Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 31

1.

Shaping of infant B cell receptor repertoires by environmental factors and infectious disease.

Nielsen SCA, Roskin KM, Jackson KJL, Joshi SA, Nejad P, Lee JY, Wagar LE, Pham TD, Hoh RA, Nguyen KD, Tsunemoto HY, Patel SB, Tibshirani R, Ley C, Davis MM, Parsonnet J, Boyd SD.

Sci Transl Med. 2019 Feb 27;11(481). pii: eaat2004. doi: 10.1126/scitranslmed.aat2004.

2.

Impact of somatic and germline mutations on the outcome of systemic mastocytosis.

Muñoz-González JI, Jara-Acevedo M, Alvarez-Twose I, Merker JD, Teodosio C, Hou Y, Henriques A, Roskin KM, Sanchez-Muñoz L, Tsai AG, Caldas C, Matito A, Sánchez-Gallego JI, Mayado A, Dasilva-Freire N, Gotlib JR, Escribano L, Orfao A, García-Montero AC.

Blood Adv. 2018 Nov 13;2(21):2814-2828. doi: 10.1182/bloodadvances.2018020628.

3.

A novel TRIP11-FLT3 fusion in a patient with a myeloid/lymphoid neoplasm with eosinophilia.

Chung A, Hou Y, Ohgami RS, Von Gehr A, Fisk DG, Roskin KM, Li X, Gojenola L, Bangs CD, Arber DA, Fire AZ, Cherry AM, Zehnder JL, Gotlib J, Merker JD.

Cancer Genet. 2017 Oct;216-217:10-15. doi: 10.1016/j.cancergen.2017.05.001. Epub 2017 May 10.

PMID:
29025582
4.

High-fat diet induces systemic B-cell repertoire changes associated with insulin resistance.

Pham TD, Chng MHY, Roskin KM, Jackson KJL, Nguyen KD, Glanville J, Lee JY, Engleman EG, Boyd SD.

Mucosal Immunol. 2017 Nov;10(6):1468-1479. doi: 10.1038/mi.2017.25. Epub 2017 Apr 19.

PMID:
28422186
5.

Defining antigen-specific plasmablast and memory B cell subsets in human blood after viral infection or vaccination.

Ellebedy AH, Jackson KJ, Kissick HT, Nakaya HI, Davis CW, Roskin KM, McElroy AK, Oshansky CM, Elbein R, Thomas S, Lyon GM, Spiropoulou CF, Mehta AK, Thomas PG, Boyd SD, Ahmed R.

Nat Immunol. 2016 Oct;17(10):1226-34. doi: 10.1038/ni.3533. Epub 2016 Aug 15.

6.

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.

PMID:
26420720
7.

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.

8.

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.

9.

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.

10.

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 KJL, Dixit VP, King J, Lyu SC, Jenks J, Hamilton RG, Nadeau KC, Boyd SD.

J Allergy Clin Immunol. 2016 Jan;137(1):157-167. doi: 10.1016/j.jaci.2015.05.029. Epub 2015 Jul 4.

11.

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.

12.

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 KJL, Roskin KM, Boyd SD, Kepler TB, Liao HX, Haynes BF.

Cell Host Microbe. 2014 Aug 13;16(2):215-226. doi: 10.1016/j.chom.2014.07.003.

13.

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, García-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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

PMID:
15338635
21.

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.

PMID:
15338624
22.

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.

PMID:
15285898
23.

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.

24.

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.

25.

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.

26.

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F; Rat Genome Sequencing Project Consortium.

Nature. 2004 Apr 1;428(6982):493-521.

PMID:
15057822
27.

The UCSC Table Browser data retrieval tool.

Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6.

28.

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution.

Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, Schwartz S, Furey TS, Whelan S, Goldman N, Smit A, Miller W, Chiaromonte F, Haussler D.

Genome Res. 2003 Jan;13(1):13-26.

29.

The UCSC Genome Browser Database.

Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ; University of California Santa Cruz.

Nucleic Acids Res. 2003 Jan 1;31(1):51-4.

30.

Initial sequencing and comparative analysis of the mouse genome.

Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES.

Nature. 2002 Dec 5;420(6915):520-62.

PMID:
12466850
31.

The human genome browser at UCSC.

Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D.

Genome Res. 2002 Jun;12(6):996-1006.

Supplemental Content

Loading ...
Support Center