IK
Ian F. Korf
SoftwarebioinformaticsGenomeAlgorithmsGenome, HumanMicrobiomeDNA MethylationEpigenesis, GeneticEvolution, MolecularGenes
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
86 papers in the corpus · 1998–2026Improve genetic quality control to increase rigor and reproducibility of mouse research.42133765 · Pardo-Manuel de Villena, Fernando, Amos-Landgraf, James M, Bell, Timothy A et al.2026 · 3 citationsScience (New York, N.Y.). 2026;392(6799):698-700
Sex and tissue resolved co-expression networks reveal a female placental-brain axis protective against prenatal PCB exposure.41943130 · Chau, Kelly H, Neier, Kari, Valenzuela, Anthony E et al.2026 · 2 citationsGenome biology. 2026;27(1)
Association of lactose intake and lactase persistence genotype with microbial taxa and function in healthy multi-ethnic U.S. adults.40880079 · Tang, Yirui, Oliver, Andrew, Alkan, Zeynep et al.2025 · 1 citationFood & function. 2025;16(18):7393-7407
Metabolic Adaptations Determine the Evolutionary Trajectory of TOR Signaling in Diverse Eukaryotes.41008602 · Johnson, Kyle, Pourkeramati, Dellaraam, Korf, Ian et al.2025 · 0 citationsBiomolecules. 2025;15(9)
Female cortical cellular mosaicism underlies shared MeCP2 and PCB impacted gene pathways.40501678 · Sharifi, Osman, Neier, Kari E, Valenzuela, Anthony et al.2026 · 2 citationsbioRxiv : the preprint server for biology. 2025
Introns increase gene expression in Caenorhabditis elegans by a mechanism that must be at least partly different than in plants.40328889 · Rose, Alan B, Baer, Aaron, Shaker, Isaac et al.2025 · 2 citationsScientific reports. 2025;15(1):15862
The mutant mouse resource and research center (MMRRC) consortium: the US-based public mouse repository system.39304538 · Agca, Yuksel, Amos-Landgraf, James, Araiza, Renee et al.2024 · 5 citationsMammalian genome : official journal of the International Mammalian Genome Society. 2024;35(4):524-536
Placental-brain axis in females detected within broadly impacted metabolic gene networks protects against prenatal PCB exposure.39071357 · Chau, Kelly, Neier, Kari, Valenzuela, Anthony E et al.2024 · 0 citationsbioRxiv : the preprint server for biology. 2024
Improving rigor and reproducibility in chromatin immunoprecipitation assay data analysis workflows with Rocketchip.39071274 · Haghani, Viktoria, Goyal, Aditi, Zhang, Alan et al.2025 · 0 citationsbioRxiv : the preprint server for biology. 2024
Sex-specific single cell-level transcriptomic signatures of Rett syndrome disease progression.38798575 · Sharifi, Osman, Haghani, Viktoria, Neier, Kari E et al.2026 · 16 citationsbioRxiv : the preprint server for biology. 2024
Do organisms need an impact factor? Citations of key biological resources including model organisms reveal usage patterns and impact.38293091 · Piekniewska, Agata, Anderson, Nathan, Roelandse, Martijn et al.2025 · 2 citationsbioRxiv : the preprint server for biology. 2024
SpecDB: A relational database for archiving biomolecular NMR spectral data.35930941 · Fraga, Keith J, Huang, Yuanpeng J, Ramelot, Theresa A et al.2022 · 6 citationsJournal of magnetic resonance (San Diego, Calif. : 1997). 2022;342:107268
Association of Diet and Antimicrobial Resistance in Healthy U.S. Adults.35536006 · Oliver, Andrew, Xue, Zhengyao, Villanueva, Yirui T et al.2022 · 104 citationsmBio. 2022;13(3):e0010122
The Mutant Mouse Resource and Research Center (MMRRC): the NIH-supported National Public Repository and Distribution Archive of Mutant Mouse Models in the USA.34313795 · Amos-Landgraf, James, Franklin, Craig, Godfrey, Virginia et al.2022 · 20 citationsMammalian genome : official journal of the International Mammalian Genome Society. 2022;33(1):203-212
Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research.33758196 · Kern, Colin, Wang, Ying, Xu, Xiaoqin et al.2021 · 255 citationsNature communications. 2021;12(1):1821
Low-pass whole genome bisulfite sequencing of neonatal dried blood spots identifies a role for RUNX1 in Down syndrome DNA methylation profiles.33001180 · Laufer, Benjamin I, Hwang, Hyeyeon, Jianu, Julia M et al.2021 · 52 citationsHuman molecular genetics. 2021;29(21):3465-3476
Association of the Lactase Persistence Haplotype Block With Disease Risk in Populations of European Descent.33193640 · Joslin, Shannon E K, Durbin-Johnson, Blythe P, Britton, Monica et al.2020 · 4 citationsFrontiers in genetics. 2020;11:558762
A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues.33028202 · Halstead, Michelle M, Kern, Colin, Saelao, Perot et al.2021 · 84 citationsBMC genomics. 2020;21(1):698
Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes.32093654 · Treiber, Michelle L, Taft, Diana H, Korf, Ian et al.2020 · 28 citationsBMC bioinformatics. 2020;21(1):74
Fecal metatranscriptomics and glycomics suggest that bovine milk oligosaccharides are fully utilized by healthy adults.32028108 · Westreich, Samuel T, Salcedo, Jaime, Durbin-Johnson, Blythe et al.2021 · 14 citationsThe Journal of nutritional biochemistry. 2020;79:108340
Laocoön: a tool for high-throughput automated cell counting10.1101/751073v3 · Lim, K. Y., Louie, M., La Torre, A. et al.2019 · 0 citationsbioRxiv
Association of Lactase Persistence Genotypes (rs4988235) and Ethnicity with Dairy Intake in a Healthy U.S. Population.31405126 · Chin, Elizabeth L, Huang, Liping, Bouzid, Yasmine Y et al.2020 · 32 citationsNutrients. 2019;11(8)
Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization.30885266 · Westreich, Samuel T, Ardeshir, Amir, Alkan, Zeynep et al.2019 · 44 citationsMicrobiome. 2019;7(1):41
Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species.30227846 · Kern, Colin, Wang, Ying, Chitwood, James et al.2018 · 111 citationsBMC genomics. 2018;19(1):684
The collaborative effect of scientific meetings: A study of the International Milk Genomics Consortium.30133459 · Kwok, Eric, Porter, Matthew, Korf, Ian et al.2019 · 12 citationsPloS one. 2018;13(8):e0201637
Correction for Gaulke et al., "Intestinal Epithelial Barrier Disruption through Altered Mucosal MicroRNA Expression in Human Immunodeficiency Virus and Simian Immunodeficiency Virus Infections".29844248 · Gaulke, Christopher A, Porter, Matthew, Han, Yan-Hong et al.2019 · 0 citationsJournal of virology. 2018;92(12)
SAMSA2: a standalone metatranscriptome analysis pipeline.29783945 · Westreich, Samuel T, Treiber, Michelle L, Mills, David A et al.2019 · 161 citationsBMC bioinformatics. 2018;19(1):175
Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins.29302007 · Yin, Da, Schwarz, Erich M, Thomas, Cristel G et al.2018 · 116 citationsScience (New York, N.Y.). 2018;359(6371):55-61
Autosomal Trisomy and Triploidy Are Corrected During Female Meiosis in Caenorhabditis elegans.28882988 · Vargas, Elizabeth, McNally, Karen, Friedman, Jacob A et al.2018 · 12 citationsGenetics. 2017;207(3):911-922
Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce.28401891 · Reyes-Chin-Wo, Sebastian, Wang, Zhiwen, Yang, Xinhua et al.2018 · 446 citationsNature communications. 2017;8:14953
Dental Pulp Stem Cells Model Early Life and Imprinted DNA Methylation Patterns.28032673 · Dunaway, Keith, Goorha, Sarita, Matelski, Lauren et al.2017 · 33 citationsStem cells (Dayton, Ohio). 2017;35(4):981-988
