individualizedPaediatricCure: Cloud-based virtual-patient models for precision paediatric oncology

Deliverables

An initial demonstrator of the platform infrastructure will be delivered, for further development and optimisation throughout the project.

Standards for data descriptions across datasets and data types and a first implementation of the iPC interface

Building of cancer type-specific multi-layered molecular and patient similarity networks

An assembly of key molecular interactions that define cancer types and subtypes as well as the positioning of patients and tumours according to their molecular similarity

Adaptation of MelanomaMine and LiMTox to the analysis of paediatric cancers and application to biomedical publications on paediatric cancers

Extraction of relationships between molecules and bioentities from the publicly available paediatric literature

Application of software enabling computational deconvolution of bulk RNA-sequencing data to immune cell profiles of patient samples

The generation of a celllevel map of the environment and composition of each tumour with a particular focus on immune cells

Identification of important regulatory elements using multi-level matrix factorization approaches

Masterregulator analysis to identify key genes and pathways whose dysregulation contribute to tumour genesis and proliferation

Synthetic data for testing and training patient, cancer, and drug models

Synthetic datasets will be assembled and distributed to modeling WPs for model construction training and testing

Collection of high-quality clinical and molecular paediatric cancer datasets, as well as other tumour types

Datasets identified will be listed and accessible and shared with WP38 for training and validating models

Collection of molecular-interaction data from high-throughput assays, perturbation and essentiality assays, molecular data and clinical annotations from ongoing and past clinical trials

A comprehensive collection and analyses of curated data and molecular assays sourced from large-scale experiments and databases.

Data-driven model for molecular targets and drug repositioning

Report on the developed software implemented in R and integrated into the iPCCP that can generate a list of small molecules and siRNAs with a potential therapeutic benefit based on omics data

Integration of INtERAcT, MelanomaMine and LiMTox and application to biomedical publications on paediatric cancers

Combination of 3 different NLP approaches for the analysis of unstructured data and application to specialised paediatric publications

Project quality plan

A handbook of the project management process, review process, quality checks, meeting organisation, which is communicated to all partners.

An interactive online atlas of interconnected network maps based on the NaviCell platform

A cloudbased platform integrated into the project data portal allowing to visualize the networks built by the consortium and visualize omics profiles from the data portal on top of them

Internal and external IT communication infrastructure and project website

This deliverable constitutes the launch of the internal iPC communication infrastructure including the establishment of mailing lists, a subversion repository server and the iPC website.

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Publications

BIODICA: a computational environment for Independent Component Analysis of omics data

Author(s): Captier, Nicolas; Merlevede, Jane; Molkenov, Askhat; Seisenova, Ainur; Zhubanchaliyev, Altynbek; Nazarov, Petr V.; Barillot, Emmanuel; Kairov, Ulykbek; Zinovyev, Andrei
Published in: Bioinformatics, Volume 38, Issue 10, 2022, Page(s) 2963–2964, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btac204

Emulating complex simulations by machine learning methods

Author(s): Paola Stolfi & Filippo Castiglione
Published in: BMC Bioinformatics, 22, Article number: 483 (2021), 2021, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-021-04354-7

STAG2 mutations alter CTCF-anchored loop extrusion, reduce cis-regulatory interactions and EWSR1-FLI1 activity in Ewing sarcoma

Author(s): Didier Surdez, Sakina Zaidi, Sandrine Grossetête, Karine Laud-Duval, Anna Sole Ferre, Lieke Mous, Thomas Vourc'h, Franck Tirode, Gaelle Pierron, Virginie Raynal, Sylvain Baulande, Erika Brunet, Véronique Hill, Olivier Delattre
Published in: Cancer Cell, 39/6, 2021, Page(s) 810-826.e9, ISSN 1535-6108
Publisher: Cell Press
DOI: 10.1016/j.ccell.2021.04.001

Hepatoblastomas with carcinoma features represent a biological spectrum of aggressive neoplasms in children and young adults

Author(s): Pavel Sumazin, Dolores H. López-Terrada
Published in: Journal of Hepatology, 2021, ISSN 0168-8278
Publisher: Elsevier BV
DOI: 10.1101/2021.07.15.445600

Estimage: a webserver hub for the computation of methylation age

Author(s): Pietro Di Lena, Claudia Sala, Christine Nardini
Published in: Nucleic Acids Research, 2021, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab426

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

Author(s): Matteo Manica, Charlotte Bunne, Roland Mathis, Joris Cadow, Mehmet Eren Ahsen, Gustavo A Stolovitzky, María Rodríguez Martínez
Published in: Bioinformatics, 2020, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa942

A single-cell analysis of breast cancer cell lines to study tumour heterogeneity and drug response

Author(s): Gambardella G, Viscido G, Tumaini B, Isacchi A, Bosotti R, di Bernardo D
Published in: Nature Communication, 13, Article number: 1714 (2022), 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-29358-6

Clinical Applications of Mass Spectrometry-Based Proteomics in Cancer: Where are we?

