Ian Korf

Title(s)Professor, Molecular and Cellular Biology
SchoolCollege of Biological Sciences
Address4333 GBSF
CA 95616
Phone530-754-4989
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Introns increase gene expression in Caenorhabditis elegans by a mechanism that must be at least partly different than in plants. Sci Rep. 2025 May 07; 15(1):15862. Rose AB, Baer A, Shaker I, Monroe JG, Korf I, Rose LS. PMID: 40328889; PMCID: PMC12055998.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    2. Sex-specific single cell-level transcriptomic signatures of Rett syndrome disease progression. Commun Biol. 2024 Oct 10; 7(1):1292. Sharifi O, Haghani V, Neier KE, Fraga KJ, Korf I, Hakam SM, Quon G, Johansen N, Yasui DH, LaSalle JM. PMID: 39384967; PMCID: PMC11464704.
      View in: PubMed   Mentions: 2  Translation:HumansAnimalsCells
    3. Placental-brain axis in females detected within broadly impacted metabolic gene networks protects against prenatal PCB exposure. bioRxiv. 2024 Jul 17. Chau K, Neier K, Valenzuela AE, Schmidt RJ, Durbin-Johnson B, Lein PJ, Korf I, LaSalle JM. PMID: 39071357; PMCID: PMC11275969.
      View in: PubMed   Mentions:
    4. Improving rigor and reproducibility in chromatin immunoprecipitation assay data analysis workflows with Rocketchip. bioRxiv. 2024 Jul 16. Haghani V, Goyal A, Zhang A, Sharifi O, Mariano N, Yasui D, Korf I, LaSalle J. PMID: 39071274; PMCID: PMC11275724.
      View in: PubMed   Mentions:
    5. Sex-specific single cell-level transcriptomic signatures of Rett syndrome disease progression. bioRxiv. 2024 May 19. Sharifi O, Haghani V, Neier KE, Fraga KJ, Korf I, Hakam SM, Quon G, Johansen N, Yasui DH, LaSalle JM. PMID: 38798575; PMCID: PMC11118571.
      View in: PubMed   Mentions:
    6. Do organisms need an impact factor? Citations of key biological resources including model organisms reveal usage patterns and impact. bioRxiv. 2024 Jan 16. Piekniewska A, Anderson N, Roelandse M, Lloyd KCK, Korf I, Voss SR, de Castro G, Magnani DM, Varga Z, James-Zorn C, Horb M, Grethe JS, Bandrowski A. PMID: 38293091; PMCID: PMC10827057.
      View in: PubMed   Mentions:
    7. SpecDB: A relational database for archiving biomolecular NMR spectral data. J Magn Reson. 2022 09; 342:107268. Fraga KJ, Huang YJ, Ramelot TA, Swapna GVT, Lashawn Anak Kendary A, Li E, Korf I, Montelione GT. PMID: 35930941; PMCID: PMC9922030.
      View in: PubMed   Mentions: 3     Fields:    
    8. Association of Diet and Antimicrobial Resistance in Healthy U.S. Adults. mBio. 2022 06 28; 13(3):e0010122. Oliver A, Xue Z, Villanueva YT, Durbin-Johnson B, Alkan Z, Taft DH, Liu J, Korf I, Laugero KD, Stephensen CB, Mills DA, Kable ME, Lemay DG. PMID: 35536006; PMCID: PMC9239165.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansAnimals
    9. Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research. Nat Commun. 2021 03 23; 12(1):1821. Kern C, Wang Y, Xu X, Pan Z, Halstead M, Chanthavixay G, Saelao P, Waters S, Xiang R, Chamberlain A, Korf I, Delany ME, Cheng HH, Medrano JF, Van Eenennaam AL, Tuggle CK, Ernst C, Flicek P, Quon G, Ross P, Zhou H. PMID: 33758196; PMCID: PMC7988148.
