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Author Details

Mar??a Rodr??guez Mart??nez
Herbert Irving Cancer Research Center, Columbia University Medical Center
2002
36
16
PMIDPaper TitleJournal TitlePublished Year
36927990Understanding repertoire sequencing data through a multiscale computational model of the germinal center.NPJ Syst Biol Appl2023
37640448Convergent evolution and B-cell recirculation in germinal centers in a human lymph node.Life Sci Alliance2023
37143924MonoNet: enhancing interpretability in neural networks via monotonic features.Bioinform Adv2023
37138881Exploring the impact of clonal definition on B-cell diversity: implications for the analysis of immune repertoires.Front Immunol2023
37031956FLAN: feature-wise latent additive neural models for biological applications.Brief Bioinform2023
35758821DECODE: a computational pipeline to discover T cell receptor binding rules.Bioinformatics2022
35724564PCfun: a hybrid computational framework for systematic characterization of protein complex function.Brief Bioinform2022
33241320COSIFER: a Python package for the consensus inference of molecular interaction networks.Bioinformatics2021
33851095PaccMann<sup>RL</sup>: De novo generation of hit-like anticancer molecules from transcriptomic data via reinforcement learning.iScience2021
33613551Multiscale Modeling of Germinal Center Recapitulates the Temporal Transition From Memory B Cells to Plasma Cells Differentiation as Regulated by Antigen Affinity-Based Tfh Cell Help.Front Immunol2021
34432947Diagnostics and correction of batch effects in large-scale proteomic studies: a tutorial.Mol Syst Biol2021
34252933On the feasibility of deep learning applications using raw mass spectrometry data.Bioinformatics2021
34179955SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems.Bioinformatics2021
32532145Computational Model Reveals a Stochastic Mechanism behind Germinal Center Clonal Bursts.Cells2020
31988302Stabilized Reconstruction of Signaling Networks from Single-Cell Cue-Response Data.Sci Rep2020
31945090Pan-cancer analysis of somatic mutations and epigenetic alterations in insulated neighbourhood boundaries.PLoS One2020
33317623Convergent network effects along the axis of gene expression during prostate cancer progression.Genome Biol2020
32850701Identifying the Potential Mechanism of Action of SNPs Associated With Breast Cancer Susceptibility With GVITamIN.Front Bioeng Biotechnol2020
32402082PaccMann: a web service for interpretable anticancer compound sensitivity prediction.Nucleic Acids Res2020
31001283A Probabilistic Model of the Germinal Center Reaction.Front Immunol2019
31685861Network-based Biased Tree Ensembles (NetBiTE) for Drug Sensitivity Prediction and Drug Sensitivity Biomarker Identification in Cancer.Sci Rep2019
31618586Toward Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-Based Convolutional Encoders.Mol Pharm2019
30982598A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer.Cell2019
30854223PIMKL: Pathway-Induced Multiple Kernel Learning.NPJ Syst Biol Appl2019
29684207The number of titrated microRNA species dictates ceRNA regulation.Nucleic Acids Res2018
29434325CellCycleTRACER accounts for cell cycle and volume in mass cytometry data.Nat Commun2018
28558729High-throughput validation of ceRNA regulatory networks.BMC Genomics2017
27185371Depletion of FOXM1 via MET Targeting Underlies Establishment of a DNA Damage-Induced Senescence Program in Gastric Cancer.Clin Cancer Res2016
26186195Elucidating Compound Mechanism of Action by Network Perturbation Analysis.Cell2015
24667158Therapeutic aphaeresis: experience in Puerto Rico.Transfus Apher Sci2014
22308355Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis.Proc Natl Acad Sci U S A2012
20365787Messenger RNA fluctuations and regulatory RNAs shape the dynamics of a negative feedback loop.Phys Rev E Stat Nonlin Soft Matter Phys2010
18772389Development of input connections in neural cultures.Proc Natl Acad Sci U S A2008
18854817Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation.Mol Syst Biol2008
18077424Input output robustness in simple bacterial signaling systems.Proc Natl Acad Sci U S A2007
12398655Cosmology of a brane radiating gravitons into the extra dimension.Phys Rev Lett2002
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Collaborators

Andrea Califano
Columbia University
Co-authored papers 5
Ruedi Aebersold
Institute of Molecular Systems Biology, ETH Zurich
Co-authored papers 4
Bernd Bodenmiller
University of Zurich
Co-authored papers 3
Mukesh Bansal
Co-authored papers 3
Gustavo Stolovitzky
IBM T.J. Watson Research Center
Co-authored papers 2
Tiannan Guo
Westlake University
Co-authored papers 2
Julio Saez-Rodriguez
Institute of Computational Biomedicine, Heidelberg University
Co-authored papers 2
Paola Nicoletti
Icahn School of Medicine at Mount Sinai
Co-authored papers 2
Patrick G A Pedrioli
Institute of Translational Medicine, Swiss Federal Institute of Technology/ETH Zurich
Co-authored papers 2
Laurence Calzone
Institut Curie, Universite PSL
Co-authored papers 2
Evan G Williams
University of Luxembourg
Co-authored papers 2
Pavel Sumazin
Baylor College of Medicine
Co-authored papers 2
Jiangning Song
Monash Data Futures Institute, Monash University
Co-authored papers 1
Rodolfo Ciuffa
Institute of Molecular Systems Biology, ETH Zurich
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Loredana Martignetti
Institut Curie, PSL Research University
Co-authored papers 1
Mehmet Eren Ahsen
Gies College of Business, University of Illinois at Urbana-Champaign.
Co-authored papers 1
Sandra Goetze
ETH Zurich
Co-authored papers 1
Bernd Wollscheid
ETH Zurich
Co-authored papers 1
Aravind Subramanian
Co-authored papers 1
Wenguang Shao
Institute of Molecular Systems Biology, ETH Zurich
Co-authored papers 1
Anthony W Purcell
Monash Biomedicine Discovery Institute, Monash University
Co-authored papers 1
Mariano J Alvarez
Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center
Co-authored papers 1
René R P de Vries
Co-authored papers 1
Andrea Jacobs
University of Zurich
Co-authored papers 1
Todd R Golub
Broad Institute of MIT and Harvard
Co-authored papers 1
Varun S Sharma
Institute of Molecular Systems Biology, ETH Zurich
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Claudine Chaouiya
Aix Marseille University CNRS
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Ben C Collins
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Release 1.2