Items: 1 to 145 of 145

1.  Validation of histopathology foundation models through whole slide image retrieval.
Alfasly S, Alabtah G, Hemati S, Kalari KR, Garcia JJ, Tizhoosh HR.
Sci Rep. 2025 Feb 1;15(1):3990. doi: 10.1038/s41598-025-88545-9.

2.  QSP Modeling Shows Pathological Synergism Between Insulin Resistance and Amyloid-Beta Exposure in Upregulating VCAM1 Expression at the BBB Endothelium.
Wang Z, Veerareddy V, Tang X, Thompson KJ, Krishnan S, Kalari KR, Kandimalla KK.
CPT Pharmacometrics Syst Pharmacol. 2024 Dec 27; doi: 10.1002/psp4.13296.

3.  Molecular Mechanisms Underlying Amyloid Beta Peptide Mediated Upregulation of Vascular Cell Adhesion Molecule-1 in Alzheimer Disease.
Salian VS, Tang X, Thompson KJ, Curan GL, Lowe VJ, Li L, Kalari KR, Kandimalla KK.
J Pharmacol Exp Ther. 2024 Nov 19;391(3):430-440. doi: 10.1124/jpet.124.002280.

4.  OmicsFootPrint: a framework to integrate and interpret multi-omics data using circular images and deep neural networks.
Tang X, Prodduturi N, Thompson KJ, Weinshilboum R, O'Sullivan CC, Boughey JC, Tizhoosh HR, Klee EW, Wang L, Goetz MP, Suman V, Kalari KR.
Nucleic Acids Res. 2024 Nov 27;52(21):e99. doi: 10.1093/nar/gkae915.

5.  Nomination of a novel plasma protein biomarker panel capable of classifying Alzheimer's disease dementia with high accuracy in an African American cohort.
Kuchenbecker LA, Thompson KJ, Hurst CD, Opdenbosch BM, Heckman MG, Reddy JS, Nguyen T, Casellas HL, Sotelo KD, Reddy DJ, Lucas JA, Day GS, Willis FB, Graff-Radford N, Ertekin-Taner N, Kalari KR, Carrasquillo MM.
bioRxiv. 2024 Jul 29; doi: 10.1101/2024.07.27.605373.

6.  ReCorDE: a framework for identifying drug classes targeting shared vulnerabilities with applications to synergistic drug discovery.
John AJ, Ghose ET, Gao H, Luck M, Jeong D, Kalari KR, Wang L.
Front Oncol. 2024;14 doi: 10.3389/fonc.2024.1343091.

7.  Pre-treatment peripheral blood immunophenotyping and response to neoadjuvant chemotherapy in operable breast cancer.
Leon-Ferre RA, Whitaker KR, Suman VJ, Hoskin T, Giridhar KV, Moore RM, Al-Jarrad A, McLaughlin SA, Northfelt DW, Hunt KN, Conners AL, Moyer A, Carter JM, Kalari K, Weinshilboum R, Wang L, Ingle JN, Knutson KL, Ansell SM, Boughey JC, Goetz MP, Villasboas JC.
Breast Cancer Res. 2024 Jun 10;26(1):97. doi: 10.1186/s13058-024-01848-z.

8.  OmicsFootPrint: a framework to integrate and interpret multi-omics data using circular images and deep neural networks.
Tang X, Prodduturi N, Thompson KJ, Weinshilboum RM, O'Sullivan CC, Boughey JC, Tizhoosh H, Klee EW, Wang L, Goetz MP, Suman V, Kalari KR.
bioRxiv. 2024 May 1; doi: 10.1101/2024.03.21.586001.

9.  Automated mitotic spindle hotspot counts are highly associated with clinical outcomes in systemically untreated early-stage triple-negative breast cancer.
Leon-Ferre RA, Carter JM, Zahrieh D, Sinnwell JP, Salgado R, Suman VJ, Hillman DW, Boughey JC, Kalari KR, Couch FJ, Ingle JN, Balkenhol M, Ciompi F, van der Laak J, Goetz MP.
NPJ Breast Cancer. 2024 Mar 29;10(1):25. doi: 10.1038/s41523-024-00629-3.

10.  Pericyte Control of Gene Expression in the Blood-Brain Barrier Endothelium: Implications for Alzheimer's Disease.
Nelson D, Thompson KJ, Wang L, Wang Z, Eberts P, Azarin SM, Kalari KR, Kandimalla KK.
J Alzheimers Dis. 2024;99(s2):S281-S297. doi: 10.3233/JAD-230907.

11.  Identification of a Notch transcriptomic signature for breast cancer.
Braune EB, Geist F, Tang X, Kalari K, Boughey J, Wang L, Leon-Ferre RA, D'Assoro AB, Ingle JN, Goetz MP, Kreis J, Wang K, Foukakis T, Seshire A, Wienke D, Lendahl U.
Breast Cancer Res. 2024 Jan 3;26(1):4. doi: 10.1186/s13058-023-01757-7.

12.  Endoxifen downregulates AKT phosphorylation through protein kinase C beta 1 inhibition in ERα+ breast cancer.
Jayaraman S, Wu X, Kalari KR, Tang X, Kuffel MJ, Bruinsma ES, Jalali S, Peterson KL, Correia C, Kudgus RA, Kaufmann SH, Renuse S, Ingle JN, Reid JM, Ames MM, Fields AP, Schellenberg MJ, Hawse JR, Pandey A, Goetz MP.
NPJ Breast Cancer. 2023 Dec 19;9(1):101. doi: 10.1038/s41523-023-00606-2.

13.  Estrogen-regulated miRs in bone enhance osteoblast differentiation and matrix mineralization.
Emch MJ, Wicik Z, Aspros KGM, Vukajlovic T, Pitel KS, Narum AK, Weivoda MM, Tang X, Kalari KR, Turner RT, Iwaniec UT, Monroe DG, Subramaniam M, Hawse JR.
Mol Ther Nucleic Acids. 2023 Sep 12;33 doi: 10.1016/j.omtn.2023.05.026.

14.  Integration of multiomics data shows down regulation of mismatch repair and tubulin pathways in triple-negative chemotherapy-resistant breast tumors.
Tang X, Thompson KJ, Kalari KR, Sinnwell JP, Suman VJ, Vedell PT, McLaughlin SA, Northfelt DW, Aspitia AM, Gray RJ, Carter JM, Weinshilboum R, Wang L, Boughey JC, Goetz MP.
Breast Cancer Res. 2023 May 24;25(1):57. doi: 10.1186/s13058-023-01656-x.

15.  Distinct spatial immune microlandscapes are independently associated with outcomes in triple-negative breast cancer.
Carter JM, Chumsri S, Hinerfeld DA, Ma Y, Wang X, Zahrieh D, Hillman DW, Tenner KS, Kachergus JM, Brauer HA, Warren SE, Henderson D, Shi J, Liu Y, Joensuu H, Lindman H, Leon-Ferre RA, Boughey JC, Liu MC, Ingle JN, Kalari KR, Couch FJ, Knutson KL, Goetz MP, Perez EA, Thompson EA.
Nat Commun. 2023 Apr 18;14(1):2215. doi: 10.1038/s41467-023-37806-0.

16.  Dynamic assessment of serum chromogranin A and treatment response with abiraterone acetate in metastatic castration-resistant prostate cancer.
Lewis AR, Costello BA, Quevedo F, Pagliaro LC, Sanhueza C, Weinshilboum RM, Kalari KR, Wang L, Kohli M, Tan W, Giridhar KV.
Prostate. 2023 May;83(7):649-655. doi: 10.1002/pros.24498.

17.  Bayesian Machine Learning Enables Identification of Transcriptional Network Disruptions Associated with Drug-Resistant Prostate Cancer.
Blatti C, de la Fuente J, Gao H, Marín-Goñi I, Chen Z, Zhao SD, Tan W, Weinshilboum R, Kalari KR, Wang L, Hernaez M.
Cancer Res. 2023 Apr 14;83(8):1361-1380. doi: 10.1158/0008-5472.CAN-22-1910.

18.  Plasma Copy Number Alteration-Based Prognostic and Predictive Multi-Gene Risk Score in Metastatic Castration-Resistant Prostate Cancer.
Huang J, Du M, Soupir A, Wang L, Tan W, Kalari KR, Kilari D, Park J, Huang CC, Kohli M, Wang L.
Cancers (Basel). 2022 Sep 28;14(19) doi: 10.3390/cancers14194714.

