Nicholas C. Spies

Nicholas C. Spies, MD

Languages spoken: English

Academic Information

Departments Primary - Pathology

Board Certification

  • American Board of Pathology (Clinical Path)

Education History

Residency Washington University School of Medicine in St. Louis
 Chief Resident
Washington University School of Medicine in St. Louis
 Resident
Residency Washington University School of Medicine in St. Louis
 Resident
Washington University School of Medicine in St. Louis
 MD
Undergraduate Washington University in St. Louis
 BA

Selected Publications

Journal Article

  1. Spies NC, Farnsworth CW, Wheeler S, McCudden C (). Validating, Implementing, and Monitoring Machine Learning Solutions Safely and Effectively in the Clinical Laboratory. (Epub ahead of print) Clin Chem.
  2. Morse P, Roberts KF, Spies NC, Padmanabhan V (2024). Process improvement in thyroid fine needle aspiration: Standardizing number of smears for enhanced adequacy and diagnosis. Diagn Cytopathol, 52(9), 519-523. (Read full article)
  3. Khonde P, Choudhury S, Spies NC, Naz N, Stoll J, Fleckenstein J, He M, Ballentine S, Kulkarni S (2024). Worse fibro-inflammatory activity on diagnostic liver biopsy adversely impacts biochemical remission in autoimmune hepatitis. Clin Res Hepatol Gastroenterol, 48(8), 102442. (Read full article)
  4. Spies NC, Hubler Z, Azimi V, Zhang R, Jackups R Jr, Gronowski AM, Farnsworth CW, Zaydman MA (2023). Automating the Detection of IV Fluid Contamination Using Unsupervised Machine Learning. Clin Chem, 70(2), 444-452. (Read full article)
  5. Spies NC, Farnsworth CW (2024). Impact and frequency of IV fluid contamination on basic metabolic panel results using quality metrics. Journal of Laboratory Medicine, 48(1), 29-36. (Read full article)
  6. Spies N, Jackups R, Zaydman M (2023). Anticoagulation management in patients tested for heparin-induced thrombocytopenia in the cardiothoracic intensive care unit diverges from expert guidelines. Am J Clin Pathol, 160(Supplement_1), S139.
  7. Spies NC, Hubler Z, Roper SM, Omosule CL, Senter-Zapata M, Roemmich BL, Brown HM, Gimple R, Farnsworth CW (2023). GPT-4 Underperforms Experts in Detecting IV Fluid Contamination. J Appl Lab Med, 8(6), 1092-1100. (Read full article)
  8. Yang HS, Pan W, Wang Y, Zaydman MA, Spies NC, Zhao Z, Guise TA, Meng QH, Wang F (2023). Generalizability of a Machine Learning Model for Improving Utilization of Parathyroid Hormone-Related Peptide Testing across Multiple Clinical Centers. Clin Chem, 69(11), 1260-1269. (Read full article)
  9. Hubler ZML, Farnsworth CW, Spies NC (2023). Asymptomatic Hyponatremia and Hyperkalemia in a Patient with Leukemic Leukocytosis. Clin Chem, 69(11), 1322-1323. (Read full article)
  10. Spies NC, Farnsworth CW, Jackups R, Zaydman MA (2023). Machine learning pipelines developed for the prediction of cancelation of inappropriate parathyroid hormone-related peptide orders demonstrate poor performance in predicting provider behavior. J Lab Precis Med, 8. (Read full article)
