2017
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2016
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Songhua Xu,
C. Markson, K. L. Costello, C. Y. Xing, K. Demissie and
Adana A. M. Llanos.
Leveraging social media to promote public health knowledge:
example of cancer awareness via Twitter.
JMIR Public Health and Surveillance,
2(1):e17, 2016.
-
Georgia Tourassi, Hong-Jun Yoon and Songhua Xu.
A novel web informatics approach for automated surveillance of
cancer mortality trends.
Journal of Biomedical Informatics,
61:110-118, 2016.
-
Abdulrhman Aljouie, Nihir Patel, Bharati Jadhav and Usman Roshan.
Cross-validation and cross-study validation of chronic
lymphocytic leukaemia with exome sequences and machine learning.
International Journal of Data Mining and Bioinformatics,
16(1):47-63, 2016.
-
Jie Zhang and Zhi Wei.
An empirical Bayes change-point model for identifying 3' and 5'
alternative splicing by next-generation RNA sequencing.
Bioinformatics,
32:1823-1831, 2016.
-
Anjana Grandhi, Wenge Guo and Shyamal D. Peddada.
A multiple testing procedure for multi-dimensional pairwise
comparisons with application to gene expression studies.
BMC Bioinformatics,
17:104, 2016.
-
Lei Hua, Yang Song, Namhee Kim, Christian Laing, Jason T. L. Wang
and Tamar Schlick.
CHSalign: a Web server that builds upon
Junction-Explorer and RNAJAG for
pairwise alignment of RNA secondary structures
with coaxial helical stacking.
PLoS ONE,
11(1):e0147097, 2016.
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2015
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B. Zhao, Songhua Xu, S. Lin, X. Luo and L. Duan.
A new visual navigation system for exploring biomedical Open
Educational Resource (OER) videos.
J Am Med Inform Assoc.,
2015.
-
A. Al-Jouie, M. Esfandiari, S. Ramakrishnan and Usman Roshan.
Chi8: a GPU program for detecting significant interacting
SNPs with the Chi-square 8-df test.
BMC Res Notes,
8:436, 2015.
-
Yang Song, Lei Hua, Bruce A. Shapiro and Jason T. L. Wang.
Effective alignment of RNA pseudoknot structures using
partition function posterior log-odds scores.
BMC Bioinformatics,
16:39, 2015.
-
Nihir Patel and Jason T. L. Wang.
Semi-supervised prediction of gene regulatory networks using
machine learning algorithms.
Journal of Biosciences,
40(4):731-740, 2015.
|
2014
|
-
Wei Wang, Zhi Wei and Hongzhe Li.
A change-point model for identifying 3'UTR switching
by next-generation RNA sequencing.
Bioinformatics,
30(15):2162-2170, 2014.
-
Turki Turki and Usman Roshan.
MaxSSmap: a GPU program for mapping divergent short reads to
genomes with the maximum scoring subsequence.
BMC Genomics,
15:969, 2014.
-
Usman Roshan.
Multiple sequence alignment using Probcons and
Probalign.
Methods in Molecular Biology,
1079:147-153, 2014.
-
Kevin Byron, Jason T. L. Wang and Dongrong Wen.
Genome-wide prediction of coaxial helical stacking using random forests and covariance models.
International Journal on Artificial Intelligence Tools,
23(3):1460008, 2014.
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2013
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-
Y. W. Yi, H. J. Kang, H. J. Kim, J. S. Hwang, Antai Wang and
I. Bae.
Inhibition of constitutively activated phosphoinositide
3-kinase/AKT pathway enhances antitumor activity of
chemotherapeutic agents in breast cancer susceptibility gene 1-defective breast
cancer cells.
Molecular Carcinogenesis,
52(9):667-675, 2013.
-
Lian Duan, M. Khoshneshin, W. N. Street and Mei Liu.
Adverse drug effect detection.
IEEE Journal of Biomedical and Health Informatics,
17(2):305-311, 2013.
-
Mei Liu, Eugenia Renne McPeek Hinz,
Michael Edwin Matheny, Joshua C. Denny,
Jonathan Scott Schildcrout, Randolph A. Miller and Hua Xu.
Comparative analysis of pharmacovigilance methods in the
detection of adverse drug reactions using electronic medical records.
Journal of the American Medical Informatics Association,
20(3):420-426, 2013.
-
Zhi Wei, Wei Wang, Jonathan Bradfield, Jin Li,
Christopher Cardinale, Edward Frackelton,
Cecilia Kim, Frank Mentch, Kristel Van Steen,
Peter M. Visscher, Robert N. Baldassano and Hakon Hakonarson.
