| Year |
Citation |
Score |
| 2021 |
Kern C, Wang Y, Xu X, Pan Z, Halstead M, Chanthavixay G, Saelao P, Waters S, Xiang R, Chamberlain A, Korf I, Delany ME, Cheng HH, Medrano JF, Van Eenennaam AL, et al. Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research. Nature Communications. 12: 1821. PMID 33758196 DOI: 10.1038/s41467-021-22100-8 |
0.321 |
|
| 2020 |
Laufer BI, Hwang H, Jianu JM, Mordaunt CE, Korf IF, Hertz-Picciotto I, LaSalle JM. Low-Pass Whole Genome Bisulfite Sequencing of Neonatal Dried Blood Spots Identifies a Role for RUNX1 in Down Syndrome DNA Methylation Profiles. Human Molecular Genetics. PMID 33001180 DOI: 10.1093/hmg/ddaa218 |
0.376 |
|
| 2020 |
Treiber ML, Taft DH, Korf I, Mills DA, Lemay DG. Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes. Bmc Bioinformatics. 21: 74. PMID 32093654 DOI: 10.1186/S12859-020-3416-Y |
0.419 |
|
| 2020 |
Westreich ST, Salcedo J, Durbin-Johnson B, Smilowitz JT, Korf I, Mills DA, Barile D, Lemay DG. Fecal metatranscriptomics and glycomics suggest that bovine milk oligosaccharides are fully utilized by healthy adults. The Journal of Nutritional Biochemistry. 79: 108340. PMID 32028108 DOI: 10.1016/J.Jnutbio.2020.108340 |
0.307 |
|
| 2018 |
Kern C, Wang Y, Chitwood J, Korf I, Delany M, Cheng H, Medrano JF, Van Eenennaam AL, Ernst C, Ross P, Zhou H. Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. Bmc Genomics. 19: 684. PMID 30227846 DOI: 10.1186/S12864-018-5037-7 |
0.386 |
|
| 2018 |
Gaulke CA, Porter M, Han YH, Sankaran-Walters S, Grishina I, George MD, Dang AT, Ding SW, Jiang G, Korf I, Dandekar S. Correction for Gaulke et al., "Intestinal Epithelial Barrier Disruption through Altered Mucosal MicroRNA Expression in Human Immunodeficiency Virus and Simian Immunodeficiency Virus Infections". Journal of Virology. 92. PMID 29844248 DOI: 10.1128/Jvi.00548-18 |
0.314 |
|
| 2018 |
Westreich ST, Treiber ML, Mills DA, Korf I, Lemay DG. SAMSA2: a standalone metatranscriptome analysis pipeline. Bmc Bioinformatics. 19: 175. PMID 29783945 DOI: 10.1186/S12859-018-2189-Z |
0.39 |
|
| 2018 |
Yin D, Schwarz EM, Thomas CG, Felde RL, Korf IF, Cutter AD, Schartner CM, Ralston EJ, Meyer BJ, Haag ES. Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins. Science (New York, N.Y.). 359: 55-61. PMID 29302007 DOI: 10.1126/Science.Aao0827 |
0.38 |
|
| 2017 |
Reyes-Chin-Wo S, Wang Z, Yang X, Kozik A, Arikit S, Song C, Xia L, Froenicke L, Lavelle DO, Truco MJ, Xia R, Zhu S, Xu C, Xu H, Xu X, ... ... Korf I, et al. Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nature Communications. 8: 14953. PMID 28401891 DOI: 10.1038/Ncomms14953 |
0.471 |
|
| 2016 |
Dunaway K, Goorha S, Matelski L, Urraca N, Lein PJ, Korf I, Reiter LT, LaSalle JM. Dental Pulp Stem Cells Model Early Life and Imprinted DNA Methylation Patterns. Stem Cells (Dayton, Ohio). PMID 28032673 DOI: 10.1002/Stem.2563 |
0.396 |
|
| 2016 |
