Publications by authors named "Gary Schroth"

88Publications

Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples.

BMC Genomics 2019 Feb 26;20(1):155. Epub 2019 Feb 26.

Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center - Frederick, Fort Detrick, Frederick, MD, 21702, USA.

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https://bmcgenomics.biomedcentral.com/articles/10.1186/s1286
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http://dx.doi.org/10.1186/s12864-019-5543-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6390631PMC
February 2019

Complete genome sequence of a KI polyomavirus isolated from an otherwise healthy child with severe lower respiratory tract infection.

J Med Virol 2017 05 9;89(5):926-930. Epub 2016 Nov 9.

Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico.

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http://dx.doi.org/10.1002/jmv.24706DOI Listing
May 2017

Molecular Evidence of Sexual Transmission of Ebola Virus.

N Engl J Med 2015 Dec 14;373(25):2448-54. Epub 2015 Oct 14.

From the Center for Genome Sciences (S.E.M., J.R.K., J.T.L., M.R.W., K.P., M.S.-L., G.P.) and Diagnostic Systems Division (R.J.S.), U.S. Army Medical Research Institute of Infectious Diseases, and the Division of Clinical Research, Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH) (J.P., L.E.H., J.H.K.) - all in Frederick, MD; the Ministry of Health and Social Welfare (T.G.N., S.B.S., M.B., F.N.K.) and the World Health Organization (WHO) (G.J.D.-W., R.M.), Monrovia, and the Liberian Institute for Biomedical Research, Charlesville (L.F., F.T., F.B.) - all in Liberia; WHO, Geneva (T.C.-L., A.G., P.F.); the Centers for Disease Control and Prevention, Atlanta (A.C., B.W.H., U.S., D.J.B., A.S.L., D.E.W., T.L., S.T.N., K.M.D.C.); Illumina, San Diego, CA (G.P.S., S.M.G.); WHO, New Delhi, India (S.A.S); Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT (E.W., N.D., V.J.M., D.S.); Naval Medical Research Unit 3, Cairo (J.W.D.); and the Foundation Mérieux, Washington, DC (J.F.).

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http://dx.doi.org/10.1056/NEJMoa1509773DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4711355PMC
December 2015

Quantitative assessment of RNA-protein interactions with high-throughput sequencing-RNA affinity profiling.

Nat Protoc 2015 Aug 16;10(8):1212-33. Epub 2015 Jul 16.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.

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http://www.nature.com/articles/nprot.2015.074
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http://dx.doi.org/10.1038/nprot.2015.074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4714542PMC
August 2015

LIN28A Modulates Splicing and Gene Expression Programs in Breast Cancer Cells.

Mol Cell Biol 2015 Sep 6;35(18):3225-43. Epub 2015 Jul 6.

Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA

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http://dx.doi.org/10.1128/MCB.00426-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4539381PMC
September 2015

Exome-level comparison of primary well-differentiated neuroendocrine tumors and their cell lines.

Cancer Genet 2015 Jul-Aug;208(7-8):374-81. Epub 2015 Apr 14.

Department of Medical Oncology, Mayo Clinic, Rochester, MN, USA; Mayo Clinic Cancer Center, Rochester, MN, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cancergen.2015.04.002DOI Listing
October 2015

Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming.

Cell Stem Cell 2015 Jan;16(1):88-101

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2014.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4291542PMC
January 2015

Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR).

Nucleic Acids Res 2015 Jan 11;43(Database issue):D737-42. Epub 2014 Nov 11.

Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA Institute for Computational Biology (ICB), Weill Cornell Medical College, New York, NY 10065, USA Feil Family Brain and Mind Research Institute (BMRI), Weill Cornell Medical College, New York, NY 10065, USA

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http://dx.doi.org/10.1093/nar/gku1110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383927PMC
January 2015

Metagenomic shotgun sequencing of a Bunyavirus in wild-caught Aedes aegypti from Thailand informs the evolutionary and genomic history of the Phleboviruses.

Virology 2014 Sep 9;464-465:312-319. Epub 2014 Aug 9.

Department of Microbiology, California Academy of Sciences, 55 Music Concourse Drive, Golden Gate Park, San Francisco, CA 94118, United States of America. Electronic address:

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http://dx.doi.org/10.1016/j.virol.2014.06.036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157124PMC
September 2014

Genomic profiling of collaborative cross founder mice infected with respiratory viruses reveals novel transcripts and infection-related strain-specific gene and isoform expression.

G3 (Bethesda) 2014 Jun 5;4(8):1429-44. Epub 2014 Jun 5.

Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research, Portland, Oregon

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http://dx.doi.org/10.1534/g3.114.011759DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132174PMC
June 2014

Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data.

