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The relationship between vitamin D status and depression in a tactical athlete population.

Schaad KA, Bukhari AS, Brooks DI, Kocher JD, Barringer ND.

J Int Soc Sports Nutr. 2019 Sep 10;16(1):40. doi: 10.1186/s12970-019-0308-5.


Prognostic subclass of intrahepatic cholangiocarcinoma by integrative molecular-clinical analysis and potential targeted approach.

Ahn KS, O'Brien D, Kang YN, Mounajjed T, Kim YH, Kim TS, Kocher JA, Allotey LK, Borad MJ, Roberts LR, Kang KJ.

Hepatol Int. 2019 Jul;13(4):490-500. doi: 10.1007/s12072-019-09954-3. Epub 2019 Jun 18.


Recurrent MSC E116K mutations in ALK-negative anaplastic large cell lymphoma.

Luchtel RA, Zimmermann MT, Hu G, Dasari S, Jiang M, Oishi N, Jacobs HK, Zeng Y, Hundal T, Rech KL, Ketterling RP, Lee JH, Eckloff BW, Yan H, Gaonkar KS, Tian S, Ye Z, Kadin ME, Sidhu J, Jiang L, Voss J, Link BK, Syrbu SI, Facchetti F, Bennani NN, Slager SL, Ordog T, Kocher JP, Cerhan JR, Ansell SM, Feldman AL.

Blood. 2019 Jun 27;133(26):2776-2789. doi: 10.1182/blood.2019000626. Epub 2019 May 17.


Ccne1 Overexpression Causes Chromosome Instability in Liver Cells and Liver Tumor Development in Mice.

Aziz K, Limzerwala JF, Sturmlechner I, Hurley E, Zhang C, Jeganathan KB, Nelson G, Bronk S, Fierro Velasco RO, van Deursen EJ, O'Brien DR, Kocher JA, Youssef SA, van Ree JH, de Bruin A, van den Bos H, Spierings DCJ, Foijer F, van de Sluis B, Roberts LR, Gores GJ, Li H, van Deursen JM.

Gastroenterology. 2019 Jul;157(1):210-226.e12. doi: 10.1053/j.gastro.2019.03.016. Epub 2019 Mar 13.


Predict drug sensitivity of cancer cells with pathway activity inference.

Wang X, Sun Z, Zimmermann MT, Bugrim A, Kocher JP.

BMC Med Genomics. 2019 Jan 31;12(Suppl 1):15. doi: 10.1186/s12920-018-0449-4.


Detection and visualization of complex structural variants from long reads.

Stephens Z, Wang C, Iyer RK, Kocher JP.

BMC Bioinformatics. 2018 Dec 21;19(Suppl 20):508. doi: 10.1186/s12859-018-2539-x.


A data science approach for the classification of low-grade and high-grade ovarian serous carcinomas.

Lin S, Wang C, Zarei S, Bell DA, Kerr SE, Runger GC, Kocher JA.

BMC Genomics. 2018 Nov 27;19(1):841. doi: 10.1186/s12864-018-5177-9.


Novel Neural Network Approach to Predict Drug-Target Interactions Based on Drug Side Effects and Genome-Wide Association Studies.

Prinz J, Koohi-Moghadam M, Sun H, Kocher JA, Wang J.

Hum Hered. 2018;83(2):79-91. doi: 10.1159/000492574. Epub 2018 Oct 22.


Indel sensitive and comprehensive variant/mutation detection from RNA sequencing data for precision medicine.

Prodduturi N, Bhagwate A, Kocher JA, Sun Z.

BMC Med Genomics. 2018 Sep 14;11(Suppl 3):67. doi: 10.1186/s12920-018-0391-5.


Microglial translational profiling reveals a convergent APOE pathway from aging, amyloid, and tau.

Kang SS, Ebbert MTW, Baker KE, Cook C, Wang X, Sens JP, Kocher JP, Petrucelli L, Fryer JD.

J Exp Med. 2018 Sep 3;215(9):2235-2245. doi: 10.1084/jem.20180653. Epub 2018 Aug 6.


Correction to: the impact of pharmacokinetic gene profiles across human cancers.

Zimmermann MT, Therneau TM, Kocher JA.

BMC Cancer. 2018 Jul 18;18(1):743. doi: 10.1186/s12885-018-4593-1.


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.


Improving Single-Nucleotide Polymorphism-Based Fetal Fraction Estimation of Maternal Plasma Circulating Cell-Free DNA Using Bayesian Hierarchical Models.

Larson NB, Wang C, Na J, Rowsey RA, Highsmith WE, Hoppman NL, Kocher JP, Klee EW.

J Comput Biol. 2018 Sep;25(9):1040-1049. doi: 10.1089/cmb.2018.0056. Epub 2018 Jun 22.


