Genomics & Bioinformatics Core Facility

Archived Publications

2013 Publications

Sarro J, Andrews E, Sun L, Behura SK, Tan JC, Zeng E et al.. Requirement for commissureless2 function during dipteran insect nerve cord development. Dev Dyn. 2013;242;(12)1466-77. PMID: 24026811
Nair SC, Pattaradilokrat S, Zilversmit MM, Dommer J, Nagarajan V, Stephens MT et al.. Genome-wide polymorphisms and development of a microarray platform to detect genetic variations in Plasmodium yoelii. Mol Biochem Parasitol. 2014;194;(1-2)9-15. PMID: 24685548
Miner, B. E., Knapp, R. A., Colbourne, J. K. and Pfrender, M. E. (2013), Evolutionary history of alpine and subalpine Daphnia in western North America. Freshwater Biology, 58: 1512–1522. doi: 10.1111/fwb.12152
Livermore JA, Emrich SJ, Tan J, Jones SE. Freshwater bacterial lifestyles inferred from comparative genomics. Environ Microbiol. 2014;16;(3)746-58. PMID: 23889754
Agrawal S, Chung DW, Ponts N, van Dooren GG, Prudhomme J, Brooks CF et al.. An apicoplast localized ubiquitylation system is required for the import of nuclear-encoded plastid proteins. PLoS Pathog. 2013;9;(6)e1003426. PMID: 23785288
Abrudan J, Ramalho-Ortigão M, O'Neil S, Stayback G, Wadsworth M, Bernard M et al.. The characterization of the Phlebotomus papatasi transcriptome. Insect Mol Biol. 2013;22;(2)211-32. PMID: 23398403

2012 Publications

O'Neil ST, Emrich SJ. Haplotype and minimum-chimerism consensus determination using short sequence data. BMC Genomics. 2012;13 Suppl 2;S4. PMID: 22537299
Christopher Moretti, Andrew Thrasher, Li Yu, Michael Olson, Scott Emrich, Douglas Thain, "A Framework for Scalable Genome Assembly on Clusters, Clouds, and Grids", IEEE Transactions on Parallel & Distributed Systems, vol.23, no. 12, pp. 2189-2197, Dec. 2012, doi:10.1109/TPDS.2012.80
Miner BE, De Meester L, Pfrender ME, Lampert W, Hairston NG. Linking genes to communities and ecosystems: Daphnia as an ecogenomic model. Proc Biol Sci. 2012;279;(1735)1873-82. PMID: 22298849
Megy K, Emrich SJ, Lawson D, Campbell D, Dialynas E, Hughes DS et al.. VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. Nucleic Acids Res. 2012;40;D729-34. PMID: 22135296
Manske M, Miotto O, Campino S, Auburn S, Almagro-Garcia J, Maslen G et al.. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature. 2012;487;(7407)375-9. PMID: 22722859
Lodge DM, Turner CR, Jerde CL, Barnes MA, Chadderton L, Egan SP et al.. Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA. Mol Ecol. 2012;21;(11)2555-8. PMID: 22624944
Latta LC, Weider LJ, Colbourne JK, Pfrender ME. The evolution of salinity tolerance in Daphnia: a functional genomics approach. Ecol Lett. 2012;15;(8)794-802. PMID: 22583985
Lanc, I., Bui, P., Thain, D. and Emrich, S. (2014), Adapting bioinformatics applications for heterogeneous systems: a case study. Concurrency Computat.: Pract. Exper., 26: 866–877. doi: 10.1002/cpe.2927
Harker BW, Hong YS, Sim C, Dana AN, Bruggner RV, Lobo NF et al.. Transcription profiling associated with life cycle of Anopheles gambiae. J Med Entomol. 2012;49;(2)316-25. PMID: 22493849
Galvan MD, Foreman DB, Zeng E, Tan JC, Bohlson SS. Complement component C1q regulates macrophage expression of Mer tyrosine kinase to promote clearance of apoptotic cells. J Immunol. 2012;188;(8)3716-23. PMID: 22422887
Feldman CR, Brodie ED, Brodie ED, Pfrender ME. Constraint shapes convergence in tetrodotoxin-resistant sodium channels of snakes. Proc Natl Acad Sci U S A. 2012;109;(12)4556-61. PMID: 22392995
Cheeseman IH, Miller BA, Nair S, Nkhoma S, Tan A, Tan JC et al.. A major genome region underlying artemisinin resistance in malaria. Science. 2012;336;(6077)79-82. PMID: 22491853
Chauhan C, Behura SK, Debruyn B, Lovin DD, Harker BW, Gomez-Machorro C et al.. Comparative expression profiles of midgut genes in dengue virus refractory and susceptible Aedes aegypti across critical period for virus infection. PLoS One. 2012;7;(10)e47350. PMID: 23077596
Cheng C, White BJ, Kamdem C, Mockaitis K, Costantini C, Hahn MW et al.. Ecological genomics of Anopheles gambiae along a latitudinal cline: a population-resequencing approach. Genetics. 2012;190;(4)1417-32. PMID: 22209907

