Computational Biology

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.

Contact

To contact the Computational Biology group at the Stowers Institute directly, please email helpcompbio@stowers.org

Resources

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

Software Tools

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.

Team Members

Hua Li

Biostatistician

Cynthia Chen

Programmer Analyst II

Malcolm Cook

Database Applications Manager

Huzaifa Hassan

Programmer Analyst II

Madelaine Gogol

Programmer Analyst III

Ariel Paulson

Programmer Analyst III

Ning Zhang

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