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Items: 1 to 50 of 115

1.

Molecular complexity of the major urinary protein system of the Norway rat, Rattus norvegicus.

Gómez-Baena G, Armstrong SD, Halstead JO, Prescott M, Roberts SA, McLean L, Mudge JM, Hurst JL, Beynon RJ.

Sci Rep. 2019 Jul 24;9(1):10757. doi: 10.1038/s41598-019-46950-x.

2.

Tracking neonicotinoids following their use as cotton seed treatments.

Kohl KL, Harrell LK, Mudge JF, Subbiah S, Kasumba J, Osma E, Barman AK, Anderson TA.

PeerJ. 2019 Apr 19;7:e6805. doi: 10.7717/peerj.6805. eCollection 2019.

3.

Experimental drought reduces genetic diversity in the grassland foundation species Bouteloua eriopoda.

Whitney KD, Mudge J, Natvig DO, Sundararajan A, Pockman WT, Bell J, Collins SL, Rudgers JA.

Oecologia. 2019 Apr;189(4):1107-1120. doi: 10.1007/s00442-019-04371-7. Epub 2019 Mar 8.

PMID:
30850884
4.

Ensembl 2019.

Cunningham F, Achuthan P, Akanni W, Allen J, Amode MR, Armean IM, Bennett R, Bhai J, Billis K, Boddu S, Cummins C, Davidson C, Dodiya KJ, Gall A, Girón CG, Gil L, Grego T, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, Kay M, Laird MR, Lavidas I, Liu Z, Loveland JE, Marugán JC, Maurel T, McMahon AC, Moore B, Morales J, Mudge JM, Nuhn M, Ogeh D, Parker A, Parton A, Patricio M, Abdul Salam AI, Schmitt BM, Schuilenburg H, Sheppard D, Sparrow H, Stapleton E, Szuba M, Taylor K, Threadgold G, Thormann A, Vullo A, Walts B, Winterbottom A, Zadissa A, Chakiachvili M, Frankish A, Hunt SE, Kostadima M, Langridge N, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Aken BL, Yates AD, Zerbino DR, Flicek P.

Nucleic Acids Res. 2019 Jan 8;47(D1):D745-D751. doi: 10.1093/nar/gky1113.

5.

Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme) and its bacterial endosymbionts.

Sun X, Chen W, Ivanov S, MacLean AM, Wight H, Ramaraj T, Mudge J, Harrison MJ, Fei Z.

New Phytol. 2019 Feb;221(3):1556-1573. doi: 10.1111/nph.15472. Epub 2018 Oct 13.

PMID:
30368822
6.

GENCODE reference annotation for the human and mouse genomes.

Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Hunt T, Izuogu OG, Lagarde J, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Xu J, Yates A, Zerbino D, Zhang Y, Aken B, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Reymond A, Tress ML, Flicek P.

Nucleic Acids Res. 2019 Jan 8;47(D1):D766-D773. doi: 10.1093/nar/gky955.

7.

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
8.

Genome-wide association study: Exploring the genetic basis for responsiveness to ketogenic dietary therapies for drug-resistant epilepsy.

Schoeler NE, Leu C, Balestrini S, Mudge JM, Steward CA, Frankish A, Leung MA, Mackay M, Scheffer I, Williams R, Sander JW, Cross JH, Sisodiya SM.

Epilepsia. 2018 Aug;59(8):1557-1566. doi: 10.1111/epi.14516. Epub 2018 Jul 16.

9.

Histone Citrullination Represses MicroRNA Expression, Resulting in Increased Oncogene mRNAs in Somatolactotrope Cells.

DeVore SB, Young CH, Li G, Sundararajan A, Ramaraj T, Mudge J, Schilkey F, Muth A, Thompson PR, Cherrington BD.

Mol Cell Biol. 2018 Sep 14;38(19). pii: e00084-18. doi: 10.1128/MCB.00084-18. Print 2018 Oct 1.

10.

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.

11.

Correction to: The transcriptome landscape of early maize meiosis.

Dukowic-Schulze S, Sundararajan A, Mudge J, Ramaraj T, Farmer AD, Wang M, Sun Q, Pillardy J, Kianian S, Retzel EF, Pawlowski WP, Chen C.

BMC Plant Biol. 2018 Jan 15;18(1):12. doi: 10.1186/s12870-017-1224-y.

12.

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, Hsu CY, Naqvi RZ, Farooq M, Li X, Gong L, Mudge J, Ramaraj T, Udall JA, Peterson DG, Wendel JF.

Genome Biol Evol. 2017 Dec 1;9(12):3328-3344. doi: 10.1093/gbe/evx248.

