| 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 |
0.805 |
|
| 2023 |
Ahuja N, Hwaun E, Pungor JR, Rafiq R, Nemes S, Sakmar T, Vogt MA, Grasse B, Diaz Quiroz J, Montague TG, Null RW, Dallis DN, Gavriouchkina D, Marletaz F, Abbo L, ... Rokhsar DS, et al. Creation of an albino squid line by CRISPR-Cas9 and its application for in vivo functional imaging of neural activity. Current Biology : Cb. PMID 37343558 DOI: 10.1016/j.cub.2023.05.066 |
0.797 |
|
| 2023 |
Session AM, Rokhsar DS. Transposon signatures of allopolyploid genome evolution. Nature Communications. 14: 3180. PMID 37263993 DOI: 10.1038/s41467-023-38560-z |
0.334 |
|
| 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 |
0.828 |
|
| 2023 |
Marlétaz F, de la Calle-Mustienes E, Acemel RD, Paliou C, Naranjo S, Martínez-García PM, Cases I, Sleight VA, Hirschberger C, Marcet-Houben M, Navon D, Andrescavage A, Skvortsova K, Duckett PE, González-Rajal Á, ... ... Rokhsar DS, et al. The little skate genome and the evolutionary emergence of wing-like fins. Nature. PMID 37046085 DOI: 10.1038/s41586-023-05868-1 |
0.752 |
|
| 2022 |
Albertin CB, Medina-Ruiz S, Mitros T, Schmidbaur H, Sanchez G, Wang ZY, Grimwood J, Rosenthal JJC, Ragsdale CW, Simakov O, Rokhsar DS. Genome and transcriptome mechanisms driving cephalopod evolution. Nature Communications. 13: 2427. PMID 35508532 DOI: 10.1038/s41467-022-29748-w |
0.393 |
|
| 2022 |
Bredeson JV, Lyons JB, Oniyinde IO, Okereke NR, Kolade O, Nnabue I, Nwadili CO, Hřibová E, Parker M, Nwogha J, Shu S, Carlson J, Kariba R, Muthemba S, Knop K, ... ... Rokhsar DS, et al. Chromosome evolution and the genetic basis of agronomically important traits in greater yam. Nature Communications. 13: 2001. PMID 35422045 DOI: 10.1038/s41467-022-29114-w |
0.338 |
|
| 2022 |
Simakov O, Bredeson J, Berkoff K, Marletaz F, Mitros T, Schultz DT, O'Connell BL, Dear P, Martinez DE, Steele RE, Green RE, David CN, Rokhsar DS. Deeply conserved synteny and the evolution of metazoan chromosomes. Science Advances. 8: eabi5884. PMID 35108053 DOI: 10.1126/sciadv.abi5884 |
0.677 |
|
| 2021 |
Sanchez G, Fernández-Álvarez FÁ, Taite M, Sugimoto C, Jolly J, Simakov O, Marlétaz F, Allcock L, Rokhsar DS. Phylogenomics illuminates the evolution of bobtail and bottletail squid (order Sepiolida). Communications Biology. 4: 819. PMID 34188187 DOI: 10.1038/s42003-021-02348-y |
0.691 |
|
| 2021 |
Lei L, Goltsman E, Goodstein D, Wu GA, Rokhsar DS, Vogel JP. Plant Pan-Genomics Comes of Age. Annual Review of Plant Biology. PMID 33848428 DOI: 10.1146/annurev-arplant-080720-105454 |
0.388 |
|
| 2021 |
Lyons JB, Bredeson JV, Mansfeld BN, Bauchet GJ, Berry J, Boyher A, Mueller LA, Rokhsar DS, Bart RS. Current status and impending progress for cassava structural genomics. Plant Molecular Biology. PMID 33604743 DOI: 10.1007/s11103-020-01104-w |
0.361 |
|
| 2020 |
Mitros T, Session AM, James BT, Wu GA, Belaffif MB, Clark LV, Shu S, Dong H, Barling A, Holmes JR, Mattick JE, Bredeson JV, Liu S, Farrar K, Głowacka K, ... ... Rokhsar DS, et al. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nature Communications. 11: 5442. PMID 33116128 DOI: 10.1038/s41467-020-18923-6 |
