Krishna R. Kalari, Ph.D. - Publications

2006 University of Iowa, Iowa City, IA 
Biomedical Engineering, Molecular Biology, Bioinformatics Biology, Pathology

38 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 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. The Microbiome of Aseptically Collected Human Breast Tissue in Benign and Malignant Disease. Scientific Reports. 6: 30751. PMID 27485780 DOI: 10.1038/srep30751  0.44
2016 Chen J, Chia N, Kalari KR, Yao JZ, Novotna M, Soldan MM, Luckey DH, Marietta EV, Jeraldo PR, Chen X, Weinshenker BG, Rodriguez M, Kantarci OH, Nelson H, Murray JA, et al. Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls. Scientific Reports. 6: 28484. PMID 27346372 DOI: 10.1038/srep28484  0.44
2016 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, et al. Determining the frequency of pathogenic germline variants from exome sequencing in patients with castrate-resistant prostate cancer. Bmj Open. 6: e010332. PMID 27084275 DOI: 10.1136/bmjopen-2015-010332  0.44
2016 Kalari KR, Thompson KJ, Nair AA, Tang X, Bockol MA, Jhawar N, Swaminathan SK, Lowe VJ, Kandimalla KK. BBBomics-Human Blood Brain Barrier Transcriptomics Hub. Frontiers in Neuroscience. 10: 71. PMID 26973449 DOI: 10.3389/fnins.2016.00071  0.44
2016 Ho MF, Bongartz T, Liu M, Kalari KR, Goss PE, Shepherd LE, Goetz MP, Kubo M, Ingle JN, Wang L, Weinshilboum RM. Estrogen, SNP-Dependent Chemokine Expression and Selective Estrogen Receptor Modulator Regulation. Molecular Endocrinology (Baltimore, Md.). me20151267. PMID 26866883 DOI: 10.1210/me.2015-1267  0.44
2015 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, et al. Correction: Folate receptor-α (FOLR1) expression and function in triple negative tumors. Plos One. 10: e0127133. PMID 25928305 DOI: 10.1371/journal.pone.0127133  0.44
2015 Necela BM, Crozier JA, Andorfer CA, Lewis-Tuffin L, Kachergus JM, Geiger XJ, Kalari KR, Serie DJ, Sun Z, Aspita AM, O'Shannessy DJ, Maltzman JD, McCullough AE, Pockaj BA, Cunliffe HE, et al. Folate receptor-α (FOLR1) expression and function in triple negative tumors. Plos One. 10: e0122209. PMID 25816016 DOI: 10.1371/journal.pone.0122209  0.44
2015 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, et al. Genomic analysis reveals that immune function genes are strongly linked to clinical outcome in the North Central Cancer Treatment Group n9831 Adjuvant Trastuzumab Trial. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 33: 701-8. PMID 25605861 DOI: 10.1200/JCO.2014.57.6298  0.44
2015 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, et al. Loss of heterozygosity at the CYP2D6 locus in breast cancer: implications for germline pharmacogenetic studies. Journal of the National Cancer Institute. 107. PMID 25490892 DOI: 10.1093/jnci/dju401  0.44
2015 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. Estrogens and their precursors in postmenopausal women with early breast cancer receiving anastrozole. Steroids. 99: 32-8. PMID 25163006 DOI: 10.1016/j.steroids.2014.08.007  0.44
2015 Necela BM, Crazier JA, Andorfer CA, Lewis-Tuffin L, Kachergus JM, Geiger XJ, Kalari KR, Serie DJ, Sun Z, Aspita AM, O'Shannessy DJ, Maltzman JD, McCullough AE, Pockaj BA, Cunliffe HE, et al. Folate receptor-a (FOLR1) expression and function in triple negative tumors Plos One. 10. DOI: 10.1371/joumal.pone.0122209  0.44
