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


Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny.
Cleary A, Farmer A. 
Bioinformatics. 2017 Nov 29. doi: 10.1093/bioinformatics/btx757. [Epub ahead of print] PMID: 29194466


Anilinopyrimidine Resistance in Botrytis cinerea Is Linked to Mitochondrial Function.
Andreas Mosbach, Dominique Edel, Andrew D. Farmer, Stephanie Widdison, Thierry Barchietto, Robert A. Dietrich, Andy Corran and Gabriel Scalliet
Front. Microbiol., 30 Nov 2017. doi: 10.3389/fmicb.2017.02361. PMID: 29250050


Comparative genomics of an unusual biogeographic disjunction in the cotton tribe (Gossypieae) yields insights into genome downsizing.
Grover CE, Arick MA 2nd, Conover JL, Thrash A, Hu G, Sanders WS, Chuan-Yu H, Naqvi RZ, Farooq M, Li X, Gong L, Mudge J, Ramaraj T, Udall JA, Peterson DG, Wendel JF. 
Genome Biol Evol. 2017 Nov 27. doi: 10.1093/gbe/evx248. [Epub ahead of print] PMID: 29194487


Transcriptomic responses of Biomphalaria pfeifferi to Schistosoma mansoni: Investigation of a neglected African snail that supports more S. mansoni transmission than any other snail species.
Buddenborg SK, Bu L, Zhang SM, Schilkey FD, Mkoji GM, Loker ES. 
PLoS Negl Trop Dis. 2017 Oct 18;11(10):e0005984. doi: 10.1371/journal.pntd.0005984. eCollection 2017 Oct. PMID: 29045404


Gene-enriched draft genome of the cattle tick Rhipicephalus microplus: assembly by the hybrid Pacific Biosciences/Illumina approach enabled analysis of the highly repetitive genome.
Barrero RA, Guerrero FD, Black M, McCooke J, Chapman B, Schilkey F, Pérez de León AA, Miller RJ, Bruns S, Dobry J, Mikhaylenko G, Stormo K, Bell C, Tao Q, Bogden R, Moolhuijzen PM, Hunter A, Bellgard MI. 
Int J Parasitol. 2017 Aug;47(9):569-583. doi: 10.1016/j.ijpara.2017.03.007. Epub 2017 Jun 1. PMID: 28577881