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Krishna R. Kalari, Ph.D. - Publications

Affiliations: 
2006 University of Iowa, Iowa City, IA 
Area:
Biomedical Engineering, Molecular Biology, Bioinformatics Biology, Pathology
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18 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
2018 Baheti S, Tang X, O'Brien DR, Chia N, Roberts LR, Nelson H, Boughey JC, Wang L, Goetz MP, Kocher JA, Kalari KR. HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data. Bmc Bioinformatics. 19: 271. PMID 30016933 DOI: 10.1186/S12859-018-2260-9  0.31
2018 Athreya AP, Gaglio AJ, Cairns J, Kalari KR, Weinshilboum RM, Wang L, Kalbarczyk ZT, Iyer RK. Machine Learning helps Identify New Drug Mechanisms in Triple-Negative Breast Cancer. Ieee Transactions On Nanobioscience. PMID 29994716 DOI: 10.1109/Tnb.2018.2851997  0.356
2018 Wieben ED, Aleff RA, Tang X, Kalari KR, Maguire LJ, Patel SV, Baratz KH, Fautsch MP. Gene expression in the corneal endothelium of Fuchs endothelial corneal dystrophy patients with and without expansion of a trinucleotide repeat in TCF4. Plos One. 13: e0200005. PMID 29966009 DOI: 10.1371/journal.pone.0200005  0.318
2018 Bidadi B, Liu D, Kalari KR, Rubner M, Hein A, Beckmann MW, Rack B, Janni W, Fasching PA, Weinshilboum RM, Wang L. Pathway-Based Analysis of Genome-Wide Association Data Identified SNPs inas Biomarker for Chemotherapy- Induced Neutropenia in Breast Cancer Patients. Frontiers in Pharmacology. 9: 158. PMID 29593529 DOI: 10.3389/Fphar.2018.00158  0.333
2017 Athreya AP, Kalari KR, Cairns J, Gaglio AJ, Wills QF, Niu N, Weinshilboum R, Iyer RK, Wang L. Model-based unsupervised learning informs metformin-induced cell-migration inhibition through an AMPK-independent mechanism in breast cancer. Oncotarget. 27199-27215. PMID 28423712 DOI: 10.18632/Oncotarget.16109  0.314
2016 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, et al. Metformin pharmacogenomics: a genome-wide association study to identify genetic and epigenetic biomarkers involved in metformin anticancer response using human lymphoblastoid cell lines. Human Molecular Genetics. 25: 4819-4834. PMID 28173075 DOI: 10.1093/Hmg/Ddw301  0.326
2016 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, et al. Metformin Pharmacogenomics: A genome-wide association study to identify genetic and epigenetic biomarkers involved in metformin anticancer response using human lymphoblastoid cell lines. Human Molecular Genetics. PMID 27616566 DOI: 10.1093/hmg/ddw301  0.326
2015 Shameer K, Tripathi LP, Kalari KR, Dudley JT, Sowdhamini R. Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment. Briefings in Bioinformatics. PMID 26494363 DOI: 10.1093/bib/bbv084  0.308
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  0.304
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  0.313
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  0.317
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  0.329
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  0.328
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  0.36
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  0.35
2009 Li L, Fridley BL, Kalari K, Jenkins G, Batzler A, Weinshilboum RM, Wang L. Gemcitabine and arabinosylcytosin pharmacogenomics: genome-wide association and drug response biomarkers. Plos One. 4: e7765. PMID 19898621 DOI: 10.1371/Journal.Pone.0007765  0.318
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  0.434
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  0.446
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