  11. Hart SN, Hoffman NG, Gershkovich P, Christenson C, McClintock DS, Miller LJ, Jackups R, Azimi V, Spies N, Brodsky V (2023). Organizational preparedness for the use of large language models in pathology informatics. J Pathol Inform, 14, 100338. (Read full article)
  12. Brown HM, Spies NC, Zaydman MA, Farnsworth CW (2023). A-015 Hemoglobin A1c Control is An Independent Predictor of Circulating Troponin Concentrations Using Machine Learning. Am J Clin Pathol, 160(Supplement_1), S141-2.
  13. Kotnik EN, Mullen MM, Spies NC, Li T, Inkman M, Zhang J, Martins-Rodrigues F, Hagemann IS, McCourt CK, Thaker PH, Hagemann AR, Powell MA, Mutch DG, Khabele D, Longmore GD, Mardis ER, Maher CA, Miller CA, Fuh KC (2023). Genetic characterization of primary and metastatic high-grade serous ovarian cancer tumors reveals distinct features associated with survival. Commun Biol, 6(1), 688. (Read full article)
  14. Barnell EK, Skidmore ZL, Newcomer KF, Chavez M, Campbell KM, Cotto KC, Spies NC, Ruzinova MB, Wang T, Abro B, Kreisel F, Parikh BA, Duncavage EJ, Frater JL, Lee YS, Hassan A, King JA, Kohnen DR, Fiala MA, Welch JS, Uy GL, Vij K, Vij R, Griffith M, Griffith OL, Wartman LD (2022). Distinct clonal identities of B-ALLs arising after lenolidomide therapy for multiple myeloma. Blood Adv, 7(2), 236-245. (Read full article)
  15. Krysiak K, Danos AM, Saliba J, McMichael JF, Coffman AC, Kiwala S, Barnell EK, Sheta L, Grisdale CJ, Kujan L, Pema S, Lever J, Ridd S, Spies NC, Andric V, Chiorean A, Rieke DT, Clark KA, Reisle C, Venigalla AC, Evans M, Jani P, Takahashi H, Suda A, Horak P, Ritter DI, Zhou X, Ainscough BJ, Delong S, Kesserwan C, Lamping M, Shen H, Marr AR, Hoang MH, Singhal K, Khanfar M, Li BV, Lin WH, Terraf P, Corson LB, Salama Y, Campbell KM, Farncombe KM, Ji J, Zhao X, Xu X, Kanagal-Shamanna R, King I, Cotto KC, Skidmore ZL, Walker JR, Zhang J, Milosavljevic A, Patel RY, Giles RH, Kim RH, Schriml LM, Mardis ER, Jones SJM, Raca G, Rao S, Madhavan S, Wagner AH, Griffith M, Griffith OL (2022). CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase. Nucleic Acids Res, 51(D1), D1230-D1241. (Read full article)
  16. Spies NC, Farnsworth CW, Jackups R (2022). Data-Driven Anomaly Detection in Laboratory Medicine: Past, Present, and Future. J Appl Lab Med, 8(1), 162-179. (Read full article)
  17. Krysiak K, Danos AM, Kiwala S, McMichael JF, Coffman AC, Barnell EK, Sheta L, Saliba J, Grisdale CJ, Kujan L, Pema S, Lever J, Spies NC, Chiorean A, Rieke DT, Clark KA, Jani P, Takahashi H, Horak P, Ritter DI, Zhou X, Ainscough BJ, Delong S, Lamping M, Marr AR, Li BV, Lin WH, Terraf P, Salama Y, Campbell KM, Farncombe KM, Ji J, Zhao X, Xu X, Kanagal-Shamanna R, Cotto KC, Skidmore ZL, Walker JR, Zhang J, Milosavljevic A, Patel RY, Giles RH, Kim RH, Schriml LM, Mardis ER, Jones SJM, Raca G, Rao S, Madhavan S, Wagner AH, Griffith OL, Griffith M (2022). A community approach to the cancer-variant-interpretation bottleneck. Nat Cancer, 3(5), 522-525. (Read full article)
