María Rodríguez Martínez  María Rodríguez Martínez photo         

contact information

Technical Leader of Computational Systems Biology
Zurich Research Laboratory, Zurich, Switzerland
  

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Professional Associations

Professional Associations:  ELIXIR Industry Advisory Committee  |  European Lab for Learning and Intelligent Systems (ELLIS)  |  International Society for Computation Biology  |  Society for Mathematical Biology


2020

PaccMann: a web service for interpretable anticancer compound sensitivity prediction
Joris Cadow, Jannis Born, Matteo Manica, Ali Oskooei, Maria Rodriguez Martinez
Nucleic Acids Research, 2020

PaccMannRL: Designing Anticancer Drugs From Transcriptomic Data via Reinforcement Learning
Jannis Born, Matteo Manica, Ali Oskooei, Joris Cadow, Maria Rodriguez Martinez
Research in Computational Molecular Biology, pp. 231--233, Springer International Publishing, 2020

Precision global health: a roadmap for augmented action
Danny J. Sheath, Rafael Ruiz de Castaneda, Nefti-Eboni Bempong, Mario Raviglione, Catherine Machalaba, Michael S. Pepper, Effy Vayena, Nicolas Ray, Didier Wernli, Gerard Escher, Francois Grey, Bernice S. Elger, Dirk Helbing, Kaj-Kolja Kleineberg, David Beran, J. Jaime Miranda, Mark D. Huffman, Fred Hersch, Fred Andayi, Samuel M. Thumbi, Valerie D'Acremont, Mary-Anne Hartley, Jakob Zinsstag, James Larus, Maria Rodriguez Martinez, Philippe J. Guerin, Laura Merson, Vinh-Kim Ngyuen, et al.
Journal of Public Health and Emergency 0(0), 2020

DeStress: Deep Learning for Unsupervised Identification of Mental Stress in Firefighters from Heart-rate Variability (HRV) Data
Ali Oskooei, Sophie Mai Chau, Jonas Weiss, Arvind Sridhar, Maria Rodriguez Martinez, Bruno Michel
W3PHIAI-20 workshop @ the 34th AAAI Conference on Artificial Intelligence (AAAI-20) 2020

Stabilized Reconstruction of Signaling Networks from Single-Cell Cue-Response Data
Sunil Kumar, Xiao-Kang Lun, Bernd Bodenmiller, Maria Rodriguez Martinez, Heinz Koeppl
Scientific Reports 10(1), 1--9, 2020
Abstract

Pan-cancer analysis of somatic mutations and epigenetic alterations in insulated neighbourhood boundaries
Pietro Pinoli, Eirini Stamoulakatou, An-Phi Nguyen, Maria Rodriguez Martinez, Stefano Ceri
PLOS ONE 15(1), 1--20, 2020
Abstract


2019

Accelerated analysis of Boolean gene regulatory networks via reconfigurable hardware
Matteo Manica, Raphael Polig, Mitra Purandare, Roland Mathis, Christoph Hagleitner, Maria Rodriguez Martinez
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1-1, 2019

A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer
Johanna Wagner, Maria Anna Rapsomaniki, Stephane Chevrier, Tobias Anzeneder, Claus Langwieder, August Dykgers, Martin Rees, Annette Ramaswamy, Simone Muenst, Savas Deniz Soysal, Andrea Jacobs, Jonas Windhager, Karina Silina, Maries van den Broek, Konstantin Johannes Dedes, Maria Rodriguez Martinez, Walter Paul Weber, Bernd Bodenmiller
Cell, 2019

edGNN: a Simple and Powerful GNN for Directed Labeled Graphs
Guillaume Jaume, An-phi Nguyen, Maria Rodriguez Martinez, Jean-Philippe Thiran, Maria Gabrani
RLGM workshop paper at ICLR 2019

Towards Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-based Convolutional Encoders
Matteo Manica, Ali Oskooei, Jannis Born, Vigneshwari Subramanian, Julio Saez-Rodriguez, Maria Rodriguez Martinez
Molecular Pharmaceutics, 2019

Context-specific interaction networks from vector representation of words
Matteo Manica, Roland Mathis, Joris Cadow, Maria Rodriguez Martinez
Nature Machine Intelligence 1(4), 181--190, 2019

