Year |
Citation |
Score |
2024 |
Nazarizadeh M, Nováková M, Drábková M, Catchen J, Olson PD, Štefka J. Highly resolved genome assembly and comparative transcriptome profiling reveal genes related to developmental stages of tapeworm . Proceedings. Biological Sciences. 291: 20232563. PMID 38290545 DOI: 10.1098/rspb.2023.2563 |
0.466 |
|
2023 |
Cheng CC, Rivera-Colón AG, Minhas BF, Wilson L, Rayamajhi N, Vargas-Chacoff L, Catchen JM. Chromosome-Level Genome Assembly and Circadian Gene Repertoire of the Patagonia Blennie -The Closest Ancestral Proxy of Antarctic Cryonotothenioids. Genes. 14. PMID 37372376 DOI: 10.3390/genes14061196 |
0.509 |
|
2023 |
Minhas BF, Beck EA, Cheng CC, Catchen J. Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes. Scientific Reports. 13: 6939. PMID 37117267 DOI: 10.1038/s41598-023-34237-1 |
0.378 |
|
2023 |
Rivera-Colón AG, Rayamajhi N, Minhas BF, Madrigal G, Bilyk KT, Yoon V, Hüne M, Gregory S, Cheng CHC, Catchen JM. Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish. Molecular Biology and Evolution. 40. PMID 36806940 DOI: 10.1093/molbev/msad029 |
0.369 |
|
2022 |
de Flamingh A, Rivera-Colón AG, Gnoske TP, Kerbis Peterhans JC, Catchen J, Malhi RS, Roca AL. Numt Parser: automated identification and removal of nuclear mitochondrial pseudogenes (numts) for accurate mitochondrial genome reconstruction in Panthera. The Journal of Heredity. PMID 36525576 DOI: 10.1093/jhered/esac065 |
0.339 |
|
2022 |
Cerca J, Petersen B, Lazaro-Guevara JM, Rivera-Colón A, Birkeland S, Vizueta J, Li S, Li Q, Loureiro J, Kosawang C, Díaz PJ, Rivas-Torres G, Fernández-Mazuecos M, Vargas P, McCauley RA, ... ... Catchen JM, et al. The genomic basis of the plant island syndrome in Darwin's giant daisies. Nature Communications. 13: 3729. PMID 35764640 DOI: 10.1038/s41467-022-31280-w |
0.405 |
|
2022 |
Small CM, Healey HM, Currey MC, Beck EA, Catchen J, Lin ASP, Cresko WA, Bassham S. Leafy and weedy seadragon genomes connect genic and repetitive DNA features to the extravagant biology of syngnathid fishes. Proceedings of the National Academy of Sciences of the United States of America. 119: e2119602119. PMID 35733255 DOI: 10.1073/pnas.2119602119 |
0.504 |
|
2022 |
Rivera-Colón AG, Catchen J. Population Genomics Analysis with RAD, Reprised: Stacks 2. Methods in Molecular Biology (Clifton, N.J.). 2498: 99-149. PMID 35727543 DOI: 10.1007/978-1-0716-2313-8_7 |
0.328 |
|
2021 |
Cerca J, Rivera-Colón AG, Ferreira MS, Ravinet M, Nowak MD, Catchen JM, Struck TH. Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species. Peerj. 9: e10896. PMID 33614296 DOI: 10.7717/peerj.10896 |
0.321 |
|
2020 |
Catchen J, Amores A, Bassham S. Chromonomer: A Tool Set for Repairing and Enhancing Assembled Genomes Through Integration of Genetic Maps and Conserved Synteny. G3: Genes, Genomes, Genetics. PMID 32912931 DOI: 10.1534/G3.120.401485 |
0.529 |
|
2020 |
Rivera-Colón AG, Rochette NC, Catchen JM. Simulation with RADinitio improves RADseq experimental design and sheds light on sources of missing data. Molecular Ecology Resources. PMID 32275349 DOI: 10.1111/1755-0998.13163 |
0.436 |
|
2020 |
Campbell-Staton SC, Winchell KM, Rochette NC, Fredette J, Maayan I, Schweizer RM, Catchen J. Parallel selection on thermal physiology facilitates repeated adaptation of city lizards to urban heat islands. Nature Ecology & Evolution. PMID 32152530 DOI: 10.1038/S41559-020-1131-8 |
0.334 |
|
2019 |
