Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 43

1.

Biophysicochemical Motifs in T-cell Receptor Sequences Distinguish Repertoires from Tumor-Infiltrating Lymphocyte and Adjacent Healthy Tissue.

Ostmeyer J, Christley S, Toby IT, Cowell LG.

Cancer Res. 2019 Apr 1;79(7):1671-1680. doi: 10.1158/0008-5472.CAN-18-2292. Epub 2019 Jan 8.

PMID:
30622114
2.

iReceptor: A platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories.

Corrie BD, Marthandan N, Zimonja B, Jaglale J, Zhou Y, Barr E, Knoetze N, Breden FMW, Christley S, Scott JK, Cowell LG, Breden F.

Immunol Rev. 2018 Jul;284(1):24-41. doi: 10.1111/imr.12666. Review.

PMID:
29944754
3.

VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements.

Christley S, Scarborough W, Salinas E, Rounds WH, Toby IT, Fonner JM, Levin MK, Kim M, Mock SA, Jordan C, Ostmeyer J, Buntzman A, Rubelt F, Davila ML, Monson NL, Scheuermann RH, Cowell LG.

Front Immunol. 2018 May 8;9:976. doi: 10.3389/fimmu.2018.00976. eCollection 2018.

4.

Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data.

Breden F, Luning Prak ET, Peters B, Rubelt F, Schramm CA, Busse CE, Vander Heiden JA, Christley S, Bukhari SAC, Thorogood A, Matsen Iv FA, Wine Y, Laserson U, Klatzmann D, Douek DC, Lefranc MP, Collins AM, Bubela T, Kleinstein SH, Watson CT, Cowell LG, Scott JK, Kepler TB.

Front Immunol. 2017 Nov 1;8:1418. doi: 10.3389/fimmu.2017.01418. eCollection 2017.

5.

Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data.

Rubelt F, Busse CE, Bukhari SAC, Bürckert JP, Mariotti-Ferrandiz E, Cowell LG, Watson CT, Marthandan N, Faison WJ, Hershberg U, Laserson U, Corrie BD, Davis MM, Peters B, Lefranc MP, Scott JK, Breden F; AIRR Community, Luning Prak ET, Kleinstein SH.

Nat Immunol. 2017 Nov 16;18(12):1274-1278. doi: 10.1038/ni.3873. No abstract available.

6.

VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data.

Christley S, Levin MK, Toby IT, Fonner JM, Monson NL, Rounds WH, Rubelt F, Scarborough W, Scheuermann RH, Cowell LG.

BMC Bioinformatics. 2017 Oct 11;18(1):448. doi: 10.1186/s12859-017-1853-z.

7.

Statistical classifiers for diagnosing disease from immune repertoires: a case study using multiple sclerosis.

Ostmeyer J, Christley S, Rounds WH, Toby I, Greenberg BM, Monson NL, Cowell LG.

BMC Bioinformatics. 2017 Sep 7;18(1):401. doi: 10.1186/s12859-017-1814-6.

8.

Peripheral VH4+ plasmablasts demonstrate autoreactive B cell expansion toward brain antigens in early multiple sclerosis patients.

Rivas JR, Ireland SJ, Chkheidze R, Rounds WH, Lim J, Johnson J, Ramirez DM, Ligocki AJ, Chen D, Guzman AA, Woodhall M, Wilson PC, Meffre E, White C 3rd, Greenberg BM, Waters P, Cowell LG, Stowe AM, Monson NL.

Acta Neuropathol. 2017 Jan;133(1):43-60. doi: 10.1007/s00401-016-1627-0. Epub 2016 Oct 11.

9.

VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.

Toby IT, Levin MK, Salinas EA, Christley S, Bhattacharya S, Breden F, Buntzman A, Corrie B, Fonner J, Gupta NT, Hershberg U, Marthandan N, Rosenfeld A, Rounds W, Rubelt F, Scarborough W, Scott JK, Uduman M, Vander Heiden JA, Scheuermann RH, Monson N, Kleinstein SH, Cowell LG.

BMC Bioinformatics. 2016 Oct 6;17(Suppl 13):333.

10.

Individual heritable differences result in unique cell lymphocyte receptor repertoires of naïve and antigen-experienced cells.

Rubelt F, Bolen CR, McGuire HM, Vander Heiden JA, Gadala-Maria D, Levin M, Euskirchen GM, Mamedov MR, Swan GE, Dekker CL, Cowell LG, Kleinstein SH, Davis MM.

Nat Commun. 2016 Mar 23;7:11112. doi: 10.1038/ncomms11112.

11.

owlcpp: a C++ library for working with OWL ontologies.

Levin MK, Cowell LG.

J Biomed Semantics. 2015 Sep 16;6:35. doi: 10.1186/s13326-015-0035-z. eCollection 2015.

12.

RAG Represents a Widespread Threat to the Lymphocyte Genome.