0.695 |
|
| 2020 |
Peng Z, Bredeson JV, Wu GA, Shu S, Rawat N, Du D, Parajuli S, Yu Q, You Q, Rokhsar DS, Gmitter FG, Deng Z. A Chromosome-scale Reference Genome of Trifoliate Orange (Poncirus trifoliata) Provides Insights into Disease Resistance, Cold Tolerance and Genome Evolution in Citrus. The Plant Journal : For Cell and Molecular Biology. PMID 32985030 DOI: 10.1111/tpj.14993 |
0.361 |
|
| 2020 |
Mudd AB, Bredeson JV, Baum R, Hockemeyer D, Rokhsar DS. Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution. Communications Biology. 3: 480. PMID 32873878 DOI: 10.1038/s42003-020-1096-9 |
0.317 |
|
| 2020 |
Gordon SP, Contreras-Moreira B, Levy JJ, Djamei A, Czedik-Eysenberg A, Tartaglio VS, Session A, Martin J, Cartwright A, Katz A, Singan VR, Goltsman E, Barry K, Dinh-Thi VH, Chalhoub B, ... ... Rokhsar D, et al. Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors. Nature Communications. 11: 3670. PMID 32728126 DOI: 10.1038/S41467-020-17302-5 |
0.475 |
|
| 2020 |
Hofmeyr S, Egan R, Georganas E, Copeland AC, Riley R, Clum A, Eloe-Fadrosh E, Roux S, Goltsman E, Buluç A, Rokhsar D, Oliker L, Yelick K. Terabase-scale metagenome coassembly with MetaHipMer. Scientific Reports. 10: 10689. PMID 32612216 DOI: 10.1038/S41598-020-67416-5 |
0.402 |
|
| 2020 |
Simakov O, Marlétaz F, Yue JX, O'Connell B, Jenkins J, Brandt A, Calef R, Tung CH, Huang TK, Schmutz J, Satoh N, Yu JK, Putnam NH, Green RE, Rokhsar DS. Deeply conserved synteny resolves early events in vertebrate evolution. Nature Ecology & Evolution. PMID 32313176 DOI: 10.1038/S41559-020-1156-Z |
0.822 |
|
| 2019 |
Sanchez G, Jolly J, Reid A, Sugimoto C, Azama C, Marlétaz F, Simakov O, Rokhsar DS. New bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu islands revealed by molecular and morphological analysis. Communications Biology. 2: 465. PMID 31840110 DOI: 10.1038/s42003-019-0661-6 |
0.649 |
|
| 2019 |
Wang B, Mojica JP, Perera N, Lee CR, Lovell JT, Sharma A, Adam C, Lipzen A, Barry K, Rokhsar DS, Schmutz J, Mitchell-Olds T. Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta. Genome Biology. 20: 126. PMID 31227026 DOI: 10.1186/S13059-019-1729-9 |
0.397 |
|
| 2019 |
Mitros T, Lyons JB, Session AM, Jenkins J, Shu S, Kwon T, Lane M, Ng C, Grammer TC, Khokha MK, Grimwood J, Schmutz J, Harland RM, Rokhsar DS. A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis. Developmental Biology. PMID 30980799 DOI: 10.1016/J.Ydbio.2019.03.015 |
0.455 |
|
| 2019 |
Gehrke AR, Neverett E, Luo YJ, Brandt A, Ricci L, Hulett RE, Gompers A, Ruby JG, Rokhsar DS, Reddien PW, Srivastava M. Acoel genome reveals the regulatory landscape of whole-body regeneration. Science (New York, N.Y.). 363. PMID 30872491 DOI: 10.1126/Science.Aau6173 |
0.804 |
|
| 2019 |
Marlétaz F, Peijnenburg KTCA, Goto T, Satoh N, Rokhsar DS. A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans. Current Biology : Cb. 29: 312-318.e3. PMID 30639106 DOI: 10.1016/J.Cub.2018.11.042 |
0.695 |
|
| 2019 |
