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Ian F Korf

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InstitutionUniversity of California Davis
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Gaulke CA, Porter M, Han YH, Sankaran-Walters S, Grishina I, George MD, Dang AT, Ding SW, Jiang G, Korf I, Dandekar S. Correction for Gaulke et al., "Intestinal Epithelial Barrier Disruption through Altered Mucosal MicroRNA Expression in Human Immunodeficiency Virus and Simian Immunodeficiency Virus Infections". J Virol. 2018 06 15; 92(12). PMID: 29844248.
      View in: PubMed
    2. Westreich ST, Treiber ML, Mills DA, Korf I, Lemay DG. SAMSA2: a standalone metatranscriptome analysis pipeline. BMC Bioinformatics. 2018 May 21; 19(1):175. PMID: 29783945.
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    3. Vargas E, McNally K, Friedman JA, Cortes DB, Wang DY, Korf I, McNally FJ. Autosomal Trisomy and Triploidy Are Corrected During Female Meiosis in Caenorhabditis elegans. Genetics. 2017 11; 207(3):911-922. PMID: 28882988.
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    4. 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. Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nat Commun. 2017 Apr 12; 8:14953. PMID: 28401891.
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    5. Dunaway K, Goorha S, Matelski L, Urraca N, Lein PJ, Korf I, Reiter LT, LaSalle JM. Dental Pulp Stem Cells Model Early Life and Imprinted DNA Methylation Patterns. Stem Cells. 2017 04; 35(4):981-988. PMID: 28032673.
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    6. 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. Cumulative Impact of Polychlorinated Biphenyl and Large Chromosomal Duplications on DNA Methylation, Chromatin, and Expression of Autism Candidate Genes. Cell Rep. 2016 12 13; 17(11):3035-3048. PMID: 27974215.
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    7. Westreich ST, Korf I, Mills DA, Lemay DG. SAMSA: a comprehensive metatranscriptome analysis pipeline. BMC Bioinformatics. 2016 Sep 29; 17(1):399. PMID: 27687690.
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    8. Rose AB, Carter A, Korf I, Kojima N. Intron sequences that stimulate gene expression in Arabidopsis. Plant Mol Biol. 2016 Oct; 92(3):337-46. PMID: 27492360.
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    9. Hartono SR, Korf I, Chédin F. GC skew is a conserved property of unmethylated CpG island promoters across vertebrates. Nucleic Acids Res. 2015 Nov 16; 43(20):9729-41. PMID: 26253743; PMCID: PMC4787789.
    10. Tan EH, Henry IM, Ravi M, Bradnam KR, Mandakova T, Marimuthu MP, Korf I, Lysak MA, Comai L, Chan SW. Catastrophic chromosomal restructuring during genome elimination in plants. Elife. 2015 May 15; 4. PMID: 25977984; PMCID: PMC4461816.
    11. Beck KL, Weber D, Phinney BS, Smilowitz JT, Hinde K, Lönnerdal B, Korf I, Lemay DG. Comparative Proteomics of Human and Macaque Milk Reveals Species-Specific Nutrition during Postnatal Development. J Proteome Res. 2015 May 01; 14(5):2143-57. PMID: 25757574.
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    12. Lockwood SH, Guan A, Yu AS, Zhang C, Zykovich A, Korf I, Rannala B, Segal DJ. The functional significance of common polymorphisms in zinc finger transcription factors. G3 (Bethesda). 2014 Jun 26; 4(9):1647-55. PMID: 24970883; PMCID: PMC4169156.
    13. Beitel CW, Froenicke L, Lang JM, Korf I, Michelmore RW, Eisen JA, Darling AE. Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ. 2014; 2:e415. PMID: 24918035; PMCID: PMC4045339.
    14. Gaulke CA, Porter M, Han YH, Sankaran-Walters S, Grishina I, George MD, Dang AT, Ding SW, Jiang G, Korf I, Dandekar S. Intestinal epithelial barrier disruption through altered mucosal microRNA expression in human immunodeficiency virus and simian immunodeficiency virus infections. J Virol. 2014 Jun; 88(11):6268-80. PMID: 24672033.