Bat Caliciviruses and Human Noroviruses Are Antigenically Similar and Have Overlapping Histo-Blood Group Antigen Binding Profiles.

Kocher JF, Lindesmith LC, Debbink K, Beall A, Mallory ML, Yount BL, Graham RL, Huynh J, Gates JE, Donaldson EF, Baric RS.

MBio. 2018 May 22;9(3). pii: e00869-18. doi: 10.1128/mBio.00869-18.


The impact of pharmacokinetic gene profiles across human cancers.

Zimmermann MT, Therneau TM, Kocher JA.

BMC Cancer. 2018 May 21;18(1):577. doi: 10.1186/s12885-018-4345-2. Erratum in: BMC Cancer. 2018 Jul 18;18(1):743.


Prevalent Homozygous Deletions of Type I Interferon and Defensin Genes in Human Cancers Associate with Immunotherapy Resistance.

Ye Z, Dong H, Li Y, Ma T, Huang H, Leong HS, Eckel-Passow J, Kocher JA, Liang H, Wang L.

Clin Cancer Res. 2018 Jul 15;24(14):3299-3308. doi: 10.1158/1078-0432.CCR-17-3008. Epub 2018 Apr 4.


Author Correction: UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq.

Sun Z, Nair A, Chen X, Prodduturi N, Wang J, Kocher JP.

Sci Rep. 2018 Mar 20;8(1):5124. doi: 10.1038/s41598-018-23183-y.


Adaptive evolution influences the infectious dose of MERS-CoV necessary to achieve severe respiratory disease.

Douglas MG, Kocher JF, Scobey T, Baric RS, Cockrell AS.

Virology. 2018 Apr;517:98-107. doi: 10.1016/j.virol.2017.12.006. Epub 2017 Dec 23.


Hybrid-denovo: a de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags.

Chen X, Johnson S, Jeraldo P, Wang J, Chia N, Kocher JA, Chen J.

Gigascience. 2018 Mar 1;7(3):1-7. doi: 10.1093/gigascience/gix129.


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 Nov 30;12(11):e0188873. doi: 10.1371/journal.pone.0188873. eCollection 2017.


Corrigendum: Linnorm: improved statistical analysis for single cell RNA-seq expression data.

Yip SH, Wang P, Kocher JA, Sham PC, Wang J.

Nucleic Acids Res. 2017 Dec 15;45(22):13097. doi: 10.1093/nar/gkx1189. No abstract available.


UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq.

Sun Z, Nair A, Chen X, Prodduturi N, Wang J, Kocher JP.

Sci Rep. 2017 Oct 27;7(1):14196. doi: 10.1038/s41598-017-14595-3. Erratum in: Sci Rep. 2018 Mar 20;8(1):5124.


Linnorm: improved statistical analysis for single cell RNA-seq expression data.

Yip SH, Wang P, Kocher JA, Sham PC, Wang J.

Nucleic Acids Res. 2017 Dec 15;45(22):e179. doi: 10.1093/nar/gkx828. Erratum in: Nucleic Acids Res. 2017 Dec 15;45(22):13097.


Comprehensive Genomic Profiling of a Rare Thyroid Follicular Dendritic Cell Sarcoma.

Davila JI, Starr JS, Attia S, Wang C, Knudson RA, Necela BM, Sarangi V, Sun Z, Ren Y, Casler JD, Menke DM, Oliver GR, Joseph RW, Copland JA, Parker AS, Kocher JA, Thompson EA, Smallridge RC, Asmann YW.

Rare Tumors. 2017 Sep 15;9(2):6834. doi: 10.4081/rt.2017.6834. eCollection 2017 Jul 3.


Emergence of Novel Human Norovirus GII.17 Strains Correlates With Changes in Blockade Antibody Epitopes.

Lindesmith LC, Kocher JF, Donaldson EF, Debbink K, Mallory ML, Swann EW, Brewer-Jensen PD, Baric RS.

J Infect Dis. 2017 Dec 5;216(10):1227-1234. doi: 10.1093/infdis/jix385.


Adipose tissue DNA methylome changes in development of new-onset diabetes after kidney transplantation.

Baheti S, Singh P, Zhang Y, Evans J, Jensen MD, Somers VK, Kocher JA, Sun Z, Chakkera HA.

Epigenomics. 2017 Nov;9(11):1423-1435. doi: 10.2217/epi-2017-0050. Epub 2017 Oct 2.


Early genetic aberrations in patients with sporadic colorectal cancer.

Druliner BR, Ruan X, Sicotte H, O'Brien D, Liu H, Kocher JA, Boardman L.

