Publications by authors named "Joshua M Francis"

27Publications

Chromatin Looping Shapes KLF5-Dependent Transcriptional Programs in Human Epithelial Cancers.

Authors:
Yanli Liu Bingqian Guo Estrella Aguilera-Jimenez Vivian S Chu Jin Zhou Zhong Wu Joshua M Francis Xiaojun Yang Peter S Choi Swneke D Bailey Xiaoyang Zhang

Cancer Res 2020 Dec 28;80(24):5464-5477. Epub 2020 Oct 28.

Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.

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December 2020

Multi-Omics Analysis Identifies MGA as a Negative Regulator of the MYC Pathway in Lung Adenocarcinoma.

Authors:
Paula Llabata Yoichiro Mitsuishi Peter S Choi Diana Cai Joshua M Francis Manuel Torres-Diz Namrata D Udeshi Lior Golomb Zhong Wu Jin Zhou Tanya Svinkina Estrella Aguilera-Jimenez Yanli Liu Steven A Carr Montse Sanchez-Cespedes Matthew Meyerson Xiaoyang Zhang

Mol Cancer Res 2020 04 20;18(4):574-584. Epub 2019 Dec 20.

Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.

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April 2020

Small-molecule targeting of brachyury transcription factor addiction in chordoma.

Authors:
Tanaz Sharifnia Mathias J Wawer Ting Chen Qing-Yuan Huang Barbara A Weir Ann Sizemore Matthew A Lawlor Amy Goodale Glenn S Cowley Francisca Vazquez Christopher J Ott Joshua M Francis Slim Sassi Patricia Cogswell Hadley E Sheppard Tinghu Zhang Nathanael S Gray Paul A Clarke Julian Blagg Paul Workman Josh Sommer Francis Hornicek David E Root William C Hahn James E Bradner Kwok K Wong Paul A Clemons Charles Y Lin Joanne D Kotz Stuart L Schreiber

Nat Med 2019 02 21;25(2):292-300. Epub 2019 Jan 21.

Broad Institute of Harvard and MIT, Cambridge, MA, USA.

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February 2019

Genotype-targeted local therapy of glioma.

Authors:
Ganesh M Shankar Ameya R Kirtane Julie J Miller Hormoz Mazdiyasni Jaimie Rogner Tammy Tai Erik A Williams Fumi Higuchi Tareq A Juratli Kensuke Tateishi Mara V A Koerner Shilpa S Tummala Alexandria L Fink Tristan Penson Stephen P Schmidt Gregory R Wojtkiewicz Aymen Baig Joshua M Francis Mikael L Rinne Julie M Batten Tracy T Batchelor Priscilla K Brastianos William T Curry Fred G Barker Justin T Jordan A John Iafrate Andrew S Chi Jochen K Lennerz Matthew Meyerson Robert Langer Hiroaki Wakimoto Giovanni Traverso Daniel P Cahill

Proc Natl Acad Sci U S A 2018 09 6;115(36):E8388-E8394. Epub 2018 Aug 6.

Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114;

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September 2018

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.

Authors:
Viktor A Adalsteinsson Gavin Ha Samuel S Freeman Atish D Choudhury Daniel G Stover Heather A Parsons Gregory Gydush Sarah C Reed Denisse Rotem Justin Rhoades Denis Loginov Dimitri Livitz Daniel Rosebrock Ignaty Leshchiner Jaegil Kim Chip Stewart Mara Rosenberg Joshua M Francis Cheng-Zhong Zhang Ofir Cohen Coyin Oh Huiming Ding Paz Polak Max Lloyd Sairah Mahmud Karla Helvie Margaret S Merrill Rebecca A Santiago Edward P O'Connor Seong H Jeong Rachel Leeson Rachel M Barry Joseph F Kramkowski Zhenwei Zhang Laura Polacek Jens G Lohr Molly Schleicher Emily Lipscomb Andrea Saltzman Nelly M Oliver Lori Marini Adrienne G Waks Lauren C Harshman Sara M Tolaney Eliezer M Van Allen Eric P Winer Nancy U Lin Mari Nakabayashi Mary-Ellen Taplin Cory M Johannessen Levi A Garraway Todd R Golub Jesse S Boehm Nikhil Wagle Gad Getz J Christopher Love Matthew Meyerson

Nat Commun 2017 11 6;8(1):1324. Epub 2017 Nov 6.

