Torsional Relaxation for Biopolymers. - Wing Hung Wong; Yan Cui 001; Run Sheng Chen (J. Comput. Biol., 1998)

Ranking Gene Regulatory Network Models with Microarray Data and Bayesian Network. - Hongqiang Li; Mi Zhou; Yan Cui 001 (CASDMKM, 2004)

GeneInfoViz: Constructing and visualizing gene relation networks. - Mi Zhou; Yan Cui 001 (Silico Biol., 2004)

Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information. - Lei Bao; Yan Cui 001 (Bioinform., 2005)

nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms. - Lei Bao; Mi Zhou; Yan Cui 001 (Nucleic Acids Res., 2005)

PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. - Lei Bao; Mi Zhou; Ligang Wu; Lu Lu 004; Dan Goldowitz; Robert W. Williams; Yan Cui 001 (Nucleic Acids Res., 2007)

CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators. - Lei Bao; Mi Zhou; Yan Cui 001 (Nucleic Acids Res., 2008)

MRI brain image segmentation for spotting tumors using improved mountain clustering approach. - Nishchal K. Verma; Payal Gupta; Pooja Agrawal; Yan Cui 001 (AIPR, 2009)

Fuzzy rule based unsupervised approach for salient gene extraction. - Nishchal K. Verma; Payal Gupta; Pooja Agrawal; Yan Cui 001 (AIPR, 2009)

Medical Image Segmentation Using Improved Mountain Clustering Approach. - Nishchal K. Verma; Payal Gupta; Pooja Agrawal; Madasu Hanmandlu; Shantaram Vasikarla; Yan Cui 001 (ITNG, 2009)

Fuzzy rule based unsupervised approach for gene saliency. - Nishchal K. Verma; Pooja Agrawal; Yan Cui 001 (BMC Bioinform., 2009)

Linking genotype to phenotype with Bayesian network modeling of Chlamydia infection. - Jesse D. Ziebarth; Bao Li; Isao Miyairi; Yan Cui 001 (BMC Bioinform., 2010)

PolymiRTS Database 2.0: linking polymorphisms in microRNA target sites with human diseases and complex traits. - Jesse D. Ziebarth; Anindya Bhattacharya; Anlong Chen; Yan Cui 001 (Nucleic Acids Res., 2012)

Bayesian Network Webserver: a comprehensive tool for biological network modeling. - Jesse D. Ziebarth; Anindya Bhattacharya; Yan Cui 001 (Bioinform., 2013)

SomamiR: a database for somatic mutations impacting microRNA function in cancer. - Anindya Bhattacharya; Jesse D. Ziebarth; Yan Cui 001 (Nucleic Acids Res., 2013)

CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization. - Jesse D. Ziebarth; Anindya Bhattacharya; Yan Cui 001 (Nucleic Acids Res., 2013)

PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways. - Anindya Bhattacharya; Jesse D. Ziebarth; Yan Cui 001 (Nucleic Acids Res., 2014)

Hausdorff distance and global silhouette index as novel measures for estimating quality of biclusters. - Nishchal K. Verma; Esha Dutta; Yan Cui 001 (BIBM, 2015)

miR2GO: comparative functional analysis for microRNAs. - Anindya Bhattacharya; Yan Cui 001 (Bioinform., 2015)

Layerwise feature selection in Stacked Sparse Auto-Encoder for tumor type prediction. - Vikas Singh; Nikhil Baranwal; Rahul Kumar Sevakula; Nishchal K. Verma; Yan Cui 001 (BIBM, 2016)

Assessing the quality of biclusters using fuzzy biclustering index. - Nishchal K. Verma; Esha Dutta; Yan Cui 001 (Int. J. Data Min. Bioinform., 2016)

SomamiR 2.0: a database of cancer somatic mutations altering microRNA-ceRNA interactions. - Anindya Bhattacharya; Yan Cui 001 (Nucleic Acids Res., 2016)

Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016: Cadiz, KY, USA. 8-10 April 2016. - Eric C. Rouchka; Julia H. Chariker; Benjamin J. Harrison; Juw Won Park; Xueyuan Cao; Stanley Pounds; Susana C. Raimondi; James R. Downing; Raul C. Ribeiro; Jeffrey Rubnitz; Jatinder Lamba; Bernie J. Daigle Jr.; et al. (BMC Bioinform., 2016)

Systematic Prediction of the Impacts of Mutations in MicroRNA Seed Sequences. - Anindya Bhattacharya; Yan Cui 001 (J. Integr. Bioinform., 2017)

Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: bioinformatics: Burns, TN, USA. April 21-23, 2017. - Eric C. Rouchka; Julia H. Chariker; David Tieri; Juw Won Park; Shreedharkumar D. Rajurkar; Vikas Singh; Nishchal K. Verma; Yan Cui 001; Mark L. Farman; Bradford Condon; Neil Moore; Jerzy W. Jaromczyk; et al. (BMC Bioinform., 2017)

Optimal Feature Selection using Fuzzy Combination of Feature Subset for Transcriptome Data. - Vikas Singh; Harsh Vardhan; Nishchal K. Verma; Yan Cui 001 (FUZZ-IEEE, 2018)

Feature Ranking using Robust Fuzzy Score Function for Gene Expression Data. - Vikas Singh; Teena Sharma; Nishchal K. Verma; Yan Cui 001 (FUZZ-IEEE, 2019)

Transfer Learning for Molecular Cancer Classification Using Deep Neural Networks. - Rahul Kumar Sevakula; Vikas Singh; Nishchal K. Verma; Chandan Kumar; Yan Cui 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Digital pathways connecting social and biological factors to health outcomes and equity. - Yan Cui 001 (npj Digit. Medicine, 2025)