A. Bhagwate

发表

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

J. Kocher, Zhifu Sun, Naresh Prodduturi, 2018, BMC Medical Genomics.

Impact of Library Preparation on Downstream Analysis and Interpretation of RNA-Seq Data: Comparison between Illumina PolyA and NuGEN Ovation Protocol

Krishna R. Kalari, Jean-Pierre A. Kocher, Asha Nair, 2013, PloS one.

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

Zhifu Sun, Sumit Middha, Huihuang Yan, 2014, BMC Genomics.

Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples

R. Vierkant, D. Radisky, A. Degnim, 2019, BMC Genomics.

Use of FFPE-Derived DNA in Next Generation Sequencing: DNA extraction methods

Zhifu Sun, Chen Wang, J. Cunningham, 2019 .

Use of FFPE-derived DNA in next generation sequencing: DNA extraction methods

J. Cunningham, Zhifu Sun, Karla J. Kopp, 2019, bioRxiv.

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

J. Cunningham, S. Baheti, Zhifu Sun, 2015, Epigenomics.

Identification of factors associated with duplicate rate in ChIP-seq data

Krutika S Gaonkar, S. Slager, J. Eckel-Passow, 2019, PloS one.

Concordance between predicted HLA type using next generation sequencing data generated for non-HLA purposes and clinical HLA type.

Krishna R. Kalari, K. Kalari, J. Black, 2020, Human immunology.

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

J. Jen, N. Chia, B. Eckloff, 2018, Journal of microbiological methods.

Somatic mutations in benign breast disease tissues and association with breast cancer risk

R. Vierkant, D. Radisky, M. Sherman, 2021, BMC medical genomics.

Somatic mutations in benign breast disease tissues and association with breast cancer risk

R. Vierkant, D. Radisky, M. Sherman, 2021, BMC Medical Genomics.

Quality control recommendations for RNASeq using FFPE samples based on pre-sequencing lab metrics and post-sequencing bioinformatics metrics

R. Vierkant, D. Radisky, A. Degnim, 2022, BMC Medical Genomics.

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

Ying Li, Jared Evans, Jean-Pierre A. Kocher, 2014, BMC Bioinformatics.

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

J. Kocher, Zhifu Sun, S. Middha, 2014, BMC Genomics.

Impact of RNA Extraction and Target Capture Methods on RNA Sequencing Using Formalin-Fixed, Paraffin Embedded Tissues

Asha A. Nair, E. Thompson, J. Jen, 2019, bioRxiv.

Gene Expression, Single Nucleotide Variant and Fusion Transcript Discovery in Archival Material from Breast Tumors

Krishna R. Kalari, Zhifu Sun, Kevin J. Thompson, 2013, PloS one.

Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples

R. Vierkant, D. Radisky, A. Degnim, 2019, BMC Genomics.

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

J. Kocher, Zhifu Sun, Naresh Prodduturi, 2018, BMC Medical Genomics.

Interactive enhancer hubs (iHUBs) mediate transcriptional reprogramming and adaptive resistance in pancreatic cancer

J. Gaedcke, S. Hahn, R. Graham, 2023, Gut.

Performance comparisons of methylation and structural variants from low-input whole-genome methylation sequencing

J. Cunningham, Zhifu Sun, Panwen Wang, 2023, Epigenomics.

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

Jared Evans, Steven N. Hart, Naresh Prodduturi, 2014, Bioinform..

RVboost: RNA-seq variants prioritization using a boosting method

Xue Wang, Saurabh Baheti, Jean-Pierre A. Kocher, 2014, Bioinform..

Epigenomics may begin to explain in vitro differential response to hypomethylating agents in MMR-D hypermethylated endometrial cancer.

Sarah H. Johnson, J. Cheville, A. Mansfield, 2023, Epigenomics.

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

Ping Yang, Naresh Prodduturi, Jean-Pierre A. Kocher, 2016, Briefings Bioinform..