2015 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, et al. Exome sequencing reveals frequent deleterious germline variants in cancer susceptibility genes in women with invasive breast cancer undergoing neoadjuvant chemotherapy Breast Cancer Research and Treatment. DOI: 10.1007/s10549-015-3545-6  0.44
2014 Tong Y, Niu N, Jenkins G, Batzler A, Li L, Kalari KR, Wang L. 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). Frontiers in Genetics. 5: 465. PMID 25628645 DOI: 10.3389/fgene.2014.00465  0.44
2014 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. The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data. Nucleic Acids Research. 42: e172. PMID 25352556 DOI: 10.1093/nar/gku1005  0.44
2014 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. MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing. Bmc Bioinformatics. 15: 224. PMID 24972667 DOI: 10.1186/1471-2105-15-224  0.44
2014 Sabarinathan R, Wenzel A, Novotny P, Tang X, Kalari KR, Gorodkin J. 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. Plos One. 9: e82699. PMID 24416147 DOI: 10.1371/journal.pone.0082699  0.44
2013 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. Gene expression, single nucleotide variant and fusion transcript discovery in archival material from breast tumors. Plos One. 8: e81925. PMID 24278466 DOI: 10.1371/journal.pone.0081925  0.44
2013 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, et al. An integrated model of the transcriptome of HER2-positive breast cancer. Plos One. 8: e79298. PMID 24223926 DOI: 10.1371/journal.pone.0079298  0.44
2013 Sun Z, Asmann YW, Nair A, Zhang Y, Wang L, Kalari KR, Bhagwate AV, Baker TR, Carr JM, Kocher JP, Perez EA, Thompson EA. Impact of library preparation on downstream analysis and interpretation of RNA-Seq data: comparison between Illumina PolyA and NuGEN Ovation protocol. Plos One. 8: e71745. PMID 23977132 DOI: 10.1371/journal.pone.0071745  0.44
2012 Raghu R, Liu CT, Tsai MH, Tang X, Kalari KR, Subramanian S, Sheen LY. Transcriptome analysis of garlic-induced hepatoprotection against alcoholic fatty liver. Journal of Agricultural and Food Chemistry. 60: 11104-19. PMID 23066854 DOI: 10.1021/jf303800p  0.44
2012 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, et al. 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. Frontiers in Oncology. 2: 12. PMID 22655260 DOI: 10.3389/fonc.2012.00012  0.44
2012 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, et al. Detection of redundant fusion transcripts as biomarkers or disease-specific therapeutic targets in breast cancer. Cancer Research. 72: 1921-8. PMID 22496456 DOI: 10.1158/0008-5472.CAN-11-3142  0.44
2012 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. Gemcitabine metabolic pathway genetic polymorphisms and response in patients with non-small cell lung cancer. Pharmacogenetics and Genomics. 22: 105-16. PMID 22173087 DOI: 10.1097/FPC.0b013e32834dd7e2  0.44
2012 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. TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. Bioinformatics (Oxford, England). 28: 277-8. PMID 22088845 DOI: 10.1093/bioinformatics/btr612  0.44
2011 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. A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines. Nucleic Acids Research. 39: e100. PMID 21622959 DOI: 10.1093/nar/gkr362  0.44
2011 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. Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing. Plos One. 6: e17490. PMID 21364760 DOI: 10.1371/journal.pone.0017490  0.44
