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Items: 1 to 50 of 86

1.

Still Something to Discover: Novel Insights intoEscherichia coli Phage Diversity and Taxonomy.

Korf IHE, Meier-Kolthoff JP, Adriaenssens EM, Kropinski AM, Nimtz M, Rohde M, van Raaij MJ, Wittmann J.

Viruses. 2019 May 17;11(5). pii: E454. doi: 10.3390/v11050454.

2.

Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization.

Westreich ST, Ardeshir A, Alkan Z, Kable ME, Korf I, Lemay DG.

Microbiome. 2019 Mar 18;7(1):41. doi: 10.1186/s40168-019-0664-z.

3.

Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species.

Kern C, Wang Y, Chitwood J, Korf I, Delany M, Cheng H, Medrano JF, Van Eenennaam AL, Ernst C, Ross P, Zhou H.

BMC Genomics. 2018 Sep 18;19(1):684. doi: 10.1186/s12864-018-5037-7.

4.

The collaborative effect of scientific meetings: A study of the International Milk Genomics Consortium.

Kwok E, Porter M, Korf I, Pasin G, German JB, Lemay DG.

PLoS One. 2018 Aug 22;13(8):e0201637. doi: 10.1371/journal.pone.0201637. eCollection 2018.

5.

Correction for Gaulke et al., "Intestinal Epithelial Barrier Disruption through Altered Mucosal MicroRNA Expression in Human Immunodeficiency Virus and Simian Immunodeficiency Virus Infections".

Gaulke CA, Porter M, Han YH, Sankaran-Walters S, Grishina I, George MD, Dang AT, Ding SW, Jiang G, Korf I, Dandekar S.

J Virol. 2018 May 29;92(12). pii: e00548-18. doi: 10.1128/JVI.00548-18. Print 2018 Jun 15. No abstract available.

6.

SAMSA2: a standalone metatranscriptome analysis pipeline.

Westreich ST, Treiber ML, Mills DA, Korf I, Lemay DG.

BMC Bioinformatics. 2018 May 21;19(1):175. doi: 10.1186/s12859-018-2189-z.

7.

Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins.

Yin D, Schwarz EM, Thomas CG, Felde RL, Korf IF, Cutter AD, Schartner CM, Ralston EJ, Meyer BJ, Haag ES.

Science. 2018 Jan 5;359(6371):55-61. doi: 10.1126/science.aao0827.

8.

Autosomal Trisomy and Triploidy Are Corrected During Female Meiosis in Caenorhabditis elegans.

Vargas E, McNally K, Friedman JA, Cortes DB, Wang DY, Korf IF, McNally FJ.

Genetics. 2017 Nov;207(3):911-922. doi: 10.1534/genetics.117.300259. Epub 2017 Sep 7.

9.

Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce.

Reyes-Chin-Wo S, Wang Z, Yang X, Kozik A, Arikit S, Song C, Xia L, Froenicke L, Lavelle DO, Truco MJ, Xia R, Zhu S, Xu C, Xu H, Xu X, Cox K, Korf I, Meyers BC, Michelmore RW.

Nat Commun. 2017 Apr 12;8:14953. doi: 10.1038/ncomms14953.

10.

Dental Pulp Stem Cells Model Early Life and Imprinted DNA Methylation Patterns.

Dunaway K, Goorha S, Matelski L, Urraca N, Lein PJ, Korf I, Reiter LT, LaSalle JM.

Stem Cells. 2017 Apr;35(4):981-988. doi: 10.1002/stem.2563. Epub 2017 Jan 19.

11.

Cumulative Impact of Polychlorinated Biphenyl and Large Chromosomal Duplications on DNA Methylation, Chromatin, and Expression of Autism Candidate Genes.

Dunaway KW, Islam MS, Coulson RL, Lopez SJ, Vogel Ciernia A, Chu RG, Yasui DH, Pessah IN, Lott P, Mordaunt C, Meguro-Horike M, Horike SI, Korf I, LaSalle JM.

