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

CORDIS bietet Links zu öffentlichen Ergebnissen und Veröffentlichungen von HORIZONT-Projekten.

Links zu Ergebnissen und Veröffentlichungen von RP7-Projekten sowie Links zu einigen Typen spezifischer Ergebnisse wie Datensätzen und Software werden dynamisch von OpenAIRE abgerufen.

Leistungen

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.

Veröffentlichungen

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

Autoren: Captier, Nicolas; Merlevede, Jane; Molkenov, Askhat; Seisenova, Ainur; Zhubanchaliyev, Altynbek; Nazarov, Petr V.; Barillot, Emmanuel; Kairov, Ulykbek; Zinovyev, Andrei
Veröffentlicht in: Bioinformatics, Volume 38, Ausgabe 10, 2022, Seite(n) 2963–2964, ISSN 1367-4803
Herausgeber: Oxford University Press
DOI: 10.1093/bioinformatics/btac204

Emulating complex simulations by machine learning methods

Autoren: Paola Stolfi & Filippo Castiglione
Veröffentlicht in: BMC Bioinformatics, Ausgabe 22, Article number: 483 (2021), 2021, ISSN 1471-2105
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Cancer Cell, Ausgabe 39/6, 2021, Seite(n) 810-826.e9, ISSN 1535-6108
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Cell Reports, 2022, ISSN 2211-1247
Herausgeber: 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

Autoren: Pavel Sumazin, Dolores H. López-Terrada
Veröffentlicht in: Journal of Hepatology, 2021, ISSN 0168-8278
Herausgeber: Elsevier BV
DOI: 10.1101/2021.07.15.445600

Estimage: a webserver hub for the computation of methylation age

Autoren: Pietro Di Lena, Claudia Sala, Christine Nardini
Veröffentlicht in: Nucleic Acids Research, 2021, ISSN 0305-1048
Herausgeber: Oxford University Press
DOI: 10.1093/nar/gkab426

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

Autoren: 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
Veröffentlicht in: Hepatology, 2023, ISSN 0270-9139
Herausgeber: John Wiley & Sons Inc.
DOI: 10.1097/hep.0000000000000601

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

Autoren: Matteo Manica, Charlotte Bunne, Roland Mathis, Joris Cadow, Mehmet Eren Ahsen, Gustavo A Stolovitzky, María Rodríguez Martínez
Veröffentlicht in: Bioinformatics, 2020, ISSN 1367-4803
Herausgeber: Oxford University Press
DOI: 10.1093/bioinformatics/btaa942

Identification and experimental validation of druggable epigenetic targets in hepatoblastoma

Autoren: 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
Veröffentlicht in: Journal of Hepatology, 2023, ISSN 1600-0641
Herausgeber: EASL
DOI: 10.1016/j.jhep.2023.05.031

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

Autoren: An-Phi Nguyen; Stefania Vasilaki; María Rodríguez Martínez
Veröffentlicht in: Briefings in Bioinformatics, 2023, ISSN 1477-4054
Herausgeber: Oxford University Press
DOI: 10.1093/bib/bbad056

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

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

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

Autoren: Emma L. Boys, Jia Liu, Phillip J Robinson, Roger R. Reddel
Veröffentlicht in: Proteomics, 2022, ISSN 1615-9861
Herausgeber: 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

Autoren: 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.
Veröffentlicht in: Cancer Cell, 2024, ISSN 1535-6108
Herausgeber: Cell Press
DOI: 10.1016/j.ccell.2023.12.008

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

Autoren: Enrico Santus, Nicola Marino, Davide Cirillo, Emmanuele Chersoni, Arnau Montagud, Antonella Santuccione Chadha, Alfonso Valencia, Kevin Hughes, Charlotta Lindvall
Veröffentlicht in: Journal of Medical Internet Research, Ausgabe 23/3, 2021, Seite(n) e22453, ISSN 1438-8871
Herausgeber: Journal of medical Internet Research
DOI: 10.2196/22453

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

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

Targeting the Unwindosome by Mebendazole Is a Vulnerability of Chemoresistant Hepatoblastoma

