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Items: 33

1.

Deep sequencing of HIV-1 variants from paired plasma and cerebrospinal fluid during primary HIV infection.

Gega A, Kozal MJ, Chiarella J, Lee E, Peterson J, Hecht FM, Liegler T, St John EP, Simen BB, Price RW, Spudich SS.

J Virus Erad. 2015;1(4):264-268.

2.

A Follow-Up of the Multicenter Collaborative Study on HIV-1 Drug Resistance and Tropism Testing Using 454 Ultra Deep Pyrosequencing.

St John EP, Simen BB, Turenchalk GS, Braverman MS, Abbate I, Aerssens J, Bouchez O, Gabriel C, Izopet J, Meixenberger K, Di Giallonardo F, Schlapbach R, Paredes R, Sakwa J, Schmitz-Agheguian GG, Thielen A, Victor M, Metzner KJ, Däumer MP; 454 HIV-1 Alpha Study Group.

PLoS One. 2016 Jan 12;11(1):e0146687. doi: 10.1371/journal.pone.0146687. eCollection 2016.

3.

Validation of a next-generation-sequencing cancer panel for use in the clinical laboratory.

Simen BB, Yin L, Goswami CP, Davis KO, Bajaj R, Gong JZ, Peiper SC, Johnson ES, Wang ZX.

Arch Pathol Lab Med. 2015 Apr;139(4):508-17. doi: 10.5858/arpa.2013-0710-OA. Epub 2014 Oct 30.

PMID:
25356985
4.

Low-frequency NNRTI-resistant HIV-1 variants and relationship to mutational load in antiretroviral-naïve subjects.

Gupta S, Lataillade M, Kyriakides TC, Chiarella J, St John EP, Webb S, Moreno EA, Simen BB, Kozal MJ.

Viruses. 2014 Sep 16;6(9):3428-37. doi: 10.3390/v6093428.

5.

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.

6.

An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing.

Simen BB, Braverman MS, Abbate I, Aerssens J, Bidet Y, Bouchez O, Gabriel C, Izopet J, Kessler HH, Stelzl E, Di Giallonardo F, Schlapbach R, Radonic A, Paredes R, Recordon-Pinson P, Sakwa J, St John EP, Schmitz-Agheguian GG, Metzner KJ, Däumer MP; 454 HIV Alphastudy Group.

J Virol Methods. 2014 Aug;204:31-7. doi: 10.1016/j.jviromet.2014.04.007. Epub 2014 Apr 13.

PMID:
24731928
7.

High-resolution antibody dynamics of vaccine-induced immune responses.

Laserson U, Vigneault F, Gadala-Maria D, Yaari G, Uduman M, Vander Heiden JA, Kelton W, Taek Jung S, Liu Y, Laserson J, Chari R, Lee JH, Bachelet I, Hickey B, Lieberman-Aiden E, Hanczaruk B, Simen BB, Egholm M, Koller D, Georgiou G, Kleinstein SH, Church GM.

Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4928-33. doi: 10.1073/pnas.1323862111. Epub 2014 Mar 17.

8.

The effects of somatic hypermutation on neutralization and binding in the PGT121 family of broadly neutralizing HIV antibodies.

Sok D, Laserson U, Laserson J, Liu Y, Vigneault F, Julien JP, Briney B, Ramos A, Saye KF, Le K, Mahan A, Wang S, Kardar M, Yaari G, Walker LM, Simen BB, St John EP, Chan-Hui PY, Swiderek K, Kleinstein SH, Alter G, Seaman MS, Chakraborty AK, Koller D, Wilson IA, Church GM, Burton DR, Poignard P.

PLoS Pathog. 2013;9(11):e1003754. doi: 10.1371/journal.ppat.1003754. Epub 2013 Nov 21. Erratum in: PLoS Pathog. 2013 Dec;9(12). doi:10.1371/annotation/f1f8c791-61e9-45c6-a455-92c6dadf9f06. Kleinstein, Stephen H [corrected to Kleinstein, Steven H].

9.

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.

10.

Next generation sequencing reveals the association of DRB3*02:02 with type 1 diabetes.

Erlich HA, Valdes AM, McDevitt SL, Simen BB, Blake LA, McGowan KR, Todd JA, Rich SS, Noble JA; Type 1 Diabetes Genetics Consortium (T1DGC).

Diabetes. 2013 Jul;62(7):2618-22. doi: 10.2337/db12-1387. Epub 2013 Mar 5.

11.

High throughput HLA genotyping using 454 sequencing and the Fluidigm Access Array™ System for simplified amplicon library preparation.

Moonsamy PV, Williams T, Bonella P, Holcomb CL, Höglund BN, Hillman G, Goodridge D, Turenchalk GS, Blake LA, Daigle DA, Simen BB, Hamilton A, May AP, Erlich HA.

