María Rodríguez Martínez

Joint Center for Systems Biology, Columbia University, New York, NY 10032;

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Papers26 papers

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Stabilized Reconstruction of Signaling Networks from Single-Cell Cue-Response Data

Sunil Kumar, Xiao-Kang Lun,Bernd Bodenmiller,María Rodríguez Martínez,Heinz Koeppl

Scientific reports, no. 1 (2020): 1233-9

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COSIFER: a Python package for the consensus inference of molecular interaction networks

Matteo Manica, Charlotte Bunne, Roland Mathis, Joris Cadow,Mehmet Eren Ahsen,Gustavo A Stolovitzky,María Rodríguez Martínez

Bioinformatics (Oxford, England), (2020)

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Pre-training Protein Language Models with Label-Agnostic Binding Pairs Enhances Performance in Downstream Tasks

Modestas Filipavicius,Matteo Manica, Joris Cadow,Maria Rodriguez Martinez

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PaccMann$^{RL}$ on SARS-CoV-2: Designing antiviral candidates with conditional generative models

Jannis Born,Matteo Manica, Joris Cadow, Greta Markert, Nil Adell Mill, Modestas Filipavicius,María Rodríguez Martínez

arXiv, (2020)

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Computational Model Reveals a Stochastic Mechanism behind Germinal Center Clonal Bursts

Aurélien Pélissier, Youcef Akrout, Katharina Jahn,Jack Kuipers, Ulf Klein,Niko Beerenwinkel,María Rodríguez Martínez

CELLS, no. 6 (2020): 1448

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Targeted design of antiviral compounds against SARS-CoV-2 with conditional generative models

Born Jannis, Manica Matteo, Cadow Joris, Markert Greta, Mill Nil Adell, Filipavicius Modestas,Martínez María Rodríguez

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PaccMann: a web service for interpretable anticancer compound sensitivity prediction

Joris Cadow, Jannis Born,Matteo Manica, Ali Oskooei,María Rodríguez Martínez

NUCLEIC ACIDS RESEARCH, no. W1 (2020): W502-W508

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Pan-cancer analysis of somatic mutations and epigenetic alterations in insulated neighbourhood boundaries

Pietro Pinoli, Eirini Stamoulakatou, An-Phi Nguyen,María Rodríguez Martínez,Stefano Ceri

PloS one, no. 1 (2020)

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PaccMannRL - Designing Anticancer Drugs From Transcriptomic Data via Reinforcement Learning

Jannis Born,Matteo Manica, Ali Oskooei, Joris Cadow,María Rodríguez Martínez

RECOMB, pp.231-233, (2020)

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Towards Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-based Convolutional Encoders

Matteo Manica, Ali Oskooei, Jannis Born, Vigneshwari Subramanian,Julio Sáez-Rodríguez,María Rodríguez Martínez

MOLECULAR PHARMACEUTICS, no. 12 (2019): 4797-4806

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PIMKL: Pathway-Induced Multiple Kernel Learning

Matteo Manica, Joris Cadow, Roland Mathis,María Rodríguez Martínez

NPJ SYSTEMS BIOLOGY AND APPLICATIONS, (2019): 8

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A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer

Johanna Wagner,Maria Anna Rapsomaniki, Stéphane Chevrier,Tobias Anzeneder,Claus Langwieder,August Dykgers,Martin Rees, Annette Ramaswamy,Simone Muenst,Savas Deniz Soysal,Andrea Jacobs, Jonas Windhager

Cell, no. 5 (2019): 1330-1345.e18

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A Probabilistic Model of the Germinal Center Reaction

Marcel Jan Thomas,Ulf Klein,John Lygeros,María Rodríguez Martínez

FRONTIERS IN IMMUNOLOGY, (2019): 689

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Network-based Biased Tree Ensembles (NetBiTE) for Drug Sensitivity Prediction and Drug Sensitivity Biomarker Identification in Cancer

Ali Oskooei,Matteo Manica, Roland Mathis,María Rodríguez Martínez

Scientific reports, no. 1 (2019): 15918-13

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A stochastic hybrid model for DNA replication incorporating protein mobility dynamics

Jonas Windhager, Amelia Paine, Patroula Nathanailidou, Eve Tasiudi,María Rodríguez Martínez,Zoi Lygerou,John Lygeros,Maria Anna Rapsomaniki

bioRxiv, pp.583187-29, (2019)

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Context-specific interaction networks from vector representation of words

Matteo Manica, Matteo Manica, Roland Mathis, Joris Cadow,María Rodríguez Martínez

Nature Machine Intelligence, no. 4 (2019): 181-190

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edGNN: a Simple and Powerful GNN for Directed Labeled Graphs

Guillaume Jaume, An-phi Nguyen,María Rodríguez Martínez,Jean-Philippe Thiran,Maria Gabrani

arXiv: Learning, (2019)

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CellCycleTRACER accounts for cell cycle and volume in mass cytometry data

Maria Anna Rapsomaniki, Xiao-Kang Lun,Stefan Woerner,Marco Laumanns,Bernd Bodenmiller,María Rodríguez Martínez

Nature communications, no. 1 (2018): 632

Cited by2WOSBibtex

PIMKL: Pathway Induced Multiple Kernel Learning

Matteo Manica, Joris Cadow, Roland Mathis,María Rodríguez Martínez

arXiv: Molecular Networks, (2018)

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INtERAcT: Interaction Network Inference from Vector Representations of Words

Matteo Manica, Roland Mathis,María Rodríguez Martínez

arXiv: Molecular Networks, (2018)

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María Rodríguez MartínezBinding

Papers26 papers

María Rodríguez Martínez