19.  Molecular Profile Changes in Patients with Castrate-Resistant Prostate Cancer Pre- and Post-Abiraterone/Prednisone Treatment.
Sicotte H, Kalari KR, Qin S, Dehm SM, Bhargava V, Gormley M, Tan W, Sinnwell JP, Hillman DW, Li Y, Vedell PT, Carlson RE, Bryce AH, Jimenez RE, Weinshilboum RM, Kohli M, Wang L.
Mol Cancer Res. 2022 Dec 2;20(12):1739-1750. doi: 10.1158/1541-7786.MCR-22-0099.

20.  Identification of Src Family Kinases as Potential Therapeutic Targets for Chemotherapy-Resistant Triple Negative Breast Cancer.
Kohale IN, Yu J, Zhuang Y, Fan X, Reddy RJ, Sinnwell J, Kalari KR, Boughey JC, Carter JM, Goetz MP, Wang L, White FM.
Cancers (Basel). 2022 Aug 30;14(17) doi: 10.3390/cancers14174220.

21.  Mapping the dynamics of insulin-responsive pathways in the blood-brain barrier endothelium using time-series transcriptomics data.
Wang Z, Tang X, Swaminathan SK, Kandimalla KK, Kalari KR.
NPJ Syst Biol Appl. 2022 Aug 16;8(1):29. doi: 10.1038/s41540-022-00235-8.

22.  DNA barcoded competitive clone-initiating cell analysis reveals novel features of metastatic growth in a cancer xenograft model.
Aalam SMM, Tang X, Song J, Ray U, Russell SJ, Weroha SJ, Bakkum-Gamez J, Shridhar V, Sherman ME, Eaves CJ, Knapp DJHF, Kalari KR, Kannan N.
NAR Cancer. 2022 Sep;4(3):zcac022. doi: 10.1093/narcan/zcac022.

23.  India's Opportunities and Challenges in Establishing a Twin Registry: An Unexplored Human Resource for the World's Second-Most Populous Nation.
Dhar R, Rana S, Srivastava TP, Nayek A, Sharma JB, Kaur D, Kalari KR, Singh H, Karmakar S.
Twin Res Hum Genet. 2022 Jun;25(3):156-164. doi: 10.1017/thg.2022.24.

24.  Luminal androgen receptor breast cancer subtype and investigation of the microenvironment and neoadjuvant chemotherapy response.
Thompson KJ, Leon-Ferre RA, Sinnwell JP, Zahrieh DM, Suman VJ, Metzger FO, Asad S, Stover DG, Carey L, Sikov WM, Ingle JN, Liu MC, Carter JM, Klee EW, Weinshilboum RM, Boughey JC, Wang L, Couch FJ, Goetz MP, Kalari KR.
NAR Cancer. 2022 Jun;4(2):zcac018. doi: 10.1093/narcan/zcac018.

25.  Implementation of preemptive DNA sequence-based pharmacogenomics testing across a large academic medical center: The Mayo-Baylor RIGHT 10K Study.
Wang L, Scherer SE, Bielinski SJ, Muzny DM, Jones LA, Black JL 3rd, Moyer AM, Giri J, Sharp RR, Matey ET, Wright JA, Oyen LJ, Nicholson WT, Wiepert M, Sullard T, Curry TB, Rohrer Vitek CR, McAllister TM, St Sauver JL, Caraballo PJ, Lazaridis KN, Venner E, Qin X, Hu J, Kovar CL, Korchina V, Walker K, Doddapaneni H, Wu TJ, Raj R, Denson S, Liu W, Chandanavelli G, Zhang L, Wang Q, Kalra D, Karow MB, Harris KJ, Sicotte H, Peterson SE, Barthel AE, Moore BE, Skierka JM, Kluge ML, Kotzer KE, Kloke K, Vander Pol JM, Marker H, Sutton JA, Kekic A, Ebenhoh A, Bierle DM, Schuh MJ, Grilli C, Erickson S, Umbreit A, Ward L, Crosby S, Nelson EA, Levey S, Elliott M, Peters SG, Pereira N, Frye M, Shamoun F, Goetz MP, Kullo IJ, Wermers R, Anderson JA, Formea CM, El Melik RM, Zeuli JD, Herges JR, Krieger CA, Hoel RW, Taraba JL, St Thomas SR, Absah I, Bernard ME, Fink SR, Gossard A, Grubbs PL, Jacobson TM, Takahashi P, Zehe SC, Buckles S, Bumgardner M, Gallagher C, Fee-Schroeder K, Nicholas NR, Powers ML, Ragab AK, Richardson DM, Stai A, Wilson J, Pacyna JE, Olson JE, Sutton EJ, Beck AT, Horrow C, Kalari KR, Larson NB, Liu H, Wang L, Lopes GS, Borah BJ, Freimuth RR, Zhu Y, Jacobson DJ, Hathcock MA, Armasu SM, McGree ME, Jiang R, Koep TH, Ross JL, Hilden MG, Bosse K, Ramey B, Searcy I, Boerwinkle E, Gibbs RA, Weinshilboum RM.
Genet Med. 2022 May;24(5):1062-1072. doi: 10.1016/j.gim.2022.01.022.

26.  Biomarkers for Predicting Abiraterone Treatment Outcome and Selecting Alternative Therapies in Castration-Resistant Prostate Cancer.
Qin S, Gao H, Kim W, Zhang H, Gu Y, Kalari KR, Sinnwell JP, Scholz JA, Xie F, Yin P, Yu J, Qin B, Zhuang Y, Wei L, Tan W, Bryce AH, Weinshilboum RM, Wang L.
Clin Pharmacol Ther. 2022 Jun;111(6):1296-1306. doi: 10.1002/cpt.2582.

27.  Estrogen receptor beta repurposes EZH2 to suppress oncogenic NFκB/p65 signaling in triple negative breast cancer.
Aspros KGM, Carter JM, Hoskin TL, Suman VJ, Subramaniam M, Emch MJ, Ye Z, Sun Z, Sinnwell JP, Thompson KJ, Tang X, Rodman EPB, Wang X, Nelson AW, Chernukhin I, Hamdan FH, Bruinsma ES, Carroll JS, Fernandez-Zapico ME, Johnsen SA, Kalari KR, Huang H, Leon-Ferre RA, Couch FJ, Ingle JN, Goetz MP, Hawse JR.
NPJ Breast Cancer. 2022 Feb 17;8(1):20. doi: 10.1038/s41523-022-00387-0.

28.  Age-Dependent Changes in the Plasma and Brain Pharmacokinetics of Amyloid-β Peptides and Insulin.
Zhou AL, Sharda N, Sarma VV, Ahlschwede KM, Curran GL, Tang X, Poduslo JF, Kalari KR, Lowe VJ, Kandimalla KK.
J Alzheimers Dis. 2022;85(3):1031-1044. doi: 10.3233/JAD-215128.

29.  Toward Individualized Prediction of Response to Methotrexate in Early Rheumatoid Arthritis: A Pharmacogenomics-Driven Machine Learning Approach.
Myasoedova E, Athreya AP, Crowson CS, Davis JM 3rd, Warrington KJ, Walchak RC, Carlson E, Kalari KR, Bongartz T, Tak PP, van Vollenhoven RF, Padyukov L, Emery P, Morgan A, Wang L, Weinshilboum RM, Matteson EL, Pharmacogenetics of Methotrexate in Rheumatoid Arthritis Consortium.
Arthritis Care Res (Hoboken). 2022 Jun;74(6):879-888. doi: 10.1002/acr.24834.

30.  Anastrozole Regulates Fatty Acid Synthase in Breast Cancer.
Cairns J, Ingle JN, Kalari KR, Goetz MP, Weinshilboum RM, Gao H, Li H, Bari MG, Wang L.
Mol Cancer Ther. 2022 Jan;21(1):206-216. doi: 10.1158/1535-7163.MCT-21-0509.

31.  Multi-Omics Analyses Show Disease, Diet, and Transcriptome Interactions With the Virome.
Mihindukulasuriya KA, Mars RAT, Johnson AJ, Ward T, Priya S, Lekatz HR, Kalari KR, Droit L, Zheng T, Blekhman R, D'Amato M, Farrugia G, Knights D, Handley SA, Kashyap PC.
Gastroenterology. 2021 Oct;161(4):1194-1207.e8. doi: 10.1053/j.gastro.2021.06.077.

32.  Establishment and characterization of immortalized human breast cancer cell lines from breast cancer patient-derived xenografts (PDX).
Zhuang Y, Grainger JM, Vedell PT, Yu J, Moyer AM, Gao H, Fan XY, Qin S, Liu D, Kalari KR, Goetz MP, Boughey JC, Weinshilboum RM, Wang L.
NPJ Breast Cancer. 2021 Jun 18;7(1):79. doi: 10.1038/s41523-021-00285-x.

