Academic and Clinical Activities

Noah Hoffman, MD, PhD is an Associate Professor at the University of Washington and Head of the Informatics Division in the Department of Laboratory Medicine and Pathology. He also serves as the Specialty CMIO for Lab and Pathology services for UW Medicine. Dr. Hoffman has interests in software development to meet the operational and analytical needs of the clinical laboratory; laboratory data analytics; bioinformatics; and process improvement. As the Co-director of the NGS Analytics Laboratory, Dr. Hoffman helps to supervise the development of analytical pipelines and scientific computing infrastructure supporting clinical assays with data intensive or computational components. His research interests include the development and application of bioinformatic tools to perform nucleic acid sequence-based identification of microbiota in both basic research and clinical settings, including studies of the human microbiome.

Dr. Hoffman received his undergraduate, MD, and PhD degrees from the University of North Carolina at Chapel Hill, where he studied HIV evolution. He performed his residency training in Clinical Pathology at the University of Washington.

Publications

  1. Whitney BM, Srinivasan S, Tapia K, Muriuki EM, Chohan BH, Wallis JM, Liu C, Guthrie BL, McClelland RS, Hoffman NG, Fredricks DN, and Roxby AC. Influence of intramuscular depot-medroxyprogesterone acetate initiation on vaginal microbiota in the postpartum period. Clin Infect Dis. 2020 Dec 23; PMID 33354707
  2. Mitchell CM, Srinivasan S, Ma N, Reed SD, Wu MC, Hoffman NG, Valint DJ, Proll S, Fiedler TL, Agnew KJ, Guthrie KA, and Fredricks DN. Bacterial communities associated with abnormal Nugent score are different in pre- versus postmenopausal women. J Infect Dis. 2020 Oct 27; PMID 33107562
  3. Rassoulian Barrett S, Hoffman NG, Rosenthal C, Bryan A, Marshall DA, Lieberman J, Greninger AL, Peddu V, Cookson BT, and Salipante SJ. Sensitive Identification of Bacterial DNA in Clinical Specimens by Broad-Range 16S rRNA Gene Enrichment. J Clin Microbiol. 2020 Nov 18;58(12) PMID 33028602
  4. Srinivasan S, Chambers LC, Tapia KA, Hoffman NG, Munch MM, Morgan JL, Domogala D, Lowens MS, Proll S, Huang ML, Soge OO, Jerome KR, Golden MR, Hughes JP, Fredricks DN, and Manhart LE. Urethral microbiota in men: Association of Haemophilus influenzae and Mycoplasma penetrans with nongonococcal urethritis. Clin Infect Dis. 2020 Aug 5; PMID 32750107
  5. Mani NS, Budak JZ, Lan KF, Bryson-Cahn C, Zelikoff A, Barker GEC, Grant CW, Hart K, Barbee CJ, Sandoval MD, Dostal CL, Corcorran M, Ungerleider HM, Gates JO, Olin SV, Bryan A, Hoffman NG, Marquis SR, Harvey ML, Nasenbeny K, Mertens K, Chew LD, Greninger AL, Jerome KR, Pottinger PS, Dellit TH, Liu C, Pergam SA, Neme S, Lynch JB, Kim HN, and Cohen SA. Prevalence of Coronavirus Disease 2019 Infection and Outcomes Among Symptomatic Healthcare Workers in Seattle, Washington. Clin Infect Dis. 2020 Dec 17;71(10):2702-2707 PMID 32548613
  6. Krumm N and Hoffman N. Practical estimation of cloud storage costs for clinical genomic data. Pract Lab Med. 2020 Aug;21:e00168 PMID 32529017
  7. Tettamanti Boshier FA, Srinivasan S, Lopez A, Hoffman NG, Proll S, Fredricks DN, and Schiffer JT. Complementing 16S rRNA Gene Amplicon Sequencing with Total Bacterial Load To Infer Absolute Species Concentrations in the Vaginal Microbiome. mSystems. 2020 Apr 7;5(2) PMID 32265316
