We are a computational biology lab that develops novel methods for analyzing DNA and RNA sequences, and that analyzes genomes to make biomedical discoveries. Our research includes software for aligning and assembling genomes, gene and transcriptome analysis, and microbiome analysis. We work closely with biomedical scientists to apply our 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 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. Computational gene finding and genome annotation. 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, called CHESS. You can read more about the CHESS project here. We’re now using ColabFold as a new way to identify functional gene variants.
2. Transcriptome (RNA sequencing) analysis. Over the past decade, members of the lab along with our collaborators have 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 100,000 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 BME Prof. Mihaela Pertea, and HISAT is led by UT Southwestern Prof. Daehwan Kim.
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 recent projects assembling the genomes of the redwood and sequoia trees. We 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 partial 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 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 the CCB website.

Interested in joining the lab? We are often interested in recruiting postdoctoral scientists, depending on funding: interested applicants should email Steven Salzberg directly. For information about applying as a graduate student, please see this page. We admit students through the Biomedical Engineering, Computer Science, and Biology Ph.D. programs.

Looking for a summer intern position? We take a limited number of summer interns each year through the BDP HOUR program. To learn more, visit the HOUR website. (Note: all positions are filled for 2024.)

The Salzberg lab is supported in part by the NIH under grants R35-GM130151, R01-HG006677, and R01-MH123567, and in the past by multiple NSF grants.