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Kyle M. Hernandez

TitleResearch Assistant Professor
InstitutionUniversity of Chicago
DepartmentMedicine-Computational Biomedicine and Biomedical Data Science
AddressChicago IL 60637
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Hernandez KM, Venkat A, Elbers DC, Bihn JR, Brophy MT, Do NV, La J, Liu Q, Prokhorenkov A, Metoki-Shlubsky N, Sung FC, Paller CJ, Fillmore NR, Grossman RL. Prostate cancer patient stratification by molecular signatures in the Veterans Precision Oncology Data Commons. Cold Spring Harb Mol Case Stud. 2023 12; 9(4). PMID: 38050021; PMCID: PMC10815278.
      Citations:    Fields:    Translation:Humans
    2. McConnell SC, Hernandez KM, Andrade J, de Jong JLO. Immune gene variation associated with chromosome-scale differences among individual zebrafish genomes. Sci Rep. 2023 05 13; 13(1):7777. PMID: 37179373; PMCID: PMC10183018.
      Citations: 1     Fields:    Translation:AnimalsCells
    3. Hernandez KM, Bramlett KS, Agius P, Baden J, Cao R, Clement O, Corner AS, Craft J, Dean DA, Dry JR, Grigaityte K, Grossman RL, Hicks J, Higa N, Holzer TR, Jensen J, Johann DJ, Katz S, Kolatkar A, Keynton JL, Lee JSH, Maar D, Martini JF, Meyer CG, Roberts PC, Ryder M, Salvatore L, Schageman JJ, Somiari S, Stetson D, Stern M, Xu L, Leiman LC. Contrived Materials and a Data Set for the Evaluation of Liquid Biopsy Tests: A Blood Profiling Atlas in Cancer (BLOODPAC) Community Study. J Mol Diagn. 2023 03; 25(3):143-155. PMID: 36828596.
      Citations:    Fields:    Translation:Humans
    4. Saravia-Butler AM, Schisler JC, Taylor D, Beheshti A, Butler D, Meydan C, Foox J, Hernandez K, Mozsary C, Mason CE, Meller R. Host transcriptional responses in nasal swabs identify potential SARS-CoV-2 infection in PCR negative patients. iScience. 2022 Nov 18; 25(11):105310. PMID: 36246576; PMCID: PMC9540688.
      Citations: 1     
    5. Arnovitz S, Mathur P, Tracy M, Mohsin A, Mondal S, Quandt J, Hernandez KM, Khazaie K, Dose M, Emmanuel AO, Gounari F. Tcf-1 promotes genomic instability and T cell transformation in response to aberrant ß-catenin activation. Proc Natl Acad Sci U S A. 2022 08 09; 119(32):e2201493119. PMID: 35921443; PMCID: PMC9371646.
      Citations: 7     Fields:    Translation:AnimalsCells
    6. Wcisel DJ, Dornburg A, McConnell SC, Hernandez KM, Andrade J, de Jong JLO, Litman GW, Yoder JA. A highly diverse set of novel immunoglobulin-like transcript (NILT) genes in zebrafish indicates a wide range of functions with complex relationships to mammalian receptors. Immunogenetics. 2023 02; 75(1):53-69. PMID: 35869336; PMCID: PMC9845131.
      Citations: 5     Fields:    Translation:AnimalsCells
    7. Barnes C, Bajracharya B, Cannalte M, Gowani Z, Haley W, Kass-Hout T, Hernandez K, Ingram M, Juvvala HP, Kuffel G, Martinov P, Maxwell JM, McCann J, Malhotra A, Metoki-Shlubsky N, Meyer C, Paredes A, Qureshi J, Ritter X, Schumm P, Shao M, Sheth U, Simmons T, VanTol A, Zhang Z, Grossman RL. The Biomedical Research Hub: a federated platform for patient research data. J Am Med Inform Assoc. 2022 03 15; 29(4):619-625. PMID: 35289369; PMCID: PMC8922179.
      Citations: 7     Fields:    Translation:Humans
    8. Kuang X, Wang F, Hernandez KM, Zhang Z, Grossman RL. Accurate and rapid prediction of tuberculosis drug resistance from genome sequence data using traditional machine learning algorithms and CNN. Sci Rep. 2022 02 14; 12(1):2427. PMID: 35165358; PMCID: PMC8844416.
      Citations: 17     Fields:    Translation:HumansCells
    9. Bao R, Spranger S, Hernandez K, Zha Y, Pytel P, Luke JJ, Gajewski TF, Volchenboum SL, Cohn SL, Desai AV. Immunogenomic determinants of tumor microenvironment correlate with superior survival in high-risk neuroblastoma. J Immunother Cancer. 2021 07; 9(7). PMID: 34272305; PMCID: PMC8287618.