      View in: PubMed   Mentions: 82     Fields:    Translation:AnimalsCells
    10. Low-pass whole genome bisulfite sequencing of neonatal dried blood spots identifies a role for RUNX1 in Down syndrome DNA methylation profiles. Hum Mol Genet. 2021 01 06; 29(21):3465-3476. Laufer BI, Hwang H, Jianu JM, Mordaunt CE, Korf IF, Hertz-Picciotto I, LaSalle JM. PMID: 33001180; PMCID: PMC7788293.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    11. Association of the Lactase Persistence Haplotype Block With Disease Risk in Populations of European Descent. Front Genet. 2020; 11:558762. Joslin SEK, Durbin-Johnson BP, Britton M, Settles ML, Korf I, Lemay DG. PMID: 33193640; PMCID: PMC7658388.
      View in: PubMed   Mentions: 1  
    12. A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues. BMC Genomics. 2020 Oct 07; 21(1):698. Halstead MM, Kern C, Saelao P, Wang Y, Chanthavixay G, Medrano JF, Van Eenennaam AL, Korf I, Tuggle CK, Ernst CW, Zhou H, Ross PJ. PMID: 33028202; PMCID: PMC7541309.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    13. Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes. BMC Bioinformatics. 2020 Feb 24; 21(1):74. Treiber ML, Taft DH, Korf I, Mills DA, Lemay DG. PMID: 32093654; PMCID: PMC7041091.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    14. Fecal metatranscriptomics and glycomics suggest that bovine milk oligosaccharides are fully utilized by healthy adults. J Nutr Biochem. 2020 05; 79:108340. Westreich ST, Salcedo J, Durbin-Johnson B, Smilowitz JT, Korf I, Mills DA, Barile D, Lemay DG. PMID: 32028108; PMCID: PMC7233280.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCellsCTClinical Trials
    15. Association of Lactase Persistence Genotypes (rs4988235) and Ethnicity with Dairy Intake in a Healthy U.S. Population. Nutrients. 2019 Aug 10; 11(8). Chin EL, Huang L, Bouzid YY, Kirschke CP, Durbin-Johnson B, Baldiviez LM, Bonnel EL, Keim NL, Korf I, Stephensen CB, Lemay DG. PMID: 31405126; PMCID: PMC6723957.
      View in: PubMed   Mentions: 17     Fields:    Translation:Humans
    16. Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization. Microbiome. 2019 03 18; 7(1):41. Westreich ST, Ardeshir A, Alkan Z, Kable ME, Korf I, Lemay DG. PMID: 30885266; PMCID: PMC6423747.
      View in: PubMed   Mentions: 17     Fields:    Translation:AnimalsCells
    17. Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. BMC Genomics. 2018 Sep 18; 19(1):684. Kern C, Wang Y, Chitwood J, Korf I, Delany M, Cheng H, Medrano JF, Van Eenennaam AL, Ernst C, Ross P, Zhou H. PMID: 30227846; PMCID: PMC6145346.
      View in: PubMed   Mentions: 67     Fields:    Translation:Animals
    18. The collaborative effect of scientific meetings: A study of the International Milk Genomics Consortium. PLoS One. 2018; 13(8):e0201637. Kwok E, Porter M, Korf I, Pasin G, German JB, Lemay DG. PMID: 30133459; PMCID: PMC6104928.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
    19. 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). Gaulke CA, Porter M, Han YH, Sankaran-Walters S, Grishina I, George MD, Dang AT, Ding SW, Jiang G, Korf I, Dandekar S. PMID: 29844248; PMCID: PMC5974476.
      View in: PubMed   Mentions:    Fields:    
    20. SAMSA2: a standalone metatranscriptome analysis pipeline. BMC Bioinformatics. 2018 05 21; 19(1):175. Westreich ST, Treiber ML, Mills DA, Korf I, Lemay DG. PMID: 29783945; PMCID: PMC5963165.
      View in: PubMed   Mentions: 64     Fields:    
    21. Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins. Science. 2018 01 05; 359(6371):55-61. Yin D, Schwarz EM, Thomas CG, Felde RL, Korf IF, Cutter AD, Schartner CM, Ralston EJ, Meyer BJ, Haag ES. PMID: 29302007; PMCID: PMC5789457.
