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Items: 22

1.

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.

PMID:
31214875
2.

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.

PMID:
30878468
3.

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.

4.

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.

PMID:
30347404
5.

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.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

PMID:
28967791
15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data.

Hart SN, Moore RM, Zimmermann MT, Oliver GR, Egan JB, Bryce AH, Kocher JA.

PeerJ. 2015 May 19;3:e970. doi: 10.7717/peerj.970. eCollection 2015.

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