Author(s): Emma L. Boys, Jia Liu, Phillip J Robinson, Roger R. Reddel
Published in: Proteomics, 2022, ISSN 1615-9861
Publisher: John Wiley & Sons
DOI: 10.1002/pmic.202200238

Artificial Intelligence–Aided Precision Medicine for COVID-19: Strategic Areas of Research and Development

Author(s): Enrico Santus, Nicola Marino, Davide Cirillo, Emmanuele Chersoni, Arnau Montagud, Antonella Santuccione Chadha, Alfonso Valencia, Kevin Hughes, Charlotta Lindvall
Published in: Journal of Medical Internet Research, 23/3, 2021, Page(s) e22453, ISSN 1438-8871
Publisher: Journal of medical Internet Research
DOI: 10.2196/22453

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

Author(s): Sunil Kumar, Xiao-Kang Lun, Bernd Bodenmiller, María Rodríguez Martínez & Heinz Koeppl
Published in: Scientific Reports, 10, Article number: 1233 (2020), 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-019-56444-5

Targeting the Unwindosome by Mebendazole Is a Vulnerability of Chemoresistant Hepatoblastoma

Author(s): Qian Li; Salih Demir, Álvaro Del Río-Álvarez; Rebecca Maxwell; Alexandra Wagner; Juan Carrillo-Reixach; Carolina Armengol; Christian Vokuhl; Beate Häberle; Dietrich von Schweinitz; Irene Schmid; Stefano Cairo; Roland Kappler
Published in: Cancers, 2022, ISSN 2072-6694
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14174196

CHAF1A Blocks Neuronal Differentiation and Promotes Neuroblastoma Oncogenesis via Metabolic Reprogramming

Author(s): Ling Tao,Myrthala Moreno-Smith,Rodrigo Ibarra-García-Padilla,Giorgio Milazzo,Nathan A. Drolet,Blanca E. Hernandez,Young S. Oh,Ivanshi Patel,Jean J. Kim,Barry Zorman,Tajhal Patel,Abu Hena Mostafa Kamal,Yanling Zhao,John Hicks,Sanjeev A. Vasudevan,Nagireddy Putluri,Cristian Coarfa,Pavel Sumazin,Giovanni Perini,Ronald J. Parchem,Rosa A. Uribe,Eveline Barbieri
Published in: Advanced Science, 2021, Page(s) e2005047, ISSN 2198-3844
Publisher: Wiley
DOI: 10.1002/advs.202005047

Mutational spectrum of <i>ATRX</i> aberrations in neuroblastoma and associated patient and tumor characteristics

Author(s): Michael R. Gerven; Eva Bozsaky; Yvette A. H. Matser; Julian Vosseberg; Sabine Taschner‐Mandl; Jan Koster; Godelieve A. M. Tytgat; Jan J. Molenaar; Marlinde Boogaard
Published in: Cancer Science, 4, 2022, ISSN 1349-7006
Publisher: John Wiley & Sons
DOI: 10.1111/cas.15363

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems

Author(s): Andreas Dräger, Tomáš Helikar, Matteo Barberis, Marc Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, Juilee Thakar
Published in: Bioinformatics, Volume 37, Issue 21, 1 November 2021, 2021, Page(s) 3702–3706, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab229

GM-CSF: Master regulator of the T cell-phagocyte interface during inflammation

Author(s): Florian Ingelfinger; Donatella De Feo; Burkhard Becher
Published in: Seminars in Immunology, Volume 56, August 2021, 2021, ISSN 1044-5323
Publisher: Academic Press
DOI: 10.1016/j.smim.2021.101518

On the feasibility of deep learning applications using raw mass spectrometry data