33.  Characteristics and Spatially Defined Immune (micro)landscapes of Early-stage PD-L1-positive Triple-negative Breast Cancer.
Carter JM, Polley MC, Leon-Ferre RA, Sinnwell J, Thompson KJ, Wang X, Ma Y, Zahrieh D, Kachergus JM, Solanki M, Boughey JC, Liu MC, Ingle JN, Kalari KR, Couch FJ, Thompson EA, Goetz MP.
Clin Cancer Res. 2021 Oct 15;27(20):5628-5637. doi: 10.1158/1078-0432.CCR-21-0343.

34.  FOXA1 overexpression suppresses interferon signaling and immune response in cancer.
He Y, Wang L, Wei T, Xiao YT, Sheng H, Su H, Hollern DP, Zhang X, Ma J, Wen S, Xie H, Yan Y, Pan Y, Hou X, Tang X, Suman VJ, Carter JM, Weinshilboum R, Wang L, Kalari KR, Weroha SJ, Bryce AH, Boughey JC, Dong H, Perou CM, Ye D, Goetz MP, Ren S, Huang H.
J Clin Invest. 2021 Jul 15;131(14) doi: 10.1172/JCI147025.

35.  Patient-Derived Xenograft Engraftment and Breast Cancer Outcomes in a Prospective Neoadjuvant Study (BEAUTY).
Boughey JC, Suman VJ, Yu J, Santo K, Sinnwell JP, Carter JM, Kalari KR, Tang X, McLaughlin SA, Moreno-Aspitia A, Northfelt DW, Gray RJ, Hunt KN, Conners AL, Ingle JN, Moyer A, Weinshilboum R, Copland JA 3rd, Wang L, Goetz MP.
Clin Cancer Res. 2021 Sep 1;27(17):4696-4699. doi: 10.1158/1078-0432.CCR-21-0641.

36.  Interaction Between SNP Genotype and Efficacy of Anastrozole and Exemestane in Early-Stage Breast Cancer.
Cairns J, Kalari KR, Ingle JN, Shepherd LE, Ellis MJ, Goss PE, Barman P, Carlson EE, Goodnature B, Goetz MP, Weinshilboum RM, Gao H, Wang L.
Clin Pharmacol Ther. 2021 Oct;110(4):1038-1049. doi: 10.1002/cpt.2311.

37.  Correction to: Establishing and characterizing patient-derived xenografts using pre-chemotherapy percutaneous biopsy and post-chemotherapy surgical samples from a prospective neoadjuvant breast cancer study.
Yu J, Qin B, Moyer AM, Sinnwell JP, Thompson KJ, Copland JA 3rd, Marlow LA, Miller JL, Yin P, Gao B, Minter-Dykhouse K, Tang X, McLaughlin SA, Moreno-Aspitia A, Schweitzer A, Lu Y, Hubbard J, Northfelt DW, Gray RJ, Hunt K, Conners AL, Suman VJ, Kalari KR, Ingle JN, Lou Z, Visscher DW, Weinshilboum R, Boughey JC, Goetz MP, Wang L.
Breast Cancer Res. 2021 Mar 25;23(1):41. doi: 10.1186/s13058-021-01420-z.

38.  SLCO1B1: Application and Limitations of Deep Mutational Scanning for Genomic Missense Variant Function.
Zhang L, Sarangi V, Ho MF, Moon I, Kalari KR, Wang L, Weinshilboum RM.
Drug Metab Dispos. 2021 May;49(5):395-404. doi: 10.1124/dmd.120.000264.

39.  COVID-19 Transmission, Current Treatment, and Future Therapeutic Strategies.
Salian VS, Wright JA, Vedell PT, Nair S, Li C, Kandimalla M, Tang X, Carmona Porquera EM, Kalari KR, Kandimalla KK.
Mol Pharm. 2021 Mar 1;18(3):754-771. doi: 10.1021/acs.molpharmaceut.0c00608.

40.  A clinical calculator to predict disease outcomes in women with triple-negative breast cancer.
Polley MC, Leon-Ferre RA, Leung S, Cheng A, Gao D, Sinnwell J, Liu H, Hillman DW, Eyman-Casey A, Gilbert JA, Negron V, Boughey JC, Liu MC, Ingle JN, Kalari K, Couch F, Carter JM, Visscher DW, Nielsen TO, Goetz MP.
Breast Cancer Res Treat. 2021 Feb;185(3):557-566. doi: 10.1007/s10549-020-06030-5.

41.  CDC25B partners with PP2A to induce AMPK activation and tumor suppression in triple negative breast cancer.
Cairns J, Ly RC, Niu N, Kalari KR, Carlson EE, Wang L.
NAR Cancer. 2020 Dec;2(4):zcaa039. doi: 10.1093/narcan/zcaa039.

42.  Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome.
Mars RAT, Yang Y, Ward T, Houtti M, Priya S, Lekatz HR, Tang X, Sun Z, Kalari KR, Korem T, Bhattarai Y, Zheng T, Bar N, Frost G, Johnson AJ, van Treuren W, Han S, Ordog T, Grover M, Sonnenburg J, D'Amato M, Camilleri M, Elinav E, Segal E, Blekhman R, Farrugia G, Swann JR, Knights D, Kashyap PC.
Cell. 2020 Nov 12;183(4):1137-1140. doi: 10.1016/j.cell.2020.10.040.

43.  Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome.
Mars RAT, Yang Y, Ward T, Houtti M, Priya S, Lekatz HR, Tang X, Sun Z, Kalari KR, Korem T, Bhattarai Y, Zheng T, Bar N, Frost G, Johnson AJ, van Treuren W, Han S, Ordog T, Grover M, Sonnenburg J, D'Amato M, Camilleri M, Elinav E, Segal E, Blekhman R, Farrugia G, Swann JR, Knights D, Kashyap PC.
Cell. 2020 Sep 17;182(6):1460-1473.e17. doi: 10.1016/j.cell.2020.08.007.

44.  Pharmacogenomics of aromatase inhibitors in postmenopausal breast cancer and additional mechanisms of anastrozole action.
Cairns J, Ingle JN, Dudenkov TM, Kalari KR, Carlson EE, Na J, Buzdar AU, Robson ME, Ellis MJ, Goss PE, Shepherd LE, Goodnature B, Goetz MP, Weinshilboum RM, Li H, Bari MG, Wang L.
JCI Insight. 2020 Aug 20;5(16) doi: 10.1172/jci.insight.137571.

45.  Single-nucleotide polymorphism biomarkers of adjuvant anastrozole-induced estrogen suppression in early breast cancer.
Ingle JN, Kalari KR, Barman P, Shepherd LE, Ellis MJ, Goss PE, Buzdar AU, Robson ME, Cairns J, Carlson EE, Eyman Casey A, Hoskin TL, Goodnature BA, Haddad TC, Goetz MP, Weinshilboum RM, Wang L.
Pharmacogenet Genomics. 2021 Jan;31(1):1-9. doi: 10.1097/FPC.0000000000000415.

46.  Frequency of MicroRNA Response Elements Identifies Pathologically Relevant Signaling Pathways in Triple-Negative Breast Cancer.
Nair AA, Tang X, Thompson KJ, Vedell PT, Kalari KR, Subramanian S.
iScience. 2020 Jun 26;23(6):101249. doi: 10.1016/j.isci.2020.101249.

47.  Concordance between predicted HLA type using next generation sequencing data generated for non-HLA purposes and clinical HLA type.
Moyer AM, Dukek B, Duellman P, Schneider B, Wakefield L, Skierka JM, Avula R, Bhagwate AV, Kalari KR, Kreuter JD, Goetz MP, Boughey JC, Black JL 3rd, Gandhi MJ.
Hum Immunol. 2020 Aug;81(8):423-429. doi: 10.1016/j.humimm.2020.06.002.

48.  Patient-specific multi-omics models and the application in personalized combination therapy.
John A, Qin B, Kalari KR, Wang L, Yu J.
Future Oncol. 2020 Aug;16(23):1737-1750. doi: 10.2217/fon-2020-0119.

49.  Antitumor activity of Z-endoxifen in aromatase inhibitor-sensitive and aromatase inhibitor-resistant estrogen receptor-positive breast cancer.
Jayaraman S, Hou X, Kuffel MJ, Suman VJ, Hoskin TL, Reinicke KE, Monroe DG, Kalari KR, Tang X, Zeldenrust MA, Cheng J, Bruinsma ES, Buhrow SA, McGovern RM, Safgren SL, Walden CA, Carter JM, Reid JM, Ingle JN, Ames MM, Hawse JR, Goetz MP.
Breast Cancer Res. 2020 May 19;22(1):51. doi: 10.1186/s13058-020-01286-7.