Eli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, 02142, MA, USA.

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November 2017

Somatic Superenhancer Duplications and Hotspot Mutations Lead to Oncogenic Activation of the KLF5 Transcription Factor.

Authors:
Xiaoyang Zhang Peter S Choi Joshua M Francis Galen F Gao Joshua D Campbell Aruna Ramachandran Yoichiro Mitsuishi Gavin Ha Juliann Shih Francisca Vazquez Aviad Tsherniak Alison M Taylor Jin Zhou Zhong Wu Ashton C Berger Marios Giannakis William C Hahn Andrew D Cherniack Matthew Meyerson

Cancer Discov 2018 01 29;8(1):108-125. Epub 2017 Sep 29.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.

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January 2018

Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia.

Authors:
Lili Wang Jean Fan Joshua M Francis George Georghiou Sarah Hergert Shuqiang Li Rutendo Gambe Chensheng W Zhou Chunxiao Yang Sheng Xiao Paola Dal Cin Michaela Bowden Dylan Kotliar Sachet A Shukla Jennifer R Brown Donna Neuberg Dario R Alessi Cheng-Zhong Zhang Peter V Kharchenko Kenneth J Livak Catherine J Wu

Genome Res 2017 08 5;27(8):1300-1311. Epub 2017 Jul 5.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.

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August 2017

Pharmacokinetics and derivation of an anticancer dosing regimen for the novel anti-cancer agent isobutyl-deoxynyboquinone (IB-DNQ), a NQO1 bioactivatable molecule, in the domestic felid species.

Authors:
Alycen P Lundberg Joshua M Francis Malgorzata Pajak Elizabeth I Parkinson Kathryn L Wycislo Thomas J Rosol Megan E Brown Cheryl A London Levent Dirikolu Paul J Hergenrother Timothy M Fan

Invest New Drugs 2017 04 14;35(2):134-144. Epub 2016 Dec 14.

Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA.

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April 2017

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma.

Authors:
Itay Tirosh Andrew S Venteicher Christine Hebert Leah E Escalante Anoop P Patel Keren Yizhak Jonathan M Fisher Christopher Rodman Christopher Mount Mariella G Filbin Cyril Neftel Niyati Desai Jackson Nyman Benjamin Izar Christina C Luo Joshua M Francis Aanand A Patel Maristela L Onozato Nicolo Riggi Kenneth J Livak Dave Gennert Rahul Satija Brian V Nahed William T Curry Robert L Martuza Ravindra Mylvaganam A John Iafrate Matthew P Frosch Todd R Golub Miguel N Rivera Gad Getz Orit Rozenblatt-Rosen Daniel P Cahill Michelle Monje Bradley E Bernstein David N Louis Aviv Regev Mario L Suvà

Nature 2016 11 2;539(7628):309-313. Epub 2016 Nov 2.

Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.

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November 2016

Kmt2a cooperates with menin to suppress tumorigenesis in mouse pancreatic islets.

Authors:
Wenchu Lin Joshua M Francis Hong Li Xiaoping Gao Chandra Sekhar Pedamallu Patricia Ernst Matthew Meyerson

Cancer Biol Ther 2016 12 1;17(12):1274-1281. Epub 2016 Nov 1.

b Department of Medical Oncology & Center for Cancer Genome Discovery , Dana-Farber Cancer Institute, Harvard Medical School , Boston , MA , USA.

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December 2016

Integrated genomic approaches identify upregulation of SCRN1 as a novel mechanism associated with acquired resistance to erlotinib in PC9 cells harboring oncogenic EGFR mutation.