Author(s): Joris Cadow, Matteo Manica, Roland Mathis, Tiannan Guo, Ruedi Aebersold, María Rodríguez Martínez
Published in: Bioinformatics, Volume 37, Issue Supplement_1, July 2021, 2021, Page(s) i245–i253, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab311

Pan-cancer proteomic map of 949 human cell lines

Author(s): Emanuel Gonçalves, Rebecca C Poulos, Zhaoxiang Cai, Syd Barthorpe, Srikanth S Manda, Natasha Lucas, Alexandra Beck, Daniel Bucio-Noble, Michael Dausmann, Caitlin Hall, Michael Hecker, Jennifer Koh, Sadia Mahboob, Iman Mali, James Morris, Laura Richardson1, Akila J Seneviratne4, Erin Sykes4, Frances Thomas, Sara Valentini, Steven G Williams, Yangxiu Wu, Dylan Xavier, Karen L MacKenzie, Peter G Hai
Published in: Cancer Cell, 2022, ISSN 1535-6108
Publisher: Cell Press
DOI: 10.1016/j.ccell.2022.06.010

MDM4 inhibition: a novel therapeutic strategy to reactivate p53 in hepatoblastoma

Author(s): Sarah E. Woodfield, Yan Shi, Roma H. Patel, Zhenghu Chen, Aayushi P. Shah, Rohit K. Srivastava, Richard S. Whitlock, Aryana M. Ibarra, Samuel R. Larson, Stephen F. Sarabia, Andrew Badachhape, Zbigniew Starosolski, Ketan B. Ghaghada, Pavel Sumazin, D. Allen Annis, Dolores López-Terrada & Sanjeev A. Vasudevan
Published in: scientific reports, 11, Article number: 2967 (2021), 2021, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-82542-4

FUNKI: Interactive functional footprint-based analysis of omics data

Author(s): Rosa Hernansaiz-Ballesteros; Christian H. Holland; Aurelien Dugourd; Julio Saez-Rodriguez
Published in: Bioinformatics, 2021, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.5281/zenodo.5779097

Restoration of the molecular clock is tumor suppressive in neuroblastoma

Author(s): Myrthala Moreno-Smith, Giorgio Milazzo, Ling Tao, Baharan Fekry, Bokai Zhu, Mahmoud A. Mohammad, Simone Di Giacomo, Roshan Borkar, Karthik Reddy Kami Reddy, Mario Capasso, Sanjeev A. Vasudevan, Pavel Sumazin, John Hicks, Nagireddy Putluri, Giovanni Perini, Kristin Eckel-Mahan, Thomas P. Burris & Eveline Barbieri
Published in: nature communications, 12, Article number: 4006 (2021), 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-24196-4

The RNA Atlas expands the catalog of human non-coding RNAs

Author(s): Lucia Lorenzi; Hua-Sheng Chiu; Francisco Avila Cobos; Stephen Gross; Pieter-Jan Volders; Robrecht Cannoodt; Justine Nuytens; Katrien Vanderheyden; Jasper Anckaert; Steve Lefever; Aidan P. Tay; Eric J. de Bony; Wim Trypsteen; Fien Gysens; Marieke Vromman; Tine Goovaerts; Thomas Birkballe Hansen; Scott Kuersten; Nele Nijs; Tom Taghon; Karim Vermaelen; Ken R. Bracke; Yvan Saeys; T
Published in: Nature Biotechnology, 2021, Page(s) 1453-1465, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.5281/zenodo.5909808

PIONEER: Pipeline for Generating High‐Quality Spectral Libraries for DIA‐MS Data

Author(s): Srikanth S. Manda, Zainab Noor, Peter G. Hains, Qing Zhong
Published in: Current Protocols, 1/3, 2021, ISSN 2691-1299
Publisher: Current Protocols in Bioinformatics
DOI: 10.1002/cpz1.69

Benchmarking of cell type deconvolution pipelines for transcriptomics data.

