Contact me via email: ifkorf@ucdavis.edu
Research Interests
My computational molecular biology research seeks to understand structure and function in genomic DNA. Since my research involves methodolgies from text processing (exact and inexact string matching) and speech recognition (hidden Markov models), and because comparative genomics provides a Rosetta Stone-like guidance, my research is very much like reading the book of life.- Gene Prediction
- Despite roughly 20 years of research, gene prediction algorithms cannot accurately derive a proteome from a genome. I'm trying to bring a biologists perspective to the field. My latest effort is called SNAP.
- Comparative Genomics
- Just as the ancient Greeks used comparative anatomy to understand the human body, I'm using comparative genomics to understand the human genome (and other genomes).
- Genome Annotation
- Genome annotation seeks to label regions of a genome with functional descriptors like "gene" or "repeat". Identifying the complete set of human genes is probably the most obvious goal of genome annotation today. Annotation often relies on expert biologists and expert systems to determine the correct labeling of a sequence. I'm interested in improving both manual and automated annotation and identifying standards in this new field.
- Developmental Regulation
- My formal training is in molecular and developmental biology and I am still very interested in this area. In a sense, all my interests are fueled by a curiosity about how genes are regulated in space, time, and clade.
Publications
- Ghedin E, Wang S, Spiro D, et al. Draft genome of the filarial nematode parasite Brugia malayi. Science. 2007 Sep 21;317(5845):1756-60
- Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics. 2007 May 1;23(9):1061-7.
- 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.
Cool Stuff
- SNAP (Semi-HMM-based Nucleic Acid Parser) is now available for download.
- The only book dedicated to BLAST!
- My unboggle programs including the YAWL word list.
- Poster on Serial BLAST Searching
(PDF)
- CSHL 2002 poster (PDF)
- Twinscan Server
Software Packages
- SNAP gene prediction program and some standard data sets of genes.
- MaskerAid Make RepeatMasker fly!
- Twinscan Genscan-like gene predictor using genomic homology.
- PolyBayes A Bayesian approach to identifying SNPs from multiple alignments.
- MyGenBank Manage a local copy of GenBank with MySQL.
- AHA Flexible sequence analysis pipeline that exports a portable ACEDB instance.
Perl Freebies
The software here is unsupported, free software. Please report bugs, but don't expect timely updates.- DataBrowser.pm Survival tool for when you're knee-deep in Perl data structures.
- BPlite.pm Simple BLAST parser with a clean, object-oriented interface.
- FAlite.pm Convenient interface for parsing FASTA files.
- GBlite.pm Parses GenBank flat files. Used by MyGenBank.
- codon.pl Ever wonder how many unambiguous translations there are for ambiguous codons?
- mpblast.pl Make BLASTN 10x faster on batch jobs of short sequences.
- plotBlast.pl Makes graphical BLAST reports.
- tregex.pl Search for protein patterns in EST databases.
- xblast.pl Perl version of Claverie's xblast.