Steven Salzberg

Steven Salzberg

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Steven Salzberg

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Author Correction: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations.

Nat Commun 2019 Sep 4;10(1):4082. Epub 2019 Sep 4.

Department of Medicine, University of Colorado Denver, Aurora, CO, 80045, USA.

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http://dx.doi.org/10.1038/s41467-019-12158-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6726619PMC
September 2019

Pavian: Interactive analysis of metagenomics data for microbiome studies and pathogen identification.

Bioinformatics 2019 Sep 25. Epub 2019 Sep 25.

Departments of Biomedical Engineering, Computer Science and Biostatistics, Johns Hopkins University, Baltimore, MD, United States.

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http://dx.doi.org/10.1093/bioinformatics/btz715DOI Listing
September 2019

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.

Nat Biotechnol 2019 08 2;37(8):907-915. Epub 2019 Aug 2.

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.

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http://dx.doi.org/10.1038/s41587-019-0201-4DOI Listing
August 2019

Human contamination in bacterial genomes has created thousands of spurious proteins.

Genome Res 2019 06 7;29(6):954-960. Epub 2019 May 7.

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.1101/gr.245373.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6581058PMC
June 2019

Next-generation genome annotation: we still struggle to get it right.

Genome Biol 2019 05 16;20(1):92. Epub 2019 May 16.

Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, 21205, USA.

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http://dx.doi.org/10.1186/s13059-019-1715-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6521345PMC
May 2019

Genomic architecture of complex traits in loblolly pine.

New Phytol 2019 03 9;221(4):1789-1801. Epub 2018 Nov 9.

Department of Plant Sciences, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA.

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http://dx.doi.org/10.1111/nph.15535DOI Listing
March 2019

The Terabase Search Engine: a large-scale relational database of short-read sequences.

Bioinformatics 2019 02;35(4):665-670

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty657DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6379032PMC
February 2019

Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations.

Nat Commun 2019 02 20;10(1):880. Epub 2019 Feb 20.

Department of Medicine, University of Colorado Denver, Aurora, CO, 80045, USA.

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http://dx.doi.org/10.1038/s41467-019-08469-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6382865PMC
February 2019

CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise.

Genome Biol 2018 11 28;19(1):208. Epub 2018 Nov 28.

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

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http://dx.doi.org/10.1186/s13059-018-1590-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6260756PMC
November 2018

Open questions: How many genes do we have?

BMC Biol 2018 08 20;16(1):94. Epub 2018 Aug 20.

Departments of Biomedical Engineering, Computer Science, and Biostatistics, Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Welch Medical Library, Rm. 107, 1900 E. Monument St, Baltimore, MD, 21205, USA.

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http://dx.doi.org/10.1186/s12915-018-0564-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6100717PMC
August 2018

Removing contaminants from databases of draft genomes.

PLoS Comput Biol 2018 06 25;14(6):e1006277. Epub 2018 Jun 25.

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1006277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6034898PMC
June 2018

Genomic characterization of chromosome translocations in patients with T/myeloid mixed-phenotype acute leukemia.

Leuk Lymphoma 2018 05 7;59(5):1231-1238. Epub 2017 Sep 7.

a Department of Pathology , Johns Hopkins University School of Medicine , Baltimore , MD , USA.

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http://dx.doi.org/10.1080/10428194.2017.1372577DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6390477PMC
May 2018

Identifying Corneal Infections in Formalin-Fixed Specimens Using Next Generation Sequencing.

Invest Ophthalmol Vis Sci 2018 01;59(1):280-288

Department of Pathology, Johns Hopkins University, Baltimore, Maryland, United States.

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http://dx.doi.org/10.1167/iovs.17-21617DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5770184PMC
January 2018

MUMmer4: A fast and versatile genome alignment system.

PLoS Comput Biol 2018 01 26;14(1):e1005944. Epub 2018 Jan 26.

Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America.

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https://dx.plos.org/10.1371/journal.pcbi.1005944
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http://dx.doi.org/10.1371/journal.pcbi.1005944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5802927PMC
January 2018

First Draft Genome Sequence of the Pathogenic Fungus (Formerly ).

G3 (Bethesda) 2017 11 6;7(11):3831-3836. Epub 2017 Nov 6.

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205

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http://dx.doi.org/10.1534/g3.117.300107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5677167PMC
November 2017

The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum.

Gigascience 2017 11;6(11):1-7

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1093/gigascience/gix097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5691383PMC
November 2017

Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs.

Ann Intern Med 2017 Jul 6;167(1):1-7. Epub 2017 Jun 6.

From Johns Hopkins University and Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.

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http://dx.doi.org/10.7326/M17-0085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5721525PMC
July 2017

16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model.

Gigascience 2017 07;6(7):1-4

Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.

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http://dx.doi.org/10.1093/gigascience/gix045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570013PMC
July 2017

Hybrid assembly of the large and highly repetitive genome of , a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm.

Genome Res 2017 05 27;27(5):787-792. Epub 2017 Jan 27.

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.1101/gr.213405.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411773PMC
May 2017

Horizontal gene transfer is not a hallmark of the human genome.

Genome Biol 2017 05 8;18(1):85. Epub 2017 May 8.

Departments of Biomedical Engineering, Computer Science and Biostatistics, Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.

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http://dx.doi.org/10.1186/s13059-017-1214-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5422933PMC
May 2017

Short Read Mapping: An Algorithmic Tour.

Proc IEEE Inst Electr Electron Eng 2017 Mar 7;105(3):436-458. Epub 2015 Sep 7.

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http://dx.doi.org/10.1109/JPROC.2015.2455551DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5425171PMC
March 2017

An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

Gigascience 2017 01;6(1):1-4

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD.

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http://dx.doi.org/10.1093/gigascience/giw016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5437942PMC
January 2017

Centrifuge: rapid and sensitive classification of metagenomic sequences.

Genome Res 2016 12 17;26(12):1721-1729. Epub 2016 Oct 17.

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.1101/gr.210641.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5131823PMC
December 2016

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.

Nat Protoc 2016 09 11;11(9):1650-67. Epub 2016 Aug 11.

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA.

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http://www.ccb.jhu.edu/people/infphilo/data/nprot.2016.095.p
Web Search
http://dx.doi.org/10.1038/nprot.2016.095DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5032908PMC
September 2016

Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system.

Neurol Neuroimmunol Neuroinflamm 2016 Aug 13;3(4):e251. Epub 2016 Jun 13.

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine (S.L.S., F.P.B.), Department of Neurology (A.K., C.A.P.), Deep Sequencing and Microarray Core (H.H.), and Departments of Pathology (P.B., F.J.R., C.A.P.), Neurosurgery (M.L., A.Q.-H., G.L.G.), and Medicine (J.A.T., M.T.M., C.L.S.), School of Medicine, and Departments of Biomedical Engineering, Computer Science, and Biostatistics (S.L.S.), Johns Hopkins University, Baltimore, MD.

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http://dx.doi.org/10.1212/NXI.0000000000000251DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907805PMC
August 2016

Reminder to deposit DNA sequences.

Science 2016 May 11;352(6287):780. Epub 2016 May 11.

Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA. Beijing Institute of Genomics, Beijing, 100101, China.

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http://dx.doi.org/10.1126/science.aaf7672DOI Listing
May 2016

Databases: Reminder to deposit DNA sequences.

Nature 2016 05;533(7602):179

Johns Hopkins University, Baltimore, USA.

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http://dx.doi.org/10.1038/533179aDOI Listing
May 2016

Use and mis-use of supplementary material in science publications.

BMC Bioinformatics 2015 Nov 3;16:237. Epub 2015 Nov 3.

