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

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Consensus multi-omics subtypes of paediatric cancers

Improving existing definition of molecular cancer subtypes in paediatric cancers, based on multiple datasets of the same and of different omics data types. Characterizing the consensus subtypes in terms of implicated molecular mechanisms and interaction with stroma.

Network models for molecular target identification

Methodology and predictions of drug mode of action on each patient, tumour, and tumour subclone.

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

Topological analysis of multi-omics and multi-cancer molecular networks resulting in the definition of molecular mechanisms

Identification of molecular mechanisms in tumour cells and in the interactions between tumour cells and stromal cells, based on simultaneous network-based analysis of several omics data types.

Final report on dissemination and communication activities

Including dissemination, communication activities and reports of executed activities.

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

Model development data including genetic perturbation screens and gene-drug synergies

A systematic collection of data generated via CRISPR-Cas perturbation screens for mechanistic model development.

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.

Updated comprehensive datasets for training, testing, and improving model predictions as additional data is gathered throughout the project's timeline

A full updated list of datasets available to the consortium for model development and testing.

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

Global report on iPC computational infrastructure

A final description of iPC’s back- and front-end, including cloud-based engine and user interface (application).

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

Identification of cell subpopulations in each tumour type, their association with response to therapy, and prediction of effective alternative therapies

Tumour decomposition into cells and subtypes and inference about the effects of treatments and perturbations on each tumour component (cell or tumor subclone).

Project quality plan

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

Software to define tumour subclones and association with therapy response

Methodology for reconstructing the clonal architecture of blood and solid tumours based on multiple biopsies across time and tumour regions.

Initial infrastructure framework

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

DAC Portal prototype, validated analytical workflows, analysis prototype, updated metadata standards and portal prototype

Implementation of a portal dedicated to managing access credentials based on strategies from the EGA archive. The deliverable will describe procedures for dissemination of access policies and will present a framework to apply for data access. DAC workflows will be presented.

Recommended metadata standards and portal prototype

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

Metabolic models

Functioning in silico prototype of hepatocyte metabolism generated.

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.

DREAM Challenge outcome

DREAM Challenge for drug response prediction in paediatric cancer completed and outcomes evaluated.

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, Issue 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, Issue 39/6, 2021, Page(s) 810-826.e9, ISSN 1535-6108
Publisher: Cell Press
DOI: 10.1016/j.ccell.2021.04.001

Systematic multi-omics cell line profiling uncovers principles of Ewing sarcoma fusion oncogene-mediated gene regulation

Author(s): Martin F. Orth, Didier Surdez, Tobias Faehling, Anna C. Ehlers, Aruna Marchetto, Sandrine Grossetête, Richard Volckmann, Danny A. Zwijnenburg, Julia S. Gerke, Sakina Zaidi, Javier Alonso, Ana Sastre, Sylvain Baulande, Martin Sill, Florencia Cidre-Aranaz, Shunya Ohmura, Thomas Kirchner, Stefanie M. Hauck, Eva Reischl, Melissa Gymrek, Stefan M. Pfister, Konstantin Strauch, Jan Koster, Olivier Delat
Published in: Cell Reports, 2022, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2022.111761

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

Computational drug prediction in hepatoblastoma by integrating pan-cancer transcriptomics with pharmacological response

Author(s): Mario Failli, Salih Demir, Álvaro Del Río-Álvarez, Juan Carrillo-Reixach, Laura Royo, Montserrat Domingo-Sàbat, Margaret Childs, Rudolf Maibach, Rita Alaggio, Piotr Czauderna, Bruce Morland, Sophie Branchereau, Stefano Cairo, Roland Kappler, Carolina Armengol, Diego di Bernardo
Published in: Hepatology, 2023, ISSN 0270-9139
Publisher: John Wiley & Sons Inc.
DOI: 10.1097/hep.0000000000000601

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

Identification and experimental validation of druggable epigenetic targets in hepatoblastoma

