Author details

Full Name

Jens Luebeck

Affiliation

University of California San Diego

ORCID

Career Start Year

2017

Papers

H Index

Expertise

CM4AI Collaborator

Trey Ideker (CM4AI)

PMID	Paper Title	Journal Title	Published Year
37162993	Transcriptional immune suppression and upregulation of double stranded DNA damage and repair repertoires in ecDNA-containing tumors.	bioRxiv	2023
37945900	Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma.	Nat Genet	2023
37503111	Coordinated inheritance of extrachromosomal DNA species in human cancer cells.	bioRxiv	2023
37425909	Immortalization and transformation of primary cells mediated by engineered ecDNAs.	bioRxiv	2023
37155843	Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneity.	Proc Natl Acad Sci U S A	2023
37046089	Extrachromosomal DNA in the cancerous transformation of Barrett's oesophagus.	Nature	2023
34930786	Plasticity of Extrachromosomal and Intrachromosomal BRAF Amplifications in Overcoming Targeted Therapy Dosage Challenges.	Cancer Discov	2022
35493723	FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA.	NAR Genom Bioinform	2022
35140399	Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA.	Nature	2022
34027500	FaNDOM: Fast nested distance-based seeding of optical maps.	Patterns (N Y)	2021
34819668	ecDNA hubs drive cooperative intermolecular oncogene expression.	Nature	2021
34548317	Extrachromosomal DNA in HPV-Mediated Oropharyngeal Cancer Drives Diverse Oncogene Transcription.	Clin Cancer Res	2021
32462051	CRISPR-Cas9 Gene Editing of Hematopoietic Stem Cells from Patients with Friedreich's Ataxia.	Mol Ther Methods Clin Dev	2020
32807987	Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers.	Nat Genet	2020
32873787	AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications.	Nat Commun	2020
30674876	Exploring the landscape of focal amplifications in cancer using AmpliconArchitect.	Nat Commun	2019
31706138	EcSeg: Semantic Segmentation of Metaphase Images Containing Extrachromosomal DNA.	iScience	2019
29226803	Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data.	Cell Syst	2018
29452643	Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis.	Mol Cell	2018
29579309	ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer.	Nucleic Acids Res	2018
28319113	Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions.	Nat Methods	2017

1 - 21 of 21

Julian M Hess

Broad Institute of MIT and Harvard

Career Start Year 2015

Number of shared co-authors 1

Stefan C Dentro

Wellcome Sanger Institute

Career Start Year 2012

Number of shared co-authors 1

Richard de Borja

The Hospital for Sick Children

Career Start Year 2012

Number of shared co-authors 1

Timothy Beck

Human Longevity Inc.

Career Start Year 2012

Number of shared co-authors 1

Matthew D Eldridge

Cancer Research UK Cambridge Institute, University of Cambridge

Career Start Year 2010

Number of shared co-authors 1

Andrew McPherson

Memorial Sloan Kettering Cancer Center

Career Start Year 2010

Number of shared co-authors 0

Rolf Kabbe

German Cancer Research Center (DKFZ)

Career Start Year 2010

Number of shared co-authors 1

Giovanni Ciriello

University of Lausanne (UNIL)