  18. Gunderson SJ, Puga Molina LC, Spies N, Balestrini PA, Buffone MG, Jungheim ES, Riley J, Santi CM (2021). Machine-learning algorithm incorporating capacitated sperm intracellular pH predicts conventional in vitro fertilization success in normospermic patients. Fertil Steril, 115(4), 930-939. (Read full article)
  19. Uppaluri R, Campbell KM, Egloff AM, Zolkind P, Skidmore ZL, Nussenbaum B, Paniello RC, Rich JT, Jackson R, Pipkorn P, Michel LS, Ley J, Oppelt P, Dunn GP, Barnell EK, Spies NC, Lin T, Li T, Mulder DT, Hanna Y, Cirlan I, Pugh TJ, Mudianto T, Riley R, Zhou L, Jo VY, Stachler MD, Hanna GJ, Kass J, Haddad R, Schoenfeld JD, Gjini E, Lako A, Thorstad W, Gay HA, Daly M, Rodig SJ, Hagemann IS, Kallogjeri D, Piccirillo JF, Chernock RD, Griffith M, Griffith OL, Adkins DR (2021). Correction: Neoadjuvant and Adjuvant Pembrolizumab in Resectable Locally Advanced, Human Papillomavirus-unrelated Head and Neck Cancer: A Multicenter, Phase II Trial. Clin Cancer Res, 27(1), 357. (Read full article)
  20. Uppaluri R, Campbell KM, Egloff AM, Zolkind P, Skidmore ZL, Nussenbaum B, Paniello RC, Rich JT, Jackson R, Pipkorn P, Michel LS, Ley J, Oppelt P, Dunn GP, Barnell EK, Spies NC, Lin T, Li T, Mulder DT, Hanna Y, Cirlan I, Pugh TJ, Mudianto T, Riley R, Zhou L, Jo VY, Stachler MD, Hanna GJ, Kass J, Haddad R, Schoenfeld JD, Gjini E, Lako A, Thorstad W, Gay HA, Daly M, Rodig SJ, Hagemann IS, Kallogjeri D, Piccirillo JF, Chernock RD, Griffith M, Griffith OL, Adkins DR (2020). Neoadjuvant and Adjuvant Pembrolizumab in Resectable Locally Advanced, Human Papillomavirus-Unrelated Head and Neck Cancer: A Multicenter, Phase II Trial. Clin Cancer Res, 26(19), 5140-5152. (Read full article)
  21. Bedrick BS, Kazarian GS, Greenwade MM, Spies N, Chen T, Maluf H, Dicke J, Thaker PH (2020). Adenomyosis presenting as a molar pregnancy: A case report. Gynecol Oncol Rep, 32. (Read full article)
  22. Danos AM, Krysiak K, Barnell EK, Coffman AC, McMichael JF, Kiwala S, Spies NC, Sheta LM, Pema SP, Kujan L, Clark KA, Wollam AZ, Rao S, Ritter DI, Sonkin D, Raca G, Lin WH, Grisdale CJ, Kim RH, Wagner AH, Madhavan S, Griffith M, Griffith OL (2019). Standard operating procedure for curation and clinical interpretation of variants in cancer. Genome Med, 11(1), 76. (Read full article)
  23. Barnell EK, Waalkes A, Mosior MC, Penewit K, Cotto KC, Danos AM, Sheta LM, Campbell KM, Krysiak K, Rieke D, Spies NC, Skidmore ZL, Pritchard CC, Fehniger TA, Uppaluri R, Govindan R, Griffith M, Salipante SJ, Griffith OL (2019). Open-Sourced CIViC Annotation Pipeline to Identify and Annotate Clinically Relevant Variants Using Single-Molecule Molecular Inversion Probes. JCO Clin Cancer Inform, 3, 1-12. (Read full article)
