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Publications

Names in bold face represent current Korf Lab members at the time of submission/publication.

2013

• Schroeder, D.I., Blair, J.D., Lott, P., Yu, H.O.K., Hong, D., Crary, F., Ashwood, P., Walker, C., Korf, I.F., Robinson, W.P., and LaSalle, J.M. The human placenta methylome, P.N.A.S, 2013, Epub ahead of print. 27 March
• Melters, D.P., Bradnam, K.R., Young, H.A., Telis, N., May, R.M., Ruby, J.G., Sebra, R., Peluso, P., Eid, J., Rank, D., Garcia, J.F., DeRisi, J.L., Smith, T., Tobias, C., Ross-Ibarra, J., Korf, I.F., and Simon W.-L. Chan. Comparative Analysis of Tandem Repeats from Hundreds of Species Reveals Unique Insights into Centromere Evolution, Genome Biology, 2013, 14:R10
• Emami, S., Arumainayagam, D., Korf, I., and Rose, A.B., The effects of a stimulating intron on the expression of heterologous genes in Arabidopsis thaliana Plant Biotechnology Journal, 2013, 28 January
• PREPRINT: Bradnam, K.R., 89 other co-authors, and Korf, I.K., Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species, arXiv:1301.5406 [q-bio.GN], 23 January

2012

• Davison, A.J., Kurobe, T., Gatherer, D., Cunningham, C., Korf, I., Fukuda, H., Hedrick, R.P., and Waltzek, T.B., Comparative genomics of carp herpesviruses J. Virol., 2012, 26 December
• Lemay, D.G., Martin, W.F., Hinrichs, A.S., Rijnkels, M., German, J.B., Korf, I., and Pollard, K.S. G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes BMC Bioinformatics, 2012, 13:253, 28 July
• Meier, J.L., Yu, A., Korf, I., Segal, DJ, and Dervan, P.B. Guiding the Design of Synthetic DNA-Binding Molecules with Massively Parallel Sequencing. J. Am. Chem. Soc., 2012, 28 July
• Bradnam, K. and Korf, I.. Unix and Perl to the RESCUE! A field guide for the life sciences (and other data-rich pursuits). Cambridge University Press
• Melters, D.P., Paliulis L.V., Korf I., and Chan SW. Holocentric chromosomes: convergent evolution, meiotic adaptations, and genomic analysis.. Chromosome Res., 2012, 7th July
• Ginno, P.A. Lott, P.L., Christensen, H.C. Korf, I., and Chédin, F. R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters. Molecular Cell, 2012, 1st March

2011

• Rose A., Emami, S., Bradnam, K., and Korf, I. Evidence for a DNA-based mechanism of intron-mediated enhancement. Frontiers in Plant Genetics and Genomics, 2011, 2, 98
• Varlakhnanova N., Cotterman, R., Bradnam, K., Korf, I. and Knoepfler, P. Myc and Miz-1 have coordinate genomic functions including targeting Hox genes in human embryonic stem cells. Epigenetics & Chromatin, 2011, 4, 20
• Earl, D., Bradnam, K., Yu, H., Korf, I. et al. Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Research, 2011, 21, 2224-2241
• Huefner, ND, Mizuno, Y, Well, CF, Korf, I., and Britt, AB. Breadth by depth: Expanding our understanding of the repair of transposon-induced DNA double strand breaks via deep-sequencing. DNA Repair, 2011
• Schroeder, DI, Lott, P., Korf, I., and LaSalle JM. Large-scale methylation domains mark a functional subset of neuronally expressed genes. Genome Research, 2011
• Parra, G., Bradnam, K., Rose, A. and Korf, I.. Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants. Nucleic Acids Research, 2011.
• Blahnik, K.R., Dou, L., Echipare, L., Iyengar, S., O'Geen, H., Sanchez, E., Zhao, Y., Marra, M.A., Hirst, M., Costello, J.F., Korf, I., and Farnham, P.J. Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes. PLoS One, 2011, 6, 2, e17121.

2010

• 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, 11, 420.
• Blahnik, K.R., Dou, L., O'Geen, H., McPhillips, T., Xu, X., Cao, A.R., Iyengar, S., Nicolet, C.M., Ludascher, Korf, I., and Farnham, P.J. Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Research, 2010, 38, 3, e13.

2009

• 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, 37, 22, e151.
• 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.

2008

• 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.

2007

• Parra G, Bradnam, K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 2007, 23(9):1061-1067.
• Ghedin E. et al. (including Korf I.) Draft Genome of the Filarial Nematode Parasite Brugia malayi Science 2007 317, 5845, 1756-1760.

Older Publications

• 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.
• Mouse Genome Sequencing Consortium. The 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. 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.

Content © Korf Lab 2012