Autoren: 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
Veröffentlicht in: Cancers, 2022, ISSN 2072-6694
Herausgeber: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14174196

Chemical Representation Learning for Toxicity Prediction

Autoren: Jannis Born, Greta Markert, Nikita Janakarajan, Talia Kimber, Andrea Volkamer, María Rodríguez Martíne, Matteo Manica
Veröffentlicht in: Digital Discovery, 2023, ISSN 2635-098X
Herausgeber: Royal Society of Chemistry
DOI: 10.1039/d2dd00099g

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

Autoren: 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
Veröffentlicht in: Molecular Cancer Therapeutics, 2023, ISSN 1535-7163
Herausgeber: American Association for Cancer Research
DOI: 10.1158/1535-7163.mct-22-0335

CHAF1A Blocks Neuronal Differentiation and Promotes Neuroblastoma Oncogenesis via Metabolic Reprogramming

Autoren: 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
Veröffentlicht in: Advanced Science, 2021, Seite(n) e2005047, ISSN 2198-3844
Herausgeber: Wiley
DOI: 10.1002/advs.202005047

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

Autoren: Dejan Štepec; Danijel Skočaj
Veröffentlicht in: Uporabna informatika, Ausgabe 1, 2021, ISSN 2630-435X
Herausgeber: Slovenian Society Informatika
DOI: 10.31449/upinf.136

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

Autoren: 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
Veröffentlicht in: Cancer Science, Ausgabe 4, 2022, ISSN 1349-7006
Herausgeber: John Wiley & Sons
DOI: 10.1111/cas.15363

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

Autoren: 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
Veröffentlicht in: Bioinformatics, Ausgabe Volume 37, Ausgabe 21, 1 November 2021, 2021, Seite(n) 3702–3706, ISSN 1367-4803
Herausgeber: Oxford University Press
DOI: 10.1093/bioinformatics/btab229

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

Autoren: Florian Ingelfinger; Donatella De Feo; Burkhard Becher
Veröffentlicht in: Seminars in Immunology, Ausgabe Volume 56, August 2021, 2021, ISSN 1044-5323
Herausgeber: Academic Press
DOI: 10.1016/j.smim.2021.101518

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

Autoren: Elisa Zappa, Alice Vitali, Kathleen Anders, Jan J Molenaar, Judith Wienke, Annette Künkele
Veröffentlicht in: European Journal of Cancer, 2023, ISSN 0959-8049
Herausgeber: 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

Autoren: Melania Franchini; Simona Pellecchia; Gaetano Viscido; Gennaro Gambardella
Veröffentlicht in: NAR Genomics and Bioinformatics, Volume 5, Ausgabe 1, March 2023,, 2023, ISSN 2631-9268
Herausgeber: Oxford University Press
DOI: 10.1093/nargab/lqad024

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

Autoren: Joris Cadow, Matteo Manica, Roland Mathis, Tiannan Guo, Ruedi Aebersold, María Rodríguez Martínez
Veröffentlicht in: Bioinformatics, Ausgabe Volume 37, Ausgabe Supplement_1, July 2021, 2021, Seite(n) i245–i253, ISSN 1367-4803
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Nature Communications, 2024, ISSN 2041-1723
Herausgeber: Nature Publishing Group
DOI: 10.1101/2023.01.19.524736

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

Autoren: 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
Veröffentlicht in: Genome Biology, 2023, ISSN 1474-760X
Herausgeber: Springer Nature
DOI: 10.1186/s13059-023-03016-6

Pan-cancer proteomic map of 949 human cell lines

Autoren: 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
Veröffentlicht in: Cancer Cell, 2022, ISSN 1535-6108
Herausgeber: Cell Press
DOI: 10.1016/j.ccell.2022.06.010

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

Autoren: 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
Veröffentlicht in: scientific reports, Ausgabe 11, Article number: 2967 (2021), 2021, ISSN 2045-2322
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Nature Communications, Ausgabe 7, 2022, ISSN 2041-1723
Herausgeber: Nature Publishing Group
DOI: 10.1038/s41467-022-31574-z

