Krishna M. Roskin, PhD

Assistant Professor, UC Department of Pediatrics

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About

Biography

With the sequencing of human genome nearing completion, there was a lot of interest in applying comparative genomics approaches to help unlock the secrets of the human genome. Dr. Roskin worked with David Haussler as part of the Mouse Genome Sequencing Consortium. Their goal was to analyze the genomic differences between mammalian species to find regions of the human genome that are conserved not by chance but because of evolutionary constraint. To that pairwise analysis, Dr. Roskin added data from the Rat Genome Sequencing Consortium to allow triangulation of evolutionary events across the whole genome.

A major result in the Mouse genome paper was Dr. Roskin's estimate of the share of the human genome under purifying selection. He developed score functions to detect unusually conserved regions in the human genome by comparing it to the mouse. By looking at the distribution of conservation scores genome-wide compared to the scores of regions under neutral section, he estimated that 5% of human genome is under purifying selection. This percentage is much higher than the fraction of the genome that codes for proteins and spurred new interest in function non-coding elements of the human genome.

BA: Mathematics, University of California, Santa Cruz, CA.

BS: Computer Science, University of California, Santa Cruz, CA.

PhD: Computer Science, University of California, Santa Cruz, CA.

Interests

Translational medicine: immunodeficiencies; autoimmunity

Interests

Computational immunology: antibody and TCR sequence analysis

Bioinformatics: large-scale biological data systems; reproducible science.

Research Areas

Biomedical Informatics, Immunobiology

Publications

Selected

High-fat diet induces systemic B-cell repertoire changes associated with insulin resistance. Pham, TD; Chng, MH Y; Roskin, KM; Jackson, KJ L; Nguyen, KD; Glanville, J; Lee, J; Engleman, EG; Boyd, SD. Mucosal Immunology. 2017; 10:1468-1479.

Selected

Defining antigen-specific plasmablast and memory B cell subsets in human blood after viral infection or vaccination. Ellebedy, AH; Jackson, KJ L; Kissick, HT; Nakaya, HI; Davis, CW; Roskin, KM; McElroy, AK; Oshansky, CM; Elbein, R; Thomas, S; Mehta, AK; Thomas, PG; Boyd, SD; Ahmed, R. Nature Immunology. 2016; 17:1226-1234.

Selected

Single B-cell deconvolution of peanut-specific antibody responses in allergic patients. Hoh, RA; Joshi, SA; Liu, Y; Wang, C; Roskin, KM; Lee, J; Pham, T; Looney, TJ; Jackson, KJ L; Dixit, VP; Jenks, J; Hamilton, RG; Nadeau, KC; Boyd, SD. Journal of Allergy and Clinical Immunology. 2016; 137:157-167.

Selected

The mouse antibody heavy chain repertoire is germline-focused and highly variable between inbred strains. Collins, AM; Wang, Y; Roskin, KM; Marquis, CP; Jackson, KJ L. Philosophical Transactions of the Royal Society of London: Biological Sciences. 2015; 370.

Selected

IgH sequences in common variable immune deficiency reveal altered B cell development and selection. Roskin, KM; Simchoni, N; Liu, Y; Lee, J; Seo, K; Hoh, RA; Pham, T; Park, JH; Furman, D; Dekker, CL; Davis, MM; James, JA; Nadeau, KC; Cunningham-Rundles, C; Boyd, SD. Science Translational Medicine. 2015; 7:302ra135.

Selected

B-cell repertoire responses to varicella-zoster vaccination in human identical twins. Wang, C; Liu, Y; Cavanagh, MM; Le Saux, S; Qi, Q; Roskin, KM; Looney, TJ; Lee, J; Dixit, V; Dekker, CL; Swan, GE; Goronzy, JJ; Boyd, SD. Proceedings of the National Academy of Sciences of USA. 2015; 112:500-505.

Selected

Human responses to influenza vaccination show seroconversion signatures and convergent antibody rearrangements. Jackson, KJ L; Liu, Y; Roskin, KM; Glanville, J; Hoh, RA; Seo, K; Marshall, EL; Gurley, TC; Moody, MA; Haynes, BF; Koller, D; Davis, MM; Fire, AZ; Boyd, SD. Cell Host and Microbe. 2014; 16:105-114.

Selected

Effects of aging, cytomegalovirus infection, and EBV infection on human B cell repertoires. Wang, C; Liu, Y; Xu, LT; Jackson, KJ L; Roskin, KM; Pham, TD; Laserson, J; Marshall, EL; Seo, K; Lee, J; Dekker, CL; Davis, MM; Fire, AZ; Boyd, SD. Journal of immunology (Baltimore, Md. : 1950). 2014; 192:603-611.

Selected

Convergent antibody signatures in human dengue. Parameswaran, P; Liu, Y; Roskin, KM; Jackson, KK L; Dixit, VP; Lee, J; Artiles, KL; Zompi, S; Jose Vargas, M; Simen, BB; Balmaseda, A; Boyd, SD; Harris, E; Fire, AZ. Cell Host and Microbe. 2013; 13:691-700.

Selected

Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Liao, H; Lynch, R; Zhou, T; Gao, F; Alam, SM; Boyd, SD; Fire, AZ; Roskin, KM; Schramm, CA; Zhang, Z; Kwong, PD; Mascola, JR; Haynes, BF; Progra, NI S C C S. Nature. 2013; 496:469-476.