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Items: 31

1.

VariantQC: a visual quality control report for variant evaluation.

Yan MY, Ferguson B, Bimber BN.

Bioinformatics. 2019 Jul 16. pii: btz560. doi: 10.1093/bioinformatics/btz560. [Epub ahead of print]

PMID:
31309221
2.
3.

Nomenclature for the KIR of non-human species.

Robinson J, Guethlein LA, Maccari G, Blokhuis J, Bimber BN, de Groot NG, Sanderson ND, Abi-Rached L, Walter L, Bontrop RE, Hammond JA, Marsh SGE, Parham P.

Immunogenetics. 2018 Sep;70(9):571-583. doi: 10.1007/s00251-018-1064-4. Epub 2018 Jun 4.

4.

Hepatocytic expression of human sodium-taurocholate cotransporting polypeptide enables hepatitis B virus infection of macaques.

Burwitz BJ, Wettengel JM, Mück-Häusl MA, Ringelhan M, Ko C, Festag MM, Hammond KB, Northrup M, Bimber BN, Jacob T, Reed JS, Norris R, Park B, Moller-Tank S, Esser K, Greene JM, Wu HL, Abdulhaqq S, Webb G, Sutton WF, Klug A, Swanson T, Legasse AW, Vu TQ, Asokan A, Haigwood NL, Protzer U, Sacha JB.

Nat Commun. 2017 Dec 15;8(1):2146. doi: 10.1038/s41467-017-01953-y.

5.

The Role of MHC-E in T Cell Immunity Is Conserved among Humans, Rhesus Macaques, and Cynomolgus Macaques.

Wu HL, Wiseman RW, Hughes CM, Webb GM, Abdulhaqq SA, Bimber BN, Hammond KB, Reed JS, Gao L, Burwitz BJ, Greene JM, Ferrer F, Legasse AW, Axthelm MK, Park BS, Brackenridge S, Maness NJ, McMichael AJ, Picker LJ, O'Connor DH, Hansen SG, Sacha JB.

J Immunol. 2018 Jan 1;200(1):49-60. doi: 10.4049/jimmunol.1700841. Epub 2017 Nov 17.

6.

Allogeneic stem cell transplantation in fully MHC-matched Mauritian cynomolgus macaques recapitulates diverse human clinical outcomes.

Burwitz BJ, Wu HL, Abdulhaqq S, Shriver-Munsch C, Swanson T, Legasse AW, Hammond KB, Junell SL, Reed JS, Bimber BN, Greene JM, Webb GM, Northrup M, Laub W, Kievit P, MacAllister R, Axthelm MK, Ducore R, Lewis A, Colgin LMA, Hobbs T, Martin LD, Ferguson B, Thomas CR Jr, Panoskaltsis-Mortari A, Meyers G, Stanton JJ, Maziarz RT, Sacha JB.

Nat Commun. 2017 Nov 10;8(1):1418. doi: 10.1038/s41467-017-01631-z.

7.

Whole genome sequencing predicts novel human disease models in rhesus macaques.

Bimber BN, Ramakrishnan R, Cervera-Juanes R, Madhira R, Peterson SM, Norgren RB Jr, Ferguson B.

Genomics. 2017 Jul;109(3-4):214-220. doi: 10.1016/j.ygeno.2017.04.001. Epub 2017 Apr 23.

8.

Cross-Species Rhesus Cytomegalovirus Infection of Cynomolgus Macaques.

Burwitz BJ, Malouli D, Bimber BN, Reed JS, Ventura AB, Hancock MH, Uebelhoer LS, Bhusari A, Hammond KB, Espinosa Trethewy RG, Klug A, Legasse AW, Axthelm MK, Nelson JA, Park BS, Streblow DN, Hansen SG, Picker LJ, Früh K, Sacha JB.

PLoS Pathog. 2016 Nov 9;12(11):e1006014. doi: 10.1371/journal.ppat.1006014. eCollection 2016 Nov.

9.

Whole-genome characterization in pedigreed non-human primates using genotyping-by-sequencing (GBS) and imputation.

Bimber BN, Raboin MJ, Letaw J, Nevonen KA, Spindel JE, McCouch SR, Cervera-Juanes R, Spindel E, Carbone L, Ferguson B, Vinson A.

BMC Genomics. 2016 Aug 24;17:676. doi: 10.1186/s12864-016-2966-x.

10.

The killer-cell immunoglobulin-like receptors of macaques.

Bimber BN, Evans DT.

Immunol Rev. 2015 Sep;267(1):246-58. doi: 10.1111/imr.12329. Review.

11.

Tertiary mutations stabilize CD8+ T lymphocyte escape-associated compensatory mutations following transmission of simian immunodeficiency virus.