2011 Publications

Tan JC, Miller BA, Tan A, Patel JJ, Cheeseman IH, Anderson TJ et al.. An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations. Genome Biol. 2011;12;(4)R35. PMID: 21477297
Singh PP, LeMaire C, Tan JC, Zeng E, Schorey JS. Exosomes released from M. tuberculosis infected cells can suppress IFN-γ mediated activation of naïve macrophages. PLoS One. 2011;6;(4)e18564. PMID: 21533172
Simon JC, Pfrender ME, Tollrian R, Tagu D, Colbourne JK. Genomics of environmentally induced phenotypes in 2 extremely plastic arthropods. J Hered. 2011;102;(5)512-25. PMID: 21525179
Samarakoon U, Regier A, Tan A, Desany BA, Collins B, Tan JC et al.. High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum. BMC Genomics. 2011;12;116. PMID: 21324207
Rund SS, Hou TY, Ward SM, Collins FH, Duffield GE. Genome-wide profiling of diel and circadian gene expression in the malaria vector Anopheles gambiae. Proc Natl Acad Sci U S A. 2011;108;(32)E421-30. PMID: 21715657
Parnell, J. , Rompato, G. , Crowl, T. , Weimer, B. , Pfrender, M. , et al. (2011). Phylogenetic distance in great salt lake microbial communities. Aquatic Microbial Ecology, 64(3), 267-273. PDF
Parnell JJ, Callister SJ, Rompato G, Nicora CD, Paša-Tolić L, Williamson A et al.. Time-course analysis of the Shewanella amazonensis SB2B proteome in response to sodium chloride shock. Sci Rep. 2011;1;25. PMID: 22355544 
Orsini L, Decaestecker E, De Meester L, Pfrender ME, Colbourne JK. Genomics in the ecological arena. Biol Lett. 2011;7;(1)2-3. PMID: 20702453
Neuman-Lee L, S McGaugh, ME Pfrender, FJ Janzen. 2011. Using Mitochondrial DNA to Determine the Origin of a Snake Found in Alaska. Journal of Herpetology 45:63-65. Full-text
Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH et al.. The ecoresponsive genome of Daphnia pulex. Science. 2011;331;(6017)555-61. PMID: 21292972
Castoe TA, Bronikowski AM, Brodie ED, Edwards SV, Pfrender ME, Shapiro MD et al.. A proposal to sequence the genome of a garter snake (Thamnophis sirtalis). Stand Genomic Sci. 2011;4;(2)257-70. PMID: 21677863
Cassone BJ, Molloy MJ, Cheng C, Tan JC, Hahn MW, Besansky NJ. Divergent transcriptional response to thermal stress by Anopheles gambiae larvae carrying alternative arrangements of inversion 2La. Mol Ecol. 2011;20;(12)2567-80. PMID: 21535279
Carrasco MA, Tan JC, Duman JG. A cross-species compendium of proteins/gene products related to cold stress identified by bioinformatic approaches. J Insect Physiol. 2011;57;(8)1127-35. PMID: 21565197