I. Korf

发表

Initial sequencing and analysis of the human genome.

J. V. Moran, V. J. Pollara, D. Haussler, 2001, Nature.

Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map.

M. Brent, P. Flicek, I. Korf, 2003, Genome research.

Initial sequencing and comparative analysis of the mouse genome.

Colin N. Dewey, Simon C. Potter, James A. Cuff, 2002 .

The Bioperl toolkit: Perl modules for the life sciences.

Matthew R. Pocock, Mark D. Wilkinson, E. Birney, 2002, Genome research.

Assemblathon 1: a competitive assessment of de novo short read assembly methods.

Nuno A. Fonseca, Shaun D. Jackman, David R. Kelley, 2011, Genome research.

A general approach to single-nucleotide polymorphism discovery

Gabor T. Marth, G. Marth, W. Gish, 1999, Nature Genetics.

Integrating genomic homology into gene structure prediction

Ian Korf, Paul Flicek, Daniel Duan, 2001, ISMB.

The DNA sequence of human chromosome 22

Melanie E. Goward, Antony V. Cox, R. Durbin, 1999, Nature.

MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes.

Sofia M. C. Robb, G. Parra, M. Yandell, 2007, Genome research.

Assessing the gene space in draft genomes

Keith Bradnam, Thomas M. Keane, Zemin Ning, 2008, Nucleic acids research.

GC skew at the 5′ and 3′ ends of human genes links R-loop formation to epigenetic regulation and transcription termination

I. Korf, F. Chédin, P. Ginno, 2013, Genome research.

formation to epigenetic regulation and transcription termination GC skew at the 5 ' and 3 ' ends of human genes links R-loop

I. Korf, F. Chédin, P. Ginno, 2013 .

Automated processing of raw DNA sequence data

L. Hillier, M. Wendl, A. Chinwalla, 2001, IEEE Engineering in Medicine and Biology Magazine.

Promoter-Proximal Introns in Arabidopsis thaliana Are Enriched in Dispersed Signals that Elevate Gene Expression[W][OA]

G. Parra, I. Korf, A. Rose, 2008, The Plant Cell Online.

Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921))

Ronald W. Davis, J. V. Moran, V. J. Pollara, 2001 .

Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

Alison L. Van Eenennaam, Hans H. Cheng, I. Korf, 2018, BMC Genomics.

Bind-n-Seq: high-throughput analysis of in vitro protein–DNA interactions using massively parallel sequencing

I. Korf, D. Segal, Artem Zykovich, 2009, Nucleic acids research.

Draft Genome of the Filarial Nematode Parasite Brugia malayi

Jonathan E. Allen, Matthew W. Dimmic, David M. A. Martin, 2007, Science.

Guiding the Design of Synthetic DNA-Binding Molecules with Massively Parallel Sequencing

I. Korf, P. Dervan, D. Segal, 2012, Journal of the American Chemical Society.

Low-pass whole genome bisulfite sequencing of neonatal dried blood spots identifies a role for RUNX1 in Down syndrome DNA methylation profiles

I. Hertz-Picciotto, I. Korf, B. Laufer, 2020, bioRxiv.

Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce

Xun Xu, Rui Xia, Blake C Meyers, 2017, Nature Communications.

The collaborative effect of scientific meetings: A study of the International Milk Genomics Consortium

Danielle G. Lemay, I. Korf, J. German, 2018, PloS one.

Longer First Introns Are a General Property of Eukaryotic Gene Structure

I. Korf, K. Bradnam, Ian Korf, 2008, PloS one.

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

Jenna M. Lang, Jonathan A. Eisen, Aaron E. Darling, 2014, PeerJ.

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

Jeffrey Ross-Ibarra, Joseph L DeRisi, Paul Peluso, 2012, Genome Biology.

Disruption of Hepatic Leptin Signaling Protects Mice From Age- and Diet-Related Glucose Intolerance

Daniël P. Melters, Scott D Covey, J. Derisi, 2010, Diabetes.

Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data

Bertram Ludäscher, Timothy McPhillips, Peggy J. Farnham, 2009, Nucleic acids research.

GC skew is a conserved property of unmethylated CpG island promoters across vertebrates

I. Korf, F. Chédin, S. Hartono, 2015, Nucleic acids research.

model organism genomes MAKER : An easy-to-use annotation pipeline designed for emerging data

Sofia M. C. Robb, G. Parra, M. Yandell, 2007 .

Comparative Proteomics of Human and Macaque Milk Reveals Species-Specific Nutrition during Postnatal Development.

Danielle G. Lemay, I. Korf, B. Phinney, 2015, Journal of proteome research.

Association of the Lactase Persistence Haplotype Block With Disease Risk in Populations of European Descent

Danielle G. Lemay, Shannon E. K. Joslin, I. Korf, 2020, Frontiers in Genetics.

From Genes to Milk: Genomic Organization and Epigenetic Regulation of the Mammary Transcriptome

Danielle G. Lemay, K. Pollard, I. Korf, 2013, PloS one.