      View in: PubMed   Mentions: 60     Fields:    Translation:AnimalsCells
    22. Autosomal Trisomy and Triploidy Are Corrected During Female Meiosis in Caenorhabditis elegans. Genetics. 2017 11; 207(3):911-922. Vargas E, McNally K, Friedman JA, Cortes DB, Wang DY, Korf IF, McNally FJ. PMID: 28882988; PMCID: PMC5676225.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    23. Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nat Commun. 2017 Apr 12; 8:14953. 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. PMID: 28401891; PMCID: PMC5394340.
      View in: PubMed   Mentions: 176     Fields:    Translation:AnimalsCells
    24. Dental Pulp Stem Cells Model Early Life and Imprinted DNA Methylation Patterns. Stem Cells. 2017 04; 35(4):981-988. Dunaway K, Goorha S, Matelski L, Urraca N, Lein PJ, Korf I, Reiter LT, LaSalle JM. PMID: 28032673; PMCID: PMC5367950.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    25. 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. 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. PMID: 27974215; PMCID: PMC5206988.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansCells
    26. SAMSA: a comprehensive metatranscriptome analysis pipeline. BMC Bioinformatics. 2016 Sep 29; 17(1):399. Westreich ST, Korf I, Mills DA, Lemay DG. PMID: 27687690; PMCID: PMC5041328.
      View in: PubMed   Mentions: 24     Fields:    
    27. Intron sequences that stimulate gene expression in Arabidopsis. Plant Mol Biol. 2016 Oct; 92(3):337-46. Rose AB, Carter A, Korf I, Kojima N. PMID: 27492360.
      View in: PubMed   Mentions: 27     Fields:    Translation:Animals
    28. GC skew is a conserved property of unmethylated CpG island promoters across vertebrates. Nucleic Acids Res. 2015 Nov 16; 43(20):9729-41. Hartono SR, Korf IF, Chédin F. PMID: 26253743; PMCID: PMC4787789.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansAnimalsCells
    29. Catastrophic chromosomal restructuring during genome elimination in plants. Elife. 2015 May 15; 4. Tan EH, Henry IM, Ravi M, Bradnam KR, Mandakova T, Marimuthu MP, Korf I, Lysak MA, Comai L, Chan SW. PMID: 25977984; PMCID: PMC4461816.
      View in: PubMed   Mentions: 53     Fields:    Translation:AnimalsCells
    30. Comparative Proteomics of Human and Macaque Milk Reveals Species-Specific Nutrition during Postnatal Development. J Proteome Res. 2015 May 01; 14(5):2143-57. Beck KL, Weber D, Phinney BS, Smilowitz JT, Hinde K, Lönnerdal B, Korf I, Lemay DG. PMID: 25757574.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansAnimals
    31. The Genome 10K Project: a way forward. Annu Rev Anim Biosci. 2015; 3:57-111. Koepfli KP, Paten B, Genome 10K Community of Scientists, O'Brien SJ. PMID: 25689317; PMCID: PMC5837290.
      View in: PubMed   Mentions: 141     Fields:    Translation:HumansAnimals
    32. The functional significance of common polymorphisms in zinc finger transcription factors. G3 (Bethesda). 2014 Jun 26; 4(9):1647-55. Lockwood SH, Guan A, Yu AS, Zhang C, Zykovich A, Korf I, Rannala B, Segal DJ. PMID: 24970883; PMCID: PMC4169156.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    33. Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ. 2014; 2:e415. Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE. PMID: 24918035; PMCID: PMC4045339.
      View in: PubMed   Mentions: 58     Fields:    
    34. 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. Gaulke CA, Porter M, Han YH, Sankaran-Walters S, Grishina I, George MD, Dang AT, Ding SW, Jiang G, Korf I, Dandekar S. PMID: 24672033; PMCID: PMC4093871.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    35. StochHMM: a flexible hidden Markov model tool and C++ library. Bioinformatics. 2014 Jun 01; 30(11):1625-6. Lott PC, Korf I. PMID: 24489371; PMCID: PMC4029032.