Authors:
Nayoung Kim Ahye Cho Hideo Watanabe Yoon-La Choi Meraj Aziz Michelle Kassner Je-Gun Joung Angela Kyung-Joo Park Joshua M Francis Joon Seol Bae Soo-Min Ahn Kyoung-Mee Kim Joon Oh Park Woong-Yang Park Myung-Ju Ahn Keunchil Park Jaehyung Koo Hongwei Holly Yin Jeonghee Cho

Oncotarget 2016 Mar;7(12):13797-809

Department of NanoBio Medical Science, Dankook University, Cheonan 31116, Republic of Korea.

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March 2016

Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers.

Authors:
Xiaoyang Zhang Peter S Choi Joshua M Francis Marcin Imielinski Hideo Watanabe Andrew D Cherniack Matthew Meyerson

Nat Genet 2016 Feb 14;48(2):176-82. Epub 2015 Dec 14.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

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February 2016

Rapid Intraoperative Molecular Characterization of Glioma.

Authors:
Ganesh M Shankar Joshua M Francis Mikael L Rinne Shakti H Ramkissoon Franklin W Huang Andrew S Venteicher Elliot H Akama-Garren Yun Jee Kang Nina Lelic James C Kim Loreal E Brown Sarah K Charbonneau Alexandra J Golby Chandra Sekhar Pedamallu Mai P Hoang Ryan J Sullivan Andrew D Cherniack Levi A Garraway Anat Stemmer-Rachamimov David A Reardon Patrick Y Wen Priscilla K Brastianos William T Curry Fred G Barker William C Hahn Brian V Nahed Keith L Ligon David N Louis Daniel P Cahill Matthew Meyerson

JAMA Oncol 2015 Aug;1(5):662-7

Cancer Program, Broad Institute, Cambridge, Massachusetts3Department of Medical Oncology, Dana-Farber Cancer Institute, Boston Massachusetts7Department of Pathology, Harvard Medical School, Boston, Massachusetts.

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August 2015

Chromothripsis from DNA damage in micronuclei.

Authors:
Cheng-Zhong Zhang Alexander Spektor Hauke Cornils Joshua M Francis Emily K Jackson Shiwei Liu Matthew Meyerson David Pellman

Nature 2015 Jun 27;522(7555):179-84. Epub 2015 May 27.

1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA [3] Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA [4] Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.

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June 2015

ARID1A and TERT promoter mutations in dedifferentiated meningioma.

Authors:
Malak S Abedalthagafi Wenya Linda Bi Parker H Merrill William J Gibson Matthew F Rose Ziming Du Joshua M Francis Rose Du Ian F Dunn Azra H Ligon Rameen Beroukhim Sandro Santagata

Cancer Genet 2015 Jun 18;208(6):345-50. Epub 2015 Mar 18.

Division of Neuropathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. Electronic address:

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June 2015

Prospective derivation of a living organoid biobank of colorectal cancer patients.

Authors:
Marc van de Wetering Hayley E Francies Joshua M Francis Gergana Bounova Francesco Iorio Apollo Pronk Winan van Houdt Joost van Gorp Amaro Taylor-Weiner Lennart Kester Anne McLaren-Douglas Joyce Blokker Sridevi Jaksani Sina Bartfeld Richard Volckman Peter van Sluis Vivian S W Li Sara Seepo Chandra Sekhar Pedamallu Kristian Cibulskis Scott L Carter Aaron McKenna Michael S Lawrence Lee Lichtenstein Chip Stewart Jan Koster Rogier Versteeg Alexander van Oudenaarden Julio Saez-Rodriguez Robert G J Vries Gad Getz Lodewyk Wessels Michael R Stratton Ultan McDermott Matthew Meyerson Mathew J Garnett Hans Clevers

Cell 2015 May;161(4):933-45

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Cancer Genomics and University Medical Center, 3584 CT Utrecht, the Netherlands; Foundation Hubrecht Organoid Technology (HUB), 3584 CT Utrecht, the Netherlands. Electronic address:

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May 2015

Constitutive asymmetric dimerization drives oncogenic activation of epidermal growth factor receptor carboxyl-terminal deletion mutants.

