Dealing with errors in interactive sequencing by hybridization. - Vinhthuy T. Phan; Steven Skiena (Bioinform., 2001)

A Time-Sensitive System for Black-Box Combinatorial Optimization. - Vinhthuy T. Phan; Pavel Sumazin; Steven Skiena (ALENEX, 2002)

A Model for Analyzing Black-Box Optimization. - Vinhthuy T. Phan; Steven Skiena; Pavel Sumazin (WADS, 2003)

The Capacity of DNA for Information Encoding. - Vinhthuy T. Phan; Max H. Garzon (DNA, 2004)

An Improved Time-Sensitive Metaheuristic Framework for Combinatorial Optimization. - Vinhthuy T. Phan; Steven Skiena (WEA, 2004)

Sensitivity and Capacity of Microarray Encodings. - Max H. Garzon; Vinhthuy T. Phan; Kiran C. Bobba; Raghuver Kontham (DNA, 2005)

"Reasoning" and "Talking" DNA: Can DNA Understand English? - Kiranchand V. Bobba; Andrew Neel; Vinhthuy T. Phan; Max H. Garzon (DNA, 2006)

In Search of Optimal Codes for DNA Computing. - Max H. Garzon; Vinhthuy T. Phan; Sujoy Roy; Andrew Neel (DNA, 2006)

Stability of RNA Structural Motifs and its Influence on Editing Efficiency by ADARS. - Vinhthuy T. Phan; Allen Thomas; Carrie Hayes Sutter (BIOCOMP, 2007)

How to Build a System that Manages Bioinformatics Content. - Vinhthuy T. Phan; Allen Thomas (Enterprise Information Systems and Web Technologies, 2007)

Synthetic Gene Design with a Large Number of Hidden Stop Codons. - Vinhthuy Phan; Sudip Saha; Ashutosh Pandey 003; Tit-Yee Wong (BIBM, 2008)

Toward a Combinatorial Approach to the Sample Size Problem in Multiple-treatment Microarray Studies. - Vinhthuy Phan; E. Olusegun George; Quynh T. Tran; Thomas R. Sutter (BIOCOMP, 2008)

Motif Tool Manager: a web-based framework for motif discovery. - Vinhthuy Phan; Nicholas A. Furlotte (Bioinform., 2008)

BioTDMS: a general-purpose system for integrative management of bioinformatics tools and data. - Vinhthuy Phan; Kriangsiri Malasri (Int. J. Comput. Biol. Drug Des., 2008)

DNA Chips for Species Identification and Biological Phylogenies. - Max H. Garzon; Tit-Yee Wong; Vinhthuy T. Phan (DNA, 2009)

Motif Tool Manager: a web-based platform for motif discovery. - Vinhthuy Phan (BMC Bioinform., 2009)

Optimal DNA Codes for Computing and Self-Assembly. - Max H. Garzon; Vinhthuy Phan; Andrew Neel (Int. J. Nanotechnol. Mol. Comput., 2009)

Analyzing microarray Data with Transitive Directed Acyclic Graphs. - Vinhthuy Phan; E. Olusegun George; Quynh T. Tran; Shirlean Goodwin; Sridevi Bodreddigari; Thomas R. Sutter (J. Bioinform. Comput. Biol., 2009)

On codeword design in metric DNA spaces. - Vinhthuy T. Phan; Max H. Garzon (Nat. Comput., 2009)

Stability of RNA structural motifs and its influence on editing efficiency by adenosine deaminases. - Vinhthuy Phan; Allen Thomas; Kriangsiri Malasri; Carrie Hayes Sutter (Int. J. Bioinform. Res. Appl., 2010)

Synthetic gene design with a large number of hidden stops. - Vinhthuy Phan; Sudip Saha; Ashutosh Pandey 003; Tit-Yee Wong (Int. J. Data Min. Bioinform., 2010)

DNA-Based Indexing. - Max H. Garzon; Kiran C. Bobba; Andrew Neel; Vinhthuy Phan (Int. J. Nanotechnol. Mol. Comput., 2010)

mDAG: a web-based tool for analyzing microarray data with multiple treatments. - Vinhthuy T. Phan; Nam S. Vo; Thomas R. Sutter (BMC Bioinform., 2011)

Latent Semantic Indexing of PubMed abstracts for identification of transcription factor candidates from microarray derived gene sets. - Sujoy Roy; Kevin Heinrich; Vinhthuy Phan; Michael W. Berry; Ramin Homayouni (BMC Bioinform., 2011)

Pattern analysis: a web-based tool for analyzing response patterns in low-replication, many-treatment gene expression data. - Nam S. Vo; Vinhthuy Phan (BCB, 2012)

Predicting possible directed-graph patterns of gene expressions in studies involving multiple treatments. - Nam S. Vo; Vinhthuy Phan; Thomas R. Sutter (BCB, 2012)

A randomized algorithm for aligning DNA sequences to reference genomes. - Nam S. Vo; Quang Tran; Nobal B. Niraula; Vinhthuy Phan (ICCABS, 2013)

Exploiting Dependencies of Patterns in Gene Expression Analysis Using Pairwise Comparisons. - Nam S. Vo; Vinhthuy Phan (ISBRA, 2013)