FUNKI: Interactive functional footprint-based analysis of omics data

Autoren: Rosa Hernansaiz-Ballesteros; Christian H. Holland; Aurelien Dugourd; Julio Saez-Rodriguez
Veröffentlicht in: Bioinformatics, 2021, ISSN 1367-4803
Herausgeber: Oxford University Press
DOI: 10.5281/zenodo.5779097

Restoration of the molecular clock is tumor suppressive in neuroblastoma

Autoren: 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
Veröffentlicht in: nature communications, Ausgabe 12, Article number: 4006 (2021), 2021, ISSN 2041-1723
Herausgeber: Nature Publishing Group
DOI: 10.1038/s41467-021-24196-4

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

Autoren: 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
Veröffentlicht in: Nature Biotechnology, 2021, Seite(n) 1453-1465, ISSN 1087-0156
Herausgeber: Nature Publishing Group
DOI: 10.5281/zenodo.5909808

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

Autoren: Srikanth S. Manda, Zainab Noor, Peter G. Hains, Qing Zhong
Veröffentlicht in: Current Protocols, Ausgabe 1/3, 2021, ISSN 2691-1299
Herausgeber: Current Protocols in Bioinformatics
DOI: 10.1002/cpz1.69

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

Autoren: 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
Veröffentlicht in: Cell Reports, 2022, ISSN 2211-1247
Herausgeber: Cell Press
DOI: 10.1016/j.celrep.2022.110988

Benchmarking of cell type deconvolution pipelines for transcriptomics data.

Autoren: Avila Cobos, Francisco; Alquicira-Hernandez, José; Powell, Joseph E.; Mestdagh, Pieter; De Preter, Katleen
Veröffentlicht in: Nature Communications, Ausgabe 1, 2020, ISSN 2041-1723
Herausgeber: Nature Publishing Group
DOI: 10.1038/s41467-020-19015-1

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

Autoren: Anna Niarakis, Juilee Thakar, Matteo Barberis, María Rodríguez Martínez, Tomáš Helikar, Marc Birtwistle, Claudine Chaouiya, Laurence Calzone, Andreas Dräger
Veröffentlicht in: Bioinformatics, 2022, ISSN 1367-4803
Herausgeber: 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

Autoren: 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,
Veröffentlicht in: Neoplasia, 2022, ISSN 1522-8002
Herausgeber: Elsevier BV
DOI: 10.1016/j.neo.2022.100846

Proteomic-based stratification of intermediate-risk prostate cancer patients

Autoren: 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,
Veröffentlicht in: 2023 Life Science Alliance LLC, February 2024 | Volume 7, No. 2, 2024, ISSN 2575-1077
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Science Advances, Ausgabe 7/6, 2021, Seite(n) eabd3311, ISSN 2375-2548
Herausgeber: Science Advances
DOI: 10.1126/sciadv.abd3311

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

Autoren: 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
Veröffentlicht in: Medical Image Analysis, Ausgabe 1, 2022, ISSN 1361-8415
Herausgeber: Elsevier BV
DOI: 10.1016/j.media.2022.102677

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

Autoren: Carolina Armengol, Stefano Cairo, Roland Kappler
Veröffentlicht in: Hepatoma Research, 2021, ISSN 2454-2520
Herausgeber: HEPATOMA RESEARCH
DOI: 10.20517/2394-5079.2021.19

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

Autoren: 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
Veröffentlicht in: BMC Bioinformatics, Ausgabe 22, Article number: 473 (2021), 2021, ISSN 1471-2105
Herausgeber: BioMed Central
DOI: 10.1186/s12859-021-04381-4

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

Autoren: 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
Veröffentlicht in: Nature Communications, 2022, ISSN 2041-1723
Herausgeber: Nature Publishing Group
DOI: 10.1038/s41467-022-31331-2

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

Autoren: Davide Cirillo, Iker Núñez‐Carpintero, Alfonso Valencia
Veröffentlicht in: Molecular Oncology, Ausgabe 15/4, 2021, Seite(n) 817-829, ISSN 1574-7891
Herausgeber: Elsevier BV
DOI: 10.1002/1878-0261.12920