Dunaway KW, Islam MS, Coulson RL, Lopez SJ, Vogel Ciernia A, Chu RG, Yasui DH, Pessah IN, Lott P, Mordaunt C, Meguro-Horike M, Horike SI, Korf I, LaSalle JM. Cumulative Impact of Polychlorinated Biphenyl and Large Chromosomal Duplications on DNA Methylation, Chromatin, and Expression of Autism Candidate Genes. Cell Reports. 17: 3035-3048. PMID 27974215 DOI: 10.1016/J.Celrep.2016.11.058 |
0.713 |
|
| 2016 |
Westreich ST, Korf I, Mills DA, Lemay DG. SAMSA: a comprehensive metatranscriptome analysis pipeline. Bmc Bioinformatics. 17: 399. PMID 27687690 DOI: 10.1186/S12859-016-1270-8 |
0.324 |
|
| 2016 |
Rose AB, Carter A, Korf I, Kojima N. Intron sequences that stimulate gene expression in Arabidopsis. Plant Molecular Biology. PMID 27492360 DOI: 10.1007/S11103-016-0516-1 |
0.388 |
|
| 2015 |
Hartono SR, Korf IF, Chédin F. GC skew is a conserved property of unmethylated CpG island promoters across vertebrates. Nucleic Acids Research. 43: 9729-41. PMID 26253743 DOI: 10.1093/Nar/Gkv811 |
0.434 |
|
| 2015 |
Tan EH, Henry IM, Ravi M, Bradnam KR, Mandakova T, Marimuthu MP, Korf I, Lysak MA, Comai L, Chan SW. Catastrophic chromosomal restructuring during genome elimination in plants. Elife. 4. PMID 25977984 DOI: 10.7554/Elife.06516 |
0.446 |
|
| 2015 |
Tan EH, Henry IM, Ravi M, Bradnam KR, Mandakova T, Marimuthu MP, Korf I, Lysak MA, Comai L, Chan SW. Author response: Catastrophic chromosomal restructuring during genome elimination in plants Elife. DOI: 10.7554/Elife.06516.029 |
0.36 |
|
| 2014 |
Lockwood SH, Guan A, Yu AS, Zhang C, Zykovich A, Korf I, Rannala B, Segal DJ. The functional significance of common polymorphisms in zinc finger transcription factors. G3 (Bethesda, Md.). 4: 1647-55. PMID 24970883 DOI: 10.1534/G3.114.012195 |
0.733 |
|
| 2014 |
Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE. Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. Peerj. 2: e415. PMID 24918035 DOI: 10.7717/Peerj.415 |
0.386 |
|
| 2014 |
Lott PC, Korf I. StochHMM: a flexible hidden Markov model tool and C++ library. Bioinformatics (Oxford, England). 30: 1625-6. PMID 24489371 DOI: 10.1093/Bioinformatics/Btu057 |
0.648 |
|
| 2014 |
Beck K, Turco G, Bradnam K, Rijnkels M, Nommsen-Rivers L, Korf I, Lemay D. Adjustment of RNA-Seq data for the effect of highly abundant transcripts: a case study in milk production (622.4) The Faseb Journal. 28. DOI: 10.1096/Fasebj.28.1_Supplement.622.4 |
0.364 |
|
| 2013 |
Korf IF. Genomics: the state of the art in RNA-seq analysis Nature Methods. 10: 1165-1166. PMID 24296473 DOI: 10.1038/Nmeth.2735 |
0.308 |
|
| 2013 |
Lemay DG, Pollard KS, Martin WF, Freeman Zadrowski C, Hernandez J, Korf I, German JB, Rijnkels M. From Genes to Milk: Genomic Organization and Epigenetic Regulation of the Mammary Transcriptome Plos One. 8. PMID 24086428 DOI: 10.1371/Journal.Pone.0075030 |
0.425 |
|
| 2013 |
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, ... ... Korf IF, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2: 10. PMID 23870653 DOI: 10.1186/2047-217X-2-10 |
0.43 |
|
| 2013 |
Ginno PA, Lim YW, Lott PL, Korf I, Chédin F. GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination. Genome Research. 23: 1590-600. PMID 23868195 DOI: 10.1101/Gr.158436.113 |
0.465 |
|
| 2013 |