J Med Primatol 2014 Oct 8;43(5):317-28. Epub 2014 May 8.

Department of Microbiology, University of Washington, Seattle, WA, USA; Washington National Primate Research Center, Seattle, WA, USA.

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http://dx.doi.org/10.1111/jmp.12125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4176519PMC
October 2014

Comprehensive analysis of RNA-protein interactions by high-throughput sequencing-RNA affinity profiling.

Nat Methods 2014 Jun 8;11(6):683-8. Epub 2014 May 8.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.

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http://www.nature.com/articles/nmeth.2970
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http://dx.doi.org/10.1038/nmeth.2970DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073888PMC
June 2014

From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing.

Genome Res 2014 Mar 3;24(3):496-510. Epub 2013 Dec 3.

Division of Biology, California Institute of Technology, Pasadena, California 91125, USA;

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http://genome.cshlp.org/cgi/doi/10.1101/gr.161034.113
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http://dx.doi.org/10.1101/gr.161034.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3941114PMC
March 2014

Cohesin-mediated interactions organize chromosomal domain architecture.

EMBO J 2013 Dec 1;32(24):3119-29. Epub 2013 Nov 1.

Research Department of Cancer Biology, Cancer Institute, University College London, London, UK.

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http://dx.doi.org/10.1038/emboj.2013.237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489921PMC
December 2013

Single-neuron RNA-Seq: technical feasibility and reproducibility.

Front Genet 2012 6;3:124. Epub 2012 Jul 6.

Zilkha Neurogenetic Institute, University of Southern California Los Angeles, CA, USA.

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http://journal.frontiersin.org/article/10.3389/fgene.2012.00
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http://dx.doi.org/10.3389/fgene.2012.00124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3407998PMC
October 2012

Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq.

Nucleic Acids Res 2011 Nov 31;39(20):e140. Epub 2011 Aug 31.

Institute of Molecular Biology and Genetics, School of Biological Sciences & Institute of Bioinformatics (BIOMAX), Seoul National University, Seoul, Republic of Korea.

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http://dx.doi.org/10.1093/nar/gkr617DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203590PMC
November 2011

Meraculous: de novo genome assembly with short paired-end reads.

PLoS One 2011 18;6(8):e23501. Epub 2011 Aug 18.

U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0023501PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158087PMC
December 2011

Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing.

Nucleic Acids Res 2011 Oct 23;39(19):e127. Epub 2011 Jul 23.

GHSU Cancer Center, Department of Biochemistry and Molecular Biology, Georgia Health Sciences University, Augusta, GA 30912, USA.

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http://dx.doi.org/10.1093/nar/gkr598DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3201883PMC
October 2011

RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries.

RNA 2011 Sep 20;17(9):1697-712. Epub 2011 Jul 20.

Howard Hughes Medical Institute, Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA.

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http://dx.doi.org/10.1261/rna.2799511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3162335PMC
September 2011

Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument.

Nat Biotechnol 2011 Jun 26;29(7):659-64. Epub 2011 Jun 26.

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.1882DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3134637PMC
June 2011

Modeling and automation of sequencing-based characterization of RNA structure.

Proc Natl Acad Sci U S A 2011 Jul 3;108(27):11069-74. Epub 2011 Jun 3.

Department of Bioengineering, University of California, Berkeley, CA 94720, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1106541108
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http://dx.doi.org/10.1073/pnas.1106541108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3131376PMC
July 2011

A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines.

Nucleic Acids Res 2011 Aug 27;39(15):e100. Epub 2011 May 27.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA.

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http://dx.doi.org/10.1093/nar/gkr362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159479PMC
August 2011

Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing.

PLoS One 2011 Feb 25;6(2):e17490. Epub 2011 Feb 25.

Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0017490PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3045451PMC
February 2011

Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq.

PLoS Biol 2011 Feb 8;9(2):e1000590. Epub 2011 Feb 8.

Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America.

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https://dx.plos.org/10.1371/journal.pbio.1000590
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http://dx.doi.org/10.1371/journal.pbio.1000590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035605PMC
February 2011

High-throughput SuperSAGE.

Methods Mol Biol 2011 ;687:135-46

Iwate Biotechnology Research Center, Kitakami, Iwate, Japan.

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http://dx.doi.org/10.1007/978-1-60761-944-4_9DOI Listing
February 2011

MetMap enables genome-scale Methyltyping for determining methylation states in populations.

PLoS Comput Biol 2010 Aug 19;6(8):e1000888. Epub 2010 Aug 19.