Author(s): Avila Cobos, Francisco; Alquicira-Hernandez, José; Powell, Joseph E.; Mestdagh, Pieter; De Preter, Katleen
Published in: Nature Communications, 1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-19015-1

Tumor to normal single-cell mRNA comparisons reveal a pan-neuroblastoma cancer cell

Author(s): Gerda Kildisiute, Waleed M. Kholosy, Matthew D. Young, Kenny Roberts, Rasa Elmentaite, Sander R. van Hooff, Clarissa N. Pacyna, Eleonora Khabirova, Alice Piapi, Christine Thevanesan, Eva Bugallo-Blanco, Christina Burke, Lira Mamanova, Kaylee M. Keller, Karin P.S. Langenberg-Ververgaert, Philip Lijnzaad, Thanasis Margaritis, Frank C.P. Holstege, Michelle L. Tas, Marc H.W.A. Wijnen, Max M. van Noese
Published in: Science Advances, 7/6, 2021, Page(s) eabd3311, ISSN 2375-2548
Publisher: Science Advances
DOI: 10.1126/sciadv.abd3311

Bridging molecular basis, prognosis, and treatment of pediatric liver tumors

Author(s): Carolina Armengol, Stefano Cairo, Roland Kappler
Published in: Hepatoma Research, 2021, ISSN 2454-2520
Publisher: HEPATOMA RESEARCH
DOI: 10.20517/2394-5079.2021.19

DECONbench: a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification

Author(s): Clémentine Decamps, Alexis Arnaud, Florent Petitprez, Mira Ayadi, Aurélia Baurès, Lucile Armenoult, HADACA consortium, Sergio Escalera, Isabelle Guyon, Rémy Nicolle, Richard Tomasini, Aurélien de Reyniès, Jérôme Cros, Yuna Blum & Magali Richard
Published in: BMC Bioinformatics, 22, Article number: 473 (2021), 2021, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-021-04381-4

Artificial intelligence in cancer research: learning at different levels of data granularity

Author(s): Davide Cirillo, Iker Núñez‐Carpintero, Alfonso Valencia
Published in: Molecular Oncology, 15/4, 2021, Page(s) 817-829, ISSN 1574-7891
Publisher: Elsevier BV
DOI: 10.1002/1878-0261.12920

Inferring clonal composition from multiple tumor biopsies

Author(s): Matteo Manica, Hyunjae Ryan Kim, Roland Mathis, Philippe Chouvarine, Dorothea Rutishauser, Laura De Vargas Roditi, Bence Szalai, Ulrich Wagner, Kathrin Oehl, Karim Saba, Arati Pati, Julio Saez-Rodriguez, Angshumoy Roy, Donald W. Parsons, Peter J. Wild, María Rodríguez Martínez, Pavel Sumazin
Published in: npj Systems Biology and Applications, 6/1, 2020, ISSN 2056-7189
Publisher: npj Sytems Biology and Applications
DOI: 10.1038/s41540-020-00147-5

Epigenetic footprint enables molecular risk stratification of hepatoblastoma with clinical implications

Author(s): Juan Carrillo-Reixach, Laura Torrens, Marina Simon-Coma, Laura Royo, Montserrat Domingo-Sàbat, Jordi Abril-Fornaguera, Nicholas Akers, Margarita Sala, Sonia Ragull, Magdalena Arnal, Núria Villalmanzo, Stefano Cairo, Alberto Villanueva, Roland Kappler, Marta Garrido, Laura Guerra, Constantino Sábado, Gabriela Guillén, Mar Mallo, David Piñeyro, María Vázquez-Vitali, Olga Kuchuk, María Elena
Published in: Journal of Hepatology, 73/2, 2020, Page(s) 328-341, ISSN 0168-8278
Publisher: Elsevier BV
DOI: 10.1016/j.jhep.2020.03.025

PaccMann: a web service for interpretable anticancer compound sensitivity prediction

Author(s): Joris Cadow, Jannis Born, Matteo Manica, Ali Oskooei, María Rodríguez Martínez
Published in: Nucleic Acids Research, 48/W1, 2020, Page(s) W502-W508, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa327

Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases

Author(s): Jean-Marie Ravel, L. Cristobal Monraz Gomez, Nicolas Sompairac, Laurence Calzone, Boris Zhivotovsky, Guido Kroemer, Emmanuel Barillot, Andrei Zinovyev, Inna Kuperstein
Published in: Cancers, 12/4, 2020, Page(s) 990, ISSN 2072-6694
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers12040990

Assessing reproducibility of matrix factorization methods in independent transcriptomes

Author(s): Laura Cantini, Ulykbek Kairov, Aurélien de Reyniès, Emmanuel Barillot, François Radvanyi, Andrei Zinovyev
Published in: Bioinformatics, 35/21, 2019, Page(s) 4307-4313, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz225