2011 Moyer AM, Fridley BL, Jenkins GD, Batzler AJ, Pelleymounter LL, Kalari KR, Ji Y, Chai Y, Nordgren KK, Weinshilboum RM. Acetaminophen-NAPQI hepatotoxicity: a cell line model system genome-wide association study. Toxicological Sciences : An Official Journal of the Society of Toxicology. 120: 33-41. PMID 21177773 DOI: 10.1093/toxsci/kfq375  0.44
2011 Murray NR, Kalari KR, Fields AP. Protein kinase Cι expression and oncogenic signaling mechanisms in cancer. Journal of Cellular Physiology. 226: 879-87. PMID 20945390 DOI: 10.1002/jcp.22463  0.44
2010 Niu N, Qin Y, Fridley BL, Hou J, Kalari KR, Zhu M, Wu TY, Jenkins GD, Batzler A, Wang L. Radiation pharmacogenomics: a genome-wide association approach to identify radiation response biomarkers using human lymphoblastoid cell lines. Genome Research. 20: 1482-92. PMID 20923822 DOI: 10.1101/gr.107672.110  0.44
2010 Li F, Fridley BL, Matimba A, Kalari KR, Pelleymounter L, Moon I, Ji Y, Jenkins GD, Batzler A, Wang L, Weinshilboum RM. Ecto-5'-nucleotidase and thiopurine cellular circulation: association with cytotoxicity. Drug Metabolism and Disposition: the Biological Fate of Chemicals. 38: 2329-38. PMID 20855458 DOI: 10.1124/dmd.110.035220  0.44
2010 Kalari KR, Hebbring SJ, Chai HS, Li L, Kocher JP, Wang L, Weinshilboum RM. Copy number variation and cytidine analogue cytotoxicity: a genome-wide association approach. Bmc Genomics. 11: 357. PMID 20525348 DOI: 10.1186/1471-2164-11-357  0.44
2009 Pei H, Li L, Fridley BL, Jenkins GD, Kalari KR, Lingle W, Petersen G, Lou Z, Wang L. FKBP51 affects cancer cell response to chemotherapy by negatively regulating Akt. Cancer Cell. 16: 259-66. PMID 19732725 DOI: 10.1016/j.ccr.2009.07.016  0.44
2009 Aksoy P, Zhu MJ, Kalari KR, Moon I, Pelleymounter LL, Eckloff BW, Wieben ED, Yee VC, Weinshilboum RM, Wang L. Cytosolic 5'-nucleotidase III (NT5C3): gene sequence variation and functional genomics. Pharmacogenetics and Genomics. 19: 567-76. PMID 19623099 DOI: 10.1097/FPC.0b013e32832c14b8  0.44
2009 Feng Q, Keshtgarpour M, Pelleymounter LL, Moon I, Kalari KR, Eckloff BW, Wieben ED, Weinshilboum RM. Human S-adenosylhomocysteine hydrolase: common gene sequence variation and functional genomic characterization. Journal of Neurochemistry. 110: 1806-17. PMID 19619139 DOI: 10.1111/j.1471-4159.2009.06276.x  0.44
2009 Niu N, Manickam V, Kalari KR, Moon I, Pelleymounter LL, Eckloff BW, Wieben ED, Schaid DJ, Wang L. Human glucocorticoid receptor alpha gene (NR3C1) pharmacogenomics: gene resequencing and functional genomics. The Journal of Clinical Endocrinology and Metabolism. 94: 3072-84. PMID 19435830 DOI: 10.1210/jc.2008-2109  0.44
2008 Kalari KR, Casavant TL, Scheetz TE. A knowledge-based approach to predict intragenic deletions or duplications. Bioinformatics (Oxford, England). 24: 1975-9. PMID 18647756 DOI: 10.1093/bioinformatics/btn370  0.44
2008 Wang L, Kumar S, Fridley BL, Kalari KR, Moon I, Pelleymounter LL, Hildebrandt MA, Batzler A, Eckloff BW, Wieben ED, Greipp PR. Proteasome beta subunit pharmacogenomics: gene resequencing and functional genomics. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 14: 3503-13. PMID 18519783 DOI: 10.1158/1078-0432.CCR-07-5150  0.44
2006 Kalari KR, Casavant M, Bair TB, Keen HL, Comeron JM, Casavant TL, Scheetz TE. First exons and introns--a survey of GC content and gene structure in the human genome. In Silico Biology. 6: 237-42. PMID 16922687  0.44
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