Using partially ordered sets to represent and predict true patterns of gene response to treatments. - Nam S. Vo; Vinhthuy Phan (BMC Bioinform., 2013)

How genome complexity can explain the hardness of aligning reads to genomes. - Vinhthuy T. Phan; Shanshan Gao; Quang Tran; Nam S. Vo (ICCABS, 2014)

Determining gene response patterns of time series gene expression data using R. - Kevin L. O'kello; Vinhthuy Phan (BMC Bioinform., 2014)

Alignment of short reads to multiple genomes using hashing. - Quang Tran; Vinhthuy Phan (BMC Bioinform., 2014)

Exploiting the bootstrap method to analyze patterns of gene expression. - Nam S. Vo; Vinhthuy Phan (BMC Bioinform., 2014)

Exploiting dependencies of pairwise comparison outcomes to predict patterns of gene response. - Nam S. Vo; Vinhthuy Phan (BMC Bioinform., 2014)

An integrated approach for SNP calling based on population of genomes. - Nam S. Vo; Quang Tran; Vinhthuy Phan (BMC Bioinform., 2014)

Alignment-free methods for metagenomic profiling. - Shanshan Gao; Diem-Trang Pham; Vinhthuy Phan (BMC Bioinform., 2015)

How genome complexity can explain the difficulty of aligning reads to genomes. - Vinhthuy Phan; Shanshan Gao; Quang Tran; Nam S. Vo (BMC Bioinform., 2015)

A linear model for predicting performance of short-read aligners using genome complexity. - Quang Tran; Shanshan Gao; Nam S. Vo; Vinhthuy Phan (BMC Bioinform., 2015)

Improving variant calling by incorporating known genetic variants into read alignment. - Nam S. Vo; Vinhthuy Phan (BMC Bioinform., 2015)

Analysis of optimal alignments unfolds aligners' bias in existing variant profiles. - Quang Tran; Shanshan Gao; Vinhthuy Phan (BMC Bioinform., 2016)

Using 16S rRNA gene as marker to detect unknown bacteria in microbial communities. - Quang Tran; Diem-Trang Pham; Vinhthuy Phan (BMC Bioinform., 2017)

An accurate and fast alignment-free method for profiling microbial communities. - Diem-Trang Pham; Shanshan Gao; Vinhthuy Phan (J. Bioinform. Comput. Biol., 2017)

Code4Brownies: an active learning solution for teaching programming and problem solving in the classroom. - Vinhthuy Phan; Eric Hicks (ITiCSE, 2018)

Leveraging known genomic variants to improve detection of variants, especially close-by Indels. - Nam S. Vo; Vinhthuy Phan (Bioinform., 2018)

icHET: interactive visualization of cytoplasmic heteroplasmy. - Vinhthuy Phan; Diem-Trang Pham; Caroline Melton; Adam J. Ramsey; Bernie J. Daigle Jr.; Jennifer R. Mandel (Bioinform., 2019)

Active Learning: The Almost Silver Bullet. - Eric Hicks; Quang Tran; Kriangsiri Malasri; Nam Sy Vo; Vinhthuy Phan (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)

Improving TA Feedback on In-Class Coding Assignments for Introductory Computer Science. - Amy Cook; Vinhthuy Phan; Alistair Windsor (ITiCSE (1), 2022)

Try That Again! How a Second Attempt on In-Class Coding Problems Benefits Students in CS1. - Amy Cook; Alina Zaman; Eric Hicks; Kriangsiri Malasri; Vinhthuy Phan (SIGCSE (1), 2022)

Keep It Relevant! Using In-class Exercises to Predict Weekly Performance in CS1. - Eric Hicks; Amy Cook; Kriangsiri Malasri; Alina Zaman; Vinhthuy Phan (SIGCSE (1), 2022)

Enabling In-Class Peer Feedback on Introductory Computer Science Coding Exercises. - Alina Zaman; Vinhthuy Phan; Amy Cook (SIGCSE (2), 2022)

Representing bacteria with unique genomic signatures. - Diem-Trang Pham; Vinhthuy Phan (Frontiers Big Data, 2022)

A Practical Strategy for Training Graduate CS Teaching Assistants to Provide Effective Feedback. - Alina Zaman; Amy Cook; Vinhthuy Phan; Alistair Windsor (ITiCSE (1), 2023)

A Cloud-Based Technology for Conducting In-class Exercises in Data Science and Machine Learning Courses. - Kritish Pahi; Vinhthuy Phan (SIGCSE (1), 2023)

Graduate Computer Science TA Perspectives on In-Person Pedagogical Training: An Experience Report. - Alina Zaman; Amy Cook; Vinhthuy Phan; Alistair Windsor (ITiCSE (1), 2025)

In-class Coding Exercises As A Mechanism To Inform Early Intervention In Programming Courses. - Eric Hicks; Vinhthuy Phan (SIGCSE (1), 2025)

Enhancing Student Performance Prediction In CS1 Via In-Class Coding. - Eric Hicks; Vinhthuy Phan; Kriangsiri Malasri (SIGCSE (1), 2025)