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Items: 44


Improved Species-Level Clinical Identification of Enterobacteriaceae through Broad-Range dnaJ PCR and Sequencing.

McLean K, Rosenthal CA, Sengupta D, Owens J, Cookson BT, Hoffman NG, Salipante SJ.

J Clin Microbiol. 2019 Oct 23;57(11). pii: e00986-19. doi: 10.1128/JCM.00986-19. Print 2019 Nov.


The Vaginal Microbiome of Transgender Men.

Winston McPherson G, Long T, Salipante SJ, Rongitsch JA, Hoffman NG, Stephens K, Penewit K, Greene DN.

Clin Chem. 2019 Jan;65(1):199-207. doi: 10.1373/clinchem.2018.293654.


Associations between improvement in genitourinary symptoms of menopause and changes in the vaginal ecosystem.

Mitchell CM, Srinivasan S, Plantinga A, Wu MC, Reed SD, Guthrie KA, LaCroix AZ, Fiedler T, Munch M, Liu C, Hoffman NG, Blair IA, Newton K, Freeman EW, Joffe H, Cohen L, Fredricks DN.

Menopause. 2018 May;25(5):500-507. doi: 10.1097/GME.0000000000001037.


Vaginal microbiota and genitourinary menopausal symptoms: a cross-sectional analysis.

Mitchell CM, Srinivasan S, Zhan X, Wu MC, Reed SD, Guthrie KA, LaCroix AZ, Fiedler T, Munch M, Liu C, Hoffman NG, Blair IA, Newton K, Freeman EW, Joffe H, Cohen L, Fredricks DN.

Menopause. 2017 Oct;24(10):1160-1166. doi: 10.1097/GME.0000000000000904.


Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities.

Golob JL, Margolis E, Hoffman NG, Fredricks DN.

BMC Bioinformatics. 2017 May 30;18(1):283. doi: 10.1186/s12859-017-1690-0.


Clinical Next Generation Sequencing Outperforms Standard Microbiological Culture for Characterizing Polymicrobial Samples.

Cummings LA, Kurosawa K, Hoogestraat DR, SenGupta DJ, Candra F, Doyle M, Thielges S, Land TA, Rosenthal CA, Hoffman NG, Salipante SJ, Cookson BT.

Clin Chem. 2016 Nov;62(11):1465-1473. Epub 2016 Sep 13.


More Easily Cultivated Than Identified: Classical Isolation With Molecular Identification of Vaginal Bacteria.

Srinivasan S, Munch MM, Sizova MV, Fiedler TL, Kohler CM, Hoffman NG, Liu C, Agnew KJ, Marrazzo JM, Epstein SS, Fredricks DN.

J Infect Dis. 2016 Aug 15;214 Suppl 1:S21-8. doi: 10.1093/infdis/jiw192.


Erratum for Salipante et al., Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling.

Salipante SJ, Kawashima T, Rosenthal C, Hoogestraat DR, Cummings LA, Sengupta DJ, Harkins TT, Cookson BT, Hoffman NG.

Appl Environ Microbiol. 2016 Jun 30;82(14):4453. doi: 10.1128/AEM.01390-16. Print 2016 Jul 15. No abstract available.


Applying Ancestry and Sex Computation as a Quality Control Tool in Targeted Next-Generation Sequencing.

Mathias PC, Turner EH, Scroggins SM, Salipante SJ, Hoffman NG, Pritchard CC, Shirts BH.

Am J Clin Pathol. 2016 Mar;145(3):308-15. doi: 10.1093/ajcp/aqv098. Epub 2016 Feb 20.


Optimizing vitamin D naming conventions in computerized order entry to support high-value care.

White AA, McKinney CM, Hoffman NG, Sutton PR.

J Am Med Inform Assoc. 2017 Jan;24(1):172-175. doi: 10.1093/jamia/ocw038. Epub 2016 Apr 23.


The Impact of the Proposed Changes for the DSM-5 on Diagnoses of First-time DUI/DWI Offenders.

Baley JW, Hoffman NG.

Subst Use Misuse. 2015;50(14):1747-52. doi: 10.3109/10826084.2015.1027923. Epub 2015 Dec 8.


Metabolic signatures of bacterial vaginosis.

Srinivasan S, Morgan MT, Fiedler TL, Djukovic D, Hoffman NG, Raftery D, Marrazzo JM, Fredricks DN.

mBio. 2015 Apr 14;6(2). pii: e00204-15. doi: 10.1128/mBio.00204-15.


Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling.

Salipante SJ, Kawashima T, Rosenthal C, Hoogestraat DR, Cummings LA, Sengupta DJ, Harkins TT, Cookson BT, Hoffman NG.

