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

Rezultaty

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

Recommended metadata standards and portal prototype

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Data-driven model for molecular targets and drug repositioning

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

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

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

Project quality plan

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

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

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

Internal and external IT communication infrastructure and project website

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

Publikacje

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

Autorzy: Captier, Nicolas; Merlevede, Jane; Molkenov, Askhat; Seisenova, Ainur; Zhubanchaliyev, Altynbek; Nazarov, Petr V.; Barillot, Emmanuel; Kairov, Ulykbek; Zinovyev, Andrei
Opublikowane w: Bioinformatics, Volume 38, Numer 10, 2022, Strona(/y) 2963–2964, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btac204

Emulating complex simulations by machine learning methods

Autorzy: Paola Stolfi & Filippo Castiglione
Opublikowane w: BMC Bioinformatics, Numer 22, Article number: 483 (2021), 2021, ISSN 1471-2105
Wydawca: 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

Autorzy: 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
Opublikowane w: Cancer Cell, Numer 39/6, 2021, Strona(/y) 810-826.e9, ISSN 1535-6108
Wydawca: 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

Autorzy: 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
Opublikowane w: Cell Reports, 2022, ISSN 2211-1247
Wydawca: 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

Autorzy: Pavel Sumazin, Dolores H. López-Terrada
Opublikowane w: Journal of Hepatology, 2021, ISSN 0168-8278
Wydawca: Elsevier BV
DOI: 10.1101/2021.07.15.445600

Estimage: a webserver hub for the computation of methylation age

Autorzy: Pietro Di Lena, Claudia Sala, Christine Nardini
Opublikowane w: Nucleic Acids Research, 2021, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkab426

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

Autorzy: 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
Opublikowane w: Hepatology, 2023, ISSN 0270-9139
Wydawca: John Wiley & Sons Inc.
DOI: 10.1097/hep.0000000000000601

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

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

Identification and experimental validation of druggable epigenetic targets in hepatoblastoma

Autorzy: 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
Opublikowane w: Journal of Hepatology, 2023, ISSN 1600-0641
Wydawca: EASL
DOI: 10.1016/j.jhep.2023.05.031

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

Autorzy: An-Phi Nguyen; Stefania Vasilaki; María Rodríguez Martínez
Opublikowane w: Briefings in Bioinformatics, 2023, ISSN 1477-4054
Wydawca: Oxford University Press
DOI: 10.1093/bib/bbad056

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

Autorzy: Gambardella G, Viscido G, Tumaini B, Isacchi A, Bosotti R, di Bernardo D
Opublikowane w: Nature Communication, Numer 13, Article number: 1714 (2022), 2022, ISSN 2041-1723
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Clinical Applications of Mass Spectrometry-Based Proteomics in Cancer: Where are we?

Autorzy: Emma L. Boys, Jia Liu, Phillip J Robinson, Roger R. Reddel
Opublikowane w: Proteomics, 2022, ISSN 1615-9861
Wydawca: 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

Autorzy: 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.
Opublikowane w: Cancer Cell, 2024, ISSN 1535-6108
Wydawca: Cell Press
DOI: 10.1016/j.ccell.2023.12.008

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

Autorzy: Enrico Santus, Nicola Marino, Davide Cirillo, Emmanuele Chersoni, Arnau Montagud, Antonella Santuccione Chadha, Alfonso Valencia, Kevin Hughes, Charlotta Lindvall
Opublikowane w: Journal of Medical Internet Research, Numer 23/3, 2021, Strona(/y) e22453, ISSN 1438-8871
Wydawca: Journal of medical Internet Research
DOI: 10.2196/22453

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

Autorzy: Sunil Kumar, Xiao-Kang Lun, Bernd Bodenmiller, María Rodríguez Martínez & Heinz Koeppl
Opublikowane w: Scientific Reports, Numer 10, Article number: 1233 (2020), 2020, ISSN 2045-2322
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Targeting the Unwindosome by Mebendazole Is a Vulnerability of Chemoresistant Hepatoblastoma

Autorzy: 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
Opublikowane w: Cancers, 2022, ISSN 2072-6694
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14174196

Chemical Representation Learning for Toxicity Prediction

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

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

Autorzy: 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
Opublikowane w: Molecular Cancer Therapeutics, 2023, ISSN 1535-7163
Wydawca: American Association for Cancer Research
DOI: 10.1158/1535-7163.mct-22-0335