Moran RL, Catchen JM, Fuller RC. Genomic resources for darters (Percidae: Etheostominae) provide insight into postzygotic barriers implicated in speciation. Molecular Biology and Evolution. PMID 31688927 DOI: 10.1093/Molbev/Msz260 |
0.568 |
|
2019 |
Rochette NC, Rivera-Colón AG, Catchen JM. Stacks 2: analytical methods for paired-end sequencing improve RADseq-based population genomics. Molecular Ecology. PMID 31550391 DOI: 10.1111/Mec.15253 |
0.444 |
|
2019 |
Nelson TC, Crandall JG, Ituarte CM, Catchen JM, Cresko WA. Selection, Linkage, and Population Structure Interact To Shape Genetic Variation Among Threespine Stickleback Genomes. Genetics. PMID 31213503 DOI: 10.1534/Genetics.119.302261 |
0.501 |
|
2019 |
Kim BM, Amores A, Kang S, Ahn DH, Kim JH, Kim IC, Lee JH, Lee SG, Lee H, Lee J, Kim HW, Desvignes T, Batzel P, Sydes J, Titus T, ... ... Catchen JM, et al. Antarctic blackfin icefish genome reveals adaptations to extreme environments. Nature Ecology & Evolution. 3: 469-478. PMID 30804520 DOI: 10.1038/S41559-019-0812-7 |
0.532 |
|
2018 |
Bassham S, Catchen J, Lescak E, von Hippel FA, Cresko WA. Repeated Selection of Alternatively Adapted Haplotypes Creates Sweeping Genomic Remodeling in Stickleback. Genetics. PMID 29794240 DOI: 10.1534/Genetics.117.300610 |
0.547 |
|
2018 |
Gomes Viana JP, Bohrer Monteiro Siqueira MV, Araujo FL, Grando C, Sanae Sujii P, Silvestre EA, Novello M, Pinheiro JB, Cavallari MM, Brancalion PHS, Rodrigues RR, Pereira de Souza A, Catchen J, Zucchi MI. Genomic diversity is similar between Atlantic Forest restorations and natural remnants for the native tree Casearia sylvestris Sw. Plos One. 13: e0192165. PMID 29513673 DOI: 10.1371/Journal.Pone.0192165 |
0.363 |
|
2018 |
Catchen J. When structure leads to sex: Untangling signals in population genetic data sets. Molecular Ecology. 26: 6763-6766. PMID 29282805 DOI: 10.1111/Mec.14422 |
0.446 |
|
2017 |
Rochette NC, Catchen JM. Deriving genotypes from RAD-seq short-read data using Stacks. Nature Protocols. 12: 2640-2659. PMID 29189774 DOI: 10.1038/Nprot.2017.123 |
0.443 |
|
2017 |
Warren WC, Kuderna L, Alexander A, Catchen J, Pérez-Silva JG, López-Otín C, Quesada V, Minx P, Tomlinson C, Montague MJ, Farias FHG, Walter RB, Marques-Bonet T, Glenn T, Kieran TJ, et al. The novel evolution of the sperm whale genome. Genome Biology and Evolution. PMID 28985367 DOI: 10.1093/Gbe/Evx187 |
0.512 |
|
2017 |
Campbell-Staton SC, Cheviron ZA, Rochette N, Catchen J, Losos JB, Edwards SV. Winter storms drive rapid phenotypic, regulatory, and genomic shifts in the green anole lizard. Science (New York, N.Y.). 357: 495-498. PMID 28774927 DOI: 10.1126/Science.Aam5512 |
0.468 |
|
2017 |
Catchen JM, Hohenlohe PA, Bernatchez L, Funk WC, Andrews KR, Allendorf FW. Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations. Molecular Ecology Resources. PMID 28319339 DOI: 10.1111/1755-0998.12669 |
0.453 |
|
2017 |
Paris JR, Stevens JR, Catchen JM. Lost in parameter space: a road map for
stacks Methods in Ecology and Evolution. 8: 1360-1373. DOI: 10.1111/2041-210X.12775 |
0.379 |
|
2017 |
Lescak EA, Wund MA, Bassham S, Catchen J, Prince DJ, Lucas R, Dominguez G, von Hippel FA, Cresko WA. Ancient three-spined stickleback (Gasterosteus aculeatus) mtDNA lineages are not associated with phenotypic or nuclear genetic variation Biological Journal of the Linnean Society. 122: 579-588. DOI: 10.1093/Biolinnean/Blx080 |
0.309 |
|
2016 |
Small CM, Bassham S, Catchen J, Amores A, Fuiten AM, Brown RS, Jones AG, Cresko WA. The genome of the Gulf pipefish enables understanding of evolutionary innovations. Genome Biology. 17: 258. PMID 27993155 DOI: 10.1186/S13059-016-1126-6 |
