| CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data Z Sun, J Evans, A Bhagwate, S Middha, M Bockol, H Yan, JP Kocher BMC genomics 15, 1-10, 2014 | 181 | 2014 |
| Use of FFPE-derived DNA in next generation sequencing: DNA extraction methods SJ McDonough, A Bhagwate, Z Sun, C Wang, M Zschunke, JA Gorman, ... PloS one 14 (4), e0211400, 2019 | 101 | 2019 |
| Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations Z Sun, A Bhagwate, N Prodduturi, P Yang, JPA Kocher Briefings in bioinformatics 18 (6), 973-983, 2017 | 69 | 2017 |
| DNA methylation profiling: comparison of genome-wide sequencing methods and the Infinium Human Methylation 450 Bead Chip DL Walker, AV Bhagwate, S Baheti, RL Smalley, CA Hilker, Z Sun, ... Epigenomics 7 (8), 1287-1302, 2015 | 67 | 2015 |
| HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data H Yan, J Evans, M Kalmbach, R Moore, S Middha, S Luban, L Wang, ... BMC bioinformatics 15, 1-12, 2014 | 67 | 2014 |
| Gene expression, single nucleotide variant and fusion transcript discovery in archival material from breast tumors N Norton, Z Sun, YW Asmann, DJ Serie, BM Necela, A Bhagwate, J Jen, ... PloS one 8 (11), e81925, 2013 | 66 | 2013 |
| Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples AV Bhagwate, Y Liu, SJ Winham, SJ McDonough, ML Stallings-Mann, ... BMC genomics 20, 1-10, 2019 | 55 | 2019 |
| RVboost: RNA-seq variants prioritization using a boosting method C Wang, JI Davila, S Baheti, AV Bhagwate, X Wang, JPA Kocher, ... Bioinformatics 30 (23), 3414-3416, 2014 | 51 | 2014 |
| PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data C Wang, JM Evans, AV Bhagwate, N Prodduturi, V Sarangi, M Middha, ... Bioinformatics 30 (18), 2678-2680, 2014 | 51 | 2014 |
| Dysfunctional ERG signaling drives pulmonary vascular aging and persistent fibrosis N Caporarello, J Lee, TX Pham, DL Jones, J Guan, PA Link, JA Meridew, ... Nature communications 13 (1), 4170, 2022 | 35 | 2022 |
| Impact of library preparation on downstream analysis and interpretation of RNA-Seq data: comparison between Illumina PolyA and NuGEN Ovation protocol Z Sun, YW Asmann, A Nair, Y Zhang, L Wang, KR Kalari, AV Bhagwate, ... PloS one 8 (8), e71745, 2013 | 27 | 2013 |
| High frequency electrical stimulation promotes expression of extracellular matrix proteins from human astrocytes JS Jang, CI Choi, J Yi, K Butters, I Kim, A Bhagwate, J Jen, S Chang Molecular biology reports 46, 4369-4375, 2019 | 15 | 2019 |
| Ex vivo cell therapy by ectopic hepatocyte transplantation treats the porcine tyrosinemia model of acute liver failure CT Nicolas, RA Kaiser, RD Hickey, KL Allen, Z Du, CJ VanLith, ... Molecular Therapy Methods & Clinical Development 18, 738-750, 2020 | 14 | 2020 |
| Comparative evaluation of cDNA library construction approaches for RNA-Seq analysis from low RNA-content human specimens TL Masters, CA Hilker, PR Jeraldo, AV Bhagwate, ... Journal of microbiological methods 154, 55-62, 2018 | 13 | 2018 |
| In vivo lentiviral vector gene therapy to cure hereditary tyrosinemia type 1 and prevent development of precancerous and cancerous lesions CT Nicolas, CJ VanLith, RD Hickey, Z Du, LG Hillin, RM Guthman, ... Nature communications 13 (1), 5012, 2022 | 12 | 2022 |
| Lactic acid induces transcriptional repression of macrophage inflammatory response via histone acetylation W Shi, TJ Cassmann, AV Bhagwate, T Hitosugi, WKE Ip Cell reports 43 (2), 2024 | 11 | 2024 |
| Quality control recommendations for RNASeq using FFPE samples based on pre-sequencing lab metrics and post-sequencing bioinformatics metrics Y Liu, A Bhagwate, SJ Winham, MT Stephens, BW Harker, ... BMC medical genomics 15 (1), 195, 2022 | 11 | 2022 |
| Human transcriptomic response to periprosthetic joint infection TL Masters, AV Bhagwate, MK Dehankar, KE Greenwood-Quaintance, ... Gene 825, 146400, 2022 | 10 | 2022 |
| Indel sensitive and comprehensive variant/mutation detection from RNA sequencing data for precision medicine N Prodduturi, A Bhagwate, JPA Kocher, Z Sun BMC medical genomics 11, 53-62, 2018 | 9 | 2018 |
| Identification of factors associated with duplicate rate in ChIP-seq data S Tian, S Peng, M Kalmbach, KS Gaonkar, A Bhagwate, W Ding, ... PloS one 14 (4), e0214723, 2019 | 8 | 2019 |
