Korf lab publications

• Zykovich, A., Korf, I., and Segal, D.J. Bind-n-Seq: high throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing Nucleic Acids Research, 2009
• Parra, G., Bradnam, K., Ning, Z., Keane, T., and Korf, I.. Assessing the gene space in draft genomes. Nucleic Acids Research 2009, 37, 1, 289-297
• Cantarel, B. Korf, I., Robb, S., Parra, G., Ross, E., Moore, B., Holt, C., Alvarado, A., Yandel M. MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes Genome Research. 2008, 18, 188-196
• Rose, A, Elfersi, T, Parra G, Korf I. Promoter-Proximal Introns in Arabidopsis thaliana are enriched in dispersed signals that elevate gene expression. Plant Cell 2008, 20:543-551
• Bradnam, K, Korf I. Longer First Introns Are a General Property of Eukaryotic Gene Structure. PLoS One 2008, 3(8), e3093
• Parra G, Bradnam, K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 2007, 23(9):1061-1067

Older publications

• Ghedin E. et al. (including Korf I.) Draft Genome of the Filarial Nematode Parasite Brugia malayi Science 2007 317, 5845, 1756-1760
• Hajarnavis A, Korf I, Durbin R. A probabilistic model of 3' end formation in Caenorhabditis elegans. Nucleic Acids Research 2004, 32:3392-3399.
• Korf I. Gene finding in novel Genomes. BMC Bioinformatics 2004, 5:59
• Korf I. Serial BLAST searching. Bioinformatics. 2003 Aug 12;19(12):1492-6.
• 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.
• The Mouse Genome Sequencing Consortium. Initial Sequencing and Comparative Analysis of the Mouse Genome. Nature. 2002 Dec 5;420(6915):520-62.
• Jason E. Stajich, David Block, Kris Boulez, Steven E. Brenner, Stephen A. Chervitz, Chris Dagdigian, Georg Fuellen, James G.R. Gilbert, Ian Korf, Hilmar Lapp, Heikki Lehv?aiho, Chad Matsalla, Chris J. Mungall, Brian I. Osborne, Matthew R. Pocock, Peter Schattner, Martin Senger, Lincoln D. Stein, Elia Stupka, Mark D. Wilkinson, and Ewan Birney. The Bioperl Toolkit: Perl Modules for the Life Sciences. (2002) Genome Res. 2002 12(10): 1611-1618.
• 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
• Korf I, Flicek P, Duan D, Brent MR. Integrating genomic homology into gene structure prediction. Bioinformatics. 2001 Jun;17 Suppl 1:S140-8.
• International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15;409(6822):860-921.
• Korf I, Gish W. MPBLAST : improved BLAST performance with multiplexed queries. Bioinformatics. 2000 Nov;16(11):1052-3.
• Bedell JA, Korf I, Gish W. MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics. 2000 Nov;16(11):1040-1.
• 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.
• Ellsworth RE et al. Comparative genomic sequence analysis of the human and mouse cystic fibrosis transmembrane conductance regulator genes. Proc Natl Acad Sci U S A. 2000 Feb 1;97(3):1172-7.
• 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.
• Dunham I et al. The DNA sequence of human chromosome 22. Nature 402(6761): 489-495 (1999).
• The C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigative biology. Science 282: 2012-2018 (1998).
• 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.