Giovanni Ciriello

Giovanni Ciriello

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Giovanni Ciriello

Giovanni Ciriello

Publications by authors named "Giovanni Ciriello"

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39Publications

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Synaptic proximity enables NMDAR signalling to promote brain metastasis.

Nature 2019 Sep 18;573(7775):526-531. Epub 2019 Sep 18.

Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.

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http://dx.doi.org/10.1038/s41586-019-1576-6DOI Listing
September 2019

EZH2 oncogenic mutations drive epigenetic, transcriptional, and structural changes within chromatin domains.

Nat Genet 2019 03 28;51(3):517-528. Epub 2019 Jan 28.

Swiss Institute for Experimental Cancer Research (ISREC), School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

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http://www.nature.com/articles/s41588-018-0338-y
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http://dx.doi.org/10.1038/s41588-018-0338-yDOI Listing
March 2019

Comparison of computational methods for the identification of topologically associating domains.

Genome Biol 2018 12 10;19(1):217. Epub 2018 Dec 10.

Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.

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http://dx.doi.org/10.1186/s13059-018-1596-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6288901PMC
December 2018

Pan-Cancer Landscape of Aberrant DNA Methylation across Human Tumors.

Cell Rep 2018 10;25(4):1066-1080.e8

Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), University of Lausanne (UNIL), Lausanne, Switzerland. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247183154
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http://dx.doi.org/10.1016/j.celrep.2018.09.082DOI Listing
October 2018

Pan-cancer inference of intra-tumor heterogeneity reveals associations with different forms of genomic instability.

PLoS Genet 2018 09 13;14(9):e1007669. Epub 2018 Sep 13.

Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1371/journal.pgen.1007669DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6155543PMC
September 2018

Pan-SRC kinase inhibition blocks B-cell receptor oncogenic signaling in non-Hodgkin lymphoma.

Blood 2018 05 22;131(21):2345-2356. Epub 2018 Mar 22.

Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1182/blood-2017-10-809210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5969377PMC
May 2018

Conditional Selection of Genomic Alterations Dictates Cancer Evolution and Oncogenic Dependencies.

Cancer Cell 2017 08 27;32(2):155-168.e6. Epub 2017 Jul 27.

Department of Computational Biology, University of Lausanne (UNIL), 1011 Lausanne, Vaud, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2017.06.010DOI Listing
August 2017

Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma.

Cell Rep 2016 Mar 3;14(10):2476-89. Epub 2016 Mar 3.

Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.02.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4794376PMC
March 2016

A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers.

PLoS Comput Biol 2016 Feb 29;12(2):e1004765. Epub 2016 Feb 29.

Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004765DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4771175PMC
February 2016

Pan-Cancer Analysis of Mutation Hotspots in Protein Domains.

Cell Syst 2015 Sep 23;1(3):197-209. Epub 2015 Sep 23.

Computational Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2015.08.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4982675PMC
September 2015

