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Laboratory and Data Analysis Methods for Characterization of Human B Cell Repertoires by High-Throughput DNA Sequencing.

Wang C, Liu Y, Roskin KM, Jackson KJ, Boyd SD.

Methods Mol Biol. 2015;1343:219-33. doi: 10.1007/978-1-4939-2963-4_17.


IgH sequences in common variable immune deficiency reveal altered B cell development and selection.

Roskin KM, Simchoni N, Liu Y, Lee JY, Seo K, Hoh RA, Pham T, Park JH, Furman D, Dekker CL, Davis MM, James JA, Nadeau KC, Cunningham-Rundles C, Boyd SD.

Sci Transl Med. 2015 Aug 26;7(302):302ra135. doi: 10.1126/scitranslmed.aab1216.


Human B-cell isotype switching origins of IgE.

Looney TJ, Lee JY, Roskin KM, Hoh RA, King J, Glanville J, Liu Y, Pham TD, Dekker CL, Davis MM, Boyd SD.

J Allergy Clin Immunol. 2016 Feb;137(2):579-586.e7. doi: 10.1016/j.jaci.2015.07.014. Epub 2015 Aug 22.


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.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 5;370(1676). pii: 20140236. doi: 10.1098/rstb.2014.0236.


Single B-cell deconvolution of peanut-specific antibody responses in allergic patients.

Hoh RA, Joshi SA, Liu Y, Wang C, Roskin KM, Lee JY, Pham T, Looney TJ, Jackson KJ, Dixit VP, King J, Lyu SC, Jenks J, Hamilton RG, Nadeau KC, Boyd SD.

J Allergy Clin Immunol. 2016 Jan;137(1):157-67. doi: 10.1016/j.jaci.2015.05.029. Epub 2015 Jul 4.


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 JY, Dixit V, Dekker CL, Swan GE, Goronzy JJ, Boyd SD.

Proc Natl Acad Sci U S A. 2015 Jan 13;112(2):500-5. doi: 10.1073/pnas.1415875112. Epub 2014 Dec 22.


HIV-1 envelope gp41 antibodies can originate from terminal ileum B cells that share cross-reactivity with commensal bacteria.

Trama AM, Moody MA, Alam SM, Jaeger FH, Lockwood B, Parks R, Lloyd KE, Stolarchuk C, Scearce R, Foulger A, Marshall DJ, Whitesides JF, Jeffries TL Jr, Wiehe K, Morris L, Lambson B, Soderberg K, Hwang KK, Tomaras GD, Vandergrift N, Jackson KJ, Roskin KM, Boyd SD, Kepler TB, Liao HX, Haynes BF.

Cell Host Microbe. 2014 Aug 13;16(2):215-26. doi: 10.1016/j.chom.2014.07.003.


Human responses to influenza vaccination show seroconversion signatures and convergent antibody rearrangements.

Jackson KJ, Liu Y, Roskin KM, Glanville J, Hoh RA, Seo K, Marshall EL, Gurley TC, Moody MA, Haynes BF, Walter EB, Liao HX, Albrecht RA, GarcĂ­a-Sastre A, Chaparro-Riggers J, Rajpal A, Pons J, Simen BB, Hanczaruk B, Dekker CL, Laserson J, Koller D, Davis MM, Fire AZ, Boyd SD.

Cell Host Microbe. 2014 Jul 9;16(1):105-14. doi: 10.1016/j.chom.2014.05.013. Epub 2014 Jun 26.


Effects of aging, cytomegalovirus infection, and EBV infection on human B cell repertoires.

Wang C, Liu Y, Xu LT, Jackson KJ, Roskin KM, Pham TD, Laserson J, Marshall EL, Seo K, Lee JY, Furman D, Koller D, Dekker CL, Davis MM, Fire AZ, Boyd SD.

J Immunol. 2014 Jan 15;192(2):603-11. doi: 10.4049/jimmunol.1301384. Epub 2013 Dec 11.


Comprehensive whole-genome sequencing of an early-stage primary myelofibrosis patient defines low mutational burden and non-recurrent candidate genes.

