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Items: 41

1.

Adjusted likelihood-ratio test for variants with unknown genotypes.

Nowling RJ, Emrich SJ.

J Bioinform Comput Biol. 2018 Oct;16(5):1840020. doi: 10.1142/S0219720018400206.

PMID:
30419783
2.

Reduced-representation sequencing identifies small effective population sizes of Anopheles gambiae in the north-western Lake Victoria basin, Uganda.

Wiltshire RM, Bergey CM, Kayondo JK, Birungi J, Mukwaya LG, Emrich SJ, Besansky NJ, Collins FH.

Malar J. 2018 Aug 6;17(1):285. doi: 10.1186/s12936-018-2432-0.

3.

HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning.

Choudhury O, Chakrabarty A, Emrich SJ.

Sci Rep. 2018 Jul 2;8(1):9936. doi: 10.1038/s41598-018-28364-3.

4.

Climate-mediated hybrid zone movement revealed with genomics, museum collection, and simulation modeling.

Ryan SF, Deines JM, Scriber JM, Pfrender ME, Jones SE, Emrich SJ, Hellmann JJ.

Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2284-E2291. doi: 10.1073/pnas.1714950115. Epub 2018 Feb 20.

5.

Single molecule sequencing-guided scaffolding and correction of draft assemblies.

Zhu S, Chen DZ, Emrich SJ.

BMC Genomics. 2017 Dec 6;18(Suppl 10):879. doi: 10.1186/s12864-017-4271-8.

6.

GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison.

Faisal FE, Newaz K, Chaney JL, Li J, Emrich SJ, Clark PL, Milenković T.

Sci Rep. 2017 Nov 2;7(1):14890. doi: 10.1038/s41598-017-14411-y.

7.

Whole-Genome Shotgun Sequencing of Two β-Proteobacterial Species in Search of the Bulgecin Biosynthetic Cluster.

Horsman ME, Marous DR, Li R, Oliver RA, Byun B, Emrich SJ, Boggess B, Townsend CA, Mobashery S.

ACS Chem Biol. 2017 Oct 20;12(10):2552-2557. doi: 10.1021/acschembio.7b00687. Epub 2017 Sep 26.

8.

Highly Accurate and Efficient Data-Driven Methods For Genotype Imputation.

Choudhury O, Chakrabarty A, Emrich SJ.

IEEE/ACM Trans Comput Biol Bioinform. 2017 May 26. doi: 10.1109/TCBB.2017.2708701. [Epub ahead of print]

PMID:
28574365
9.

Chromosomal inversions and ecotypic differentiation in Anopheles gambiae: the perspective from whole-genome sequencing.

Love RR, Steele AM, Coulibaly MB, Traore SF, Emrich SJ, Fontaine MC, Besansky NJ.

Mol Ecol. 2016 Dec;25(23):5889-5906. doi: 10.1111/mec.13888. Epub 2016 Nov 9.

10.

High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti.

Behura SK, Sarro J, Li P, Mysore K, Severson DW, Emrich SJ, Duman-Scheel M.

BMC Genomics. 2016 May 10;17:341. doi: 10.1186/s12864-016-2468-x.

11.

Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes.

Hall AB, Papathanos PA, Sharma A, Cheng C, Akbari OS, Assour L, Bergman NH, Cagnetti A, Crisanti A, Dottorini T, Fiorentini E, Galizi R, Hnath J, Jiang X, Koren S, Nolan T, Radune D, Sharakhova MV, Steele A, Timoshevskiy VA, Windbichler N, Zhang S, Hahn MW, Phillippy AM, Emrich SJ, Sharakhov IV, Tu ZJ, Besansky NJ.

Proc Natl Acad Sci U S A. 2016 Apr 12;113(15):E2114-23. doi: 10.1073/pnas.1525164113. Epub 2016 Mar 29.

12.

Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection.

