Ankit Malhotra

Ankit Malhotra

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Ankit Malhotra

Ankit Malhotra

Publications by authors named "Ankit Malhotra"

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Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Nat Commun 2019 04 16;10(1):1784. Epub 2019 Apr 16.

The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.

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http://www.nature.com/articles/s41467-018-08148-z
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http://dx.doi.org/10.1038/s41467-018-08148-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467913PMC
April 2019

Computational inference of a genomic pluripotency signature in human and mouse stem cells.

Biol Direct 2016 09 17;11:47. Epub 2016 Sep 17.

The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA.

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http://dx.doi.org/10.1186/s13062-016-0148-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5027095PMC
September 2016

An integrated map of structural variation in 2,504 human genomes.

Nature 2015 Oct;526(7571):75-81

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature15394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617611PMC
October 2015

Efficient CRISPR/Cas9-Mediated Genome Editing in Mice by Zygote Electroporation of Nuclease.

Genetics 2015 Jun 27;200(2):423-30. Epub 2015 Mar 27.

The Jackson Laboratory, Bar Harbor, Maine 04609 State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100090, China

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http://www.genetics.org/content/genetics/200/2/423.full.pdf
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http://www.genetics.org/cgi/doi/10.1534/genetics.115.176594
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http://dx.doi.org/10.1534/genetics.115.176594DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4492369PMC
June 2015

Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations.

Genome Med 2015 28;7(1). Epub 2015 Jan 28.

Department of Genetics, MD Anderson Cancer Center, Houston, TX USA ; Department of Bioinformatics, MD Anderson Cancer Center, Houston, TX USA ; Graduate Program in Genes and Development, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, TX USA.

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http://dx.doi.org/10.1186/s13073-015-0127-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343275PMC
March 2015

Systems consequences of amplicon formation in human breast cancer.

Genome Res 2014 Oct 3;24(10):1559-71. Epub 2014 Sep 3.

Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Genome, Singapore 138672, Singapore; The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06030, USA; The Jackson Laboratory, Bar Harbor, Maine 04609, USA;

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http://dx.doi.org/10.1101/gr.164871.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4199368PMC
October 2014

Facile and rapid thermo-regulated biomineralization of gold by pullulan and study of its thermodynamic parameters.

Carbohydr Polym 2014 Jun 7;106:154-9. Epub 2014 Feb 7.

CSIR - Institute of Microbial Technology (IMTECH), Council of Scientific and Industrial Research, Sector 39A, Chandigarh 160 036, India.

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http://dx.doi.org/10.1016/j.carbpol.2014.01.072DOI Listing
June 2014

Chromosomal structural variations during progression of a prostate epithelial cell line to a malignant metastatic state inactivate the NF2, NIPSNAP1, UGT2B17, and LPIN2 genes.

Cancer Biol Ther 2013 Sep 26;14(9):840-52. Epub 2013 Jul 26.

Department of Biochemistry and Molecular Genetics; University of Virginia School of Medicine; Charlottesville, VA USA.

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http://dx.doi.org/10.4161/cbt.25329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3909553PMC
September 2013

Biosynthesis of gold and silver nanoparticles using a novel marine strain of Stenotrophomonas.

Bioresour Technol 2013 Aug 31;142:727-31. Epub 2013 May 31.

CSIR-Institute of Microbial Technology (IMTECH), Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh 160 036, India.

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http://dx.doi.org/10.1016/j.biortech.2013.05.109DOI Listing
August 2013

In-Ear Pulse Wave Measurements: A Pilot Study.

Biomed Tech (Berl) 2013 08 7;58 Suppl 1. Epub 2013 Sep 7.

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http://dx.doi.org/10.1515/bmt-2013-4128DOI Listing
August 2013

Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms.

Genome Res 2013 May 14;23(5):762-76. Epub 2013 Feb 14.

Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22903, USA.

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http://dx.doi.org/10.1101/gr.143677.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3638133PMC
May 2013

Abberantly placed impacted mandibular canine.

Contemp Clin Dent 2013 Apr;4(2):217-9

Department of Oral and Maxillofacial Surgery, Genesis Institute of Dental Sciences and Research, Ferozepur, Punjab, India.

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http://dx.doi.org/10.4103/0976-237X.114850DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3757885PMC
April 2013

Detection of DNA fusion junctions for BCR-ABL translocations by Anchored ChromPET.

Genome Med 2010 Sep 22;2(9):70. Epub 2010 Sep 22.

Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, 1300 Jefferson Pk Ave, Charlottesville, VA 22908-0733, USA.

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http://dx.doi.org/10.1186/gm191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3092121PMC
September 2010

Genomic study of replication initiation in human chromosomes reveals the influence of transcription regulation and chromatin structure on origin selection.

Mol Biol Cell 2010 Feb 2;21(3):393-404. Epub 2009 Dec 2.

Departments of *Biochemistry and Molecular Genetics and Computer Science, University of Virginia, Charlottesville, VA 22908, USA.

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http://www.molbiolcell.org/doi/10.1091/mbc.e09-08-0707
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http://dx.doi.org/10.1091/mbc.e09-08-0707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2814785PMC
February 2010

A novel class of small RNAs: tRNA-derived RNA fragments (tRFs).

Genes Dev 2009 Nov;23(22):2639-49

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

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http://genesdev.cshlp.org/content/23/22/2639.full.pdf
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http://genesdev.cshlp.org/lookup/doi/10.1101/gad.1837609
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http://dx.doi.org/10.1101/gad.1837609DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779758PMC
November 2009

Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas.

Genome Res 2007 Jun;17(6):865-76

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

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http://www.genome.org/cgi/doi/10.1101/gr.5427007
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http://dx.doi.org/10.1101/gr.5427007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891345PMC
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

Targeted comparative RNA interference analysis reveals differential requirement of genes essential for cell proliferation.

Mol Biol Cell 2006 Nov 6;17(11):4837-45. Epub 2006 Sep 6.

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

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http://dx.doi.org/10.1091/mbc.e06-04-0340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635399PMC
November 2006

Muscle-specific microRNA miR-206 promotes muscle differentiation.

J Cell Biol 2006 Aug 21;174(5):677-87. Epub 2006 Aug 21.

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

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http://dx.doi.org/10.1083/jcb.200603008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2064311PMC
August 2006