NCGR Publications - 2017

Dengue virus serotype 2 infection alters midgut and carcass gene expression in the Asian tiger mosquito, Aedes albopictus.
Tsujimoto H, Hanley KA, Sundararajan A, Devitt NP, Schilkey FD, Hansen IA. 
PLoS One. 2017 Feb 2;12(2):e0171345. doi: 10.1371/journal.pone.0171345. eCollection 2017. PMID: 28152011

 

Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes.
Zhou P, Silverstein KA, Ramaraj T, Guhlin J, Denny R, Liu J, Farmer AD, Steele KP, Stupar RM, Miller JR, Tiffin P, Mudge J, Young ND. 
BMC Genomics. 2017 Mar 27;18(1):261. doi: 10.1186/s12864-017-3654-1. PMID: 28347275

 

Zinc-Dependent Transcriptional Regulation in Paracoccus denitrificans.
Neupane DP, Jacquez B, Sundararajan A, Ramaraj T, Schilkey FD, Yukl ET. 
Front Microbiol. 2017 Apr 11;8:569. doi: 10.3389/fmicb.2017.00569. eCollection 2017. PMID: 28443074

 

Crude oil impairs immune function and increases susceptibility to pathogenic bacteria in southern flounder.
Bayha KM, Ortell N, Ryan CN, Griffitt KJ, Krasnec M, Sena J, Ramaraj T, Takeshita R, Mayer GD, Schilkey F, Griffitt RJ. 
PLoS One. 2017 May 2;12(5):e0176559. doi:10.1371/journal.pone.0176559. eCollection 2017. PMID: 28464028

 

Hybrid assembly with long and short reads improves discovery of gene family expansions.
Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu J, Stupar RM, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, Schatz MC, Tiffin P, Young ND, Silverstein KAT. 
BMC Genomics. 2017 Jul 19;18(1):541. doi: 10.1186/s12864-017-3927-8. PMID: 28724409

 

Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula.
Moll KM, Zhou P, Ramaraj T, Fajardo D, Devitt NP, Sadowsky MJ, Stupar RM, Tiffin P, Miller JR, Young ND, Silverstein KAT, Mudge J. 
BMC Genomics. 2017 Aug 4;18(1):578. doi: 10.1186/s12864-017-3971-4. PMID: 28778149

 

Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution.
Lightfoot DJ, Jarvis DE, Ramaraj T, Lee R, Jellen EN, Maughan PJ 
BMC Biol. 2017 Aug 31;15(1):74. doi: 10.1186/s12915-017-0412-4. PMID: 28854926