Links within this page: Richard Durbin | Carlos D Bustamante | Partha P Majumder | Marinka Zitnik | Olga Troyanskaya

More applications of the Burrows-Wheeler transform in computational genomics

I will discuss a series of applications of the Burrows-Wheeler transform, based on suffix sorting, for sequence matching and compression in computational genomics.  Initial applications, as in bwa with Heng Li, were for finding maximal exact matches as an alternative to fixed length seeds based on hashing  for sequence read mapping.  Next the Positional Burrows-Wheeler Transform (PBWT) incorporating run-length encoding gave both excellent compression and very fast maximal matching of haplotype sequences; this underlies most modern genotype imputation tools.  More recently, the Graph Burrows-Wheeler Transform (GBWT) was introduced to provide path indices over pangenome graphs,  again providing both compression and efficient search. Finally, I will describe a new dynamic GBWT framework based on doubly-linked skip lists that when implemented over a sparse de-Bruijn graph enables rapid O(log_N) time insertion and matching, supporting single-threaded pangenome graph construction and indexing at ~15 seconds per gigabase.

Biography

Richard Durbin has worked for over 30 years in computational genomics.  He started with a BA in Mathematics from Cambridge (1982), then switched to biology for his PhD  on C. elegans neural development at the MRC Laboratory of Molecular Biology. After a short postdoc in neural modelling, he joined John Sulston and colleagues in 1990 at the start of the genome sequencing project,  both developing and applying a variety of computational tools and approaches for genome assembly and analysis. After completion of the initial human genome, and helping establish Pfam and Ensembl, he co-led the 1000 Genomes Project to provide a foundation reference for human sequence diversity, along the way leading the development of computational tools still widely used for studying sequence variation (including bwa, BAM files, VCF format).

In 2017, Richard moved to the Department of Genetics, University of Cambridge, where he and his group have applied computational and evolutionary genomics approaches to  speciation in the Lake Malawi cichlid fish radiation, ancient DNA , statistical genetics methods for demographic inference, and pangenome and genome assembly methods. Recently, he has been involved in efforts to extend reference genome sequencing across the diversity of life and has come to appreciate how important mobile elements are in genome and potentially species evolution, making these a new focus for his research.

Richard was elected a Fellow of the Royal Society in 2004, a member of the European Molecular Biology Organisation in 2009, and an International Honorary Member of the American Academy of Arts and Sciences in 2019. He received the Gabor Medal of the Royal Society in 2017 and the International Prize for Biology in 2023.

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Biography

Coming soon.

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Biography

Partha P. Majumder is a Distinguished Professor of the John C. Martin Centre for Liver Research & Innovations, Kolkata; and, an Emeritus Professor of the Indian Statistical Institute.  Until recently, he was a National Science Chair in India.  He has made significant contributions to human-, statistical- and population genetics and genomics. He has developed methodologies for mapping human disease genes, identified genomic factors underlying many diseases notably oral cancer, and has reconstructed the ancestries and relationships of ethnic populations groups of India and Asia using genomic methods. He has immensely contributed to capacity-building in human and statistical genetics in India. He has founded the National Institute of Biomedical Genomics, India.

He is an elected Fellow of all the three national science academies of India, The World Academy of Sciences (TWAS) and the International Statistical Institute. He has served as the President of the Indian Academy of Sciences and of the West Bengal Academy of Science & Technology.

He is a Member of the Executive Committees of the international Human Cell Atlas consortium and the International Common Disease Alliance.  He serves as an expert on genomics for the World Health Organization.

He has received many awards and honours, including the G.N. Ramachandran Gold Medal (2021) of the Government of India; Barclay Memorial Medal (2020) of The Asiatic Society; Golden Jubilee Commemoration Medal (2018) of the Indian National Science Academy; TWAS Prize in Biology (2009) of The World Academy of Sciences, Trieste.

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Biography

Marinka Zitnik is an Associate Professor of Biomedical Informatics at Harvard Medical School, Associate Faculty at the Kempner Institute for the Study of Natural and Artificial Intelligence at Harvard University, and an Associate Member at the Broad Institute of MIT and Harvard. Zitnik investigates the foundations of AI that contribute to the scientific understanding of medicine and therapeutic design, with the goal of enabling AI to learn and innovate on its own. Her research has received numerous awards, including Kavli Fellowship of the National Academy of Sciences, NSF CAREER Award, and awards from the International Conference on Machine Learning, Bayer Early Excellence in Science, Amazon Faculty Research, Google Faculty Research, Roche Alliance with Distinguished Scientists, and Sanofi iDEA-iTECH. Zitnik founded Therapeutics Data Commons, a global open-science initiative to evaluate AI across stages of development and therapeutic modalities. Through the AI4Science initiative, she develops foundation models, benchmarks, and open datasets to empower discovery across biology and medicine.

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Biography

Dr. Carlos Bustamante is one of the world’s foremost thought leaders in population genetics and genomics and brings immense knowledge and relationships key to the company’s success. A leading academic in the field of medical and population genomics, his background includes roles as a Venture Partner at F-Prime Capital, SAB member with Digitalis Ventures, Founder of Arc Bio, advisor to numerous startups, and former Professor of Genetics / Biomedical Data Science at Stanford University (now adjunct). Dr. Bustamante was also awarded a MacArthur Fellowship in 2010 for his contributions to population genetics (mining DNA sequence data to address fundamental questions about mechanisms of evolution, origins of human genetic diversity, and patterns of population migration).

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