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Submissions from 2018

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A Cyberinfrastructure for BigData Transportation Engineering, Md Johirul Islam, Anuj Sharma, and Hridesh Rajan

Submissions from 2017

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NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences, Philip L. Tzou, Xiaoqiu Huang, and Robert W. Shafer

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Optimization of SAMtools sorting using OpenMP tasks, Nathan T. Weeks and Glenn R. Luecke

Submissions from 2016

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Identification of Highly Variable Supernumerary Chromosome Segments in an Asexual Pathogen, Xiaoqiu Huang, Anindya Das, Binod B. Sahu, Subodh K. Srivastava, Leonor F. S. Leandro, Kerry O'Donnell, and Madan K. Bhattacharyya

Submissions from 2015

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Boa: Ultra-large-scale software repository and source-code mining, Robert Dyer, Hoan Anh Nguyen, Hridesh Rajan, and Tien N. Nguyen

Submissions from 2014

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EvoMiner: frequent subtree mining in phylogenetic databases, Akshay Deepak, David Fernández-Baca, Srikanta Tirthapura, Michael J. Sanderson, and Michelle M. McMahon

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Horizontal transfer generates genetic variation in an asexual pathogen, Xiaoqiu Huang

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Genetic architecture and evolution of the mating type locus in fusaria that cause soybean sudden death syndrome and bean root rot, Teresa J. Hughes, Kerry O'Donnell, Stacy Sink, Alejandro P. Rooney, Maria Mercedes Scandiani, Alicia Luque, Madan Bhattacharyya, and Xiaoqiu Huang

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The Genome Sequence of the Fungal Pathogen Fusarium virguliforme That Causes Sudden Death Syndrome in Soybean, Subodh K. Srivastava; Xiaoqiu Huang; Hargeet K. Brar; Ahmad M. Fakhoury; and Burton H, Bluhm

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RNABindRPlus: A Predictor that Combines Machine Learning and Sequence Homology-Based Methods to Improve the Reliability of Predicted RNA-Binding Residues in Proteins, Rasna R. Walia, Li C. Xue, Katherine E. Wilkins, Yasser El-Manzalawy, Drena L. Dobbs, and Vasant G. Honavar

Submissions from 2013

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Language Features for Software Evolution and Aspect-Oriented Interfaces: An Exploratory Study, Robert Dyer, Hridesh Rajan, and Yuanfang Cai

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Association between Experiences and Representations: Memory, Dreaming, Dementia and Consciousness, Xiaoqiu Huang

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A Genome-Wide Survey of Highly Expressed Non-Coding RNAs and Biological Validation of Selected Candidates in Agrobacterium tumefaciens, Keunsub Lee, Xiaoqiu Huang, Chichun Yang, Danny Lee, Kan Nobuta, Jian-Bing Fan, and Kan Wang

Submissions from 2012

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Frances: A Tool for Understanding Computer Architecture and Assembly Language, Tyler Sondag, Kian L. Pokorny, and Hridesh Rajan

Submissions from 2011

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Assemblathon 1: A competitive assessment of de novo short read assembly methods, Dent A. Earl, Isaac Y. Ho, Daniel S. Rokhsar, Jarrod A. Chapman, Adam M. Phillippy, Sergey Koren, Xiaoqiu Huang, and et al.

Submissions from 2010

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Supporting dynamic aspect-oriented features, Hridesh Rajan and Robert Dyer

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Modular aspect-oriented design with XPIs, Kevin Sullivan, Wiilliam G. Griswold, Hridesh Rajan, Yuanyuan Song, Yuanfang Cai, Macneil Shonle, and Nishit Tewari

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Detection of gene orthology from gene co-expression and protein interaction networks, Fadi George Towfic, Susan R. VanderPlas, Casey A. Oiver, Oliver Couture, Christopher K. Tuggle, M. Heather West Greenlee, and Vasant Honavar

Submissions from 2009

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Unifying aspect- and object-oriented design, Hridesh Rajan and Kevin J. Sullivan

Submissions from 2008

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Tisa: Toward Trustworthy Services in a Service-Oriented Architecture, Hridesh Rajan and Mahantesh Hosamani

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Genome analysis of the platypus reveals unique signatures of evolution, Wesley C. Warren, Xiaoqiu Huang, and et al.

Submissions from 2007

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Dynamic use of multiple parameter sets in sequence alignment, Xiaoqiu Huang and Douglas L. Brutlag

Submissions from 2006

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Modular software design with crosscutting interfaces, W. G. Griswold, M. Shonle, K. Sullivan, Y. Song, N. Tewari, Y. Cai, and Hridesh Rajan

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Application of a superword array in genome assembly, Xiaoqiu Huang, Shiaw-Pyng Yang, Asif T. Chinwalla, LaDeana W. Hillier, Patrick Minx, Elaine R. Mardis, and Richard K. Wilson

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Evolution of Alternative Splicing after Gene Duplication, Zhixi Su, Jianmin Wang, Xiaoqiu Huang, and Xun Gu

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Physical map-assisted whole-genome shotgun sequence assemblies, René L. Warren, Dmitry Varabei, Darren Platt, Xiaoqiu Huang, David Messina, Shiaw-Pyng Yang, James W. Kronstad, Martin Krzywinski, Wesley C. Warren, John W. Wallis, LaDeana W. Hillier, Asif T. Chinwalla, Jacqueline E. Schein, Asim S. Siddiqui, Marco A. Marra, Richard K. Wilson, and Steven J. M. Jones

Submissions from 2005

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A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage, Jianmin Wang and Xiaoqiu Huang

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MAP2: multiple alignment of syntenic genomic sequences, Liang Ye and Xiaoqiu Huang

Submissions from 2004

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Over 20% of human transcripts might form sense–antisense pairs, Jianjun Chen, Miao Sun, James Kent, Xiaoqiu Huang, Hanqing Xie, Wenquan Wang, Guolin Zhou, Run Zhang Shi, and Janet D. Rowley

Submissions from 2003

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PCAP: A Whole-Genome Assembly Program, Xiaoqiu Huang, Jianmin Wang, Srinivas Aluru, Shiaw-Pyng Yang, and LaDeana Hillier

Submissions from 2002

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Bio‐sequence comparison and applications, Xiaoqiu Huang

Submissions from 1999

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CAP3: A DNA Sequence Assembly Program, Xiaoqiu Huang and Anup Madan

Submissions from 1996

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Methods for Comparing a DNA Sequence with a Protein Sequence, Xiaoqiu Huang and Jinghui Zhang