Bhagwate AV - Search Results

1

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. Sun Z, et al. Among authors: bhagwate av. PLoS One. 2013 Aug 19;8(8):e71745. doi: 10.1371/journal.pone.0071745. eCollection 2013. PLoS One. 2013. PMID: 23977132 Free PMC article.

2

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. Norton N, et al. PLoS One. 2013 Nov 22;8(11):e81925. doi: 10.1371/journal.pone.0081925. eCollection 2013. PLoS One. 2013. PMID: 24278466 Free PMC article.

3

PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data.

Wang C, Evans JM, Bhagwate AV, Prodduturi N, Sarangi V, Middha M, Sicotte H, Vedell PT, Hart SN, Oliver GR, Kocher JP, Maurer MJ, Novak AJ, Slager SL, Cerhan JR, Asmann YW. Wang C, et al. Among authors: bhagwate av. Bioinformatics. 2014 Sep 15;30(18):2678-80. doi: 10.1093/bioinformatics/btu363. Epub 2014 May 29. Bioinformatics. 2014. PMID: 24876377 Free PMC article.

4

CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data.

Sun Z, Evans J, Bhagwate A, Middha S, Bockol M, Yan H, Kocher JP. Sun Z, et al. BMC Genomics. 2014 Jun 3;15(1):423. doi: 10.1186/1471-2164-15-423. BMC Genomics. 2014. PMID: 24894665 Free PMC article.

5

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data.

Yan H, Evans J, Kalmbach M, Moore R, Middha S, Luban S, Wang L, Bhagwate A, Li Y, Sun Z, Chen X, Kocher JP. Yan H, et al. BMC Bioinformatics. 2014 Aug 15;15(1):280. doi: 10.1186/1471-2105-15-280. BMC Bioinformatics. 2014. PMID: 25128017 Free PMC article.

6

RVboost: RNA-seq variants prioritization using a boosting method.

Wang C, Davila JI, Baheti S, Bhagwate AV, Wang X, Kocher JP, Slager SL, Feldman AL, Novak AJ, Cerhan JR, Thompson EA, Asmann YW. Wang C, et al. Among authors: bhagwate av. Bioinformatics. 2014 Dec 1;30(23):3414-6. doi: 10.1093/bioinformatics/btu577. Epub 2014 Aug 27. Bioinformatics. 2014. PMID: 25170027 Free PMC article.

7

DNA methylation profiling: comparison of genome-wide sequencing methods and the Infinium Human Methylation 450 Bead Chip.

Walker DL, Bhagwate AV, Baheti S, Smalley RL, Hilker CA, Sun Z, Cunningham JM. Walker DL, et al. Among authors: bhagwate av. Epigenomics. 2015;7(8):1287-302. doi: 10.2217/EPI.15.64. Epub 2015 Jul 20. Epigenomics. 2015. PMID: 26192535

8

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. Sun Z, et al. Brief Bioinform. 2017 Nov 1;18(6):973-983. doi: 10.1093/bib/bbw069. Brief Bioinform. 2017. PMID: 27473065 Free PMC article.

9

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

Prodduturi N, Bhagwate A, Kocher JA, Sun Z. Prodduturi N, et al. BMC Med Genomics. 2018 Sep 14;11(Suppl 3):67. doi: 10.1186/s12920-018-0391-5. BMC Med Genomics. 2018. PMID: 30255803 Free PMC article.

10

Comparative evaluation of cDNA library construction approaches for RNA-Seq analysis from low RNA-content human specimens.

Masters TL, Hilker CA, Jeraldo PR, Bhagwate AV, Greenwood-Quaintance KE, Eckloff BW, Chia N, Hanssen AD, Abdel MP, Yao JZ, Jen J, Patel R. Masters TL, et al. Among authors: bhagwate av. J Microbiol Methods. 2018 Nov;154:55-62. doi: 10.1016/j.mimet.2018.10.008. Epub 2018 Oct 14. J Microbiol Methods. 2018. PMID: 30332617 Free PMC article.

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