  8. Cummings LA, Hoogestraat DR, Rassoulian-Barrett SL, Rosenthal CA, Salipante SJ, Cookson BT, and Hoffman NG. Comprehensive evaluation of complex polymicrobial specimens using next generation sequencing and standard microbiological culture. Sci Rep. 2020 Mar 25;10(1):5446 PMID 32214207
  9. McLean K, Rosenthal CA, Sengupta D, Owens J, Cookson BT, Hoffman NG, and Salipante SJ. Improved Species-Level Clinical Identification of Enterobacteriaceae through Broad-Range dnaJ PCR and Sequencing. J Clin Microbiol. 2019 Nov;57(11) PMID 31434720
  10. Winston McPherson G, Long T, Salipante SJ, Rongitsch JA, Hoffman NG, Stephens K, Penewit K, and Greene DN. The Vaginal Microbiome of Transgender Men. Clin Chem. 2019 Jan;65(1):199-207 PMID 30602481
  11. 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, and Fredricks DN. Associations between improvement in genitourinary symptoms of menopause and changes in the vaginal ecosystem. Menopause. 2018 May;25(5):500-507 PMID 29206774
  12. 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, and Fredricks DN. Vaginal microbiota and genitourinary menopausal symptoms: a cross-sectional analysis. Menopause. 2017 Oct;24(10):1160-1166 PMID 28640154
  13. Golob JL, Margolis E, Hoffman NG, and Fredricks DN. Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities. BMC Bioinformatics. 2017 May 30;18(1):283 PMID 28558684
  14. Cummings LA, Kurosawa K, Hoogestraat DR, SenGupta DJ, Candra F, Doyle M, Thielges S, Land TA, Rosenthal CA, Hoffman NG, Salipante SJ, and Cookson BT. Clinical Next Generation Sequencing Outperforms Standard Microbiological Culture for Characterizing Polymicrobial Samples. Clin Chem. 2016 Nov;62(11):1465-1473 PMID 27624135
  15. Srinivasan S, Munch MM, Sizova MV, Fiedler TL, Kohler CM, Hoffman NG, Liu C, Agnew KJ, Marrazzo JM, Epstein SS, and Fredricks DN. More Easily Cultivated Than Identified: Classical Isolation With Molecular Identification of Vaginal Bacteria. J Infect Dis. 2016 Aug 15;214 Suppl 1:S21-8 PMID 27449870
  16. Salipante SJ, Kawashima T, Rosenthal C, Hoogestraat DR, Cummings LA, Sengupta DJ, Harkins TT, Cookson BT, and Hoffman NG. Erratum for Salipante et al., Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling. Appl Environ Microbiol. 2016 Jul 15;82(14):4453 PMID 27364849
  17. Mathias PC, Turner EH, Scroggins SM, Salipante SJ, Hoffman NG, Pritchard CC, and Shirts BH. Applying Ancestry and Sex Computation as a Quality Control Tool in Targeted Next-Generation Sequencing. Am J Clin Pathol. 2016 Mar;145(3):308-15 PMID 27124912
  18. White AA, McKinney CM, Hoffman NG, and Sutton PR. Optimizing vitamin D naming conventions in computerized order entry to support high-value care. J Am Med Inform Assoc. 2017 Jan;24(1):172-175 PMID 27107453
  19. Srinivasan S, Morgan MT, Fiedler TL, Djukovic D, Hoffman NG, Raftery D, Marrazzo JM, and Fredricks DN. Metabolic signatures of bacterial vaginosis. mBio. 2015 Apr 14;6(2) PMID 25873373
  20. Salipante SJ, Kawashima T, Rosenthal C, Hoogestraat DR, Cummings LA, Sengupta DJ, Harkins TT, Cookson BT, and Hoffman NG. Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling. Appl Environ Microbiol. 2014 Dec;80(24):7583-91 PMID 25261520
