Venkat S Malladi

Venkat S Malladi

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Venkat S Malladi

Venkat S Malladi

Publications by authors named "Venkat S Malladi"

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29Publications

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Activation of PARP-1 by snoRNAs Controls Ribosome Biogenesis and Cell Growth via the RNA Helicase DDX21.

Mol Cell 2019 09 24;75(6):1270-1285.e14. Epub 2019 Jul 24.

Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2019.06.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6754283PMC
September 2019

Cardiac Reprogramming Factors Synergistically Activate Genome-wide Cardiogenic Stage-Specific Enhancers.

Cell Stem Cell 2019 Jul 9;25(1):69-86.e5. Epub 2019 May 9.

Department of Molecular Biology, the Hamon Center for Regenerative Science and Medicine, and Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2019.03.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6754266PMC
July 2019

Open collaborative writing with Manubot.

PLoS Comput Biol 2019 06 24;15(6):e1007128. Epub 2019 Jun 24.

Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1007128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6611653PMC
June 2019

Identification of a multipotent Twist2-expressing cell population in the adult heart.

Proc Natl Acad Sci U S A 2018 09 20;115(36):E8430-E8439. Epub 2018 Aug 20.

Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390;

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http://dx.doi.org/10.1073/pnas.1800526115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6130356PMC
September 2018

Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis.

Genome Res 2018 02 22;28(2):159-170. Epub 2017 Dec 22.

Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.

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http://dx.doi.org/10.1101/gr.226019.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793780PMC
February 2018

Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes.

BMC Genomics 2018 02 20;19(1):150. Epub 2018 Feb 20.

The Department of Epigenetics and Molecular Carcinogenesis, University of Texas Graduate School of Biomedical Sciences at Houston and The Center for Cancer Epigenetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA.

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http://dx.doi.org/10.1186/s12864-018-4533-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5819162PMC
February 2018

Computational Approaches for Mining GRO-Seq Data to Identify and Characterize Active Enhancers.

Methods Mol Biol 2017 ;1468:121-38

The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8511, USA.

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http://dx.doi.org/10.1007/978-1-4939-4035-6_10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5522910PMC
January 2018

Transcription pausing regulates mouse embryonic stem cell differentiation.

Stem Cell Res 2017 12 16;25:250-255. Epub 2017 Nov 16.

Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S18735061173024
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http://dx.doi.org/10.1016/j.scr.2017.11.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5732849PMC
December 2017

Ontology application and use at the ENCODE DCC.

Database (Oxford) 2015 16;2015. Epub 2015 Mar 16.

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA and Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA

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http://dx.doi.org/10.1093/database/bav010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4360730PMC
September 2015

A comparative encyclopedia of DNA elements in the mouse genome.

Authors:
Feng Yue Yong Cheng Alessandra Breschi Jeff Vierstra Weisheng Wu Tyrone Ryba Richard Sandstrom Zhihai Ma Carrie Davis Benjamin D Pope Yin Shen Dmitri D Pervouchine Sarah Djebali Robert E Thurman Rajinder Kaul Eric Rynes Anthony Kirilusha Georgi K Marinov Brian A Williams Diane Trout Henry Amrhein Katherine Fisher-Aylor Igor Antoshechkin Gilberto DeSalvo Lei-Hoon See Meagan Fastuca Jorg Drenkow Chris Zaleski Alex Dobin Pablo Prieto Julien Lagarde Giovanni Bussotti Andrea Tanzer Olgert Denas Kanwei Li M A Bender Miaohua Zhang Rachel Byron Mark T Groudine David McCleary Long Pham Zhen Ye Samantha Kuan Lee Edsall Yi-Chieh Wu Matthew D Rasmussen Mukul S Bansal Manolis Kellis Cheryl A Keller Christapher S Morrissey Tejaswini Mishra Deepti Jain Nergiz Dogan Robert S Harris Philip Cayting Trupti Kawli Alan P Boyle Ghia Euskirchen Anshul Kundaje Shin Lin Yiing Lin Camden Jansen Venkat S Malladi Melissa S Cline Drew T Erickson Vanessa M Kirkup Katrina Learned Cricket A Sloan Kate R Rosenbloom Beatriz Lacerda de Sousa Kathryn Beal Miguel Pignatelli Paul Flicek Jin Lian Tamer Kahveci Dongwon Lee W James Kent Miguel Ramalho Santos Javier Herrero Cedric Notredame Audra Johnson Shinny Vong Kristen Lee Daniel Bates Fidencio Neri Morgan Diegel Theresa Canfield Peter J Sabo Matthew S Wilken Thomas A Reh Erika Giste Anthony Shafer Tanya Kutyavin Eric Haugen Douglas Dunn Alex P Reynolds Shane Neph Richard Humbert R Scott Hansen Marella De Bruijn Licia Selleri Alexander Rudensky Steven Josefowicz Robert Samstein Evan E Eichler Stuart H Orkin Dana Levasseur Thalia Papayannopoulou Kai-Hsin Chang Arthur Skoultchi Srikanta Gosh Christine Disteche Piper Treuting Yanli Wang Mitchell J Weiss Gerd A Blobel Xiaoyi Cao Sheng Zhong Ting Wang Peter J Good Rebecca F Lowdon Leslie B Adams Xiao-Qiao Zhou Michael J Pazin Elise A Feingold Barbara Wold James Taylor Ali Mortazavi Sherman M Weissman John A Stamatoyannopoulos Michael P Snyder Roderic Guigo Thomas R Gingeras David M Gilbert Ross C Hardison Michael A Beer Bing Ren

Nature 2014 Nov;515(7527):355-64

Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature13992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106PMC
November 2014

ENCODE data in the UCSC Genome Browser: year 5 update.

Nucleic Acids Res 2013 Jan 27;41(Database issue):D56-63. Epub 2012 Nov 27.

Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gks1172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531152PMC
January 2013

An encyclopedia of mouse DNA elements (Mouse ENCODE).

August 2012

The effect of SNP discovery method and sample size on estimation of population genetic data for Chinese and Indian rhesus macaques (Macaca mulatta).

Primates 2011 Apr 5;52(2):129-38. Epub 2011 Jan 5.

Department of Anthropology, University of California, Davis, 330 Young Hall, One Shields Avenue, Davis, CA 95616, USA.

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http://dx.doi.org/10.1007/s10329-010-0232-4DOI Listing
April 2011

ENCODE whole-genome data in the UCSC genome browser (2011 update).

Nucleic Acids Res 2011 Jan 30;39(Database issue):D871-5. Epub 2010 Oct 30.

Center for Biomolecular Science and Engineering, School of Engineering and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gkq1017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013645PMC
January 2011

Analysis of forensic SNPs in the canine mtDNA HV1 mutational hotspot region.

J Forensic Sci 2008 Nov 18;53(6):1325-33. Epub 2008 Sep 18.

The Jan Bashinski DNA Laboratory, California Department of Justice, Richmond, CA 94804, USA.

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http://dx.doi.org/10.1111/j.1556-4029.2008.00880.xDOI Listing
November 2008