Hamid Bolouri, PhD
Background Information
Hamid Bolouri received his PhD from Brunel University (London, UK) in 1990. From 1987 to 2002, he was a faculty member at the University of Hertfordshire (UK), becoming Professor of Neural Systems in 1998. In 2002, he joined the Institute for Systems Biology (Seattle) as a Professor of Computational Biology. He was visiting faculty in the Divisions of Biology and Control & Dynamical Systems at Caltech for periods spanning 1996-2010. In 2010, Bolouri joined the Division of Human Biology at the Fred Hutchinson Cancer Research Center (Seattle) as a Research Full Member. Before joining BRI, he was Director of Informatics & Computational Biology at the Allen Institute for Immunology.
Area of Research
We are interested in discovering and decoding the molecular interaction networks that regulate immune cell function and behavior in both healthy and disease settings. To this end, we develop and use machine learning, bioinformatics, and other statistical/mathematical methods to integrate diverse and usually large-scale data types (e.g. single-cell omics, FACS, CyTOF, and patient data).
Featured Publications
Hamid Bolouri, Cate Speake, David Skibinski, S. Alice Long, Anne M. Hocking, Daniel J. Campbell, Jessica A. Hamerman, Uma Malhotra, Jane H. Buckner, and the Benaroya Research Institute COVID-19 Research Team, The COVID-19 immune landscape is dynamically and reversibly correlated with disease severity. J Clin Invest. 2021; 131(3):e143648.
Julia Kargl, Xiaodong Zhu, Huajia Zhang, Grace HY Yang, Travis J Friesen, Melissa Shipley, Dean Y Maeda, John A Zebala, Jill McKay-Fleisch, Gavin Meredith, Afshin Mashadi-Hossein, Christina Baik, Robert H Pierce, Mary W Redman, Jeffrey C Thompson, Steven M Albelda, Hamid Bolouri, A McGarry Houghton, Neutrophil content predicts lymphocyte depletion and anti-PD1 treatment failure in NSCLC.
* Highlighted in the NIH Director's Blog on January 30th, 2020 by Dr. Francis Collins.
Hamid Bolouri#, Mary Young, Joshua Beilke, Rebecca Johnson, Brian Fox, Lu Huang, Cristina Costa Santini, Christopher Mark Hill, Anne-Renee van der Vuurst de Vries, Paul Shannon, Andrew Dervan, Pallavur Sivakumar, Matthew Trotter, Douglas Bassett, and Alexander Ratushny#, Integrative network modeling reveals mechanisms underlying T cell exhaustion. Scientific Reports. 2020. 10, 1915
Arora S, Pattwell SS, Holland EC, Bolouri H#. Variability in estimated gene expression among commonly used RNA-seq pipelines. Sci Rep. 2020;10(1):2734.
Lisa G. McFerrin, Michael Zager, Jianan Zhang, Gretchen Krenn, Robert McDermott, Desert Horse-Grant, Emily Silgard, Kara Colevas, Paul Shannon, Hamid Bolouri & Eric C. Holland, Analysis and visualization of linked molecular and clinical cancer data by using Oncoscape, Nature Genetics, 2018, (50):1203–1204.
Bolouri H#, Farrar JE, Triche T Jr, Ries RE, Lim EL, Alonzo TA, Ma Y, Moore R, Mungall AJ, Marra MA, Zhang J, Ma X, Liu Y, Liu Y, Auvil JMG, Davidsen TM, Gesuwan P, Hermida LC, Salhia B, Capone S, Ramsingh G, Zwaan CM, Noort S, Piccolo SR, Kolb EA, Gamis AS, Smith MA, Gerhard DS, Meshinchi S#. The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions. Nat Med. 2018; 24(1):103-112.
Bolouri H#, Zhao LP, Holland EC, Big data visualization identifies the multidimensional molecular landscape of human gliomas, Proceedings of the National Academy of Sciences of the United States of America, 2016; 113(19):5394-9.
# Corresponding Author
Most Cited Articles
M Hucka, A Finney, HM Sauro, H Bolouri, JC Doyle, H Kitano, AP Arkin, etl. al., The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics 2003; 19 (4), 524-531.
Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh CH, Minokawa T, Amore G, Hinman V, Arenas-Mena C, Otim O, Brown CT, Livi CB, Lee PY, Revilla R, Rust AG, Pan Zj, Schilstra MJ, Clarke PJ, Arnone MI, Rowen L, Cameron RA, McClay DR, Hood L, Bolouri H, A genomic regulatory network for development, Science; 2002, 295 (5560), 1669-1678
CH Yuh, H Bolouri, EH Davidson, Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene, Science 1998; 279 (5358), 1896-1902
List of Published Work
To view a full list of published work, please visit Dr Bolouri's Google Scholar Page.
Books
Bolouri H, Personal Genomics and Personalized Medicine, Imperial College Press, 2010. Reviewed in Nature, 1st April 2010, (464):680.
Bolouri H, Computational Modeling of Genetic Regulatory Networks – a primer, Imperial College Press, 2008. (an IPC all-time best-seller)
Bower J and Bolouri H (Eds.), Computational Modeling of Genetic and Biochemical Networks, MIT Press. Hardcover January 2001. Paperback March 2004.
Paton R, Bolouri H, Holcombe M, Parish JH, Tateson R (Eds.), Computation in Cells and Tissues, Springer-Verlag, 2004.