Appl Environ Microbiol. 2014 Dec;80(24):7583-91. doi: 10.1128/AEM.02206-14. Epub 2014 Sep 26. Erratum in: Appl Environ Microbiol. 2016 Jul 15;82(14):4453.


Coinfection of Fusobacterium nucleatum and Actinomyces israelii in mastoiditis diagnosed by next-generation DNA sequencing.

Salipante SJ, Hoogestraat DR, Abbott AN, SenGupta DJ, Cummings LA, Butler-Wu SM, Stephens K, Cookson BT, Hoffman NG.

J Clin Microbiol. 2014 May;52(5):1789-92. doi: 10.1128/JCM.03133-13. Epub 2014 Feb 26.


More than meets the eye: associations of vaginal bacteria with gram stain morphotypes using molecular phylogenetic analysis.

Srinivasan S, Morgan MT, Liu C, Matsen FA, Hoffman NG, Fiedler TL, Agnew KJ, Marrazzo JM, Fredricks DN.

PLoS One. 2013 Oct 24;8(10):e78633. doi: 10.1371/journal.pone.0078633. eCollection 2013.


Molecular diagnosis of Actinomadura madurae infection by 16S rRNA deep sequencing.

Salipante SJ, Sengupta DJ, Hoogestraat DR, Cummings LA, Bryant BH, Natividad C, Thielges S, Monsaas PW, Chau M, Barbee LA, Rosenthal C, Cookson BT, Hoffman NG.

J Clin Microbiol. 2013 Dec;51(12):4262-5. doi: 10.1128/JCM.02227-13. Epub 2013 Oct 9.


Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections.

Salipante SJ, Sengupta DJ, Rosenthal C, Costa G, Spangler J, Sims EH, Jacobs MA, Miller SI, Hoogestraat DR, Cookson BT, McCoy C, Matsen FA, Shendure J, Lee CC, Harkins TT, Hoffman NG.

PLoS One. 2013 May 29;8(5):e65226. doi: 10.1371/journal.pone.0065226. Print 2013.


Nestly--a framework for running software with nested parameter choices and aggregating results.

McCoy CO, Gallagher A, Hoffman NG, Matsen FA.

Bioinformatics. 2013 Feb 1;29(3):387-8. doi: 10.1093/bioinformatics/bts696. Epub 2012 Dec 6.


Admission oxygenation and ventilation parameters associated with discharge survival in severe pediatric traumatic brain injury.

Ramaiah VK, Sharma D, Ma L, Prathep S, Hoffman NG, Vavilala MS.

Childs Nerv Syst. 2013 Apr;29(4):629-34. doi: 10.1007/s00381-012-1984-5. Epub 2012 Dec 4.


Design and implementation of software for automated quality control and data analysis for a complex LC/MS/MS assay for urine opiates and metabolites.

Dickerson JA, Schmeling M, Hoofnagle AN, Hoffman NG.

Clin Chim Acta. 2013 Jan 16;415:290-4. doi: 10.1016/j.cca.2012.10.055. Epub 2012 Nov 15.


Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria.

Srinivasan S, Hoffman NG, Morgan MT, Matsen FA, Fiedler TL, Hall RW, Ross FJ, McCoy CO, Bumgarner R, Marrazzo JM, Fredricks DN.

PLoS One. 2012;7(6):e37818. doi: 10.1371/journal.pone.0037818. Epub 2012 Jun 18.


A format for phylogenetic placements.

Matsen FA, Hoffman NG, Gallagher A, Stamatakis A.

PLoS One. 2012;7(2):e31009. doi: 10.1371/journal.pone.0031009. Epub 2012 Feb 22.


Rapid high-resolution mapping of balanced chromosomal rearrangements on tiling CGH arrays.

Greisman HA, Hoffman NG, Yi HS.

J Mol Diagn. 2011 Nov;13(6):621-33. doi: 10.1016/j.jmoldx.2011.07.005. Epub 2011 Sep 9.


Simulations of delta check rule performance to detect specimen mislabeling using historical laboratory data.

Strathmann FG, Baird GS, Hoffman NG.

Clin Chim Acta. 2011 Oct 9;412(21-22):1973-7. doi: 10.1016/j.cca.2011.07.007. Epub 2011 Jul 19.


Hyperglycemia during craniotomy for adult traumatic brain injury.

Pecha T, Sharma D, Hoffman NG, Sookplung P, Curry P, Vavilala MS.

Anesth Analg. 2011 Aug;113(2):336-42. doi: 10.1213/ANE.0b013e31821d3dde. Epub 2011 May 19.