Teng G, Maman Y, Resch W, Kim M, Yamane A, Qian J, Kieffer-Kwon KR, Mandal M, Ji Y, Meffre E, Clark MR, Cowell LG, Casellas R, Schatz DG.

Cell. 2015 Aug 13;162(4):751-65. doi: 10.1016/j.cell.2015.07.009. Epub 2015 Jul 30.

13.

MSPrecise: A molecular diagnostic test for multiple sclerosis using next generation sequencing.

Rounds WH, Salinas EA, Wilks TB 2nd, Levin MK, Ligocki AJ, Ionete C, Pardo CA, Vernino S, Greenberg BM, Bigwood DW, Eastman EM, Cowell LG, Monson NL.

Gene. 2015 Nov 10;572(2):191-7. doi: 10.1016/j.gene.2015.07.011. Epub 2015 Jul 11.

14.

The antibody genetics of multiple sclerosis: comparing next-generation sequencing to sanger sequencing.

Rounds WH, Ligocki AJ, Levin MK, Greenberg BM, Bigwood DW, Eastman EM, Cowell LG, Monson NL.

Front Neurol. 2014 Sep 16;5:166. doi: 10.3389/fneur.2014.00166. eCollection 2014.

15.

Design and evaluation of a bacterial clinical infectious diseases ontology.

Gordon CL, Pouch S, Cowell LG, Boland MR, Platt HL, Goldfain A, Weng C.

AMIA Annu Symp Proc. 2013 Nov 16;2013:502-11. eCollection 2013.

16.

A genome-wide association study of variants associated with acquisition of Staphylococcus aureus bacteremia in a healthcare setting.

Nelson CL, Pelak K, Podgoreanu MV, Ahn SH, Scott WK, Allen AS, Cowell LG, Rude TH, Zhang Y, Tong A, Ruffin F, Sharma-Kuinkel BK, Fowler VG Jr.

BMC Infect Dis. 2014 Feb 13;14:83. doi: 10.1186/1471-2334-14-83.

17.

Expansion of CD27high plasmablasts in transverse myelitis patients that utilize VH4 and JH6 genes and undergo extensive somatic hypermutation.

Ligocki AJ, Rounds WH, Cameron EM, Harp CT, Frohman EM, Courtney AM, Vernino S, Cowell LG, Greenberg B, Monson NL.

Genes Immun. 2013 Jul-Aug;14(5):291-301. doi: 10.1038/gene.2013.18. Epub 2013 Apr 18.

18.

CD19-targeted T cells rapidly induce molecular remissions in adults with chemotherapy-refractory acute lymphoblastic leukemia.

Brentjens RJ, Davila ML, Riviere I, Park J, Wang X, Cowell LG, Bartido S, Stefanski J, Taylor C, Olszewska M, Borquez-Ojeda O, Qu J, Wasielewska T, He Q, Bernal Y, Rijo IV, Hedvat C, Kobos R, Curran K, Steinherz P, Jurcic J, Rosenblat T, Maslak P, Frattini M, Sadelain M.

Sci Transl Med. 2013 Mar 20;5(177):177ra38. doi: 10.1126/scitranslmed.3005930.

19.

Ontology for vector surveillance and management.

Lozano-Fuentes S, Bandyopadhyay A, Cowell LG, Goldfain A, Eisen L.

J Med Entomol. 2013 Jan;50(1):1-14.

20.

Haplotype Association Mapping Identifies a Candidate Gene Region in Mice Infected With Staphylococcus aureus.

Johnson NV, Ahn SH, Deshmukh H, Levin MK, Nelson CL, Scott WK, Allen A, Fowler VG Jr, Cowell LG.

G3 (Bethesda). 2012 Jun;2(6):693-700. doi: 10.1534/g3.112.002501. Epub 2012 Jun 1.

21.

Logical development of the cell ontology.

Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD.

BMC Bioinformatics. 2011 Jan 5;12:6. doi: 10.1186/1471-2105-12-6.

22.

Two genes on A/J chromosome 18 are associated with susceptibility to Staphylococcus aureus infection by combined microarray and QTL analyses.

Ahn SH, Deshmukh H, Johnson N, Cowell LG, Rude TH, Scott WK, Nelson CL, Zaas AK, Marchuk DA, Keum S, Lamlertthon S, Sharma-Kuinkel BK, Sempowski GD, Fowler VG Jr.

PLoS Pathog. 2010 Sep 2;6(9):e1001088. doi: 10.1371/journal.ppat.1001088.

23.

Memory B cells from a subset of treatment-naïve relapsing-remitting multiple sclerosis patients elicit CD4(+) T-cell proliferation and IFN-γ production in response to myelin basic protein and myelin oligodendrocyte glycoprotein.

Harp CT, Ireland S, Davis LS, Remington G, Cassidy B, Cravens PD, Stuve O, Lovett-Racke AE, Eagar TN, Greenberg BM, Racke MK, Cowell LG, Karandikar NJ, Frohman EM, Monson NL.