Atovaquone is active against AML by upregulating the integrated stress pathway and suppressing oxidative phosphorylation

Author(s): Alexandra M. Stevens, Michael Xiang, Lisa N. Heppler, Isidora Tošić, Kevin Jiang, Jaime O. Munoz, Amos S. Gaikwad, Terzah M. Horton, Xin Long, Padmini Narayanan, Elizabeth L. Seashore, Maci C. Terrell, Raushan Rashid, Michael J. Krueger, Alicia E. Mangubat-Medina, Zachary T. Ball, Pavel Sumazin, Sarah R. Walker, Yoshimasa Hamada, Seiichi Oyadomari, Michele S. Redell, David A. Frank
Published in: Blood Advances, 3/24, 2019, Page(s) 4215-4227, ISSN 2473-9529
Publisher: The American Society of Hematology
DOI: 10.1182/bloodadvances.2019000499

Computer Modeling of Clonal Dominance: Memory-Anti-Naïve and Its Curbing by Attrition

Author(s): Filippo Castiglione, Dario Ghersi, Franco Celada
Published in: Frontiers in Immunology, 10, 2019, ISSN 1664-3224
Publisher: Frontiers in Immunology
DOI: 10.3389/fimmu.2019.01513

Toward Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-Based Convolutional Encoders

Author(s): Matteo Manica, Ali Oskooei, Jannis Born, Vigneshwari Subramanian, Julio Sáez-Rodríguez, María Rodríguez Martínez
Published in: Molecular Pharmaceutics, 16/12, 2019, Page(s) 4797-4806, ISSN 1543-8384
Publisher: American Chemical Society
DOI: 10.1021/acs.molpharmaceut.9b00520

Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets

Author(s): Nicolas Sompairac, Petr V. Nazarov, Urszula Czerwinska, Laura Cantini, Anne Biton, Askhat Molkenov, Zhaxybay Zhumadilov, Emmanuel Barillot, Francois Radvanyi, Alexander Gorban, Ulykbek Kairov, Andrei Zinovyev
Published in: International Journal of Molecular Sciences, 20/18, 2019, Page(s) 4414, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms20184414

Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution

Author(s): Marie-Ming Aynaud, Olivier Mirabeau, Nadege Gruel, Sandrine Grossetête, Valentina Boeva, Simon Durand, Didier Surdez, Olivier Saulnier, Sakina Zaïdi, Svetlana Gribkova, Aziz Fouché, Ulykbek Kairov, Virginie Raynal, Franck Tirode, Thomas G.P. Grünewald, Mylene Bohec, Sylvain Baulande, Isabelle Janoueix-Lerosey, Jean-Philippe Vert, Emmanuel Barillot, Olivier Delattre, Andrei Zinovyev
Published in: Cell Reports, 30/6, 2020, Page(s) 1767-1779.e6, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2020.01.049

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats

Author(s): Irina Balaur, Ludovic Roy, Alexander Mazein, S Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Zinovyev
Published in: Bioinformatics, 36/8, 2020, Page(s) 2620-2622, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz969

Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph

Author(s): Luca Albergante, Evgeny Mirkes, Jonathan Bac, Huidong Chen, Alexis Martin, Louis Faure, Emmanuel Barillot, Luca Pinello, Alexander Gorban, Andrei Zinovyev
Published in: Entropy, 22/3, 2020, Page(s) 296, ISSN 1099-4300
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/e22030296

Adaptation through the lens of single-cell multi-omics data: Comment on “Dynamic and thermodynamic models of adaptation” by A.N. Gorban et al.

Author(s): Andrei Zinovyev
Published in: Physics of Life Reviews, 2021, Page(s) 132-134, ISSN 1571-0645
Publisher: Elsevier BV
DOI: 10.1016/j.plrev.2021.05.004

The Multiple Dimensions of Networks in Cancer: A Perspective

Author(s): Cristian Axenie, Roman Bauer and María Rodríguez Martínez
Published in: Symmetry 2021, 2021, ISSN 2073-8994
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/sym13091559

Applications of single-cell and bulk RNA sequencing in onco-immunology

Author(s): Maria Kuksin, Daphné Morel, Marine Aglave, François-Xavier Danlos, Aurélien Marabelle, Andrei Zinovyev, Daniel Gautheret, Loïc Verlingue
Published in: European Journal of Cancer, 149, 2021, Page(s) 193-210, ISSN 0959-8049
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.ejca.2021.03.005