Inferring clonal composition from multiple tumor biopsies

Autoren: 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
Veröffentlicht in: npj Systems Biology and Applications, Ausgabe 6/1, 2020, ISSN 2056-7189
Herausgeber: npj Sytems Biology and Applications
DOI: 10.1038/s41540-020-00147-5

MonoNet: Enhancing interpretability in neural networks via Monotonic Features

Autoren: An-phi Nguyen, Dana Lea Moreno, Nicolas Le Bel, Maria Rodriguez Martinez
Veröffentlicht in: Bioinformatics Advances, 2023, ISSN 2635-0041
Herausgeber: Oxford University Press
DOI: 10.1093/bioadv/vbad016

Epigenetic footprint enables molecular risk stratification of hepatoblastoma with clinical implications

Autoren: 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
Veröffentlicht in: Journal of Hepatology, Ausgabe 73/2, 2020, Seite(n) 328-341, ISSN 0168-8278
Herausgeber: Elsevier BV
DOI: 10.1016/j.jhep.2020.03.025

PaccMann: a web service for interpretable anticancer compound sensitivity prediction

Autoren: Joris Cadow, Jannis Born, Matteo Manica, Ali Oskooei, María Rodríguez Martínez
Veröffentlicht in: Nucleic Acids Research, Ausgabe 48/W1, 2020, Seite(n) W502-W508, ISSN 0305-1048
Herausgeber: Oxford University Press
DOI: 10.1093/nar/gkaa327

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

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

Assessing reproducibility of matrix factorization methods in independent transcriptomes

Autoren: Laura Cantini, Ulykbek Kairov, Aurélien de Reyniès, Emmanuel Barillot, François Radvanyi, Andrei Zinovyev
Veröffentlicht in: Bioinformatics, Ausgabe 35/21, 2019, Seite(n) 4307-4313, ISSN 1367-4803
Herausgeber: Oxford University Press
DOI: 10.1093/bioinformatics/btz225

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

Autoren: 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
Veröffentlicht in: Blood Advances, Ausgabe 3/24, 2019, Seite(n) 4215-4227, ISSN 2473-9529
Herausgeber: The American Society of Hematology
DOI: 10.1182/bloodadvances.2019000499

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

Autoren: Filippo Castiglione, Dario Ghersi, Franco Celada
Veröffentlicht in: Frontiers in Immunology, Ausgabe 10, 2019, ISSN 1664-3224
Herausgeber: Frontiers in Immunology
DOI: 10.3389/fimmu.2019.01513

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

Autoren: Matteo Manica, Ali Oskooei, Jannis Born, Vigneshwari Subramanian, Julio Sáez-Rodríguez, María Rodríguez Martínez
Veröffentlicht in: Molecular Pharmaceutics, Ausgabe 16/12, 2019, Seite(n) 4797-4806, ISSN 1543-8384
Herausgeber: American Chemical Society
DOI: 10.1021/acs.molpharmaceut.9b00520

Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets

Autoren: 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
Veröffentlicht in: International Journal of Molecular Sciences, Ausgabe 20/18, 2019, Seite(n) 4414, ISSN 1422-0067
Herausgeber: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms20184414

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

Autoren: 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
Veröffentlicht in: Cell Reports, Ausgabe 30/6, 2020, Seite(n) 1767-1779.e6, ISSN 2211-1247
Herausgeber: Cell Press
DOI: 10.1016/j.celrep.2020.01.049

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats

Autoren: Irina Balaur, Ludovic Roy, Alexander Mazein, S Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Zinovyev
Veröffentlicht in: Bioinformatics, Ausgabe 36/8, 2020, Seite(n) 2620-2622, ISSN 1367-4803
Herausgeber: Oxford University Press
DOI: 10.1093/bioinformatics/btz969

Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph

Autoren: Luca Albergante, Evgeny Mirkes, Jonathan Bac, Huidong Chen, Alexis Martin, Louis Faure, Emmanuel Barillot, Luca Pinello, Alexander Gorban, Andrei Zinovyev
Veröffentlicht in: Entropy, Ausgabe 22/3, 2020, Seite(n) 296, ISSN 1099-4300
Herausgeber: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/e22030296

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

Autoren: 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
Veröffentlicht in: Molecular Cell, 2022, Seite(n) P2458-2471.E9, ISSN 1097-2765
Herausgeber: 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.

