NCGR Publications - 2018

Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content.
Tran HTM, Ramaraj T, Furtado A, Lee LS, Henry RJ. 
Plant Biotechnol J. 2018 Mar 6. doi: 10.1111/pbi.12912. [Epub ahead of print] PMID: 29509991

 

A transcriptome-SNP-derived linkage map of Apios americana (potato bean) provides insights about genome re-organization and synteny conservation in the phaseoloid legumes.
Jugpreet Singh, Scott R. Kalberer, Vikas Belamkar, Teshale Assefa, Matthew N. Nelson, Andrew D. Farmer, William J. Blackmon, Steven B. Cannon 
Theor Appl Genet. 2018 Feb;131(2):333-351. doi: 10.1007/s00122-017-3004-3. PMID: 29071392

 

Histone citrullination represses miRNA expression resulting in increased oncogene mRNAs in somatolactotrope cells.
JDeVore SB, Young CH, Li G, Sundararajan A, Ramaraj T, Mudge J, Schilkey F, Muth A, Thompson PR, Cherrington BD. 
Mol Cell Biol. 2018 Jul 9. pii: MCB.00084-18. doi: 10.1128/MCB.00084-18. [Epub ahead of print] PMID: 29987187

 

High-resolution crossover mapping reveals similarities and differences of male and female recombination in maize.
Kianian PMA, Wang M, Simons K, Ghavami F, He Y, Dukowic-Schulze S, Sundararajan A, Sun Q, Pillardy J, Mudge J, Chen C, Kianian SF, Pawlowski WP. 
Nat Commun. 2018 Jun 18;9(1):2370. doi: 10.1038/s41467-018-04562-5. PMID: 29915302

 

Exploring Frequented Regions in Pan-Genomic Graphs.
Cleary A, Ramaraj T, Kahanda I, Mudge J, Mumey B. 
IEEE/ACM Trans Comput Biol Bioinform. 2018 Aug 9. doi: 10.1109/TCBB.2018.2864564. [Epub ahead of print] PMID: 30106690

 

Cranberry-derived proanthocyanidins induce a differential transcriptomic response within Candida albicans urinary biofilms.
Sundararajan A, Rane HS, Ramaraj T, Sena J, Howell AB, Bernardo SM, Schilkey FD, Lee SA. 
PLoS One. 2018 Aug 8;13(8):e0201969. doi: 10.1371/journal.pone.0201969. eCollection 2018. PMID: 30089157

 

Salt and oxidative stresses uniquely regulate tomato cytokinin levels and transcriptomic response.
Erika A. Keshishian, H. Tucker Hallmark, Thiruvarangan Ramaraj, Lenka Plačková, Anitha Sundararajan, Faye Schilkey, Ondřej Novák Aaron M. Rashotte. 
Plant Direct 2 (7), e00071 19 July 2018.

 

Transcriptome analysis reveals a stress response of Shewanella oneidensis deprived of background levels of ionizing radiation.
Castillo H, Li X, Schilkey F, Smith GB. 
PLoS One. 2018 Aug 8;13(8):e0201969. doi: 10.1371/journal.pone.0201969. eCollection 2018. PMID: 29768440

 

A Whole Genome Assembly of the Horn Fly, Haematobia irritans, and Prediction of Genes with Roles in Metabolism and Sex Determination.
Konganti K, Guerrero FD, Schilkey F, Ngam P, Jacobi JL, Umale PE, Perez de Leon AA, Threadgill DW. 
G3 (Bethesda). 2018 May 4;8(5):1675-1686. doi: 10.1534/g3.118.200154. PMID: 29602812

 

Correction: 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. 2018 Jan 25;13(1):e0192128. doi: 10.1371/journal.pone.0192128. eCollection 2018. PMID: 29370309

 

Unique Molecular Identifiers reveal a novel sequencing artefact with implications for RNA-Seq based gene expression analysis.
Sena, J.A., Galotto, G., Devitt, N.P., Connick, M.C., Jacobi, J.L., Umale, P.E., Vidali, L., Bell, C.J. 
Scientific Reports 8, 13121. PMID: 30177820