Schroeder DI, Blair JD, Lott P, Yu HO, Hong D, Crary F, Ashwood P, Walker C, Korf I, Robinson WP, LaSalle JM. The human placenta methylome. Proceedings of the National Academy of Sciences of the United States of America. 110: 6037-42. PMID 23530188 DOI: 10.1073/Pnas.1215145110 |
0.727 |
|
| 2013 |
Melters DP, Bradnam KR, Young HA, Telis N, May MR, Ruby JG, Sebra R, Peluso P, Eid J, Rank D, Garcia JF, DeRisi JL, Smith T, Tobias C, Ross-Ibarra J, ... Korf I, et al. Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biology. 14: R10. PMID 23363705 DOI: 10.1186/Gb-2013-14-1-R10 |
0.75 |
|
| 2013 |
Emami S, Arumainayagam D, Korf I, Rose AB. The effects of a stimulating intron on the expression of heterologous genes in Arabidopsis thaliana. Plant Biotechnology Journal. 11: 555-63. PMID 23347383 DOI: 10.1111/Pbi.12043 |
0.334 |
|
| 2013 |
Davison AJ, Kurobe T, Gatherer D, Cunningham C, Korf I, Fukuda H, Hedrick RP, Waltzek TB. Comparative genomics of carp herpesviruses. Journal of Virology. 87: 2908-22. PMID 23269803 DOI: 10.1128/Jvi.03206-12 |
0.48 |
|
| 2012 |
Lemay DG, Martin WF, Hinrichs AS, Rijnkels M, German JB, Korf I, Pollard KS. G-NEST: A gene neighborhood scoring tool to identify co-conserved, co-expressed genes Bmc Bioinformatics. 13. PMID 23020263 DOI: 10.1186/1471-2105-13-253 |
0.4 |
|
| 2012 |
Meier JL, Yu AS, Korf I, Segal DJ, Dervan PB. Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing. Journal of the American Chemical Society. 134: 17814-22. PMID 23013524 DOI: 10.1021/Ja308888C |
0.409 |
|
| 2012 |
Melters DP, Paliulis LV, Korf IF, Chan SW. Holocentric chromosomes: convergent evolution, meiotic adaptations, and genomic analysis. Chromosome Research : An International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology. 20: 579-93. PMID 22766638 DOI: 10.1007/S10577-012-9292-1 |
0.704 |
|
| 2012 |
Ginno PA, Lott PL, Christensen HC, Korf I, Chédin F. R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Molecular Cell. 45: 814-25. PMID 22387027 DOI: 10.1016/J.Molcel.2012.01.017 |
0.393 |
|
| 2012 |
Wingfield BD, Steenkamp ET, Santana QC, Coetzee MP, Bam S, Barnes I, Beukes CW, Chan WY, De Vos L, Fourie G, Friend M, Gordon TR, Herron DA, Holt C, Korf I, et al. First fungal genome sequence from Africa: A preliminary analysis South African Journal of Science. 108. DOI: 10.4102/Sajs.V108I1/2.537 |
0.47 |
|
| 2011 |
Rose AB, Emami S, Bradnam K, Korf I. Evidence for a DNA-Based Mechanism of Intron-Mediated Enhancement. Frontiers in Plant Science. 2: 98. PMID 22645558 DOI: 10.3389/Fpls.2011.00098 |
0.401 |
|
| 2011 |
Varlakhanova N, Cotterman R, Bradnam K, Korf I, Knoepfler PS. Myc and Miz-1 have coordinate genomic functions including targeting Hox genes in human embryonic stem cells. Epigenetics & Chromatin. 4: 20. PMID 22053792 DOI: 10.1186/1756-8935-4-20 |
0.365 |
|
| 2011 |
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, ... ... Korf I, et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Research. 21: 2224-41. PMID 21926179 DOI: 10.1101/Gr.126599.111 |
0.381 |
|
| 2011 |
