GLOSSI: a method to assess the association of genetic loci-sets with complex diseases. - High-Seng Chai; Hugues Sicotte; Kent R. Bailey; Stephen T. Turner; Yan W. Asmann; Jean-Pierre A. Kocher (BMC Bioinform., 2009)

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)

SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. - Zhifu Sun; Saurabh Baheti; Sumit Middha; Rahul Kanwar; Yuji Zhang 001; Xing Li; Andreas S. Beutler; Eric W. Klee; Yan W. Asmann; E. Aubrey Thompson; Jean-Pierre A. Kocher (Bioinform., 2012)

RVboost: RNA-seq variants prioritization using a boosting method. - Chen Wang 001; Jaime I. Dávila; Saurabh Baheti; Aditya Bhagwate; Xue Wang; Jean-Pierre A. Kocher; Susan L. Slager; Andrew L. Feldman; Anne J. Novak; James R. Cerhan; E. Aubrey Thompson; Yan W. Asmann (Bioinform., 2014)

PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data. - Chen Wang 001; Jared Evans; Aditya Bhagwate; Naresh Prodduturi; Vivekananda Sarangi; Mridu Middha; Hugues Sicotte; Peter T. Vedell; Steven N. Hart; Gavin R. Oliver; Jean-Pierre A. Kocher; Matthew J. Maurer; et al. (Bioinform., 2014)

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)

Identification of missing variants by combining multiple analytic pipelines. - Yingxue Ren; Joseph S. Reddy; Cyril Pottier; Vivekananda Sarangi; Shulan Tian; Jason P. Sinnwell; Shannon K. McDonnell; Joanna M. Biernacka; Minerva M. Carrasquillo; Owen A. Ross; Nilüfer Ertekin-Taner; Rosa Rademakers; et al. (BMC Bioinform., 2018)

NucMap: a database of genome-wide nucleosome positioning map across species. - Yongbing Zhao; Jinyue Wang; Fang Liang; Yanxia Liu; Qi Wang 072; Hao Zhang; Meiye Jiang; Zhewen Zhang; Wenming Zhao; Yiming Bao; Zhang Zhang 002; Jiayan Wu; et al. (Nucleic Acids Res., 2019)

Somatic selection distinguishes oncogenes and tumor suppressor genes. - Pramod Chandrashekar; Navid Ahmadinejad; Junwen Wang; Aleksandar Sekulic; Jan B. Egan; Yan W. Asmann; Sudhir Kumar 001; Carlo Maley; Li Liu 035 (Bioinform., 2020)

Assessment and Optimization of Explainable Machine Learning Models Applied to Transcriptomic Data. - Yongbing Zhao; Jinfeng Shao; Yan W. Asmann (Genom. Proteom. Bioinform., 2022)

Identification of gene regulatory networks associated with breast cancer patient survival using an interpretable deep neural network model. - Xue Wang; Vivekananda Sarangi; Daniel P. Wickland; Shaoyu Li; Duan Chen; E. Aubrey Thompson; Garrett Jenkinson; Yan W. Asmann (Expert Syst. Appl., 2025)

Corrigendum to "Identification of gene regulatory networks associated with breast cancer patient survival using an interpretable deep neural network model" [Expert Syst. Appl. 262 (2025) 125632]. - Xue Wang; Vivekananda Sarangi; Daniel P. Wickland; Shaoyu Li; Duan Chen; E. Aubrey Thompson; Garrett Jenkinson; Yan W. Asmann (Expert Syst. Appl., 2025)