A Probabilistic Model of the Germinal Center Reaction
Marcel Jan Thomas, Ulf Klein, John Lygeros, Maria Rodriguez Martinez
Frontiers in Immunology10, 689, 2019

A stochastic hybrid model for DNA replication incorporating protein mobility dynamics View ORCID Profile
Jonas Windhager, Amelia Paine, Patroula Nathanailidou, Eve Tasiudi, Maria Rodriguez Martinez, Zoi Lygerou, John Lygeros, Maria Anna Rapsomaniki
preprint @ biorxiv.org/content/10.1101/583187v1, 2019

MonoNet: Towards interpretable models by learning monotonic features.
An-phi Nguyen and Maria Rodriguez Martinez
Human-Centric Machine Learning workshop, NeurIPS 2019.

PaccManna^RL: Designing anticancer drugs from transcriptomic data via reinforcement learning
Jannis Born, Matteo Manica, Ali Oskooei, Maria Rodriguez Martinez
preprint arxiv.org/abs/1909.05114, 2019


PIMKL: Pathway Induced Multiple Kernel Learning
Matteo Manica, Joris Cadow, Roland Mathis, Maria Rodriguez Martinez
npj Systems Biology and Applications 5(8), 2019


2018

Inference of the three-dimensional chromatin structure and its temporal behavior
Bianca-Cristina Cristescu, Zalan Borsos, John Lygeros, Maria Rodriguez Martinez, Maria Anna Rapsomaniki
Machine Learning for Molecules and Materials NIPS 2018 Workshop

PaccMann: Prediction of anticancer compound sensitivity with multi-modal attention-based neural networks
Ali Oskooei, Jannis Born, Matteo Manica, Vigneshwari Subramanian, Julio Saez-Rodriguez, Maria Rodriguez Martinez
Machine Learning for Molecules and Materials NIPS 2018 Workshop

The number of titrated microRNA species dictates ceRNA regulation
Hua-Sheng Chiu, Maria Rodriguez Martinez, Elena V Komissarova, David Llobet-Navas, Mukesh Bansal, Evan O Paull, Jose Silva, Xuerui Yang, Pavel Sumazin, Andrea Califano
Nucleic Acids Research, 2018

INtERAcT: Interaction Network Inference from Vector Representations of Words
Matteo Manica, Roland Mathis, Maria Rodriguez Martinez
arXiv preprint arXiv:1801.03011 , 2018

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 Communications9, 2018


2017

Inferring clonal composition from multiple tumor biopsies
M. Manica, P. Chouvarine, R. Mathis, U. Wagner, K. Oehl, K. Saba, L. De Vargas Roditi, A. N Pati, M. Rodríguez-Martínez, P. J. Wild, P. Sumazin
arXiv preprint arXiv:1701.07940, 2017

High-throughput validation of ceRNA regulatory networks
Hua-Sheng Chiu, María Rodríguez-Martínez, Mukesh Bansal, Aravind Subramanian, Todd R Golub, Xuerui Yang, Pavel Sumazin, and Andrea Califano.
BMC genomics 18(1), 418, BioMed Central, 2017


2016

Depletion of FOXM1 via MET targeting underlies establishment of a DNA damage-induced senescence program in gastric cancer
Paola Francica, Lluis Nisa, Daniel M Aebersold, Rupert Langer, Friedhelm Bladt, Andree Blaukat, Deborah Stroka, María Rodríguez-Martínez, Yitzhak Zimmer and Michaela Medova
Clinical Cancer Research, clincanres-2987, AACR, 2016

Marginalized Continuous Time Bayesian Networks for Network Reconstruction from Incomplete Observations
Lukas Studer, Loic Pauleve, Christoph Zechner, Matthias Reumann, María Rodríguez-Martínez and Heinz Koeppl
AAAI Conference on Artificial Intelligence, 2016


2015

Elucidating compound mechanism of action by network perturbation analysis
Jung Hoon Woo, Yishai Shimoni, Wan Seok Yang, Prem Subramaniam, Archana Iyer, Paola Nicoletti, María Rodríguez-Martínez, Gonzalo López, Michela Mattioli, Ronald Realubit, Charles Karan, Brent R. Stockwell, Mukesh Bansal and And
Cell 162(2), 441-451, 2015


