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Author Details

Julio Saez-Rodriguez
Institute of Computational Biomedicine, Heidelberg University
2004
245
62
Kirsten Obernier (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36688815Pan-Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival.Mol Syst Biol2023
37488529A network medicine approach to study comorbidities in heart failure with preserved ejection fraction.BMC Med2023
37486964Hepatocytes reprogram liver macrophages involving control of TGF-β activation, influencing liver regeneration and injury.Hepatol Commun2023
37842805Enablers and challenges of spatial omics, a melting pot of technologies.Mol Syst Biol2023
37991480Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease.Elife2023
37873403Microbiome-based risk prediction in incident heart failure: a community challenge.medRxiv2023
37318792Single-cell biology: what does the future hold?Mol Syst Biol2023
37343696Proteomic Dynamics of Breast Cancer Cell Lines Identifies Potential Therapeutic Protein Targets.Mol Cell Proteomics2023
36973489A T follicular helper cell origin for T regulatory type 1 cells.Cell Mol Immunol2023
37337100Democratizing knowledge representation with BioCypher.Nat Biotechnol2023
37365273Gene regulatory network inference in the era of single-cell multi-omics.Nat Rev Genet2023
37162916Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples.bioRxiv2023
36781298Phosphoproteomic analysis of metformin signaling in colorectal cancer cells elucidates mechanism of action and potential therapeutic opportunities.Clin Transl Med2023
33332571Experimental and computational technologies to dissect the kidney at the single-cell level.Nephrol Dial Transplant2022
35680885Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data.Nat Commun2022
35803930Imbalanced gut microbiota fuels hepatocellular carcinoma development by shaping the hepatic inflammatory microenvironment.Nat Commun2022
35550039Reducing lipid bilayer stress by monounsaturated fatty acids protects renal proximal tubules in diabetes.Elife2022
35404937Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity.PLoS Comput Biol2022
35347318Molecular consequences of SARS-CoV-2 liver tropism.Nat Metab2022
35501398Mapping the epithelial-immune cell interactome upon infection in the gut and the upper airways.NPJ Syst Biol Appl2022
35760868Cancer-associated fibroblasts require proline synthesis by PYCR1 for the deposition of pro-tumorigenic extracellular matrix.Nat Metab2022
35422018Explainable multiview framework for dissecting spatial relationships from highly multiplexed data.Genome Biol2022
36591270Dissecting CD8+ T cell pathology of severe SARS-CoV-2 infection by single-cell immunoprofiling.Front Immunol2022
36539415Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression.Nat Commun2022
36605986Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis.Front Mol Biosci2022
36462502B cell expansion hinders the stroma-epithelium regenerative cross talk during mucosal healing.Immunity2022
36699385decoupleR: ensemble of computational methods to infer biological activities from omics data.Bioinform Adv2022
36112223Cross-regional homeostatic and reactive glial signatures in multiple sclerosis.Acta Neuropathol2022
36303074Adult human kidney organoids originate from CD24<sup>+</sup> cells and represent an advanced model for adult polycystic kidney disease.Nat Genet2022
35927357Author Correction: Cancer-associated fibroblasts require proline synthesis by PYCR1 for the deposition of pro-tumorigenic extracellular matrix.Nat Metab2022
36261631A microfluidic Braille valve platform for on-demand production, combinatorial screening and sorting of chemically distinct droplets.Nat Protoc2022
35948637Spatial multi-omic map of human myocardial infarction.Nature2022
35947955Phosphoproteomics of primary AML patient samples reveals rationale for AKT combination therapy and p53 context to overcome selinexor resistance.Cell Rep2022
35880747Integrating knowledge and omics to decipher mechanisms via large-scale models of signaling networks.Mol Syst Biol2022