Merker JD, Roskin KM, Ng D, Pan C, Fisk DG, King JJ, Hoh R, Stadler M, Okumoto LM, Abidi P, Hewitt R, Jones CD, Gojenola L, Clark MJ, Zhang B, Cherry AM, George TI, Snyder M, Boyd SD, Zehnder JL, Fire AZ, Gotlib J.

Haematologica. 2013 Nov;98(11):1689-96. doi: 10.3324/haematol.2013.092379. Epub 2013 Jul 19.


Convergent antibody signatures in human dengue.

Parameswaran P, Liu Y, Roskin KM, Jackson KK, Dixit VP, Lee JY, Artiles KL, Zompi S, Vargas MJ, Simen BB, Hanczaruk B, McGowan KR, Tariq MA, Pourmand N, Koller D, Balmaseda A, Boyd SD, Harris E, Fire AZ.

Cell Host Microbe. 2013 Jun 12;13(6):691-700. doi: 10.1016/j.chom.2013.05.008.


Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus.

Liao HX, Lynch R, Zhou T, Gao F, Alam SM, Boyd SD, Fire AZ, Roskin KM, Schramm CA, Zhang Z, Zhu J, Shapiro L; NISC Comparative Sequencing Program, Mullikin JC, Gnanakaran S, Hraber P, Wiehe K, Kelsoe G, Yang G, Xia SM, Montefiori DC, Parks R, Lloyd KE, Scearce RM, Soderberg KA, Cohen M, Kamanga G, Louder MK, Tran LM, Chen Y, Cai F, Chen S, Moquin S, Du X, Joyce MG, Srivatsan S, Zhang B, Zheng A, Shaw GM, Hahn BH, Kepler TB, Korber BT, Kwong PD, Mascola JR, Haynes BF.

Nature. 2013 Apr 25;496(7446):469-76. doi: 10.1038/nature12053. Epub 2013 Apr 3.


Meta-alignment with crumble and prune: partitioning very large alignment problems for performance and parallelization.

Roskin KM, Paten B, Haussler D.

BMC Bioinformatics. 2011 May 10;12:144. doi: 10.1186/1471-2105-12-144.


ENCODE whole-genome data in the UCSC genome browser (2011 update).

Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, Fujita PA, Rhead B, Smith KE, Pohl A, Kuhn RM, Karolchik D, Haussler D, Kent WJ.

Nucleic Acids Res. 2011 Jan;39(Database issue):D871-5. doi: 10.1093/nar/gkq1017. Epub 2010 Oct 30.


Global predictions and tests of erythroid regulatory regions.

Hardison RC, Chiaromonte F, Kolbe D, Wang H, Petrykowska H, Elnitski L, Yang S, Giardine B, Zhang Y, Riemer C, Schwartz S, Haussler D, Roskin KM, Weber RJ, Diekhans M, Kent WJ, Weiss MJ, Welch J, Miller W.

Cold Spring Harb Symp Quant Biol. 2003;68:335-44. No abstract available.


The share of human genomic DNA under selection estimated from human-mouse genomic alignments.

Chiaromonte F, Weber RJ, Roskin KM, Diekhans M, Kent WJ, Haussler D.

Cold Spring Harb Symp Quant Biol. 2003;68:245-54. No abstract available.


Score functions for determining regional conservation in two-species local alignments.

Roskin KM, Diekhans M, Haussler D.

J Comput Biol. 2004;11(2-3):395-411.


Aligning multiple genomic sequences with the threaded blockset aligner.

Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W.

Genome Res. 2004 Apr;14(4):708-15.


Comparative recombination rates in the rat, mouse, and human genomes.

Jensen-Seaman MI, Furey TS, Payseur BA, Lu Y, Roskin KM, Chen CF, Thomas MA, Haussler D, Jacob HJ.

Genome Res. 2004 Apr;14(4):528-38.


Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes.

Yang S, Smit AF, Schwartz S, Chiaromonte F, Roskin KM, Haussler D, Miller W, Hardison RC.

Genome Res. 2004 Apr;14(4):517-27.

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