  21. Salipante SJ, Hoogestraat DR, Abbott AN, SenGupta DJ, Cummings LA, Butler-Wu SM, Stephens K, Cookson BT, and Hoffman NG. Coinfection of Fusobacterium nucleatum and Actinomyces israelii in mastoiditis diagnosed by next-generation DNA sequencing. J Clin Microbiol. 2014 May;52(5):1789-92 PMID 24574281
  22. Srinivasan S, Morgan MT, Liu C, Matsen FA, Hoffman NG, Fiedler TL, Agnew KJ, Marrazzo JM, and Fredricks DN. More than meets the eye: associations of vaginal bacteria with gram stain morphotypes using molecular phylogenetic analysis. PLoS One. 2013;8(10):e78633 PMID 24302980
  23. Salipante SJ, Sengupta DJ, Hoogestraat DR, Cummings LA, Bryant BH, Natividad C, Thielges S, Monsaas PW, Chau M, Barbee LA, Rosenthal C, Cookson BT, and Hoffman NG. Molecular diagnosis of Actinomadura madurae infection by 16S rRNA deep sequencing. J Clin Microbiol. 2013 Dec;51(12):4262-5 PMID 24108607
  24. 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, and Hoffman NG. Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections. PLoS One. 2013;8(5):e65226 PMID 23734239
  25. McCoy CO, Gallagher A, Hoffman NG, and Matsen FA. Nestly--a framework for running software with nested parameter choices and aggregating results. Bioinformatics. 2013 Feb 1;29(3):387-8 PMID 23220574
  26. Ramaiah VK, Sharma D, Ma L, Prathep S, Hoffman NG, and Vavilala MS. Admission oxygenation and ventilation parameters associated with discharge survival in severe pediatric traumatic brain injury. Childs Nerv Syst. 2013 Apr;29(4):629-34 PMID 23207977
  27. Dickerson JA, Schmeling M, Hoofnagle AN, and Hoffman NG. Design and implementation of software for automated quality control and data analysis for a complex LC/MS/MS assay for urine opiates and metabolites. Clin Chim Acta. 2013 Jan 16;415:290-4 PMID 23159299
  28. Srinivasan S, Hoffman NG, Morgan MT, Matsen FA, Fiedler TL, Hall RW, Ross FJ, McCoy CO, Bumgarner R, Marrazzo JM, and Fredricks DN. Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria. PLoS One. 2012;7(6):e37818 PMID 22719852
  29. Matsen FA, Hoffman NG, Gallagher A, and Stamatakis A. A format for phylogenetic placements. PLoS One. 2012;7(2):e31009 PMID 22383988
  30. Greisman HA, Hoffman NG, and Yi HS. Rapid high-resolution mapping of balanced chromosomal rearrangements on tiling CGH arrays. J Mol Diagn. 2011 Nov;13(6):621-33 PMID 21907824
  31. Strathmann FG, Baird GS, and Hoffman NG. Simulations of delta check rule performance to detect specimen mislabeling using historical laboratory data. Clin Chim Acta. 2011 Oct 9;412(21-22):1973-7 PMID 21782806
  32. Pecha T, Sharma D, Hoffman NG, Sookplung P, Curry P, and Vavilala MS. Hyperglycemia during craniotomy for adult traumatic brain injury. Anesth Analg. 2011 Aug;113(2):336-42 PMID 21596888
  33. Hoffman NG, Cook L, Atienza EE, Limaye AP, and Jerome KR. Marked variability of BK virus load measurement using quantitative real-time PCR among commonly used assays. J Clin Microbiol. 2008 Aug;46(8):2671-80 PMID 18562587
  34. Knies JL, Dang KK, Vision TJ, Hoffman NG, Swanstrom R, and Burch CL. Compensatory evolution in RNA secondary structures increases substitution rate variation among sites. Mol Biol Evol. 2008 Aug;25(8):1778-87 PMID 18535013
  35. Patel MB, Hoffman NG, and Swanstrom R. Subtype-specific conformational differences within the V3 region of subtype B and subtype C human immunodeficiency virus type 1 Env proteins. J Virol. 2008 Jan;82(2):903-16 PMID 18003735