Center for Computational Biology McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/s12859-015-0668-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4630891PMC
November 2015

Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms.

Genome Res 2015 Sep;25(9):1401-9

Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.

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http://dx.doi.org/10.1101/gr.193607.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561498PMC
September 2015

Re-analysis of metagenomic sequences from acute flaccid myelitis patients reveals alternatives to enterovirus D68 infection.

F1000Res 2015 2;4:180. Epub 2015 Jul 2.

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA ; Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, 21218, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4536609PMC
http://dx.doi.org/10.12688/f1000research.6743.2DOI Listing
August 2015

HISAT: a fast spliced aligner with low memory requirements.

Nat Methods 2015 Apr 9;12(4):357-60. Epub 2015 Mar 9.

1] Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. [2] Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA. [3] Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1038/nmeth.3317DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4655817PMC
April 2015

The genomes of two key bumblebee species with primitive eusocial organization.

Authors:
Ben M Sadd Seth M Barribeau Guy Bloch Dirk C de Graaf Peter Dearden Christine G Elsik Jürgen Gadau Cornelis J P Grimmelikhuijzen Martin Hasselmann Jeffrey D Lozier Hugh M Robertson Guy Smagghe Eckart Stolle Matthias Van Vaerenbergh Robert M Waterhouse Erich Bornberg-Bauer Steffen Klasberg Anna K Bennett Francisco Câmara Roderic Guigó Katharina Hoff Marco Mariotti Monica Munoz-Torres Terence Murphy Didac Santesmasses Gro V Amdam Matthew Beckers Martin Beye Matthias Biewer Márcia M G Bitondi Mark L Blaxter Andrew F G Bourke Mark J F Brown Severine D Buechel Rossanah Cameron Kaat Cappelle James C Carolan Olivier Christiaens Kate L Ciborowski David F Clarke Thomas J Colgan David H Collins Andrew G Cridge Tamas Dalmay Stephanie Dreier Louis du Plessis Elizabeth Duncan Silvio Erler Jay Evans Tiago Falcon Kevin Flores Flávia C P Freitas Taro Fuchikawa Tanja Gempe Klaus Hartfelder Frank Hauser Sophie Helbing Fernanda C Humann Frano Irvine Lars S Jermiin Claire E Johnson Reed M Johnson Andrew K Jones Tatsuhiko Kadowaki Jonathan H Kidner Vasco Koch Arian Köhler F Bernhard Kraus H Michael G Lattorff Megan Leask Gabrielle A Lockett Eamonn B Mallon David S Marco Antonio Monika Marxer Ivan Meeus Robin F A Moritz Ajay Nair Kathrin Näpflin Inga Nissen Jinzhi Niu Francis M F Nunes John G Oakeshott Amy Osborne Marianne Otte Daniel G Pinheiro Nina Rossié Olav Rueppell Carolina G Santos Regula Schmid-Hempel Björn D Schmitt Christina Schulte Zilá L P Simões Michelle P M Soares Luc Swevers Eva C Winnebeck Florian Wolschin Na Yu Evgeny M Zdobnov Peshtewani K Aqrawi Kerstin P Blankenburg Marcus Coyle Liezl Francisco Alvaro G Hernandez Michael Holder Matthew E Hudson LaRonda Jackson Joy Jayaseelan Vandita Joshi Christie Kovar Sandra L Lee Robert Mata Tittu Mathew Irene F Newsham Robin Ngo Geoffrey Okwuonu Christopher Pham Ling-Ling Pu Nehad Saada Jireh Santibanez DeNard Simmons Rebecca Thornton Aarti Venkat Kimberly K O Walden Yuan-Qing Wu Griet Debyser Bart Devreese Claire Asher Julie Blommaert Ariel D Chipman Lars Chittka Bertrand Fouks Jisheng Liu Meaghan P O'Neill Seirian Sumner Daniela Puiu Jiaxin Qu Steven L Salzberg Steven E Scherer Donna M Muzny Stephen Richards Gene E Robinson Richard A Gibbs Paul Schmid-Hempel Kim C Worley

Genome Biol 2015 Apr 24;16:76. Epub 2015 Apr 24.