      View in: PubMed
    15. Lott PC, Korf I. StochHMM: a flexible hidden Markov model tool and C++ library. Bioinformatics. 2014 Jun 01; 30(11):1625-6. PMID: 24489371; PMCID: PMC4029032.
    16. 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. Sequencing the transcriptome of milk production: milk trumps mammary tissue. BMC Genomics. 2013 Dec 12; 14:872. PMID: 24330573; PMCID: PMC3871720.
    17. Korf I. Genomics: the state of the art in RNA-seq analysis. Nat Methods. 2013 Dec; 10(12):1165-6. PMID: 24296473.
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    18. Lemay DG, Pollard KS, Martin WF, Freeman Zadrowski C, Hernandez J, Korf I, German JB, Rijnkels M. From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome. PLoS One. 2013; 8(9):e75030. PMID: 24086428; PMCID: PMC3784412.
    19. 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 I. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2013 Jul 22; 2(1):10. PMID: 23870653; PMCID: PMC3844414.
    20. Ginno PA, Lim YW, Lott PL, Korf I, Chédin F. GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination. Genome Res. 2013 Oct; 23(10):1590-600. PMID: 23868195; PMCID: PMC3787257.
    21. Schroeder DI, Blair JD, Lott P, Yu HO, Hong D, Crary F, Ashwood P, Walker C, Korf I, Robinson WP, LaSalle JM. The human placenta methylome. Proc Natl Acad Sci U S A. 2013 Apr 09; 110(15):6037-42. PMID: 23530188; PMCID: PMC3625261.
    22. 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. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biol. 2013 Jan 30; 14(1):R10. PMID: 23363705; PMCID: PMC4053949.
    23. Emami S, Arumainayagam D, Korf I, Rose AB. The effects of a stimulating intron on the expression of heterologous genes in Arabidopsis thaliana. Plant Biotechnol J. 2013 Jun; 11(5):555-63. PMID: 23347383.
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    24. Davison AJ, Kurobe T, Gatherer D, Cunningham C, Korf I, Fukuda H, Hedrick RP, Waltzek TB. Comparative genomics of carp herpesviruses. J Virol. 2013 Mar; 87(5):2908-22. PMID: 23269803; PMCID: PMC3571366.
    25. Meier JL, Yu AS, Korf I, Segal DJ, Dervan PB. Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing. J Am Chem Soc. 2012 Oct 24; 134(42):17814-22. PMID: 23013524; PMCID: PMC3483022.
    26. Lemay DG, Martin WF, Hinrichs AS, Rijnkels M, German JB, Korf I, Pollard KS. G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes. BMC Bioinformatics. 2012 Sep 28; 13:253. PMID: 23020263; PMCID: PMC3575404.
    27. Melters DP, Paliulis LV, Korf I, Chan SW. Holocentric chromosomes: convergent evolution, meiotic adaptations, and genomic analysis. Chromosome Res. 2012 Jul; 20(5):579-93. PMID: 22766638.
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    28. Ginno PA, Lott PL, Christensen HC, Korf I, Chédin F. R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol Cell. 2012 Mar 30; 45(6):814-25. PMID: 22387027; PMCID: PMC3319272.
    29. Rose AB, Emami S, Bradnam K, Korf I. Evidence for a DNA-Based Mechanism of Intron-Mediated Enhancement. Front Plant Sci. 2011; 2:98. PMID: 22645558; PMCID: PMC3355757.
    30. Varlakhanova N, Cotterman R, Bradnam K, Korf I, Knoepfler PS. Myc and Miz-1 have coordinate genomic functions including targeting Hox genes in human embryonic stem cells. Epigenetics Chromatin. 2011 Nov 04; 4:20. PMID: 22053792; PMCID: PMC3226433.
    31. 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 I, 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. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 2011 Dec; 21(12):2224-41. PMID: 21926179; PMCID: PMC3227110.
    32. Huefner ND, Mizuno Y, Weil CF, Korf I, Britt AB. Breadth by depth: expanding our understanding of the repair of transposon-induced DNA double strand breaks via deep-sequencing. DNA Repair (Amst). 2011 Oct 10; 10(10):1023-33. PMID: 21889425.