Designing a Network Proximity-Based Drug Repurposing Strategy for COVID-19

Author(s): Paola Stolfi, Luigi Manni, Marzia Soligo, Davide Vergni, Paolo Tieri
Published in: Frontiers in Cell and Developmental Biology, 8, 2020, ISSN 2296-634X
Publisher: Front Cell Dev Biol.
DOI: 10.3389/fcell.2020.545089

FPGA Accelerated Analysis of Boolean Gene Regulatory Networks

Author(s): Matteo Manica, Raphael Polig, Mitra Purandare, Roland Mathis, Christoph Hagleitner, Maria Rodriguez Martinez
Published in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 17/6, 2020, Page(s) 2141-2147, ISSN 1545-5963
Publisher: IEEE Computer Society
DOI: 10.1109/tcbb.2019.2936836

Data-driven molecular design for discovery and synthesis of novel ligands: a case study on SARS-CoV-2

Author(s): Jannis Born, Matteo Manica, Joris Cadow, Greta Markert, Nil Adell Mill, Modestas Filipavicius, Nikita Janakarajan, Antonio Cardinale, Teodoro Laino, María Rodríguez Martínez
Published in: Machine Learning: Science and Technology, 2/2, 2021, Page(s) 025024, ISSN 2632-2153
Publisher: Machine Learning: Science and Technology
DOI: 10.1088/2632-2153/abe808

Modeling progression of single cell populations through the cell cycle as a sequence of switches

Author(s): Zinovyev A, Sadovsky M, Calzone L, Fouche A, Groeneveld CS, Chervov A, Barillot E, Gorban AN
Published in: Frontiers in Molecular Biosciences, 2022, ISSN 2296-889X
Publisher: Lausanne: Frontiers Media S.A.,
DOI: 10.3389/fmolb.2021.793912

Deep learning in systems medicine

Author(s): Haiying Wang, Estelle Pujos-Guillot, Blandine Comte, Joao Luis de Miranda, Vojtech Spiwok, Ivan Chorbev, Filippo Castiglione, Paolo Tieri, Steven Watterson, Roisin McAllister, Tiago de Melo Malaquias, Massimiliano Zanin, Taranjit Singh Rai, Huiru Zheng
Published in: Briefings in Bioinformatics, Volume 22, Issue 2, March 2021, 2021, Page(s) 1543–1559, ISSN 1477-4054
Publisher: Oxford University Press
DOI: 10.1093/bib/bbaa237

Methylation data imputation performances under different representations and missingness patterns

Author(s): Pietro Di Lena, Claudia Sala, Andrea Prodi, Christine Nardini
Published in: BMC Bioinformatics, 21/1, 2020, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-020-03592-5

Identification and validation of viral antigens sharing sequence and structural homology with tumor-associated antigens (TAAs).

Author(s): Concetta Ragone, Carmen Manolio, Beatrice Cavalluzzo, Angela Mauriello, Maria Lina Tornesello, Franco M Buonaguro, Filippo Castiglione, Luigi Vitagliano, Emanuela Iaccarino, Menotti Ruvo, Maria Tagliamonte, Luigi Buonaguro
Published in: Journal for ImmunoTherapy of Cancer, 9/5, 2021, Page(s) e002694, ISSN 2051-1426
Publisher: Journal for ImmunoTherapy of Cancer
DOI: 10.1136/jitc-2021-002694

Improved identification and quantification of peptides in mass spectrometry data via chemical and random additive noise elimination (CRANE)

Author(s): Akila J Seneviratne, Sean Peters, David Clarke, Michael Dausmann, Michael Hecker, Brett Tully, Peter G Hains, Qing Zhong
Published in: Bioinformatics, Volume 37, Issue 24, 2021, Page(s) 4719-4726, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab563

TITAN: T Cell Receptor Specificity Prediction with Bimodal Attention Networks

Author(s): Weber, Anna; Born, Jannis; Martínez, María Rodríguez
Published in: Bioinformatics, Volume 37, Issue Supplement_1, July 2021, 2021, Page(s) i237–i244, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab294

The multilayer community structure of medulloblastoma

Author(s): Iker Núñez-Carpintero, Marianyela Petrizzelli, Andrei Zinovyev, Davide Cirillo, Alfonso Valencia
Published in: iScience, 24/4, 2021, Page(s) 102365, ISSN 2589-0042
Publisher: iScience
DOI: 10.1016/j.isci.2021.102365

