| Year |
Citation |
Score |
| 2024 |
Marlétaz F, Timoshevskaya N, Timoshevskiy VA, Parey E, Simakov O, Gavriouchkina D, Suzuki M, Kubokawa K, Brenner S, Smith JJ, Rokhsar DS. The hagfish genome and the evolution of vertebrates. Nature. PMID 38262590 DOI: 10.1038/s41586-024-07070-3 |
0.462 |
|
| 2023 |
Marlétaz F, Timoshevskaya N, Timoshevskiy V, Simakov O, Parey E, Gavriouchkina D, Suzuki M, Kubokawa K, Brenner S, Smith J, Rokhsar DS. The hagfish genome and the evolution of vertebrates. Biorxiv : the Preprint Server For Biology. PMID 37131617 DOI: 10.1101/2023.04.17.537254 |
0.818 |
|
| 2023 |
Kabangu M, Cecil R, Strohl L, Timoshevskaya N, Smith JJ, Voss SR. () Is the Mendelian Determinant of the Axolotl Melanoid Color Variant. Genes. 14. PMID 37107662 DOI: 10.3390/genes14040904 |
0.781 |
|
| 2023 |
Timoshevskaya N, Eşkut KI, Timoshevskiy VA, Robb SMC, Holt C, Hess JE, Parker HJ, Baker CF, Miller AK, Saraceno C, Yandell M, Krumlauf R, Narum SR, Lampman RT, Gemmell NJ, ... ... Smith JJ, et al. An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes. Cell Reports. 42: 112263. PMID 36930644 DOI: 10.1016/j.celrep.2023.112263 |
0.811 |
|
| 2022 |
Gatto KP, Timoshevskaya N, Smith JJ, Lourenço LB. Sequencing of laser captured Z and W chromosomes of the tocantins paradoxical frog (Pseudis tocantins) provides insights on repeatome and chromosomal homology. Journal of Evolutionary Biology. PMID 35642451 DOI: 10.1111/jeb.14027 |
0.769 |
|
| 2022 |
Miller AK, Timoshevskaya N, Smith JJ, Gillum J, Sharif S, Clarke S, Baker C, Kitson J, Gemmell NJ, Alexander A. Population genomics of New Zealand pouched lamprey (kanakana; piharau; Geotria australis). The Journal of Heredity. PMID 35439308 DOI: 10.1093/jhered/esac014 |
0.786 |
|
| 2021 |
Voss SR, Smith JJ, Cecil RF, Kabangu M, Duerr TJ, Monaghan JR, Timoshevskaya N, Ponomareva LV, Thorson JS, Veliz-Cuba A, Murrugarra D. HDAC Inhibitor Titration of Transcription and Axolotl Tail Regeneration. Frontiers in Cell and Developmental Biology. 9: 767377. PMID 35036404 DOI: 10.3389/fcell.2021.767377 |
0.765 |
|
| 2021 |
Schloissnig S, Kawaguchi A, Nowoshilow S, Falcon F, Otsuki L, Tardivo P, Timoshevskaya N, Keinath MC, Smith JJ, Voss SR, Tanaka EM. The giant axolotl genome uncovers the evolution, scaling, and transcriptional control of complex gene loci. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33827918 DOI: 10.1073/pnas.2017176118 |
0.827 |
|
| 2020 |
Timoshevskaya N, Voss SR, Labianca CN, High CR, Smith JJ. Large-scale variation in SNP density within the laboratory axolotl (Ambystoma mexicanum). Developmental Dynamics : An Official Publication of the American Association of Anatomists. PMID 33001517 DOI: 10.1002/dvdy.257 |
0.81 |
|
| 2020 |
Hess JE, Smith JJ, Timoshevskaya N, Baker C, Caudill CC, Graves D, Keefer ML, Kinziger AP, Moser ML, Porter LL, Silver G, Whitlock SL, Narum SR. Genomic islands of divergence infer a phenotypic landscape in Pacific lamprey. Molecular Ecology. PMID 32814354 DOI: 10.1111/Mec.15605 |
0.796 |
|
| 2020 |
Arenas Gómez CM, Woodcock MR, Smith JJ, Voss SR, Delgado JP. A reference transcriptome for , an Andean mountain salamander in Colombia. Data in Brief. 29: 105256. PMID 32123704 DOI: 10.1016/j.dib.2020.105256 |
0.501 |
|
| 2019 |
Timoshevskiy VA, Timoshevskaya NY, Smith JJ. Germline-Specific Repetitive Elements in Programmatically Eliminated Chromosomes of the Sea Lamprey (). Genes. 10. PMID 31652530 DOI: 10.3390/genes10100832 |
0.773 |
