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Ian F Korf

Title(s)Professor, Molecular and Cellular Biology
SchoolUniversity of California, Davis
Phone530-754-4989
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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. Westreich ST, Salcedo J, Durbin-Johnson B, Smilowitz JT, Korf I, Mills DA, Barile D, Lemay DG. Fecal metatranscriptomics and glycomics suggest that bovine milk oligosaccharides are fully utilized by healthy adults. J Nutr Biochem. 2020 Jan 17; 79:108340. PMID: 32028108.
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    2. Chin EL, Huang L, Bouzid YY, Kirschke CP, Durbin-Johnson B, Baldiviez LM, Bonnel EL, Keim NL, Korf I, Stephensen CB, Lemay DG. Association of Lactase Persistence Genotypes (rs4988235) and Ethnicity with Dairy Intake in a Healthy U.S. Population. Nutrients. 2019 Aug 10; 11(8). PMID: 31405126.
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    3. Westreich ST, Ardeshir A, Alkan Z, Kable ME, Korf I, Lemay DG. Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization. Microbiome. 2019 03 18; 7(1):41. PMID: 30885266.
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    4. Kern C, Wang Y, Chitwood J, Korf I, Delany M, Cheng H, Medrano JF, Van Eenennaam AL, Ernst C, Ross P, Zhou H. Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. BMC Genomics. 2018 Sep 18; 19(1):684. PMID: 30227846.
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    5. Kwok E, Porter M, Korf I, Pasin G, German JB, Lemay DG. The collaborative effect of scientific meetings: A study of the International Milk Genomics Consortium. PLoS One. 2018; 13(8):e0201637. PMID: 30133459.
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    6. 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.
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    7. Westreich ST, Treiber ML, Mills DA, Korf I, Lemay DG. SAMSA2: a standalone metatranscriptome analysis pipeline. BMC Bioinformatics. 2018 05 21; 19(1):175. PMID: 29783945.
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    8. Yin D, Schwarz EM, Thomas CG, Felde RL, Korf IF, Cutter AD, Schartner CM, Ralston EJ, Meyer BJ, Haag ES. Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins. Science. 2018 01 05; 359(6371):55-61. PMID: 29302007.
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    9. Vargas E, McNally K, Friedman JA, Cortes DB, Wang DY, Korf IF, 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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    10. 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 04 12; 8:14953. PMID: 28401891.
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    11. 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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    12. 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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    13. 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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    14. 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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    15. Hartono SR, Korf IF, 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.
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    16. 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.
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    17. 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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    18. 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.
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    19. Beitel CW, Froenicke L, Lang JM, Korf IF, 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.
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    20. 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.
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    21. Lott PC, Korf I. StochHMM: a flexible hidden Markov model tool and C++ library. Bioinformatics. 2014 Jun 01; 30(11):1625-6. PMID: 24489371.
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    22. 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.
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    23. 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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    24. 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.
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    25. 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. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2013 Jul 22; 2(1):10. PMID: 23870653.
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    26. 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.
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    27. 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.
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    28. 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.
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    29. 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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    30. 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.
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    31. 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.
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    32. 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.
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    33. Melters DP, Paliulis LV, Korf IF, 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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    34. 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.
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    35. 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.
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    36. 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.
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    37. 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.
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    38. 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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    39. 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.
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    40. 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.
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    41. 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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    42. 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.
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    43. 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.
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    44. 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.
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    45. Korf IF, Rose AB. Applying word-based algorithms: the IMEter. Methods Mol Biol. 2009; 553:287-301. PMID: 19588111.
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    46. 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.
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    47. 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.
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    48. 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.
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    49. 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.
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    50. 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.
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    51. Huang D, Chow TW. Identifying the biologically relevant gene categories based on gene expression and biological data: an example on prostate cancer. Bioinformatics. 2007 Jun 15; 23(12):1503-10. PMID: 17463028.
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    52. 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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    53. 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 IF, 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.
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    54. 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.
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    55. Korf I. Gene finding in novel genomes. BMC Bioinformatics. 2004 May 14; 5:59. PMID: 15144565.
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    56. Korf I. Serial BLAST searching. Bioinformatics. 2003 Aug 12; 19(12):1492-6. PMID: 12912829.
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    57. 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.
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    58. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 05; 420(6915):520-62. PMID: 12466850.
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    59. 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.
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    60. Wendl MC, Korf I, Chinwalla AT, Hillier LW. Automated processing of raw DNA sequence data. IEEE Eng Med Biol Mag. 2001 Jul-Aug; 20(4):41-8. PMID: 11494768.
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    61. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15; 409(6822):860-921. PMID: 11237011.
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    62. Korf I, Flicek P, Duan D, Brent MR. Integrating genomic homology into gene structure prediction. Bioinformatics. 2001; 17 Suppl 1:S140-8. PMID: 11473003.
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    63. Bedell JA, Korf I, Gish W. MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics. 2000 Nov; 16(11):1040-1. PMID: 11159316.
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    64. Korf I, Gish W. MPBLAST : improved BLAST performance with multiplexed queries. Bioinformatics. 2000 Nov; 16(11):1052-3. PMID: 11159321.
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    65. Barbazuk WB, Korf I, Kadavi C, Heyen J, Tate S, Wun E, Bedell JA, McPherson JD, Johnson SL. The syntenic relationship of the zebrafish and human genomes. Genome Res. 2000 Sep; 10(9):1351-8. PMID: 10984453.
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    66. Ellsworth RE, Jamison DC, Touchman JW, Chissoe SL, Braden Maduro VV, Bouffard GG, Dietrich NL, Beckstrom-Sternberg SM, Iyer LM, Weintraub LA, Cotton M, Courtney L, Edwards J, Maupin R, Ozersky P, Rohlfing T, Wohldmann P, Miner T, Kemp K, Kramer J, Korf I, Pepin K, Antonacci-Fulton L, Fulton RS, Minx P, Hillier LW, Wilson RK, Waterston RH, Miller W, Green ED. Comparative genomic sequence analysis of the human and mouse cystic fibrosis transmembrane conductance regulator genes. Proc Natl Acad Sci U S A. 2000 Feb 01; 97(3):1172-7. PMID: 10655503.
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    67. Dunham I, Shimizu N, Roe BA, Chissoe S, Hunt AR, Collins JE, Bruskiewich R, Beare DM, Clamp M, Smink LJ, Ainscough R, Almeida JP, Babbage A, Bagguley C, Bailey J, Barlow K, Bates KN, Beasley O, Bird CP, Blakey S, Bridgeman AM, Buck D, Burgess J, Burrill WD, O'Brien KP. The DNA sequence of human chromosome 22. Nature. 1999 Dec 02; 402(6761):489-95. PMID: 10591208.
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    68. Marth GT, Korf I, Yandell MD, Yeh RT, Gu Z, Zakeri H, Stitziel NO, Hillier L, Kwok PY, Gish WR. A general approach to single-nucleotide polymorphism discovery. Nat Genet. 1999 Dec; 23(4):452-6. PMID: 10581034.
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    69. Korf I, Fan Y, Strome S. The Polycomb group in Caenorhabditis elegans and maternal control of germline development. Development. 1998 Jul; 125(13):2469-78. PMID: 9609830.
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