  36. Hoffman NG and Cookson BT. Case 8-2007: a man with chest pain followed by cardiac arrest. N Engl J Med. 2007 Jun 21;356(25):2652-3; author reply 2652-3 PMID 17582082
  37. Henderson GJ, Hoffman NG, Ping LH, Fiscus SA, Hoffman IF, Kitrinos KM, Banda T, Martinson FE, Kazembe PN, Chilongozi DA, Cohen MS, and Swanstrom R. HIV-1 populations in blood and breast milk are similar. Virology. 2004 Dec 5;330(1):295-303 PMID 15527854
  38. Ritola K, Pilcher CD, Fiscus SA, Hoffman NG, Nelson JA, Kitrinos KM, Hicks CB, Eron JJ Jr, and Swanstrom R. Multiple V1/V2 env variants are frequently present during primary infection with human immunodeficiency virus type 1. J Virol. 2004 Oct;78(20):11208-18 PMID 15452240
  39. Brumme ZL, Dong WW, Yip B, Wynhoven B, Hoffman NG, Swanstrom R, Jensen MA, Mullins JI, Hogg RS, Montaner JS, and Harrigan PR. Clinical and immunological impact of HIV envelope V3 sequence variation after starting initial triple antiretroviral therapy. AIDS. 2004 Mar 5;18(4):F1-9 PMID 15090786
  40. Hoffman NG, Schiffer CA, and Swanstrom R. Covariation of amino acid positions in HIV-1 protease. Virology. 2003 Sep 30;314(2):536-48 PMID 14554082
  41. Kitrinos KM, Hoffman NG, Nelson JA, and Swanstrom R. Turnover of env variable region 1 and 2 genotypes in subjects with late-stage human immunodeficiency virus type 1 infection. J Virol. 2003 Jun;77(12):6811-22 PMID 12768001
  42. Hoffman NG, Seillier-Moiseiwitsch F, Ahn J, Walker JM, and Swanstrom R. Variability in the human immunodeficiency virus type 1 gp120 Env protein linked to phenotype-associated changes in the V3 loop. J Virol. 2002 Apr;76(8):3852-64 PMID 11907225
  43. Resch W, Hoffman N, and Swanstrom R. Improved success of phenotype prediction of the human immunodeficiency virus type 1 from envelope variable loop 3 sequence using neural networks. Virology. 2001 Sep 15;288(1):51-62 PMID 11543657
  44. McGrath KM, Hoffman NG, Resch W, Nelson JA, and Swanstrom R. Using HIV-1 sequence variability to explore virus biology. Virus Res. 2001 Aug;76(2):137-60 PMID 11410314
  45. Kurakin A, Hoffman NG, and Kay BK. Molecular recognition properties of the C-terminal Sh3 domain of the Cbl associated protein, Cap. J Pept Res. 1998 Nov;52(5):331-7 PMID 9894838
  46. Yamabhai M, Hoffman NG, Hardison NL, McPherson PS, Castagnoli L, Cesareni G, and Kay BK. Intersectin, a novel adaptor protein with two Eps15 homology and five Src homology 3 domains. J Biol Chem. 1998 Nov 20;273(47):31401-7 PMID 9813051
  47. Ribon V, Printen JA, Hoffman NG, Kay BK, and Saltiel AR. A novel, multifuntional c-Cbl binding protein in insulin receptor signaling in 3T3-L1 adipocytes. Mol Cell Biol. 1998 Feb;18(2):872-9 PMID 9447983
  48. Hoffman NG, Sparks AB, Carter JM, and Kay BK. Binding properties of SH3 peptide ligands identified from phage-displayed random peptide libraries. Mol Divers. 1996 Oct;2(1-2):5-12 PMID 9238627
  49. Sparks AB, Hoffman NG, McConnell SJ, Fowlkes DM, and Kay BK. Cloning of ligand targets: systematic isolation of SH3 domain-containing proteins. Nat Biotechnol. 1996 Jun;14(6):741-4 PMID 9630982
  50. Sparks AB, Rider JE, Hoffman NG, Fowlkes DM, Quillam LA, and Kay BK. Distinct ligand preferences of Src homology 3 domains from Src, Yes, Abl, Cortactin, p53bp2, PLCgamma, Crk, and Grb2. Proc Natl Acad Sci U S A. 1996 Feb 20;93(4):1540-4 PMID 8643668

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