Publications by authors named "Alexei Protopopov"

78Publications

A Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases.

Cell Rep 2018 07;24(2):515-527

Dan L. Duncan Comprehensive Cancer 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; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.06.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6092947PMC
July 2018

A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations.

Cancer Cell 2017 06 18;31(6):820-832.e3. Epub 2017 May 18.

Dan L. Duncan Comprehensive Cancer 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; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2017.04.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502825PMC
June 2017

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

Telomere dysfunction suppresses multiple endocrine neoplasia in mice.

Genes Cancer 2014 Sep;5(9-10):306-19

Diabetes, Endocrinology & Obesity Branch, National Institute of Diabetes & Digestive & Kidney Diseases, Bethesda, MD.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4209601PMC
http://dx.doi.org/10.18632/genesandcancer.31DOI Listing
September 2014

Identification of double-stranded genomic DNA spanning all chromosomes with mutated KRAS and p53 DNA in the serum exosomes of patients with pancreatic cancer.

J Biol Chem 2014 Feb 7;289(7):3869-75. Epub 2014 Jan 7.

From the Department of Cancer Biology, Metastasis Research Center, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030.

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http://dx.doi.org/10.1074/jbc.C113.532267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3924256PMC
February 2014

Role of telomere dysfunction in cardiac failure in Duchenne muscular dystrophy.

Nat Cell Biol 2013 Aug 7;15(8):895-904. Epub 2013 Jul 7.

Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Clinical Sciences Research Center, Stanford University School of Medicine, Stanford, California 94305, USA.

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http://dx.doi.org/10.1038/ncb2790DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3774175PMC
August 2013

ZNF365 promotes stability of fragile sites and telomeres.

Cancer Discov 2013 Jul 17;3(7):798-811. Epub 2013 Jun 17.

Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, USA.

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http://dx.doi.org/10.1158/2159-8290.CD-12-0536DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3710545PMC
July 2013

Quantitative imaging of haematopoietic stem and progenitor cell localization and hypoxic status in the bone marrow microenvironment.

Nat Cell Biol 2013 May 28;15(5):533-43. Epub 2013 Apr 28.

Division of Transfusion Medicine, Department of Laboratory Medicine, Children's Hospital Boston, 300 Longwood Avenue, Boston, Massachusetts 02115, USA. [corrected]

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http://dx.doi.org/10.1038/ncb2730DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156024PMC
May 2013

Spectrum of somatic mitochondrial mutations in five cancers.

Proc Natl Acad Sci U S A 2012 Aug 13;109(35):14087-91. Epub 2012 Aug 13.

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1073/pnas.1211502109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3435197PMC
August 2012

DNA breaks and chromosome pulverization from errors in mitosis.

Nature 2012 Jan 18;482(7383):53-8. Epub 2012 Jan 18.

Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nature10802DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3271137PMC
January 2012

Cloning and Initial Functional Characterization of Mlk4α and Mlk4β.

Genomics Insights 2011 22;4:1-12. Epub 2011 Mar 22.

Department of Microbiology, Tumor and Cell Biology, Department of Clinical Science and Education, Södersjukhuset, Karolinska Institute, Stockholm, 17177, Sweden. ; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.

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http://dx.doi.org/10.4137/GEI.S6092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510602PMC
July 2015

Telomerase reactivation reverses tissue degeneration in aged telomerase-deficient mice.

Nature 2011 Jan 28;469(7328):102-6. Epub 2010 Nov 28.

Belfer Institute for Applied Cancer Science and Departments of Medical Oncology, Medicine and Genetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nature09603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057569PMC
January 2011

Altered antisense-to-sense transcript ratios in breast cancer.

Proc Natl Acad Sci U S A 2012 Feb 22;109(8):2820-4. Epub 2010 Nov 22.

Department of Medical Oncology, and Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02115, USA.

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http://www.pnas.org/content/109/8/2820.full.pdf
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http://www.pnas.org/cgi/doi/10.1073/pnas.1010559107
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http://dx.doi.org/10.1073/pnas.1010559107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3286925PMC
February 2012

Glioma oncoprotein Bcl2L12 inhibits the p53 tumor suppressor.

Genes Dev 2010 Oct 13;24(19):2194-204. Epub 2010 Sep 13.

Belfer Institute for Applied Cancer Science, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1101/gad.1924710DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2947771PMC
October 2010

Oncogenesis of T-ALL and nonmalignant consequences of overexpressing intracellular NOTCH1.

J Exp Med 2008 Nov 3;205(12):2851-61. Epub 2008 Nov 3.

Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1084/jem.20081561DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2585834PMC
November 2008

Bcl2L12-mediated inhibition of effector caspase-3 and caspase-7 via distinct mechanisms in glioblastoma.

Proc Natl Acad Sci U S A 2008 Aug 31;105(31):10703-8. Epub 2008 Jul 31.

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

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http://dx.doi.org/10.1073/pnas.0712034105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2504776PMC
August 2008

Full complexity genomic hybridization on 60-mer oligonucleotide microarrays for array comparative genomic hybridization (aCGH).

Methods Mol Biol 2008 ;439:87-100

Center for Applied Cancer Science, Belfer Institute for Innovative Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1007/978-1-59745-188-8_6DOI Listing
June 2008

A comparison of DNA copy number profiling platforms.

Cancer Res 2007 Nov 29;67(21):10173-80. Epub 2007 Oct 29.

Translational Medicine, GlaxoSmithKline, King of Prussia, Pennsylvania, USA.

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http://dx.doi.org/10.1158/0008-5472.CAN-07-2102DOI Listing
November 2007

Epigenetic transdifferentiation of normal melanocytes by a metastatic melanoma microenvironment.

Cancer Res 2005 Nov;65(22):10164-9

Children's Memorial Research Center and Robert H. Lurie Comprehensive Cancer Center at Northwestern University, Chicago, IL 60614, USA.

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http://dx.doi.org/10.1158/0008-5472.CAN-05-2497DOI Listing
November 2005

High-resolution global profiling of genomic alterations with long oligonucleotide microarray.

Cancer Res 2004 Jul;64(14):4744-8

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

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http://dx.doi.org/10.1158/0008-5472.CAN-04-1241DOI Listing
July 2004

mSin3-associated protein, mSds3, is essential for pericentric heterochromatin formation and chromosome segregation in mammalian cells.

Genes Dev 2003 Oct;17(19):2396-405

Departments of Medical Oncology, Medicine, and Genetics, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1101/gad.1109403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC218077PMC
October 2003

An integrated physical and gene map of the 3.5-Mb chromosome 3p21.3 (AP20) region implicated in major human epithelial malignancies.

Cancer Res 2003 Jan;63(2):404-12

Microbiology and Tumor Biology Center, Karolinska Institute, 171 77 Stockholm, Sweden.

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January 2003