Author(s): Alex Clavería-Cabello, Jose Maria Herranz, Maria Ujue Latasa, Maria Arechederra, Iker Uriarte, Antonio Pineda-Lucena, Felipe Prosper, Pedro Berraondo, Cristina Alonso, Bruno Sangro, Jose Juan García Marin, Maria Luz Martinez-Chantar, Sergio Ciordia, Fernando José Corrales, Paola Francalanci, Rita Alaggio, Jessica Zucman-Rossi, Emilie Indersie, Stefano Cairo, Montserrat Domingo-Sàbat, Laura Zan
Published in: Journal of Hepatology, 2023, ISSN 1600-0641
Publisher: EASL
DOI: 10.1016/j.jhep.2023.05.031

FLAN: feature-wise latent additive neural models for biological applications

Author(s): An-Phi Nguyen; Stefania Vasilaki; María Rodríguez Martínez
Published in: Briefings in Bioinformatics, 2023, ISSN 1477-4054
Publisher: Oxford University Press
DOI: 10.1093/bib/bbad056

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, Issue 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

Integrative analysis of neuroblastoma by single-cell RNA sequencing indentifies the NECTIN2-TIGIT axis as a target for immunotherapy

Author(s): Judith Wienke, Lindy L. Visser, Waleed M. Kholosy, Kaylee M. Keller, Marta Barisa, Sophie Munnings-Tomes, Elizabeth Carlton, Evon Poon, Ana Rodriguez, Ronald Bernardi, Femke van den Ham, Sander R. van Hooff, Yvette A.H. Matser, Michelle L. Tas, Karin P.S. Langenberg, Philip Lijnzaad, Josephine G.M. Strijker, Alvaro Sanchez-Bernabeu, Annelisa M. Cornel, Frank C.P. Holstege, Juliet Gray, Lieve A.M.
Published in: Cancer Cell, 2024, ISSN 1535-6108
Publisher: Cell Press
DOI: 10.1016/j.ccell.2023.12.008

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, Issue 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, Issue 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

Chemical Representation Learning for Toxicity Prediction

Author(s): Jannis Born, Greta Markert, Nikita Janakarajan, Talia Kimber, Andrea Volkamer, María Rodríguez Martíne, Matteo Manica
Published in: Digital Discovery, 2023, ISSN 2635-098X
Publisher: Royal Society of Chemistry
DOI: 10.1039/d2dd00099g

Identification of IGF2 as Genomic Driver and Actionable Therapeutic Target in Hepatoblastoma

Author(s): Jordi Abril-Fornaguera; Laura Torrens; Carmen Andreu-Oller; Juan Carrillo-Reixach; Alex Rialdi; Ugne Balaseviciute; Roser Pinyol; Carla Montironi; Philipp K. Haber; Álvaro Del Río-Álvarez; Montserrat Domingo-Sàbat; Laura Royo; Nicholas K. Akers; Catherine E. Willoughby; Judit Peix; Miguel Torres-Martin; Marc Puigvehi; Stefano Cairo; Margaret Childs; Rudolf Maibach; Rita Alaggio; Piotr Czaudern
Published in: Molecular Cancer Therapeutics, 2023, ISSN 1535-7163
Publisher: American Association for Cancer Research
DOI: 10.1158/1535-7163.mct-22-0335

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

Image-to-Image Translation as a Pretext for Unsupervised Detection of Cancerous Regions in Histology Imagery

Author(s): Dejan Štepec; Danijel Skočaj
Published in: Uporabna informatika, Issue 1, 2021, ISSN 2630-435X
Publisher: Slovenian Society Informatika
DOI: 10.31449/upinf.136

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, Issue 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, Issue 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, Issue Volume 56, August 2021, 2021, ISSN 1044-5323
Publisher: Academic Press
DOI: 10.1016/j.smim.2021.101518

