Genomics & Bioinformatics Core Facility


Select 2016 Publications

Asselman J, De Coninck DIM, Pfrender ME, De Schamphelaere KAC. Gene Body Methylation Patterns in Daphnia Are Associated with Gene Family Size. Genome Biology and Evolution. 2016;8(4):1185-96. doi: 10.1093/gbe/evw069 

Behura SK, Sarro J, Li P, Mysore K, Severson DW, Emrich SJ, et al. High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti. Bmc Genomics. 2016;17:11. doi: 10.1186/s12864-016-2468-x.

Dowle EJ, Bracewell R, Pfrender M, Mock K, Bentz B, Ragland G. Reproductive isolation and environmental adaptation shape the phylogeography of Mountain Pine Beetle (Dendroctonus ponderosae). Integrative and Comparative Biology. 2016;56:E57-E.DOI:10.1111/ele.12460

Evans NT, Olds BP, Renshaw MA, Turner CR, Li YY, Jerde CL, et al. Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Molecular Ecology Resources. 2016;16(1):29-41. doi: 10.1111/1755-0998.12433.

Feldman CR, Durso AM, Hanifin CT, Pfrender ME, Ducey PK, Stokes AN, et al. Is there more than one way to skin a newt? Convergent toxin resistance in snakes is not due to a common genetic mechanism. Heredity. 2016;116(1):84-91. doi: 10.1038/hdy.2015.73. 

Hall AB, Papathanos PA, Sharma A, Cheng CD, Akbari OS, Assour L, et al. Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes. Proceedings of the National Academy of Sciences of the United States of America. 2016;113(15):E2114-E23. doi: 10.1073/pnas.1525164113

Olds BP, Jerde CL, Renshaw MA, Li YY, Evans NT, Turner CR, et al. Estimating species richness using environmental DNA. Ecology and Evolution. 2016;6(12):4214-26. doi: 10.1002/ece3.2186.

Evans NT, Olds BP, Renshaw MA, Turner CR, Li Y, Jerde CL et al.. Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Mol Ecol Resour. 2015.

Paiva MHS, Lovin DD, Mori A, Melo-Santos MAV, Severson DW, Ayres CFJ. Identification of a major Quantitative Trait Locus determining resistance to the organophosphate temephos in the dengue vector mosquito Aedes aegypti. Genomics. 2016;107(1):40-8. doi: 10.1016/j.ygeno.2015.11.004

Reyna C, Medie FM, Champion MM, Champion PA. Rational engineering of a virulence gene from Mycobacterium tuberculosis facilitates proteomic analysis of a natural protein N-terminus. Scientific Reports. 2016;6:11. doi: 10.1038/srep33265.

Rosenzweig BK, Pease JB, Besansky NJ, Hahn MW. Powerful methods for detecting introgressed regions from population genomic data. Molecular Ecology. 2016;25(11):2387-97. doi: 10.1111/mec.13610.

Uyhelji HA, Cheng CD, Besansky NJ. Transcriptomic differences between euryhaline and stenohaline malaria vector sibling species in response to salinity stress. Molecular Ecology. 2016;25(10):2210-25. doi: 10.1111/mec.13609

Vacchina P, Norris-Mullins B, Abengozar MA, Viamontes CG, Sarro J, Stephens MT, et al. Genomic Appraisal of the Multifactorial Basis for In Vitro Acquisition of Miltefosine Resistance in Leishmania donovani. Antimicrobial Agents and Chemotherapy. 2016;60(7):4089-100. doi: 10.1128/aac.00478-16

2015 Publications

Feldman CR, Durso AM, Hanifin CT, Pfrender ME, Ducey PK, Stokes AN et al.. Is there more than one way to skin a newt? Convergent toxin resistance in snakes is not due to a common genetic mechanism. Heredity.2015; PMID:26374236

Siwo G, Rider A, Tan A et al. Prediction of fine-tuned promoter activity from DNA sequence. F1000Research 2016, 5:158. DOI: 10.12688/f1000research.7485.1

Egan SP, Ragland GJ, Assour L, Powell TH, Hood GR, Emrich S et al. Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow.Ecol Lett.2015.18;8;817-25.PMID:26077935.DOI:10.1111/ele.12460

Choudhury O, Hazekamp N, Thain D, Emrich S. Accelerating Comparative Genomics Workflows in a Distributed Environment with Optimized Data Partitioning and Workflow Fusion. Scalable Computing: Practice and Expereience. 2015;16;(1)53-70

Ramalho-Ortigão M, Coutinho-Abreu IV, Balbino VQ, Figueiredo CA, Mukbel R, Dayem H et al. Phlebotomus papatasi SP15: mRNA expression variability and amino acid sequence polymorphisms of field populations. Parasit Vectors. 2015;8;298.PMID:26022221.DOI:10.1186/s13071-015-0914-2

Siwo GH, Rider A, Tan A, Pinapati RS, Emrich S, Chawla N, Ferdit MT. Predicition of Fine-tuned Promoter Activity from DNA Sequence.bioRxiv.2015.DOI:10.1101/030049

Giraldo-Calderón GI, Emrich SJ, MacCallum RM, Maslen G, Dialynas E, Topalis P et al.VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases.Nucleic Acids Res.2015;43; D707-13.PMID:25510499.DOI:10.1093/nar/gku1117

Evans NT, Olds BP, Renshaw MA, Turner CR, Li Y, Jerde CL et al.. Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Mol Ecol Resour. 2015;PMID: 26032773