|
| 2019 |
Hockman D, Chong-Morrison V, Green SA, Gavriouchkina D, Candido-Ferreira I, Ling ITC, Williams RM, Amemiya CT, Smith JJ, Bronner ME, Sauka-Spengler T. A genome-wide assessment of the ancestral neural crest gene regulatory network. Nature Communications. 10: 4689. PMID 31619682 DOI: 10.1038/S41467-019-12687-4 |
0.62 |
|
| 2019 |
Marks RA, Smith JJ, Cronk Q, Grassa CJ, McLetchie DN. Genome of the tropical plant Marchantia inflexa: implications for sex chromosome evolution and dehydration tolerance. Scientific Reports. 9: 8722. PMID 31217536 DOI: 10.1038/S41598-019-45039-9 |
0.417 |
|
| 2019 |
Smith JJ, Timoshevskaya N, Timoshevskiy VA, Keinath MC, Hardy D, Voss SR. A chromosome-scale assembly of the axolotl genome. Genome Research. 29: 317-324. PMID 30679309 DOI: 10.1101/gr.241901.118 |
0.828 |
|
| 2018 |
Gatto KP, Smith JJ, Lourenço LB. The mitochondrial genome of the endemic Brazilian paradoxical frog (Hylidae). Mitochondrial Dna. Part B, Resources. 3: 1106-1107. PMID 33474435 DOI: 10.1080/23802359.2018.1508385 |
0.362 |
|
| 2018 |
Keinath MC, Timoshevskaya N, Timoshevskiy VA, Voss SR, Smith JJ. Miniscule differences between sex chromosomes in the giant genome of a salamander. Scientific Reports. 8: 17882. PMID 30552368 DOI: 10.1038/s41598-018-36209-2 |
0.809 |
|
| 2018 |
Smith JJ, Timoshevskaya N, Ye C, Holt C, Keinath MC, Parker HJ, Cook ME, Hess JE, Narum SR, Lamanna F, Kaessmann H, Timoshevskiy VA, Waterbury CKM, Saraceno C, Wiedemann LM, et al. Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nature Genetics. PMID 30224652 DOI: 10.1038/S41588-018-0199-4 |
0.794 |
|
| 2018 |
Smith JJ. Programmed DNA Elimination: Keeping Germline Genes in Their Place. Current Biology : Cb. 28: R601-R603. PMID 29787722 DOI: 10.1016/j.cub.2018.03.057 |
0.306 |
|
| 2018 |
Smith JJ, Timoshevskaya N, Ye C, Holt C, Keinath MC, Parker HJ, Cook ME, Hess JE, Narum SR, Lamanna F, Kaessmann H, Timoshevskiy VA, Waterbury CKM, Saraceno C, Wiedemann LM, et al. Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nature Genetics. PMID 29674745 DOI: 10.1038/S41588-018-0075-2 |
0.801 |
|
| 2018 |
Smith JJ, Timoshevskaya N, Ye C, Holt C, Keinath MC, Parker HJ, Cook ME, Hess JE, Narum SR, Lamanna F, Kaessmann H, Timoshevskiy VA, Waterbury CKM, Saraceno C, Wiedemann LM, et al. The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nature Genetics. PMID 29358652 DOI: 10.1038/S41588-017-0036-1 |
0.837 |
|
| 2017 |
Timoshevskiy VA, Lampman RT, Hess JE, Porter LL, Smith JJ. Deep Ancestry of Programmed Genome Rearrangement in Lampreys. Developmental Biology. PMID 28669817 DOI: 10.1016/j.ydbio.2017.06.032 |
0.436 |
|
| 2017 |
Woodcock MR, Vaughn-Wolfe J, Elias A, Kump DK, Kendall KD, Timoshevskaya N, Timoshevskiy V, Perry DW, Smith JJ, Spiewak JE, Parichy DM, Voss SR. Identification of Mutant Genes and Introgressed Tiger Salamander DNA in the Laboratory Axolotl, Ambystoma mexicanum. Scientific Reports. 7: 6. PMID 28127056 DOI: 10.1038/s41598-017-00059-1 |
0.787 |
|
| 2017 |
Smith J. A Deep Evolutionary Perspective on Vertebrate Genome Biology Mechanisms of Development. 145. DOI: 10.1016/J.Mod.2017.04.294 |
0.506 |
|
| 2016 |
Timoshevskiy VA, Herdy JR, Keinath MC, Smith JJ. Cellular and Molecular Features of Developmentally Programmed Genome Rearrangement in a Vertebrate (Sea Lamprey: Petromyzon marinus). Plos Genetics. 12: e1006103. PMID 27341395 DOI: 10.1371/journal.pgen.1006103 |
0.353 |
|
| 2016 |