Adoptive cell therapy in pediatric extracranial solid tumors: current approaches and future challenges

Author(s): Elisa Zappa, Alice Vitali, Kathleen Anders, Jan J Molenaar, Judith Wienke, Annette Künkele
Published in: European Journal of Cancer, 2023, ISSN 0959-8049
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.ejca.2023.113347

Single-cell gene set enrichment analysis and transfer learning for functional annotation of scRNA-seq data

Author(s): Melania Franchini; Simona Pellecchia; Gaetano Viscido; Gennaro Gambardella
Published in: NAR Genomics and Bioinformatics, Volume 5, Issue 1, March 2023,, 2023, ISSN 2631-9268
Publisher: Oxford University Press
DOI: 10.1093/nargab/lqad024

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, Issue Volume 37, Issue Supplement_1, July 2021, 2021, Page(s) i245–i253, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab311

Rare disease research workflow using multilayer networks elucidates the molecular determinants of severity in Congenital Myasthenic Syndromes

Author(s): Iker Núñez-Carpintero, Emily O'Connor, Maria Rigau, Mattia Bosio, Yoshiteru Azuma, Ana Topf, Rachel Thompson, Peter A.C. ’t Hoen, Teodora Chamova, Ivailo Tournev, Velina Guergueltcheva, Steven Laurie, Sergi Beltran, Salvador Capella, Davide Cirillo, Hanns Lochmüller, Alfonso Valencia
Published in: Nature Communications, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/2023.01.19.524736

Effective methods for bulk RNA-Seq deconvolution using scnRNA-Seq transcriptomes

Author(s): Cobos, Francisco Avila; Panah, Mohammad Javad Najaf; Epps, Jessica; Long, Xiaochen; Man, Tsz-Kwong; Chiu, Hua-Sheng; Chomsky, Elad; Kiner, Evgeny; Krueger, Michael J.; di Bernado, Diego; Voloch, Luis; Molenaar, Jan; von Hooff, Sander R.; Westermann, Frank; Jansky, Selina; Redell, Michele L.; Mestdagh, Pieter; Sumazin, Pavel
Published in: Genome Biology, 2023, ISSN 1474-760X
Publisher: Springer Nature
DOI: 10.1186/s13059-023-03016-6

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, Issue 11, Article number: 2967 (2021), 2021, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-82542-4

The HHIP-AS1 lncRNA promotes tumorigenicity through stabilization of dynein complex 1 in human SHH-driven tumors

Author(s): Jasmin Bartl; Marco Zanini; Flavia Bernardi; Antoine Forget; Lena Blümel; Julie Talbot; Daniel Picard; Nan Qin; Gabriele Cancila; Qingsong Gao; Soumav Nath; Idriss Mahoungou Koumba; Marietta Wolter; François Kuonen; Maike Langini; Thomas Beez; Christopher Munoz; David Pauck; Viktoria Marquardt; Hua Yu; Judith Souphron; Mascha Korsch; Christina Mölders; Daniel Berger; Sarah Göbbels; Frauke-Doro
Published in: Nature Communications, Issue 7, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-31574-z

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, Issue 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, Issue 1/3, 2021, ISSN 2691-1299
Publisher: Current Protocols in Bioinformatics
DOI: 10.1002/cpz1.69

MacroH2As regulate enhancer-promoter contacts affecting enhancer activity and sensitivity to inflammatory cytokines

Author(s): David Corujo, Roberto Malinverni, Juan Carrillo-Reixach, Oliver Meers, Arce Garcia-Jaraquemada, Marguerite-Marie Le Pannérer, Vanesa Valero, Ainhoa Pérez, Álvaro Del Río-Álvarez, Laura Royo, Beatriz Pérez-González, Helena Raurell, Rafael D Acemel, José M Santos-Pereira, Marta Garrido-Pontnou, José Luis Gómez-Skarmeta, Lorenzo Pasquali, Josep Manyé, Carolina Armengol, Marcus Buschbeck
Published in: Cell Reports, 2022, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2022.110988