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s13059-015-0623-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4414376PMC
April 2015

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.

Nat Biotechnol 2015 Mar 18;33(3):290-5. Epub 2015 Feb 18.

1] Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA. [2] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA. [3] Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA. [4] Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1038/nbt.3122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4643835PMC
March 2015

Ballgown bridges the gap between transcriptome assembly and expression analysis.

Nat Biotechnol 2015 Mar;33(3):243-6

1] Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA. [2] Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1038/nbt.3172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4792117PMC
March 2015

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space.

PeerJ 2015 3;3:e808. Epub 2015 Mar 3.

Department of Physics and Astronomy, Johns Hopkins University , Baltimore, MD , USA ; Department of Computer Science, Johns Hopkins University , USA.

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http://dx.doi.org/10.7717/peerj.808DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4358639PMC
March 2015

Unexpected cross-species contamination in genome sequencing projects.

PeerJ 2014 20;2:e675. Epub 2014 Nov 20.

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University , Baltimore, MD , USA ; Department of Computer Science, Johns Hopkins University , USA ; Department of Biomedical Engineering, Johns Hopkins University , USA.

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http://dx.doi.org/10.7717/peerj.675DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4243333PMC
November 2014

Genomic features of a bumble bee symbiont reflect its host environment.

Appl Environ Microbiol 2014 Jul 18;80(13):3793-803. Epub 2014 Apr 18.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA.

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http://dx.doi.org/10.1128/AEM.00322-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4054214PMC
July 2014

DIAMUND: direct comparison of genomes to detect mutations.

Hum Mutat 2014 Mar;35(3):283-8

Center for Computational Biology, Johns Hopkins School of Medicine, Baltimore, Maryland, 21205; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, 21205.

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http://dx.doi.org/10.1002/humu.22503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4031744PMC
March 2014

Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues.

F1000Res 2013 16;2:188. Epub 2013 Sep 16.

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA ; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA ; Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA.

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http://dx.doi.org/10.12688/f1000research.2-188.v2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892928PMC
February 2014

The MaSuRCA genome assembler.

Bioinformatics 2013 Nov 29;29(21):2669-77. Epub 2013 Aug 29.

Institute for Physical Sciences and Technology, University of Maryland, College Park, MD 20742, USA, Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA, Department of Mathematics and Department of Physics, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt476DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799473PMC
November 2013

GAGE-B: an evaluation of genome assemblers for bacterial organisms.

Bioinformatics 2013 Jul 10;29(14):1718-25. Epub 2013 May 10.

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21025, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3702249PMC
July 2013

EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes.

Evol Bioinform Online 2013 10;9:127-36. Epub 2013 Mar 10.

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

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http://dx.doi.org/10.4137/EBO.S11250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603529PMC
March 2013

Mis-assembled "segmental duplications" in two versions of the Bos taurus genome.

PLoS One 2012 3;7(8):e42680. Epub 2012 Aug 3.

Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0042680PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411808PMC
January 2013

NIH funding: It does support innovators.

Nature 2013 Jan;493(7430):26

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http://dx.doi.org/10.1038/493026bDOI Listing
January 2013

A scientist and an advocate. An interview with Steven Salzberg by Kristie Nybo.

Authors:
Steven Salzberg

Biotechniques 2012 Aug;53(2):71

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http://dx.doi.org/10.2144/000113898DOI Listing
August 2012

Fast gapped-read alignment with Bowtie 2.

Nat Methods 2012 Mar 4;9(4):357-9. Epub 2012 Mar 4.

Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, USA.

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http://www.nature.com/articles/nmeth.1923
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http://dx.doi.org/10.1038/nmeth.1923DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322381PMC
March 2012

Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths.