Srivastava AK, Wang Y, Huang R, Skinner C, Thompson T, Pollard L, Wood T, Luo F, Stevenson R, Polimanti R, Gelernter J, Lin X, Lim IY, Wu Y, Teh AL, ... ... Smith J, et al. Human genome meeting 2016: Houston, TX, USA. 28 February - 2 March 2016 Human Genomics. 10: 12-12. PMID 27294413 DOI: 10.1186/S40246-016-0063-5 |
0.337 |
|
| 2016 |
Bryant SA, Herdy JR, Amemiya CT, Smith JJ. Characterization of Somatically-Eliminated Genes During Development of the Sea Lamprey (Petromyzon marinus). Molecular Biology and Evolution. PMID 27288344 DOI: 10.1093/molbev/msw104 |
0.662 |
|
| 2016 |
Keinath MC, Voss SR, Tsonis PA, Smith JJ. A linkage map for the Newt Notophthalmus viridescens: Insights in vertebrate genome and chromosome evolution. Developmental Biology. PMID 27265323 DOI: 10.1016/J.Ydbio.2016.05.027 |
0.552 |
|
| 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 |
0.818 |
|
| 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 |
0.839 |
|
| 2015 |
Turner TN, Hormozdiari F, Duyzend MH, McClymont SA, Hook PW, Iossifov I, Raja A, Baker C, Hoekzema K, Stessman HA, Zody MC, Nelson BJ, Huddleston J, Sandstrom R, Smith JD, et al. Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA. American Journal of Human Genetics. PMID 26749308 DOI: 10.1016/J.Ajhg.2015.11.023 |
0.822 |
|
| 2015 |
Keinath MC, Timoshevskiy VA, Timoshevskaya NY, Tsonis PA, Voss SR, Smith JJ. Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing. Scientific Reports. 5: 16413. PMID 26553646 DOI: 10.1038/Srep16413 |
0.836 |
|
| 2015 |
Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Lyons E, Wang ML, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, ... ... Smith JA, et al. The pineapple genome and the evolution of CAM photosynthesis. Nature Genetics. 47: 1435-42. PMID 26523774 DOI: 10.1038/Ng.3435 |
0.413 |
|
| 2015 |
Peters MJ, Joehanes R, Pilling LC, Schurmann C, Conneely KN, Powell J, Reinmaa E, Sutphin GL, Zhernakova A, Schramm K, Wilson YA, Kobes S, Tukiainen T, Ramos YF, ... ... Smith JA, et al. The transcriptional landscape of age in human peripheral blood. Nature Communications. 6: 8570. PMID 26490707 DOI: 10.1038/Ncomms9570 |
0.313 |
|
| 2015 |
Joshi PK, Esko T, Mattsson H, Eklund N, Gandin I, Nutile T, Jackson AU, Schurmann C, Smith AV, Zhang W, Okada Y, Stančáková A, Faul JD, Zhao W, Bartz TM, ... ... Smith JA, et al. Directional dominance on stature and cognition in diverse human populations. Nature. 523: 459-62. PMID 26131930 DOI: 10.1038/Nature14618 |
0.301 |
|
| 2015 |
Smith JJ, Keinath MC. The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications. Genome Research. PMID 26048246 DOI: 10.1101/gr.184135.114 |
0.421 |
|
| 2014 |
Iossifov I, O'Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, Smith JD, Paeper B, Nickerson DA, Dea J, Dong S, et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature. 515: 216-21. PMID 25363768 DOI: 10.1038/Nature13908 |
0.778 |
|
| 2014 |
He Z, O'Roak BJ, Smith JD, Wang G, Hooker S, Santos-Cortez RL, Li B, Kan M, Krumm N, Nickerson DA, Shendure J, Eichler EE, Leal SM. Rare-variant extensions of the transmission disequilibrium test: application to autism exome sequence data. American Journal of Human Genetics. 94: 33-46. PMID 24360806 DOI: 10.1016/J.Ajhg.2013.11.021 |
0.77 |
|
| 2013 |
Decatur WA, Hall JA, Smith JJ, Li W, Sower SA. Insight from the lamprey genome: glimpsing early vertebrate development via neuroendocrine-associated genes and shared synteny of gonadotropin-releasing hormone (GnRH). General and Comparative Endocrinology. 192: 237-45. PMID 23770021 DOI: 10.1016/J.Ygcen.2013.05.020 |