Career Start Year 2008

Number of shared co-authors 2

Lixing Yang

University of Chicago, USA University of Chicago Comprehensive Cancer Center

Career Start Year 2008

Number of shared co-authors 1

Ignaty Leshchiner

Broad Institute of Massachusetts Institute of Technology and Harvard

Career Start Year 2008

Number of shared co-authors 0

Ken Chen

University of Texas MD Anderson Cancer Center

Career Start Year 2007

Number of shared co-authors 3

Moritz Gerstung

German Cancer Research Centre DKFZ

Career Start Year 2007

Number of shared co-authors 1

David C Wedge

Manchester Cancer Research Centre, University of Manchester

Career Start Year 2006

Number of shared co-authors 5

Paz Polak

McGill University

Career Start Year 2006

Number of shared co-authors 1

David Jones

Wellcome Sanger Institute

Career Start Year 2005

Number of shared co-authors 2

Keiran Raine

Wellcome Sanger Institute

Career Start Year 2004

Number of shared co-authors 2

Matthias Schlesner

University of Augsburg

Career Start Year 2004

Number of shared co-authors 3

Chip Stewart

Broad Institute of MIT and Harvard

Career Start Year 2004

Number of shared co-authors 1

Sohrab P Shah

Memorial Sloan Kettering Cancer Center

Career Start Year 2003

Number of shared co-authors 2

Benjamin J Raphael

Princeton University

Career Start Year 2003

Number of shared co-authors 5

Trevor J Pugh

Princess Margaret Cancer Centre, University Health Network

Career Start Year 2003

Number of shared co-authors 5

Peter Van Loo

The Francis Crick Institute

Career Start Year 2003

Number of shared co-authors 4

Peter J Campbell

Wellcome Sanger Institute

Career Start Year 2003

Number of shared co-authors 5

Olivier Harismendy

University of California

Career Start Year 2003

Number of shared co-authors 13

Mark Maddison

Wellcome Sanger Institute

Career Start Year 2002

Number of shared co-authors 2

Jan O Korbel

European Bioinformatics Institute (EMBL-EBI)

Career Start Year 2001

Number of shared co-authors 8

Gad Getz

Broad Institute of the Massachusetts Institute of Technology and Harvard

Career Start Year 2000

Number of shared co-authors 8

Serena Nik-Zainal

Early Cancer Institute, University of Cambridge

Career Start Year 1999

Number of shared co-authors 2

Li Ding

McDonnell Genome Institute, Washington University School of Medicine

Career Start Year 1997

Number of shared co-authors 4

Adam Butler

Wellcome Sanger Institute

Career Start Year 1996

Number of shared co-authors 3

row(s) 1 - 30 of 30

Vineet Bafna

University of California San Diego

Co-authored papers 17

Paul S Mischel

Stanford University

Co-authored papers 13

Howard Y Chang

Center for Personal Dynamic Regulomes, Stanford University

Co-authored papers 4

Anton G Henssen

Co-authored papers 3

Prashant Mali (CM4AI)

University of California San Diego

Co-authored papers 3

Hannah Carter

University of California San Diego

Co-authored papers 2

Trey Ideker (CM4AI)

University of California San Diego

Co-authored papers 2

Amanda Birmingham

Center for Computational Biology & Bioinformatics , University of California

Co-authored papers 2

Dongxin Zhao

University of California

Co-authored papers 2

Roel G W Verhaak

Yale School of Medicine

Co-authored papers 2

Roman Sasik

Center for Computational Biology & Bioinformatics (CCBB), University of California

Co-authored papers 2

Ludmil B Alexandrov

Moores Cancer Center, university of california san diego

Co-authored papers 2

Kyle S Sanchez

University of California San Diego

Co-authored papers 1

Douglas M Fowler

University of Washington, USA Brotman Baty Institute for Precision Medicine

Co-authored papers 1

Ana Bojorquez-Gomez

University of California

Co-authored papers 1

Shuling Ren

Beijing Friendship Hospital, Capital Medical University

Co-authored papers 1

Jill P Mesirov

University of California San Diego

Co-authored papers 1

Zhen Ye

Ludwig Institute for Cancer Research, University of California San Diego

Co-authored papers 1

Daniel Pekin

University of California

Co-authored papers 1

Nevan J Krogan (CM4AI)

University of California San Francisco

Co-authored papers 1

Yanmeng Shi

University of California riverside

Co-authored papers 1

Mitchell Flagg

University of California San Diego

Co-authored papers 1

Theresa Guo

Moores Cancer Center, University of California

Co-authored papers 1

Rongxin Fang

Ludwig Institute for Cancer Research, University of California San Diego

Co-authored papers 1

Jee Yun Han

Co-authored papers 1

Johanna Ten Hoeve

California Nanosystems Institute, University of California los angeles

Co-authored papers 1

Gabriel Karin

David Geffen School of Medicine, University of California los angeles

Co-authored papers 1

Johannes H Schulte

Co-authored papers 1

Jason F Kreisberg

University of California San Diego

Co-authored papers 1

Jeremy N Rich

UPMC Hillman Cancer Center, University of Pittsburgh Medical Center

Co-authored papers 1

1 - 30

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