Collaborators

Kathy Yelick is the Principal Investigator of the ExaBiome project. She is also the Associate Laboratory Director for Computing Sciences at Lawrence Berkeley National Laboratory (Berkeley Lab) and a Professor of Electrical Engineering and Computer Sciences at UC Berkeley. Her research interests include programming languages, parallel algorithms, computational biology, and high performance data analytics.

photo of Lenny Oliker

Lenny Oliker is the Executive Director of the ExaBiome project. He is a Senior Computer Scientist in the Computational Research Division at Lawrence Berkeley National Laboratory. His research interests include optimization of scientific methods, performance evaluation of extreme-scale applications, autotuning, domain-optimized computational architectures, and large-scale de novo genome assembly and genetic mapping.

Aydin Buluc is a Staff Scientist at the Lawrence Berkeley National Lab and an Adjunct Assistant Professor of Electrical Engineering and Computer Sciences at UC Berkeley. His research focuses on high-performance graph analysis and libraries, parallel sparse matrix computations, communication-avoiding algorithms, with applications in computational genomics and biology.

Dan Rokhsar is the Chief Scientist of the ExaBiome project. He is Program Head for Computational Genomics at the Department of Energy Joint Genome Institute, Faculty Scientist at the Lawrence Berkeley National Laboratory, and Professor of Genetics, Genomics, and Development, and Physics, at UC Berkeley. He is interested in the evolution of complex genomes and metagenomes.

Steven Hofmeyr is in the Computational Research Division at Lawrence Berkeley National Laboratory. His research interests include genome assembly, modeling of large-scale complex systems (such as the Internet), Information Security, Operating Systems, and scheduling and load-balancing of parallel applications.

Rob Egan is a software developer at the DOE Joint Genome Institute in the research and development department. His interests include metagenome assembly, binning and analysis, along with high performance computing, high throughput computing, software optimization and algorithm development.

Ariful Azad is a Research Scientist in the Computational Research Division at the Lawrence Berkeley National Laboratory (LBNL). His research interests are in parallel graph algorithms, high performance computing, data analytics and bioinformatics. Ariful finished his Ph.D. in Computer Science from Purdue University in 2014.

Patrick Chain is currently leading the Bioinformatics and Analytics Team and the Metagenomics Program within the Biosecurity and Public Health group at Los Alamos National Laboratory. His interests include algorithms and strategies for the biological interpretation of massively parallel sequencing data.

Migun Shakya is a Computational Biologist at Los Alamos National Laboratory in the Biosecurity and Public Health team (B-10). His research interests are in microbiome analysis, comparative genomics, statistics, and molecular biology and genetics.

Nikos Kyrpides leads the combined Microbial Genomes and Metagenomes Program at the Joint Genome Institute. His research includes environmental genomics and analysis techniques for metagenomic data sets.

Evangelos Georganas is a research scientist at Intel. HIs research interested include high performance computing, machine learning, parallel algorithms, and computational biology. He was the primary author of the original version of the HipMer code and continues to collaborate with the ExaBiome team.


Former team members

Pavel Senin was a postdoctoral research associate in the Biosecurity and Public Health team (B-10) at the Los Alamos National Laboratory (LANL). He worked on GOTTCHA code within ExaBiome. He is currently at Altran. His research interests are in data mining, knowledge discovery, and software engineering.