Autoren: Andrei Zinovyev
Veröffentlicht in: Physics of Life Reviews, 2021, Seite(n) 132-134, ISSN 1571-0645
Herausgeber: 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

Autoren: Dylan XavierNatasha LucasSteven G WilliamsJennifer M. S. KohKeith AshmanClare LoudonRoger ReddelPeter G. HainsPhillip J. Robinson
Veröffentlicht in: Analytical Chemistry, 2023, ISSN 0003-2700
Herausgeber: American Chemical Society
DOI: 10.1101/2023.09.27.559846

The Multiple Dimensions of Networks in Cancer: A Perspective

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

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

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

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

Autoren: Paola Stolfi, Luigi Manni, Marzia Soligo, Davide Vergni, Paolo Tieri
Veröffentlicht in: Frontiers in Cell and Developmental Biology, Ausgabe 8, 2020, ISSN 2296-634X
Herausgeber: Front Cell Dev Biol.
DOI: 10.3389/fcell.2020.545089

FPGA Accelerated Analysis of Boolean Gene Regulatory Networks

Autoren: Matteo Manica, Raphael Polig, Mitra Purandare, Roland Mathis, Christoph Hagleitner, Maria Rodriguez Martinez
Veröffentlicht in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, Ausgabe 17/6, 2020, Seite(n) 2141-2147, ISSN 1545-5963
Herausgeber: 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

Autoren: Jannis Born, Matteo Manica, Joris Cadow, Greta Markert, Nil Adell Mill, Modestas Filipavicius, Nikita Janakarajan, Antonio Cardinale, Teodoro Laino, María Rodríguez Martínez
Veröffentlicht in: Machine Learning: Science and Technology, Ausgabe 2/2, 2021, Seite(n) 025024, ISSN 2632-2153
Herausgeber: Machine Learning: Science and Technology
DOI: 10.1088/2632-2153/abe808

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

Autoren: Salih Demir, Negin Razizadeh, Emilie Indersie, Sophie Branchereau, Stefano Cairo, Roland Kappler
Veröffentlicht in: Hepatology Communications, 2024, ISSN 2471-254x
Herausgeber: Hepatology Communications
DOI: 10.1097/hc9.0000000000000378

Two opposing gene expression patterns within ATRX aberrant neuroblastoma

Autoren: 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
Veröffentlicht in: PLOS ONE, 2023, ISSN 1932-6203
Herausgeber: 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

Autoren: Zinovyev A, Sadovsky M, Calzone L, Fouche A, Groeneveld CS, Chervov A, Barillot E, Gorban AN
Veröffentlicht in: Frontiers in Molecular Biosciences, 2022, ISSN 2296-889X
Herausgeber: Lausanne: Frontiers Media S.A.,
DOI: 10.3389/fmolb.2021.793912

Deep learning in systems medicine

Autoren: 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
Veröffentlicht in: Briefings in Bioinformatics, Ausgabe Volume 22, Ausgabe 2, March 2021, 2021, Seite(n) 1543–1559, ISSN 1477-4054
Herausgeber: Oxford University Press
DOI: 10.1093/bib/bbaa237

Methylation data imputation performances under different representations and missingness patterns

Autoren: Pietro Di Lena, Claudia Sala, Andrea Prodi, Christine Nardini
Veröffentlicht in: BMC Bioinformatics, Ausgabe 21/1, 2020, ISSN 1471-2105
Herausgeber: 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).