Marked variability of BK virus load measurement using quantitative real-time PCR among commonly used assays.

Hoffman NG, Cook L, Atienza EE, Limaye AP, Jerome KR.

J Clin Microbiol. 2008 Aug;46(8):2671-80. doi: 10.1128/JCM.00258-08. Epub 2008 Jun 18.


Compensatory evolution in RNA secondary structures increases substitution rate variation among sites.

Knies JL, Dang KK, Vision TJ, Hoffman NG, Swanstrom R, Burch CL.

Mol Biol Evol. 2008 Aug;25(8):1778-87. doi: 10.1093/molbev/msn130. Epub 2008 Jun 4.


Case 8-2007: a man with chest pain followed by cardiac arrest.

Hoffman NG, Cookson BT.

N Engl J Med. 2007 Jun 21;356(25):2652-3; author reply 2652-3. No abstract available.


HIV-1 populations in blood and breast milk are similar.

Henderson GJ, Hoffman NG, Ping LH, Fiscus SA, Hoffman IF, Kitrinos KM, Banda T, Martinson FE, Kazembe PN, Chilongozi DA, Cohen MS, Swanstrom R.

Virology. 2004 Dec 5;330(1):295-303.


Multiple V1/V2 env variants are frequently present during primary infection with human immunodeficiency virus type 1.

Ritola K, Pilcher CD, Fiscus SA, Hoffman NG, Nelson JA, Kitrinos KM, Hicks CB, Eron JJ Jr, Swanstrom R.

J Virol. 2004 Oct;78(20):11208-18.


Clinical and immunological impact of HIV envelope V3 sequence variation after starting initial triple antiretroviral therapy.

Brumme ZL, Dong WW, Yip B, Wynhoven B, Hoffman NG, Swanstrom R, Jensen MA, Mullins JI, Hogg RS, Montaner JS, Harrigan PR.

AIDS. 2004 Mar 5;18(4):F1-9.


Covariation of amino acid positions in HIV-1 protease.

Hoffman NG, Schiffer CA, Swanstrom R.

Virology. 2003 Sep 30;314(2):536-48. Erratum in: Virology. 2005 Jan 5;331(1):206-7.


Variability in the human immunodeficiency virus type 1 gp120 Env protein linked to phenotype-associated changes in the V3 loop.

Hoffman NG, Seillier-Moiseiwitsch F, Ahn J, Walker JM, Swanstrom R.

J Virol. 2002 Apr;76(8):3852-64.


Using HIV-1 sequence variability to explore virus biology.

McGrath KM, Hoffman NG, Resch W, Nelson JA, Swanstrom R.

Virus Res. 2001 Aug;76(2):137-60. Review. Erratum in: Virus Res 2001 Nov 28;80(1-2):125.


Molecular recognition properties of the C-terminal Sh3 domain of the Cbl associated protein, Cap.

Kurakin A, Hoffman NG, Kay BK.

J Pept Res. 1998 Nov;52(5):331-7.


Intersectin, a novel adaptor protein with two Eps15 homology and five Src homology 3 domains.

Yamabhai M, Hoffman NG, Hardison NL, McPherson PS, Castagnoli L, Cesareni G, Kay BK.

J Biol Chem. 1998 Nov 20;273(47):31401-7.


A novel, multifuntional c-Cbl binding protein in insulin receptor signaling in 3T3-L1 adipocytes.

Ribon V, Printen JA, Hoffman NG, Kay BK, Saltiel AR.

Mol Cell Biol. 1998 Feb;18(2):872-9.


Binding properties of SH3 peptide ligands identified from phage-displayed random peptide libraries.

Hoffman NG, Sparks AB, Carter JM, Kay BK.

Mol Divers. 1996 Oct;2(1-2):5-12.


Cloning of ligand targets: systematic isolation of SH3 domain-containing proteins.

Sparks AB, Hoffman NG, McConnell SJ, Fowlkes DM, Kay BK.

Nat Biotechnol. 1996 Jun;14(6):741-4.


Distinct ligand preferences of Src homology 3 domains from Src, Yes, Abl, Cortactin, p53bp2, PLCgamma, Crk, and Grb2.

Sparks AB, Rider JE, Hoffman NG, Fowlkes DM, Quillam LA, Kay BK.

Proc Natl Acad Sci U S A. 1996 Feb 20;93(4):1540-4.


Elderly alcohol misuse.

Gurnack AM, Hoffman NG.

Int J Addict. 1992;27(7):869-78.


Patient variations in alcohol treatment utilization.

Hoffman NG, Harrison PA.

Bus Health. 1987 Mar;4(5):16-8. No abstract available.


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