13.

Ensembl 2018.

Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J, Billis K, Cummins C, Gall A, Girón CG, Gil L, Gordon L, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, To JK, Laird MR, Lavidas I, Liu Z, Loveland JE, Maurel T, McLaren W, Moore B, Mudge J, Murphy DN, Newman V, Nuhn M, Ogeh D, Ong CK, Parker A, Patricio M, Riat HS, Schuilenburg H, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Zadissa A, Frankish A, Hunt SE, Kostadima M, Langridge N, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Aken BL, Cunningham F, Yates A, Flicek P.

Nucleic Acids Res. 2018 Jan 4;46(D1):D754-D761. doi: 10.1093/nar/gkx1098.

14.

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.

Pujar S, O'Leary NA, Farrell CM, Loveland JE, Mudge JM, Wallin C, Girón CG, Diekhans M, Barnes I, Bennett R, Berry AE, Cox E, Davidson C, Goldfarb T, Gonzalez JM, Hunt T, Jackson J, Joardar V, Kay MP, Kodali VK, Martin FJ, McAndrews M, McGarvey KM, Murphy M, Rajput B, Rangwala SH, Riddick LD, Seal RL, Suner MM, Webb D, Zhu S, Aken BL, Bruford EA, Bult CJ, Frankish A, Murphy T, Pruitt KD.

Nucleic Acids Res. 2018 Jan 4;46(D1):D221-D228. doi: 10.1093/nar/gkx1031.

15.

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.

16.

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.

17.

Optimal alpha reduces error rates in gene expression studies: a meta-analysis approach.

Mudge JF, Martyniuk CJ, Houlahan JE.

BMC Bioinformatics. 2017 Jun 21;18(1):312. doi: 10.1186/s12859-017-1728-3.

18.

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.

19.

Temporal monitoring of perfluorooctane sulfonate accumulation in aquatic biota downstream of historical aqueous film forming foam use areas.

Lanza HA, Cochran RS, Mudge JF, Olson AD, Blackwell BR, Maul JD, Salice CJ, Anderson TA.

Environ Toxicol Chem. 2017 Aug;36(8):2022-2029. doi: 10.1002/etc.3726. Epub 2017 Feb 2.

PMID:
28029183
20.

The state of play in higher eukaryote gene annotation.

Mudge JM, Harrow J.

Nat Rev Genet. 2016 Dec;17(12):758-772. doi: 10.1038/nrg.2016.119. Epub 2016 Oct 24. Review.

21.

Flexible Data Analysis Pipeline for High-Confidence Proteogenomics.

Weisser H, Wright JC, Mudge JM, Gutenbrunner P, Choudhary JS.

J Proteome Res. 2016 Dec 2;15(12):4686-4695. Epub 2016 Nov 10.

22.

Transcriptome Sequencing of Diverse Peanut (Arachis) Wild Species and the Cultivated Species Reveals a Wealth of Untapped Genetic Variability.

Chopra R, Burow G, Simpson CE, Chagoya J, Mudge J, Burow MD.

G3 (Bethesda). 2016 Dec 7;6(12):3825-3836. doi: 10.1534/g3.115.026898.

23.

Gene Evolutionary Trajectories and GC Patterns Driven by Recombination in Zea mays.

Sundararajan A, Dukowic-Schulze S, Kwicklis M, Engstrom K, Garcia N, Oviedo OJ, Ramaraj T, Gonzales MD, He Y, Wang M, Sun Q, Pillardy J, Kianian SF, Pawlowski WP, Chen C, Mudge J.

Front Plant Sci. 2016 Sep 22;7:1433. eCollection 2016.

24.

Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).

Lagarde J, Uszczynska-Ratajczak B, Santoyo-Lopez J, Gonzalez JM, Tapanari E, Mudge JM, Steward CA, Wilming L, Tanzer A, Howald C, Chrast J, Vela-Boza A, Rueda A, Lopez-Domingo FJ, Dopazo J, Reymond A, Guigó R, Harrow J.

Nat Commun. 2016 Aug 17;7:12339. doi: 10.1038/ncomms12339.

25.

Augmenting Chinese hamster genome assembly by identifying regions of high confidence.

Vishwanathan N, Bandyopadhyay AA, Fu HY, Sharma M, Johnson KC, Mudge J, Ramaraj T, Onsongo G, Silverstein KA, Jacob NM, Le H, Karypis G, Hu WS.

Biotechnol J. 2016 Sep;11(9):1151-7. doi: 10.1002/biot.201500455. Epub 2016 Jul 19.

PMID:
27374913
26.

Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens.

