People

Kathy Yelick is the Principal Investigator of the ExaBiome project. She is a Senior Scientist in the Computational Research Division 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 in the Computaitonal Research Division at Berkeley 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 Berkeley Lab. 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 an Assistant Professor of Intelligent Systems Engineering at Indiana University, Bloomington. He is also an Affiliate Scientist in the Computational Research Division at Lawrence Berkeley National Laboratory. His research focuses on parallel graph algorithms, high performance computing and bioinformatics.

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.

Marquita Ellis is a Postdoctoral Research at Berkeley Lab and recently completed her PhD at UC Berkeley. Her work is on performance modeling and high performance computing. She is working on the long read overlapping and alignment.

Oguz Selvitopi is a Postdoctoral Research Fellow in the Computational Researh Division at Berkeley Lab. His research interests are high performance computing, parallel sparse matrix computations, combinatorial scientific computing, and bioinformatics.

Muaaz Awan is an Application Performance Specialist at NERSC working on high performance data analytics, including the use of hardware accelerators for Bioinformatics and data mining algorithms.

Andrew Tritt is a data engineer in Computational Research Division at Berkeley lab. His work in ExaBiome focuses on using deep neural network sequence embeddings for addressing computationally expensive problems in genomics.

Giulia Guidi is a Ph.D. student in Computer Science at UC Berkeley, advised by Aydın Buluç and Kathy Yelick. Giulia's research is focused on the development of a novel algorithm to de novo assemble genomes using long-read sequencing data.

Prashant Pandey is a Postdoctoral Research Fellow in the Performance and Algorithms group at Berkeley Lab. He designs and builds theoretically well-founded data structures for massive data problems in computational biology, storage, and streaming.

Israt Nisa is a Postdoctoral Research Fellow in the Computational Research Division at Berkeley Lab. Her research is in parallelization of machine learning and numeric algorithms, especially sparse matrices, graphs, and tensors.

Md. Taufique Hussain is a PhD student at Indiana University, Bloominton, working with Professor Azad on parallel graph algorithms and clustering.

Alicia Clum is the Group Lead for the Genome Assembly and Analysis Group at the Joint Genome Institute. She is an expert in assembly and alignment algorithms for 1st-3rd generation sequencing platforms.

Robert Riley is a Staff Scientist at the Joint Genome Institute with expertise i microbiology, metagenomics, infectious disease, bioenergy, ecology, and the structure, function, evolution, and interactions of biomolecules, genomes, and organism communities.

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.

Saliya Ekanayake was a Postdoctoral Fellow at Berkeley Lab. His research is in scalable parallel machine learning algorithms for Big Data problems and he built the PISA protein similiary software. He is currently at Microsoft Research.