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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

Oct 2025: New lab member! Harun Mustafa joins the lab as a postdoctoral fellow, joining us from his previous postdoc at ETH Zürich.
Sept 2025: Lab member Peter Ge leads a major new paper in Science Translational Medicine debunking recent claims of a microbiome in cancer.
Sept 2025: New lab member! Nikola Zadorozhny joins the Salzberg and Pertea labs as a Ph.D. candidate in Computer Science.
Aug 26 2025: Kuan-Hao Chao successfully defends his Ph.D. thesis!
Apr 2025: Postdoctoral fellow Ilia Minkin publishes a new analysis of splice site conservation across 470 mammals, in the journal Nucleic Acids Research.
Jan 2025: Kuan-Hao Chao and 3 other lab members publish LiftOn, a new genome annotation system, in the journal Genome Research.
Nov 2024: Hayden (Hyun Joo) Ji publishes a paper describing 100s of novel human exons found in upstream ORFs, in the journal PLoS Computational Biology.
Sept 2024: Kuan-Hao Chao publishes a paper on Splam, a new, highly accurate splice site prediction program, in the journal Genome Biology.
June 2024: New lab member! David Bass joins the lab as a Ph.D. candidate in Cell, Molecular, and Developmental Biology (CMDB).
February 2024: Congratulations! to former postdoc Martin Steinegger, who was announced as the 2024 winner of the Overton Prize from ISCB.
October 7 2023: In "Major data analysis errors invalidate cancer microbiome findings", published in mBio, we describe how a major cancer microbiome study was fatally flawed.
October 4 2023: Our Nature paper on "The status of the human gene catalog", provides a broad look at how complete and accurate today's human annotation is.
August 7 2023: Markus Sommer successfully defends his Ph.D. thesis!
August 1 2023: Ales Varabyou successfully defends his Ph.D. thesis! Ales was jointly advised by Mihaela Pertea and Steven Salzberg.
July 2023: A new paper in Nature Computational Science, led by Ales Varabyou, describes ORFanage, a system that finds protein-coding regions in RNA-seq assemblies, guided by annotation.

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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