Vinhthuy T. Phan

Proceedings of the 54th ACM Technical Symposium on Computer Science Education, Volume 1, 2023

A Practical Strategy for Training Graduate CS Teaching Assistants to Provide Effective Feedback.

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[DOI]

Proceedings of the 2023 Conference on Innovation and Technology in Computer Science Education V. 1, 2023

2022

Representing bacteria with unique genomic signatures.

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[DOI]

Frontiers Big Data, 2022

Enabling In-Class Peer Feedback on Introductory Computer Science Coding Exercises.

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[DOI]

Alina Zaman

Amy Cook

Proceedings of the SIGCSE 2022: The 53rd ACM Technical Symposium on Computer Science Education, 2022

Keep It Relevant! Using In-class Exercises to Predict Weekly Performance in CS1.

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[DOI]

Proceedings of the SIGCSE 2022: The 53rd ACM Technical Symposium on Computer Science Education, 2022

Try That Again! How a Second Attempt on In-Class Coding Problems Benefits Students in CS1.

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[DOI]

Proceedings of the SIGCSE 2022: The 53rd ACM Technical Symposium on Computer Science Education, 2022

Improving TA Feedback on In-Class Coding Assignments for Introductory Computer Science.

[BibT_eX]

[DOI]

Amy Cook

Alistair Windsor

Proceedings of the ITiCSE 2022: Innovation and Technology in Computer Science Education, Dublin, Ireland, July 8, 2022

2020

Analysis of Short-read Aligners using Genome Sequence Complexity.

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[DOI]

Proceedings of the 12th International Conference on Knowledge and Systems Engineering, 2020

Active Learning: The Almost Silver Bullet.

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[DOI]

Proceedings of the 12th International Conference on Knowledge and Systems Engineering, 2020

2019

icHET: interactive visualization of cytoplasmic heteroplasmy.

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[DOI]

Bioinform., 2019

2018

Leveraging known genomic variants to improve detection of variants, especially close-by Indels.

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[DOI]

Bioinform., 2018

Code4Brownies: an active learning solution for teaching programming and problem solving in the classroom.

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[DOI]

Eric Hicks

Proceedings of the 23rd Annual ACM Conference on Innovation and Technology in Computer Science Education, 2018

2017

An accurate and fast alignment-free method for profiling microbial communities.

[BibT_eX]

[DOI]

Shanshan Gao

J. Bioinform. Comput. Biol., 2017

Using 16S rRNA gene as marker to detect unknown bacteria in microbial communities.

[BibT_eX]

[DOI]

BMC Bioinform., 2017

2016

Analysis of optimal alignments unfolds aligners' bias in existing variant profiles.

[BibT_eX]

[DOI]

Shanshan Gao

BMC Bioinform., 2016

2015

Improving variant calling by incorporating known genetic variants into read alignment.

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[DOI]

BMC Bioinform., December, 2015

A linear model for predicting performance of short-read aligners using genome complexity.

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[DOI]

BMC Bioinform., December, 2015

How genome complexity can explain the difficulty of aligning reads to genomes.

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[DOI]

BMC Bioinform., December, 2015

Alignment-free methods for metagenomic profiling.

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[DOI]

Shanshan Gao

BMC Bioinform., December, 2015

2014

An integrated approach for SNP calling based on population of genomes.

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[DOI]

BMC Bioinform., 2014

Exploiting dependencies of pairwise comparison outcomes to predict patterns of gene response.

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[DOI]

BMC Bioinform., 2014

Exploiting the bootstrap method to analyze patterns of gene expression.

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[DOI]

BMC Bioinform., 2014

Alignment of short reads to multiple genomes using hashing.

[BibT_eX]

[DOI]

BMC Bioinform., 2014

Determining gene response patterns of time series gene expression data using R.

[BibT_eX]

[DOI]

Kevin L. O'kello

BMC Bioinform., 2014

How genome complexity can explain the hardness of aligning reads to genomes.

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[DOI]

Proceedings of the IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, 2014

2013

Using partially ordered sets to represent and predict true patterns of gene response to treatments.

[BibT_eX]

[DOI]

BMC Bioinform., 2013

Exploiting Dependencies of Patterns in Gene Expression Analysis Using Pairwise Comparisons.

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[DOI]

Proceedings of the Bioinformatics Research and Applications, 9th International Symposium, 2013

A randomized algorithm for aligning DNA sequences to reference genomes.

