News
31 March 2022
Completing the sequence
Stowers Institute researchers help assemble the complete human genome
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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.
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 Institute 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.
Team Contact
Head of Computational Imaging
Stowers Institute for Medical Research
Sean McKinney, Ph.D., joined the Stowers Institute in 2009 as the group head of Optics Development. He was named manager of Microscopy in 2015, head in 2019, and in 2023 he was appointed Head of Computational Imaging.
Sean McKinney, Ph.D., joined the Stowers Institute in 2009 as the group head of Optics Development. He was named manager of Microscopy in 2015, head in 2019, and in 2023 he was appointed Head of Computational Imaging.
Team Contact
Genomics Scientist
Stowers Institute for Medical Research
Sofia Robb graduated with a B.S. 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, Ph.D., in the Department of Embryology at the Carnegie Institute.
Robb remained with the Sánchez Alvarado Lab 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 mediterranea. She 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, Ph.D., and Susan Wessler, Ph.D., studying active transposable elements in rice.
At the Stowers Institute, Robb is involved in several genomics initiatives, including establishing a collection of tools for the analysis of genomes and genome-wide data of research organisms.
Sofia Robb graduated with a B.S. 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, Ph.D., in the Department of Embryology at the Carnegie Institute.
Robb remained with the Sánchez Alvarado Lab 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 mediterranea. She 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, Ph.D., and Susan Wessler, Ph.D., studying active transposable elements in rice.
At the Stowers Institute, Robb is involved in several genomics initiatives, including establishing a collection of tools for the analysis of genomes and genome-wide data of research organisms.
Team Contact
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.
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.
Team Contact
Genomics Scientist
Stowers Institute for Medical Research
Chris Seidel is an experienced bench biologist who leverages his experimental background when developing approaches for big data analysis. 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, Ph.D.. 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, Ph.D., at the University of California, San Francisco.
After building microarray robots at the University of California, 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.
Chris Seidel is an experienced bench biologist who leverages his experimental background when developing approaches for big data analysis. 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, Ph.D.. 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, Ph.D., at the University of California, San Francisco.
After building microarray robots at the University of California, 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.
Exponential increases in technology produce vast quantities of data. How to handle that data and to extract the essentials requires expertise in computation and machine learning, or artificial intelligence (AI). Whole genome assembly is a perfect example of really big data and the necessity of computers to parse information.
In bioinformatics, BLAST (Basic Local Alignment Search Tool) is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold. Different types of BLASTs are available according to the query sequences. For example, following the discovery of a previously unknown gene in the mouse, a scientist will typically perform a BLAST search of the human genome to see if humans carry a similar gene; BLAST will identify sequences in the human genome that resemble the mouse gene based on similarity of sequence.
Find homologous genes across transcriptomes. Software to quickly map IDs to a reference sequence or other transcriptome IDs.
Search for transcripts by ID, experimentally determined tissue/pattern, homologs (best BLAST hits), GO terms, and PFAM protein domain terms. All the following search fields are cumulative, meaning the results need to meet all provided criteria.
SIMRbase is the place for assembled genomes and genome related data at the Stowers Institute for Medical Research. Here you can find tools to search sequences with BLAST, keywords, GO terms, tools to browse genomes, and tools to manually curate gene models. Currently SIMRbase has public access to Petromyzon marinus, the sea lamprey and its germline genome assembly, Nothobranchius furzeri, African killifish or turquoise killifish, Scolanthus callimorphus, the worm anemone, and Nematostella vectensis the starlet sea anemone. For more information or to get help contact Sofia Robb (simrbase@stowers.org).
Planosphere is a collection of data and tools from the Sánchez Alvarado lab planarian publications.
News
31 March 2022
Stowers Institute researchers help assemble the complete human genome
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Press Release
21 June 2022
An ancient stinging organelle that evolved to deliver toxins could inspire the design of new medical delivery devices
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News
13 May 2022
Genomic analysis of cavefish DNA provides clues to their unique metabolic adaptations
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The architecture and operating mechanism of a cnidarian stinging organelle
Karabulut A, McClain M, Rubinstein B, Sabin KZ, McKinney SA, Gibson MC. Nat Commun. 2022;13:3494. doi: 10.1038/s41467-41022-31090.
The Planarian Anatomy Ontology: A resource to connect data within and across experimental platforms
Nowotarski SH, Davies EL, Robb SMC, Ross EJ, Matentzoglu N, Doddihal V, Mir M, McClain M, Sánchez Alvarado A. Development. 2021;148:dev196097. doi: 196010.191242/dev.196097.
The SAGA core module is critical during Drosophila oogenesis and is broadly recruited to promoters
Soffers JHM, Alcantara SG, Li X, Shao W, Seidel CW, Li H, Zeitlinger J, Abmayr SM, Workman JL. PLoS Genet. 2021;17:e1009668. doi: 10.1371/journal.pgen.1009668.
Salim D, Bradford WD, Rubinstein B, Gerton JL. G3 (Bethesda). 2021:jkab082. doi:010.1093/g1093journal/jkab1082.
Hox genes regulate asexual reproductive behavior and tissue segmentation in adult animals
Arnold CP, Lozano AM, Mann FG, Jr., Nowotarski SH, Haug JO, Lange JJ, Seidel CW, Sánchez Alvarado A. Nat Commun. 2021;12:6706. doi: 6710.1038/s41467-41021-26986-41462.
Changes in regeneration-responsive enhancers shape regenerative capacities in vertebrates
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, Sanchez Alvarado A. Science. 2020;369: eaaz3090. doi: 10.1126/science.aaz3090.