Overview

The Salzberg lab is a computational biology lab that develops novel methods for analyzing DNA and RNA sequences. Our research includes software for aligning and assembling genomes from a wide range of species, transcriptome analysis, 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 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 four related but distinct areas:

  1. Transcriptome (RNA sequencing) analysis. 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, and more recently the HISAT and StringTie programs, with over 50,000 citations collectively. 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.
  2. Computational gene finding. We have been working for many years on methods to identify genes, ranging from methods for bacterial gene finding to the development of a new human gene database. Our work on the human gene database called CHESS, which you can read about here, is a major current focus of the lab.
  3. 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.
  4. Metagenomics and microbiome analysis.  We have developed a variety of tools to analyze metagenomics data sets, including the widely-used Kraken and Centrifuge systems. We have a special focus here on using metagenomic sequencing to diagnose infections in human patients. Here’s a paper that describes one of our efforts to use direct DNA sequencing to diagnose brain infections.

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 take a limited number of summer intern through the BDP HOUR program. Our openings have been filled for 2021, but if you are interested in the future, visit the HOUR website, which will be updated during the 2021-22 academic year.

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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).