Mesquita RD, Vionette-Amaral RJ, Lowenberger C, Rivera-Pomar R, Monteiro FA, Minx P, Spieth J, Carvalho AB, Panzera F, Lawson D, Torres AQ, Ribeiro JM, Sorgine MH, Waterhouse RM, Montague MJ, Abad-Franch F, Alves-Bezerra M, Amaral LR, Araujo HM, Araujo RN, Aravind L, Atella GC, Azambuja P, Berni M, Bittencourt-Cunha PR, Braz GR, Calderón-Fernández G, Carareto CM, Christensen MB, Costa IR, Costa SG, Dansa M, Daumas-Filho CR, De-Paula IF, Dias FA, Dimopoulos G, Emrich SJ, Esponda-Behrens N, Fampa P, Fernandez-Medina RD, da Fonseca RN, Fontenele M, Fronick C, Fulton LA, Gandara AC, Garcia ES, Genta FA, Giraldo-Calderón GI, Gomes B, Gondim KC, Granzotto A, Guarneri AA, Guigó R, Harry M, Hughes DS, Jablonka W, Jacquin-Joly E, Juárez MP, Koerich LB, Lange AB, Latorre-Estivalis JM, Lavore A, Lawrence GG, Lazoski C, Lazzari CR, Lopes RR, Lorenzo MG, Lugon MD, Majerowicz D, Marcet PL, Mariotti M, Masuda H, Megy K, Melo AC, Missirlis F, Mota T, Noriega FG, Nouzova M, Nunes RD, Oliveira RL, Oliveira-Silveira G, Ons S, Orchard I, Pagola L, Paiva-Silva GO, Pascual A, Pavan MG, Pedrini N, Peixoto AA, Pereira MH, Pike A, Polycarpo C, Prosdocimi F, Ribeiro-Rodrigues R, Robertson HM, Salerno AP, Salmon D, Santesmasses D, Schama R, Seabra-Junior ES, Silva-Cardoso L, Silva-Neto MA, Souza-Gomes M, Sterkel M, Taracena ML, Tojo M, Tu ZJ, Tubio JM, Ursic-Bedoya R, Venancio TM, Walter-Nuno AB, Wilson D, Warren WC, Wilson RK, Huebner E, Dotson EM, Oliveira PL.

Proc Natl Acad Sci U S A. 2015 Dec 1;112(48):14936-41. doi: 10.1073/pnas.1506226112. Epub 2015 Nov 16. Erratum in: Proc Natl Acad Sci U S A. 2016 Mar 8;113(10):E1415-6. Lange, Angela B [added]; Orchard, Ian [added].

13.

Phlebotomus papatasi SP15: mRNA expression variability and amino acid sequence polymorphisms of field populations.

Ramalho-Ortigão M, Coutinho-Abreu IV, Balbino VQ, Figueiredo CA Jr, Mukbel R, Dayem H, Hanafi HA, El-Hossary SS, Fawaz Eel-D, Abo-Shehada M, Hoel DF, Stayback G, Wadsworth M, Shoue DA, Abrudan J, Lobo NF, Mahon AR, Emrich SJ, Kamhawi S, Collins FH, McDowell MA.

Parasit Vectors. 2015 May 29;8:298. doi: 10.1186/s13071-015-0914-2.

14.

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.

Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arcà B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, Brockman AI, Burkot TR, Burt A, Chan CS, Chauve C, Chiu JC, Christensen M, Costantini C, Davidson VL, Deligianni E, Dottorini T, Dritsou V, Gabriel SB, Guelbeogo WM, Hall AB, Han MV, Hlaing T, Hughes DS, Jenkins AM, Jiang X, Jungreis I, Kakani EG, Kamali M, Kemppainen P, Kennedy RC, Kirmitzoglou IK, Koekemoer LL, Laban N, Langridge N, Lawniczak MK, Lirakis M, Lobo NF, Lowy E, MacCallum RM, Mao C, Maslen G, Mbogo C, McCarthy J, Michel K, Mitchell SN, Moore W, Murphy KA, Naumenko AN, Nolan T, Novoa EM, O'Loughlin S, Oringanje C, Oshaghi MA, Pakpour N, Papathanos PA, Peery AN, Povelones M, Prakash A, Price DP, Rajaraman A, Reimer LJ, Rinker DC, Rokas A, Russell TL, Sagnon N, Sharakhova MV, Shea T, Simão FA, Simard F, Slotman MA, Somboon P, Stegniy V, Struchiner CJ, Thomas GW, Tojo M, Topalis P, Tubio JM, Unger MF, Vontas J, Walton C, Wilding CS, Willis JH, Wu YC, Yan G, Zdobnov EM, Zhou X, Catteruccia F, Christophides GK, Collins FH, Cornman RS, Crisanti A, Donnelly MJ, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Hansen IA, Howell PI, Kafatos FC, Kellis M, Lawson D, Louis C, Luckhart S, Muskavitch MA, Ribeiro JM, Riehle MA, Sharakhov IV, Tu Z, Zwiebel LJ, Besansky NJ.