0.553 |
|
2016 |
Hoffberg SL, Kieran TJ, Catchen JM, Devault A, Faircloth BC, Mauricio R, Glenn TC. RADcap: Sequence Capture of Dual-digest RADseq Libraries with Identifiable Duplicates and Reduced Missing Data. Molecular Ecology Resources. PMID 27416967 DOI: 10.1111/1755-0998.12566 |
0.36 |
|
2016 |
Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, et al. Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics. 48: 700. PMID 27230688 DOI: 10.1038/Ng0616-700C |
0.513 |
|
2016 |
Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, et al. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics. 48: 427-37. PMID 26950095 DOI: 10.1038/Ng.3526 |
0.57 |
|
2015 |
Lescak EA, Bassham SL, Catchen J, Gelmond O, Sherbick ML, von Hippel FA, Cresko WA. Evolution of stickleback in 50 years on earthquake-uplifted islands. Proceedings of the National Academy of Sciences of the United States of America. PMID 26668399 DOI: 10.1073/Pnas.1512020112 |
0.421 |
|
2014 |
Amores A, Catchen J, Nanda I, Warren W, Walter R, Schartl M, Postlethwait JH. A RAD-tag genetic map for the platyfish (Xiphophorus maculatus) reveals mechanisms of karyotype evolution among teleost fish. Genetics. 197: 625-41. PMID 24700104 DOI: 10.1534/Genetics.114.164293 |
0.516 |
|
2013 |
Rodríguez-Marí A, Cañestro C, BreMiller RA, Catchen JM, Yan YL, Postlethwait JH. Retinoic acid metabolic genes, meiosis, and gonadal sex differentiation in zebrafish. Plos One. 8: e73951. PMID 24040125 DOI: 10.1371/Journal.Pone.0073951 |
0.304 |
|
2013 |
Merz C, Catchen JM, Hanson-Smith V, Emerson KJ, Bradshaw WE, Holzapfel CM. Replicate phylogenies and post-glacial range expansion of the pitcher-plant mosquito, Wyeomyia smithii, in North America. Plos One. 8: e72262. PMID 24039746 DOI: 10.1371/Journal.Pone.0072262 |
0.337 |
|
2013 |
Zhang G, Hoersch S, Amsterdam A, Whittaker CA, Beert E, Catchen JM, Farrington S, Postlethwait JH, Legius E, Hopkins N, Lees JA. Comparative oncogenomic analysis of copy number alterations in human and zebrafish tumors enables cancer driver discovery. Plos Genetics. 9: e1003734. PMID 24009526 DOI: 10.1371/Journal.Pgen.1003734 |
0.354 |
|
2013 |
Catchen J, Bassham S, Wilson T, Currey M, O'Brien C, Yeates Q, Cresko WA. The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing. Molecular Ecology. 22: 2864-83. PMID 23718143 DOI: 10.1111/Mec.12330 |
0.468 |
|
2013 |
Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA. Stacks: an analysis tool set for population genomics. Molecular Ecology. 22: 3124-40. PMID 23701397 DOI: 10.1111/Mec.12354 |
0.509 |
|
2013 |
Schartl M, Walter RB, Shen Y, Garcia T, Catchen J, Amores A, Braasch I, Chalopin D, Volff JN, Lesch KP, Bisazza A, Minx P, Hillier L, Wilson RK, Fuerstenberg S, et al. The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. Nature Genetics. 45: 567-72. PMID 23542700 DOI: 10.1038/Ng.2604 |
0.548 |
|
2012 |
Bradshaw WE, Emerson KJ, Catchen JM, Cresko WA, Holzapfel CM. Footprints in time: Comparative quantitative trait loci mapping of the pitcher-plant mosquito, Wyeomyia smithii Proceedings of the Royal Society B: Biological Sciences. 279: 4551-4558. PMID 23015622 DOI: 10.1098/Rspb.2012.1917 |
0.433 |
|
2012 |
Hohenlohe PA, Catchen J, Cresko WA. Population genomic analysis of model and nonmodel organisms using sequenced RAD tags. Methods in Molecular Biology (Clifton, N.J.). 888: 235-60. PMID 22665285 DOI: 10.1007/978-1-61779-870-2_14 |