Burwitz BJ, Wu HL, Reed JS, Hammond KB, Newman LP, Bimber BN, Nimiyongskul FA, Leon EJ, Maness NJ, Friedrich TC, Yokoyama M, Sato H, Matano T, O'Connor DH, Sacha JB.

J Virol. 2014 Mar;88(6):3598-604. doi: 10.1128/JVI.03304-13. Epub 2013 Dec 26.

12.

Acute phase CD8+ T lymphocytes against alternate reading frame epitopes select for rapid viral escape during SIV infection.

Walsh AD, Bimber BN, Das A, Piaskowski SM, Rakasz EG, Bean AT, Mudd PA, Ericsen AJ, Wilson NA, Hughes AL, O'Connor DH, Maness NJ.

PLoS One. 2013 May 6;8(5):e61383. doi: 10.1371/journal.pone.0061383. Print 2013.

13.

Low-cost ultra-wide genotyping using Roche/454 pyrosequencing for surveillance of HIV drug resistance.

Dudley DM, Chin EN, Bimber BN, Sanabani SS, Tarosso LF, Costa PR, Sauer MM, Kallas EG, O'Connor DH.

PLoS One. 2012;7(5):e36494. doi: 10.1371/journal.pone.0036494. Epub 2012 May 4.

14.

Pyrosequencing reveals restricted patterns of CD8+ T cell escape-associated compensatory mutations in simian immunodeficiency virus.

Burwitz BJ, Sacha JB, Reed JS, Newman LP, Norante FA, Bimber BN, Wilson NA, Watkins DI, O'Connor DH.

J Virol. 2011 Dec;85(24):13088-96. doi: 10.1128/JVI.05650-11. Epub 2011 Oct 12.

15.

Differential MHC class I expression in distinct leukocyte subsets.

Greene JM, Wiseman RW, Lank SM, Bimber BN, Karl JA, Burwitz BJ, Lhost JJ, Hawkins OE, Kunstman KJ, Broman KW, Wolinsky SM, Hildebrand WH, O'Connor DH.

BMC Immunol. 2011 Jul 15;12:39. doi: 10.1186/1471-2172-12-39.

16.

Characterization of killer immunoglobulin-like receptor genetics and comprehensive genotyping by pyrosequencing in rhesus macaques.

Moreland AJ, Guethlein LA, Reeves RK, Broman KW, Johnson RP, Parham P, O'Connor DH, Bimber BN.

BMC Genomics. 2011 Jun 7;12:295. doi: 10.1186/1471-2164-12-295.

17.

Characterization of full-length MHC class II sequences in Indonesian and Vietnamese cynomolgus macaques.

Creager HM, Becker EA, Sandman KK, Karl JA, Lank SM, Bimber BN, Wiseman RW, Hughes AL, O'Connor SL, O'Connor DH.

Immunogenetics. 2011 Sep;63(9):611-8. doi: 10.1007/s00251-011-0537-5. Epub 2011 May 26.

18.

KIR polymorphisms modulate peptide-dependent binding to an MHC class I ligand with a Bw6 motif.

Colantonio AD, Bimber BN, Neidermyer WJ Jr, Reeves RK, Alter G, Altfeld M, Johnson RP, Carrington M, O'Connor DH, Evans DT.

PLoS Pathog. 2011 Mar;7(3):e1001316. doi: 10.1371/journal.ppat.1001316. Epub 2011 Mar 10.

19.

Transcriptionally abundant major histocompatibility complex class I alleles are fundamental to nonhuman primate simian immunodeficiency virus-specific CD8+ T cell responses.

Budde ML, Lhost JJ, Burwitz BJ, Becker EA, Burns CM, O'Connor SL, Karl JA, Wiseman RW, Bimber BN, Zhang GL, Hildebrand W, Brusic V, O'Connor DH.

J Virol. 2011 Apr;85(7):3250-61. doi: 10.1128/JVI.02355-10. Epub 2011 Jan 26.

20.

Simian immunodeficiency virus SIVmac239Deltanef vaccination elicits different Tat28-35SL8-specific CD8+ T-cell clonotypes compared to a DNA prime/adenovirus type 5 boost regimen in rhesus macaques.

Burwitz BJ, Ende Z, Sudolcan B, Reynolds MR, Greene JM, Bimber BN, Almeida JR, Kurniawan M, Venturi V, Gostick E, Wiseman RW, Douek DC, Price DA, O'Connor DH.

J Virol. 2011 Apr;85(7):3683-9. doi: 10.1128/JVI.02112-10. Epub 2011 Jan 26.

21.

Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing.