Science. 2015 Jan 2;347(6217):1258522. doi: 10.1126/science.1258522. Epub 2014 Nov 27.

15.

VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases.

Giraldo-Calderón GI, Emrich SJ, MacCallum RM, Maslen G, Dialynas E, Topalis P, Ho N, Gesing S; VectorBase Consortium, Madey G, Collins FH, Lawson D.

Nucleic Acids Res. 2015 Jan;43(Database issue):D707-13. doi: 10.1093/nar/gku1117. Epub 2014 Dec 15.

16.

Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics.

Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, Jiang X, Hall AB, Catteruccia F, Kakani E, Mitchell SN, Wu YC, Smith HA, Love RR, Lawniczak MK, Slotman MA, Emrich SJ, Hahn MW, Besansky NJ.

Science. 2015 Jan 2;347(6217):1258524. doi: 10.1126/science.1258524. Epub 2014 Nov 27.

17.

Networks' Characteristics Matter for Systems Biology.

Rider AK, Milenković T, Siwo GH, Pinapati RS, Emrich SJ, Ferdig MT, Chawla NV.

Netw Sci (Camb Univ Press). 2014 Aug;2(2):139-161. Epub 2014 Sep 3.

18.

Standardized metadata for human pathogen/vector genomic sequences.

Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ Jr, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH.

PLoS One. 2014 Jun 17;9(6):e99979. doi: 10.1371/journal.pone.0099979. eCollection 2014.

19.

A supervised learning approach to the ensemble clustering of genes.

Rider AK, Siwo G, Emrich SJ, Ferdig MT, Chawla NV.

Int J Data Min Bioinform. 2014;9(2):199-219.

PMID:
24864378
20.

Gene expression in closely related species mirrors local adaptation: consequences for responses to a warming world.

O'Neil ST, Dzurisin JD, Williams CM, Lobo NF, Higgins JK, Deines JM, Carmichael RD, Zeng E, Tan JC, Wu GC, Emrich SJ, Hellmann JJ.

Mol Ecol. 2014 Jun;23(11):2686-98. doi: 10.1111/mec.12773.

PMID:
24766086
21.

Examination of the genetic basis for sexual dimorphism in the Aedes aegypti (dengue vector mosquito) pupal brain.

Tomchaney M, Mysore K, Sun L, Li P, Emrich SJ, Severson DW, Duman-Scheel M.

Biol Sex Differ. 2014 Oct 21;5:10. doi: 10.1186/s13293-014-0010-x. eCollection 2014.

22.

Freshwater bacterial lifestyles inferred from comparative genomics.

Livermore JA, Emrich SJ, Tan J, Jones SE.

Environ Microbiol. 2014 Mar;16(3):746-58. doi: 10.1111/1462-2920.12199. Epub 2013 Jul 26.

PMID:
23889754
23.

Assessing De Novo transcriptome assembly metrics for consistency and utility.

O'Neil ST, Emrich SJ.

BMC Genomics. 2013 Jul 9;14:465. doi: 10.1186/1471-2164-14-465.

24.

The evolution of the Anopheles 16 genomes project.

Neafsey DE, Christophides GK, Collins FH, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Howell PI, Kafatos FC, Lawson D, Muskavitch MA, Waterhouse RM, Williams LJ, Besansky NJ.

G3 (Bethesda). 2013 Jul 8;3(7):1191-4. doi: 10.1534/g3.113.006247.

25.

Haplotype and minimum-chimerism consensus determination using short sequence data.

O'Neil ST, Emrich SJ.

BMC Genomics. 2012 Apr 12;13 Suppl 2:S4. doi: 10.1186/1471-2164-13-S2-S4.

26.

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics.

Megy K, Emrich SJ, Lawson D, Campbell D, Dialynas E, Hughes DS, Koscielny G, Louis C, Maccallum RM, Redmond SN, Sheehan A, Topalis P, Wilson D; VectorBase Consortium.

Nucleic Acids Res. 2012 Jan;40(Database issue):D729-34. doi: 10.1093/nar/gkr1089. Epub 2011 Dec 1.

27.

High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum.

Samarakoon U, Regier A, Tan A, Desany BA, Collins B, Tan JC, Emrich SJ, Ferdig MT.

BMC Genomics. 2011 Feb 17;12:116. doi: 10.1186/1471-2164-12-116.

28.