Cumulative Impact of Polychlorinated Biphenyl and Large Chromosomal Duplications on DNA Methylation, Chromatin, and Expression of Autism Candidate Genes.27974215 · Dunaway, Keith W, Islam, M Saharul, Coulson, Rochelle L et al.2017 · 73 citationsCell reports. 2016;17(11):3035-3048
SAMSA: a comprehensive metatranscriptome analysis pipeline.27687690 · Westreich, Samuel T, Korf, Ian, Mills, David A et al.2019 · 56 citationsBMC bioinformatics. 2016;17(1):399
Intron sequences that stimulate gene expression in Arabidopsis.27492360 · Rose, Alan B, Carter, Amanda, Korf, Ian et al.2017 · 61 citationsPlant molecular biology. 2016;92(3):337-46
GC skew is a conserved property of unmethylated CpG island promoters across vertebrates.26253743 · Hartono, Stella R, Korf, Ian F, Chédin, Frédéric2016 · 61 citationsNucleic acids research. 2015;43(20):9729-41
Catastrophic chromosomal restructuring during genome elimination in plants.25977984 · Tan, Ek Han, Henry, Isabelle M, Ravi, Maruthachalam et al.2016 · 121 citationseLife. 2015;4
Comparative Proteomics of Human and Macaque Milk Reveals Species-Specific Nutrition during Postnatal Development.25757574 · Beck, Kristen L, Weber, Darren, Phinney, Brett S et al.2016 · 78 citationsJournal of proteome research. 2015;14(5):2143-57
The functional significance of common polymorphisms in zinc finger transcription factors.24970883 · Lockwood, Sarah H, Guan, Anna, Yu, Abigail S et al.2015 · 13 citationsG3 (Bethesda, Md.). 2014;4(9):1647-55
Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products.24918035 · Beitel, Christopher W, Froenicke, Lutz, Lang, Jenna M et al.2014 · 134 citationsPeerJ. 2014;2:e415
Intestinal epithelial barrier disruption through altered mucosal microRNA expression in human immunodeficiency virus and simian immunodeficiency virus infections.24672033 · Gaulke, Christopher A, Porter, Matthew, Han, Yan-Hong et al.2014 · 31 citationsJournal of virology. 2014;88(11):6268-80
StochHMM: a flexible hidden Markov model tool and C++ library.24489371 · Lott, Paul C, Korf, Ian2014 · 18 citationsBioinformatics (Oxford, England). 2014;30(11):1625-6
Sequencing the transcriptome of milk production: milk trumps mammary tissue.24330573 · Lemay, Danielle G, Hovey, Russell C, Hartono, Stella R et al.2014 · 59 citationsBMC genomics. 2013;14:872
Genomics: the state of the art in RNA-seq analysis.24296473 · Korf, Ian2014 · 28 citationsNature methods. 2013;10(12):1165-6
From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome.24086428 · Lemay, Danielle G, Pollard, Katherine S, Martin, William F et al.2014 · 21 citationsPloS one. 2013;8(9):e75030
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.23870653 · Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton et al.2014 · 671 citationsGigaScience. 2013;2(1):10
GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination.23868195 · Ginno, Paul A, Lim, Yoong Wearn, Lott, Paul L et al.2014 · 352 citationsGenome research. 2013;23(10):1590-600
The human placenta methylome.23530188 · Schroeder, Diane I, Blair, John D, Lott, Paul et al.2013 · 310 citationsProceedings of the National Academy of Sciences of the United States of America. 2013;110(15):6037-42
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution.23363705 · Melters, Daniël P, Bradnam, Keith R, Young, Hugh A et al.2015 · 526 citationsGenome biology. 2013;14(1):R10
The effects of a stimulating intron on the expression of heterologous genes in Arabidopsis thaliana.23347383 · Emami, Shahram, Arumainayagam, Dinah, Korf, Ian et al.2014 · 51 citationsPlant biotechnology journal. 2013;11(5):555-63
Comparative genomics of carp herpesviruses.23269803 · Davison, Andrew J, Kurobe, Tomofumi, Gatherer, Derek et al.2013 · 153 citationsJournal of virology. 2013;87(5):2908-22
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