Belcaid M, Casaburi G, McAnulty SJ, Schmidbaur H, Suria AM, Moriano-Gutierrez S, Pankey MS, Oakley TH, Kremer N, Koch EJ, Collins AJ, Nguyen H, Lek S, Goncharenko-Foster I, Minx P, ... ... Rokhsar DS, et al. Symbiotic organs shaped by distinct modes of genome evolution in cephalopods. Proceedings of the National Academy of Sciences of the United States of America. PMID 30635418 DOI: 10.1073/Pnas.1817322116 |
0.437 |
|
| 2018 |
Lovell JT, Jenkins J, Lowry DB, Mamidi S, Sreedasyam A, Weng X, Barry K, Bonnette J, Campitelli B, Daum C, Gordon SP, Gould BA, Khasanova A, Lipzen A, MacQueen A, ... ... Rokhsar D, et al. The genomic landscape of molecular responses to natural drought stress in Panicum hallii. Nature Communications. 9: 5213. PMID 30523281 DOI: 10.1038/S41467-018-07669-X |
0.414 |
|
| 2018 |
Kliver S, Rayko M, Komissarov A, Bakin E, Zhernakova D, Prasad K, Rushworth C, Baskar R, Smetanin D, Schmutz J, Rokhsar DS, Mitchell-Olds T, Grossniklaus U, Brukhin V. Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes. Genes. 9. PMID 29597328 DOI: 10.3390/Genes9040185 |
0.43 |
|
| 2018 |
Wu GA, Terol J, Ibanez V, López-García A, Pérez-Román E, Borredá C, Domingo C, Tadeo FR, Carbonell-Caballero J, Alonso R, Curk F, Du D, Ollitrault P, Roose ML, Dopazo J, ... ... Rokhsar DS, et al. Genomics of the origin and evolution of Citrus. Nature. PMID 29414943 DOI: 10.1038/Nature25447 |
0.425 |
|
| 2017 |
Lee CR, Wang B, Mojica JP, Mandáková T, Prasad KVSK, Goicoechea JL, Perera N, Hellsten U, Hundley HN, Johnson J, Grimwood J, Barry K, Fairclough S, Jenkins JW, Yu Y, ... ... Rokhsar DS, et al. Young inversion with multiple linked QTLs under selection in a hybrid zone. Nature Ecology & Evolution. 1: 119. PMID 28812690 DOI: 10.1038/S41559-017-0119 |
0.333 |
|
| 2017 |
Brawley SH, Blouin NA, Ficko-Blean E, Wheeler GL, Lohr M, Goodson HV, Jenkins JW, Blaby-Haas CE, Helliwell KE, Chan CX, Marriage TN, Bhattacharya D, Klein AS, Badis Y, Brodie J, ... ... Rokhsar DS, et al. Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta). Proceedings of the National Academy of Sciences of the United States of America. PMID 28716924 DOI: 10.1073/Pnas.1703088114 |
0.385 |
|
| 2016 |
Morales J, Kokkori S, Weidauer D, Chapman J, Goltsman E, Rokhsar D, Grossman AR, Nowack EC. Development of a toolbox to dissect host-endosymbiont interactions and protein trafficking in the trypanosomatid Angomonas deanei. Bmc Evolutionary Biology. 16: 247. PMID 27835948 DOI: 10.1186/S12862-016-0820-Z |
0.554 |
|
| 2016 |
Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, ... ... Rokhsar DS, et al. Genome evolution in the allotetraploid frog Xenopus laevis. Nature. 538: 336-343. PMID 27762356 DOI: 10.1038/Nature19840 |
0.807 |
|
| 2016 |
Suzuki A, Uno Y, Takahashi S, Grimwood J, Schmutz J, Mawaribuchi S, Yoshida H, Takebayashi-Suzuki K, Ito M, Matsuda Y, Rokhsar D, Taira M. Genome organization of the vg1 and nodal3 gene clusters in the allotetraploid frog Xenopus laevis. Developmental Biology. PMID 27720224 DOI: 10.1016/J.Ydbio.2016.04.014 |
0.349 |
|
| 2016 |
Farley EK, Olson KM, Zhang W, Rokhsar DS, Levine MS. Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers. Proceedings of the National Academy of Sciences of the United States of America. PMID 27155014 DOI: 10.1073/pnas.1605085113 |
0.54 |
|
| 2016 |