Breakpoint structure of the Anopheles gambiae 2Rb chromosomal inversion.

Lobo NF, Sangaré DM, Regier AA, Reidenbach KR, Bretz DA, Sharakhova MV, Emrich SJ, Traore SF, Costantini C, Besansky NJ, Collins FH.

Malar J. 2010 Oct 25;9:293. doi: 10.1186/1475-2875-9-293.

29.

Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences.

Lawniczak MK, Emrich SJ, Holloway AK, Regier AP, Olson M, White B, Redmond S, Fulton L, Appelbaum E, Godfrey J, Farmer C, Chinwalla A, Yang SP, Minx P, Nelson J, Kyung K, Walenz BP, Garcia-Hernandez E, Aguiar M, Viswanathan LD, Rogers YH, Strausberg RL, Saski CA, Lawson D, Collins FH, Kafatos FC, Christophides GK, Clifton SW, Kirkness EF, Besansky NJ.

Science. 2010 Oct 22;330(6003):512-4. doi: 10.1126/science.1195755.

30.

A statistical approach to finding overlooked genetic associations.

Rider AK, Siwo G, Chawla NV, Ferdig M, Emrich SJ.

BMC Bioinformatics. 2010 Oct 21;11:526. doi: 10.1186/1471-2105-11-526.

31.

Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon.

O'Neil ST, Dzurisin JD, Carmichael RD, Lobo NF, Emrich SJ, Hellmann JJ.

BMC Genomics. 2010 May 17;11:310. doi: 10.1186/1471-2164-11-310.

32.

The B73 maize genome: complexity, diversity, and dynamics.

Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK.

Science. 2009 Nov 20;326(5956):1112-5. doi: 10.1126/science.1178534. Erratum in: Science. 2012 Aug 31;337(6098):1040.

33.

High-throughput genetic mapping of mutants via quantitative single nucleotide polymorphism typing.

Liu S, Chen HD, Makarevitch I, Shirmer R, Emrich SJ, Dietrich CR, Barbazuk WB, Springer NM, Schnable PS.

Genetics. 2010 Jan;184(1):19-26. doi: 10.1534/genetics.109.107557. Epub 2009 Nov 2.

34.

Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.).

Ohtsu K, Smith MB, Emrich SJ, Borsuk LA, Zhou R, Chen T, Zhang X, Timmermans MC, Beck J, Buckner B, Janick-Buckner D, Nettleton D, Scanlon MJ, Schnable PS.

Plant J. 2007 Nov;52(3):391-404. Epub 2007 Aug 23.

35.

SNP discovery via 454 transcriptome sequencing.

Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS.

Plant J. 2007 Sep;51(5):910-8. Epub 2007 Jul 27.

36.

Nearly identical paralogs: implications for maize (Zea mays L.) genome evolution.

Emrich SJ, Li L, Wen TJ, Yandeau-Nelson MD, Fu Y, Guo L, Chou HH, Aluru S, Ashlock DA, Schnable PS.

Genetics. 2007 Jan;175(1):429-39. Epub 2006 Nov 16.

37.

Gene discovery and annotation using LCM-454 transcriptome sequencing.

Emrich SJ, Barbazuk WB, Li L, Schnable PS.

Genome Res. 2007 Jan;17(1):69-73. Epub 2006 Nov 9.

38.

Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes.

Fu Y, Emrich SJ, Guo L, Wen TJ, Ashlock DA, Aluru S, Schnable PS.

Proc Natl Acad Sci U S A. 2005 Aug 23;102(34):12282-7. Epub 2005 Aug 15.

39.

Evaluation of five ab initio gene prediction programs for the discovery of maize genes.

Yao H, Guo L, Fu Y, Borsuk LA, Wen TJ, Skibbe DS, Cui X, Scheffler BE, Cao J, Emrich SJ, Ashlock DA, Schnable PS.

Plant Mol Biol. 2005 Feb;57(3):445-60.

PMID:
15830133
40.

A strategy for assembling the maize (Zea mays L.) genome.

Emrich SJ, Aluru S, Fu Y, Wen TJ, Narayanan M, Guo L, Ashlock DA, Schnable PS.

Bioinformatics. 2004 Jan 22;20(2):140-7.

PMID:
14734303
41.

PROBEmer: A web-based software tool for selecting optimal DNA oligos.

Emrich SJ, Lowe M, Delcher AL.

Nucleic Acids Res. 2003 Jul 1;31(13):3746-50.

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