Older Lab News (archive)

  • 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.
  • April 2019: The first draft of the redwood genome is released. The giant genome (26.5 Gb) of this giant tree was sequenced and assembled by the Salzberg and Timp labs at Hopkins, in collaboration with David Neale at UC Davis and the Save the Redwoods League.
  • November 2018: Ph.D. student Rachel Sherman leads a a new study in Nature Genetics describing the African pan-genome.
  • November 2018: The CHESS human gene catalog is published in Genome Biology, in a paper led by Ela Pertea and including lab members Ales Varabyou, Alaina Shumate, and Florian Breitwieser.
  • July 2018: Our collaborator Prof. Mihaela (Ela) Pertea is awarded a 3-year, $993,000 NSF grant to support her work on transcriptome assembly from RNA-seq data.
  • July 6, 2018: Steven Salzberg gave the opening keynote talk for ISMB 2018, the Intelligent Systems for Molecular Biology conference, in Chicago.
  • May 2018: Associate Research Scientist Aleksey Zimin is awarded a 3-year, $500,000 USDA grant to support his work on genome assembly.
  • Apr 2018: Steven Salzberg elected a member of the American Academy of Arts & Sciences. Founded in 1780, the Academy honors exceptional scholars, leaders, artists, and innovators and engages them in sharing knowledge and addressing challenges facing the world.
  • Feb 2018: Former student Cole Trapnell, an Asst. Prof at U. Washington, wins this year’s Overton Prize from ISCB.
  • Feb 7, 2018: Our work on the redwood genome is featured on the front page of the Washington Post.
  • Dec 2017: See Steven Salzberg’s talk on genome assembly at the Oxford Nanopore Community Meeting in NYC.
  • 31 Oct 2017: “Small group scoops international effort to sequence huge wheat genome.” This is us: read the story in Nature.
    Oct 2017. Re-released the Kraken! (v1.0 that is.) See ccb.jhu.edu/software/krakenfor details.
  • Sept 2017. Two new Ph.D. students join the lab, Alaina Shumate in the BME program, and Ales Varabyou in the CS program.
  • May 2017. Steven Salzberg publishes a paper refuting a recent claim that horizontal gene transfer is a widespread phenomenon in animal species.
  • July 2016. Steven Salzberg gives a keynote talk on open science at BOSC 2016. See the talk on YouTube.
  • June 2016. Steven Salzberg, Florian Breitwieser, and other scientists including Hopkins neurologist Carlos Pardo publish a landmark study on the use of sequencing to diagnose brain infections in critically ill patients.
  • May 2016. Former student Mike Schatz joins Hopkins as a Bloomberg Distinguished Associate Professor of Computer Science and Biology.
  • Feb. 2016. Daehwan Kim, Li Song and Florian Breitwieser release Centrifuge, a new metagenomics classifier.
  • December 2015. Steven Salzberg is named a Highly Cited Researcher by Thomson Reuters, in the areas of both computer science and microbiology.
  • October 2015. Postdocs Daehwan Kim and Florian Breitwieser each give plenary talks at the 2015 Genome Informatics Conference at Cold Spring Harbor Laboratory.
  • September 2015. Two new Ph.D. students join the lab: Jennifer Lu in Biomedical Engineering, and Rachel Sherman in Computer Science.
  • June 22, 2015. NIH awards a new 3-year grant to Steven Salzberg, Kathleen Barnes, and Alex Szalay for a new database to explore 1,000 genomes of African descent.
  • June 1, 2015. NSF awards a new 3-year research grant to Mihaela Pertea for her work on transcriptome reconstruction.
  • May 14, 2015. A consortium including 3 Salzberg lab members publishes a major new study of bee evolution in the journal Science.
  • Mar 30, 2015. Steven Salzberg is named as one of four new Bloomberg Distinguished Professors at Johns Hopkins University.
  • March 9, 2015. Daehwan Kim and colleagues publish HISAT, a highly efficient new method for alignment of RNA-seq reads, in Nature Methods.
  • Feb 23, 2015. Former Salzberg lab students Mike Schatz and Cole Trapnell are both selected as 2015 Sloan Research Fellows.
  • Feb 18, 2015. Ela Pertea and colleagues publish StringTie, a new method for assembly of RNA-seq data, in Nature Biotechnology.
  • Feb. 2, 2015. Florian Breitwieser joins the lab as a new postdoc.
  • Jan 2015. Computer Science Ph.D. student Rachel Coston joins the lab.
  • Sept. 2014. Postdoc Stefan Canzar departs for a new position as Research Assistant Professor at TTIC, Univ. of Chicago.