iQuant: A fast yet accurate GUI tool for transcript quantification. - Tin Chi Nguyen; Nan Deng; Guorong Xu; Zhansheng Duan; Dongxiao Zhu (BIBM Workshops, 2011)

SPATA: A highly accurate GUI tool for de novo transcriptome assembly. - Tin Chi Nguyen; Zhiyu Zhao; Dongxiao Zhu (BIBM Workshops, 2011)

SPATA: A seeding and patching algorithm for de novo transcriptome assembly. - Zhiyu Zhao; Tin Chi Nguyen; Nan Deng; Kristen Marie Johnson; Dongxiao Zhu (BIBM Workshops, 2011)

QSEA for fuzzy subgraph querying of KEGG pathways. - Thair Judeh; Tin Chi Nguyen; Dongxiao Zhu (BCB, 2012)

SASeq: A Selective and Adaptive Shrinkage Approach to Detect and Quantify Active Transcripts using RNA-Seq - Tin Chi Nguyen; Nan Deng; Dongxiao Zhu (CoRR, 2012)

MarkovBin: An Algorithm to Cluster Metagenomic Reads Using a Mixture Modeling of Hierarchical Distributions. - Tin Chi Nguyen; Dongxiao Zhu (BCB, 2013)

SPATA: A Seeding and Patching Algorithm for Hybrid Transcriptome Assembly. - Tin Chi Nguyen; Zhiyu Zhao; Dongxiao Zhu (CoRR, 2013)

TOMAS: A novel TOpology-aware Meta-Analysis approach applied to System biology. - Tin Chi Nguyen; Diana Diaz; Sorin Draghici (BCB, 2016)

A Systems Biology Approach for Unsupervised Clustering of High-Dimensional Data. - Diana Diaz; Tin Chi Nguyen; Sorin Draghici (MOD, 2016)

A novel bi-level meta-analysis approach: applied to biological pathway analysis. - Tin Chi Nguyen; Rebecca Tagett; Michele Donato; Cristina Mitrea; Sorin Draghici (Bioinform., 2016)

MicroRNA-Augmented Pathways (mirAP) and Their Applications to Pathway Analysis and Disease Subtyping. - Diana Diaz; Michele Donato; Tin Nguyen 001; Sorin Draghici (PSB, 2017)

DANUBE: Data-Driven Meta-ANalysis Using UnBiased Empirical Distributions - Applied to Biological Pathway Analysis. - Tin Chi Nguyen; Cristina Mitrea; Rebecca Tagett; Sorin Draghici (Proc. IEEE, 2017)

MIA: Multi-cohort Integrated Analysis for Biomarker Identification. - Brian Marks; Nina Hees; Hung Nguyen 005; Tin Nguyen 001 (BCB, 2018)

A survey of the approaches for identifying differential methylation using bisulfite sequencing data. - Adib Shafi; Cristina Mitrea; Tin Chi Nguyen; Sorin Draghici (Briefings Bioinform., 2018)

MGKA: A genetic algorithm-based clustering technique for genomic data. - Hung Nguyen 005; Sushil J. Louis; Tin Nguyen 001 (CEC, 2019)

RIA: a novel Regression-based Imputation Approach for single-cell RNA sequencing. - Bang Tran; Duc Tran; Hung Nguyen 005; Nam Sy Vo; Tin Nguyen 001 (KSE, 2019)

PINSPlus: a tool for tumor subtype discovery in integrated genomic data. - Hung Nguyen 005; Sangam Shrestha; Sorin Draghici; Tin Nguyen 001 (Bioinform., 2019)

Disease subtyping using community detection from consensus networks. - Hung Nguyen 005; Bang Tran; Duc Tran; Quang-Huy Nguyen; Duc-Hau Le; Tin Nguyen 001 (KSE, 2020)

Analysis of Short-read Aligners using Genome Sequence Complexity. - Quang Tran; Nam Sy Vo; Eric Hicks; Tin Chi Nguyen; Vinhthuy Phan (KSE, 2020)

Integrated Cancer Subtyping using Heterogeneous Genome-Scale Molecular Datasets. - Suzan Arslanturk; Sorin Draghici; Tin Nguyen 001 (PSB, 2020)

GSMA: an approach to identify robust global and test Gene Signatures using Meta-Analysis. - Adib Shafi; Tin Nguyen 001; Azam Peyvandi-Pour; Sorin Draghici (Bioinform., 2020)

Single-cell RNA sequencing data imputation using similarity preserving network. - Duc Tran; Hung Nguyen 005; Frederick C. Harris Jr.; Tin Nguyen 001 (KSE, 2021)

scIDS: Single-cell Imputation by combining Deep autoencoder neural networks and Subspace regression. - Bang Tran; Quyen Nguyen; Sangam Shrestha; Tin Nguyen 001 (KSE, 2021)

A comprehensive survey of regulatory network inference methods using single cell RNA sequencing data. - Hung Nguyen 005; Duc Tran; Bang Tran; Bahadir Pehlivan; Tin Nguyen 001 (Briefings Bioinform., 2021)

CPA: a web-based platform for consensus pathway analysis and interactive visualization. - Hung Nguyen 005; Duc Tran; Jonathan M. Galazka; Sylvain V. Costes; Afshin Beheshti; Juli Petereit; Sorin Draghici; Tin Nguyen 001 (Nucleic Acids Res., 2021)

DWEN: A novel method for accurate estimation of cell type compositions from bulk data samples. - Duc Tran; Ha Nguyen; Hung Nguyen 005; Tin Nguyen 001 (KSE, 2022)

DrGA: cancer driver gene analysis in a simpler manner. - Quang-Huy Nguyen; Tin Nguyen 001; Duc-Hau Le (BMC Bioinform., 2022)

ViT-DeiT: An Ensemble Model for Breast Cancer Histopathological Images Classification. - Amira Alotaibi; Tarik Alafif; Faris Alkhilaiwi; Yasser Alatawi; Hassan Althobaiti; Abdulmajeed Alrefaei; Yousef M. Hawsawi; Tin Nguyen 001 (CoRR, 2022)

A comprehensive survey of the approaches for pathway analysis using multi-omics data integration. - Zeynab Maghsoudi; Ha Nguyen; Alireza Tavakkoli; Tin Nguyen 001 (Briefings Bioinform., 2022)

Provenance documentation to enable explainable and trustworthy AI: A literature review. - Amruta Kale; Tin Nguyen 001; Frederick C. Harris Jr.; Chenhao Li; Jiyin Zhang; Xiaogang Ma 001 (Data Intell., 2023)

A robust and accurate single-cell data trajectory inference method using ensemble pseudotime. - Yifan Zhang; Duc Tran; Tin Nguyen 001; Sergiu M. Dascalu; Frederick C. Harris Jr. (BMC Bioinform., 2023)

CCPA: cloud-based, self-learning modules for consensus pathway analysis using GO, KEGG and Reactome. - Ha Nguyen; Van-Dung Pham; Hung Nguyen 005; Bang Tran; Juli Petereit; Tin Nguyen 001 (Briefings Bioinform., 2024)