50.  Anastrozole has an Association between Degree of Estrogen Suppression and Outcomes in Early Breast Cancer and is a Ligand for Estrogen Receptor α.
Ingle JN, Cairns J, Suman VJ, Shepherd LE, Fasching PA, Hoskin TL, Singh RJ, Desta Z, Kalari KR, Ellis MJ, Goss PE, Chen BE, Volz B, Barman P, Carlson EE, Haddad T, Goetz MP, Goodnature B, Cuellar ME, Walters MA, Correia C, Kaufmann SH, Weinshilboum RM, Wang L.
Clin Cancer Res. 2020 Jun 15;26(12):2986-2996. doi: 10.1158/1078-0432.CCR-19-3091.

51.  Folate receptor alpha expression associates with improved disease-free survival in triple negative breast cancer patients.
Norton N, Youssef B, Hillman DW, Nassar A, Geiger XJ, Necela BM, Liu H, Ruddy KJ, Polley MC, Ingle JN, Couch FJ, Perez EA, Liu MC, Carter JM, Leon-Ferre RA, Boughey JC, Somers EB, Kalari KR, Visscher DW, Goetz MP, Knutson KL.
NPJ Breast Cancer. 2020;6 doi: 10.1038/s41523-020-0147-1.

52.  CYP2C9 and CYP2C19: Deep Mutational Scanning and Functional Characterization of Genomic Missense Variants.
Zhang L, Sarangi V, Moon I, Yu J, Liu D, Devarajan S, Reid JM, Kalari KR, Wang L, Weinshilboum R.
Clin Transl Sci. 2020 Jul;13(4):727-742. doi: 10.1111/cts.12758.

53.  Knowledge-guided analysis of omics data using the KnowEnG cloud platform.
Blatti C 3rd, Emad A, Berry MJ, Gatzke L, Epstein M, Lanier D, Rizal P, Ge J, Liao X, Sobh O, Lambert M, Post CS, Xiao J, Groves P, Epstein AT, Chen X, Srinivasan S, Lehnert E, Kalari KR, Wang L, Weinshilboum RM, Song JS, Jongeneel CV, Han J, Ravaioli U, Sobh N, Bushell CB, Sinha S.
PLoS Biol. 2020 Jan;18(1):e3000583. doi: 10.1371/journal.pbio.3000583.

54.  A Transcriptionally Definable Subgroup of Triple-Negative Breast and Ovarian Cancer Samples Shows Sensitivity to HSP90 Inhibition.
Shee K, Wells JD, Ung M, Hampsch RA, Traphagen NA, Yang W, Liu SC, Zeldenrust MA, Wang L, Kalari KR, Yu J, Boughey JC, Demidenko E, Kettenbach AN, Cheng C, Goetz MP, Miller TW.
Clin Cancer Res. 2020 Jan 1;26(1):159-170. doi: 10.1158/1078-0432.CCR-18-2213.

55.  Gene Expression and Missplicing in the Corneal Endothelium of Patients With a TCF4 Trinucleotide Repeat Expansion Without Fuchs' Endothelial Corneal Dystrophy.
Wieben ED, Baratz KH, Aleff RA, Kalari KR, Tang X, Maguire LJ, Patel SV, Fautsch MP.
Invest Ophthalmol Vis Sci. 2019 Aug 1;60(10):3636-3643. doi: 10.1167/iovs.19-27689.

56.  Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data.
Deng W, Mou T, Kalari KR, Niu N, Wang L, Pawitan Y, Vu TN.
Bioinformatics. 2020 Feb 1;36(3):805-812. doi: 10.1093/bioinformatics/btz640.

57.  Stochastic changes in gene expression promote chaotic dysregulation of homeostasis in clonal breast tumors.
Felts SJ, Tang X, Willett B, Van Keulen VP, Hansen MJ, Kalari KR, Pease LR.
Commun Biol. 2019;2 doi: 10.1038/s42003-019-0460-0.

58.  Deep sequencing across germline genome-wide association study signals relating to breast cancer events in women receiving aromatase inhibitors for adjuvant therapy of early breast cancer.
Ingle JN, Kalari KR, Momozawa Y, Kubo M, Furukawa Y, Shepherd LE, Ellis MJ, Goss PE, Barman P, Carlson EE, Sinnwell JP, Tang X, Goetz MP, Chen BE, Cairns J, Weinshilboum RM, Wang L.
Pharmacogenet Genomics. 2019 Oct;29(8):183-191. doi: 10.1097/FPC.0000000000000382.

59.  Comparison of (99m)Tc-Sestamibi Molecular Breast Imaging and Breast MRI in Patients With Invasive Breast Cancer Receiving Neoadjuvant Chemotherapy.
Hunt KN, Conners AL, Goetz MP, O'Connor MK, Suman V, Kalari K, Weinshilboum R, Wang L, Carter J, McLaughlin S, Aspitia AM, Gray R, Northfelt D, Boughey JC.
AJR Am J Roentgenol. 2019 Oct;213(4):932-943. doi: 10.2214/AJR.18.20628.

60.  Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders.
Saffouri GB, Shields-Cutler RR, Chen J, Yang Y, Lekatz HR, Hale VL, Cho JM, Battaglioli EJ, Bhattarai Y, Thompson KJ, Kalari KK, Behera G, Berry JC, Peters SA, Patel R, Schuetz AN, Faith JJ, Camilleri M, Sonnenburg JL, Farrugia G, Swann JR, Grover M, Knights D, Kashyap PC.
Nat Commun. 2019 May 1;10(1):2012. doi: 10.1038/s41467-019-09964-7.

61.  Cell-level somatic mutation detection from single-cell RNA sequencing.
Vu TN, Nguyen HN, Calza S, Kalari KR, Wang L, Pawitan Y.
Bioinformatics. 2019 Nov 1;35(22):4679-4687. doi: 10.1093/bioinformatics/btz288.

62.  The lncRNA MIR2052HG regulates ERα levels and aromatase inhibitor resistance through LMTK3 by recruiting EGR1.
Cairns J, Ingle JN, Kalari KR, Shepherd LE, Kubo M, Goetz MP, Weinshilboum RM, Wang L.
Breast Cancer Res. 2019 Apr 3;21(1):47. doi: 10.1186/s13058-019-1130-3.

63.  PANOPLY: Omics-Guided Drug Prioritization Method Tailored to an Individual Patient.
Kalari KR, Sinnwell JP, Thompson KJ, Tang X, Carlson EE, Yu J, Vedell PT, Ingle JN, Weinshilboum RM, Boughey JC, Wang L, Goetz MP, Suman V.
JCO Clin Cancer Inform. 2018 Dec;2 doi: 10.1200/CCI.18.00012.

64.  Anastrozole Aromatase Inhibitor Plasma Drug Concentration Genome-Wide Association Study: Functional Epistatic Interaction Between SLC38A7 and ALPPL2.
Dudenkov TM, Liu D, Cairns J, Devarajan S, Zhuang Y, Ingle JN, Buzdar AU, Robson ME, Kubo M, Batzler A, Barman P, Jenkins GD, Carlson EE, Goetz MP, Northfelt DW, Moreno-Aspitia A, Desta Z, Reid JM, Kalari KR, Wang L, Weinshilboum RM.
Clin Pharmacol Ther. 2019 Jul;106(1):219-227. doi: 10.1002/cpt.1359.

65.  Your brain scan may be a reflection of your genes.
Lowe VJ, Kalari KR, Kandimalla KK.
Brain. 2018 Sep 1;141(9):2539-2541. doi: 10.1093/brain/awy226.

66.  ATR Inhibition Is a Promising Radiosensitizing Strategy for Triple-Negative Breast Cancer.
Tu X, Kahila MM, Zhou Q, Yu J, Kalari KR, Wang L, Harmsen WS, Yuan J, Boughey JC, Goetz MP, Sarkaria JN, Lou Z, Mutter RW.
Mol Cancer Ther. 2018 Nov;17(11):2462-2472. doi: 10.1158/1535-7163.MCT-18-0470.

67.  HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data.
Baheti S, Tang X, O'Brien DR, Chia N, Roberts LR, Nelson H, Boughey JC, Wang L, Goetz MP, Kocher JA, Kalari KR.
BMC Bioinformatics. 2018 Jul 17;19(1):271. doi: 10.1186/s12859-018-2260-9.

68.  Machine Learning Helps Identify New Drug Mechanisms in Triple-Negative Breast Cancer.
Athreya AP, Gaglio AJ, Cairns J, Kalari KR, Weinshilboum RM, Wang L, Kalbarczyk ZT, Iyer RK.
IEEE Trans Nanobioscience. 2018 Jul;17(3):251-259. doi: 10.1109/TNB.2018.2851997.