Mol Carcinog. 2018 Jan;57(1):114-124. doi: 10.1002/mc.22738. Epub 2017 Oct 18. Erratum in: Mol Carcinog. 2018 May;57(5):684.


Impact of enzalutamide and its main metabolite N-desmethyl enzalutamide on pharmacokinetically important drug metabolizing enzymes and drug transporters.

Weiss J, Kocher J, Mueller C, Rosenzweig S, Theile D.

Biopharm Drug Dispos. 2017 Dec;38(9):517-525. doi: 10.1002/bdd.2103. Epub 2017 Oct 30.


MERS-CoV Accessory ORFs Play Key Role for Infection and Pathogenesis.

Menachery VD, Mitchell HD, Cockrell AS, Gralinski LE, Yount BL Jr, Graham RL, McAnarney ET, Douglas MG, Scobey T, Beall A, Dinnon K 3rd, Kocher JF, Hale AE, Stratton KG, Waters KM, Baric RS.

MBio. 2017 Aug 22;8(4). pii: e00665-17. doi: 10.1128/mBio.00665-17.


Allelic Variation in the Toll-Like Receptor Adaptor Protein Ticam2 Contributes to SARS-Coronavirus Pathogenesis in Mice.

Gralinski LE, Menachery VD, Morgan AP, Totura AL, Beall A, Kocher J, Plante J, Harrison-Shostak DC, Schäfer A, Pardo-Manuel de Villena F, Ferris MT, Baric RS.

G3 (Bethesda). 2017 Jun 7;7(6):1653-1663. doi: 10.1534/g3.117.041434.


CircularLogo: A lightweight web application to visualize intra-motif dependencies.

Ye Z, Ma T, Kalmbach MT, Dasari S, Kocher JA, Wang L.

BMC Bioinformatics. 2017 May 22;18(1):269. doi: 10.1186/s12859-017-1680-2.


mTCTScan: a comprehensive platform for annotation and prioritization of mutations affecting drug sensitivity in cancers.

Li MJ, Yao H, Huang D, Liu H, Liu Z, Xu H, Qin Y, Prinz J, Xia W, Wang P, Yan B, Tran NL, Kocher JP, Sham PC, Wang J.

Nucleic Acids Res. 2017 Jul 3;45(W1):W215-W221. doi: 10.1093/nar/gkx400.


Exploring genetic associations with ceRNA regulation in the human genome.

Li MJ, Zhang J, Liang Q, Xuan C, Wu J, Jiang P, Li W, Zhu Y, Wang P, Fernandez D, Shen Y, Chen Y, Kocher JA, Yu Y, Sham PC, Wang J, Liu JS, Liu XS.

Nucleic Acids Res. 2017 Jun 2;45(10):5653-5665. doi: 10.1093/nar/gkx331.


Experience with precision genomics and tumor board, indicates frequent target identification, but barriers to delivery.

Bryce AH, Egan JB, Borad MJ, Stewart AK, Nowakowski GS, Chanan-Khan A, Patnaik MM, Ansell SM, Banck MS, Robinson SI, Mansfield AS, Klee EW, Oliver GR, McCormick JB, Huneke NE, Tagtow CM, Jenkins RB, Rumilla KM, Kerr SE, Kocher JA, Beck SA, Fernandez-Zapico ME, Farrugia G, Lazaridis KN, McWilliams RR.

Oncotarget. 2017 Apr 18;8(16):27145-27154. doi: 10.18632/oncotarget.16057.


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.


cepip: context-dependent epigenomic weighting for prioritization of regulatory variants and disease-associated genes.

Li MJ, Li M, Liu Z, Yan B, Pan Z, Huang D, Liang Q, Ying D, Xu F, Yao H, Wang P, Kocher JA, Xia Z, Sham PC, Liu JS, Wang J.

Genome Biol. 2017 Mar 16;18(1):52. doi: 10.1186/s13059-017-1177-3.


Molecular Modeling and Functional Analysis of Exome Sequencing-Derived Variants of Unknown Significance Identify a Novel, Constitutively Active FGFR2 Mutant in Cholangiocarcinoma.

Egan JB, Marks DL, Hogenson TL, Vrabel AM, Sigafoos AN, Tolosa EJ, Carr RM, Safgren SL, Hesles EE, Almada LL, Romecin-Duran PA, Iguchi E, Ala'Aldeen A, Kocher JA, Oliver GR, Prodduturi N, Mead DW, Hossain A, Huneke NE, Tagtow CM, Ailawadhi S, Ansell SM, Banck MS, Bryce AH, Carballido EM, Chanan-Khan AA, Curtis KK, Resnik E, Gawryletz CD, Go RS, Halfdanarson TR, Ho TH, Joseph RW, Kapoor P, Mansfield AS, Meurice N, Nageswara Rao AA, Nowakowski GS, Pardanani A, Parikh SA, Cheville JC, Feldman AL, Ramanathan RK, Robinson SI, Tibes R, Finnes HD, McCormick JB, McWilliams RR, Jatoi A, Patnaik MM, Silva AC, Wieben ED, McAllister TM, Rumilla KM, Kerr SE, Lazaridis KN, Farrugia G, Stewart AK, Clark KJ, Kennedy EJ, Klee EW, Borad MJ, Fernandez-Zapico ME.

