First Exons and Introns - A Survey of GC Content and Gene Structure in the Human Genome. - Krishna R. Kalari; Melanie Casavant; Thomas B. Bair; Henry L. Keen; Josep M. Comeron; Thomas L. Casavant; Todd E. Scheetz (Silico Biol., 2006)

A knowledge-based approach to predict intragenic deletions or duplications. - Krishna R. Kalari; Thomas L. Casavant; Todd E. Scheetz (Bioinform., 2008)

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. - Yan W. Asmann; Sumit Middha; Asif Hossain; Saurabh Baheti; Ying Li; High-Seng Chai; Zhifu Sun; Patrick H. Duffy; Ahmed A. Hadad; Asha A. Nair; Xiaoyu Liu; Yuji Zhang 001; et al. (Bioinform., 2012)

MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing. - Krishna R. Kalari; Asha A. Nair; Jaysheel D. Bhavsar; Daniel R. O'Brien; Jaime I. Dávila; Matthew A. Bockol; Jinfu J. Nie; Xiaojia Tang; Saurabh Baheti; Jay B. Doughty; Sumit Middha; Hugues Sicotte; et al. (BMC Bioinform., 2014)

Unsupervised single-cell analysis in triple-negative breast cancer: A case study. - Arjun P. Athreya; Alan J. Gaglio; Zbigniew T. Kalbarczyk; Ravishankar K. Iyer; Junmei Cairns; Krishna R. Kalari; Richard M. Weinshilboum; Liewei Wang (BIBM, 2016)

Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment. - Khader Shameer; Lokesh P. Tripathi; Krishna R. Kalari; Joel T. Dudley; Ramanathan Sowdhamini (Briefings Bioinform., 2016)

Beta-Poisson model for single-cell RNA-seq data analyses. - Trung-Nghia Vu; Quin F. Wills; Krishna R. Kalari; Nifang Niu; Liewei Wang; Mattias Rantalainen; Yudi Pawitan (Bioinform., 2016)

Isoform-level gene expression patterns in single-cell RNA-sequencing data. - Trung-Nghia Vu; Quin F. Wills; Krishna R. Kalari; Nifang Niu; Liewei Wang; Yudi Pawitan; Mattias Rantalainen (Bioinform., 2018)

HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data. - Saurabh Baheti; Xiaojia Tang; Daniel R. O'Brien; Nicholas Chia; Lewis R. Roberts; Heidi Nelson; Judy C. Boughey; Liewei Wang; Matthew P. Goetz; Jean-Pierre A. Kocher; Krishna R. Kalari (BMC Bioinform., 2018)

Cell-level somatic mutation detection from single-cell RNA sequencing. - Trung-Nghia Vu; Ha-Nam Nguyen; Stefano Calza; Krishna R. Kalari; Liewei Wang; Yudi Pawitan (Bioinform., 2019)

Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data. - Wenjiang Deng; Tian Mou; Krishna R. Kalari; Nifang Niu; Liewei Wang; Yudi Pawitan; Trung-Nghia Vu (Bioinform., 2020)

A Short Survey on Set-Based Aggregation Techniques for Single-Vector WSI Representation in Digital Pathology. - Sobhan Hemati; Krishna R. Kalari; Hamid R. Tizhoosh (CoRR, 2024)