69.  Single Nucleotide Polymorphisms (SNPs) Distant from Xenobiotic Response Elements Can Modulate Aryl Hydrocarbon Receptor Function: SNP-Dependent CYP1A1 Induction.
Liu D, Qin S, Ray B, Kalari KR, Wang L, Weinshilboum RM.
Drug Metab Dispos. 2018 Sep;46(9):1372-1381. doi: 10.1124/dmd.118.082164.

70.  Gene expression in the corneal endothelium of Fuchs endothelial corneal dystrophy patients with and without expansion of a trinucleotide repeat in TCF4.
Wieben ED, Aleff RA, Tang X, Kalari KR, Maguire LJ, Patel SV, Baratz KH, Fautsch MP.
PLoS One. 2018;13(7):e0200005. doi: 10.1371/journal.pone.0200005.

71.  Germline genome-wide association studies in women receiving neoadjuvant chemotherapy with or without bevacizumab.
Ingle JN, Kalari KR, Wickerham DL, von Minckwitz G, Fasching PA, Furukawa Y, Mushiroda T, Goetz MP, Barman P, Carlson EE, Rastogi P, Costantino JP, Cairns J, Paik S, Bear HD, Kubo M, Wang L, Wolmark N, Weinshilboum RM.
Pharmacogenet Genomics. 2018 Jun;28(6):147-152. doi: 10.1097/FPC.0000000000000337.

72.  DNA methyltransferase expression in triple-negative breast cancer predicts sensitivity to decitabine.
Yu J, Qin B, Moyer AM, Nowsheen S, Liu T, Qin S, Zhuang Y, Liu D, Lu SW, Kalari KR, Visscher DW, Copland JA, McLaughlin SA, Moreno-Aspitia A, Northfelt DW, Gray RJ, Lou Z, Suman VJ, Weinshilboum R, Boughey JC, Goetz MP, Wang L.
J Clin Invest. 2018 Jun 1;128(6):2376-2388. doi: 10.1172/JCI97924.

73.  Discovery of a Glucocorticoid Receptor (GR) Activity Signature Using Selective GR Antagonism in ER-Negative Breast Cancer.
West DC, Kocherginsky M, Tonsing-Carter EY, Dolcen DN, Hosfield DJ, Lastra RR, Sinnwell JP, Thompson KJ, Bowie KR, Harkless RV, Skor MN, Pierce CF, Styke SC, Kim CR, de Wet L, Greene GL, Boughey JC, Goetz MP, Kalari KR, Wang L, Fleming GF, Györffy B, Conzen SD.
Clin Cancer Res. 2018 Jul 15;24(14):3433-3446. doi: 10.1158/1078-0432.CCR-17-2793.

74.  Pathway-Based Analysis of Genome-Wide Association Data Identified SNPs in HMMR as Biomarker for Chemotherapy- Induced Neutropenia in Breast Cancer Patients.
Bidadi B, Liu D, Kalari KR, Rubner M, Hein A, Beckmann MW, Rack B, Janni W, Fasching PA, Weinshilboum RM, Wang L.
Front Pharmacol. 2018;9 doi: 10.3389/fphar.2018.00158.

75.  Isoform-level gene expression patterns in single-cell RNA-sequencing data.
Vu TN, Wills QF, Kalari KR, Niu N, Wang L, Pawitan Y, Rantalainen M.
Bioinformatics. 2018 Jul 15;34(14):2392-2400. doi: 10.1093/bioinformatics/bty100.

76.  Differential Effects of Alzheimer's Disease Aβ40 and 42 on Endocytosis and Intraneuronal Trafficking.
Omtri RS, Thompson KJ, Tang X, Gali CC, Panzenboeck U, Davidson MW, Kalari KR, Kandimalla KK.
Neuroscience. 2018 Mar 1;373 doi: 10.1016/j.neuroscience.2018.01.003.

77.  Beta-defensin 1, aryl hydrocarbon receptor and plasma kynurenine in major depressive disorder: metabolomics-informed genomics.
Liu D, Ray B, Neavin DR, Zhang J, Athreya AP, Biernacka JM, Bobo WV, Hall-Flavin DK, Skime MK, Zhu H, Jenkins GD, Batzler A, Kalari KR, Boakye-Agyeman F, Matson WR, Bhasin SS, Mushiroda T, Nakamura Y, Kubo M, Iyer RK, Wang L, Frye MA, Kaddurah-Daouk R, Weinshilboum RM.
Transl Psychiatry. 2018 Jan 10;8(1):10. doi: 10.1038/s41398-017-0056-8.

78.  Establishing and characterizing patient-derived xenografts using pre-chemotherapy percutaneous biopsy and post-chemotherapy surgical samples from a prospective neoadjuvant breast cancer study.
Yu J, Qin B, Moyer AM, Sinnwell JP, Thompson KJ, Copland JA 3rd, Marlow LA, Miller JL, Yin P, Gao B, Minter-Dykhouse K, Tang X, McLaughlin SA, Moreno-Aspitia A, Schweitzer A, Lu Y, Hubbard J, Northfelt DW, Gray RJ, Hunt K, Conners AL, Suman VJ, Kalari KR, Ingle JN, Lou Z, Visscher DW, Weinshilboum R, Boughey JC, Goetz MP, Wang L.
Breast Cancer Res. 2017 Dec 6;19(1):130. doi: 10.1186/s13058-017-0920-8.

79.  A comprehensive analysis of breast cancer microbiota and host gene expression.
Thompson KJ, Ingle JN, Tang X, Chia N, Jeraldo PR, Walther-Antonio MR, Kandimalla KK, Johnson S, Yao JZ, Harrington SC, Suman VJ, Wang L, Weinshilboum RL, Boughey JC, Kocher JP, Nelson H, Goetz MP, Kalari KR.
PLoS One. 2017;12(11):e0188873. doi: 10.1371/journal.pone.0188873.

80.  Vitamin D Levels, Vitamin D Receptor Polymorphisms, and Inflammatory Cytokines in Aromatase Inhibitor-Induced Arthralgias: An Analysis of CCTG MA.27.
Niravath P, Chen B, Chapman JW, Agarwal SK, Welschhans RL, Bongartz T, Kalari KR, Shepherd LE, Bartlett J, Pritchard K, Gelmon K, Hilsenbeck SG, Rimawi MF, Osborne CK, Goss PE, Ingle JN.
Clin Breast Cancer. 2018 Feb;18(1):78-87. doi: 10.1016/j.clbc.2017.10.009.

81.  A prospective genome-wide study of prostate cancer metastases reveals association of wnt pathway activation and increased cell cycle proliferation with primary resistance to abiraterone acetate-prednisone.
Wang L, Dehm SM, Hillman DW, Sicotte H, Tan W, Gormley M, Bhargava V, Jimenez R, Xie F, Yin P, Qin S, Quevedo F, Costello BA, Pitot HC, Ho T, Bryce AH, Ye Z, Li Y, Eiken P, Vedell PT, Barman P, McMenomy BP, Atwell TD, Carlson RE, Ellingson M, Eckloff BW, Qin R, Ou F, Hart SN, Huang H, Jen J, Wieben ED, Kalari KR, Weinshilboum RM, Wang L, Kohli M.
Ann Oncol. 2018 Feb 1;29(2):352-360. doi: 10.1093/annonc/mdx689.

82.  Impact of histopathology, tumor-infiltrating lymphocytes, and adjuvant chemotherapy on prognosis of triple-negative breast cancer.
Leon-Ferre RA, Polley MY, Liu H, Gilbert JA, Cafourek V, Hillman DW, Elkhanany A, Akinhanmi M, Lilyquist J, Thomas A, Negron V, Boughey JC, Liu MC, Ingle JN, Kalari KR, Couch FJ, Visscher DW, Goetz MP.
Breast Cancer Res Treat. 2018 Jan;167(1):89-99. doi: 10.1007/s10549-017-4499-7.

83.  Breast cancer chemoprevention pharmacogenomics: Deep sequencing and functional genomics of the ZNF423 and CTSO genes.
Liu D, Ho MF, Schaid DJ, Scherer SE, Kalari K, Liu M, Biernacka J, Yee V, Evans J, Carlson E, Goetz MP, Kubo M, Wickerham DL, Wang L, Ingle JN, Weinshilboum RM.
NPJ Breast Cancer. 2017;3 doi: 10.1038/s41523-017-0036-4.

84.  Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistance.
Emad A, Cairns J, Kalari KR, Wang L, Sinha S.
Genome Biol. 2017 Aug 11;18(1):153. doi: 10.1186/s13059-017-1282-3.