0.327 |
|
| 2013 |
Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, et al. The African coelacanth genome provides insights into tetrapod evolution. Nature. 496: 311-6. PMID 23598338 DOI: 10.1038/Nature12027 |
0.826 |
|
| 2013 |
Voss SR, Putta S, Walker JA, Smith JJ, Maki N, Tsonis PA. Salamander Hox clusters contain repetitive DNA and expanded non-coding regions: a typical Hox structure for non-mammalian tetrapod vertebrates? Human Genomics. 7: 9. PMID 23561734 DOI: 10.1186/1479-7364-7-9 |
0.5 |
|
| 2013 |
Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, et al. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nature Genetics. 45: 415-21, 421e1-2. PMID 23435085 DOI: 10.1038/Ng.2568 |
0.7 |
|
| 2012 |
Smith JJ, Baker C, Eichler EE, Amemiya CT. Genetic consequences of programmed genome rearrangement. Current Biology : Cb. 22: 1524-9. PMID 22818913 DOI: 10.1016/j.cub.2012.06.028 |
0.738 |
|
| 2012 |
O'Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N, Coe BP, Levy R, Ko A, Lee C, Smith JD, Turner EH, Stanaway IB, Vernot B, Malig M, Baker C, et al. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature. 485: 246-50. PMID 22495309 DOI: 10.1038/Nature10989 |
0.768 |
|
| 2012 |
Smith JJ, Sumiyama K, Amemiya CT. A living fossil in the genome of a living fossil: Harbinger transposons in the coelacanth genome. Molecular Biology and Evolution. 29: 985-93. PMID 22045999 DOI: 10.1093/molbev/msr267 |
0.707 |
|
| 2011 |
Voss SR, Kump DK, Putta S, Pauly N, Reynolds A, Henry RJ, Basa S, Walker JA, Smith JJ. Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes. Genome Research. 21: 1306-12. PMID 21482624 DOI: 10.1101/gr.116491.110 |
0.583 |
|
| 2010 |
Itsara A, Wu H, Smith JD, Nickerson DA, Romieu I, London SJ, Eichler EE. De novo rates and selection of large copy number variation. Genome Research. 20: 1469-81. PMID 20841430 DOI: 10.1101/Gr.107680.110 |
0.809 |
|
| 2010 |
Page RB, Boley MA, Smith JJ, Putta S, Voss SR. Microarray analysis of a salamander hopeful monster reveals transcriptional signatures of paedomorphic brain development. Bmc Evolutionary Biology. 10: 199. PMID 20584293 DOI: 10.1186/1471-2148-10-199 |
0.443 |
|
| 2010 |
Smith JJ, Stuart AB, Sauka-Spengler T, Clifton SW, Amemiya CT. Development and analysis of a germline BAC resource for the sea lamprey, a vertebrate that undergoes substantial chromatin diminution Chromosoma. 119: 381-389. PMID 20195622 DOI: 10.1007/S00412-010-0263-Z |
0.708 |
|
| 2010 |
Fitzpatrick BM, Johnson JR, Kump DK, Smith JJ, Voss SR, Shaffer HB. Rapid spread of invasive genes into a threatened native species. Proceedings of the National Academy of Sciences of the United States of America. 107: 3606-10. PMID 20133596 DOI: 10.1073/Pnas.0911802107 |
0.617 |
|
| 2010 |
Saha NR, Smith J, Amemiya CT. Evolution of adaptive immune recognition in jawless vertebrates. Seminars in Immunology. 22: 25-33. PMID 20056434 DOI: 10.1016/J.Smim.2009.12.002 |
0.587 |
|
| 2009 |
Fitzpatrick BM, Johnson JR, Kump DK, Shaffer HB, Smith JJ, Voss SR. Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders. Bmc Evolutionary Biology. 9: 176. PMID 19630983 DOI: 10.1186/1471-2148-9-176 |
0.649 |
|
| 2009 |
Smith JJ, Antonacci F, Eichler EE, Amemiya CT. Programmed loss of millions of base pairs from a vertebrate genome. Proceedings of the National Academy of Sciences of the United States of America. 106: 11212-7. PMID 19561299 DOI: 10.1073/Pnas.0902358106 |