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    33. Schroeder DI, Lott P, Korf I, LaSalle JM. Large-scale methylation domains mark a functional subset of neuronally expressed genes. Genome Res. 2011 Oct; 21(10):1583-91. PMID: 21784875; PMCID: PMC3202276.
    34. Parra G, Bradnam K, Rose AB, Korf I. Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants. Nucleic Acids Res. 2011 Jul; 39(13):5328-37. PMID: 21427088; PMCID: PMC3141229.
    35. 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. Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes. PLoS One. 2011 Feb 15; 6(2):e17121. PMID: 21347206.
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    36. Kovach A, Wegrzyn JL, Parra G, Holt C, Bruening GE, Loopstra CA, Hartigan J, Yandell M, Langley CH, Korf I, Neale DB. The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics. 2010 Jul 07; 11:420. PMID: 20609256; PMCID: PMC2996948.
    37. Zykovich A, Korf I, Segal DJ. Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing. Nucleic Acids Res. 2009 Dec; 37(22):e151. PMID: 19843614; PMCID: PMC2794170.
    38. Blahnik KR, Dou L, O'Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Ludäscher B, Korf I, Farnham PJ. Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res. 2010 Jan; 38(3):e13. PMID: 19906703; PMCID: PMC2817454.
    39. Korf I, Rose AB. Applying word-based algorithms: the IMEter. Methods Mol Biol. 2009; 553:287-301. PMID: 19588111.
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    40. Parra G, Bradnam K, Ning Z, Keane T, Korf I. Assessing the gene space in draft genomes. Nucleic Acids Res. 2009 Jan; 37(1):289-97. PMID: 19042974; PMCID: PMC2615622.
    41. Bradnam KR, Korf I. Longer first introns are a general property of eukaryotic gene structure. PLoS One. 2008 Aug 29; 3(8):e3093. PMID: 18769727; PMCID: PMC2518113.
    42. Rose AB, Elfersi T, Parra G, Korf I. Promoter-proximal introns in Arabidopsis thaliana are enriched in dispersed signals that elevate gene expression. Plant Cell. 2008 Mar; 20(3):543-51. PMID: 18319396; PMCID: PMC2329928.
    43. Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sánchez Alvarado A, Yandell M. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 2008 Jan; 18(1):188-96. PMID: 18025269; PMCID: PMC2134774.
    44. 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. Draft genome of the filarial nematode parasite Brugia malayi. Science. 2007 Sep 21; 317(5845):1756-60. PMID: 17885136; PMCID: PMC2613796.
    45. Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics. 2007 May 01; 23(9):1061-7. PMID: 17332020.
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    46. Bedell JA, Budiman MA, Nunberg A, Citek RW, Robbins D, Jones J, Flick E, Rholfing T, Fries J, Bradford K, McMenamy J, Smith M, Holeman H, Roe BA, Wiley G, Korf I, Rabinowicz PD, Lakey N, McCombie WR, Jeddeloh JA, Martienssen RA. Sorghum genome sequencing by methylation filtration. PLoS Biol. 2005 Jan; 3(1):e13. PMID: 15660154; PMCID: PMC539327.
    47. Hajarnavis A, Korf I, Durbin R. A probabilistic model of 3' end formation in Caenorhabditis elegans. Nucleic Acids Res. 2004; 32(11):3392-9. PMID: 15247332; PMCID: PMC443532.
    48. Korf I. Gene finding in novel genomes. BMC Bioinformatics. 2004 May 14; 5:59. PMID: 15144565; PMCID: PMC421630.
    49. Korf I. Serial BLAST searching. Bioinformatics. 2003 Aug 12; 19(12):1492-6. PMID: 12912829.
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    50. Flicek P, Keibler E, Hu P, Korf I, Brent MR. Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. Genome Res. 2003 Jan; 13(1):46-54. PMID: 12529305; PMCID: PMC430948.
    51. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 05; 420(6915):520-62. PMID: 12466850.
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    52. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002 Oct; 12(10):1611-8. PMID: 12368254; PMCID: PMC187536.