Big Data, AI, & Genomics

The Big Data, Artificial Intelligence, and Genomics group consists of computational experts in genomics, mathematical modeling, scientific software, big data analytics, and the use of artificial intelligence to understand biological systems.

Research Services 

Extensive experience in both molecular biology and computational sciences aids in the development and applications of novel genomic and computational methods for solving biological problems. Members of the Big Data, AI, and Genomics group provide advanced expertise, analytical support, and comprehensive collaborative services to Stowers scientists. Genomics support focuses on the latest approaches for making effective use of an immense amount of generated data. In particular, the Stowers SIMRbase platform provides assembled genomes and related data for various research organisms plus a toolkit for investigating these resources. Biomathematics support includes complex data analysis, modeling, and numerical/symbolic programming. Researchers can also tap into expertise in biophysical and systems biology, as well as image processing and analysis. Additionally, the team supports many of the scientific software packages used by Stowers researchers.

Technology 
Team Contact 
Boris Rubinstein, PhD
Research Advisor, Biomathematics

As a biomathematician, Boris Rubinstein primarily assists Stowers researchers with complex data analysis, modeling, and numerical/symbolic programming but his expertise extends to biophysical and systems biology questions, image processing and analysis, and protein interaction network analysis.

Rubinstein received a MSc in nuclear physics from the Ural State Technical University in Sverdlovsk and a PhD in optics from Irkutsk State University in Siberia, Russia. After two years at the Metal Physics Institute, USSR Academy of Sciences in Sverdlovsk, he accepted a postdoctoral position at the Technion in Haifa, Israel. After a short stint at a small start-up company called Kernel Knowledge, where he helped to develop a widely used symbolic computer algebra software Mathematica, he returned to the Technion as a research engineer.

In 2000, he accepted a postdoctoral position at Northwestern University, Chicago, where he focused on the numerical stability analysis of two-phase hydrodynamic flows and discovered a new type of crystallization process dynamics. Prior to joining the Stowers Institute as a biomathematician in 2007, Rubinstein spent five years in the Department of Mathematics at the University of California, Davis, where he became interested in biological questions and started to study the motion of living cells. During that time he also solved an old number theory problem posed by Euler in 1748.

Sofia Robb, PhD
Genomics Scientist

Sofia Robb graduated with a BS degree in biology from the University of Maryland, Baltimore in 1999. She began integrating scripting and the use of databases with her experiments while working as a technician in the laboratory of Alejandro Sánchez Alvarado, PhD, in the Department of Embryology at the Carnegie Institute.

Robb remained with the Sánchez laboratory after its move to the University of Utah for her doctoral work where she studied histone modifying enzymes and their role in stem cells and regeneration in the planarian flatworm, Schmidtea mediterranean. Robb also constructed numerous genomic tools for this emerging non-model organism and continued integrating the genome with bioinformatic tools as a postdoctoral associate at the University of California Riverside with Jason Stajich, PhD, and Susan Wessler, PhD, studying active transposable elements in rice. At the Stowers Institute, Robb is currently involved in several genomics initiatives, including establishing a collection of tools for the analysis of genomes and genome-wide data of research organisms.

Chris Seidel, PhD
Genomics Scientist
Faculty, The Graduate School of the Stowers Institute

Chris Seidel has many years of experience as a biologist and an experimentalist. He works closely with Stowers researchers to develop and execute strategies for bringing genomics to bear on biological problems, including experimental design, data analysis, development of novel reagents, and bioinformatics.

Seidel grew up in the San Francisco Bay Area and studied biochemistry and molecular biology at the University of California, Santa Cruz. He completed graduate work at the University of California, Berkeley, studying transcription elongation in the laboratory of Caroline Kane, PhD. He has worked in the biotech industry as a senior scientist and led a small team of researchers to develop the first bioinformatically optimized reagents for spotted microarray production, including an array to tackle malaria in collaboration with Joseph DeRisi, PhD, at UCSF. After building microarray robots at UC Berkeley and Children’s Hospital of Oakland Research Institute, Seidel joined the Stowers Institute where he develops novel genomic approaches and analysis pipelines and continues to do research in genomics.

Featured Publications 
Nowotarski SH, Davies EL, Robb SMC, Ross EJ, Matentzoglu N, Doddihal V, Mir M, McClain M, Sánchez Alvarado A. BioRxiv. 2020.
Wang W, Hu CK, Zeng A, Alegre D, Hu D, Gotting K, Ortega Granillo A, Wang Y, Robb S, Schnittker R, Zhang S, Alegre D, Li H, Ross E, Zhang N, Brunet A, Sánchez Alvarado A. Science. 2020; 369.
Dash S, Bhatt S, Sandell L, Seidel C, Ahn Y, Krumlauf R, Trainor P. Front Physiol. 2020; 11:531933.
Cheng LC, Tu KC, Seidel CW, Robb SMC, Guo F, Sánchez Alvarado A. Dev Biol. 2018;433:357-373.
Khan T, Kandola TS, Wu J, Venkatesan S, Ketter E, Lange JJ, Rodriguez Gama A, Box A, Unruh JR, Cook M, Halfmann R. Mol Cell. 2018; 71:155.
Dhatchinamoorthy K, Shivaraju M, Lange JJ, Rubinstein B, Unruh JR, Slaughter BD, Gerton JL. J Cell Biol. 2017; 216:3551.
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