  24. Danos AM, Krysiak K, Barnell EK, Coffman AC, McMichael JF, Kiwala S, Spies NC, Sheta LM, Pema SP, Kujan L, Clark KA, Wollam AZ, Rao S, Ritter DI, Sonkin D, Raca G, Lin WH, Grisdale CJ, Kim RH, Wagner AH, Madhavan S, Griffith M, Griffith OL (2019). The CIViC knowledge model and standard operating procedures for curation and clinical interpretation of variants in cancer. bioRxiv, 700179.
  25. Barnell EK, Ronning P, Campbell KM, Krysiak K, Ainscough BJ, Sheta LM, Pema SP, Schmidt AD, Richters M, Cotto KC, Danos AM, Ramirez C, Skidmore ZL, Spies NC, Hundal J, Sediqzad MS, Kunisaki J, Gomez F, Trani L, Matlock M, Wagner AH, Swamidass SJ, Griffith M, Griffith OL (2018). Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples. Genet Med, 21(4), 972-981. (Read full article)
  26. Griffith OL, Spies NC, Anurag M, Griffith M, Luo J, Tu D, Yeo B, Kunisaki J, Miller CA, Krysiak K, Hundal J, Ainscough BJ, Skidmore ZL, Campbell K, Kumar R, Fronick C, Cook L, Snider JE, Davies S, Kavuri SM, Chang EC, Magrini V, Larson DE, Fulton RS, Liu S, Leung S, Voduc D, Bose R, Dowsett M, Wilson RK, Nielsen TO, Mardis ER, Ellis MJ (2018). Author Correction: The prognostic effects of somatic mutations in ER-positive breast cancer. Nat Commun, 9(1), 4850. (Read full article)
  27. Wagner AH, Devarakonda S, Skidmore ZL, Krysiak K, Ramu A, Trani L, Kunisaki J, Masood A, Waqar SN, Spies NC, Morgensztern D, Waligorski J, Ponce J, Fulton RS, Maggi LB Jr, Weber JD, Watson MA, OConor CJ, Ritter JH, Olsen RR, Cheng H, Mukhopadhyay A, Can I, Cessna MH, Oliver TG, Mardis ER, Wilson RK, Griffith M, Griffith OL, Govindan R (2018). Recurrent WNT pathway alterations are frequent in relapsed small cell lung cancer. Nat Commun, 9(1), 3787. (Read full article)
  28. Griffith OL, Spies NC, Anurag M, Griffith M, Luo J, Tu D, Yeo B, Kunisaki J, Miller CA, Krysiak K, Hundal J, Ainscough BJ, Skidmore ZL, Campbell K, Kumar R, Fronick C, Cook L, Snider JE, Davies S, Kavuri SM, Chang EC, Magrini V, Larson DE, Fulton RS, Liu S, Leung S, Voduc D, Bose R, Dowsett M, Wilson RK, Nielsen TO, Mardis ER, Ellis MJ (2018). The prognostic effects of somatic mutations in ER-positive breast cancer. Nat Commun, 9(1), 3476. (Read full article)
  29. Cotto KC, Wagner AH, Feng YY, Kiwala S, Coffman AC, Spies G, Wollam A, Spies NC, Griffith OL, Griffith M (2017). DGIdb 3.0: a redesign and expansion of the drug-gene interaction database. Nucleic Acids Res, 46(D1), D1068-D1073. (Read full article)
  30. Leung W, Shaffer CD, Chen EJ, Quisenberry TJ, Ko K, Braverman JM, Giarla TC, Mortimer NT, Reed LK, Smith ST, Robic S, McCartha SR, Perry DR, Prescod LM, Sheppard ZA, Saville KJ, McClish A, Morlock EA, Sochor VR, Stanton B, Veysey-White IC, Revie D, Jimenez LA, Palomino JJ, Patao MD, Patao SM, Himelblau ET, Campbell JD, Hertz AL, McEvilly MF, Wagner AR, Youngblom J, Bedi B, Bettincourt J, Duso E, Her M, Hilton W, House S, Karimi M, Kumimoto K, Lee R, Lopez D, Odisho G, Prasad R, Robbins HL, Sandhu T, Selfridge T, Tsukashima K, Yosif H, Kokan NP, Britt L, Zoellner A, Spana EP, Chlebina BT, Chong I, Friedman H, Mammo DA, Ng CL, Nikam VS, Schwartz