35915108Combi-seq for multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets.Nat Commun2022
33913468Deficiency of myeloid PHD proteins aggravates atherogenesis via macrophage apoptosis and paracrine fibrotic signalling.Cardiovasc Res2022
34978927Stabilization but No Functional Influence of HIF-1α Expression in the Intestinal Epithelium during Salmonella Typhimurium Infection.Infect Immun2022
35149721The spatial transcriptomic landscape of the healing mouse intestine following damage.Nat Commun2022
35106508A community challenge for a pancancer drug mechanism of action inference from perturbational profile data.Cell Rep Med2022
35134857FUNKI: interactive functional footprint-based analysis of omics data.Bioinformatics2022
35164900Patient-specific Boolean models of signalling networks guide personalised treatments.Elife2022
34558834Transcriptomic Cross-Species Analysis of Chronic Liver Disease Reveals Consistent Regulation Between Humans and Mice.Hepatol Commun2022
34775100MAGED2 controls vasopressin-induced aquaporin-2 expression in collecting duct cells.J Proteomics2022
32313939Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.Brief Bioinform2021
33795376Corrigendum: Benchmark and integration of resources for the estimation of human transcription factor activities.Genome Res2021
33682416PHONEMeS: Efficient Modeling of Signaling Networks Derived from Large-Scale Mass Spectrometry Data.J Proteome Res2021
33484195Norepinephrine promotes triglyceride storage in macrophages via beta2-adrenergic receptor activation.FASEB J2021
33787284Consensus Transcriptional Landscape of Human End-Stage Heart Failure.J Am Heart Assoc2021
33692771Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions.Front Microbiol2021
33932331Deciphering the signaling network of breast cancer improves drug sensitivity prediction.Cell Syst2021
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Collaborators

Aurelien Dugourd
Institute of Experimental Medicine and Systems Biology, RWTH Aachen University
Co-authored papers 24
Mathew J Garnett
Wellcome Sanger Institute
Co-authored papers 20
Gustavo Stolovitzky
IBM T.J. Watson Research Center
Co-authored papers 15
Douglas A Lauffenburger
Massachusetts Institute of Technology
Co-authored papers 14
D??nes T??rei
Heidelberg University
Co-authored papers 14
Peter K Sorger
Co-authored papers 11
Ultan McDermott
Wellcome Sanger Institute
Co-authored papers 10
Ruedi Aebersold
Institute of Molecular Systems Biology, ETH Zurich
Co-authored papers 7
Alberto Valdeolivas
Roche Pharma Research and Early Development
Co-authored papers 7
Claudine Chaouiya
Aix Marseille University CNRS
Co-authored papers 7
Laurence Calzone
Institut Curie, Universite PSL
Co-authored papers 7
Markus M Rinschen
Co-authored papers 6
Pedro Beltrao
Institute of Molecular Systems Biology, ETH Zurich
Co-authored papers 6
Justin Guinney
University of Washington
Co-authored papers 6
Denis Thieffry
Institut de Biologie de l'Ecole Normale Superieure, Inserm, CNRS, Universite PSL
Co-authored papers 5
Aur??lien Naldi
Institut de Biologie de l'Ecole Normale Superieure, Inserm, CNRS, Universite PSL
Co-authored papers 5
Thea Norman
Bill & Melinda Gates Foundation
Co-authored papers 5
Cyril H Benes
Co-authored papers 5
Oliver Stegle
Wellcome Sanger Institute
Co-authored papers 4
Kosuke Yusa
Wellcome Sanger Institute
Co-authored papers 4
Jonathan R Dry
Present Address: Tempus Labs Inc.
Co-authored papers 4
Michael R Stratton
Wellcome Sanger Institute
Co-authored papers 4
Fabian J Theis
Technical University of Munich
Co-authored papers 4
Henning Hermjakob
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 4
Thomas Yu
Co-authored papers 4
Michael R Kellen
University of Washington
Co-authored papers 4
Augustin Luna
Harvard Medical School
Co-authored papers 4
Chris Sander
Broad Institute of MIT and Harvard
Co-authored papers 4
Stephen H Friend
University of Oxford
Co-authored papers 4
Euan A Stronach
Imperial College London
Co-authored papers 4
Release 1.2