Computer Science Division, University of California at Berkeley, Berkeley, California, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1000888DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2924245PMC
August 2010

Genome-wide analysis of DNA methylation and gene expression changes in the mouse lung following subchronic arsenate exposure.

Toxicol Sci 2010 Oct 28;117(2):404-17. Epub 2010 Jul 28.

The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709, USA.

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http://dx.doi.org/10.1093/toxsci/kfq225DOI Listing
October 2010

High-resolution analysis of parent-of-origin allelic expression in the mouse brain.

Science 2010 Aug 8;329(5992):643-8. Epub 2010 Jul 8.

Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1126/science.1190830DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3005244PMC
August 2010

Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome.

Nat Protoc 2009 ;4(3):356-62

Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA.

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http://dx.doi.org/10.1038/nprot.2009.8DOI Listing
April 2009

Accurate whole human genome sequencing using reversible terminator chemistry.

Authors:
David R Bentley Shankar Balasubramanian Harold P Swerdlow Geoffrey P Smith John Milton Clive G Brown Kevin P Hall Dirk J Evers Colin L Barnes Helen R Bignell Jonathan M Boutell Jason Bryant Richard J Carter R Keira Cheetham Anthony J Cox Darren J Ellis Michael R Flatbush Niall A Gormley Sean J Humphray Leslie J Irving Mirian S Karbelashvili Scott M Kirk Heng Li Xiaohai Liu Klaus S Maisinger Lisa J Murray Bojan Obradovic Tobias Ost Michael L Parkinson Mark R Pratt Isabelle M J Rasolonjatovo Mark T Reed Roberto Rigatti Chiara Rodighiero Mark T Ross Andrea Sabot Subramanian V Sankar Aylwyn Scally Gary P Schroth Mark E Smith Vincent P Smith Anastassia Spiridou Peta E Torrance Svilen S Tzonev Eric H Vermaas Klaudia Walter Xiaolin Wu Lu Zhang Mohammed D Alam Carole Anastasi Ify C Aniebo David M D Bailey Iain R Bancarz Saibal Banerjee Selena G Barbour Primo A Baybayan Vincent A Benoit Kevin F Benson Claire Bevis Phillip J Black Asha Boodhun Joe S Brennan John A Bridgham Rob C Brown Andrew A Brown Dale H Buermann Abass A Bundu James C Burrows Nigel P Carter Nestor Castillo Maria Chiara E Catenazzi Simon Chang R Neil Cooley Natasha R Crake Olubunmi O Dada Konstantinos D Diakoumakos Belen Dominguez-Fernandez David J Earnshaw Ugonna C Egbujor David W Elmore Sergey S Etchin Mark R Ewan Milan Fedurco Louise J Fraser Karin V Fuentes Fajardo W Scott Furey David George Kimberley J Gietzen Colin P Goddard George S Golda Philip A Granieri David E Green David L Gustafson Nancy F Hansen Kevin Harnish Christian D Haudenschild Narinder I Heyer Matthew M Hims Johnny T Ho Adrian M Horgan Katya Hoschler Steve Hurwitz Denis V Ivanov Maria Q Johnson Terena James T A Huw Jones Gyoung-Dong Kang Tzvetana H Kerelska Alan D Kersey Irina Khrebtukova Alex P Kindwall Zoya Kingsbury Paula I Kokko-Gonzales Anil Kumar Marc A Laurent Cynthia T Lawley Sarah E Lee Xavier Lee Arnold K Liao Jennifer A Loch Mitch Lok Shujun Luo Radhika M Mammen John W Martin Patrick G McCauley Paul McNitt Parul Mehta Keith W Moon Joe W Mullens Taksina Newington Zemin Ning Bee Ling Ng Sonia M Novo Michael J O'Neill Mark A Osborne Andrew Osnowski Omead Ostadan Lambros L Paraschos Lea Pickering Andrew C Pike Alger C Pike D Chris Pinkard Daniel P Pliskin Joe Podhasky Victor J Quijano Come Raczy Vicki H Rae Stephen R Rawlings Ana Chiva Rodriguez Phyllida M Roe John Rogers Maria C Rogert Bacigalupo Nikolai Romanov Anthony Romieu Rithy K Roth Natalie J Rourke Silke T Ruediger Eli Rusman Raquel M Sanches-Kuiper Martin R Schenker Josefina M Seoane Richard J Shaw Mitch K Shiver Steven W Short Ning L Sizto Johannes P Sluis Melanie A Smith Jean Ernest Sohna Sohna Eric J Spence Kim Stevens Neil Sutton Lukasz Szajkowski Carolyn L Tregidgo Gerardo Turcatti Stephanie Vandevondele Yuli Verhovsky Selene M Virk Suzanne Wakelin Gregory C Walcott Jingwen Wang Graham J Worsley Juying Yan Ling Yau Mike Zuerlein Jane Rogers James C Mullikin Matthew E Hurles Nick J McCooke John S West Frank L Oaks Peter L Lundberg David Klenerman Richard Durbin Anthony J Smith

Nature 2008 Nov;456(7218):53-9

Illumina Cambridge Ltd. (Formerly Solexa Ltd), Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex CB10 1XL, UK.