85.  TCL1A Single-Nucleotide Polymorphisms and Estrogen-Mediated Toll-Like Receptor-MYD88-Dependent Nuclear Factor-κB Activation: Single-Nucleotide Polymorphism- and Selective Estrogen Receptor Modulator-Dependent Modification of Inflammation and Immune Response.
Ho MF, Ingle JN, Bongartz T, Kalari KR, Goss PE, Shepherd LE, Mushiroda T, Kubo M, Wang L, Weinshilboum RM.
Mol Pharmacol. 2017 Aug;92(2):175-184. doi: 10.1124/mol.117.108340.

86.  SLCO1B1 polymorphisms and plasma estrone conjugates in postmenopausal women with ER+ breast cancer: genome-wide association studies of the estrone pathway.
Dudenkov TM, Ingle JN, Buzdar AU, Robson ME, Kubo M, Ibrahim-Zada I, Batzler A, Jenkins GD, Pietrzak TL, Carlson EE, Barman P, Goetz MP, Northfelt DW, Moreno-Aspita A, Williard CV, Kalari KR, Nakamura Y, Wang L, Weinshilboum RM.
Breast Cancer Res Treat. 2017 Jul;164(1):189-199. doi: 10.1007/s10549-017-4243-3.

87.  Model-based unsupervised learning informs metformin-induced cell-migration inhibition through an AMPK-independent mechanism in breast cancer.
Athreya AP, Kalari KR, Cairns J, Gaglio AJ, Wills QF, Niu N, Weinshilboum R, Iyer RK, Wang L.
Oncotarget. 2017 Apr 18;8(16):27199-27215. doi: 10.18632/oncotarget.16109.

88.  Tumor Sequencing and Patient-Derived Xenografts in the Neoadjuvant Treatment of Breast Cancer.
Goetz MP, Kalari KR, Suman VJ, Moyer AM, Yu J, Visscher DW, Dockter TJ, Vedell PT, Sinnwell JP, Tang X, Thompson KJ, McLaughlin SA, Moreno-Aspitia A, Copland JA, Northfelt DW, Gray RJ, Hunt K, Conners A, Sicotte H, Eckel-Passow JE, Kocher JP, Ingle JN, Ellingson MS, McDonough M, Wieben ED, Weinshilboum R, Wang L, Boughey JC.
J Natl Cancer Inst. 2017 Jul 1;109(7) doi: 10.1093/jnci/djw306.

89.  Metformin pharmacogenomics: a genome-wide association study to identify genetic and epigenetic biomarkers involved in metformin anticancer response using human lymphoblastoid cell lines.
Niu N, Liu T, Cairns J, Ly RC, Tan X, Deng M, Fridley BL, Kalari KR, Abo RP, Jenkins G, Batzler A, Carlson EE, Barman P, Moran S, Heyn H, Esteller M, Wang L.
Hum Mol Genet. 2016 Nov 1;25(21):4819-4834. doi: 10.1093/hmg/ddw301.

90.  Trinucleotide Repeat Expansion in the Transcription Factor 4 (TCF4) Gene Leads to Widespread mRNA Splicing Changes in Fuchs' Endothelial Corneal Dystrophy.
Wieben ED, Aleff RA, Tang X, Butz ML, Kalari KR, Highsmith EW, Jen J, Vasmatzis G, Patel SV, Maguire LJ, Baratz KH, Fautsch MP.
Invest Ophthalmol Vis Sci. 2017 Jan 1;58(1):343-352. doi: 10.1167/iovs.16-20900.

91.  Circular RNAs and their associations with breast cancer subtypes.
Nair AA, Niu N, Tang X, Thompson KJ, Wang L, Kocher JP, Subramanian S, Kalari KR.
Oncotarget. 2016 Dec 6;7(49):80967-80979. doi: 10.18632/oncotarget.13134.

92.  Genetic Polymorphisms in the Long Noncoding RNA MIR2052HG Offer a Pharmacogenomic Basis for the Response of Breast Cancer Patients to Aromatase Inhibitor Therapy.
Ingle JN, Xie F, Ellis MJ, Goss PE, Shepherd LE, Chapman JW, Chen BE, Kubo M, Furukawa Y, Momozawa Y, Stearns V, Pritchard KI, Barman P, Carlson EE, Goetz MP, Weinshilboum RM, Kalari KR, Wang L.
Cancer Res. 2016 Dec 1;76(23):7012-7023. doi: 10.1158/0008-5472.CAN-16-1371.

93.  The Microbiome of Aseptically Collected Human Breast Tissue in Benign and Malignant Disease.
Hieken TJ, Chen J, Hoskin TL, Walther-Antonio M, Johnson S, Ramaker S, Xiao J, Radisky DC, Knutson KL, Kalari KR, Yao JZ, Baddour LM, Chia N, Degnim AC.
Sci Rep. 2016 Aug 3;6 doi: 10.1038/srep30751.

94.  Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls.
Chen J, Chia N, Kalari KR, Yao JZ, Novotna M, Paz Soldan MM, Luckey DH, Marietta EV, Jeraldo PR, Chen X, Weinshenker BG, Rodriguez M, Kantarci OH, Nelson H, Murray JA, Mangalam AK.
Sci Rep. 2016 Jun 27;6 doi: 10.1038/srep28484.

95.  Clonal expansion of antitumor T cells in breast cancer correlates with response to neoadjuvant chemotherapy.
Park JH, Jang M, Tarhan YE, Katagiri T, Sasa M, Miyoshi Y, Kalari KR, Suman VJ, Weinshilboum R, Wang L, Boughey JC, Goetz MP, Nakamura Y.
Int J Oncol. 2016 Aug;49(2):471-8. doi: 10.3892/ijo.2016.3540.

96.  Beta-Poisson model for single-cell RNA-seq data analyses.
Vu TN, Wills QF, Kalari KR, Niu N, Wang L, Rantalainen M, Pawitan Y.
Bioinformatics. 2016 Jul 15;32(14):2128-35. doi: 10.1093/bioinformatics/btw202.

97.  Determining the frequency of pathogenic germline variants from exome sequencing in patients with castrate-resistant prostate cancer.
Hart SN, Ellingson MS, Schahl K, Vedell PT, Carlson RE, Sinnwell JP, Barman P, Sicotte H, Eckel-Passow JE, Wang L, Kalari KR, Qin R, Kruisselbrink TM, Jimenez RE, Bryce AH, Tan W, Weinshilboum R, Wang L, Kohli M.
BMJ Open. 2016 Apr 15;6(4):e010332. doi: 10.1136/bmjopen-2015-010332.

98.  BBBomics-Human Blood Brain Barrier Transcriptomics Hub.
Kalari KR, Thompson KJ, Nair AA, Tang X, Bockol MA, Jhawar N, Swaminathan SK, Lowe VJ, Kandimalla KK.
Front Neurosci. 2016;10 doi: 10.3389/fnins.2016.00071.

99.  TSPAN5, ERICH3 and selective serotonin reuptake inhibitors in major depressive disorder: pharmacometabolomics-informed pharmacogenomics.
Gupta M, Neavin D, Liu D, Biernacka J, Hall-Flavin D, Bobo WV, Frye MA, Skime M, Jenkins GD, Batzler A, Kalari K, Matson W, Bhasin SS, Zhu H, Mushiroda T, Nakamura Y, Kubo M, Wang L, Kaddurah-Daouk R, Weinshilboum RM.
Mol Psychiatry. 2016 Dec;21(12):1717-1725. doi: 10.1038/mp.2016.6.

100.  Estrogen, SNP-Dependent Chemokine Expression and Selective Estrogen Receptor Modulator Regulation.
Ho MF, Bongartz T, Liu M, Kalari KR, Goss PE, Shepherd LE, Goetz MP, Kubo M, Ingle JN, Wang L, Weinshilboum RM.
Mol Endocrinol. 2016 Mar;30(3):382-98. doi: 10.1210/me.2015-1267.

101.  A cell cycle-dependent BRCA1-UHRF1 cascade regulates DNA double-strand break repair pathway choice.
Zhang H, Liu H, Chen Y, Yang X, Wang P, Liu T, Deng M, Qin B, Correia C, Lee S, Kim J, Sparks M, Nair AA, Evans DL, Kalari KR, Zhang P, Wang L, You Z, Kaufmann SH, Lou Z, Pei H.
Nat Commun. 2016 Jan 5;7 doi: 10.1038/ncomms10201.

102.  Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.
Shameer K, Tripathi LP, Kalari KR, Dudley JT, Sowdhamini R.
Brief Bioinform. 2016 Sep;17(5):841-62. doi: 10.1093/bib/bbv084.