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, Issue 1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-19015-1

Computational modelling in health and disease: highlights of the 6th annual SysMod meeting

Author(s): Anna Niarakis, Juilee Thakar, Matteo Barberis, María Rodríguez Martínez, Tomáš Helikar, Marc Birtwistle, Claudine Chaouiya, Laurence Calzone, Andreas Dräger
Published in: Bioinformatics, 2022, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btac609

The children's brain tumor network (CBTN) - Accelerating research in pediatric central nervous system tumors through collaboration and open science

Author(s): Jena V. Lilly, Jo Lynne Rokita, Jennifer L. Mason, Tatiana Patton, Stephanie Stefankiewiz, David Higgins, Gerri Trooskin, Carina A. Larouci, Kamnaa Arya, Elizabeth Appert, Allison P. Heath, Yuankun Zhu, Miguel A. Brown, Bo Zhang, Bailey K. Farrow, Shannon Robins, Allison M. Morgan, Thinh Q. Nguyen, Elizabeth Frenkel, Kaitlin Lehmann, Emily Drake, Catherine Sullivan, Alexa Plisiewicz, Noel Coleman,
Published in: Neoplasia, 2022, ISSN 1522-8002
Publisher: Elsevier BV
DOI: 10.1016/j.neo.2022.100846

Proteomic-based stratification of intermediate-risk prostate cancer patients

Author(s): Qing Zhong, Sun Rui, Adel T. Aref, Zainab Noor, Asim Anees, Yi Zhu, Natasha Lucas, Rebecca C. Poulos, Mengge Lyu, Tiansheng Zhu, Bo Wang, Guo-Bo Chen, Yingrui Wang, Xuan Ding, Dorothea Rutishauser, Niels J. Rupp, Jan H. Rueschoff, Cédric Poyet, Thomas Hermanns, Christian Fankhauser, María Rodríguez Martínez, Wenguang Shao, Marija Buljan, Janis Frederick Neumann, Andreas Beyer, Peter G. Hains,
Published in: 2023 Life Science Alliance LLC, February 2024 | Volume 7, No. 2, 2024, ISSN 2575-1077
Publisher: 2023 Life Science Alliance LLC
DOI: 10.1101/2023.03.03.530910

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, Issue 7/6, 2021, Page(s) eabd3311, ISSN 2375-2548
Publisher: Science Advances
DOI: 10.1126/sciadv.abd3311

SegPC-2021: A challenge & dataset on segmentation of Multiple Myeloma plasma cells from microscopic images

Author(s): Anubha Gupta; Shiv Gehlot; Shubham Goswami; Sachin Motwani; Ritu Gupta; Álvaro García Faura; Dejan Štepec; Tomaž Martinčič; Reza Azad; Dorit Merhof; Afshin Bozorgpour; Babak Azad; Alaa Sulaiman; Deepanshu Pandey; Pradyumna Gupta; Sumit Bhattacharya; Aman Sinha; Rohit Agarwal; Xinyun Qiu; Yucheng Zhang; Ming Fan; Yoonbeom Park; Daehong Lee; Joon Sik Park; Kwangyeol Lee; Jaehyung Ye
Published in: Medical Image Analysis, Issue 1, 2022, ISSN 1361-8415
Publisher: Elsevier BV
DOI: 10.1016/j.media.2022.102677

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, Issue 22, Article number: 473 (2021), 2021, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-021-04381-4

MYCN-driven Fatty Acid Uptake is a Novel Metabolic Vulnerability in Neuroblastoma

