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Topic: Bioinformatics

Easton Li Xu, Xiaoning Qian, Qilian Yu, Han Zhang, Shuguang Cui, "Feature selection with interactions in logistic regression models using multivariate synergies for a GWAS application", BMC Genomics, 19(Suppl 4): 170, 9 pages, doi: 10.1186/s12864-018-4552-x, 2018.  (Journal Publication)  [More Details]  [Online]

A. Katiyar, A. Mohanty, C. Sima, J. Hua, R. Lopes, A. Datta and M. L. Bittner, "A Bayesian Approach to Determine the Composition of Heterogeneous Cancer Tissue", BMC Bioinformatics  (Journal Publication)  [More Details]  [Online]

A. Al Kawam, A. Sen, A. Datta and N. Dickey, "Understanding the Bioinformatics Challenges of Integrating Genomics into Healthcare", IEEE Journal of Biomedical and Health Informatics, DOI: 10.1109/JBHI.2017.2778263, to appear.  (Journal Publication)  [More Details]  [Online]

Navadon Khunlertgit and Byung-Jun Yoon, "Incorporating topological information for predicting robust cancer subnetwork markers in human protein-protein interaction network", BMC Bioinformatics, 17(Suppl 13):351, 2016  (Journal Publication)  [More Details]  [Online]

Roozbeh Dehghannasiri, Byung-Jun Yoon, and Edward R. Dougherty, "Optimal experimental design for gene regulatory networks in the presence of uncertainty", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.12, no.4, pp.938-950, 2015.  (Journal Publication)  [More Details]  [Online]

Yvette A. Halley, Scot E. Dowd, Jared E. Decker, Paul M. Seabury, Eric Bhattarai, Charles D. Johnson, Dale Rollins, Ian R. Tizard, Donald J. Brightsmith, Markus J. Peterson, Jeremy F. Taylor, Christopher M. Seabury, "A Draft De Novo Genome Assembly for the Northern Bobwhite (Colinus virginianus) Reveals Evidence for a Rapid Decline in Effective Population Size Beginning in the Late Pleistocene", PLOS ONE, March 2014, Volume 9, Issue 3  (Journal Publication)  [More Details]  [Online]

U.M. Braga-Neto, A. Zollanvari, and E.R. Dougherty, "Cross-validation under separate sampling: strong bias and how to correct it", Bioinformatics, Vol. 30, No. 23, Dec 1 2014, pp. 3349-3355.  (Journal Publication)  [More Details]  [Online]

SEQC/MAQC-III Consortium, "A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium", Nature Biotechnology (2014) doi:10.1038/nbt.2957  (Journal Publication)  [More Details]  [Online]

Noushin Ghaffari, Alejandro Sanchez-Flores, Ryan Doan, Karina D. Garcia-Orozco, Patricia L. Chen, Adrian Ochoa-Leyva, Alonso A. Lopez-Zavala, J. Salvador Carrasco, Chris Hong, Luis G. Brieba, Enrique Rudiño-Piñera, Philip D. Blood, Jason E. Sawyer, Charles D. Johnson, Scott V. Dindot, Rogerio R. Sotelo-Mundo, Michael F. Criscitiello, "Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture", Nature Scientific Reports 4, Article number: 7081  (Journal Publication)  [More Details]  [Online]

Fangjun Li, Cheng Cheng, Fuhao Cui, Marcos VV de Oliveira, Xiao Yu, Xiangzong Meng, Aline C Intorne, Kevin Babilonia, Maoying Li, Bo Li, Sixue Chen, Xianfeng Ma, Shunyuan Xiao, Yi Zheng, Zhangjun Fei, Richard P Metz, Charles D Johnson, Hisashi Koiwa, Wenxian Sun, Zhaohu Li, Gonçalo A de Souza Filho, Libo Shan, Ping He, "Modulation of RNA Polymerase II Phosphorylation Downstream of Pathogen Perception Orchestrates Plant Immunity", Cell Host & Microbe doi:10.1016/j.chom.2014.10.018  (Journal Publication)  [More Details]  [Online]

Noushin Ghaffari, Mohammadmahdi R Yousefi, Charles D Johnson, Ivan Ivanov and Edward R Dougherty, "Modeling the next generation sequencing sample processing pipeline for the purposes of classification", BMC Bioinformatics 2013, 14:307  (Journal Publication)  [More Details]  [Online]

Ryan Doan, Noah D Cohen, Jason Sawyer, Noushin Ghaffari, Charles D Johnson, Scott V Dindot, "Whole-Genome Sequencing and Genetic Variant Analysis of a Quarter Horse Mare", BMC Genomics, 2012; 13 (1): 78  (Journal Publication)  [More Details]  [Online]

Alfonso Clavijo, Amir Nikooienejad, Mohammad Shahrokh , Richard P. Metz, Scott Schwartz, Esmaeil Atashpaz Gargari, Thomas J. Deliberto, Mark W. Lutman, Kerri Pedersen , Luis R. Bazan, Leo G. Koster, Melinda Jenkins-Moore, Sabrina L. Swenson, Mike Zang, Tammy Beckham, Charles D. Johnson , Mangkey Bounpheng, "Identification and Analysis of the First 2009 Pandemic H1N1 Influenza Virus from U.S. Feral Swine", Zoonoses and Public Health. DOI: 10.1111/zph.12006  (Journal Publication)  [More Details]  [Online]

Y. Wang, N. Ghaffari, C. D. Johnson, U. M. Braga-Neto, H. Wang, R. Chen, and H. Zhou, "Evaluation of Coverage and Depth of Transcriptome by RNA-Seq in Chickens", BMC Bioinformatics, 12 (Suppl 10):S5, 2011  (Journal Publication)  [More Details]  [Online]