Matteo Manica  Matteo Manica photo         

contact information

Research Staff Member in Cognitive Health Care and Life Sciences
Zurich Research Laboratory, Zurich, Switzerland
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Professional Associations

Professional Associations:  International Society for Computational Biology


2020

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, Maria Rodriguez Martinez
Bioinformatics, 2020
btaa942

On the Role of Artificial Intelligence in Medical Imaging of COVID-19
Jannis Born, David Beymer, Deepta Rajan, Adam Coy, Vandana V Mukherjee, Matteo Manica, Prasanth Prasanna, Deddeh Ballah, Pallav L Shah, Emmanouil Karteris, Jan Lukas Robertus, Maria Gabrani, Michal Rosen-Zvi
medRxiv, Cold Spring Harbor Laboratory Press, 2020

CogMol: Target-Specific and Selective Drug Design for COVID-19 Using Deep Generative Models
Vijil Chenthamarakshan, Payel Das, Inkit Padhi, Hendrik Strobelt, Kar Wai Lim, Ben Hoover, Samuel C Hoffman, Matteo Manica, Jannis Born, Teodoro Laino, others
NeurIPS, 2020

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, Maria Rodriguez Martinez
WCB ICML, 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

Guider l'attention dans les modeles de sequence a sequence pour la prediction des actes de dialogue
Pierre Colombo, Emile Chapuis, Matteo Manica, Emmanuel Vignon, Giovanna Varni, Chloe Clavel
arXiv preprint arXiv:2002.09419, 2020

Proteogenomic heterogeneity of localized human prostate cancer progression
Konstantina Charmpi, Tiannan Guo, Qing Zhong, Ulrich Wagner, Rui Sun, Nora C Toussaint, Christine Fritz, Chunhui Yuan, Hao Chen, Niels J Rupp, Ailsa Christiansen, Dorothea Rutishauser, Jan H Ruschoff, Christian Fankhauser, Karim Saba, Cedric Poyet, Thomas Hermanns, Kathrin Oehl, Ariane Leoni Moore, Christian Beisel, Laurence Calzone, Loredana Martignetti, Qiushi Zhang, Yi Judy Zhu, Maria Rodriguez Martinez, Matteo Manica, Michael C Haffner, Ruedi Aebersold, Peter J Wild, Andreas Beyer
bioRxiv, Cold Spring Harbor Laboratory, 2020

Inferring clonal composition from multiple tumor biopsies
Matteo Manica, Hyunjae Ryan Kim, Roland Mathis, Philippe Chouvarine, Dorothea Rutishauser, Laura De Vargas Roditi, Bence Szalai, Ulrich Wagner, Kathrin Oehl, Karim Saba, others
npj Systems Biology and Applications 6(1), 1--13, Nature Publishing Group, 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

Convergent network effects along the axis of gene expression during prostate cancer progression
Konstantina Charmpi, Tiannan Guo, Qing Zhong, Ulrich Wagner, Rui Sun, Nora C Toussaint, Christine Fritz, Chunhui Yuan, Hao Chen, Niels J Rupp, Ailsa Christiansen, Dorothea Rutishauser, Jan H Ruschoff, Christian Fankhauser, Karim Saba, Cedric Poyet, Thomas Hermanns, Kathrin Oehl, Ariane Leoni Moore, Christian Beisel, Laurence Calzone, Loredana Martignetti, Qiushi Zhang, Yi Judy Zhu, Maria Rodriguez Martinez, Matteo Manica, Michael C Haffner, Ruedi Aebersold, Peter J Wild, Andreas Beyer
bioRxiv, 2020

Guiding attention in Sequence-to-sequence models for Dialogue Act prediction
Pierre Colombo, Emile Chapuis, Matteo Manica, Emmanuel Vignon, Giovanna Varni, Chloe Clavel
AAAI, 2020


2019

AI Enables Explainable Drug Sensitivity Screenings
Matteo Manica, Ali Oskooei, Jannis Born
Digital Health, 23, 2019


Toward 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
PMID: 31618586

Accelerated analysis of Boolean gene regulatory networks via reconfigurable hardware
M. Manica, R. Polig, M. Purandare, R. Mathis, C. Hagleitner, M. Rodriguez-Martinez
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1-1, 2019

An Information Extraction and Knowledge Graph Platform for Accelerating Biochemical Discoveries
Matteo Manica, Christoph Auer, Valery Weber, Federico Zipoli, Michele Dolfi, Peter Staar, Teodoro Laino, Costas Bekas, Akihiro Fujita, Hiroki Toda, Shuichi Hirose, Yasumitsu Orii
Workshop on Applied Data Science for Healthcare at KDD, 2019

PIMKL: Pathway-Induced Multiple Kernel Learning
Matteo Manica, Joris Cadow, Roland Mathis, Maria Rodriguez-Martinez
npj Systems Biology and Applications 5(1), 8, Nature Publishing Group, 2019

NeuNetS: An Automated Synthesis Engine for Neural Network Design
Atin Sood, Benjamin Elder, Benjamin Herta, Chao Xue, Costas Bekas, A. Cristiano I. Malossi, Debashish Saha, Florian Scheidegger, Ganesh Venkataraman, Gegi Thomas, Giovanni Mariani, Hendrik Strobelt, Horst Samulowitz, Martin Wistuba, Matteo Manica, Mihir Choudhury, Rong Yan, Roxana Istrate, Ruchir Puri, Tejaswini Pedapati
arXiv preprint arXiv:1901.06261, 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, Nature Publishing Group, 2019


2018


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
Workshop on Machine Learning for Molecule and Materials NeurIPS, 2018

Mixed-precision in-memory computing
Manuel Le Gallo, Abu Sebastian, Roland Mathis, Matteo Manica, Tomas Tuma, Costas Bekas, Alessandro Curioni, Evangelos Eleftheriou
Nature Electronics, 2018


2013