Publications

Publications

Title: DEEP LEARNING FOR COMPUTATIONAL BIOLOGY

Authors: Christof Angermueller, Tanel Pärnamaa, Leopold Parts, Oliver Stegle

Published online 29.07.2016 Molecular Systems Biology (2016) 12, 878

 

Title: BAYESIAN INFERENCE OF CANCER DRIVER GENES USING SIGNATURES OF POSITIVE SELECTION

Authors: Luis Zapata, Hana Susak, Oliver Drechsel, Marc R. Friedländer, Xavier Estivill, and Stephan Ossowski

This article is a preprint and has not been peer-reviewed

 

Title: SIGNATURES OF POSITIVE SELECTION REVEAL A UNIVERSAL ROLE OF CHROMATIN MODIFIERS AS CANCER DRIVER GENES

Authors: Luis Zapata, Hana Susak, Oliver Drechsel, Marc R. Friedländer, Xavier Estivill, and Stephan Ossowski

Published online 2017 Oct 13 at Sci Rep. 2017; 7: 13124

 

Title: GERMLINE DETERMINANTS OF THE SOMATIC MUTATION LANDSCAPE IN 2,642 CANCER GENOMES

Authors: Sebastian M. Waszak, Grace Tiao, Bin Zhu, Tobias Rausch, Francesc Muyas, Bernardo Rodriguez-Martin, Raquel Rabionet, Sergei Yakneen, Georgia Escaramis, Yilong Li, Natalie Saini, Steven A. Roberts, German M. Demidov, Esa Pitkanen, Olivier Delaneau, Jose M. Heredia-Genestar, Joachim Weischenfeldt, Suyash S. Shringarpure, Jieming Chen, Hidewaki Nakagawa, Ludmil B. Alexandrov, Oliver Drechsel, L. Jonathan Dursi, Ayellet V. Segre, Erik Garrison, Serap Erkek, Nina Habermann, Lara Urban, Ekta Khurana, Andy Cafferkey, Shuto Hayashi, Seiya Imoto, Lauri A. Aaltonen, Eva G. Alvarez, Adrian Baez-Ortega, Matthew Bailey, Mattia Bosio, Alicia L. Bruzos, Ivo Buchhalter, Carlos D. Bustamante, Claudia Calabrese, Anthony DiBiase, Mark Gerstein, Aliaksei Z. Holik, Xing Hua, Kuan-lin Huang, Ivica Letunic, Leszek J. Klimczak, Roelof Koster, Sushant Kumar, Mike McLellan, Jay Mashl, Lisa Mirabello, Steven Newhouse, Aparna Prasad, Gunnar Raetsch, Matthias Schlesner, Roland Schwarz, Pramod Sharma, Tal Shmaya, Nikos Sidiropoulos, Lei Song, Hana Susak, Tomas Tanskanen, Marta Tojo, David C. Wedge, Mark Wright, Ying Wu, Kai Ye, Venkata D. Yellapantula, Jorge Zamora, Atul J. Butte, Gad Getz, Jared Simpson, Li Ding, Tomas Marques-Bonet, Arcadi Navarro, Alvis Brazma, Peter Campbell, Stephen J. Chanock, Nilanjan Chatterjee, Oliver Stegle, Reiner Siebert, Stephan Ossowski, Olivier Harismendy, Dmitry A. Gordenin, Jose M. C. Tubio, Francisco M. De La Vega, Douglas F. Easton, Xavier Estivill, Jan Korbel, PCAWG Germline Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Net

This article is a preprint and has not been peer-reviewed

 

Title: ASSESSING THE GENE REGULATORY LANDSCAPE IN 1,188 HUMAN TUMORS

Authors: PCAWG Transcriptome Core Group, Claudia Calabrese, Natalie R Davidson, Nuno A Fonseca, Yao He, André Kahles, Kjong-Van Lehmann, Fenglin Liu, Yuichi Shiraishi, Cameron M Soulette, Lara Urban, Deniz Demircioğlu, Liliana Greger, Siliang Li, Dongbing Liu, Marc D Perry, Linda Xiang, Fan Zhang, Junjun Zhang, Peter Bailey, Serap Erkek, Katherine A Hoadley, Yong Hou, Helena Kilpinen, Jan O Korbel, Maximillian G Marin, Julia Markowski, Tannistha Nandi, Qiang Pan-Hammarström, Chandra Sekhar Pedamallu, Reiner Siebert, Stefan G Stark, Hong Su, Patrick Tan, Sebastian M Waszak, Christina Yung, Shida Zhu, PCAWG Transcriptome Working Group, Philip Awadalla, Chad J Creighton, Matthew Meyerson, B.F. Francis Ouellette, Kui Wu, Huanming Yang, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network, Alvis Brazma, Angela N Brooks, Jonathan Göke, Gunnar Rätsch, Roland F Schwarz, Oliver Stegle, Zemin Zhang