Bimber BN, Dudley DM, Lauck M, Becker EA, Chin EN, Lank SM, Grunenwald HL, Caruccio NC, Maffitt M, Wilson NA, Reed JS, Sosman JM, Tarosso LF, Sanabani S, Kallas EG, Hughes AL, O'Connor DH.

J Virol. 2010 Nov;84(22):12087-92. doi: 10.1128/JVI.01378-10. Epub 2010 Sep 15.

22.

Biological and structural characterization of a host-adapting amino acid in influenza virus.

Yamada S, Hatta M, Staker BL, Watanabe S, Imai M, Shinya K, Sakai-Tagawa Y, Ito M, Ozawa M, Watanabe T, Sakabe S, Li C, Kim JH, Myler PJ, Phan I, Raymond A, Smith E, Stacy R, Nidom CA, Lank SM, Wiseman RW, Bimber BN, O'Connor DH, Neumann G, Stewart LJ, Kawaoka Y.

PLoS Pathog. 2010 Aug 5;6(8):e1001034. doi: 10.1371/journal.ppat.1001034.

23.

MHC heterozygote advantage in simian immunodeficiency virus-infected Mauritian cynomolgus macaques.

O'Connor SL, Lhost JJ, Becker EA, Detmer AM, Johnson RC, Macnair CE, Wiseman RW, Karl JA, Greene JM, Burwitz BJ, Bimber BN, Lank SM, Tuscher JJ, Mee ET, Rose NJ, Desrosiers RC, Hughes AL, Friedrich TC, Carrington M, O'Connor DH.

Sci Transl Med. 2010 Mar 10;2(22):22ra18. doi: 10.1126/scitranslmed.3000524.

24.

Dynamics of haplotype frequency change in a CD8+TL epitope of simian immunodeficiency virus.

Hughes AL, O'Connor S, Dudley DM, Burwitz BJ, Bimber BN, O'Connor D.

Infect Genet Evol. 2010 May;10(4):555-60. doi: 10.1016/j.meegid.2010.02.001. Epub 2010 Feb 10.

25.

Major histocompatibility complex genotyping with massively parallel pyrosequencing.

Wiseman RW, Karl JA, Bimber BN, O'Leary CE, Lank SM, Tuscher JJ, Detmer AM, Bouffard P, Levenkova N, Turcotte CL, Szekeres E Jr, Wright C, Harkins T, O'Connor DH.

Nat Med. 2009 Nov;15(11):1322-6. doi: 10.1038/nm.2038. Epub 2009 Oct 11.

26.

Identification of novel MHC class I sequences in pig-tailed macaques by amplicon pyrosequencing and full-length cDNA cloning and sequencing.

O'Leary CE, Wiseman RW, Karl JA, Bimber BN, Lank SM, Tuscher JJ, O'Connor DH.

Immunogenetics. 2009 Oct;61(10):689-701. doi: 10.1007/s00251-009-0397-4. Epub 2009 Sep 24.

27.

Ultradeep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in simian immunodeficiency virus-infected macaques.

Bimber BN, Burwitz BJ, O'Connor S, Detmer A, Gostick E, Lank SM, Price DA, Hughes A, O'Connor D.

J Virol. 2009 Aug;83(16):8247-53. doi: 10.1128/JVI.00897-09. Epub 2009 Jun 10.

28.

Nef gene evolution from a single transmitted strain in acute SIV infection.

Bimber BN, Chugh P, Giorgi EE, Kim B, Almudevar AL, Dewhurst S, O'Connor DH, Lee HY.

Retrovirology. 2009 Jun 8;6:57. doi: 10.1186/1742-4690-6-57.

29.

Mauritian cynomolgus macaques share two exceptionally common major histocompatibility complex class I alleles that restrict simian immunodeficiency virus-specific CD8+ T cells.

Burwitz BJ, Pendley CJ, Greene JM, Detmer AM, Lhost JJ, Karl JA, Piaskowski SM, Rudersdorf RA, Wallace LT, Bimber BN, Loffredo JT, Cox DG, Bardet W, Hildebrand W, Wiseman RW, O'Connor SL, O'Connor DH.

J Virol. 2009 Jun;83(12):6011-9. doi: 10.1128/JVI.00199-09. Epub 2009 Apr 1.

30.

Characterization of 47 MHC class I sequences in Filipino cynomolgus macaques.

Campbell KJ, Detmer AM, Karl JA, Wiseman RW, Blasky AJ, Hughes AL, Bimber BN, O'Connor SL, O'Connor DH.

Immunogenetics. 2009 Mar;61(3):177-87. doi: 10.1007/s00251-008-0351-x. Epub 2008 Dec 24.

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