      View in: PubMed   Mentions: 8     Fields:    
    36. Sequencing the transcriptome of milk production: milk trumps mammary tissue. BMC Genomics. 2013 Dec 12; 14:872. 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. PMID: 24330573; PMCID: PMC3871720.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansAnimalsCells
    37. Genomics: the state of the art in RNA-seq analysis. Nat Methods. 2013 Dec; 10(12):1165-6. Korf I. PMID: 24296473.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    38. From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome. PLoS One. 2013; 8(9):e75030. Lemay DG, Pollard KS, Martin WF, Freeman Zadrowski C, Hernandez J, Korf I, German JB, Rijnkels M. PMID: 24086428; PMCID: PMC3784412.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    39. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2013 Jul 22; 2(1):10. 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. PMID: 23870653; PMCID: PMC3844414.
      View in: PubMed   Mentions: 299     Fields:    
    40. 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. Ginno PA, Lim YW, Lott PL, Korf I, Chédin F. PMID: 23868195; PMCID: PMC3787257.
      View in: PubMed   Mentions: 186     Fields:    Translation:HumansCells
    41. The human placenta methylome. Proc Natl Acad Sci U S A. 2013 Apr 09; 110(15):6037-42. Schroeder DI, Blair JD, Lott P, Yu HO, Hong D, Crary F, Ashwood P, Walker C, Korf I, Robinson WP, LaSalle JM. PMID: 23530188; PMCID: PMC3625261.
      View in: PubMed   Mentions: 161     Fields:    Translation:HumansCells
    42. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biol. 2013 Jan 30; 14(1):R10. 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. PMID: 23363705; PMCID: PMC4053949.
      View in: PubMed   Mentions: 241     Fields:    Translation:AnimalsCells
    43. The effects of a stimulating intron on the expression of heterologous genes in Arabidopsis thaliana. Plant Biotechnol J. 2013 Jun; 11(5):555-63. Emami S, Arumainayagam D, Korf I, Rose AB. PMID: 23347383.
      View in: PubMed   Mentions: 25     Fields:    Translation:AnimalsCells
    44. Comparative genomics of carp herpesviruses. J Virol. 2013 Mar; 87(5):2908-22. Davison AJ, Kurobe T, Gatherer D, Cunningham C, Korf I, Fukuda H, Hedrick RP, Waltzek TB. PMID: 23269803; PMCID: PMC3571366.
      View in: PubMed   Mentions: 33     Fields:    
    45. Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing. J Am Chem Soc. 2012 Oct 24; 134(42):17814-22. Meier JL, Yu AS, Korf I, Segal DJ, Dervan PB. PMID: 23013524; PMCID: PMC3483022.
      View in: PubMed   Mentions: 23     Fields:    
    46. G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes. BMC Bioinformatics. 2012 Sep 28; 13:253. Lemay DG, Martin WF, Hinrichs AS, Rijnkels M, German JB, Korf I, Pollard KS. PMID: 23020263; PMCID: PMC3575404.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    47. Holocentric chromosomes: convergent evolution, meiotic adaptations, and genomic analysis. Chromosome Res. 2012 Jul; 20(5):579-93. Melters DP, Paliulis LV, Korf IF, Chan SW. PMID: 22766638.
      View in: PubMed   Mentions: 129     Fields:    Translation:AnimalsCells
    48. R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol Cell. 2012 Mar 30; 45(6):814-25. Ginno PA, Lott PL, Christensen HC, Korf I, Chédin F. PMID: 22387027; PMCID: PMC3319272.
      View in: PubMed   Mentions: 436     Fields:    
    49. Evidence for a DNA-Based Mechanism of Intron-Mediated Enhancement. Front Plant Sci. 2011; 2:98. Rose AB, Emami S, Bradnam K, Korf I. PMID: 22645558; PMCID: PMC3355757.
      View in: PubMed   Mentions: 22  
    50. Myc and Miz-1 have coordinate genomic functions including targeting Hox genes in human embryonic stem cells. Epigenetics Chromatin. 2011 Nov 04; 4:20. Varlakhanova N, Cotterman R, Bradnam K, Korf I, Knoepfler PS. PMID: 22053792; PMCID: PMC3226433.
