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Salzberg Lab

Computational biology and genomics @JHU

Publications

Under construction!

Until this is ready, please see my old Publications page or my Google Scholar page, which has links to most of my publications.

Meanwhile here is our newest paper:

M. Pertea, G.M. Pertea, C.M. Antonescu, T.C. Chang, J.T. Mendell, and S.L. Salzberg (2015). StringTie enables improved reconstruction of a transcriptome from RNA-seq reads Nature Biotechnology 33 (3), 290-295. Publ. online 18 February 2015.

Lab news

Jan 2023: A new paper in G3: Genes, Genomes, Genetics, led by Kuan-Hao Chao (a joint member of the Salzberg and Pertea labs), describes the first gap-free assembly of a Han Chinese human. See the paper here.
Dec 2022: A new paper in eLife, led by Markus Sommer, shows how protein structure can yield remarkable insights into gene function. See the paper here.
Aug 2022: New lab members! Hayden Ji and Celine Hoh join the lab as Ph.D. candidates in Computer Science.
March 31, 2022: A team of over 100 scientists, including lab member Alaina Shumate, publishes the first-ever truly complete human genome in the journal Science. See the paper here, and see a perspective about the work here.
March 18, 2022: Alaina Shumate successfully defends her Ph.D. thesis!
Dec 2021: Our paper on a high-quality genome of a Puerto Rican individual, with authors from both the Salzberg and Pertea labs, appears in the journal Genetics.
Aug 2021: New lab members! Kuan-Hao Chao joins both our lab and Ela Pertea's lab as a Ph.D. candidate in Computer Science.
July 2021: Ales Varabyou and Christopher Pockrandt publish a novel method to find recombination events in COVID-19 viruses in the journal Genetics.
June 2021: Alaina Shumate publishes Liftoff, a new genome annotation tool, in the journal Bioinformatics.
Feb 2021: Markus Sommer publishes Balrog, a new bacterial gene finding system, in PLoS Computational Biology.
Jan 2021: Rachel Sherman successfully defends her Ph.D. thesis.
Nov 2020: New lab members! Ilia Minkin, Ph.D. joins the lab as a postdoctoral fellow, and Jennifer Lu successfully defends her Ph.D thesis and stays on as a postdoc.
Oct 2020: Genetics features our new wheat genome assembly on its cover. We discovered 5,799 new genes, in work led by Mike Alonge and Alaina Shumate.
Aug 2020: New lab members! Natalia Rincon, Beril Erdogdu, and Yuchen (Peter) Ge join the lab as new Ph.D. students.
Aug 2020: Genome Biology selects 3 papers from the lab for its list of the 20 most-accessed papers of their first 20 years. Lead authors were Ben Langmead, Aleksey Zimin, and Daeahwan Kim.
June 2020: Ph.D. student Alaina Shumate and Research Scientist Aleksey Zimin lead a new paper describing the first-ever human reference genome based on a single individual, published in Genome Biology.
Feb 2020: ISCB announces that Steven Salzberg will receive the Accomplishments by a Senior Scientist Award at the 2020 ISMB conference.
Feb 2020: Ph.D. student Rachel Sherman publishes a major review of pan-genomes in Nature Reviews Genetics.
Nov 2019: 3 lab alumni make 2019 list of world's most highly-cited researchers: Mike Schatz, Adam Phillippy, and Cole Trapnell. CCB colleague Ela Pertea also made the list, in a previous year.
Aug 2019: HISAT2 and HISAT-genotype are published in Nature Biotechnology, led by former lab member Daehwan Kim, now an Asst. Professor at UT Southwestern.
May 2019: We discovered 3437 bogus proteins in 2250 contaminated microbial genomes, described in our new Genome Research paper. Supplemental files are on our ftp site, here.

Related links

Steven Salzberg's biosketch
Steven Salzberg's blog at Forbes
Center for Computational Biology
Directions to Hopkins
Blog at WordPress.com.
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