Eur J Immunol. 2010 Oct;40(10):2942-56. doi: 10.1002/eji.201040516.

24.

Towards an ontological representation of resistance: the case of MRSA.

Goldfain A, Smith B, Cowell LG.

J Biomed Inform. 2011 Feb;44(1):35-41. doi: 10.1016/j.jbi.2010.02.008. Epub 2010 Mar 2.

25.

Hematopoietic cell types: prototype for a revised cell ontology.

Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ.

J Biomed Inform. 2011 Feb;44(1):75-9. doi: 10.1016/j.jbi.2010.01.006. Epub 2010 Feb 1.

26.

Conserved cryptic recombination signals in Vkappa gene segments are cleaved in small pre-B cells.

Lieberman AE, Kuraoka M, Davila M, Kelsoe G, Cowell LG.

BMC Immunol. 2009 Jun 25;10:37. doi: 10.1186/1471-2172-10-37.

27.

An improved ontological representation of dendritic cells as a paradigm for all cell types.

Masci AM, Arighi CN, Diehl AD, Lieberman AE, Mungall C, Scheuermann RH, Smith B, Cowell LG.

BMC Bioinformatics. 2009 Feb 25;10:70. doi: 10.1186/1471-2105-10-70.

28.

Multiple, conserved cryptic recombination signals in VH gene segments: detection of cleavage products only in pro B cells.

Davila M, Liu F, Cowell LG, Lieberman AE, Heikamp E, Patel A, Kelsoe G.

J Exp Med. 2007 Dec 24;204(13):3195-208. Epub 2007 Dec 3.

29.

Reassignment of the murine 3'TRDD1 recombination signal sequence.

Touvrey C, Cowell LG, Lieberman AE, Marche PN, Jouvin-Marche E, Candéias SM.

Immunogenetics. 2006 Nov;58(11):895-903. Epub 2006 Oct 5.

30.

V(D)J recombinase-mediated processing of coding junctions at cryptic recombination signal sequences in peripheral T cells during human development.

Murray JM, O'Neill JP, Messier T, Rivers J, Walker VE, McGonagle B, Trombley L, Cowell LG, Kelsoe G, McBlane F, Finette BA.

J Immunol. 2006 Oct 15;177(8):5393-404.

31.

Neonate-primed CD8+ memory cells rival adult-primed memory cells in antigen-driven expansion and anti-viral protection.

Fadel SA, Cowell LG, Cao S, Ozaki DA, Kepler TB, Steeber DA, Sarzotti M.

Int Immunol. 2006 Feb;18(2):249-57. Epub 2006 Jan 17.

PMID:
16418189
32.

SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations.

Volpe JM, Cowell LG, Kepler TB.

Bioinformatics. 2006 Feb 15;22(4):438-44. Epub 2005 Dec 15.

PMID:
16357034
33.

The recombination difference between mouse kappa and lambda segments is mediated by a pair-wise regulation mechanism.

Larijani M, Chen S, Cunningham LA, Volpe JM, Cowell LG, Lewis SM, Wu GE.

Mol Immunol. 2006 Mar;43(7):870-81. Epub 2005 Jul 27.

PMID:
16054218
34.

Computational tools for understanding sequence variability in recombination signals.

Cowell LG, Davila M, Ramsden D, Kelsoe G.

Immunol Rev. 2004 Aug;200:57-69. Review.

PMID:
15242396
35.

A functional analysis of the spacer of V(D)J recombination signal sequences.

Lee AI, Fugmann SD, Cowell LG, Ptaszek LM, Kelsoe G, Schatz DG.

PLoS Biol. 2003 Oct;1(1):E1. Epub 2003 Oct 13.

36.
37.

Identification and utilization of arbitrary correlations in models of recombination signal sequences.

Cowell LG, Davila M, Kepler TB, Kelsoe G.

Genome Biol. 2002;3(12):RESEARCH0072. Epub 2002 Nov 21.

38.

The "dispensable" portion of RAG2 is necessary for efficient V-to-DJ rearrangement during B and T cell development.

Liang HE, Hsu LY, Cado D, Cowell LG, Kelsoe G, Schlissel MS.

Immunity. 2002 Nov;17(5):639-51.

39.

The targeting of somatic hypermutation closely resembles that of meiotic mutation.

Oprea M, Cowell LG, Kepler TB.

J Immunol. 2001 Jan 15;166(2):892-9.

41.

Enhanced evolvability in immunoglobulin V genes under somatic hypermutation.

Cowell LG, Kim HJ, Humaljoki T, Berek C, Kepler TB.

J Mol Evol. 1999 Jul;49(1):23-6.

PMID:
10368430
42.
43.

The distribution of variation in regulatory gene segments, as present in MHC class II promoters.

Cowell LG, Kepler TB, Janitz M, Lauster R, Mitchison NA.

Genome Res. 1998 Feb;8(2):124-34.

Supplemental Content

Loading ...
Support Center