The Salzberg lab is a computational biology lab that develops novel methods for analysis of DNA and RNA sequences. Our research includes software for aligning and assembling RNA-seq data, whole-genome assembly, and microbiome analysis. We work closely with biomedical scientists to apply these methods to current problems arising in a broad spectrum of biological and medical research areas. We’re also part of the Center for Computational Biology, a group of 20+ faculty members and their labs at Johns Hopkins working on computational, statistical, and mathematical methods that can turn massive genomic data sets into biologically and clinically useful information.

Research Project Areas. Our lab currently works in three related but distinct areas:

  1. Genome Assembly. We develop genome assembly algorithms to use the latest generation of sequencing technologies, pushing the technology to take on ever-larger and more complex genomes, such as our current project to assemble the mega-genomes of the redwood and sequoia trees. We also apply these methods in collaborations with biologists to sequence the genomes of species ranging from bacteria to plants and animals. See our Genome Projects page for a list of the many genomes we have assembled and published over the years.
  2. Transcriptome (RNA sequencing) analysis and gene finding. Over the past decade, members of the lab developed multiple programs for RNA-seq analysis that have been adopted around the world. These include the Bowtie, TopHat, and Cufflinks programs, each with over 5000 citations to date, and more recently the HISAT and StringTie programs. Together these programs align and assemble RNA sequencing data to reconstruct a detailed picture of all the genes and gene variants that are expressed in a tissue sample. The StringTie project is led by Prof. Ela Pertea, whose lab works closely with ours.
  3. Metagenomics and microbiome analysis.  Our particular focus here is using metagenomic sequencing to diagnose infections. Here’s a paper that
    describes one of our efforts to use direct DNA sequencing to diagnose brain infections. We also design software to analyze metagenomics datasets, including the widely-used Kraken and Centrifuge systems.

For a broader look at our software, see our software page or the larger software page on the CCB website.

Interested in joining the lab? See this page for information about postdoctoral or graduate student positions in the lab. We admit students through both the Biomedical Engineering and Computer Science Ph.D. programs. We are actively looking for Ph.D. students!

Looking for a summer intern position? We have a limited number of summer intern positions through the BDP HOUR program. Our openings have been filled for 2020, but if you are interested in the future, visit the HOUR website, which will be updated during the 2020-21 academic year.


Our lab stands with #BlackLivesMatter, and we condemn the racism that continues to affect Black communities across the U.S.

The Salzberg lab is supported in part by the NIH under grants R35-GM130151, R01-HG006677, by the NSF under grant IOS-1744309, and by the Save the Redwoods League (for our redwood genome project).