Authors:
Angela K J Park Joshua M Francis Woong-Yang Park Joon-Oh Park Jeonghee Cho

Oncotarget 2015 Apr;6(11):8839-50

Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.

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April 2015

Sporadic hemangioblastomas are characterized by cryptic VHL inactivation.

Authors:
Ganesh M Shankar Amaro Taylor-Weiner Nina Lelic Robert T Jones James C Kim Joshua M Francis Malak Abedalthagafi Lawrence F Borges Jean-Valery Coumans William T Curry Brian V Nahed John H Shin Sun Ha Paek Sung-Hye Park Chip Stewart Michael S Lawrence Kristian Cibulskis Aaron R Thorner Paul Van Hummelen Anat O Stemmer-Rachamimov Tracy T Batchelor Scott L Carter Mai P Hoang Sandro Santagata David N Louis Fred G Barker Matthew Meyerson Gad Getz Priscilla K Brastianos Daniel P Cahill

Acta Neuropathol Commun 2014 Dec 24;2:167. Epub 2014 Dec 24.

Departments of Neurosurgery, Massachusetts General Hospital, Boston, MA, USA.

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December 2014

Dynamic epigenetic regulation by menin during pancreatic islet tumor formation.

Authors:
Wenchu Lin Hideo Watanabe Shouyong Peng Joshua M Francis Nathan Kaplan Chandra Sekhar Pedamallu Aruna Ramachandran Agoston Agoston Adam J Bass Matthew Meyerson

Mol Cancer Res 2015 Apr 23;13(4):689-98. Epub 2014 Dec 23.

Department of Medical Oncology, Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts. Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts. Cancer program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts.

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April 2015

Angiomatous meningiomas have a distinct genetic profile with multiple chromosomal polysomies including polysomy of chromosome 5.

Authors:
Malak S Abedalthagafi Parker H Merrill Wenya Linda Bi Robert T Jones Marc L Listewnik Shakti H Ramkissoon Aaron R Thorner Ian F Dunn Rameen Beroukhim Brian M Alexander Priscilla K Brastianos Joshua M Francis Rebecca D Folkerth Keith L Ligon Paul Van Hummelen Azra H Ligon Sandro Santagata

Oncotarget 2014 Nov;5(21):10596-606

Department of Pathology, Division of Neuropathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.

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November 2014

EGFR variant heterogeneity in glioblastoma resolved through single-nucleus sequencing.

Authors:
Joshua M Francis Cheng-Zhong Zhang Cecile L Maire Joonil Jung Veronica E Manzo Viktor A Adalsteinsson Heather Homer Sam Haidar Brendan Blumenstiel Chandra Sekhar Pedamallu Azra H Ligon J Christopher Love Matthew Meyerson Keith L Ligon

Cancer Discov 2014 Aug 3;4(8):956-71. Epub 2014 Jun 3.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts. Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts. Department of Pathology, Boston Children's Hospital, Boston, Massachusetts. Department of Pathology, Harvard Medical School, Boston, Massachusetts.

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August 2014

Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer.

Authors:
Jens G Lohr Viktor A Adalsteinsson Kristian Cibulskis Atish D Choudhury Mara Rosenberg Peter Cruz-Gordillo Joshua M Francis Cheng-Zhong Zhang Alex K Shalek Rahul Satija John J Trombetta Diana Lu Naren Tallapragada Narmin Tahirova Sora Kim Brendan Blumenstiel Carrie Sougnez Alarice Lowe Bang Wong Daniel Auclair Eliezer M Van Allen Mari Nakabayashi Rosina T Lis Gwo-Shu M Lee Tiantian Li Matthew S Chabot Amy Ly Mary-Ellen Taplin Thomas E Clancy Massimo Loda Aviv Regev Matthew Meyerson William C Hahn Philip W Kantoff Todd R Golub Gad Getz Jesse S Boehm J Christopher Love

Nat Biotechnol 2014 May 20;32(5):479-84. Epub 2014 Apr 20.

1] The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3] Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.

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May 2014

SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas.