      View in: PubMed   Mentions: 23     Fields:    
    51. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 2011 Dec; 21(12):2224-41. 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. PMID: 21926179; PMCID: PMC3227110.
      View in: PubMed   Mentions: 213     Fields:    
    52. 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. Huefner ND, Mizuno Y, Weil CF, Korf I, Britt AB. PMID: 21889425.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    53. Large-scale methylation domains mark a functional subset of neuronally expressed genes. Genome Res. 2011 Oct; 21(10):1583-91. Schroeder DI, Lott P, Korf I, LaSalle JM. PMID: 21784875; PMCID: PMC3202276.
      View in: PubMed   Mentions: 53     Fields:    Translation:HumansCells
    54. Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants. Nucleic Acids Res. 2011 Jul; 39(13):5328-37. Parra G, Bradnam K, Rose AB, Korf I. PMID: 21427088; PMCID: PMC3141229.
      View in: PubMed   Mentions: 67     Fields:    Translation:Animals
    55. Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes. PLoS One. 2011 Feb 15; 6(2):e17121. 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. PMID: 21347206; PMCID: PMC3039671.
      View in: PubMed   Mentions: 48     Fields:    Translation:HumansCells
    56. The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics. 2010 Jul 07; 11:420. Kovach A, Wegrzyn JL, Parra G, Holt C, Bruening GE, Loopstra CA, Hartigan J, Yandell M, Langley CH, Korf I, Neale DB. PMID: 20609256; PMCID: PMC2996948.
      View in: PubMed   Mentions: 62     Fields:    Translation:AnimalsCells
    57. Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing. Nucleic Acids Res. 2009 Dec; 37(22):e151. Zykovich A, Korf I, Segal DJ. PMID: 19843614; PMCID: PMC2794170.
      View in: PubMed   Mentions: 69     Fields:    
    58. Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res. 2010 Jan; 38(3):e13. Blahnik KR, Dou L, O'Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Ludäscher B, Korf I, Farnham PJ. PMID: 19906703; PMCID: PMC2817454.
      View in: PubMed   Mentions: 75     Fields:    
    59. Applying word-based algorithms: the IMEter. Methods Mol Biol. 2009; 553:287-301. Korf IF, Rose AB. PMID: 19588111.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    60. Assessing the gene space in draft genomes. Nucleic Acids Res. 2009 Jan; 37(1):289-97. Parra G, Bradnam K, Ning Z, Keane T, Korf I. PMID: 19042974; PMCID: PMC2615622.
      View in: PubMed   Mentions: 259     Fields:    Translation:HumansAnimals
    61. Longer first introns are a general property of eukaryotic gene structure. PLoS One. 2008 Aug 29; 3(8):e3093. Bradnam KR, Korf I. PMID: 18769727; PMCID: PMC2518113.
      View in: PubMed   Mentions: 67     Fields:    Translation:Animals
    62. Promoter-proximal introns in Arabidopsis thaliana are enriched in dispersed signals that elevate gene expression. Plant Cell. 2008 Mar; 20(3):543-51. Rose AB, Elfersi T, Parra G, Korf I. PMID: 18319396; PMCID: PMC2329928.
      View in: PubMed   Mentions: 86     Fields:    Translation:AnimalsCells
    63. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 2008 Jan; 18(1):188-96. Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sánchez Alvarado A, Yandell M. PMID: 18025269; PMCID: PMC2134774.
      View in: PubMed   Mentions: 969     Fields:    Translation:Animals
    64. Draft genome of the filarial nematode parasite Brugia malayi. Science. 2007 Sep 21; 317(5845):1756-60. 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. PMID: 17885136; PMCID: PMC2613796.
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    65. 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. Huang D, Chow TW. PMID: 17463028.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    66. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics. 2007 May 01; 23(9):1061-7. Parra G, Bradnam K, Korf I. PMID: 17332020.