Large sample size, wide variant spectrum, and advanced
machine-learning technique boost risk prediction for inflammatory bowel
disease.
The American Journal of Human Genetics,
92(6):1008-1012, 2013.
-
Palak Sheth, Miguel Cervantes-Cervantes, Akhila Nagula,
Christian Laing and Jason T. L. Wang.
Novel features for identifying A-minors in three-dimensional
RNA molecules.
Computational Biology and Chemistry,
47:240-245, 2013.
-
Ling Zhong, Jason T. L. Wang, Dongrong Wen,
Virginie Aris, Patricia Soteropoulos and Bruce A. Shapiro.
Effective classification of microRNA precursors using
feature mining and AdaBoost algorithms.
OMICS: A Journal of Integrative Biology,
17:486-493, 2013.
-
Kevin Byron, Christian Laing, Dongrong Wen and Jason T. L. Wang.
A computational approach to finding RNA tertiary motifs
in genomic sequences: a case study.
Recent Patents on DNA & Gene Sequences,
7(2):115-122, 2013.
|
2012
|
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Wenge Guo, M. Yang, C. Xing and S. D. Peddada.
Analysis of high dimensional data using pre-defined set and
subset information, with applications to genomic data.
BMC Bioinformatics,
13:177, 2012.
-
Mei Liu, Yonghui Wu, Yukun Chen, Jingchun Sun,
Zhongming Zhao, Xue-wen Chen, Michael E. Matheny and Hua Xu.
Large-scale
prediction of adverse drug reactions
using chemical, biological, and phenotypic properties of drugs.
Journal of the American Medical Informatics Association,
19:e28-e35, 2012.
-
Yanxin Lu, Hua Xu, Neeraja B. Peterson, Qi Dai, Min Jiang, Joshua C. Denny
and Mei Liu.
Extracting
epidemiologic exposure and outcome terms from literature using
machine learning approaches.
International Journal of Data Mining and Bioinformatics,
6(4):447-459, 2012.
-
W. Wang, W. Hu, F. Hou, P. Hu and
Zhi Wei.
SNVerGUI: a desktop tool for variant
analysis of next-generation sequencing data.
Journal of Medical Genetics,
49(12):753-755, 2012.
-
Z. John Daye, Hongzhe Li and Zhi Wei.
A powerful test for multiple rare variants association studies that
incorporates sequencing qualities.
Nucleic Acids Research,
40(8):e60, 2012.
-
Christian Laing, Dongrong Wen, Jason T. L. Wang and
Tamar Schlick.
Predicting coaxial helical stacking in RNA junctions.
Nucleic Acids Research,
40(2):487-498, 2012.
-
Xin Zhang, Dennis Shasha, Yang Song and Jason T. L. Wang.
Fast elastic peak detection for mass spectrometry data mining.
IEEE Transactions on Knowledge and Data Engineering,
24(4):634-648, 2012.
-
Junilda Spirollari, Shawn X. Wang and Jason T. L. Wang.
Using folding ensemble and stem probability maximization
methods to predict RNA H-type pseudoknots.
Tsinghua Science and Technology,
Special Issue on Bioinformatics and Computational Biology,
17(6):691-700, 2012.
-
Lei Hua, Jason T. L. Wang, X. Ji, A. Malhotra,
M. Khaladkar, B. A. Shapiro and K. Zhang.
A method for discovering common patterns from two RNA secondary structures
and its application to structural repeat detection.
Journal of Bioinformatics and Computational Biology,
10(4):1250001, 2012.
-
M. Bao, M. Cervantes-Cervantes, Ling Zhong and Jason T. L. Wang.
Searching for non-coding RNAs in genomic sequences using ncRNAscout.
Genomics, Proteomics & Bioinformatics,
10(2):114-121, 2012.
|
2011
|
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Min Jiang, Yukun Chen, Mei Liu, S. Trent Rosenbloom,
Subramani Mani, Joshua C. Denny and Hua Xu.
A study of machine-learning-based approaches to extract clinical
entities and their assertions from discharge summaries.
Journal of the American Medical Informatics Association,
18(5):601-606, 2011.
-
Weixin Wang, Zhi Wei, Tak-Wah Lam and Junwen Wang.
Next generation sequencing has lower sequence coverage and poorer SNP-detection
capability in the regulatory regions.
Scientific Reports,
1(55), 2011.