      Citations: 19     Fields:    Translation:Humans
    10. Heath AP, Ferretti V, Agrawal S, An M, Angelakos JC, Arya R, Bajari R, Baqar B, Barnowski JHB, Burt J, Catton A, Chan BF, Chu F, Cullion K, Davidsen T, Do PM, Dompierre C, Ferguson ML, Fitzsimons MS, Ford M, Fukuma M, Gaheen S, Ganji GL, Garcia TI, George SS, Gerhard DS, Gerthoffert F, Gomez F, Han K, Hernandez KM, Issac B, Jackson R, Jensen MA, Joshi S, Kadam A, Khurana A, Kim KMJ, Kraft VE, Li S, Lichtenberg TM, Lodato J, Lolla L, Martinov P, Mazzone JA, Miller DP, Miller I, Miller JS, Miyauchi K, Murphy MW, Nullet T, Ogwara RO, Pham PL, Popov MY, Porter JJ, Powell R, Rademacher K, Reid CP, Rich S, Rogel B, Sahni H, Savage JH, Schmitt KA, Simmons TJ, Sislow J, Spring J, Stein L, Sullivan S, Tang Y, Thiagarajan M, Troyer HD, Wang C, Wang Z, West BL, Wilmer A, Wilson S, Wu K, Wysocki WP, Xiang L, Yamada JT, Yang L, Yu C, Yung CK, Zenklusen JC, Zhang J, Zhang Z, Zhao Y, Zubair A, Staudt LM, Grossman RL, Ortuño FM, Pedrosa J. Author Correction: The NCI Genomic Data Commons. Nat Genet. 2021 Jun; 53(6):935. PMID: 34007079.
      Citations:    Fields:    
    11. Singh U, Hernandez KM, Aronow BJ, Wurtele ES. African Americans and European Americans exhibit distinct gene expression patterns across tissues and tumors associated with immunologic functions and environmental exposures. Sci Rep. 2021 05 10; 11(1):9905. PMID: 33972602; PMCID: PMC8110974.
      Citations: 12     Fields:    Translation:HumansCellsPHPublic Health
    12. Heath AP, Ferretti V, Agrawal S, An M, Angelakos JC, Arya R, Bajari R, Baqar B, Barnowski JHB, Burt J, Catton A, Chan BF, Chu F, Cullion K, Davidsen T, Do PM, Dompierre C, Ferguson ML, Fitzsimons MS, Ford M, Fukuma M, Gaheen S, Ganji GL, Garcia TI, George SS, Gerhard DS, Gerthoffert F, Gomez F, Han K, Hernandez KM, Issac B, Jackson R, Jensen MA, Joshi S, Kadam A, Khurana A, Kim KMJ, Kraft VE, Li S, Lichtenberg TM, Lodato J, Lolla L, Martinov P, Mazzone JA, Miller DP, Miller I, Miller JS, Miyauchi K, Murphy MW, Nullet T, Ogwara RO, Pham PL, Popov MY, Porter JJ, Powell R, Rademacher K, Reid CP, Rich S, Rogel B, Sahni H, Savage JH, Schmitt KA, Simmons TJ, Sislow J, Spring J, Stein L, Sullivan S, Tang Y, Thiagarajan M, Troyer HD, Wang C, Wang Z, West BL, Wilmer A, Wilson S, Wu K, Wysocki WP, Xiang L, Yamada JT, Yang L, Yu C, Yung CK, Zenklusen JC, Zhang J, Zhang Z, Zhao Y, Zubair A, Staudt LM, Grossman RL, Ortuño FM, Pedrosa J. The NCI Genomic Data Commons. Nat Genet. 2021 03; 53(3):257-262. PMID: 33619384.
      Citations: 39     Fields:    Translation:Humans
    13. Zhang Z, Hernandez K, Savage J, Li S, Miller D, Agrawal S, Ortuno F, Staudt LM, Heath A, Grossman RL. Uniform genomic data analysis in the NCI Genomic Data Commons. Nat Commun. 2021 02 22; 12(1):1226. PMID: 33619257; PMCID: PMC7900240.
      Citations: 52     Fields:    Translation:HumansCells
    14. Sapoval N, Mahmoud M, Jochum MD, Liu Y, Elworth RAL, Wang Q, Albin D, Ogilvie HA, Lee MD, Villapol S, Hernandez KM, Maljkovic Berry I, Foox J, Beheshti A, Ternus K, Aagaard KM, Posada D, Mason CE, Sedlazeck FJ, Treangen TJ. SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission. Genome Res. 2021 04; 31(4):635-644. PMID: 33602693; PMCID: PMC8015855.