Tissue Antigens. 2013 Mar;81(3):141-9. doi: 10.1111/tan.12071.

PMID:
23398507
12.

Assuring the quality of next-generation sequencing in clinical laboratory practice.

Gargis AS, Kalman L, Berry MW, Bick DP, Dimmock DP, Hambuch T, Lu F, Lyon E, Voelkerding KV, Zehnbauer BA, Agarwala R, Bennett SF, Chen B, Chin EL, Compton JG, Das S, Farkas DH, Ferber MJ, Funke BH, Furtado MR, Ganova-Raeva LM, Geigenmüller U, Gunselman SJ, Hegde MR, Johnson PL, Kasarskis A, Kulkarni S, Lenk T, Liu CS, Manion M, Manolio TA, Mardis ER, Merker JD, Rajeevan MS, Reese MG, Rehm HL, Simen BB, Yeakley JM, Zook JM, Lubin IM.

Nat Biotechnol. 2012 Nov;30(11):1033-6. doi: 10.1038/nbt.2403. No abstract available.

13.

Deep sequencing does not reveal additional transmitted mutations in patients diagnosed with HIV-1 variants with single nucleoside reverse transcriptase inhibitor resistance mutations.

Pingen M, van der Ende ME, Wensing AM, el Barzouhi A, Simen BB, Schutten M, Boucher CA.

HIV Med. 2013 Mar;14(3):176-81. doi: 10.1111/j.1468-1293.2012.01037.x. Epub 2012 Sep 19.

14.

Therapy failure resulting from superinfection by a drug-resistant HIV variant.

Pingen M, Nouwen JL, Dinant S, Albert J, Mild M, Brodin J, Simen BB, Walsh S, Kayser M, van der Ende ME, Schutten M, Boucher CA.

Antivir Ther. 2012;17(8):1621-5. doi: 10.3851/IMP2267. Epub 2012 Jul 31.

PMID:
22846173
15.

Initial antibodies binding to HIV-1 gp41 in acutely infected subjects are polyreactive and highly mutated.

Liao HX, Chen X, Munshaw S, Zhang R, Marshall DJ, Vandergrift N, Whitesides JF, Lu X, Yu JS, Hwang KK, Gao F, Markowitz M, Heath SL, Bar KJ, Goepfert PA, Montefiori DC, Shaw GC, Alam SM, Margolis DM, Denny TN, Boyd SD, Marshal E, Egholm M, Simen BB, Hanczaruk B, Fire AZ, Voss G, Kelsoe G, Tomaras GD, Moody MA, Kepler TB, Haynes BF.

J Exp Med. 2011 Oct 24;208(11):2237-49. doi: 10.1084/jem.20110363. Epub 2011 Oct 10.

16.

High-throughput sequencing of PCR products tagged with universal primers using 454 life sciences systems.

Daigle D, Simen BB, Pochart P.

Curr Protoc Mol Biol. 2011 Oct;Chapter 7:Unit7.5. doi: 10.1002/0471142727.mb0705s96.

PMID:
21987058
17.

Use of dried-blood-spot samples and in-house assays to identify antiretroviral drug resistance in HIV-infected children in resource-constrained settings.

Ziemniak C, Mengistu Y, Ruff A, Chen YH, Khaki L, Bedri A, Simen BB, Palumbo P, Eshleman SH, Persaud D.

J Clin Microbiol. 2011 Dec;49(12):4077-82. doi: 10.1128/JCM.01004-11. Epub 2011 Sep 28.

18.

Prevalence of low-level HIV-1 variants with reverse transcriptase mutation K65R and the effect of antiretroviral drug exposure on variant levels.

Kozal MJ, Chiarella J, St John EP, Moreno EA, Simen BB, Arnold TE, Lataillade M.

Antivir Ther. 2011;16(6):925-9. doi: 10.3851/IMP1851.

PMID:
21900725
19.

A multi-site study using high-resolution HLA genotyping by next generation sequencing.

Holcomb CL, Höglund B, Anderson MW, Blake LA, Böhme I, Egholm M, Ferriola D, Gabriel C, Gelber SE, Goodridge D, Hawbecker S, Klein R, Ladner M, Lind C, Monos D, Pando MJ, Pröll J, Sayer DC, Schmitz-Agheguian G, Simen BB, Thiele B, Trachtenberg EA, Tyan DB, Wassmuth R, White S, Erlich HA.

Tissue Antigens. 2011 Mar;77(3):206-17. doi: 10.1111/j.1399-0039.2010.01606.x.

20.

Characterization of Mauritian cynomolgus macaque major histocompatibility complex class I haplotypes by high-resolution pyrosequencing.

Budde ML, Wiseman RW, Karl JA, Hanczaruk B, Simen BB, O'Connor DH.