-
Zhi Wei, Wei Wang, Pingzhao Hu, Gholson J. Lyon and Hakon Hakonarson.
SNVer: a statistical tool for variant calling in analysis of pooled or
individual next-generation sequencing data.
Nucleic Acids Research,
39:e132, 2011.
-
Usman Roshan, Satish Chikkagoudar,
Zhi Wei,
Kai Wang and Hakon Hakonarson.
Ranking causal variants and associated regions in genome-wide association
studies by the support vector machine and random forest.
Nucleic Acids Research,
39(9):e62, 2011.
-
Stephen J. Griesmer, Miguel Cervantes-Cervantes, Yang Song and
Jason T. L. Wang.
In silico prediction of noncoding RNAs using supervised learning and feature
ranking methods.
International Journal of Bioinformatics Research and Applications,
7(4):355-375, 2011.
|
2010
|
-
Mei Liu, Joshua C. Denny, Subramani Mani, Yukun Chen,
Yong Hu and Hua Xu.
Identifying potential drugs that induce QT prolongation using electronic
medical records.
BMC Bioinformatics,
11(S-4):P2, 2010.
-
Caiyan Li, Zhi Wei and Hongzhe Li.
Network-based empirical Bayes methods for linear models with applications to
genomic data.
Journal of Biopharmaceutical Statistics,
20(2):209-222, 2010.
-
H. Li, Zhi Wei and J. Maris.
A hidden Markov random field model for genome-wide association studies.
Biostatistics, 11(1):139-150, 2010.
-
Satish Chikkagoudar, Dennis R. Livesay and Usman Roshan.
PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding
RNA sequences.
Nucleic Acids Research,
38(Web Server issue):W59-W63, 2010.
-
Kevin Byron, M. Cervantes-Cervantes,
Jason T. L. Wang, W.C. Lin and Y. Park.
Mining roX1 RNA in Drosophila
genomes using covariance models.
International Journal of Computational Bioscience,
1(1):22-32, 2010.
-
Richipal Singh Bindra, Jason T. L. Wang and
Paramjeet Singh Bagga.
Bioinformatics methods for studying microRNA and ARE-mediated regulation of
post-transcriptional gene expression.
International Journal of Knowledge Discovery in Bioinformatics,
1(3):97-112, 2010.
-
Vandanaben Patel,
Jason T. L. Wang,
Shefali Setia,
Anurag Verma,
Charles D. Warden
and
Kaizhong Zhang.
On comparing two structured RNA multiple alignments.
Journal of Bioinformatics and Computational Biology,
8(6):967-980, 2010.
|
2009
|
-
Mei Liu, Xue-wen Chen and Raja Jothi.
Knowledge-guided inference of domain-domain
interactions from incomplete protein-protein interaction networks.
Bioinformatics,
25(19):2492-2499, 2009.
-
Xiaotong Lin, Mei Liu and Xue-wen Chen.
Assessing reliability of protein-protein
interactions by integrative analysis of data in model organisms.
BMC Bioinformatics,
10(S-4):S5, 2009.
-
Zhi Wei, Kai Wang, Hui-Qi Qu, Haitao Zhang, Jonathan Bradfield,
Cecilia Kim, Edward Frackleton, Cuiping Hou, Joseph T. Glessner,
Rosetta Chiavacci, Charles Stanley, Dimitri Monos,
Struan F. A. Grant, Constantin Polychronakos and Hakon Hakonarson.
From disease association to risk assessment: an optimistic view from
genome-wide association studies on type 1 diabetes.
PLoS Genetics, 5(10):e1000678, 2009.
-
Zhi Wei, Wenguang Sun, Kai Wang and Hakon Hakonarson.
Multiple testing in genome-wide association studies
via hidden Markov models.
Bioinformatics, 25(21):2802-2808, 2009.
-
Junilda Spirollari, Jason T. L. Wang,
Kaizhong Zhang, Vivian Bellofatto,
Yongkyu Park and Bruce A. Shapiro.
Predicting consensus structures for RNA
alignments via pseudo-energy minimization.
Bioinformatics and Biology Insights,
3:51-69, 2009.
-
Dongrong Wen and Jason T. L. Wang.
Design of an RNA structural motif database.
International Journal of Computational Intelligence in
Bioinformatics and Systems Biology, 1:32-41, 2009.
|
2008
|
-
Zhi Wei,
M. Li, T. Rebeck and H. Li.
U-statistics-based tests for multiple genes
in genetic association studies.
