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Topic: Next Generation Sequencing

A. Bahadorinejad and U.M. Braga-Neto, "Optimal Fault Detection and Diagnosis in Transcriptional Circuits using Next-Generation Sequencing", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 15, Issue 2, Mar-Apr 2018  (Journal Publication)  [More Details]  [Online]

A. Al-Kawam, S. Khatri and A. Datta, "A GPU-CPU heterogeneous algorithm for NGS read alignment", International Journal of Computational Biology and Drug Design, Vol. 11, Nos. 1/2, 52-66, 2018.  (Journal Publication)  [More Details]  [Online]

A. Al-Kawam, S. Khatri and A. Datta, "A Survey of Software and Hardware Approaches to Short Read Alignment in Next Generation Sequencing", IEEE/ACM Trans. on Computational Biology and Bioinformatics, Vol. 14, No. 6, 1202-1213, Nov.-Dec. 2017. DOI: 10.1109/TCBB.2016.2586070.  (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]

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]

Madina BR, Kumar V1 Metz R, Mooers BH, Bundschuh R, Cruz-Reyes J., "Native mitochondrial RNA-binding complexes in kinetoplastid RNA editing differ in guide RNA composition", RNA. 2014 Jul;20(7):1142-52. doi: 10.1261/rna.044495.114. Epub 2014 May 27.  (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]

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]