Machine learning for multi-omics data integration in cancer

Author(s): Zhaoxiang Cai, Rebecca C. Poulos, Jia Liu, Qing Zhong
Published in: iScience, Volume 25, Issue 2, 2022, 103798, 2022, ISSN 2589-0042
Publisher: Elsevier Inc.
DOI: 10.1016/j.isci.2022.103798

DECODE: a computational pipeline to discover T-cell receptor binding rules

Author(s): Iliana Papadopoulou, An-phi Nguyen, Anna Weber, Maria Rodriguez Martinez
Published in: Bioinformatics, 2022, ISSN 1460-2059
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btac257

From Infection to Immunity: Understanding the Response to SARS-CoV2 Through In-Silico Modeling

Author(s): Filippo Castiglione, Debashrito Deb, Anurag P. Srivastava, Pietro Liò and Arcangelo Liso
Published in: Frontiers in Immunology, 2021, ISSN 1664-3224
Publisher: Lausanne: Frontiers Media S.A., 2010-
DOI: 10.3389/fimmu.2021.646972

Opportunities for pharmacoproteomics in biomarker discovery

Author(s): Rebecca C Poulos, Zhaoxiang Cai, Phillip J Robinson, Qing Zhong
Published in: Proteomics, 16159861, 2022, ISSN 1615-9861
Publisher: John Wiley & Sons
DOI: 10.1002/pmic.202200031

Additional file 2 of Methylation data imputation performances under different representations and missingness patterns

Author(s): Lena, Pietro Di; Sala, Claudia; Prodi, Andrea; Nardini, Christine
Published in: 1, 2020
Publisher: Springer
DOI: 10.6084/m9.figshare.12585955

Additional file 1 of Methylation data imputation performances under different representations and missingness patterns

Author(s): Lena, Pietro Di; Sala, Claudia; Prodi, Andrea; Nardini, Christine
Published in: 2020
Publisher: Springer Nature
DOI: 10.6084/m9.figshare.12585952.v1

Additional file 3 of Methylation data imputation performances under different representations and missingness patterns

Author(s): Lena, Pietro Di; Sala, Claudia; Prodi, Andrea; Nardini, Christine
Published in: 2020
Publisher: Springer
DOI: 10.6084/m9.figshare.12585958.v1

Trajectories, bifurcations and pseudotime in large clinical datasets

Author(s): Sergey E. Golovenkin, Jonathan Bac, Alexander Chervov, Evgeny M. Mirkes, Yuliya V. Orlova, Emmanuel Barillot, Alexander N. Gorban and Andrei Zinovyev
Published in: 2020
Publisher: ArXiv
DOI: 10.5281/zenodo.4018714

Loss of p16INK4a in neuroblastoma cells induces shift to an immature state with mesenchymal characteristics and increases sensitivity to EGFR inhibitors

Author(s): Nil A. Schubert, Sander R. van Hooff, Linda Schild, Kimberley Ober, Marjolein Hortensius, Kim van den Handel, Anke H.W. Essing, Bianca Koopmans, Manon Boeije, Natalie Proost, Marieke van de Ven, Selina Jansky, Sabine A. Stainczyk, Umut H. Toprak, Frank Westermann, Selma Eising, Jan J. Molenaar, Marlinde L. van den Boogaard
Published in: 2021
Publisher: bioRxiv
DOI: 10.1101/2021.10.27.465137

The RNA Atlas, a single nucleotide resolution map of the human transcriptome

Author(s): Lorenzi, Lucia; Chiu, Hua-Sheng; Cobos, Francisco Avila; Gross, Stephen; Volders, Pieter-Jan; Cannoodt, Robrecht; Nuytens, Justine; Vanderheyden, Katrien; Anckaert, Jasper; Lefever, Steve; Goovaerts, Tine; Birkballe Hansen, Thomas; Kuersten, Scott; Nijs, Nele; Taghon, Tom; Vermaelen, Karim; Bracke, Ken R.; Saeys, Yvan; De Meyer, Tim; Deshpande, Nandan; Anande, Govardhan; Chen, Ting-Wen; Wilkins, M
Published in: 7, 2019
Publisher: Biorixv - The Preprint server for biology
DOI: 10.1101/807529

