Philipp Kapranov

Philipp Kapranov

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Philipp Kapranov

Philipp Kapranov

Publications by authors named "Philipp Kapranov"

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Diversification of retinoblastoma protein function associated with cis and trans adaptations.

Mol Biol Evol 2019 Aug 16. Epub 2019 Aug 16.

Graduate Program in Cell and Molecular Biology, Michigan State University, East Lansing, MI.

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http://dx.doi.org/10.1093/molbev/msz187DOI Listing
August 2019

Strategies to Annotate and Characterize Long Noncoding RNAs: Advantages and Pitfalls.

Trends Genet 2018 09 17;34(9):704-721. Epub 2018 Jul 17.

Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 201 Pan-Chinese S & T Building, 668 Jimei Road, Xiamen 361021, China. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2018.06.002DOI Listing
September 2018

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.

Nucleic Acids Res 2016 Apr 21;44(7):3233-52. Epub 2016 Mar 21.

Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen 361021, China St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA

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http://dx.doi.org/10.1093/nar/gkw162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838384PMC
April 2016

The Bromodomain protein BRD4 controls HOTAIR, a long noncoding RNA essential for glioblastoma proliferation.

Proc Natl Acad Sci U S A 2015 Jul 25;112(27):8326-31. Epub 2015 Jun 25.

Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL 33136;

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http://dx.doi.org/10.1073/pnas.1424220112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4500283PMC
July 2015

The Landscape of long noncoding RNA classification.

Trends Genet 2015 May 10;31(5):239-51. Epub 2015 Apr 10.

Institute of Genomics, School of Biomedical Sciences, Huaqiao Univerisity, 668 Jimei Road, Xiamen, China 361021; St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801 USA. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2015.03.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417002PMC
May 2015

Proteomics analysis of co-purifying cellular proteins associated with rAAV vectors.

PLoS One 2014 3;9(2):e86453. Epub 2014 Feb 3.

Department of Microbiology and Immunology, Sol Sherry Thrombosis Research Center, Temple University, Philadelphia, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0086453PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3911921PMC
December 2014

RNA editing regulates transposon-mediated heterochromatic gene silencing.

Nat Commun 2013 ;4:2745

Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, Rhode Island 02912, USA.

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http://dx.doi.org/10.1038/ncomms3745DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3992701PMC
June 2014

Dark matter RNA illuminates the puzzle of genome-wide association studies.

BMC Med 2014 Jun 12;12:97. Epub 2014 Jun 12.

St, Laurent Institute, 317 New Boston St, Suite 201, Woburn, MA 01801, USA.

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http://dx.doi.org/10.1186/1741-7015-12-97DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4054906PMC
June 2014

Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila.

Nat Struct Mol Biol 2013 Nov 29;20(11):1333-9. Epub 2013 Sep 29.

1] Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA. [2] St. Laurent Institute, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nsmb.2675DOI Listing
November 2013

Genomics in the assessment of a multi-component, multi-target medication in soft tissue disorders.

Curr Med Res Opin 2013 ;29 Suppl 2:11-4

St Laurent Institute, Cambridge, MA, USA.

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http://dx.doi.org/10.1185/03007995.2013.779879DOI Listing
October 2013

On the importance of small changes in RNA expression.

Methods 2013 Sep 4;63(1):18-24. Epub 2013 Apr 4.

Immunovirology - Biogenisis Group, University of Antioquia, A.A. 1226, Medellin, Colombia; St. Laurent Institute, One Kendall Square, Cambridge, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2013.03.027DOI Listing
September 2013

A concept of eliminating nonhomologous recombination for scalable and safe AAV vector generation for human gene therapy.

Nucleic Acids Res 2013 Jul 15;41(13):6609-17. Epub 2013 May 15.

Department of Microbiology and Immunology, Sol Sherry Thrombosis Research Center, Temple University, Philadelphia, PA 19140, USA.

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http://dx.doi.org/10.1093/nar/gkt404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711426PMC
July 2013

and Model Systems for Hemophilia A Gene Therapy.

J Genet Syndr Gene Ther 2013 Jan;Suppl 1

Department of Microbiology and Immunology, Sol Sherry Thrombosis Research Center, Temple University, Philadelphia, PA, USA.

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http://dx.doi.org/10.4172/2157-7412.S1-014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4229687PMC
January 2013

Dark Matter RNA: Existence, Function, and Controversy.

Front Genet 2012 23;3:60. Epub 2012 Apr 23.

St. Laurent Institute Cambridge, MA, USA.

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http://dx.doi.org/10.3389/fgene.2012.00060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3332219PMC
October 2012

Landscape of transcription in human cells.

Nature 2012 Sep;489(7414):101-8

Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.