Deschamps S, Mudge J, Cameron C, Ramaraj T, Anand A, Fengler K, Hayes K, Llaca V, Jones TJ, May G.

Sci Rep. 2016 Jun 28;6:28625. doi: 10.1038/srep28625.

27.

Novel Meiotic miRNAs and Indications for a Role of PhasiRNAs in Meiosis.

Dukowic-Schulze S, Sundararajan A, Ramaraj T, Kianian S, Pawlowski WP, Mudge J, Chen C.

Front Plant Sci. 2016 Jun 2;7:762. doi: 10.3389/fpls.2016.00762. eCollection 2016.

28.

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.

Wright JC, Mudge J, Weisser H, Barzine MP, Gonzalez JM, Brazma A, Choudhary JS, Harrow J.

Nat Commun. 2016 Jun 2;7:11778. doi: 10.1038/ncomms11778.

29.

The combined influence of two agricultural contaminants on natural communities of phytoplankton and zooplankton.

Baker LF, Mudge JF, Thompson DG, Houlahan JE, Kidd KA.

Ecotoxicology. 2016 Jul;25(5):1021-32. doi: 10.1007/s10646-016-1659-1. Epub 2016 Apr 25.

PMID:
27112456
30.

Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes.

Suh A, Witt CC, Menger J, Sadanandan KR, Podsiadlowski L, Gerth M, Weigert A, McGuire JA, Mudge J, Edwards SV, Rheindt FE.

Nat Commun. 2016 Apr 21;7:11396. doi: 10.1038/ncomms11396.

31.

The plant-specific protein FEHLSTART controls male meiotic entry, initializing meiotic synchronization in Arabidopsis.

Li J, Dukowic-Schulze S, Lindquist IE, Farmer AD, Kelly B, Li T, Smith AG, Retzel EF, Mudge J, Chen C.

Plant J. 2015 Nov;84(4):659-71. doi: 10.1111/tpj.13026. Epub 2015 Oct 22.

32.

Creating reference gene annotation for the mouse C57BL6/J genome assembly.

Mudge JM, Harrow J.

Mamm Genome. 2015 Oct;26(9-10):366-78. doi: 10.1007/s00335-015-9583-x. Epub 2015 Jul 18.

33.

Monte Carlo-based distance analysis using unit mass resolution ICP-MS data for shellfish site of origin verification.

Mudge JF, Engel ME, Ryan CN, Klein DM.

Integr Environ Assess Manag. 2015 Jul;11(3):515-6. doi: 10.1002/ieam.1648. No abstract available.

PMID:
26119767
34.

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.

Frankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D, Petryszak R, Mudge JM, Fonseca N, Brazma A, Guigo R, Harrow J.

BMC Genomics. 2015;16 Suppl 8:S2. doi: 10.1186/1471-2164-16-S8-S2. Epub 2015 Jun 18.

35.

Polarimetric characterization of birefringent filter components.

Mudge J, Mitchell K, Tarbell T.

Appl Opt. 2015 Jan 10;54(2):259-65. doi: 10.1364/AO.54.000259.

PMID:
25967624
36.

Comparative genome analysis of non-toxigenic non-O1 versus toxigenic O1 Vibrio cholerae.

Mukherjee M, Kakarla P, Kumar S, Gonzalez E, Floyd JT, Inupakutika M, Devireddy AR, Tirrell SR, Bruns M, He G, Lindquist IE, Sundararajan A, Schilkey FD, Mudge J, Varela MF.

Genom Discov. 2014;2(1):1-15.

37.

Next-generation transcriptome sequencing, SNP discovery and validation in four market classes of peanut, Arachis hypogaea L.

Chopra R, Burow G, Farmer A, Mudge J, Simpson CE, Wilkins TA, Baring MR, Puppala N, Chamberlin KD, Burow MD.

Mol Genet Genomics. 2015 Jun;290(3):1169-80. doi: 10.1007/s00438-014-0976-4. Epub 2015 Feb 7.

PMID:
25663138
38.

Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-Seq data.

Chopra R, Burow G, Farmer A, Mudge J, Simpson CE, Burow MD.

PLoS One. 2014 Dec 31;9(12):e115055. doi: 10.1371/journal.pone.0115055. eCollection 2014.

39.

Draft Genome Sequences of Vancomycin-Susceptible Staphylococcus aureus Related to Heterogeneous Vancomycin-Intermediate S. aureus.

Ramaraj T, Matyi SA, Sundararajan A, Lindquist IE, Devitt NP, Schilkey FD, Lamichhane-Khadka R, Hoyt PR, Mudge J, Gustafson JE.