103.  Exome sequencing reveals frequent deleterious germline variants in cancer susceptibility genes in women with invasive breast cancer undergoing neoadjuvant chemotherapy.
Ellingson MS, Hart SN, Kalari KR, Suman V, Schahl KA, Dockter TJ, Felten SJ, Sinnwell JP, Thompson KJ, Tang X, Vedell PT, Barman P, Sicotte H, Eckel-Passow JE, Northfelt DW, Gray RJ, McLaughlin SA, Moreno-Aspitia A, Ingle JN, Moyer AM, Visscher DW, Jones K, Conners A, McDonough M, Wieben ED, Wang L, Weinshilboum R, Boughey JC, Goetz MP.
Breast Cancer Res Treat. 2015 Sep;153(2):435-43. doi: 10.1007/s10549-015-3545-6.

104.  Correction: Folate receptor-α (FOLR1) expression and function in triple negative tumors.
Necela BM, Crozier JA, Andorfer CA, Lewis-Tuffin L, Kachergus JM, Geiger XJ, Kalari KR, Serie DJ, Sun Z, Moreno-Aspitia A, O'Shannessy DJ, Maltzman JD, McCullough AE, Pockaj BA, Cunliffe HE, Ballman KV, Thompson EA, Perez EA.
PLoS One. 2015;10(4):e0127133. doi: 10.1371/journal.pone.0127133.

105.  Folate receptor-α (FOLR1) expression and function in triple negative tumors.
Necela BM, Crozier JA, Andorfer CA, Lewis-Tuffin L, Kachergus JM, Geiger XJ, Kalari KR, Serie DJ, Sun Z, Moreno-Aspitia A, O'Shannessy DJ, Maltzman JD, McCullough AE, Pockaj BA, Cunliffe HE, Ballman KV, Thompson EA, Perez EA.
PLoS One. 2015;10(3):e0122209. doi: 10.1371/journal.pone.0122209.

106.  Identification of genetic variants or genes that are associated with Homoharringtonine (HHT) response through a genome-wide association study in human lymphoblastoid cell lines (LCLs).
Tong Y, Niu N, Jenkins G, Batzler A, Li L, Kalari KR, Wang L.
Front Genet. 2014;5 doi: 10.3389/fgene.2014.00465.

107.  Genomic analysis reveals that immune function genes are strongly linked to clinical outcome in the North Central Cancer Treatment Group n9831 Adjuvant Trastuzumab Trial.
Perez EA, Thompson EA, Ballman KV, Anderson SK, Asmann YW, Kalari KR, Eckel-Passow JE, Dueck AC, Tenner KS, Jen J, Fan JB, Geiger XJ, McCullough AE, Chen B, Jenkins RB, Sledge GW, Winer EP, Gralow JR, Reinholz MM.
J Clin Oncol. 2015 Mar 1;33(7):701-8. doi: 10.1200/JCO.2014.57.6298.

108.  RNA toxicity and missplicing in the common eye disease fuchs endothelial corneal dystrophy.
Du J, Aleff RA, Soragni E, Kalari K, Nie J, Tang X, Davila J, Kocher JP, Patel SV, Gottesfeld JM, Baratz KH, Wieben ED.
J Biol Chem. 2015 Mar 6;290(10):5979-90. doi: 10.1074/jbc.M114.621607.

109.  IM-TORNADO: a tool for comparison of 16S reads from paired-end libraries.
Jeraldo P, Kalari K, Chen X, Bhavsar J, Mangalam A, White B, Nelson H, Kocher JP, Chia N.
PLoS One. 2014;9(12):e114804. doi: 10.1371/journal.pone.0114804.

110.  Loss of heterozygosity at the CYP2D6 locus in breast cancer: implications for germline pharmacogenetic studies.
Goetz MP, Sun JX, Suman VJ, Silva GO, Perou CM, Nakamura Y, Cox NJ, Stephens PJ, Miller VA, Ross JS, Chen D, Safgren SL, Kuffel MJ, Ames MM, Kalari KR, Gomez HL, Gonzalez-Angulo AM, Burgues O, Brauch HB, Ingle JN, Ratain MJ, Yelensky R.
J Natl Cancer Inst. 2014 Dec 8;107(2) doi: 10.1093/jnci/dju401.

111.  The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data.
Tang X, Baheti S, Shameer K, Thompson KJ, Wills Q, Niu N, Holcomb IN, Boutet SC, Ramakrishnan R, Kachergus JM, Kocher JP, Weinshilboum RM, Wang L, Thompson EA, Kalari KR.
Nucleic Acids Res. 2014 Dec 16;42(22):e172. doi: 10.1093/nar/gku1005.

112.  Estrogens and their precursors in postmenopausal women with early breast cancer receiving anastrozole.
Ingle JN, Kalari KR, Buzdar AU, Robson ME, Goetz MP, Desta Z, Barman P, Dudenkov TT, Northfelt DW, Perez EA, Flockhart DA, Williard CV, Wang L, Weinshilboum RM.
Steroids. 2015 Jul;99(Pt A):32-8. doi: 10.1016/j.steroids.2014.08.007.

113.  MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing.
Kalari KR, Nair AA, Bhavsar JD, O'Brien DR, Davila JI, Bockol MA, Nie J, Tang X, Baheti S, Doughty JB, Middha S, Sicotte H, Thompson AE, Asmann YW, Kocher JP.
BMC Bioinformatics. 2014 Jun 27;15 doi: 10.1186/1471-2105-15-224.

114.  Inverse association between programmed death ligand 1 and genes in the VEGF pathway in primary clear cell renal cell carcinoma.
Joseph RW, Parasramka M, Eckel-Passow JE, Serie D, Wu K, Jiang L, Kalari K, Thompson RH, Huu Ho T, Castle EP, Cheville J, Kwon ED, Thompson EA, Parker A.
Cancer Immunol Res. 2013 Dec;1(6):378-85. doi: 10.1158/2326-6066.CIR-13-0042.

115.  Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines.
Li L, Fridley BL, Kalari K, Niu N, Jenkins G, Batzler A, Abo RP, Schaid D, Wang L.
BMC Genomics. 2014 Feb 1;15 doi: 10.1186/1471-2164-15-93.

116.  Transcriptome-wide analysis of UTRs in non-small cell lung cancer reveals cancer-related genes with SNV-induced changes on RNA secondary structure and miRNA target sites.
Sabarinathan R, Wenzel A, Novotny P, Tang X, Kalari KR, Gorodkin J.
PLoS One. 2014;9(1):e82699. doi: 10.1371/journal.pone.0082699.

117.  Gene expression, single nucleotide variant and fusion transcript discovery in archival material from breast tumors.
Norton N, Sun Z, Asmann YW, Serie DJ, Necela BM, Bhagwate A, Jen J, Eckloff BW, Kalari KR, Thompson KJ, Carr JM, Kachergus JM, Geiger XJ, Perez EA, Thompson EA.
PLoS One. 2013;8(11):e81925. doi: 10.1371/journal.pone.0081925.

118.  An integrated model of the transcriptome of HER2-positive breast cancer.
Kalari KR, Necela BM, Tang X, Thompson KJ, Lau M, Eckel-Passow JE, Kachergus JM, Anderson SK, Sun Z, Baheti S, Carr JM, Baker TR, Barman P, Radisky DC, Joseph RW, McLaughlin SA, Chai HS, Camille S, Rossell D, Asmann YW, Thompson EA, Perez EA.
PLoS One. 2013;8(11):e79298. doi: 10.1371/journal.pone.0079298.

119.  Impact of library preparation on downstream analysis and interpretation of RNA-Seq data: comparison between Illumina PolyA and NuGEN Ovation protocol.
Sun Z, Asmann YW, Nair A, Zhang Y, Wang L, Kalari KR, Bhagwate AV, Baker TR, Carr JM, Kocher JP, Perez EA, Thompson EA.
PLoS One. 2013;8(8):e71745. doi: 10.1371/journal.pone.0071745.

120.  Transcriptome analysis of garlic-induced hepatoprotection against alcoholic fatty liver.
Raghu R, Liu CT, Tsai MH, Tang X, Kalari KR, Subramanian S, Sheen LY.
J Agric Food Chem. 2012 Nov 7;60(44):11104-19. doi: 10.1021/jf303800p.

121.  Genetic association with overall survival of taxane-treated lung cancer patients - a genome-wide association study in human lymphoblastoid cell lines followed by a clinical association study.
Niu N, Schaid DJ, Abo RP, Kalari K, Fridley BL, Feng Q, Jenkins G, Batzler A, Brisbin AG, Cunningham JM, Li L, Sun Z, Yang P, Wang L.
BMC Cancer. 2012 Sep 24;12 doi: 10.1186/1471-2407-12-422.