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Authors:
Daniel J Brat Roel G W Verhaak Kenneth D Aldape W K Alfred Yung Sofie R Salama Lee A D Cooper Esther Rheinbay C Ryan Miller Mark Vitucci Olena Morozova A Gordon Robertson Houtan Noushmehr Peter W Laird Andrew D Cherniack Rehan Akbani Jason T Huse Giovanni Ciriello Laila M Poisson Jill S Barnholtz-Sloan Mitchel S Berger Cameron Brennan Rivka R Colen Howard Colman Adam E Flanders Caterina Giannini Mia Grifford Antonio Iavarone Rajan Jain Isaac Joseph Jaegil Kim Katayoon Kasaian Tom Mikkelsen Bradley A Murray Brian Patrick O'Neill Lior Pachter Donald W Parsons Carrie Sougnez Erik P Sulman Scott R Vandenberg Erwin G Van Meir Andreas von Deimling Hailei Zhang Daniel Crain Kevin Lau David Mallery Scott Morris Joseph Paulauskis Robert Penny Troy Shelton Mark Sherman Peggy Yena Aaron Black Jay Bowen Katie Dicostanzo Julie Gastier-Foster Kristen M Leraas Tara M Lichtenberg Christopher R Pierson Nilsa C Ramirez Cynthia Taylor Stephanie Weaver Lisa Wise Erik Zmuda Tanja Davidsen John A Demchok Greg Eley Martin L Ferguson Carolyn M Hutter Kenna R Mills Shaw Bradley A Ozenberger Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean Claude Zenklusen Brenda Ayala Julien Baboud Sudha Chudamani Mark A Jensen Jia Liu Todd Pihl Rohini Raman Yunhu Wan Ye Wu Adrian Ally J Todd Auman Miruna Balasundaram Saianand Balu Stephen B Baylin Rameen Beroukhim Moiz S Bootwalla Reanne Bowlby Christopher A Bristow Denise Brooks Yaron Butterfield Rebecca Carlsen Scott Carter Lynda Chin Andy Chu Eric Chuah Kristian Cibulskis Amanda Clarke Simon G Coetzee Noreen Dhalla Tim Fennell Sheila Fisher Stacey Gabriel Gad Getz Richard Gibbs Ranabir Guin Angela Hadjipanayis D Neil Hayes Toshinori Hinoue Katherine Hoadley Robert A Holt Alan P Hoyle Stuart R Jefferys Steven Jones Corbin D Jones Raju Kucherlapati Phillip H Lai Eric Lander Semin Lee Lee Lichtenstein Yussanne Ma Dennis T Maglinte Harshad S Mahadeshwar Marco A Marra Michael Mayo Shaowu Meng Matthew L Meyerson Piotr A Mieczkowski Richard A Moore Lisle E Mose Andrew J Mungall Angeliki Pantazi Michael Parfenov Peter J Park Joel S Parker Charles M Perou Alexei Protopopov Xiaojia Ren Jeffrey Roach Thaís S Sabedot Jacqueline Schein Steven E Schumacher Jonathan G Seidman Sahil Seth Hui Shen Janae V Simons Payal Sipahimalani Matthew G Soloway Xingzhi Song Huandong Sun Barbara Tabak Angela Tam Donghui Tan Jiabin Tang Nina Thiessen Timothy Triche David J Van Den Berg Umadevi Veluvolu Scot Waring Daniel J Weisenberger Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Andrew W Xu Lixing Yang Travis I Zack Jianhua Zhang B Arman Aksoy Harindra Arachchi Chris Benz Brady Bernard Daniel Carlin Juok Cho Daniel DiCara Scott Frazer Gregory N Fuller JianJiong Gao Nils Gehlenborg David Haussler David I Heiman Lisa Iype Anders Jacobsen Zhenlin Ju Sol Katzman Hoon Kim Theo Knijnenburg Richard Bailey Kreisberg Michael S Lawrence William Lee Kalle Leinonen Pei Lin Shiyun Ling Wenbin Liu Yingchun Liu Yuexin Liu Yiling Lu Gordon Mills Sam Ng Michael S Noble Evan Paull Arvind Rao Sheila Reynolds Gordon Saksena Zack Sanborn Chris Sander Nikolaus Schultz Yasin Senbabaoglu Ronglai Shen Ilya Shmulevich Rileen Sinha Josh Stuart S Onur Sumer Yichao Sun Natalie Tasman Barry S Taylor Doug Voet Nils Weinhold John N Weinstein Da Yang Kosuke Yoshihara Siyuan Zheng Wei Zhang Lihua Zou Ty Abel Sara Sadeghi Mark L Cohen Jenny Eschbacher Eyas M Hattab Aditya Raghunathan Matthew J Schniederjan Dina Aziz Gene Barnett Wendi Barrett Darell D Bigner Lori Boice Cathy Brewer Chiara Calatozzolo Benito Campos Carlos Gilberto Carlotti Timothy A Chan Lucia Cuppini Erin Curley Stefania Cuzzubbo Karen Devine Francesco DiMeco Rebecca Duell J Bradley Elder Ashley Fehrenbach Gaetano Finocchiaro William Friedman Jordonna Fulop Johanna Gardner Beth Hermes Christel Herold-Mende Christine Jungk Ady Kendler Norman L Lehman Eric Lipp Ouida Liu Randy Mandt Mary McGraw Roger Mclendon Christopher McPherson Luciano Neder Phuong Nguyen Ardene Noss Raffaele Nunziata Quinn T Ostrom Cheryl Palmer Alessandro Perin Bianca Pollo Alexander Potapov Olga Potapova W Kimryn Rathmell Daniil Rotin Lisa Scarpace Cathy Schilero Kelly Senecal Kristen Shimmel Vsevolod Shurkhay Suzanne Sifri Rosy Singh Andrew E Sloan Kathy Smolenski Susan M Staugaitis Ruth Steele Leigh Thorne Daniela P C Tirapelli Andreas Unterberg Mahitha Vallurupalli Yun Wang Ronald Warnick Felicia Williams Yingli Wolinsky Sue Bell Mara Rosenberg Chip Stewart Franklin Huang Jonna L Grimsby Amie J Radenbaugh Jianan Zhang
June 2015

Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations.

Genome Biol 2015 Feb 26;16:45. Epub 2015 Feb 26.

Computational Biology Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 460, New York, 10065, USA.

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http://genomebiology.com/2015/16/1/45
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http://dx.doi.org/10.1186/s13059-015-0612-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381444PMC
February 2015

Frequent disruption of the RB pathway in indolent follicular lymphoma suggests a new combination therapy.

