Department faculty were recognized for their contributions to the field of computational biology at the 28th Annual International Conference on Research in Computational Molecular Biology held April 26 through May 2 in Cambridge, Massachusetts. RECOMB is a leading international conference on algorithmic computational biology, bridging computational, mathematical, statistical, and biological sciences.
Ben Langmead, an associate professor of computer science, and Li Song, an alumnus of the department and now an assistant professor at Dartmouth College, won this year’s Best Paper Award for their work, “Centrifuger: Lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification.” Available in Genome Biology, the paper presents Centrifuger, an efficient taxonomic classification method that compares sequencing reads against a microbial genome database. With its lossless compression and unconstrained match length, Centrifuger achieves greater accuracy than competing methods at lower taxonomic levels.
On April 30, Steven Salzberg, Bloomberg Distinguished Professor of Biomedical Engineering, Computer Science, and Biostatistics, was invited to give one of five distinguished keynotes. His talk “The status of the human genome catalogue: Where are we now, and how do we finish it?” reviewed the course of the Human Genome Project and described recent efforts to use large RNA sequencing resources to create a comprehensive human gene database.
Johns Hopkins teams additionally presented the following posters at the main conference:
- “Compressed Indexing for Pangenome Substring Queries” by Stephen Hwang, Nathaniel Brown, Omar Ahmed, Katharine Jenike, Sam Kovaka, Michael Schatz, and Ben Langmead—also selected for a short talk at RECOMB-Seq, a satellite workshop on biological sequence analysis held prior to the main conference
- “Combining DNA and protein alignments to improve genome annotation with LiftOn” by Kuan-Hao Chao, Jakob M. Heinz, Celine Hoh, Alan Mao, Alaina Shumate, Mihaela Pertea, and Steven Salzberg—also selected for a short talk at RECOMB-Seq
- “Detecting differential transcript usage in complex diseases with SPIT” by Beril Erdogdu, Ales Varabyou, Stephanie Hicks, Steven Salzberg, and Mihaela Pertea
- “Quality assessment of splice site annotation based on conservation across multiple species” by Ilia Minkin and Steven Salzberg—also an Overlay Track talk at RECOMB-Seq
Hopkins researchers also presented the following work at RECOMB-Seq:
- “Movi: A fast and cache-efficient full-text pangenome index” by Mohsen Zakeri, Nathaniel Brown, Omar Ahmed, Travis Gagie, and Ben Langmead—one of six proceedings papers published in the workshop
- “Mumemto: Efficient maximal matching across multiple genomes” by Vikram Shivakumar and Ben Langmead—selected for a short talk