Huefner ND, Mizuno Y, Weil CF, Korf I, Britt AB. Breadth by depth: Expanding our understanding of the repair of transposon-induced DNA double strand breaks via deep-sequencing Dna Repair. 10: 1023-1033. PMID 21889425 DOI: 10.1016/J.Dnarep.2011.07.011 |
0.335 |
|
| 2011 |
Schroeder DI, Lott P, Korf I, LaSalle JM. Large-scale methylation domains mark a functional subset of neuronally expressed genes. Genome Research. 21: 1583-91. PMID 21784875 DOI: 10.1101/Gr.119131.110 |
0.728 |
|
| 2011 |
Parra G, Bradnam K, Rose AB, Korf I. Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants. Nucleic Acids Research. 39: 5328-37. PMID 21427088 DOI: 10.1093/Nar/Gkr043 |
0.407 |
|
| 2011 |
Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF, Korf I, Farnham PJ. Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes. Plos One. 6: e17121. PMID 21347206 DOI: 10.1371/Journal.Pone.0017121 |
0.439 |
|
| 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. 11: 420. PMID 20609256 DOI: 10.1186/1471-2164-11-420 |
0.467 |
|
| 2010 |
Blahnik KR, Dou L, O'Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Ludäscher B, Korf I, Farnham PJ. Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Research. 38: e13. PMID 19906703 DOI: 10.1093/Nar/Gkp1012 |
0.463 |
|
| 2009 |
Zykovich A, Korf I, Segal DJ. Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing. Nucleic Acids Research. 37: e151. PMID 19843614 DOI: 10.1093/Nar/Gkp802 |
0.732 |
|
| 2009 |
Korf IF, Rose AB. Applying word-based algorithms: the IMEter. Methods in Molecular Biology (Clifton, N.J.). 553: 287-301. PMID 19588111 DOI: 10.1007/978-1-60327-563-7_14 |
0.349 |
|
| 2009 |
Parra G, Bradnam K, Ning Z, Keane T, Korf I. Assessing the gene space in draft genomes. Nucleic Acids Research. 37: 289-97. PMID 19042974 DOI: 10.1093/Nar/Gkn916 |
0.466 |
|
| 2008 |
Bradnam KR, Korf I. Longer First Introns Are a General Property of Eukaryotic Gene Structure Plos One. 3. PMID 18769727 DOI: 10.1371/Journal.Pone.0003093 |
0.389 |
|
| 2008 |
Rose AB, Elfersi T, Parra G, Korf I. Promoter-proximal introns in Arabidopsis thaliana are enriched in dispersed signals that elevate gene expression. The Plant Cell. 20: 543-51. PMID 18319396 DOI: 10.1105/Tpc.107.057190 |
0.403 |
|
| 2008 |
Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sánchez Alvarado A, Yandell M. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Research. 18: 188-96. PMID 18025269 DOI: 10.1101/Gr.6743907 |
0.452 |
|
| 2007 |
Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, Delcher AL, Guiliano DB, Miranda-Saavedra D, Angiuoli SV, Creasy T, Amedeo P, Haas B, El-Sayed NM, ... ... Korf I, et al. Draft genome of the filarial nematode parasite Brugia malayi. Science (New York, N.Y.). 317: 1756-60. PMID 17885136 DOI: 10.1126/Science.1145406 |
0.438 |
|
| 2007 |
Parra G, Bradnam K, Korf I. CEGMA: A pipeline to accurately annotate core genes in eukaryotic genomes Bioinformatics. 23: 1061-1067. PMID 17332020 DOI: 10.1093/Bioinformatics/Btm071 |
0.449 |
|
| 2005 |
