Publications

Genomic basis for RNA alterations in cancer

Authors (1461)

Claudia Calabrese
Natalie R Davidson
Deniz Demircioğlu
Nuno A Fonseca
Yao He
André Kahles
[...]
Marc J van de Vijver
L van’t Veer
Christian von Mering
PCAWG Transcriptome Core Group
PCAWG Consortium

Nature

Published 6 February 2020

Crick labs

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Genomic footprints of activated telomere maintenance mechanisms in cancer

Authors (1413)

Lina Sieverling
Chen Hong
Sandra D Koser
Philip Ginsbach
Kortine Kleinheinz
Barbara Hutter
[...]
Nicholas van As
Carolien HM van Deurzen
Marc J van de Vijver
L van’t Veer
Christian von Mering

Nature Communications

Published 5 February 2020

Crick labs

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High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

Authors (12)

Yiqun Zhang
Fengju Chen
Nuno A Fonseca
Yao He
Masashi Fujita
Hidewaki Nakagawa
[...]
Alvis Brazma
PCAWG Transcriptome Working Group
PCAWG Structural Variation Working Group
Chad J Creighton
PCAWG Consortium

Nature Communications

Published 5 February 2020

Crick labs

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Inferring structural variant cancer cell fraction

Authors (11)

Marek Cmero
Ke Yuan
Cheng Soon Ong
Jan Schröder
PCAWG Evolution and Heterogeneity Working Group
Niall M Corcoran
Tony Papenfuss
Christopher M Hovens
Florian Markowetz
Geoff Macintyre
PCAWG Consortium

Nature Communications

Published 5 February 2020

Crick labs

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Integrative pathway enrichment analysis of multivariate omics data

Authors (1459)

Marta Paczkowska
Jonathan Barenboim
Nardnisa Sintupisut
Natalie S Fox
Helen Zhu
Diala Abd-Rabbo
[...]
Nicholas van As
Carolien HM van Deurzen
Marc J van de Vijver
L van’t Veer
Christian von Mering

Nature Communications

Published 5 February 2020

Crick labs

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Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

Authors (53)

Bernardo Rodriguez-Martin
Eva G Alvarez
Adrian Baez-Ortega
Jorge Zamora
Fran Supek
Jonas Demeulemeester
[...]
Kathleen H Burns
PCAWG Structural Variation Working Group
Peter J Campbell
Jose MC Tubio
PCAWG Consortium

Nature Genetics

Published 1 March 2020

Crick labs

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Pan-cancer analysis of whole genomes

Authors (1)

ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium

Nature

Published 5 February 2020

Crick labs

Peter Van Loo

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Pathway and network analysis of more than 2500 whole cancer genomes

Authors (1453)

Matthew A Reyna
David Haan
Marta Paczkowska
Lieven PC Verbeke
Miguel Vazquez
Abdullah Kahraman
[...]
Nicholas van As
Carolien HM van Deurzen
Marc J van de Vijver
L van’t Veer
Christian von Mering

Nature Communications

Published 5 February 2020

Crick labs

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Patterns of somatic structural variation in human cancer genomes

Authors (1411)

Yilong Li
Nicola D Roberts
Jeremiah A Wala
Ofer Shapira
Steven E Schumacher
Kiran Kumar
[...]
Carolien HM van Deurzen
Marc J van de Vijver
L van’t Veer
Christian von Mering
PCAWG Consortium

Nature

Published 6 February 2020

Crick labs

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Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig

Authors (10)

Yulia Rubanova
Ruian Shi
Caitlin F Harrigan
Roujia Li
Jeff Wintersinger
Nil Sahin
Amit Deshwar
PCAWG Evolution and Heterogeneity Working Group
Quaid Morris
PCAWG Consortium

Nature Communications

Published 5 February 2020

Crick labs

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The evolutionary history of 2,658 cancers

Authors (48)

Moritz Gerstung
Clemency Jolly
Ignaty Leshchiner
Stefan C Dentro
Santiago Gonzalez
Daniel Rosebrock
[...]
PCAWG Evolution & Heterogeneity Working Group
Paul T Spellman
David C Wedge
Peter Van Loo
PCAWG Consortium

Nature

Published 6 February 2020

Crick labs/ facilities

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The landscape of viral associations in human cancers

Authors (15)

Marc Zapatka
Ivan Borozan
Daniel S Brewer
Murat Iskar
Adam Grundhoff
Malik Alawi
[...]
Colin S Cooper
Roland Eils
Vincent Ferretti
Peter Lichter
PCAWG Consortium

