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 sequencing data (RNA-seq, scRNA-seq, ChIP-seq, ATAC-seq, Ribo-profiling, anything-else-seq). We also provide general statistical and numerical analysis as well as support for scientific software, databases, and training.
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 use several CentOS servers and clusters to analyze our data. Some of the computational resources available at Stowers include the following:
- A 24 CPU machine with 128 GB of RAM
- Two 32 CPU machines with 400-900 GB of RAM
- Two 64 CPU machines with 512 GB of RAM each, one queued.
- An 80 CPU machine with 528 GB of RAM.
- A 37 node (424 CPU) cluster
- A 160 node (2728 CPU) cluster
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 are a few tools we currently use to process NGS data:
- Bowtie2, STAR, and RSEM are used for basic alignment and analysis of ChIP-seq and RNA-seq.
- R is used heavily for statistical analysis and data visualization. We commonly use edgeR and Seurat.
- Many of us use RMarkdown to prepare our analysis reports.
Programmer Analyst II
Database Applications Manager
Programmer Analyst II
Programmer Analyst III
Programmer Analyst III
Bioinformatics Specialist I
Selected Publications with Bioinformatics Support
High-throughput sequencing data analysis:
Gao X, Hu D, Gogol M, Li H. ClusterMap: compare multiple single cell RNA-Seq datasets across different experimental conditions. Bioinformatics. 2019.
Qian P, De Kumar B, He X, Nolte C, Gogol M, Ahn Y, Chen S, Li Z, Xu H, Perry J, Hu D, Tao F, Zhao M, Han Y, Hall K, Peak A, Paulson A, Zhao C, Venkatraman A, Box A, Perera A, Haug J, Parmely T, Li H, Krumlauf R, Li L. Retinoid-Sensitive Epigenetic Regulation of the Hoxb Cluster Maintains Normal Hematopoiesis and Inhibits Leukemogenesis. Cell Stem Cell. 2018;22(5):740-754.
Morrison JA, McLennan R, Wolfe L, Gogol M, Meier S, McKinney M, Teddy J, Holmes L, Semerad C, Box A, Li H, Hall K, Perera A, Kulesa A. Single-cell transcriptome analysis of avian neural crest migration reveals signatures of invasion and molecular transitions. Elife. 2017;6:e28415.
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