The Functional Significance of Common Polymorphisms in Zinc Finger Transcription Factors

B. Rannala, I. Korf, D. Segal, 2014, G3: Genes, Genomes, Genetics.

Association of Diet and Antimicrobial Resistance in Healthy U.S. Adults

Danielle G. Lemay, I. Korf, B. Durbin-Johnson, 2022, mBio.

Sorghum Genome Sequencing by Methylation Filtration

W. Richard McCombie, Ian F Korf, B. Roe, 2005, PLoS biology.

The Genome 10K Project: A Way Forward Further

D. Haussler, R. Durbin, M. Diekhans, 2015 .

Marth, G.T. et al. A general approach to single-nucleotide polymorphism discovery. Nat. Genet. 23, 452-456

Mark Yandell, Gabor T. Marth, Warren Gish, 2000 .

Holocentric chromosomes: convergent evolution, meiotic adaptations, and genomic analysis

Daniël P. Melters, I. Korf, S. Chan, 2012, Chromosome Research.

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes

Keith Bradnam, Ian Korf, Genis Parra, 2007, Bioinform..

Gene finding in novel genomes

Ian Korf, I. Korf, 2004, BMC Bioinformatics.

Serial BLAST searching

Ian Korf, I. Korf, 2003, Bioinform..

First fungal genome sequence from Africa: A preliminary analysis

Simon H. Martin, M. Yandell, I. Korf, 2012 .

Comparative Genomics of Carp Herpesviruses

I. Korf, A. Davison, D. Gatherer, 2012, Journal of Virology.

The human placenta methylome

Wendy P Robinson, I. Korf, D. Schroeder, 2013, Proceedings of the National Academy of Sciences.

A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues

Alison L. Van Eenennaam, I. Korf, C. Ernst, 2020, bioRxiv.

Gene Prediction Methods

Uwe Ohler, William H. Majoros, Ian F Korf, 2009 .

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

Mark Yandell, Carson Holt, David B Neale, 2010, BMC Genomics.

The syntenic relationship of the zebrafish and human genomes.

J. McPherson, S. Johnson, I. Korf, 2000, Genome research.

R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters.

I. Korf, F. Chédin, P. Ginno, 2012, Molecular cell.

Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research

Alison L. Van Eenennaam, Hans H. Cheng, P. Flicek, 2021, Nature Communications.

Large-scale methylation domains mark a functional subset of neuronally expressed genes.

I. Korf, D. Schroeder, J. LaSalle, 2011, Genome research.

Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins

Cristel G. Thomas, Ian F Korf, Barbara J Meyer, 2018, Science.

Characterization of the Contradictory Chromatin Signatures at the 3′ Exons of Zinc Finger Genes

M. Marra, P. Farnham, M. Hirst, 2011, PloS one.

The Polycomb group in Caenorhabditis elegans and maternal control of germline development.

I. Korf, S. Strome, Yuan Fan, 1998, Development.

Cumulative Impact of Polychlorinated Biphenyl and Large Chromosomal Duplications on DNA Methylation, Chromatin, and Expression of Autism Candidate Genes.

I. Korf, S. J. Lopez, J. LaSalle, 2016, Cell reports.

Fecal metatranscriptomics and glycomics suggest that bovine milk oligosaccharides are fully utilized by healthy adults.

Danielle G. Lemay, Samuel T. Westreich, I. Korf, 2020, The Journal of nutritional biochemistry.

Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization

Danielle G. Lemay, Samuel T. Westreich, I. Korf, 2019, Microbiome.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Inanç Birol, Dominique Lavenier, Hamidreza Chitsaz, 2013, GigaScience.

Catastrophic chromosomal restructuring during genome elimination in plants

I. Korf, K. Bradnam, S. Chan, 2015, eLife.

MaskerAid : a performance enhancement to RepeatMasker

Ian Korf, Joseph A. Bedell, Warren Gish, 2000, Bioinform..

Dental Pulp Stem Cells Model Early Life and Imprinted DNA Methylation Patterns

I. Korf, J. LaSalle, L. Reiter, 2017, Stem cells.

Breadth by depth: expanding our understanding of the repair of transposon-induced DNA double strand breaks via deep-sequencing.

I. Korf, C. Weil, A. Britt, 2011, DNA repair.

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes

Ian Korf, Danielle G. Lemay, Angie S. Hinrichs, 2012, BMC Bioinformatics.

SAMSA2: a standalone metatranscriptome analysis pipeline

Danielle G. Lemay, Samuel T. Westreich, I. Korf, 2017, bioRxiv.

Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes

Michelle L. Treiber, Diana H. Taft, David A. Mills, 2019, BMC Bioinformatics.

The effects of a stimulating intron on the expression of heterologous genes in Arabidopsis thaliana.