Genome Announc. 2014 Oct 9;2(5). pii: e01033-14. doi: 10.1128/genomeA.01033-14.

40.

In situ calibration of tunable filters: Lyot and Michelson.

Mudge J, Tarbell T.

Appl Opt. 2014 Aug 1;53(22):4978-86. doi: 10.1364/AO.53.004978.

PMID:
25090330
41.

Draft Genomes of Heterogeneous Vancomycin-Intermediate Staphylococcus aureus Strain MM66 and MM66 Derivatives with Altered Vancomycin Resistance Levels.

Matyi SA, Ramaraj T, Sundararajan A, Lindquist IE, Devitt NP, Schilkey FD, Lamichhane-Khadka R, Hoyt PR, Mudge J, Gustafson JE.

Genome Announc. 2014 Jul 10;2(4). pii: e00688-14. doi: 10.1128/genomeA.00688-14.

42.

The direct and indirect effects of a glyphosate-based herbicide and nutrients on Chironomidae (Diptera) emerging from small wetlands.

Baker LF, Mudge JF, Houlahan JE, Thompson DG, Kidd KA.

Environ Toxicol Chem. 2014 Sep;33(9):2076-85. doi: 10.1002/etc.2657. Epub 2014 Aug 7.

PMID:
24899169
43.

SNP markers identify widely distributed clonal lineages of Phytophthora colocasiae in Vietnam, Hawaii and Hainan Island, China.

Shrestha S, Hu J, Fryxell RT, Mudge J, Lamour K.

Mycologia. 2014 Jul-Aug;106(4):676-85. doi: 10.3852/13-165. Epub 2014 Jun 3.

PMID:
24895424
44.

The transcriptome landscape of early maize meiosis.

Dukowic-Schulze S, Sundararajan A, Mudge J, Ramaraj T, Farmer AD, Wang M, Sun Q, Pillardy J, Kianian S, Retzel EF, Pawlowski WP, Chen C.

BMC Plant Biol. 2014 May 3;14:118. doi: 10.1186/1471-2229-14-118. Erratum in: BMC Plant Biol. 2018 Jan 15;18(1):12.

45.

Improved Hybrid Genome Assemblies of Two Strains of Bacteroides xylanisolvens, SD_CC_1b and SD_CC_2a, Obtained Using Illumina and 454 Sequencing Technologies.

Ramaraj T, Sundararajan A, Schilkey FD, Delvecchio VG, Donlon M, Ziemer C, Mudge J.

Genome Announc. 2014 Apr 3;2(2). pii: e00237-14. doi: 10.1128/genomeA.00237-14.

46.

Comparative transcriptomics of early meiosis in Arabidopsis and maize.

Dukowic-Schulze S, Harris A, Li J, Sundararajan A, Mudge J, Retzel EF, Pawlowski WP, Chen C.

J Genet Genomics. 2014 Mar 20;41(3):139-52. doi: 10.1016/j.jgg.2013.11.007. Epub 2013 Dec 14.

47.

Sequencing-based large-scale genomics approaches with small numbers of isolated maize meiocytes.

Dukowic-Schulze S, Sundararajan A, Ramaraj T, Mudge J, Chen C.

Front Plant Sci. 2014 Feb 25;5:57. doi: 10.3389/fpls.2014.00057. eCollection 2014.

48.

C60 fullerene soil sorption, biodegradation, and plant uptake.

Avanasi R, Jackson WA, Sherwin B, Mudge JF, Anderson TA.

Environ Sci Technol. 2014;48(5):2792-7. doi: 10.1021/es405306w. Epub 2014 Feb 21.

PMID:
24521447
49.

The Vertebrate Genome Annotation browser 10 years on.

Harrow JL, Steward CA, Frankish A, Gilbert JG, Gonzalez JM, Loveland JE, Mudge J, Sheppard D, Thomas M, Trevanion S, Wilming LG.

Nucleic Acids Res. 2014 Jan;42(Database issue):D771-9. doi: 10.1093/nar/gkt1241. Epub 2013 Dec 6.

50.

High-density genome-wide association mapping implicates an F-box encoding gene in Medicago truncatula resistance to Aphanomyces euteiches.

Bonhomme M, André O, Badis Y, Ronfort J, Burgarella C, Chantret N, Prosperi JM, Briskine R, Mudge J, Debéllé F, Navier H, Miteul H, Hajri A, Baranger A, Tiffin P, Dumas B, Pilet-Nayel ML, Young ND, Jacquet C.

New Phytol. 2014 Mar;201(4):1328-42. doi: 10.1111/nph.12611. Epub 2013 Nov 28.

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