      Citations: 40     Fields:    Translation:HumansCells
    15. Sapoval N, Mahmoud M, Jochum MD, Liu Y, Elworth RAL, Wang Q, Albin D, Ogilvie H, Lee MD, Villapol S, Hernandez KM, Berry IM, Foox J, Beheshti A, Ternus K, Aagaard KM, Posada D, Mason CE, Sedlazeck F, Treangen TJ. Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission. bioRxiv. 2020 Jul 02. PMID: 32637955; PMCID: PMC7337385.
      Citations: 1     
    16. Bao R, Hernandez K, Huang L, Luke JJ. ACE2 and TMPRSS2 expression by clinical, HLA, immune, and microbial correlates across 34 human cancers and matched normal tissues: implications for SARS-CoV-2 COVID-19. J Immunother Cancer. 2020 07; 8(2). PMID: 32675312; PMCID: PMC7372174.
      Citations: 31     Fields:    Translation:HumansCellsPHPublic Health
    17. Pekow J, Hernandez K, Meckel K, Deng Z, Haider HI, Khalil A, Zhang C, Talisila N, Siva S, Jasmine F, Li YC, Rubin DT, Hyman N, Bissonnette M, Weber C, Kibriya MG. IBD-associated Colon Cancers Differ in DNA Methylation and Gene Expression Profiles Compared With Sporadic Colon Cancers. J Crohns Colitis. 2019 Jul 25; 13(7):884-893. PMID: 30753380; PMCID: PMC7327274.
      Citations: 13     Fields:    Translation:HumansCells
    18. Gao GF, Parker JS, Reynolds SM, Wang LB, Zhou W, Akbani R, Bailey M, Balu S, Berman BP, Brooks D, Chen H, Cherniack AD, Demchok JA, Ding L, Felau I, Gaheen S, Gerhard DS, Heiman DI, Hernandez KM, Hoadley KA, Jayasinghe R, Kemal A, Knijnenburg TA, Laird PW, Mensah MKA, Mungall AJ, Robertson AG, Shen H, Tarnuzzer R, Wang Z, Wyczalkowski M, Yang L, Zenklusen JC, Zhang Z, Genomic Data Analysis Network, Liang H, Noble MS, Silva TC. Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data. Cell Syst. 2019 07 24; 9(1):24-34.e10. PMID: 31344359; PMCID: PMC6707074.
      Citations: 77     Fields:    Translation:Humans
    19. Tonsing-Carter E, Hernandez KM, Kim CR, Harkless RV, Oh A, Bowie KR, West-Szymanski DC, Betancourt-Ponce MA, Green BD, Lastra RR, Fleming GF, Chandarlapaty S, Conzen SD. Glucocorticoid receptor modulation decreases ER-positive breast cancer cell proliferation and suppresses wild-type and mutant ER chromatin association. Breast Cancer Res. 2019 07 24; 21(1):82. PMID: 31340854; PMCID: PMC6651939.
      Citations: 31     Fields:    Translation:HumansAnimalsCells
    20. Eckert MA, Coscia F, Chryplewicz A, Chang JW, Hernandez KM, Pan S, Tienda SM, Nahotko DA, Li G, Lastra RR, Curtis M, Yamada SD, Perets R, McGregor SM, Andrade J, Fiehn O, Moellering RE, Mann M, Lengyel E, Blaženovic I. Proteomics reveals NNMT as a master metabolic regulator of cancer-associated fibroblasts. Nature. 2019 05; 569(7758):723-728. PMID: 31043742; PMCID: PMC6690743.
      Citations: 210     Fields:    Translation:HumansCells
    21. Weafer J, Gray JC, Hernandez K, Palmer AA, MacKillop J, de Wit H. Hierarchical investigation of genetic influences on response inhibition in healthy young adults. Exp Clin Psychopharmacol. 2017 12; 25(6):512-520. PMID: 29251981; PMCID: PMC5737791.
      Citations: 8     Fields:    Translation:Humans
    22. Yang Y, Zapata L, Rodgers C, Hernandez K, Iyer M, Jia G, Hynan LS, Pandya AG. Quality of life in patients with vitiligo using the Short Form-36. Br J Dermatol. 2017 12; 177(6):1764-1766. PMID: 28872663.
      Citations: 5     Fields:    Translation:Humans
    23. Gray JC, MacKillop J, Weafer J, Hernandez KM, Gao J, Palmer AA, de Wit H. Genetic analysis of impulsive personality traits: Examination of a priori candidates and genome-wide variation. Psychiatry Res. 2018 01; 259:398-404. PMID: 29120849; PMCID: PMC5742029.
      Citations: 20     Fields:    Translation:Humans
    24. Applebaum MA, Jha AR, Kao C, Hernandez KM, DeWane G, Salwen HR, Chlenski A, Dobratic M, Mariani CJ, Godley LA, Prabhakar N, White K, Stranger BE, Cohn SL. Integrative genomics reveals hypoxia inducible genes that are associated with a poor prognosis in neuroblastoma patients. Oncotarget. 2016 Nov 22; 7(47):76816-76826. PMID: 27765905; PMCID: PMC5340231.