Immunogenetics. 2010 Dec;62(11-12):773-80. doi: 10.1007/s00251-010-0481-9. Epub 2010 Sep 30.

21.

Individual variation in the germline Ig gene repertoire inferred from variable region gene rearrangements.

Boyd SD, Gaëta BA, Jackson KJ, Fire AZ, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, Jones CD, Simen BB, Hanczaruk B, Nguyen KD, Nadeau KC, Egholm M, Miklos DB, Zehnder JL, Collins AM.

J Immunol. 2010 Jun 15;184(12):6986-92. doi: 10.4049/jimmunol.1000445. Epub 2010 May 21.

22.

Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing.

Boyd SD, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, Jones CD, Simen BB, Hanczaruk B, Nguyen KD, Nadeau KC, Egholm M, Miklos DB, Zehnder JL, Fire AZ.

Sci Transl Med. 2009 Dec 23;1(12):12ra23.

23.

Minority variants associated with transmitted and acquired HIV-1 nonnucleoside reverse transcriptase inhibitor resistance: implications for the use of second-generation nonnucleoside reverse transcriptase inhibitors.

Varghese V, Shahriar R, Rhee SY, Liu T, Simen BB, Egholm M, Hanczaruk B, Blake LA, Gharizadeh B, Babrzadeh F, Bachmann MH, Fessel WJ, Shafer RW.

J Acquir Immune Defic Syndr. 2009 Nov 1;52(3):309-15. doi: 10.1097/QAI.0b013e3181bca669.

24.

Low-abundance HIV drug-resistant viral variants in treatment-experienced persons correlate with historical antiretroviral use.

Le T, Chiarella J, Simen BB, Hanczaruk B, Egholm M, Landry ML, Dieckhaus K, Rosen MI, Kozal MJ.

PLoS One. 2009 Jun 29;4(6):e6079. doi: 10.1371/journal.pone.0006079.

25.

Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patients.

Margeridon-Thermet S, Shulman NS, Ahmed A, Shahriar R, Liu T, Wang C, Holmes SP, Babrzadeh F, Gharizadeh B, Hanczaruk B, Simen BB, Egholm M, Shafer RW.

J Infect Dis. 2009 May 1;199(9):1275-85. doi: 10.1086/597808.

26.

Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes.

Simen BB, Simons JF, Hullsiek KH, Novak RM, Macarthur RD, Baxter JD, Huang C, Lubeski C, Turenchalk GS, Braverman MS, Desany B, Rothberg JM, Egholm M, Kozal MJ; Terry Beirn Community Programs for Clinical Research on AIDS.

J Infect Dis. 2009 Mar 1;199(5):693-701. doi: 10.1086/596736.

PMID:
19210162
27.

Gene expression profiling in postmortem prefrontal cortex of major depressive disorder.

Kang HJ, Adams DH, Simen A, Simen BB, Rajkowska G, Stockmeier CA, Overholser JC, Meltzer HY, Jurjus GJ, Konick LC, Newton SS, Duman RS.

J Neurosci. 2007 Nov 28;27(48):13329-40.

28.

GRP94 is essential for mesoderm induction and muscle development because it regulates insulin-like growth factor secretion.

Wanderling S, Simen BB, Ostrovsky O, Ahmed NT, Vogen SM, Gidalevitz T, Argon Y.

Mol Biol Cell. 2007 Oct;18(10):3764-75. Epub 2007 Jul 18.

29.

TNFalpha signaling in depression and anxiety: behavioral consequences of individual receptor targeting.

Simen BB, Duman CH, Simen AA, Duman RS.

Biol Psychiatry. 2006 May 1;59(9):775-85. Epub 2006 Feb 3.

PMID:
16458261
30.

Radicicol-sensitive peptide binding to the N-terminal portion of GRP94.

Vogen S, Gidalevitz T, Biswas C, Simen BB, Stein E, Gulmen F, Argon Y.

J Biol Chem. 2002 Oct 25;277(43):40742-50. Epub 2002 Aug 19.

31.

The C terminus of the Ca channel alpha1B subunit mediates selective inhibition by G-protein-coupled receptors.

Simen AA, Lee CC, Simen BB, Bindokas VP, Miller RJ.

J Neurosci. 2001 Oct 1;21(19):7587-97.

32.

GRP94, an ER chaperone with protein and peptide binding properties.

Argon Y, Simen BB.

Semin Cell Dev Biol. 1999 Oct;10(5):495-505. Review.

PMID:
10597632
33.

Interaction of radicicol with members of the heat shock protein 90 family of molecular chaperones.

Schulte TW, Akinaga S, Murakata T, Agatsuma T, Sugimoto S, Nakano H, Lee YS, Simen BB, Argon Y, Felts S, Toft DO, Neckers LM, Sharma SV.

Mol Endocrinol. 1999 Sep;13(9):1435-48.

PMID:
10478836

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