Autoren: 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
Veröffentlicht in: Journal for ImmunoTherapy of Cancer, Ausgabe 9/5, 2021, Seite(n) e002694, ISSN 2051-1426
Herausgeber: 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

Autoren: 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.
Veröffentlicht in: PNAS, Ausgabe 1, 2021, ISSN 0027-8424
Herausgeber: 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)

Autoren: Akila J Seneviratne, Sean Peters, David Clarke, Michael Dausmann, Michael Hecker, Brett Tully, Peter G Hains, Qing Zhong
Veröffentlicht in: Bioinformatics, Ausgabe Volume 37, Ausgabe 24, 2021, Seite(n) 4719-4726, ISSN 1367-4803
Herausgeber: Oxford University Press
DOI: 10.1093/bioinformatics/btab563

TITAN: T Cell Receptor Specificity Prediction with Bimodal Attention Networks

Autoren: Weber, Anna; Born, Jannis; Martínez, María Rodríguez
Veröffentlicht in: Bioinformatics, Ausgabe Volume 37, Ausgabe Supplement_1, July 2021, 2021, Seite(n) i237–i244, ISSN 1367-4803
Herausgeber: Oxford University Press
DOI: 10.1093/bioinformatics/btab294

The multilayer community structure of medulloblastoma

Autoren: Iker Núñez-Carpintero, Marianyela Petrizzelli, Andrei Zinovyev, Davide Cirillo, Alfonso Valencia
Veröffentlicht in: iScience, Ausgabe 24/4, 2021, Seite(n) 102365, ISSN 2589-0042
Herausgeber: iScience
DOI: 10.1016/j.isci.2021.102365

Machine learning for multi-omics data integration in cancer

Autoren: Zhaoxiang Cai, Rebecca C. Poulos, Jia Liu, Qing Zhong
Veröffentlicht in: iScience, Volume 25, Ausgabe 2, 2022, 103798, 2022, ISSN 2589-0042
Herausgeber: Elsevier Inc.
DOI: 10.1016/j.isci.2022.103798

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

Autoren: Iliana Papadopoulou, An-phi Nguyen, Anna Weber, Maria Rodriguez Martinez
Veröffentlicht in: Bioinformatics, 2022, ISSN 1460-2059
Herausgeber: Oxford University Press
DOI: 10.1093/bioinformatics/btac257

Quantitative proteomic studies addressing unmet clinical needs in sarcoma

Autoren: Elizabeth A. Connolly, Peter S. Grimison, Lisa G. Horvath, Phillip J. Robinson and Roger R. Reddel
Veröffentlicht in: Frontiers in Oncology, 2023, ISSN 2234-943X
Herausgeber: Frontiers Media S. A.
DOI: 10.3389/fonc.2023.1126736

Opportunities for pharmacoproteomics in biomarker discovery

Autoren: Rebecca C Poulos, Zhaoxiang Cai, Phillip J Robinson, Qing Zhong
Veröffentlicht in: Proteomics, Ausgabe 16159861, 2022, ISSN 1615-9861
Herausgeber: John Wiley & Sons
DOI: 10.1002/pmic.202200031

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

Autoren: Filippo Castiglione; Debashrito Deb; Anurag P. Srivastava; Pietro Liò; Arcangelo Liso
Veröffentlicht in: Front. Immunol., 07 September 2021 Sec. Viral Immunology Volume 12 - 2021, Ausgabe 15, 2021, ISSN 1664-3224
Herausgeber: Frontiers in Immunology
DOI: 10.17863/cam.75782

Scalable Inference in Graph-coupled Continuous-time Markov Chains

Autoren: Linzner, Dominik
Veröffentlicht in: Ausgabe 1, 2021
Herausgeber: TUprints
DOI: 10.12921/tuprints-00017403

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

Autoren: Lena, Pietro Di; Sala, Claudia; Prodi, Andrea; Nardini, Christine
Veröffentlicht in: Ausgabe 1, 2020
Herausgeber: Springer
DOI: 10.6084/m9.figshare.12585955

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

Autoren: Lena, Pietro Di; Sala, Claudia; Prodi, Andrea; Nardini, Christine
Veröffentlicht in: 2020
Herausgeber: Springer Nature
DOI: 10.6084/m9.figshare.12585952.v1

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

Autoren: An-phi Nguyen, Maria Rodriguez Martinez
Veröffentlicht in: 2021
Herausgeber: arXiv
DOI: 10.48550/arxiv.2106.10086

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

Autoren: Lena, Pietro Di; Sala, Claudia; Prodi, Andrea; Nardini, Christine
Veröffentlicht in: 2020
Herausgeber: Springer
DOI: 10.6084/m9.figshare.12585958.v1