Author(s): Ling Tao, Mahmoud A. Mohammad, Giorgio Milazzo, Myrthala Moreno-Smith, Tajhal Patel, Barry Zorman, Andrew Badachhape, Blanca E. Hernandez, Amber B. Wolf, Zihua Zeng, Jennifer H. Foster, Sara Aloisi, Pavel Sumazin, Youli Zu, John Hicks, Ketan B. Ghaghada, Nagireddy Putluri, Giovanni Perini, Cristian Coarfa, and Eveline Barbieri
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-31331-2

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, Issue 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, Issue 6/1, 2020, ISSN 2056-7189
Publisher: npj Sytems Biology and Applications
DOI: 10.1038/s41540-020-00147-5

MonoNet: Enhancing interpretability in neural networks via Monotonic Features

Author(s): An-phi Nguyen, Dana Lea Moreno, Nicolas Le Bel, Maria Rodriguez Martinez
Published in: Bioinformatics Advances, 2023, ISSN 2635-0041
Publisher: Oxford University Press
DOI: 10.1093/bioadv/vbad016

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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 22/3, 2020, Page(s) 296, ISSN 1099-4300
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/e22030296

Oncogenic chimeric transcription factors drive tumor-specific transcription, processing, and translation of silent genomic regions

Author(s): Julien Vibert, Olivier Saulnier, Celine Collin, Floriane Petit, Kyra J.E. Borgman, Jeromine Vigneau, Maud Gautier, Sakina Zaidi, Gaelle Pierron, Sarah Watson, Nadege Gruel, Clemence Henon, Sophie Postel-Vinay, Marc Deloger, Virginie Raynal, Sylvain Baulande, Karine Laud-Duval, Veronique Hill, Sandrine Grossetete, Florent Dingli,Damarys Loew, Jacob Torrejon, Olivier Ayrault, Martin F. Orth, Thomas
Published in: Molecular Cell, 2022, Page(s) P2458-2471.E9, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2022.04.019

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

Heat ‘n Beat: A universal high-throughput end-to-end proteomics sample processing platform in under an hour

Author(s): Dylan XavierNatasha LucasSteven G WilliamsJennifer M. S. KohKeith AshmanClare LoudonRoger ReddelPeter G. HainsPhillip J. Robinson
Published in: Analytical Chemistry, 2023, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1101/2023.09.27.559846

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, Issue 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, Issue 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, Issue 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, Issue 2/2, 2021, Page(s) 025024, ISSN 2632-2153
Publisher: Machine Learning: Science and Technology
DOI: 10.1088/2632-2153/abe808

Targeting G9a/DNMT1 methyltransferase activity impedes IGF2-mediated survival in hepatoblastoma

Author(s): Salih Demir, Negin Razizadeh, Emilie Indersie, Sophie Branchereau, Stefano Cairo, Roland Kappler
Published in: Hepatology Communications, 2024, ISSN 2471-254x
Publisher: Hepatology Communications
DOI: 10.1097/hc9.0000000000000378

Two opposing gene expression patterns within ATRX aberrant neuroblastoma

Author(s): Michael R. van Gerven, Linda Schild, Jennemiek van Arkel, Bianca Koopmans, Luuk A. Broeils, Loes A. M. Meijs, Romy van Oosterhout, Max M. van Noesel, Jan Koster, Sander R. van Hooff, Jan J. Molenaar, Marlinde L. van den Boogaard
Published in: PLOS ONE, 2023, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0289084

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, Issue 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, Issue 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, Issue 9/5, 2021, Page(s) e002694, ISSN 2051-1426
Publisher: Journal for ImmunoTherapy of Cancer
DOI: 10.1136/jitc-2021-002694

Defects in 8-oxo-guanine repair pathway cause high frequency of C > A substitutions in neuroblastoma

Author(s): van den Boogaard, M.L.; Oka, R.; Hakkert, A.; Schild, L.; Ebus, M.E.; van Gerven, M.R.; Zwijnenburg, D.A.; Molenaar, P.; Hoyng, L.L.; Dolman, M.E.M.; Essing, A.H.W.; Koopmans, B.; Helleday, T.; Drost, J.; van Boxtel, R.; Versteeg, R.; Koster, J.; Molenaar, J.J.
Published in: PNAS, Issue 1, 2021, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2007898118

