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 and the Center for Brain Science.
Recent publications
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Cellular Evolution of the Hypothalmic Preoptic Area of Behaviorally Divergent Deer Mice.
J. Chen, P. R. Richardson, C. Kirby, S. R. Eddy, H. E. Hoekstra.
eLife, 13:RP103019, 2025.Download software : [analysis scripts (github)]abstract reprint
Supplementary material : [supplemental figures (PDF)] [supplemental tables (xlsx)] -
Protein Sequence Domain Annotation using Language Models.
A. Sarkar, K. Krishnan, S. R. Eddy.
bioRxiv preprint and manuscript submitted, 2024.
preprint
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 seed funding available.
Graduate students in the group come from many different Harvard programs, including Systems, Synthetic, and Quantitative Biology, MCO (Molecules, Cells, and Organisms), and Biophysics.
We have an open position for a bioinformatics scientist to help us develop and support HMMER and Infernal.
How to find us
Department of Molecular & Cellular BiologyBiological Laboratories 1008A
16 Divinity Avenue
Harvard University
Cambridge MA 02138, USA
HMMER
Hidden Markov models for sequence profile analysis.
Infernal
RNA structure analysis using covariance models.
Pfam
Database of protein family alignments and hidden Markov models.
Rfam
The Rfam database of RNA alignments, consensus secondary structures, and profile SCFGs.
Dfam
The Dfam database of repetitive DNA sequence elements.