Warren AS, Aurrecoechea C, Brunk B, Desai P, Emrich S, Giraldo-Calderón GI et al.. RNA-Rocket: an RNA-Seq analysis resource for infectious disease research. Bioinformatics. 2015;31;(9)1496-8. PMID: 25573919

Singh PP, Li L, Schorey JS. Exosomal RNA from Mycobacterium tuberculosis-Infected Cells Is Functional in Recipient Macrophages. Traffic. 2015;16;(6)555-71. PMID: 25753779

Mbengue A, Bhattacharjee S, Pandharkar T, Liu H, Estiu G, Stahelin RV et al.. A molecular mechanism of artemisinin resistance in Plasmodium falciparum malaria. Nature. 2015;520;(7549)683-7. PMID: 25874676

Evans NT, Olds BP, Renshaw MA, Turner CR, Li Y, Jerde CL et al.. Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Mol Ecol Resour. 2015; PMID: 26032773

Laricchia K.M., McCleary T.S., Hoban S.M., Borkowski D., Romero-Severson J.2015. Chloroplast haplotypes suggest preglacial differentiation and separate postglacial migration paths for the threatened North American forest tree Juglans cinerea L. Tree Genetics and Genomes 11:30. DOI:10.1007/s11295-015-0852-3

Hickner PV, Mori A, Zeng E, Tan JC, Severson DW. Whole transcriptome responses among females of the filariasis and arbovirus vector mosquito Culex pipiens implicate TGF-β signaling and chromatin modification as key drivers of diapause induction. Funct Integr Genomics. 2015;PMID: 25634120

Geraci NS, Tan JC, McDowell MA. Characterization of microRNA expression profiles in Leishmania-infected human phagocytes. Parasite Immunol. 2015;37;(1)43-51. PMID: 25376316
Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV et al.. Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science. 2015;347;(6217)1258524. PMID: 25431491

Asselman J, Pfrender ME, Lopez JA, De Coninck DI, Janssen CR, Shaw JR et al.. Conserved transcriptional responses to cyanobacterial stressors are mediated by alternate regulation of paralogous genes in Daphnia. Mol Ecol. 2015;24;(8)1844-55. PMID: 25754071

Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE et al. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science. 2015; PMID:25554792

Mesquita RD et al. Genome Of Rhodnius Prolixus, An Insect Vector Of Chagas Disease, Reveals Unique Adaptations To Hematophagy And Parasite Infection. Proceedings of the National Academy of Sciences. 2015.

2014 Publications

Mysore K, Andrews E, Li P, Duman-Scheel M. Chitosan/siRNA nanoparticle targeting demonstrates a requirement for single-minded during larval and pupal olfactory system development of the vector mosquito Aedes aegypti. BMC Dev Biol. 2014;14;9. PMID: 24552425

Tomchaney M, Mysore K, Sun L, Li P, Emrich SJ, Severson DW et al.. Examination of the genetic basis for sexual dimorphism in the Aedes aegypti (dengue vector mosquito) pupal brain. Biol Sex Differ. 2014;5;10. PMID: 25729562

Zhang W, Zeng E, Liu D, Jones SE, Emrich S. Mapping genomic features to functional traits through microbial whole genome sequences. Int J Bioinform Res Appl. 2014;10;(4-5)461-78. PMID: 24989863
Yampolsky LY, Zeng E, Lopez J, Williams PJ, Dick KB, Colbourne JK et al.. Functional genomics of acclimation and adaptation in response to thermal stress in Daphnia. BMC Genomics. 2014;15;859. PMID: 25282344

Xiao Q, Vakulenko S, Chang M, Mobashery S. Mutations in mmpL and in the cell wall stress stimulon contribute to resistance to oxadiazole antibiotics in methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother. 2014;58;(10)5841-7. PMID: 25049248

Thrasher A, Musgrave Z, Kachmarck B, Thain D, Emrich S. Scaling up genome annotation using MAKER and work queue. Int J Bioinform Res Appl. 2014;10;(4-5)447-60. PMID: 24989862

Stokes AN, Ducey PK, Neuman-Lee L, Hanifin CT, French SS, Pfrender ME et al.. Confirmation and distribution of tetrodotoxin for the first time in terrestrial invertebrates: two terrestrial flatworm species (Bipalium adventitium and Bipalium kewense). PLoS One. 2014;9;(6)e100718. PMID: 24963791

Routtu J, Hall MD, Albere B, Beisel C, Bergeron RD, Chaturvedi A et al.. An SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traits. BMC Genomics. 2014;15;1033. PMID: 25431334

O'Neil ST, Dzurisin JD, Williams CM, Lobo NF, Higgins JK, Deines JM et al.. Gene expression in closely related species mirrors local adaptation: consequences for responses to a warming world. Mol Ecol. 2014;23;(11)2686-98. PMID: 24766086

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

McGlothlin JW, Chuckalovcak JP, Janes DE, Edwards SV, Feldman CR, Brodie ED et al.. Parallel evolution of tetrodotoxin resistance in three voltage-gated sodium channel genes in the garter snake Thamnophis sirtalis. Mol Biol Evol. 2014;31;(11)2836-46. PMID: 25135948

Favila MA, Geraci NS, Zeng E, Harker B, Condon D, Cotton RN et al.. Human dendritic cells exhibit a pronounced type I IFN signature following Leishmania major infection that is required for IL-12 induction. J Immunol. 2014;192;(12)5863-72. PMID: 24808365

Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE et al.. Standardized metadata for human pathogen/vector genomic sequences. PLoS One. 2014;9;(6)e99979. PMID: 24936976