Annals of Human Genetics, 72:821-833, 2008.
-
Zhi Wei and Hongzhe Li.
A hidden spatial-temporal Markov random field model for
network-based analysis of time course gene expression data.
Annals of Applied Statistics, 2:408-429, 2008.
-
Usman Roshan, Satish Chikkagoudar and Dennis R. Livesay.
Searching for evolutionary distant RNA homologs within
genomic sequences using partition function posterior
probabilities.
BMC Bioinformatics,
9:61, 2008.
-
Mugdha Khaladkar, Jianghui Liu, Dongrong Wen,
Jason T. L. Wang and Bin Tian.
Mining small RNA structure elements
in untranslated regions of human and mouse
mRNAs using structure-based alignment.
BMC Genomics, 9:189, 2008.
-
Mugdha Khaladkar, Vandanaben Patel, Vivian Bellofatto,
Jeffrey Wilusz and Jason T. L. Wang.
Detecting conserved secondary structures in RNA
molecules using constrained structural alignment.
Computational Biology and Chemistry,
32:264-272, 2008.
-
Sen Zhang and Jason T. L. Wang.
Discovering frequent agreement subtrees from phylogenetic data.
IEEE Transactions on Knowledge and Data Engineering,
20(1):68-82, 2008.
|
2007
|
-
Zhi Wei and Hongzhe Li.
A Markov random field model for network-based analysis of
genomic data.
Bioinformatics,
23(12):1537-1544, 2007.
-
Zhi Wei and Hongzhe Li.
Nonparametric pathway-based regression models for analysis of
genomic data.
Biostatistics,
8(2):265-284, 2007.
-
Dennis R. Livesay, Patrick D. Kidd, Sepehr Eskandari and
Usman Roshan.
Assessing the ability of sequence-based methods to provide functional insight
within membrane integral proteins: a case study analyzing the
neurotransmitter/Na+ symporter family.
BMC Bioinformatics,
8:397, 2007.
-
Satish Chikkagoudar, Usman Roshan and Dennis Livesay.
eProbalign: generation and manipulation of multiple sequence alignments
using partition function posterior probabilities.
Nucleic Acids Research,
35(Web Server issue):W675-W677, 2007.
-
Marc Q. Ma, Kai Zhang, Hui-Yun Wang and Frank Y. Shih.
ELB-Q, a new method for improving the robustness
in DNA microarray image quantification.
IEEE Transactions on Information Technology in Biomedicine,
11(5):574-582, 2007.
-
Mugdha Khaladkar, Vivian Bellofatto, Jason T. L. Wang,
Bin Tian and Bruce A. Shapiro.
RADAR: a web server for RNA data analysis and research.
Nucleic Acids Research,
35(Web Server issue):W300-W304, 2007.
|
2006
|
-
Zhi Wei and Shane T. Jensen.
GAME: detecting cis-regulatory elements
using a genetic algorithm.
Bioinformatics,
22(13):1577-1584, 2006.
-
Yuri Dotsenko, Cristian Coarfa, Luay Nakhleh, John Mellor-Crummey
and Usman Roshan.
PRec-I-DCM3:
a parallel framework for fast and accurate large scale phylogeny
reconstruction.
International Journal on Bioinformatics Research and
Applications,
2(4):407-419, 2006.
-
Usman Roshan and Dennis R. Livesay.
Probalign: multiple sequence alignment using partition
function posterior probabilities.
Bioinformatics,
22(22):2715-2721, 2006.
-
Quanzhi Li and Yi-fang Brook Wu.
Identifying
important concepts from medical documents.
Journal of Biomedical Informatics, 39(6):668-679, 2006.
-
Jason T. L. Wang and Xiaoming Wu.
Kernel design for RNA classification
using support vector machines.
International Journal of Data Mining and
Bioinformatics, 1:57-76, 2006.
|
2005
|
-
Zhihua Du, Feng Lin and Usman Roshan.
Reconstruction of large phylogenetic trees: a parallel
approach.
Computational Biology and Chemistry, 29(4):273-280, 2005.
-
Jason T. L. Wang, Huiyuan Shan, Dennis Shasha and William H. Piel.
Fast
structural search in phylogenetic databases.
Evolutionary Bioinformatics,
1:37-46, 2005.
-
Jianghui Liu, Jason T. L. Wang, Jun Hu and Bin Tian.
A method for aligning RNA
secondary structures and its application to RNA motif detection.
BMC Bioinformatics, 6:89, 2005.
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