0.575 |
|
2012 |
Garcia TI, Shen Y, Catchen J, Amores A, Schartl M, Postlethwait J, Walter RB. Effects of short read quality and quantity on a de novo vertebrate transcriptome assembly. Comparative Biochemistry and Physiology. Toxicology & Pharmacology : Cbp. 155: 95-101. PMID 21651990 DOI: 10.1016/J.Cbpc.2011.05.012 |
0.343 |
|
2012 |
Shen Y, Catchen J, Garcia T, Amores A, Beldorth I, Wagner J, Zhang Z, Postlethwait J, Warren W, Schartl M, Walter RB. Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within Fâ‚ interspecies hybrids. Comparative Biochemistry and Physiology. Toxicology & Pharmacology : Cbp. 155: 102-8. PMID 21466860 DOI: 10.1016/J.Cbpc.2011.03.012 |
0.351 |
|
2011 |
Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH. Stacks: building and genotyping Loci de novo from short-read sequences. G3 (Bethesda, Md.). 1: 171-82. PMID 22384329 DOI: 10.1534/G3.111.000240 |
0.489 |
|
2011 |
Catchen JM, Braasch I, Postlethwait JH. Conserved synteny and the zebrafish genome. Methods in Cell Biology. 104: 259-85. PMID 21924168 DOI: 10.1016/B978-0-12-374814-0.00015-X |
0.533 |
|
2011 |
Amores A, Catchen J, Ferrara A, Fontenot Q, Postlethwait JH. Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication. Genetics. 188: 799-808. PMID 21828280 DOI: 10.1534/Genetics.111.127324 |
0.558 |
|
2011 |
Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews. Genetics. 12: 499-510. PMID 21681211 DOI: 10.1038/Nrg3012 |
0.538 |
|
2011 |
Hohenlohe PA, Amish SJ, Catchen JM, Allendorf FW, Luikart G. Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout Molecular Ecology Resources. 11: 117-122. PMID 21429168 DOI: 10.1111/J.1755-0998.2010.02967.X |
0.515 |
|
2010 |
Emerson KJ, Merz CR, Catchen JM, Hohenlohe PA, Cresko WA, Bradshaw WE, Holzapfel CM. Resolving postglacial phylogeography using high-throughput sequencing Proceedings of the National Academy of Sciences of the United States of America. 107: 16196-16200. PMID 20798348 DOI: 10.1073/Pnas.1006538107 |
0.496 |
|
2010 |
Jovelin R, Yan YL, He X, Catchen J, Amores A, Canestro C, Yokoi H, Postlethwait JH. Evolution of developmental regulation in the vertebrate FgfD subfamily. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 314: 33-56. PMID 19562753 DOI: 10.1002/Jez.B.21307 |
0.388 |
|
2009 |
Cañestro C, Catchen JM, Rodríguez-Marí A, Yokoi H, Postlethwait JH. Consequences of lineage-specific gene loss on functional evolution of surviving paralogs: ALDH1A and retinoic acid signaling in vertebrate genomes. Plos Genetics. 5: e1000496. PMID 19478994 DOI: 10.1371/Journal.Pgen.1000496 |
0.531 |
|
2009 |
Catchen JM, Conery JS, Postlethwait JH. Automated identification of conserved synteny after whole-genome duplication. Genome Research. 19: 1497-505. PMID 19465509 DOI: 10.1101/Gr.090480.108 |
0.708 |
|
2008 |
Bridgham JT, Brown JE, Rodríguez-Marí A, Catchen JM, Thornton JW. Evolution of a new function by degenerative mutation in cephalochordate steroid receptors. Plos Genetics. 4: e1000191. PMID 18787702 DOI: 10.1371/Journal.Pgen.1000191 |
0.361 |
|
2008 |
Catchen JM, Conery JS, Postlethwait JH. Inferring ancestral gene order. Methods in Molecular Biology (Clifton, N.J.). 452: 365-83. PMID 18566773 DOI: 10.1007/978-1-60327-159-2_17 |
0.71 |
|
2005 |
Conery JS, Catchen JM, Lynch M. Rule-based workflow management for bioinformatics Vldb Journal. 14: 318-329. DOI: 10.1007/s00778-005-0153-9 |
0.579 |
|
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