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http://dx.doi.org/10.1038/nature11233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684276PMC
September 2012

Dark matter RNA: an intelligent scaffold for the dynamic regulation of the nuclear information landscape.

Front Genet 2012 26;3:57. Epub 2012 Apr 26.

Immunovirology - Biogenesis Group, University of Antioquia, Medellin, Colombia.

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http://dx.doi.org/10.3389/fgene.2012.00057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3336093PMC
July 2012

Profiling of short RNAs using Helicos single-molecule sequencing.

Methods Mol Biol 2012 ;822:219-32

Helicos BioSciences Corporation, Cambridge, MA, USA.

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http://dx.doi.org/10.1007/978-1-61779-427-8_15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272357PMC
April 2012

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells.

Nature 2011 May 8;473(7347):394-7. Epub 2011 May 8.

Harvard Medical School, Immune Disease Institute and Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/nature10102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3124347PMC
May 2011

Protocol dependence of sequencing-based gene expression measurements.

PLoS One 2011 May 6;6(5):e19287. Epub 2011 May 6.

Applications, Methods, and Collaborations Group, Helicos BioSciences, Cambridge, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019287PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3089619PMC
May 2011

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Science 2010 Dec 22;330(6012):1787-97. Epub 2010 Dec 22.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.

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http://compbio.mit.edu/publications/46_modENCODE_Science_10.
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http://www.sciencemag.org/cgi/doi/10.1126/science.1198374
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http://dx.doi.org/10.1126/science.1198374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495PMC
December 2010

Error tolerant indexing and alignment of short reads with covering template families.

J Comput Biol 2010 Oct;17(10):1397-1411

Helicos BioSciences Corporation, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1089/cmb.2010.0005DOI Listing
October 2010

Genome-wide mapping indicates that p73 and p63 co-occupy target sites and have similar dna-binding profiles in vivo.

PLoS One 2010 Jul 14;5(7):e11572. Epub 2010 Jul 14.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0011572PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2904373PMC
July 2010

High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans.

Genome Biol 2009 24;10(9):R101. Epub 2009 Sep 24.

Donnelly CCBR, College Street, University of Toronto, Toronto, M5S 3E1, Canada.

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http://dx.doi.org/10.1186/gb-2009-10-9-r101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768976PMC
February 2010

From transcription start site to cell biology.

Authors:
Philipp Kapranov

Genome Biol 2009 20;10(4):217. Epub 2009 Apr 20.

Helicos BioSciences Corporation, One Kendall Square Building 700, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1186/gb-2009-10-4-217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688922PMC
September 2009

Studying chromosome-wide transcriptional networks: new insights into disease?

Authors:
Philipp Kapranov

Genome Med 2009 May 11;1(5):50. Epub 2009 May 11.

Helicos BioSciences Corporation, One Kendall Square Bldg 700, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1186/gm50DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689442PMC
May 2009

Differential analysis for high density tiling microarray data.

BMC Bioinformatics 2007 Sep 24;8:359. Epub 2007 Sep 24.

Affymetrix Inc,, Santa Clara, CA 95051, USA.

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http://dx.doi.org/10.1186/1471-2105-8-359DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2231405PMC
September 2007

Genome-wide transcription and the implications for genomic organization.

Nat Rev Genet 2007 Jun 8;8(6):413-23. Epub 2007 May 8.

Affymetrix, Inc., 3420 Central Expressway, Santa Clara, California 95051, USA.

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http://dx.doi.org/10.1038/nrg2083DOI Listing
June 2007

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells.

Mol Cell 2006 Nov;24(4):593-602

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1016/j.molcel.2006.10.018DOI Listing
November 2006

Microarray-based DNA methylation profiling: technology and applications.

Nucleic Acids Res 2006 20;34(2):528-42. Epub 2006 Jan 20.

The Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, 250 College Street, Toronto, ON, Canada M5T 1R8.

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http://dx.doi.org/10.1093/nar/gkj461DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1345696PMC
February 2006

Temporal profile of replication of human chromosomes.

Proc Natl Acad Sci U S A 2005 May 21;102(18):6419-24. Epub 2005 Apr 21.

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.

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http://dx.doi.org/10.1073/pnas.0405088102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088349PMC
May 2005

Beyond expression profiling: next generation uses of high density oligonucleotide arrays.

Brief Funct Genomic Proteomic 2003 Apr;2(1):47-56

Affymetrix, Inc., Santa Clara, CA 95051, USA.

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http://dx.doi.org/10.1093/bfgp/2.1.47DOI Listing
April 2003

Large-scale transcriptional activity in chromosomes 21 and 22.

Science 2002 May;296(5569):916-9

Affymetrix, Santa Clara, CA 95051, USA., National Cancer Institute, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1126/science.1068597DOI Listing
May 2002