JCO Precis Oncol. 2017;2017. doi: 10.1200/PO.17.00018. Epub 2017 Aug 1.


High Protective Efficacy of Probiotics and Rice Bran against Human Norovirus Infection and Diarrhea in Gnotobiotic Pigs.

Lei S, Ramesh A, Twitchell E, Wen K, Bui T, Weiss M, Yang X, Kocher J, Li G, Giri-Rachman E, Trang NV, Jiang X, Ryan EP, Yuan L.

Front Microbiol. 2016 Nov 2;7:1699. eCollection 2016.


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.


Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations.

Sun Z, Bhagwate A, Prodduturi N, Yang P, Kocher JA.

Brief Bioinform. 2017 Nov 1;18(6):973-983. doi: 10.1093/bib/bbw069.


Lactobacillus rhamnosus GG modulates innate signaling pathway and cytokine responses to rotavirus vaccine in intestinal mononuclear cells of gnotobiotic pigs transplanted with human gut microbiota.

Wang H, Gao K, Wen K, Allen IC, Li G, Zhang W, Kocher J, Yang X, Giri-Rachman E, Li GH, Clark-Deener S, Yuan L.

BMC Microbiol. 2016 Jun 14;16(1):109. doi: 10.1186/s12866-016-0727-2.


Predicting regulatory variants with composite statistic.

Li MJ, Pan Z, Liu Z, Wu J, Wang P, Zhu Y, Xu F, Xia Z, Sham PC, Kocher JP, Li M, Liu JS, Wang J.

Bioinformatics. 2016 Sep 15;32(18):2729-36. doi: 10.1093/bioinformatics/btw288. Epub 2016 Jun 6.


Erratum to: Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature.

Ravikumar KE, Wagholikar KB, Li D, Kocher JP, Liu H.

BMC Bioinformatics. 2016 Apr 13;17:162. doi: 10.1186/s12859-016-0974-0. No abstract available.


Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data.

Baheti S, Kanwar R, Goelzenleuchter M, Kocher JP, Beutler AS, Sun Z.

BMC Genomics. 2016 Feb 27;17:149. doi: 10.1186/s12864-016-2494-8.


Measure transcript integrity using RNA-seq data.

Wang L, Nie J, Sicotte H, Li Y, Eckel-Passow JE, Dasari S, Vedell PT, Barman P, Wang L, Weinshiboum R, Jen J, Huang H, Kohli M, Kocher JP.

BMC Bioinformatics. 2016 Feb 3;17:58. doi: 10.1186/s12859-016-0922-z.


B-Cell-Deficient and CD8 T-Cell-Depleted Gnotobiotic Pigs for the Study of Human Rotavirus Vaccine-Induced Protective Immune Responses.

Wen K, Bui T, Weiss M, Li G, Kocher J, Yang X, Jobst PM, Vaught T, Ramsoondar J, Ball S, Clark-Deener S, Ayares D, Yuan L.

Viral Immunol. 2016 Mar;29(2):112-27. doi: 10.1089/vim.2015.0105. Epub 2016 Jan 29.


GWASdb v2: an update database for human genetic variants identified by genome-wide association studies.

Li MJ, Liu Z, Wang P, Wong MP, Nelson MR, Kocher JP, Yeager M, Sham PC, Chanock SJ, Xia Z, Wang J.

Nucleic Acids Res. 2016 Jan 4;44(D1):D869-76. doi: 10.1093/nar/gkv1317. Epub 2015 Nov 28.


High protective efficacy of rice bran against human rotavirus diarrhea via enhancing probiotic growth, gut barrier function, and innate immunity.

Yang X, Twitchell E, Li G, Wen K, Weiss M, Kocher J, Lei S, Ramesh A, Ryan EP, Yuan L.

Sci Rep. 2015 Oct 13;5:15004. doi: 10.1038/srep15004.


CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies.

Chen J, Just AC, Schwartz J, Hou L, Jafari N, Sun Z, Kocher JP, Baccarelli A, Lin X.

Bioinformatics. 2016 Feb 1;32(3):469-71. doi: 10.1093/bioinformatics/btv577. Epub 2015 Oct 7.

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