What We Do
The Computational Biology group at the Stowers Institute is a core facility that works with investigators to analyze biological data. We combine our software development and technical skills with biological insights to help find answers in complex and massive data-sets. We primarily work with high-throughput sequence data, ChIP data, and other expression-based datasets. We also provide general statistical and numerical analysis as well as support for scientific software and databases.
To contact the Computational Biology group at the Stowers Institute directly, please email email@example.com
With assistance and support from the Stowers IT group, we help to manage and maintain several servers that are used to manage and manipulate our data. The computational resources available at Stowers include the following:
- A 8 CPU, 3.0 GHz each machine with 64 GB of RAM
- A 24 CPU, 2.4 GHz each machine with 128 GB of RAM
- A 32 CPU, 2.3 GHz each (4 8-core hyperthreaded) machine with 915 GB of RAM
- A 20 (160 CPU) node cluster with 448 GHz total processing power and 160 GB of combined RAM
- A 180 (1440 CPU) node cluster with 1500 GHz total processing power and 1080 GB of combined RAM
Tools We Use
The Computational Biology group uses a variety of software packages, both open-source and commercial, to assist us in our analysis process. Here is a small sampling of the tools we are currently using to process NGS data:
- Bowtie, Cufflinks, and Tophat are used for basic alignment and analysis.
- Trinity and Trans-ABySS are used for assembly of model organisms.
- R is used heavily for statistical analysis and data visualization.
Programmer Analyst I
Database Applications Manager
Programmer Analyst I
Programmer Analyst III
Programmer Analyst III
Selected Publications with Bioinformatics Support
High-throughput sequencing data analysis:
Huang F, Paulson A, Dutta A, Venkatesh S, Smolle M, Abmayr S, Workman JL. Histone acetyltransferase Enok regulates oocyte polarization by promoting expression of the actin nucleation factor spire. Genes & development. 2014;28(24):2750-2763.
Dutta A, Gogol M, Kim JH, Smolle M, Venkatesh S, Gilmore J, Florens L, Washburn M, Workman JL. Swi/Snf dynamics on stress-responsive genes is governed by competitive bromodomain interactions. Genes & development. 2014;28(20):2314-2330.
Venkatraman A, He XC, Thorvaldsen JL, Sugimura R, Perry JM, Tao F, Zhao M, Christenson MK, Sanchez R, Yu JY, Peng L, Haug JS, Paulson A, Li H, Zhong XB, Clemens TL, Bartolomei MS, Li L. Maternal imprinting at the H19-Igf2 locus maintains adult haematopoietic stem cell quiescence. Nature.2013;500:345-349. Abstract
Venkatesh S, Smolle M, Li H, Gogol MM, Saint M, Kumar S, Natarajan K, Workman J. Set2 methylation of histone H3 lysine 36 suppresses histone exchange on transcribed genes. Nature.2012;489:452-455. Abstract
Miller D, Takeo S, Nandanan K, Paulson A, Gogol MM, Noll A, Perera A, Walton K, Gilliland W, Li H, Staehling K, Blumenstiel J, Hawley RS. A whole-chromosome analysis of meiotic recombination in Drosophila melanogaster. G3: Genes| Genomes| Genetics.2012;2:249-260. Abstract
He Q, Bardet AF, Patton B, Purvis J, Johnston J, Paulson A, Gogol MM, Stark A, Zeitlinger J. High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. Nat Genet.2011;43:414-420. Abstract
High-throughput array-based data analysis:
Lin C, Garrett AS, De Kumar B, Smith ER, Gogol MM, Seidel C, Krumlauf R, Shilatifard A. Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC). Genes Dev. 2011;25:1486-1498. Abstract
Gardner JM, Smoyer CJ, Stensrud ES, Alexander R, Gogol MM, Wiegraebe W, Jaspersen SL. Targeting of the SUN protein Mps3 to the inner nuclear membrane by the histone variant H2A.Z. J Cell Biol. 2011;193:489-507. Abstract
Statistical Modeling and Numerical Data Analysis
Gao JT, Guimera R, Li H, Pinto IM, Sales-Pardo M, Wai SC, Rubinstein B, Li R. Modular coherence of protein dynamics in yeast cell polarity system. Proc Natl Acad Sci U S A. 2011;108:7647-7652. Abstract
Zeng Y, Li H, Schweppe NM, Hawley RS, Gilliland WD. Statistical analysis of nondisjunction assays in Drosophila. Genetics. 2010;186:505-513. Abstract