Genome Biol 2011 31;12(5):R51. Epub 2011 May 31.

McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L9, Canada.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2011-12-5-r51DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3219973PMC
February 2012

Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering.

Nucleic Acids Res 2012 Jan 18;40(1):e9. Epub 2011 Nov 18.

Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, Department of Computer Science, 3115 Biomolecular Sciences Building 296, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1093/nar/gkr1067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245904PMC
January 2012

Genome assembly has a major impact on gene content: a comparison of annotation in two Bos taurus assemblies.

PLoS One 2011 22;6(6):e21400. Epub 2011 Jun 22.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021400PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3120881PMC
November 2011

FLASH: fast length adjustment of short reads to improve genome assemblies.

Bioinformatics 2011 Nov 7;27(21):2957-63. Epub 2011 Sep 7.

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3198573PMC
November 2011

Repetitive DNA and next-generation sequencing: computational challenges and solutions.

Nat Rev Genet 2011 Nov 29;13(1):36-46. Epub 2011 Nov 29.

McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

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http://www.nature.com/articles/nrg3117
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http://dx.doi.org/10.1038/nrg3117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3324860PMC
November 2011

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.

Genome Biol 2011 Aug 11;12(8):R72. Epub 2011 Aug 11.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1186/gb-2011-12-8-r72DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245612PMC
August 2011

Detection of lineage-specific evolutionary changes among primate species.

BMC Bioinformatics 2011 Jul 4;12:274. Epub 2011 Jul 4.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.

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http://dx.doi.org/10.1186/1471-2105-12-274DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143108PMC
July 2011

Do-it-yourself genetic testing.

Genome Biol 2010 7;11(10):404. Epub 2010 Oct 7.

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http://dx.doi.org/10.1186/gb-2010-11-10-404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218655PMC
June 2011

Quake: quality-aware detection and correction of sequencing errors.

Genome Biol 2010 29;11(11):R116. Epub 2010 Nov 29.

Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, and Department of Computer Science, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1186/gb-2010-11-11-r116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3156955PMC
June 2011

Improving pan-genome annotation using whole genome multiple alignment.

BMC Bioinformatics 2011 Jun 30;12:272. Epub 2011 Jun 30.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1186/1471-2105-12-272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142524PMC
June 2011

Mugsy: fast multiple alignment of closely related whole genomes.

Bioinformatics 2011 Feb 9;27(3):334-42. Epub 2010 Dec 9.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq665DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3031037PMC
February 2011

Genome sequence of the dioxin-mineralizing bacterium Sphingomonas wittichii RW1.

J Bacteriol 2010 Nov 10;192(22):6101-2. Epub 2010 Sep 10.

Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1128/JB.01030-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2976435PMC
November 2010

Clustering metagenomic sequences with interpolated Markov models.

BMC Bioinformatics 2010 Nov 2;11:544. Epub 2010 Nov 2.

Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, College Park, MD 20742, USA.

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http://dx.doi.org/10.1186/1471-2105-11-544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098094PMC
November 2010

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

PLoS Biol 2010 Sep 7;8(9). Epub 2010 Sep 7.

Avian Immunobiology Laboratory, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1000475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935454PMC
September 2010

Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification.

BMC Genomics 2010 Sep 16;11:500. Epub 2010 Sep 16.

National Center for Food Safety and Technology, Illinois Institute of Technology, Summit, Illinois 60501, USA.

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http://dx.doi.org/10.1186/1471-2164-11-500DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996996PMC
September 2010

Recent advances in RNA sequence analysis.

F1000 Biol Rep 2010 Aug 19;2:64. Epub 2010 Aug 19.

Center for Bioinformatics and Computational Biology and Department of Computer Science, University of Maryland College Park, MD 20742 USA.

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http://dx.doi.org/10.3410/B2-64DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990453PMC
August 2010