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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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    Collapse Bibliographic 
    Collapse selected publications
    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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    1. 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.
      View in: PubMed
    2. 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, Ortuño FM, Pedrosa J, 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. Author Correction: The NCI Genomic Data Commons. Nat Genet. 2021 Jun; 53(6):935. PMID: 34007079.
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    3. 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.
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    4. 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, Ortuño FM, Pedrosa J, 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. The NCI Genomic Data Commons. Nat Genet. 2021 03; 53(3):257-262. PMID: 33619384.
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    5. 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.
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    6. 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.
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    7. 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.
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    8. 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.
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    9. 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.
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    10. Gao GF, Parker JS, Reynolds SM, Silva TC, 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. 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.
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    11. 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.
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    12. Eckert MA, Coscia F, Chryplewicz A, Chang JW, Hernandez KM, Pan S, Tienda SM, Nahotko DA, Li G, Blaženovic I, Lastra RR, Curtis M, Yamada SD, Perets R, McGregor SM, Andrade J, Fiehn O, Moellering RE, Mann M, Lengyel E. Proteomics reveals NNMT as a master metabolic regulator of cancer-associated fibroblasts. Nature. 2019 05; 569(7758):723-728. PMID: 31043742.
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    13. 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.
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    14. 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.
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    15. 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.
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    16. 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.
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    17. 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.
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    18. 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.
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    19. 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.
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    20. 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.
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    21. Pagano MJ, Weinberg AC, Deibert CM, Hernandez K, Alukal J, Zhao L, Wilson SK, Egydio PH, Valenzuela RJ. 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.
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    22. 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. . 2016 Oct; 251:2-11. PMID: 27593458.
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    23. Hernandez KM. Understanding the genetic architecture of complex traits using the function-valued approach. . 2015 Oct; 208(1):1-3. PMID: 26311281.
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    24. 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.
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    25. 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.
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    26. 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. . 2015 Jan; 205(2):841-51. PMID: 25264298.
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    27. 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.
      View in: PubMed
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