I. Korf, A. Rose, S. Emami, 2013, Plant biotechnology journal.

Evidence for a DNA-Based Mechanism of Intron-Mediated Enhancement

I. Korf, K. Bradnam, A. Rose, 2011, Front. Plant Sci..

Intestinal Epithelial Barrier Disruption through Altered Mucosal MicroRNA Expression in Human Immunodeficiency Virus and Simian Immunodeficiency Virus Infections

Michael D. George, I. Korf, G. Jiang, 2014, Journal of Virology.

StochHMM: a flexible hidden Markov model tool and C++ library

Ian Korf, Paul C. Lott, I. Korf, 2014, Bioinform..

Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants

G. Parra, I. Korf, K. Bradnam, 2011, Nucleic acids research.

Intron sequences that stimulate gene expression in Arabidopsis

I. Korf, A. Rose, N. Kojima, 2016, Plant Molecular Biology.

Sequencing the transcriptome of milk production: milk trumps mammary tissue

Danielle G. Lemay, I. Korf, J. German, 2013, BMC Genomics.

Association of Diet and Antimicrobial Resistance in Healthy U.S. Adults

Danielle G. Lemay, I. Korf, B. Durbin-Johnson, 2022, mBio.

Myc and Miz-1 have coordinate genomic functions including targeting Hox genes in human embryonic stem cells

I. Korf, K. Bradnam, P. Knoepfler, 2011, Epigenetics & Chromatin.

Comparative genomic sequence analysis of the human and mouse cystic fibrosis transmembrane conductance regulator genes.

W Miller, R. Fulton, W. Miller, 2000, Proceedings of the National Academy of Sciences of the United States of America.

BLAST - an essential guide to the basic local alignment search tool

Ian Korf, Mark Yandell, Joseph A. Bedell, 2003 .

Association of Lactase Persistence Genotypes (rs4988235) and Ethnicity with Dairy Intake in a Healthy U.S. Population

Danielle G. Lemay, Elizabeth L Chin, Yasmine Y Bouzid, 2019, Nutrients.

Applying word-based algorithms: the IMEter.

I. Korf, A. Rose, 2009, Methods in molecular biology.

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

Daniël P. Melters, J. Derisi, J. Eid, 2013, Genome Biology.

A probabilistic model of 3' end formation in Caenorhabditis elegans.

Richard Durbin, R. Durbin, I. Korf, 2004, Nucleic acids research.

Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization

Danielle G. Lemay, Samuel T. Westreich, I. Korf, 2019, Microbiome.

SpecDB: A Relational Database for Archiving Biomolecular NMR Spectra Data

G. Montelione, I. Korf, T. Ramelot, 2022, bioRxiv.

SAMSA: a comprehensive metatranscriptome analysis pipeline

Danielle G. Lemay, Samuel T. Westreich, I. Korf, 2016, bioRxiv.

A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues

Alison L. Van Eenennaam, I. Korf, C. Ernst, 2020, BMC Genomics.

Autosomal Trisomy and Triploidy Are Corrected During Female Meiosis in Caenorhabditis elegans

I. Korf, F. McNally, K. McNally, 2017, Genetics.

UNIX and Perl to the Rescue!: A Field Guide for the Life Sciences (and Other Data-rich Pursuits)

Keith Bradnam, Ian F Korf, I. Korf, 2012 .

Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

Alison L. Van Eenennaam, Hans H. Cheng, I. Korf, 2018, BMC Genomics.

Laocoön: a tool for high-throughput automated cell counting

Ian F Korf, Kaitlin Y Lim, Mikaela Louie, 2019, bioRxiv.

The Mutant Mouse Resource and Research Center (MMRRC): the NIH-supported National Public Repository and Distribution Archive of Mutant Mouse Models in the USA

Samit J. Patel, I. Korf, L. Reinholdt, 2021, Mammalian genome : official journal of the International Mammalian Genome Society.

SAMSA: a comprehensive metatranscriptome analysis pipeline

Ian Korf, Danielle G. Lemay, Samuel T. Westreich, 2016, BMC Bioinformatics.

SAMSA2: a standalone metatranscriptome analysis pipeline

Michelle L. Treiber, Ian Korf, Danielle G. Lemay, 2017, BMC Bioinformatics.

Holocentric chromosomes: convergent evolution, meiotic adaptations, and genomic analysis

Daniël P. Melters, I. Korf, S. Chan, 2012, Chromosome Research.

Genomics: the state of the art in RNA-seq analysis

I. Korf, 2013, Nature Methods.

The effects of a stimulating intron on the expression of heterologous genes in Arabidopsis thaliana.

I. Korf, A. Rose, S. Emami, 2013, Plant biotechnology journal.

Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins

Cristel G. Thomas, I. Korf, E. Schwarz, 2018, Science.

Distributed under Creative Commons Cc-by 4.0 Strain-and Plasmid-level Deconvolution of a Synthetic Metagenome by Sequencing Proximity Ligation Products

I. Korf, J. Eisen, R. Michelmore, 2022 .

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

D. Neale, M. Yandell, I. Korf, 2010, BMC Genomics.