Cell Rep. 2016 Dec 13;17(11):3035-3048. doi: 10.1016/j.celrep.2016.11.058.

12.

SAMSA: a comprehensive metatranscriptome analysis pipeline.

Westreich ST, Korf I, Mills DA, Lemay DG.

BMC Bioinformatics. 2016 Sep 29;17(1):399.

13.

Intron sequences that stimulate gene expression in Arabidopsis.

Rose AB, Carter A, Korf I, Kojima N.

Plant Mol Biol. 2016 Oct;92(3):337-46. doi: 10.1007/s11103-016-0516-1. Epub 2016 Aug 5.

PMID:
27492360
14.

GC skew is a conserved property of unmethylated CpG island promoters across vertebrates.

Hartono SR, Korf IF, Chédin F.

Nucleic Acids Res. 2015 Nov 16;43(20):9729-41. doi: 10.1093/nar/gkv811. Epub 2015 Aug 7.

15.

Catastrophic chromosomal restructuring during genome elimination in plants.

Tan EH, Henry IM, Ravi M, Bradnam KR, Mandakova T, Marimuthu MP, Korf I, Lysak MA, Comai L, Chan SW.

Elife. 2015 May 15;4. pii: e06516. doi: 10.7554/eLife.06516.

16.

Comparative Proteomics of Human and Macaque Milk Reveals Species-Specific Nutrition during Postnatal Development.

Beck KL, Weber D, Phinney BS, Smilowitz JT, Hinde K, Lönnerdal B, Korf I, Lemay DG.

J Proteome Res. 2015 May 1;14(5):2143-57. doi: 10.1021/pr501243m. Epub 2015 Apr 6.

PMID:
25757574
17.

The functional significance of common polymorphisms in zinc finger transcription factors.

Lockwood SH, Guan A, Yu AS, Zhang C, Zykovich A, Korf I, Rannala B, Segal DJ.

G3 (Bethesda). 2014 Jun 26;4(9):1647-55. doi: 10.1534/g3.114.012195.

18.

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products.

Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE.

PeerJ. 2014 May 27;2:e415. doi: 10.7717/peerj.415. eCollection 2014.

19.

Intestinal epithelial barrier disruption through altered mucosal microRNA expression in human immunodeficiency virus and simian immunodeficiency virus infections.

Gaulke CA, Porter M, Han YH, Sankaran-Walters S, Grishina I, George MD, Dang AT, Ding SW, Jiang G, Korf I, Dandekar S.

J Virol. 2014 Jun;88(11):6268-80. doi: 10.1128/JVI.00097-14. Epub 2014 Mar 26. Erratum in: J Virol. 2018 May 29;92(12):.

20.

StochHMM: a flexible hidden Markov model tool and C++ library.

Lott PC, Korf I.

Bioinformatics. 2014 Jun 1;30(11):1625-6. doi: 10.1093/bioinformatics/btu057. Epub 2014 Jan 30.

21.

Sequencing the transcriptome of milk production: milk trumps mammary tissue.

Lemay DG, Hovey RC, Hartono SR, Hinde K, Smilowitz JT, Ventimiglia F, Schmidt KA, Lee JW, Islas-Trejo A, Silva PI, Korf I, Medrano JF, Barry PA, German JB.

BMC Genomics. 2013 Dec 12;14:872. doi: 10.1186/1471-2164-14-872.

22.

Genomics: the state of the art in RNA-seq analysis.

Korf I.

Nat Methods. 2013 Dec;10(12):1165-6. doi: 10.1038/nmeth.2735. No abstract available.

PMID:
24296473
23.

From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome.

Lemay DG, Pollard KS, Martin WF, Freeman Zadrowski C, Hernandez J, Korf I, German JB, Rijnkels M.

PLoS One. 2013 Sep 26;8(9):e75030. doi: 10.1371/journal.pone.0075030. eCollection 2013.

24.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF.

Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10.

25.

GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination.