0.801 |
|
| 2009 |
Mefford HC, Cooper GM, Zerr T, Smith JD, Baker C, Shafer N, Thorland EC, Skinner C, Schwartz CE, Nickerson DA, Eichler EE. A method for rapid, targeted CNV genotyping identifies rare variants associated with neurocognitive disease. Genome Research. 19: 1579-85. PMID 19506092 DOI: 10.1101/Gr.094987.109 |
0.67 |
|
| 2009 |
Smith JJ, Putta S, Zhu W, Pao GM, Verma IM, Hunter T, Bryant SV, Gardiner DM, Harkins TT, Voss SR. Genic regions of a large salamander genome contain long introns and novel genes. Bmc Genomics. 10: 19. PMID 19144141 DOI: 10.1186/1471-2164-10-19 |
0.62 |
|
| 2008 |
Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, Haugen E, Zerr T, Yamada NA, Tsang P, Newman TL, ... ... Smith JD, et al. Mapping and sequencing of structural variation from eight human genomes. Nature. 453: 56-64. PMID 18451855 DOI: 10.1038/Nature06862 |
0.825 |
|
| 2008 |
Page RB, Voss SR, Samuels AK, Smith JJ, Putta S, Beachy CK. Effect of thyroid hormone concentration on the transcriptional response underlying induced metamorphosis in the Mexican axolotl (Ambystoma). Bmc Genomics. 9: 78. PMID 18267027 DOI: 10.1186/1471-2164-9-78 |
0.385 |
|
| 2007 |
Putta S, Smith JJ, Staben C, Voss SR. MapToGenome: a comparative genomic tool that aligns transcript maps to sequenced genomes. Evolutionary Bioinformatics Online. 3: 15-25. PMID 19430601 DOI: 10.1177/117693430700300023 |
0.594 |
|
| 2007 |
Smith JJ, Voss SR. Bird and mammal sex-chromosome orthologs map to the same autosomal region in a salamander (ambystoma). Genetics. 177: 607-13. PMID 17660573 DOI: 10.1534/genetics.107.072033 |
0.484 |
|
| 2007 |
Page RB, Monaghan JR, Samuels AK, Smith JJ, Beachy CK, Voss SR. Microarray analysis identifies keratin loci as sensitive biomarkers for thyroid hormone disruption in the salamander Ambystoma mexicanum. Comparative Biochemistry and Physiology. Toxicology & Pharmacology : Cbp. 145: 15-27. PMID 16926121 DOI: 10.1016/j.cbpc.2006.06.003 |
0.727 |
|
| 2006 |
Smith JJ, Voss SR. Gene order data from a model amphibian (Ambystoma): new perspectives on vertebrate genome structure and evolution. Bmc Genomics. 7: 219. PMID 16939647 DOI: 10.1186/1471-2164-7-219 |
0.619 |
|
| 2006 |
Newman TL, Rieder MJ, Morrison VA, Sharp AJ, Smith JD, Sprague LJ, Kaul R, Carlson CS, Olson MV, Nickerson DA, Eichler EE. High-throughput genotyping of intermediate-size structural variation. Human Molecular Genetics. 15: 1159-67. PMID 16497726 DOI: 10.1093/Hmg/Ddl031 |
0.58 |
|
| 2005 |
Smith JJ, Putta S, Walker JA, Kump DK, Samuels AK, Monaghan JR, Weisrock DW, Staben C, Voss SR. Sal-Site: integrating new and existing ambystomatid salamander research and informational resources. Bmc Genomics. 6: 181. PMID 16359543 DOI: 10.1186/1471-2164-6-181 |
0.723 |
|
| 2005 |
Samuels AK, Weisrock DW, Smith JJ, France KJ, Walker JA, Putta S, Voss SR. Transcriptional and phylogenetic analysis of five complete ambystomatid salamander mitochondrial genomes. Gene. 349: 43-53. PMID 15780978 DOI: 10.1016/J.Gene.2004.12.037 |
0.522 |
|
| 2004 |
Putta S, Smith JJ, Walker JA, Rondet M, Weisrock DW, Monaghan J, Samuels AK, Kump K, King DC, Maness NJ, Habermann B, Tanaka E, Bryant SV, Gardiner DM, Parichy DM, et al. From biomedicine to natural history research: EST resources for ambystomatid salamanders. Bmc Genomics. 5: 54. PMID 15310388 DOI: 10.1186/1471-2164-5-54 |
0.733 |
|
| Show low-probability matches. |
