Eddy Lab: Home

Reading genomes, bit by bit

Because of rapid advances in genome sequencing technology, we can finally see the source code for life: the complete genomic DNA sequences that specify development, regulation, and function of organisms. Our laboratory develops computational methods for genome sequence analysis. We are particularly interested in methods for identifying remote evolutionary relationships between distantly related protein and RNA sequences.

We're a Howard Hughes Medical Institute laboratory at Harvard University, in Molecular & Cellular Biology in Biolabs on the Cambridge campus. We're affiliated with the Harvard Data Science Initiative, the Quantative Biology Initative, and the Center for Brain Science.

Recent publications

ORFeus: A Computational Method to Detect Programmed Ribosomal Frameshifts and Other Non-Canonical Translation Events.
M. O. Richardson, S. R. Eddy.
bioRxiv, and manuscript submitted, 2023.
Download software : [ORFeus github]
Supplementary material : [ORFeus code and data tarball]
preprint
End-to-End Learning of Multiple Sequence Alignments with Differentiable Smith-Waterman.
S. Petti, N. Bhattacharya, R. Rao, J. Dauparas, N. Thomas, J. Zhou, A. M. Rush, P. K. Koo, S. Ovchinnikov.
Bioinformatics, 39:btac724, 2023.
abstract reprint

How to join us

If you're interested in doing a postdoc with us, contact me and propose a project idea. We usually have space and initial funding available.

Graduate students in the group come from many different Harvard programs, including MCO (Molecules, Cells, and Organisms), Systems Biology, Biophysics, Applied Math, and Physics.

We have an open position for a bioinformatics scientist to help us develop and support HMMER and Infernal. To see the job description and application instructions, see here.