Authors:
Hideo Watanabe Qiuping Ma Shouyong Peng Guillaume Adelmant Danielle Swain Wenyu Song Cameron Fox Joshua M Francis Chandra Sekhar Pedamallu David S DeLuca Angela N Brooks Su Wang Jianwen Que Anil K Rustgi Kwok-kin Wong Keith L Ligon X Shirley Liu Jarrod A Marto Matthew Meyerson Adam J Bass

J Clin Invest 2014 Apr 3;124(4):1636-45. Epub 2014 Mar 3.

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April 2014

Somatic mutation of CDKN1B in small intestine neuroendocrine tumors.

Authors:
Joshua M Francis Adam Kiezun Alex H Ramos Stefano Serra Chandra Sekhar Pedamallu Zhi Rong Qian Michaela S Banck Rahul Kanwar Amit A Kulkarni Anna Karpathakis Veronica Manzo Tanupriya Contractor Juliet Philips Elizabeth Nickerson Nam Pho Susanne M Hooshmand Lauren K Brais Michael S Lawrence Trevor Pugh Aaron McKenna Andrey Sivachenko Kristian Cibulskis Scott L Carter Akinyemi I Ojesina Samuel Freeman Robert T Jones Douglas Voet Gordon Saksena Daniel Auclair Robert Onofrio Erica Shefler Carrie Sougnez Jonna Grimsby Lisa Green Niall Lennon Tim Meyer Martyn Caplin Daniel C Chung Andreas S Beutler Shuji Ogino Christina Thirlwell Ramesh Shivdasani Sylvia L Asa Chris R Harris Gad Getz Matthew Kulke Matthew Meyerson

Nat Genet 2013 Dec 3;45(12):1483-6. Epub 2013 Nov 3.

1] Broad Institute, Cambridge, Massachusetts, USA. [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [3].

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December 2013

Cetuximab response of lung cancer-derived EGF receptor mutants is associated with asymmetric dimerization.

Authors:
Jeonghee Cho Liang Chen Naveen Sangji Takafumi Okabe Kimio Yonesaka Joshua M Francis Richard J Flavin William Johnson Jihyun Kwon Soyoung Yu Heidi Greulich Bruce E Johnson Michael J Eck Pasi A Jänne Kwok-Kin Wong Matthew Meyerson

Cancer Res 2013 Nov 24;73(22):6770-9. Epub 2013 Sep 24.

Authors' Affiliations: Departments of Medical Oncology and Cancer Biology; Center for Cancer Genome Discovery, Lowe Center for Thoracic Oncology, and Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute; Departments of Medicine, Brigham and Women's Hospital; Departments of Biological Chemistry and Molecular Pharmacology and Pathology, Harvard Medical School, Boston, Massachusetts; Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea; and The Broad Institute of Harvard and MIT, Cambridge, Massachusetts.

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November 2013

Integrated cistromic and expression analysis of amplified NKX2-1 in lung adenocarcinoma identifies LMO3 as a functional transcriptional target.

Authors:
Hideo Watanabe Joshua M Francis Michele S Woo Banafsheh Etemad Wenchu Lin Daniel F Fries Shouyong Peng Eric L Snyder Purushothama Rao Tata Francesca Izzo Anna C Schinzel Jeonghee Cho Peter S Hammerman Roel G Verhaak William C Hahn Jayaraj Rajagopal Tyler Jacks Matthew Meyerson

Genes Dev 2013 Jan 15;27(2):197-210. Epub 2013 Jan 15.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.

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January 2013

The tumor suppressor Cdc73 functionally associates with CPSF and CstF 3' mRNA processing factors.

Authors:
Orit Rozenblatt-Rosen Takashi Nagaike Joshua M Francis Syuzo Kaneko Karen A Glatt Christina M Hughes Thomas LaFramboise James L Manley Matthew Meyerson

Proc Natl Acad Sci U S A 2009 Jan 9;106(3):755-60. Epub 2009 Jan 9.

Department of Medical Oncology, Dana-Farber Cancer Institute, and Harvard Medical School, Boston, MA 02115, USA.

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January 2009