Bedell JA, Budiman MA, Nunberg A, Citek RW, Robbins D, Jones J, Flick E, Rohlfing T, Fries J, Bradford K, McMenamy J, Smith M, Holeman H, Roe BA, Wiley G, ... Korf IF, et al. Sorghum genome sequencing by methylation filtration Plos Biology. 3. PMID 15660154 DOI: 10.1371/Journal.Pbio.0030013 |
0.5 |
|
| 2004 |
Hajarnavis A, Korf IF, Durbin R. A probabilistic model of 3' end formation in Caenorhabditis elegans Nucleic Acids Research. 32: 3392-3399. PMID 15247332 DOI: 10.1093/Nar/Gkh656 |
0.417 |
|
| 2004 |
Korf IF. Gene finding in novel genomes Bmc Bioinformatics. 5: 59-59. PMID 15144565 DOI: 10.1186/1471-2105-5-59 |
0.425 |
|
| 2003 |
Korf IF. Serial BLAST searching. Bioinformatics. 19: 1492-1496. PMID 12912829 DOI: 10.1093/Bioinformatics/Btg199 |
0.343 |
|
| 2003 |
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 Research. 13: 46-54. PMID 12529305 DOI: 10.1101/Gr.830003 |
0.468 |
|
| 2002 |
Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, ... ... Korf I, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/Nature01262 |
0.483 |
|
| 2001 |
Wendl MC, Korf I, Chinwalla AT, Hillier LW. Automated processing of raw DNA sequence data Ieee Engineering in Medicine and Biology Magazine. 20: 41-48. PMID 11494768 DOI: 10.1109/51.940044 |
0.41 |
|
| 2001 |
Korf I, Flicek P, Duan D, Brent MR. Integrating genomic homology into gene structure prediction. Bioinformatics (Oxford, England). 17: S140-8. PMID 11473003 DOI: 10.1093/Bioinformatics/17.Suppl_1.S140 |
0.491 |
|
| 2001 |
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, ... ... Korf I, et al. Initial sequencing and analysis of the human genome. Nature. 409: 860-921. PMID 11237011 DOI: 10.1038/35057062 |
0.444 |
|
| 2001 |
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, Fitzhugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, ... ... Korf I, et al. Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921)) Nature. 412: 565-566. DOI: 10.1038/35087627 |
0.443 |
|
| 2000 |
Korf I, Gish W. MPBLAST: Improved BLAST performance with multiplexed queries Bioinformatics. 16: 1052-1053. PMID 11159321 DOI: 10.1093/Bioinformatics/16.11.1052 |
0.337 |
|
| 2000 |
Bedell JA, Korf I, Gish W. MaskerAid: A performance enhancement to RepeatMasker Bioinformatics. 16: 1040-1041. PMID 11159316 DOI: 10.1093/Bioinformatics/16.11.1040 |
0.379 |
|
| 2000 |
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 Research. 10: 1351-8. PMID 10984453 DOI: 10.1101/Gr.144700 |
0.443 |
|
| 2000 |
Ellsworth RE, Jamison DC, Touchman JW, Chissoe SL, Braden Maduro VV, Bouffard GG, Dietrich NL, Beckstrom-Sternberg SM, Lyer LM, Weintraub LA, Cotton M, Courtney L, Edwards J, Maupin R, Ozersky P, ... ... Korf I, et al. Comparative genomic sequence analysis of the human and mouse cystic fibrosis transmembrane conductance regulator genes Proceedings of the National Academy of Sciences of the United States of America. 97: 1172-1177. PMID 10655503 DOI: 10.1073/Pnas.97.3.1172 |
0.477 |
|
| 1999 |
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. Nature Genetics. 23: 452-6. PMID 10581034 DOI: 10.1038/70570 |
0.456 |
|
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