Trajectories, bifurcations and pseudotime in large clinical datasets

Autoren: Sergey E. Golovenkin, Jonathan Bac, Alexander Chervov, Evgeny M. Mirkes, Yuliya V. Orlova, Emmanuel Barillot, Alexander N. Gorban and Andrei Zinovyev
Veröffentlicht in: 2020
Herausgeber: 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

Autoren: 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
Veröffentlicht in: 2021
Herausgeber: bioRxiv
DOI: 10.1101/2021.10.27.465137

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

Autoren: 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
Veröffentlicht in: Ausgabe 7, 2019
Herausgeber: 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

Autoren: 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
Veröffentlicht in: Ausgabe 12, 2021
Herausgeber: Springer Nature
DOI: 10.6084/m9.figshare.16726873

Computational challenges of cell cycle analysis using single cell transcriptomic data

Autoren: Alexander Chervov, Andrei Zinovyev
Veröffentlicht in: 2022
Herausgeber: arXiv
DOI: 10.48550/arxiv.2208.05229

Isotropic Gaussian Processes on Finite Spaces of Graphs

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

Active Learning of Continuous-time Bayesian Networks through Interventions

Autoren: "Dominik Linzner, Heinz Koeppl """
Veröffentlicht in: 2021
Herausgeber: 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

Autoren: Alexander Chervov; Andrei Zinovyev
Veröffentlicht in: Crossref, Ausgabe 6, 2021
Herausgeber: Zenodo
DOI: 10.1109/ijcnn52387.2021.9534249

Aligned Diffusion Schrödinger Bridges

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

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

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

Image Synthesis as a Pretext for Unsupervised Histopathological Diagnosis

Autoren: Stepec, D.; Skocaj, D.
Veröffentlicht in: Ausgabe 1, 2020
Herausgeber: Springer
DOI: 10.5281/zenodo.4288328

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

Autoren: Dominik Linzner Michael Schmidt Heinz Koeppl
Veröffentlicht in: 33rd Conference on Neural Information Processing Systems (NeurIPS 2019), 2019
Herausgeber: NIPS

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

Autoren: Dominik Linzner Heinz Koeppl
Veröffentlicht in: Association for the Advancement of Artificial Intelligence, 2019
Herausgeber: Association for the Advancement of Artificial Intelligence

Continuous-Time Bayesian Networks with Clocks

Autoren: Engelmann, Nikolai; Linzner, Dominik; Koeppl, Heinz
Veröffentlicht in: Ausgabe 10, 2020
Herausgeber: 37th International Conference on Machine Learning (ICML)
DOI: 10.5281/zenodo.3957199

PaccMannRL: Designing anticancer drugs from transcriptomic data via reinforcement learning

Autoren: Jannis Born, Matteo Manica, Ali Oskooei, María Rodríguez Martínez
Veröffentlicht in: 2019
Herausgeber: 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

Autoren: Dejan Štepec, Danijel Skočaj
Veröffentlicht in: 2020, ISBN 9789-612863371
Herausgeber: University of Maribor Press
DOI: 10.18690/978-961-286-337-1

Why is the winner the best

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

Is Attention Interpretation? A Quantitative Assessment On Sets

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

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

Autoren: Dejan Stepec, Danijel Skocaj
Veröffentlicht in: 2021
Herausgeber: 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

Autoren: Álvaro García Faura, Dejan Štepec, Tomaž Martinčič, Danijel Skočaj
Veröffentlicht in: 2021
Herausgeber: arXiv.org

Systems biology analysis for Ewing sarcoma

Autoren: Petrizzelli, Marianyela; Merlevede, Jane; Zinovyev, Andrei
Veröffentlicht in: Ausgabe 2, 2020, ISBN 978-1-0716-1019-0
Herausgeber: Springer
DOI: 10.5281/zenodo.3952244

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

Autoren: Ali Oskooei, Sophie Mai Chau, Jonas Weiss, Arvind Sridhar, María Rodríguez Martínez, Bruno Michel
Veröffentlicht in: Explainable AI in Healthcare and Medicine, 2021, Seite(n) 93-105, ISBN 978-3-030-53352-6
Herausgeber: Springer

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