Nature Genetics

Published 2 March 2020

Crick labs

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The repertoire of mutational signatures in human cancer

Authors (1383)

Ludmil B Alexandrov
Jaegil Kim
Nicholas J Haradhvala
Mi Ni Huang
Alvin Wei Tian Ng
Yang Wu
[...]
Nicholas van As
Carolien HM van Deurzen
Marc J van de Vijver
L van’t Veer
Christian von Mering

Nature

Published 6 February 2020

Crick labs

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A community effort to create standards for evaluating tumor subclonal reconstruction

Authors (33)

Adriana Salcedo
Maxime Tarabichi
Shadrielle Melijah G Espiritu
Amit G Deshwar
Matei David
Nathan M Wilson
[...]
Kyle Ellrott
David C Wedge
Quaid Morris
Peter Van Loo
Paul C Boutros

Nature Biotechnology

Published 9 January 2020

Crick labs

Peter Van Loo

Full details

Investigation of somatic CNVs in brains of synucleinopathy cases using targeted SNCA analysis and single cell sequencing

Authors (16)

Diego Perez-Rodriguez
Maria Kalyva
Melissa Leija-Salazar
Tammaryn Lashley
Maxime Tarabichi
Viorica Chelban
[...]
Anthony HV Schapira
Thomas T Warner
Janice L Holton
Zane Jaunmuktane
Christos Proukakis

Acta Neuropathologica Communications

Published 23 December 2019

Crick labs

Peter Van Loo

Full details

Translating insights into tumor evolution to clinical practice: promises and challenges

Authors (2)

Genome Medicine

Published 29 March 2019

Crick labs

Peter Van Loo

Full details

Neoantigen-directed immune escape in lung cancer evolution

Authors (29)

Rachel Rosenthal
Elizabeth Larose Cadieux
Roberto Salgado
Maise Al Bakir
David A Moore
Crispin T Hiley
[...]
Peter Van Loo
Stephan Beck
Nicholas McGranahan
Charles Swanton
The TRACERx Consortium

Nature

Published 20 March 2019

Crick labs/ facilities

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Undifferentiated sarcomas develop through distinct evolutionary pathways

Authors (25)

Christopher D Steele
Maxime Tarabichi
Dahmane Oukrif
Amy P Webster
Hongtao Ye
Matthew Fittall
[...]
Peter J Campbell
Ludmil B Alexandrov
Peter Van Loo
Adrienne M Flanagan
Nischalan Pillay

Cancer Cell

Published 18 March 2019

Crick labs

Peter Van Loo

Full details

Time series analysis of neoadjuvant chemotherapy and bevacizumab-treated breast carcinomas reveals a systemic shift in genomic aberrations

Authors (19)

Elen Kristine Höglander
Silje Nord
David C Wedge
Ole Christian Lingjaerde
Laxmi Silwal-Pandit
Hedda vdL Gythfeldt
[...]
Bjørn Naume
Peter Van Loo
Anne-Lise Børresen-Dale
Olav Engebraaten
Vessela Kristensen

Genome Medicine

Published 29 November 2018

Crick labs

Peter Van Loo

Full details

Neutral tumor evolution?

Authors (11)

Maxime Tarabichi
Iñigo Martincorena
Moritz Gerstung
Armand M Leroi
Florian Markowetz
The PCAWG Evolution and Heterogeneity Working Group
Paul T Spellman
Quaid D Morris
Ole Christian Lingjærde
David C Wedge
Peter Van Loo

Nature Genetics

Published 29 October 2018

Crick labs

Peter Van Loo

Full details

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Genomic basis for RNA alterations in cancer

Genomic footprints of activated telomere maintenance mechanisms in cancer

High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

Inferring structural variant cancer cell fraction

Integrative pathway enrichment analysis of multivariate omics data

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

Pan-cancer analysis of whole genomes

Pathway and network analysis of more than 2500 whole cancer genomes

Patterns of somatic structural variation in human cancer genomes

Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig

The evolutionary history of 2,658 cancers

The landscape of viral associations in human cancers

The repertoire of mutational signatures in human cancer

A community effort to create standards for evaluating tumor subclonal reconstruction

Investigation of somatic CNVs in brains of synucleinopathy cases using targeted SNCA analysis and single cell sequencing

Translating insights into tumor evolution to clinical practice: promises and challenges

Neoantigen-directed immune escape in lung cancer evolution

Undifferentiated sarcomas develop through distinct evolutionary pathways

Time series analysis of neoadjuvant chemotherapy and bevacizumab-treated breast carcinomas reveals a systemic shift in genomic aberrations

Neutral tumor evolution?

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