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, Issue 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, Issue 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, Issue 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

Quantitative proteomic studies addressing unmet clinical needs in sarcoma

Author(s): Elizabeth A. Connolly, Peter S. Grimison, Lisa G. Horvath, Phillip J. Robinson and Roger R. Reddel
Published in: Frontiers in Oncology, 2023, ISSN 2234-943X
Publisher: Frontiers Media S. A.
DOI: 10.3389/fonc.2023.1126736

Opportunities for pharmacoproteomics in biomarker discovery

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

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: Front. Immunol., 07 September 2021 Sec. Viral Immunology Volume 12 - 2021, Issue 15, 2021, ISSN 1664-3224
Publisher: Frontiers in Immunology
DOI: 10.17863/cam.75782

Scalable Inference in Graph-coupled Continuous-time Markov Chains

Author(s): Linzner, Dominik
Published in: Issue 1, 2021
Publisher: TUprints
DOI: 10.12921/tuprints-00017403

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: Issue 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

It's FLAN time! Summing feature-wise latent representations for interpretability

Author(s): An-phi Nguyen, Maria Rodriguez Martinez
Published in: 2021
Publisher: arXiv
DOI: 10.48550/arxiv.2106.10086

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: Issue 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: Issue 12, 2021
Publisher: Springer Nature
DOI: 10.6084/m9.figshare.16726873

Computational challenges of cell cycle analysis using single cell transcriptomic data

Author(s): Alexander Chervov, Andrei Zinovyev
Published in: 2022
Publisher: arXiv
DOI: 10.48550/arxiv.2208.05229

Isotropic Gaussian Processes on Finite Spaces of Graphs

Author(s): Borovitskiy, Viacheslav; Karimi, Mohammad Reza; Somnath, Vignesh Ram; Krause, Andreas
Published in: 26th International Conference on Artificial Intelligence and Statistics (AISTATS), 2022
Publisher: arXiv
DOI: 10.48550/arxiv.2211.01689

Active Learning of Continuous-time Bayesian Networks through Interventions

Author(s): "Dominik Linzner, Heinz Koeppl """
Published in: 2021
Publisher: 38th International Conference on Machine Learning (ICML 2021)
DOI: 10.5281/zenodo.5234917

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

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

Aligned Diffusion Schrödinger Bridges

Author(s): Somnath, Vignesh Ram; Pariset, Matteo; Hsieh, Ya-Ping; Martinez, Maria Rodriguez; Krause, Andreas; Bunne, Charlotte
Published in: 39th Conference on Uncertainty in Artificial Intelligence (UAI 2023, 2023
Publisher: arXiv
DOI: 10.48550/arxiv.2302.11419

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: Issue 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: Issue 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

Why is the winner the best

Author(s): Matthias Eisenmann; Dejan Štepec; et. al.
Published in: IEEE / CVF Computer Vision and Pattern Recognition Conference (CVPR), 2023
Publisher: IEEE Xplore
DOI: 10.1109/cvpr52729.2023.01911

Is Attention Interpretation? A Quantitative Assessment On Sets

Author(s): Haab, Jonathan; Deutschmann, Nicolas; Martínez, Maria Rodríguez
Published in: ECML PKDD International Workshop on eXplainable Knowledge Discovery in Data Mining, Grenoble/France (19 September 2022), 2022
Publisher: arXiv
DOI: 10.48550/arxiv.2207.13018

Unsupervised Detection of Cancerous Regions in Histology Imagery using Image-to-Image Translation

Author(s): Dejan Stepec, Danijel Skocaj
Published in: 2021
Publisher: Computer Vision for Microscopy Image Analysis (CVMI) workshop
DOI: 10.5281/zenodo.5158712

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: Issue 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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