540-019-0118-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6848167PMC
April 2020

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

Cell Rep 2019 10;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
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6899515PMC
October 2019

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

Nucleic Acids Res 2019 11;47(19):10010-10026

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
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821211PMC
November 2019

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

Biochim Biophys Acta Gene Regul Mech 2020 06 13;1863(6):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
June 2020

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

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

Big science and big data in nephrology.

Kidney Int 2019 06 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

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

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

How to find the right drug for each patient? Advances and challenges in pharmacogenomics.

Curr Opin Syst Biol 2018 Aug;10:53-62

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

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http://dx.doi.org/10.1016/j.coisb.2018.07.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6855262PMC
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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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