CHAF1A Blocks Neuronal Differentiation and Promotes Neuroblastoma Oncogenesis via Metabolic Reprogramming

Autorzy: 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
Opublikowane w: Advanced Science, 2021, Strona(/y) e2005047, ISSN 2198-3844
Wydawca: Wiley
DOI: 10.1002/advs.202005047

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

Autorzy: Dejan Štepec; Danijel Skočaj
Opublikowane w: Uporabna informatika, Numer 1, 2021, ISSN 2630-435X
Wydawca: Slovenian Society Informatika
DOI: 10.31449/upinf.136

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

Autorzy: 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
Opublikowane w: Cancer Science, Numer 4, 2022, ISSN 1349-7006
Wydawca: John Wiley & Sons
DOI: 10.1111/cas.15363

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

Autorzy: 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
Opublikowane w: Bioinformatics, Numer Volume 37, Numer 21, 1 November 2021, 2021, Strona(/y) 3702–3706, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btab229

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

Autorzy: Florian Ingelfinger; Donatella De Feo; Burkhard Becher
Opublikowane w: Seminars in Immunology, Numer Volume 56, August 2021, 2021, ISSN 1044-5323
Wydawca: Academic Press
DOI: 10.1016/j.smim.2021.101518

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

Autorzy: Elisa Zappa, Alice Vitali, Kathleen Anders, Jan J Molenaar, Judith Wienke, Annette Künkele
Opublikowane w: European Journal of Cancer, 2023, ISSN 0959-8049
Wydawca: 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

Autorzy: Melania Franchini; Simona Pellecchia; Gaetano Viscido; Gennaro Gambardella
Opublikowane w: NAR Genomics and Bioinformatics, Volume 5, Numer 1, March 2023,, 2023, ISSN 2631-9268
Wydawca: Oxford University Press
DOI: 10.1093/nargab/lqad024

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

Autorzy: Joris Cadow, Matteo Manica, Roland Mathis, Tiannan Guo, Ruedi Aebersold, María Rodríguez Martínez
Opublikowane w: Bioinformatics, Numer Volume 37, Numer Supplement_1, July 2021, 2021, Strona(/y) i245–i253, ISSN 1367-4803
Wydawca: 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

Autorzy: 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
Opublikowane w: Nature Communications, 2024, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1101/2023.01.19.524736

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

Autorzy: 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
Opublikowane w: Genome Biology, 2023, ISSN 1474-760X
Wydawca: Springer Nature
DOI: 10.1186/s13059-023-03016-6

Pan-cancer proteomic map of 949 human cell lines

Autorzy: 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
Opublikowane w: Cancer Cell, 2022, ISSN 1535-6108
Wydawca: Cell Press
DOI: 10.1016/j.ccell.2022.06.010

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

Autorzy: 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
Opublikowane w: scientific reports, Numer 11, Article number: 2967 (2021), 2021, ISSN 2045-2322
Wydawca: 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

Autorzy: 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
Opublikowane w: Nature Communications, Numer 7, 2022, ISSN 2041-1723
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FUNKI: Interactive functional footprint-based analysis of omics data

Autorzy: Rosa Hernansaiz-Ballesteros; Christian H. Holland; Aurelien Dugourd; Julio Saez-Rodriguez
Opublikowane w: Bioinformatics, 2021, ISSN 1367-4803
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Restoration of the molecular clock is tumor suppressive in neuroblastoma

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

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Opublikowane w: Nature Biotechnology, 2021, Strona(/y) 1453-1465, ISSN 1087-0156
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PIONEER: Pipeline for Generating High‐Quality Spectral Libraries for DIA‐MS Data

Autorzy: Srikanth S. Manda, Zainab Noor, Peter G. Hains, Qing Zhong
Opublikowane w: Current Protocols, Numer 1/3, 2021, ISSN 2691-1299
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MacroH2As regulate enhancer-promoter contacts affecting enhancer activity and sensitivity to inflammatory cytokines

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Opublikowane w: Cell Reports, 2022, ISSN 2211-1247
Wydawca: Cell Press
DOI: 10.1016/j.celrep.2022.110988

Benchmarking of cell type deconvolution pipelines for transcriptomics data.