NU, Xu TQ, Burg MG, Batten SM, Corbeill LM, Enoch E, Ensign JJ, Franks ME, Haiker B, Ingles JA, Kirkland LD, Lorenz-Guertin JM, Matthews J, Mittig CM, Monsma N, Olson KJ, Perez-Aragon G, Ramic A, Ramirez JR, Scheiber C, Schneider PA, Schultz DE, Simon M, Spencer E, Wernette AC, Wykle ME, Zavala-Arellano E, McDonald MJ, Ostby K, Wendland P, DiAngelo JR, Ceasrine AM, Cox AH, Docherty JEB, Gingras RM, Grieb SM, Pavia MJ, Personius CL, Polak GL, Beach DL, Cerritos HL, Horansky EA, Sharif KA, Moran R, Parrish S, Bickford K, Bland J, Broussard J, Campbell K, Deibel KE, Forka R, Lemke MC, Nelson MB, OKeeffe C, Ramey SM, Schmidt L, Villegas P, Jones CJ, Christ SL, Mamari S, Rinaldi AS, Stity G, Hark AT, Scheuerman M, Silver Key SC, McRae BD, Haberman AS, Asinof S, Carrington H, Drumm K, Embry T, McGuire R, Miller-Foreman D, Rosen S, Safa N, Schultz D, Segal M, Shevin Y, Svoronos P, Vuong T, Skuse G, Paetkau DW, Bridgman RK, Brown CM, Carroll AR, Gifford FM, Gillespie JB, Herman SE, Holtcamp KL, Host MA, Hussey G, Kramer DM, Lawrence JQ, Martin MM, Niemiec EN, OReilly AP, Pahl OA, Quintana G, Rettie EAS, Richardson TL, Rodriguez AE, Rodriguez MO, Schiraldi L, Smith JJ, Sugrue KF, Suriano LJ, Takach KE, Vasquez AM, Velez X, Villafuerte EJ, Vives LT, Zellmer VR, Hauke J, Hauser CR, Barker K, Cannon L, Parsamian P, Parsons S, Wichman Z, Bazinet CW, Johnson DE, Bangura A, Black JA, Chevee V, Einsteen SA, Hilton SK, Kollmer M, Nadendla R, Stamm J, Fafara-Thompson AE, Gygi AM, Ogawa EE, Van Camp M, Kocsisova Z, Leatherman JL, Modahl CM, Rubin MR, Apiz-Saab SS, Arias-Mejias SM, Carrion-Ortiz CF, Claudio-Vazquez PN, Espada-Green DM, Feliciano-Camacho M, Gonzalez-Bonilla KM, Taboas-Arroyo M, Vargas-Franco D, Montaez-Gonzalez R, Perez-Otero J, Rivera-Burgos M, Rivera-Rosario FJ, Eisler HL, Alexander J, Begley SK, Gabbard D, Allen RJ, Aung WY, Barshop WD, Boozalis A, Chu VP, Davis JS, Duggal RN, Franklin R, Gavinski K, Gebreyesus H, Gong HZ, Greenstein RA, Guo AD, Hanson C, Homa KE, Hsu SC, Huang Y, Huo L, Jacobs S, Jia S, Jung KL, Wai-Chee Kong S, Kroll MR, Lee BM, Lee PF, Levine KM, Li AS, Liu C, Liu MM, Lousararian AP, Lowery PB, Mallya AP, Marcus JE, Ng PC, Nguyen HP, Patel R, Precht H, Rastogi S, Sarezky JM, Schefkind A, Schultz MB, Shen D, Skorupa T, Spies NC, Stancu G, Vivian Tsang HM, Turski AL, Venkat R, Waldman LE, Wang K, Wang T, Wei JW, Wu DY, Xiong DD, Yu J, Zhou K, McNeil GP, Fernandez RW, Menzies PG, Gu T, Buhler J, Mardis ER, Elgin SCR (2017). Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element. G3 (Bethesda), 7(8), 2439-2460. (Read full article)
  31. Ma CX, Gao F, Luo J, Northfelt DW, Goetz M, Forero A, Hoog J, Naughton M, Ademuyiwa F, Suresh R, Anderson KS, Margenthaler J, Aft R, Hobday T, Moynihan T, Gillanders W, Cyr A, Eberlein TJ, Hieken T, Krontiras H, Guo Z, Lee MV, Spies NC, Skidmore ZL, Griffith OL, Griffith M, Thomas S, Bumb C, Vij K, Bartlett CH, Koehler M, Al-Kateb H, Sanati S, Ellis MJ (2017). NeoPalAna: Neoadjuvant Palbociclib, a Cyclin-Dependent Kinase 4/6 Inhibitor, and Anastrozole for Clinical Stage 2 or 3 Estrogen Receptor-Positive Breast Cancer. Clin Cancer Res, 23(15), 4055-4065. (Read full article)