Ginno PA, Lim YW, Lott PL, Korf I, Chédin F.

Genome Res. 2013 Oct;23(10):1590-600. doi: 10.1101/gr.158436.113. Epub 2013 Jul 18.

26.

The human placenta methylome.

Schroeder DI, Blair JD, Lott P, Yu HO, Hong D, Crary F, Ashwood P, Walker C, Korf I, Robinson WP, LaSalle JM.

Proc Natl Acad Sci U S A. 2013 Apr 9;110(15):6037-42. doi: 10.1073/pnas.1215145110. Epub 2013 Mar 25.

27.

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution.

Melters DP, Bradnam KR, Young HA, Telis N, May MR, Ruby JG, Sebra R, Peluso P, Eid J, Rank D, Garcia JF, DeRisi JL, Smith T, Tobias C, Ross-Ibarra J, Korf I, Chan SW.

Genome Biol. 2013 Jan 30;14(1):R10. doi: 10.1186/gb-2013-14-1-r10.

28.

The effects of a stimulating intron on the expression of heterologous genes in Arabidopsis thaliana.

Emami S, Arumainayagam D, Korf I, Rose AB.

Plant Biotechnol J. 2013 Jun;11(5):555-63. doi: 10.1111/pbi.12043. Epub 2013 Jan 24.

29.

Comparative genomics of carp herpesviruses.

Davison AJ, Kurobe T, Gatherer D, Cunningham C, Korf I, Fukuda H, Hedrick RP, Waltzek TB.

J Virol. 2013 Mar;87(5):2908-22. doi: 10.1128/JVI.03206-12. Epub 2012 Dec 26.

30.

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes.

Lemay DG, Martin WF, Hinrichs AS, Rijnkels M, German JB, Korf I, Pollard KS.

BMC Bioinformatics. 2012 Sep 28;13:253. doi: 10.1186/1471-2105-13-253.

31.

Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing.

Meier JL, Yu AS, Korf I, Segal DJ, Dervan PB.

J Am Chem Soc. 2012 Oct 24;134(42):17814-22. doi: 10.1021/ja308888c. Epub 2012 Oct 10.

32.

Holocentric chromosomes: convergent evolution, meiotic adaptations, and genomic analysis.

Melters DP, Paliulis LV, Korf IF, Chan SW.

Chromosome Res. 2012 Jul;20(5):579-93. doi: 10.1007/s10577-012-9292-1. Review.

PMID:
22766638
33.

R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters.

Ginno PA, Lott PL, Christensen HC, Korf I, Chédin F.

Mol Cell. 2012 Mar 30;45(6):814-25. doi: 10.1016/j.molcel.2012.01.017. Epub 2012 Mar 1.

34.

[Effect of fatty component in ration and coenzyme Q10 on indices of rat lipid metabolism in ontogenesis].

Kulakova SN, Korf II, Baturina VA, Sharanova NE, Karagodina ZV, Arutiunova MB, Tarasova IB.

Vopr Pitan. 2011;80(5):24-9. Russian.

PMID:
22238945
35.

Myc and Miz-1 have coordinate genomic functions including targeting Hox genes in human embryonic stem cells.

Varlakhanova N, Cotterman R, Bradnam K, Korf I, Knoepfler PS.

Epigenetics Chromatin. 2011 Nov 4;4:20. doi: 10.1186/1756-8935-4-20.

36.

Assemblathon 1: a competitive assessment of de novo short read assembly methods.

Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B.

Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16.

37.

Breadth by depth: expanding our understanding of the repair of transposon-induced DNA double strand breaks via deep-sequencing.

Huefner ND, Mizuno Y, Weil CF, Korf I, Britt AB.

DNA Repair (Amst). 2011 Oct 10;10(10):1023-33. doi: 10.1016/j.dnarep.2011.07.011. Epub 2011 Sep 1.

PMID:
21889425
38.

Large-scale methylation domains mark a functional subset of neuronally expressed genes.

