Julian M. Catchen, Ph.D. - Publications

2009 University of Oregon, Eugene, OR, United States 
Bioinformatics Biology

54 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

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  0.411
2023 de Flamingh A, Gnoske TP, Rivera-Colón AG, Simeonovski VA, Kerbis Peterhans JC, Yamaguchi N, Witt KE, Catchen J, Roca AL, Malhi RS. Genomic analysis supports Cape Lion population connectivity prior to colonial eradication and extinction. The Journal of Heredity. PMID 38150491 DOI: 10.1093/jhered/esad081  0.416
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  0.428
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  0.361
2023 Rochette NC, Rivera-Colón AG, Walsh J, Sanger TJ, Campbell-Staton SC, Catchen JM. On the causes, consequences, and avoidance of PCR duplicates: Towards a theory of library complexity. Molecular Ecology Resources. PMID 37062860 DOI: 10.1111/1755-0998.13800  0.701
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  0.322
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  0.368
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  0.356
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  0.426
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  0.376
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  0.326
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  0.497
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  0.776
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  0.684
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  0.509
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  0.773
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  0.479
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  0.484
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  0.546
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  0.4
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  0.44
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  0.776
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  0.474
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  0.751
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  0.442
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  0.418
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  0.302
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  0.481
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  0.432
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  0.431
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  0.504
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  0.466
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  0.425
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  0.403
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  0.337
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  0.493
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  0.533
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  0.489
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  0.428
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  0.56
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  0.401
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 F₁ interspecies hybrids. Comparative Biochemistry and Physiology. Toxicology & Pharmacology : Cbp. 155: 102-8. PMID 21466860 DOI: 10.1016/J.Cbpc.2011.03.012  0.363
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  0.522
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  0.477
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  0.512
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  0.545
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  0.519
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  0.507
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  0.359
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  0.465
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  0.748
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  0.352
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  0.749
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  0.631
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