2014

Observational Consequences of a Landscape: Epilogue
Ben Freivogel, Matthew Kleban, María Rodríguez-Martínez, Leonard Susskind
Cosmology and Nongalactic Astrophysics, 2014


2013

Highly conserved ceRNA regulatory interactions cooperate with genomic variability to modulate drivers of tumorigenesis
Hua-Sheng Chiu, María Rodríguez-Martínez, David Llobet-Navas, Aravind Subramanian, Archana Iyer, Yishai Shimoni, Mukesh Bansal, Todd R. Golub, Jose Silva, Xuerui Yang, Pavel Sumazin, Andrea Califano.
Proceedings: AACR 104th Annual Meeting, 2013

GWAS next generation: identifying mechanisms of action in association studies
María Rodríguez-Martínez, Paola Nicoletti, Gonzalo López, Mukesh Bansal, Yishai Shimoni, Andrea Califano
Regulatory Genomics Special Interest Group (RegGen SIG) Program, 2013


2012

Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis
M. Rodríguez-Martínez, A. Corradin, U. Klein, M.J. Alvarez, G.M. Toffolo, B. di Camillo, A. Califano, G.A. Stolovitzky
Proceedings of the National Academy of Sciences 109(7), 2672-2677, 2012


2010

Quorum percolation in living neural networks
Or Cohen, Anna Keselman, Elisha Moses, María Rodríguez-Martínez, Jordi Soriano, Tsvi Tlusty
EPL (Europhysics Letters) 89(1), 18008, IOP Publishing, 2010

Messenger RNA fluctuations and regulatory RNAs shape the dynamics of a negative feedback loop
María Rodríguez Martínez, Jordi Soriano, Tsvi Tlusty, Yitzhak Pilpel, Itay Furman
Physical Review E 81(3), 031924, APS, 2010


2008

Development of input connections in neural cultures
Jordi Soriano, María Rodríguez-Martínez, Tsvi Tlusty, Elisha Moses
Proceedings of the National Academy of Sciences 105(37), 13758-13763, 2008

Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation
Ophir Shalem, Orna Dahan, Michal Levo, María Rodríguez-Martínez, Itay Furman, Eran Segal, Yitzhak Pilpel
Molecular Systems Biology 4(1), 223, 2008


2007

Input-output robustness in simple bacterial signaling systems
Guy Shinar, Ron Milo, María Rodríguez Martínez, Uri Alon
Proceedings of the National Academy of Sciences 104(50), 19931-19935, 2007


2006

Observational consequences of a landscape
Ben Freivogel, Matthew Kleban, María Rodríguez Martínez, Leonard Susskind
Journal of High Energy Physics0603, 039, 2006

Constraining Lorentz violations with gamma-ray bursts
María Rodríguez Martínez, Tsvi Piran
Journal of Cosmology and Astroparticle Physics604, 6, 2006

Gamma-ray bursts and new physics
Tsvi Piran, Dafne Guetta, María Rodríguez Martínez
Progress of Theoretical Physics Supplement163, 23-37, 2006

GRB 051221A and tests of Lorentz symmetry
María Rodríguez Martínez, Tsvi Piran, Yonatan Oren
Journal of Cosmology and Astroparticle Physics0605, 017, 2006


2003

Defining perturbations on submanifolds
Karim A Malik, María Rodríguez-Martínez, David Langlois
Physical Review D 68(12), 123517, APS, 2003


2002

Fluctuating brane in a dilatonic bulk
Philippe Brax, David Langlois, María Rodríguez-Martínez
Phys.Rev. D67, 104022, 2002

Brane Cosmology with a Bulk Scalar Field
María Rodríguez-Martínez
International Journal of Modern Physics A 17(20), 2774-2774, World Scientific, 2002

Cosmology of a brane radiating gravitons into the extra dimension
David Langlois, Lorenzo Sorbo, María Rodríguez-Martínez
Physical Review Letters 89(17), 171301, APS, 2002


2001

Brane cosmology with a bulk scalar field
David Langlois and María Rodríguez-Martínez
Phys. Rev. D64, 123507, 2001