  32. Griffith M, Spies NC, Krysiak K, McMichael JF, Coffman AC, Danos AM, Ainscough BJ, Ramirez CA, Rieke DT, Kujan L, Barnell EK, Wagner AH, Skidmore ZL, Wollam A, Liu CJ, Jones MR, Bilski RL, Lesurf R, Feng YY, Shah NM, Bonakdar M, Trani L, Matlock M, Ramu A, Campbell KM, Spies GC, Graubert AP, Gangavarapu K, Eldred JM, Larson DE, Walker JR, Good BM, Wu C, Su AI, Dienstmann R, Margolin AA, Tamborero D, Lopez-Bigas N, Jones SJ, Bose R, Spencer DH, Wartman LD, Wilson RK, Mardis ER, Griffith OL (2017). CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nat Genet, 49(2), 170-174. (Read full article)
  33. Griffith M, Griffith OL, Krysiak K, Skidmore ZL, Christopher MJ, Klco JM, Ramu A, Lamprecht TL, Wagner AH, Campbell KM, Lesurf R, Hundal J, Zhang J, Spies NC, Ainscough BJ, Larson DE, Heath SE, Fronick C, OLaughlin S, Fulton RS, Magrini V, McGrath S, Smith SM, Miller CA, Maher CA, Payton JE, Walker JR, Eldred JM, Walter MJ, Link DC, Graubert TA, Westervelt P, Kulkarni S, DiPersio JF, Mardis ER, Wilson RK, Ley TJ (2016). Comprehensive genomic analysis reveals FLT3 activation and a therapeutic strategy for a patient with relapsed adult B-lymphoblastic leukemia. Exp Hematol, 44(7), 603-13. (Read full article)
  34. Ma CX, Luo J, Naughton M, Ademuyiwa F, Suresh R, Griffith M, Griffith OL, Skidmore ZL, Spies NC, Ramu A, Trani L, Pluard T, Nagaraj G, Thomas S, Guo Z, Hoog J, Han J, Mardis E, Lockhart C, Ellis MJ (2015). A Phase I Trial of BKM120 (Buparlisib) in Combination with Fulvestrant in Postmenopausal Women with Estrogen Receptor-Positive Metastatic Breast Cancer. Clin Cancer Res, 22(7), 1583-91. (Read full article)
  35. Wagner AH, Coffman AC, Ainscough BJ, Spies NC, Skidmore ZL, Campbell KM, Krysiak K, Pan D, McMichael JF, Eldred JM, Walker JR, Wilson RK, Mardis ER, Griffith M, Griffith OL (2015). DGIdb 2.0: mining clinically relevant drug-gene interactions. Nucleic Acids Res, 44(D1), D1036-44. (Read full article)
  36. Griffith M, Walker JR, Spies NC, Ainscough BJ, Griffith OL (2015). Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud. PLoS Comput Biol, 11(8), e1004393. (Read full article)
  37. Griffith M, Griffith OL, Coffman AC, Weible JV, McMichael JF, Spies NC, Koval J, Das I, Callaway MB, Eldred JM, Miller CA, Subramanian J, Govindan R, Kumar RD, Bose R, Ding L, Walker JR, Larson DE, Dooling DJ, Smith SM, Ley TJ, Mardis ER, Wilson RK (2013). DGIdb: mining the druggable genome. Nat Methods, 10(12), 1209-10. (Read full article)

Review

  1. Hart SN, Hoffman NG, Gershkovich P, Christenson C, McClintock DS, Miller LJ, Jackups R, Azimi V, Spies N, Brodsky V (2023). Organizational preparedness for the use of large language models in pathology informatics. [Review]. J Pathol Inform, 14. (Read full article)