This article is a preprint and has not been peer-reviewed

 

Title: COMBINED SINGLE CELL PROFILING OF EXPRESSION AND DNA METHYLATION REVEALS SPLICING REGULATION AND HETEROGENEITY

Authors: Stephanie Linker, Lara Urban, Stephen Clark, Mariya Chhatriwala, Shradha Amatya, Davis McCarthy, Ingo Ebersberger, Ludovic Vallier, Wolf Reik, Oliver Stegle1, Marc Jan Bonder

This article is a preprint and has not been peer-reviewed

 

Title: NEGATIVE SELECTION IN TUMOR GENOME EVOLUTION ACTS ON ESSENTIAL CELLULAR FUNCTIONS AND THE IMMUNOPEPTIDOME

Authors: Luis Zapata, Oriol Pich, Luis Serrano, Fyodor A. Kondrashov, Stephan Ossowski and Martin H. Schaefer

Published: 31 May 2018

 

Title: ALLELE BALANCE BIAS IDENTIFIES SYSTEMATIC GENOTYPING ERRORS AND FALSE DISEASE ASSOCIATIONS

Authors: Francesc Muyas, Mattia Bosio, Anna Puig, Hana Susak, Laura Domènech‐Salgado, Georgia Escaramis, Luis Zapata, German Demidov, Xavier Estivill, Raquel Rabionet, Stephan Ossowski

Published: 24 October 2018

 

Comunications & Posters

 

Title: SIGNATURES OF POSITIVE AND NEGATIVE SELECTION IDENTIFY CANCER DRIVER GENES

Authors: Zapata L., Susak H. & Ossowski S.

Presented atthe Cancer Genomics Conference (Heidelberg), November 2015

 

Title: eDiVA: EXOME SEQUENCING ANALYSIS PIPELINE FOR DISEASE GENE IDENTIFICATION.

Authors: Bosio M., Drechsel O., Rahman R., Ossowski S.

Presented at NGS2016 (Barcelona, Spain)

 

Title: eDiVA: EXOME SEQUENCING ANALYSIS PIPELINE FOR DISEASE GENE IDENTIFICATION.

Authors: Poster presentation Bosio M., Drechsel O., Rahman R., Ossowski S.

Presented in 2016 at the Biology of Genomes Meeting (Cold Spring Harbor, US)

 

Title: IMPLEMENTATION OF A MULTI-GENE PANEL TESTING FOR HEREDITARY CANCER (QCANCERISK) IN A HEREDITARY CANCER AND GENETIC COUNSELLING UNIT

Authors: Palacios-Verdú MG, Abulí A; Rodríguez-Santiago B; Armengol L; Fábregas R; Cusidó M; Estivill X

Presented in 2017 at the American Society of Human Genetics meeting (Vancouver, Canada).

 

Title: NEW DNA BINDING SITE IN BRCA2 THAT MEDIATES HOMOLOGOUS RECOMBINATION

Author: Aura Carreira

Presented at the Fusion Conference: 2nd DNA replication as a source of DNA damage: From Molecules to Human Health Conference (Rome, Italy), July 2017

 

Title: CLINCNV: LARGE-SCALE GERMLINE CNV DISCOVERY IN THE PCAWG COHORT

Author: German Demidov

Presented at the Cancer Genomics  Meeting 2017 (Heidelberg, Germany).

 

Title: CONTROL OF THE EXTENT OF DNA SYNTHESIS DURING MEIOTIC RECOMBINATION

Author:Valerie Borde

Presented at the Abcam Mechanisms of Recombination meeting (London, UK), May 2018

 

Title: ASSESSING THE IMPACT OF GENE REGULATORY VARIATION ON MUTATIONAL PROCESSES ACTIVE IN CÁNCER

Author: Urban, Lara

Presented at the Biology of Genomes 2018 meeting (Cold Spring Harbour, USA)

 

Title: PanCanRisk’s RESULTS

Author: Ceres Fernández-Rozadilla

Conference at the V edition Biomedical Cancer Research Conference (A Coruña, Spain), October 2018

 

Participation to a workshop

  • Genomics on the Move workshop on NGS based cancer diagnostics. WITS University Johannesburg (South Africa), September 2015
  • PAWG F2F Meeting (Cambridge, UK), October 2015
  • 11th ICGC Scientific Workshop (Mumbai, India ), December 2015
  • Computational Cancer Workshop (Berkeley), February 2016
  • PCAWG F2F Meeting (Barcelona), April 2016
  • NGS Workshop at FAPESP – EU Life Meeting (Sao Paulo, Brazil), June 2016
  • 12th Scientific Workshop of the International Cancer Genome Consortium (ICGC) (Boston, USA), September 2016