      Citations: 23     Fields:    Translation:HumansCells
    25. Spranger S, Luke JJ, Bao R, Zha Y, Hernandez KM, Li Y, Gajewski AP, Andrade J, Gajewski TF. Density of immunogenic antigens does not explain the presence or absence of the T-cell-inflamed tumor microenvironment in melanoma. Proc Natl Acad Sci U S A. 2016 11 29; 113(48):E7759-E7768. PMID: 27837020; PMCID: PMC5137753.
      Citations: 208     Fields:    Translation:HumansCells
    26. Eckert MA, Pan S, Hernandez KM, Loth RM, Andrade J, Volchenboum SL, Faber P, Montag A, Lastra R, Peter ME, Yamada SD, Lengyel E. Genomics of Ovarian Cancer Progression Reveals Diverse Metastatic Trajectories Including Intraepithelial Metastasis to the Fallopian Tube. Cancer Discov. 2016 12; 6(12):1342-1351. PMID: 27856443; PMCID: PMC5164915.
      Citations: 98     Fields:    Translation:HumansCells
    27. McConnell SC, Hernandez KM, Wcisel DJ, Kettleborough RN, Stemple DL, Yoder JA, Andrade J, de Jong JL. Alternative haplotypes of antigen processing genes in zebrafish diverged early in vertebrate evolution. Proc Natl Acad Sci U S A. 2016 08 23; 113(34):E5014-23. PMID: 27493218; PMCID: PMC5003237.
      Citations: 29     Fields:    Translation:AnimalsCells
    28. West DC, Pan D, Tonsing-Carter EY, Hernandez KM, Pierce CF, Styke SC, Bowie KR, Garcia TI, Kocherginsky M, Conzen SD. GR and ER Coactivation Alters the Expression of Differentiation Genes and Associates with Improved ER+ Breast Cancer Outcome. Mol Cancer Res. 2016 08; 14(8):707-19. PMID: 27141101; PMCID: PMC5008962.
      Citations: 58     Fields:    Translation:HumansCells
    29. Pagano MJ, Weinberg AC, Deibert CM, Hernandez K, Alukal J, Zhao L, Wilson SK, Valenzuela RJ, Egydio PH. Penile intracavernosal pillars: lessons from anatomy and potential implications for penile prosthesis placement. Int J Impot Res. 2016 May; 28(3):114-9. PMID: 27053154.
      Citations: 4     Fields:    Translation:Humans
    30. Des Marais DL, Razzaque S, Hernandez KM, Garvin DF, Juenger TE. Quantitative trait loci associated with natural diversity in water-use efficiency and response to soil drying in Brachypodium distachyon. Plant Sci. 2016 Oct; 251:2-11. PMID: 27593458.
      Citations: 11     Fields:    Translation:Animals
    31. Hernandez KM. Understanding the genetic architecture of complex traits using the function-valued approach. New Phytol. 2015 Oct; 208(1):1-3. PMID: 26311281.
      Citations: 2     Fields:    Translation:Animals
    32. Singh P, Brock CO, Volden PA, Hernandez K, Skor M, Kocherginsky M, Park JE, Brady MJ, Conzen SD. Glucocorticoid receptor ChIP-sequencing of subcutaneous fat reveals modulation of inflammatory pathways. Obesity (Silver Spring). 2015 Nov; 23(11):2286-93. PMID: 26408078; PMCID: PMC4818951.
      Citations: 5     Fields:    Translation:HumansCells
    33. Bao R, Hernandez K, Huang L, Kang W, Bartom E, Onel K, Volchenboum S, Andrade J. ExScalibur: A High-Performance Cloud-Enabled Suite for Whole Exome Germline and Somatic Mutation Identification. PLoS One. 2015; 10(8):e0135800. PMID: 26271043; PMCID: PMC4535852.
      Citations: 8     Fields:    Translation:Humans
    34. Malcom JW, Hernandez KM, Likos R, Wayne T, Leibold MA, Juenger TE. Extensive cross-environment fitness variation lies along few axes of genetic variation in the model alga, Chlamydomonas reinhardtii. New Phytol. 2015 Jan; 205(2):841-51. PMID: 25264298.
      Citations: 7     Fields:    Translation:Animals
    35. Lowry DB, Hernandez K, Taylor SH, Meyer E, Logan TL, Barry KW, Chapman JA, Rokhsar DS, Schmutz J, Juenger TE. The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii. New Phytol. 2015 Jan; 205(1):402-14. PMID: 25252269; PMCID: PMC4265272.
      Citations: 27     Fields:    Translation:Animals
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