Schroeder DI, Lott P, Korf I, LaSalle JM.

Genome Res. 2011 Oct;21(10):1583-91. doi: 10.1101/gr.119131.110. Epub 2011 Jul 22.

39.

Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants.

Parra G, Bradnam K, Rose AB, Korf I.

Nucleic Acids Res. 2011 Jul;39(13):5328-37. doi: 10.1093/nar/gkr043. Epub 2011 Mar 22.

40.

Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.

Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ.

PLoS One. 2011 Feb 15;6(2):e17121. doi: 10.1371/journal.pone.0017121.

41.

Evidence for a DNA-Based Mechanism of Intron-Mediated Enhancement.

Rose AB, Emami S, Bradnam K, Korf I.

Front Plant Sci. 2011 Dec 13;2:98. doi: 10.3389/fpls.2011.00098. eCollection 2011.

42.

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences.

Kovach A, Wegrzyn JL, Parra G, Holt C, Bruening GE, Loopstra CA, Hartigan J, Yandell M, Langley CH, Korf I, Neale DB.

BMC Genomics. 2010 Jul 7;11:420. doi: 10.1186/1471-2164-11-420.

43.

Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data.

Blahnik KR, Dou L, O'Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Ludäscher B, Korf I, Farnham PJ.

Nucleic Acids Res. 2010 Jan;38(3):e13. doi: 10.1093/nar/gkp1012. Epub 2009 Nov 11.

44.

Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing.

Zykovich A, Korf I, Segal DJ.

Nucleic Acids Res. 2009 Dec;37(22):e151. doi: 10.1093/nar/gkp802.

45.

Applying word-based algorithms: the IMEter.

Korf IF, Rose AB.

Methods Mol Biol. 2009;553:287-301. doi: 10.1007/978-1-60327-563-7_14. Review.

PMID:
19588111
46.

Assessing the gene space in draft genomes.

Parra G, Bradnam K, Ning Z, Keane T, Korf I.

Nucleic Acids Res. 2009 Jan;37(1):289-97. doi: 10.1093/nar/gkn916. Epub 2008 Nov 28.

47.

Longer first introns are a general property of eukaryotic gene structure.

Bradnam KR, Korf I.

PLoS One. 2008 Aug 29;3(8):e3093. doi: 10.1371/journal.pone.0003093.

48.

Promoter-proximal introns in Arabidopsis thaliana are enriched in dispersed signals that elevate gene expression.

Rose AB, Elfersi T, Parra G, Korf I.

Plant Cell. 2008 Mar;20(3):543-51. doi: 10.1105/tpc.107.057190. Epub 2008 Mar 4.

49.

MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes.

Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sánchez Alvarado A, Yandell M.

Genome Res. 2008 Jan;18(1):188-96. Epub 2007 Nov 19.

50.

Draft genome of the filarial nematode parasite Brugia malayi.

Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, Delcher AL, Guiliano DB, Miranda-Saavedra D, Angiuoli SV, Creasy T, Amedeo P, Haas B, El-Sayed NM, Wortman JR, Feldblyum T, Tallon L, Schatz M, Shumway M, Koo H, Salzberg SL, Schobel S, Pertea M, Pop M, White O, Barton GJ, Carlow CK, Crawford MJ, Daub J, Dimmic MW, Estes CF, Foster JM, Ganatra M, Gregory WF, Johnson NM, Jin J, Komuniecki R, Korf I, Kumar S, Laney S, Li BW, Li W, Lindblom TH, Lustigman S, Ma D, Maina CV, Martin DM, McCarter JP, McReynolds L, Mitreva M, Nutman TB, Parkinson J, Peregrín-Alvarez JM, Poole C, Ren Q, Saunders L, Sluder AE, Smith K, Stanke M, Unnasch TR, Ware J, Wei AD, Weil G, Williams DJ, Zhang Y, Williams SA, Fraser-Liggett C, Slatko B, Blaxter ML, Scott AL.

Science. 2007 Sep 21;317(5845):1756-60.

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