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[DOI]

Proceedings of the IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences, 2013

2012

Predicting possible directed-graph patterns of gene expressions in studies involving multiple treatments.

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[DOI]

Thomas R. Sutter

Proceedings of the ACM International Conference on Bioinformatics, 2012

<i>Pattern analysis</i>: a web-based tool for analyzing response patterns in low-replication, many-treatment gene expression data.

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[DOI]

Proceedings of the ACM International Conference on Bioinformatics, 2012

2011

Latent Semantic Indexing of PubMed abstracts for identification of transcription factor candidates from microarray derived gene sets.

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[DOI]

BMC Bioinform., 2011

mDAG: a web-based tool for analyzing microarray data with multiple treatments.

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[DOI]

Thomas R. Sutter

BMC Bioinform., 2011

2010

DNA-Based Indexing.

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[DOI]

Int. J. Nanotechnol. Mol. Comput., 2010

Synthetic gene design with a large number of hidden stops.

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[DOI]

Int. J. Data Min. Bioinform., 2010

Stability of RNA structural motifs and its influence on editing efficiency by adenosine deaminases.

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[DOI]

Int. J. Bioinform. Res. Appl., 2010

2009

On codeword design in metric DNA spaces.

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[DOI]

Nat. Comput., 2009

Analyzing microarray Data with Transitive Directed Acyclic Graphs.

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[DOI]

J. Bioinform. Comput. Biol., 2009

Optimal DNA Codes for Computing and Self-Assembly.

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[DOI]

Andrew Neel

Int. J. Nanotechnol. Mol. Comput., 2009

Motif Tool Manager: a web-based platform for motif discovery.

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[DOI]

BMC Bioinform., 2009

DNA Chips for Species Identification and Biological Phylogenies.

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[DOI]

Tit-Yee Wong

Proceedings of the DNA Computing and Molecular Programming, 15th International Conference, 2009

2008

BioTDMS: a general-purpose system for integrative management of bioinformatics tools and data.

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[DOI]

Kriangsiri Malasri

Int. J. Comput. Biol. Drug Des., 2008

Motif Tool Manager: a web-based framework for motif discovery.

[BibT_eX]

[DOI]

Nicholas A. Furlotte

Bioinform., 2008

Toward a Combinatorial Approach to the Sample Size Problem in Multiple-treatment Microarray Studies.

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Proceedings of the International Conference on Bioinformatics & Computational Biology, 2008

Synthetic Gene Design with a Large Number of Hidden Stop Codons.

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[DOI]

Proceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine, 2008

2007

How to Build a System that Manages Bioinformatics Content.

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Allen Thomas

Proceedings of the International Conference on Enterprise Information Systems and Web Technologies, 2007

Stability of RNA Structural Motifs and its Influence on Editing Efficiency by ADARS.

[BibT_eX]

Allen Thomas

Carrie Hayes Sutter

Proceedings of the International Conference on Bioinformatics & Computational Biology, 2007

2006

In Search of Optimal Codes for DNA Computing.

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[DOI]

Proceedings of the DNA Computing, 12th International Meeting on DNA Computing, 2006

"Reasoning" and "Talking" DNA: Can DNA Understand English?

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[DOI]

Proceedings of the DNA Computing, 12th International Meeting on DNA Computing, 2006

2005

Sensitivity and Capacity of Microarray Encodings.

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[DOI]

Proceedings of the DNA Computing, 11th International Workshop on DNA Computing, 2005

2004

An Improved Time-Sensitive Metaheuristic Framework for Combinatorial Optimization.

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[DOI]

Proceedings of the Experimental and Efficient Algorithms, Third International Workshop, 2004

The Capacity of DNA for Information Encoding.

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[DOI]

Proceedings of the DNA Computing, 10th International Workshop on DNA Computing, 2004

2003

A Model for Analyzing Black-Box Optimization.

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[DOI]

Pavel Sumazin

Proceedings of the Algorithms and Data Structures, 8th International Workshop, 2003

2002

A Time-Sensitive System for Black-Box Combinatorial Optimization.

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[DOI]

Pavel Sumazin

Proceedings of the Algorithm Engineering and Experiments, 4th International Workshop, 2002

2001

Dealing with errors in interactive sequencing by hybridization.

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[DOI]