J Exp Med 2014 Jun 9;211(7):1379-91. Epub 2014 Jun 9.

Cancer Biology & Genetics Program, Computational Biology Program, Department of Medicine, Human Oncology and Pathogenesis Program, Genomics Core Facility, Molecular Pharmacology Program, Department of Pathology, Department of Epidemiology and Biostatistics, and Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065

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http://dx.doi.org/10.1084/jem.20132120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4076578PMC
June 2014

Collection, integration and analysis of cancer genomic profiles: from data to insight.

Curr Opin Genet Dev 2014 Feb 27;24:92-8. Epub 2014 Feb 27.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, Box 460, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2013.12.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4084973PMC
February 2014

An epidemiologic and genomic investigation into the obesity paradox in renal cell carcinoma.

J Natl Cancer Inst 2013 Dec 27;105(24):1862-70. Epub 2013 Nov 27.

Affiliations of authors: Urology Service, Department of Surgery (AAH, NM, BF, PHK, PR), Human Oncology & Pathogenesis Program (AAH, JJH); Epidemiology and Biostatistics (HF, ECZ), Computational Biology (AJ, NS, GC, CS), Genitourinary Oncology (MHV, RJM, JJH), and Department of Pathology (VER), Memorial Sloan-Kettering Cancer Center, New York, NY; USC Epigenome Center, University of Southern California, Los Angeles, California (HS, PWL); Weill Medical College, Cornell University, New York, NY (RJM, JJH, PR).

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http://dx.doi.org/10.1093/jnci/djt310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866155PMC
December 2013

SQSTM1 is a pathogenic target of 5q copy number gains in kidney cancer.

Cancer Cell 2013 Dec;24(6):738-50

Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccr.2013.10.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910168PMC
December 2013

Generation of tumor-targeted human T lymphocytes from induced pluripotent stem cells for cancer therapy.

Nat Biotechnol 2013 Oct 11;31(10):928-33. Epub 2013 Aug 11.

Center for Cell Engineering, Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.

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http://dx.doi.org/10.1038/nbt.2678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5722218PMC
October 2013

Emerging landscape of oncogenic signatures across human cancers.

Nat Genet 2013 Oct;45(10):1127-33

Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.

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http://dx.doi.org/10.1038/ng.2762DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4320046PMC
October 2013

The molecular diversity of Luminal A breast tumors.

Breast Cancer Res Treat 2013 Oct 6;141(3):409-20. Epub 2013 Oct 6.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA,

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http://dx.doi.org/10.1007/s10549-013-2699-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3824397PMC
October 2013

The somatic genomic landscape of glioblastoma.

Cell 2013 Oct;155(2):462-77

Human Oncology and Pathogenesis Program, Brain Tumor Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Neurosurgery, Memorial Sloan-Kettering Cancer Center, Department of Neurological Surgery, Weill Cornell Medical Center, New York, NY 10065, USA. Electronic address:

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https://www.genome.gov/Multimedia/Slides/TCGA2/27_Verhaak.pd
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http://linkinghub.elsevier.com/retrieve/pii/S009286741301208
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http://dx.doi.org/10.1016/j.cell.2013.09.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910500PMC
October 2013

Using MEMo to discover mutual exclusivity modules in cancer.

Curr Protoc Bioinformatics 2013 Mar;Chapter 8:Unit 8.17

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.

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http://dx.doi.org/10.1002/0471250953.bi0817s41DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5563973PMC
March 2013

Mutual exclusivity analysis identifies oncogenic network modules.

Genome Res 2012 Feb 9;22(2):398-406. Epub 2011 Sep 9.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.

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http://dx.doi.org/10.1101/gr.125567.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3266046PMC
February 2012

Analysis of interactions between ribosomal proteins and RNA structural motifs.

BMC Bioinformatics 2010 Jan 18;11 Suppl 1:S41. Epub 2010 Jan 18.

Dept, of Information Engineering, University of Padova, Via Gradenigo 6a, 35131 Padova, Italy.

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http://dx.doi.org/10.1186/1471-2105-11-S1-S41DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009514PMC
January 2010

Finding 3D motifs in ribosomal RNA structures.

Nucleic Acids Res 2009 Mar 21;37(4):e29. Epub 2009 Jan 21.

College of Computing, Georgia Institute of Technology, Atlanta, GA 30332-0280, USA.

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http://dx.doi.org/10.1093/nar/gkn1044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651809PMC
March 2009

A review on models and algorithms for motif discovery in protein-protein interaction networks.

Brief Funct Genomic Proteomic 2008 Mar 28;7(2):147-56. Epub 2008 Apr 28.

Department of Information Engineering, University of Padova Via Gradenigo 6a, 35131 Padova, Italy.

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http://dx.doi.org/10.1093/bfgp/eln015DOI Listing
March 2008