122.  Deep Sequence Analysis of Non-Small Cell Lung Cancer: Integrated Analysis of Gene Expression, Alternative Splicing, and Single Nucleotide Variations in Lung Adenocarcinomas with and without Oncogenic KRAS Mutations.
Kalari KR, Rossell D, Necela BM, Asmann YW, Nair A, Baheti S, Kachergus JM, Younkin CS, Baker T, Carr JM, Tang X, Walsh MP, Chai HS, Sun Z, Hart SN, Leontovich AA, Hossain A, Kocher JP, Perez EA, Reisman DN, Fields AP, Thompson EA.
Front Oncol. 2012;2 doi: 10.3389/fonc.2012.00012.

123.  Detection of redundant fusion transcripts as biomarkers or disease-specific therapeutic targets in breast cancer.
Asmann YW, Necela BM, Kalari KR, Hossain A, Baker TR, Carr JM, Davis C, Getz JE, Hostetter G, Li X, McLaughlin SA, Radisky DC, Schroth GP, Cunliffe HE, Perez EA, Thompson EA.
Cancer Res. 2012 Apr 15;72(8):1921-8. doi: 10.1158/0008-5472.CAN-11-3142.

124.  Gemcitabine metabolic pathway genetic polymorphisms and response in patients with non-small cell lung cancer.
Li L, Schaid DJ, Fridley BL, Kalari KR, Jenkins GD, Abo RP, Batzler A, Moon I, Pelleymounter L, Eckloff BW, Wieben ED, Sun Z, Yang P, Wang L.
Pharmacogenet Genomics. 2012 Feb;22(2):105-16. doi: 10.1097/FPC.0b013e32834dd7e2.

125.  TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data.
Asmann YW, Middha S, Hossain A, Baheti S, Li Y, Chai HS, Sun Z, Duffy PH, Hadad AA, Nair A, Liu X, Zhang Y, Klee EW, Kalari KR, Kocher JP.
Bioinformatics. 2012 Jan 15;28(2):277-8. doi: 10.1093/bioinformatics/btr612.

126.  Detecting gene-gene interactions in prostate disease in African American men.
Reams RR, Kalari KR, Wang H, Odedina FT, Soliman KF, Yates C.
Infect Agent Cancer. 2011 Sep 23;6 Suppl 2(Suppl 2):S1. doi: 10.1186/1750-9378-6-S2-S1.

127.  Gemcitabine Cytotoxicity: Interaction of Efflux and Deamination.
Rudin D, Li L, Niu N, Kalari KR, Gilbert JA, Ames MM, Wang L.
J Drug Metab Toxicol. 2011 Feb 2;2(107):1-10. doi: 10.4172/2157-7609.1000107.

128.  A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines.
Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, Chai HS, Williamson DW, Radisky D, Schroth GP, Kocher JP, Perez EA, Thompson EA.
Nucleic Acids Res. 2011 Aug;39(15):e100. doi: 10.1093/nar/gkr362.

129.  Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing.
Sun Z, Asmann YW, Kalari KR, Bot B, Eckel-Passow JE, Baker TR, Carr JM, Khrebtukova I, Luo S, Zhang L, Schroth GP, Perez EA, Thompson EA.
PLoS One. 2011 Feb 25;6(2):e17490. doi: 10.1371/journal.pone.0017490.

130.  Acetaminophen-NAPQI hepatotoxicity: a cell line model system genome-wide association study.
Moyer AM, Fridley BL, Jenkins GD, Batzler AJ, Pelleymounter LL, Kalari KR, Ji Y, Chai Y, Nordgren KK, Weinshilboum RM.
Toxicol Sci. 2011 Mar;120(1):33-41. doi: 10.1093/toxsci/kfq375.

131.  Betaine-homocysteine methyltransferase: human liver genotype-phenotype correlation.
Feng Q, Kalari K, Fridley BL, Jenkins G, Ji Y, Abo R, Hebbring S, Zhang J, Nye MD, Leeder JS, Weinshilboum RM.
Mol Genet Metab. 2011 Feb;102(2):126-33. doi: 10.1016/j.ymgme.2010.10.010.

132.  Protein kinase Cι expression and oncogenic signaling mechanisms in cancer.
Murray NR, Kalari KR, Fields AP.
J Cell Physiol. 2011 Apr;226(4):879-87. doi: 10.1002/jcp.22463.

133.  Radiation pharmacogenomics: a genome-wide association approach to identify radiation response biomarkers using human lymphoblastoid cell lines.
Niu N, Qin Y, Fridley BL, Hou J, Kalari KR, Zhu M, Wu TY, Jenkins GD, Batzler A, Wang L.
Genome Res. 2010 Nov;20(11):1482-92. doi: 10.1101/gr.107672.110.

134.  Ecto-5'-nucleotidase and thiopurine cellular circulation: association with cytotoxicity.
Li F, Fridley BL, Matimba A, Kalari KR, Pelleymounter L, Moon I, Ji Y, Jenkins GD, Batzler A, Wang L, Weinshilboum RM.
Drug Metab Dispos. 2010 Dec;38(12):2329-38. doi: 10.1124/dmd.110.035220.

135.  Copy number variation and cytidine analogue cytotoxicity: a genome-wide association approach.
Kalari KR, Hebbring SJ, Chai HS, Li L, Kocher JP, Wang L, Weinshilboum RM.
BMC Genomics. 2010 Jun 4;11 doi: 10.1186/1471-2164-11-357.

136.  CD38 expression, function, and gene resequencing in a human lymphoblastoid cell line-based model system.
Hartman WR, Pelleymounter LL, Moon I, Kalari K, Liu M, Wu TY, Escande C, Nin V, Chini EN, Weinshilboum RM.
Leuk Lymphoma. 2010 Jul;51(7):1315-25. doi: 10.3109/10428194.2010.483299.

137.  Gemcitabine and arabinosylcytosin pharmacogenomics: genome-wide association and drug response biomarkers.
Li L, Fridley BL, Kalari K, Jenkins G, Batzler A, Weinshilboum RM, Wang L.
PLoS One. 2009 Nov 9;4(11):e7765. doi: 10.1371/journal.pone.0007765.

138.  FKBP51 affects cancer cell response to chemotherapy by negatively regulating Akt.
Pei H, Li L, Fridley BL, Jenkins GD, Kalari KR, Lingle W, Petersen G, Lou Z, Wang L.
Cancer Cell. 2009 Sep 8;16(3):259-66. doi: 10.1016/j.ccr.2009.07.016.

139.  Cytosolic 5'-nucleotidase III (NT5C3): gene sequence variation and functional genomics.
Aksoy P, Zhu MJ, Kalari KR, Moon I, Pelleymounter LL, Eckloff BW, Wieben ED, Yee VC, Weinshilboum RM, Wang L.
Pharmacogenet Genomics. 2009 Aug;19(8):567-76. doi: 10.1097/FPC.0b013e32832c14b8.

140.  Human S-adenosylhomocysteine hydrolase: common gene sequence variation and functional genomic characterization.
Feng Q, Keshtgarpour M, Pelleymounter LL, Moon I, Kalari KR, Eckloff BW, Wieben ED, Weinshilboum RM.
J Neurochem. 2009 Sep;110(6):1806-17. doi: 10.1111/j.1471-4159.2009.06276.x.

141.  Human glucocorticoid receptor alpha gene (NR3C1) pharmacogenomics: gene resequencing and functional genomics.
Niu N, Manickam V, Kalari KR, Moon I, Pelleymounter LL, Eckloff BW, Wieben ED, Schaid DJ, Wang L.
J Clin Endocrinol Metab. 2009 Aug;94(8):3072-84. doi: 10.1210/jc.2008-2109.

142.  Gemcitabine and cytosine arabinoside cytotoxicity: association with lymphoblastoid cell expression.
Li L, Fridley B, Kalari K, Jenkins G, Batzler A, Safgren S, Hildebrandt M, Ames M, Schaid D, Wang L.
Cancer Res. 2008 Sep 1;68(17):7050-8. doi: 10.1158/0008-5472.CAN-08-0405.

143.  A knowledge-based approach to predict intragenic deletions or duplications.
Kalari KR, Casavant TL, Scheetz TE.
Bioinformatics. 2008 Sep 15;24(18):1975-9. doi: 10.1093/bioinformatics/btn370.

144.  Proteasome beta subunit pharmacogenomics: gene resequencing and functional genomics.
Wang L, Kumar S, Fridley BL, Kalari KR, Moon I, Pelleymounter LL, Hildebrandt MA, Batzler A, Eckloff BW, Wieben ED, Greipp PR.
Clin Cancer Res. 2008 Jun 1;14(11):3503-13. doi: 10.1158/1078-0432.CCR-07-5150.

145.  First exons and introns--a survey of GC content and gene structure in the human genome.
Kalari KR, Casavant M, Bair TB, Keen HL, Comeron JM, Casavant TL, Scheetz TE.
In Silico Biol. 2006;6(3):237-42.