      View in: PubMed   Mentions: 1181     Fields:    Translation:HumansAnimalsCells
    67. Sorghum genome sequencing by methylation filtration. PLoS Biol. 2005 Jan; 3(1):e13. 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. PMID: 15660154; PMCID: PMC539327.
      View in: PubMed   Mentions: 50     Fields:    Translation:AnimalsCells
    68. A probabilistic model of 3' end formation in Caenorhabditis elegans. Nucleic Acids Res. 2004; 32(11):3392-9. Hajarnavis A, Korf I, Durbin R. PMID: 15247332; PMCID: PMC443532.
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    69. Gene finding in novel genomes. BMC Bioinformatics. 2004 May 14; 5:59. Korf I. PMID: 15144565; PMCID: PMC421630.
      View in: PubMed   Mentions: 1566     Fields:    Translation:Animals
    70. Serial BLAST searching. Bioinformatics. 2003 Aug 12; 19(12):1492-6. Korf I. PMID: 12912829.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    71. 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. Flicek P, Keibler E, Hu P, Korf I, Brent MR. PMID: 12529305; PMCID: PMC430948.
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    72. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 Dec 05; 420(6915):520-62. Mouse Genome Sequencing Consortium, 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. PMID: 12466850.
      View in: PubMed   Mentions: 2488     Fields:    Translation:HumansAnimalsCells
    73. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002 Oct; 12(10):1611-8. 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. PMID: 12368254; PMCID: PMC187536.
      View in: PubMed   Mentions: 789     Fields:    Translation:HumansAnimals
    74. Automated processing of raw DNA sequence data. IEEE Eng Med Biol Mag. 2001 Jul-Aug; 20(4):41-8. Wendl MC, Korf I, Chinwalla AT, Hillier LW. PMID: 11494768.
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    75. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15; 409(6822):860-921. 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, International Human Genome Sequencing Consortium. PMID: 11237011.
      View in: PubMed   Mentions: 7123     Fields:    Translation:HumansAnimalsCells
    76. Integrating genomic homology into gene structure prediction. Bioinformatics. 2001; 17 Suppl 1:S140-8. Korf I, Flicek P, Duan D, Brent MR. PMID: 11473003.
      View in: PubMed   Mentions: 148     Fields:    Translation:HumansAnimalsCells
    77. MPBLAST : improved BLAST performance with multiplexed queries. Bioinformatics. 2000 Nov; 16(11):1052-3. Korf I, Gish W. PMID: 11159321.
      View in: PubMed   Mentions: 9     Fields:    
    78. MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics. 2000 Nov; 16(11):1040-1. Bedell JA, Korf I, Gish W. PMID: 11159316.
      View in: PubMed   Mentions: 122     Fields:    Translation:HumansAnimalsCells
    79. The syntenic relationship of the zebrafish and human genomes. Genome Res. 2000 Sep; 10(9):1351-8. Barbazuk WB, Korf I, Kadavi C, Heyen J, Tate S, Wun E, Bedell JA, McPherson JD, Johnson SL. PMID: 10984453; PMCID: PMC310919.
      View in: PubMed   Mentions: 184     Fields:    Translation:HumansAnimalsCells
    80. 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. 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. PMID: 10655503; PMCID: PMC15558.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    81. The DNA sequence of human chromosome 22. Nature. 1999 Dec 02; 402(6761):489-95. 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, et al. PMID: 10591208.
      View in: PubMed   Mentions: 224     Fields:    Translation:HumansAnimalsCells
    82. A general approach to single-nucleotide polymorphism discovery. Nat Genet. 1999 Dec; 23(4):452-6. Marth GT, Korf I, Yandell MD, Yeh RT, Gu Z, Zakeri H, Stitziel NO, Hillier L, Kwok PY, Gish WR. PMID: 10581034.
      View in: PubMed   Mentions: 150     Fields:    Translation:Humans
    83. The Polycomb group in Caenorhabditis elegans and maternal control of germline development. Development. 1998 Jul; 125(13):2469-78. Korf I, Fan Y, Strome S. PMID: 9609830.
      View in: PubMed   Mentions: 40     Fields:    Translation:AnimalsCells
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