Autorzy: Avila Cobos, Francisco; Alquicira-Hernandez, José; Powell, Joseph E.; Mestdagh, Pieter; De Preter, Katleen
Opublikowane w: Nature Communications, Numer 1, 2020, ISSN 2041-1723
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Computational modelling in health and disease: highlights of the 6th annual SysMod meeting

Autorzy: Anna Niarakis, Juilee Thakar, Matteo Barberis, María Rodríguez Martínez, Tomáš Helikar, Marc Birtwistle, Claudine Chaouiya, Laurence Calzone, Andreas Dräger
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Wydawca: Oxford University Press
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The children's brain tumor network (CBTN) - Accelerating research in pediatric central nervous system tumors through collaboration and open science

Autorzy: 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,
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Proteomic-based stratification of intermediate-risk prostate cancer patients

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

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

Autorzy: 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
Opublikowane w: Medical Image Analysis, Numer 1, 2022, ISSN 1361-8415
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Bridging molecular basis, prognosis, and treatment of pediatric liver tumors

Autorzy: Carolina Armengol, Stefano Cairo, Roland Kappler
Opublikowane w: Hepatoma Research, 2021, ISSN 2454-2520
Wydawca: HEPATOMA RESEARCH
DOI: 10.20517/2394-5079.2021.19

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

Autorzy: 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
Opublikowane w: BMC Bioinformatics, Numer 22, Article number: 473 (2021), 2021, ISSN 1471-2105
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DOI: 10.1186/s12859-021-04381-4

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

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

Autorzy: Davide Cirillo, Iker Núñez‐Carpintero, Alfonso Valencia
Opublikowane w: Molecular Oncology, Numer 15/4, 2021, Strona(/y) 817-829, ISSN 1574-7891
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Inferring clonal composition from multiple tumor biopsies

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

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Quantitative proteomic studies addressing unmet clinical needs in sarcoma

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Scalable Inference in Graph-coupled Continuous-time Markov Chains

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

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

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

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

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

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

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Computational challenges of cell cycle analysis using single cell transcriptomic data

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Isotropic Gaussian Processes on Finite Spaces of Graphs

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Opublikowane w: 26th International Conference on Artificial Intelligence and Statistics (AISTATS), 2022
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Active Learning of Continuous-time Bayesian Networks through Interventions

Autorzy: "Dominik Linzner, Heinz Koeppl """
Opublikowane w: 2021
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Clinical trajectories estimated from bulk tumoral molecular profiles using elastic principal trees

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Aligned Diffusion Schrödinger Bridges

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

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Image Synthesis as a Pretext for Unsupervised Histopathological Diagnosis

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

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

Autorzy: Dominik Linzner Heinz Koeppl
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Continuous-Time Bayesian Networks with Clocks

Autorzy: Engelmann, Nikolai; Linzner, Dominik; Koeppl, Heinz
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PaccMannRL: Designing anticancer drugs from transcriptomic data via reinforcement learning

Autorzy: Jannis Born, Matteo Manica, Ali Oskooei, María Rodríguez Martínez
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ROSUS 2020 - Računalniška obdelava slik in njena uporaba v Sloveniji 2020: Zbornik 15. strokovne konference

Autorzy: Dejan Štepec, Danijel Skočaj
Opublikowane w: 2020, ISBN 9789-612863371
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Why is the winner the best

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Is Attention Interpretation? A Quantitative Assessment On Sets

Autorzy: Haab, Jonathan; Deutschmann, Nicolas; Martínez, Maria Rodríguez
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Unsupervised Detection of Cancerous Regions in Histology Imagery using Image-to-Image Translation

Autorzy: Dejan Stepec, Danijel Skocaj
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Segmentation of multiple myeloma plasma cells in microscopy images with noisy labels

Autorzy: Álvaro García Faura, Dejan Štepec, Tomaž Martinčič, Danijel Skočaj
Opublikowane w: 2021
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Systems biology analysis for Ewing sarcoma

Autorzy: Petrizzelli, Marianyela; Merlevede, Jane; Zinovyev, Andrei
Opublikowane w: Numer 2, 2020, ISBN 978-1-0716-1019-0
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DeStress: Deep Learning for Unsupervised Identification of Mental Stress in Firefighters from Heart-Rate Variability (HRV) Data

Autorzy: Ali Oskooei, Sophie Mai Chau, Jonas Weiss, Arvind Sridhar, María Rodríguez Martínez, Bruno Michel
Opublikowane w: Explainable AI in Healthcare and Medicine, 2021, Strona(/y) 93-105, ISBN 978-3-030-53352-6
Wydawca: Springer

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