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http://dx.doi.org/10.1038/nature07517DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581791PMC
November 2008

Alternative isoform regulation in human tissue transcriptomes.

Nature 2008 Nov;456(7221):470-6

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1038/nature07509DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593745PMC
November 2008

Highly sensitive and specific microRNA expression profiling using BeadArray technology.

Nucleic Acids Res 2008 Aug 25;36(14):e87. Epub 2008 Jun 25.

Illumina, Inc. 9885 Towne Centre Drive, San Diego, CA 92121, USA.

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http://dx.doi.org/10.1093/nar/gkn387DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2504321PMC
August 2008

Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends.

Nat Biotechnol 2008 Aug 9;26(8):941-6. Epub 2008 Jun 9.

Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA.

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http://dx.doi.org/10.1038/nbt1417DOI Listing
August 2008

Differences in hepatotoxicity and gene expression profiles by anti-diabetic PPAR gamma agonists on rat primary hepatocytes and human HepG2 cells.

Mol Divers 2006 Aug 21;10(3):349-60. Epub 2006 Sep 21.

Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.

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http://dx.doi.org/10.1007/s11030-006-9038-0DOI Listing
August 2006

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.

Authors:
Leming Shi Laura H Reid Wendell D Jones Richard Shippy Janet A Warrington Shawn C Baker Patrick J Collins Francoise de Longueville Ernest S Kawasaki Kathleen Y Lee Yuling Luo Yongming Andrew Sun James C Willey Robert A Setterquist Gavin M Fischer Weida Tong Yvonne P Dragan David J Dix Felix W Frueh Frederico M Goodsaid Damir Herman Roderick V Jensen Charles D Johnson Edward K Lobenhofer Raj K Puri Uwe Schrf Jean Thierry-Mieg Charles Wang Mike Wilson Paul K Wolber Lu Zhang Shashi Amur Wenjun Bao Catalin C Barbacioru Anne Bergstrom Lucas Vincent Bertholet Cecilie Boysen Bud Bromley Donna Brown Alan Brunner Roger Canales Xiaoxi Megan Cao Thomas A Cebula James J Chen Jing Cheng Tzu-Ming Chu Eugene Chudin John Corson J Christopher Corton Lisa J Croner Christopher Davies Timothy S Davison Glenda Delenstarr Xutao Deng David Dorris Aron C Eklund Xiao-hui Fan Hong Fang Stephanie Fulmer-Smentek James C Fuscoe Kathryn Gallagher Weigong Ge Lei Guo Xu Guo Janet Hager Paul K Haje Jing Han Tao Han Heather C Harbottle Stephen C Harris Eli Hatchwell Craig A Hauser Susan Hester Huixiao Hong Patrick Hurban Scott A Jackson Hanlee Ji Charles R Knight Winston P Kuo J Eugene LeClerc Shawn Levy Quan-Zhen Li Chunmei Liu Ying Liu Michael J Lombardi Yunqing Ma Scott R Magnuson Botoul Maqsodi Tim McDaniel Nan Mei Ola Myklebost Baitang Ning Natalia Novoradovskaya Michael S Orr Terry W Osborn Adam Papallo Tucker A Patterson Roger G Perkins Elizabeth H Peters Ron Peterson Kenneth L Philips P Scott Pine Lajos Pusztai Feng Qian Hongzu Ren Mitch Rosen Barry A Rosenzweig Raymond R Samaha Mark Schena Gary P Schroth Svetlana Shchegrova Dave D Smith Frank Staedtler Zhenqiang Su Hongmei Sun Zoltan Szallasi Zivana Tezak Danielle Thierry-Mieg Karol L Thompson Irina Tikhonova Yaron Turpaz Beena Vallanat Christophe Van Stephen J Walker Sue Jane Wang Yonghong Wang Russ Wolfinger Alex Wong Jie Wu Chunlin Xiao Qian Xie Jun Xu Wen Yang Liang Zhang Sheng Zhong Yaping Zong William Slikker

Nat Biotechnol 2006 Sep;24(9):1151-61

National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA.

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http://dx.doi.org/10.1038/nbt1239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272078PMC
September 2006