Additional file 1 of DECONbench: a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification

Author(s): Decamps, Clémentine; Arnaud, Alexis; Petitprez, Florent; Ayadi, Mira; Baurès, Aurélia; Armenoult, Lucile; Escalera, Sergio; Guyon, Isabelle; Nicolle, Rémy; Tomasini, Richard; de Reyniès, Aurélien; Cros, Jérôme; Blum, Yuna; Richard, Magali
Published in: 12, 2021
Publisher: Springer Nature
DOI: 10.6084/m9.figshare.16726873

From infection to immunity: understanding the response to SARS-CoV2 through in-silico modeling

Author(s): Filippo Castiglione; Debashrito Deb; Anurag P. Srivastava; Pietro Liò; Arcangelo Liso
Published in: Frontiers in Immunology, 15, 2021
Publisher: Frontiers Media S.A.
DOI: 10.17863/cam.75782

Clinical trajectories estimated from bulk tumoral molecular profiles using elastic principal trees

Author(s): Alexander Chervov; Andrei Zinovyev
Published in: Crossref, 6, 2021
Publisher: Zenodo
DOI: 10.1109/ijcnn52387.2021.9534249

Towards Visual Anomaly Detection in Domains with Limited Amount of Labeled Data

Author(s): Dejan Štepec, Danijel Skočaj
Published in: ROSUS 2020 - Računalniška obdelava slik in njena uporaba v Sloveniji 2020: Zbornik 15. strokovne konference, 2020, Page(s) 7-26, ISBN 9789612863371
Publisher: University of Maribor Press
DOI: 10.18690/978-961-286-337-1.1

Image Synthesis as a Pretext for Unsupervised Histopathological Diagnosis

Author(s): Stepec, D.; Skocaj, D.
Published in: 1, 2020
Publisher: Springer
DOI: 10.5281/zenodo.4288328

Scalable Structure Learning of Continuous-Time Bayesian Networks from Incomplete Data

Author(s): Dominik Linzner Michael Schmidt Heinz Koeppl
Published in: 33rd Conference on Neural Information Processing Systems (NeurIPS 2019), 2019
Publisher: NIPS

A Variational Perturbative Approach to Planning in Graph-based Markov Decision Processes

Author(s): Dominik Linzner Heinz Koeppl
Published in: Association for the Advancement of Artificial Intelligence, 2019
Publisher: Association for the Advancement of Artificial Intelligence

Continuous-Time Bayesian Networks with Clocks

Author(s): Engelmann, Nikolai; Linzner, Dominik; Koeppl, Heinz
Published in: 10, 2020
Publisher: 37th International Conference on Machine Learning (ICML)
DOI: 10.5281/zenodo.3957199

PaccMannRL: Designing anticancer drugs from transcriptomic data via reinforcement learning

Author(s): Jannis Born, Matteo Manica, Ali Oskooei, María Rodríguez Martínez
Published in: 2019
Publisher: Workshop for Physical Sciences at NeurIPS
DOI: 10.5281/zenodo.3610233

ROSUS 2020 - Računalniška obdelava slik in njena uporaba v Sloveniji 2020: Zbornik 15. strokovne konference

Author(s): Dejan Štepec, Danijel Skočaj
Published in: 2020, ISBN 9789-612863371
Publisher: University of Maribor Press
DOI: 10.18690/978-961-286-337-1

Segmentation of multiple myeloma plasma cells in microscopy images with noisy labels

Author(s): Álvaro García Faura, Dejan Štepec, Tomaž Martinčič, Danijel Skočaj
Published in: 2021
Publisher: arXiv.org

Systems biology analysis for Ewing sarcoma

Author(s): Petrizzelli, Marianyela; Merlevede, Jane; Zinovyev, Andrei
Published in: 2, 2020, ISBN 978-1-0716-1019-0
Publisher: Springer
DOI: 10.5281/zenodo.3952244

DeStress: Deep Learning for Unsupervised Identification of Mental Stress in Firefighters from Heart-Rate Variability (HRV) Data

Author(s): Ali Oskooei, Sophie Mai Chau, Jonas Weiss, Arvind Sridhar, María Rodríguez Martínez, Bruno Michel
Published in: Explainable AI in Healthcare and Medicine, 2021, Page(s) 93-105, ISBN 978-3-030-53352-6
Publisher: Springer

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