Bredeson JV, Lyons JB, Prochnik SE, Wu GA, Ha CM, Edsinger-Gonzales E, Grimwood J, Schmutz J, Rabbi IY, Egesi C, Nauluvula P, Lebot V, Ndunguru J, Mkamilo G, Bart RS, ... ... Rokhsar DS, et al. Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity. Nature Biotechnology. PMID 27088722 DOI: 10.1038/Nbt.3535 |
0.425 |
|
| 2016 |
Putnam NH, O'Connell BL, Stites JC, Rice BJ, Blanchette M, Calef R, Troll CJ, Fields A, Hartley PD, Sugnet CW, Haussler D, Rokhsar DS, Green RE. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Research. PMID 26848124 DOI: 10.1101/Gr.193474.115 |
0.718 |
|
| 2015 |
Simakov O, Kawashima T, Marlétaz F, Jenkins J, Koyanagi R, Mitros T, Hisata K, Bredeson J, Shoguchi E, Gyoja F, Yue JX, Chen YC, Freeman RM, Sasaki A, Hikosaka-Katayama T, ... ... Rokhsar DS, et al. Hemichordate genomes and deuterostome origins. Nature. PMID 26580012 DOI: 10.1038/Nature16150 |
0.828 |
|
| 2015 |
Farley EK, Olson KM, Zhang W, Brandt AJ, Rokhsar DS, Levine MS. Suboptimization of developmental enhancers. Science (New York, N.Y.). 350: 325-8. PMID 26472909 DOI: 10.1126/science.aac6948 |
0.532 |
|
| 2015 |
Albertin CB, Simakov O, Mitros T, Wang ZY, Pungor JR, Edsinger-Gonzales E, Brenner S, Ragsdale CW, Rokhsar DS. The octopus genome and the evolution of cephalopod neural and morphological novelties. Nature. 524: 220-4. PMID 26268193 DOI: 10.1038/nature14668 |
0.476 |
|
| 2015 |
Glazer AM, Killingbeck EE, Mitros T, Rokhsar DS, Miller CT. Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing. G3 (Bethesda, Md.). 5: 1463-72. PMID 26044731 DOI: 10.1534/G3.115.017905 |
0.374 |
|
| 2015 |
Lowe CJ, Clarke DN, Medeiros DM, Rokhsar DS, Gerhart J. The deuterostome context of chordate origins. Nature. 520: 456-65. PMID 25903627 DOI: 10.1038/Nature14434 |
0.342 |
|
| 2015 |
Matsuda Y, Uno Y, Kondo M, Gilchrist MJ, Zorn AM, Rokhsar DS, Schmid M, Taira M. A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis. Cytogenetic and Genome Research. PMID 25871511 DOI: 10.1159/000381292 |
0.333 |
|
| 2015 |
Chapman JA, Mascher M, Buluç A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Sehgal S, Oliker L, Schmutz J, Yelick KA, Scholz U, Waugh R, Poland JA, ... ... Rokhsar DS, et al. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biology. 16: 26. PMID 25637298 DOI: 10.1186/S13059-015-0582-8 |
0.644 |
|
| 2015 |
Lowry DB, Hernandez K, Taylor SH, Meyer E, Logan TL, Barry KW, Chapman JA, Rokhsar DS, Schmutz J, Juenger TE. The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii. The New Phytologist. 205: 402-14. PMID 25252269 DOI: 10.1111/Nph.13027 |
0.558 |
|
| 2014 |
Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, Jenkins J, Lindquist E, Tice H, Bauer D, Goodstein DM, Dubchak I, Poliakov A, Mizrachi E, Kullan AR, ... ... Rokhsar DS, et al. The genome of Eucalyptus grandis. Nature. 510: 356-62. PMID 24919147 DOI: 10.1038/Nature13308 |
0.474 |
|
| 2014 |
Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, Perrier X, Ruiz M, Scalabrin S, Terol J, Takita MA, Labadie K, Poulain J, Couloux A, Jabbari K, ... ... Rokhsar D, et al. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nature Biotechnology. 32: 656-62. PMID 24908277 DOI: 10.1038/Nbt.2906 |
0.64 |
|
| 2014 |
Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, Torres-Torres M, Geffroy V, Moghaddam SM, Gao D, Abernathy B, ... ... Rokhsar DS, et al. A reference genome for common bean and genome-wide analysis of dual domestications. Nature Genetics. 46: 707-13. PMID 24908249 DOI: 10.1038/Ng.3008 |
0.489 |
|
| 2014 |
Wang W, Haberer G, Gundlach H, Gläßer C, Nussbaumer T, Luo MC, Lomsadze A, Borodovsky M, Kerstetter RA, Shanklin J, Byrant DW, Mockler TC, Appenroth KJ, Grimwood J, Jenkins J, ... ... Rokhsar D, et al. The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nature Communications. 5: 3311. PMID 24548928 DOI: 10.1038/Ncomms4311 |
0.471 |
|
| 2014 |
Lukaszewski AJ, Alberti A, Sharpe A, Kilian A, Stanca AM, Keller B, Clavijo BJ, Friebe B, Gill B, Wulff B, Chapman B, Steuernagel B, Feuillet C, Viseux C, Pozniak C, ... Rokhsar DS, et al. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome Science. 345. DOI: 10.1126/science.1251788 |
0.605 |
|
| 2014 |
Georganas E, Buluç A, Chapman J, Oliker L, Rokhsar D, Yelick K. Parallel de Bruijn Graph Construction and Traversal for de Novo Genome Assembly International Conference For High Performance Computing, Networking, Storage and Analysis, Sc. 2015: 437-448. DOI: 10.1109/SC.2014.41 |
0.549 |
|
| 2014 |
Strnadová V, Buluc A, Chapman J, Gilbert JR, Gonzalez J, Jegelka S, Rokhsar D, Oliker L. Efficient and accurate clustering for large-scale genetic mapping Proceedings - 2014 Ieee International Conference On Bioinformatics and Biomedicine, Ieee Bibm 2014. 3-10. DOI: 10.1109/BIBM.2014.6999119 |
0.467 |
|
| 2013 |
Barling A, Swaminathan K, Mitros T, James BT, Morris J, Ngamboma O, Hall MC, Kirkpatrick J, Alabady M, Spence AK, Hudson ME, Rokhsar DS, Moose SP. A detailed gene expression study of the Miscanthus genus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes. Bmc Genomics. 14: 864. PMID 24320546 DOI: 10.1186/1471-2164-14-864 |
0.397 |
|
| 2013 |
Hellsten U, Wright KM, Jenkins J, Shu S, Yuan Y, Wessler SR, Schmutz J, Willis JH, Rokhsar DS. Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing. Proceedings of the National Academy of Sciences of the United States of America. 110: 19478-82. PMID 24225854 DOI: 10.1073/Pnas.1319032110 |
0.586 |
|
| 2013 |
Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, Schmutz J, Barry K, Muñoz-AmatriaÃn M, Close TJ, Wise RP, Schulman AH, Himmelbach A, Mayer KF, Scholz U, Poland JA, Stein N, et al. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). The Plant Journal : For Cell and Molecular Biology. 76: 718-27. PMID 23998490 DOI: 10.1111/Tpj.12319 |
0.667 |
|
| 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, ... ... Rokhsar DS, 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 |
0.649 |
|
| 2013 |
Slotte T, Hazzouri KM, Ågren JA, Koenig D, Maumus F, Guo YL, Steige K, Platts AE, Escobar JS, Newman LK, Wang W, Mandáková T, Vello E, Smith LM, Henz SR, ... ... Rokhsar D, et al. The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nature Genetics. 45: 831-5. PMID 23749190 DOI: 10.1038/Ng.2669 |
0.64 |
|
| 2013 |
Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F, Zhebentyayeva T, Dettori MT, Grimwood J, Cattonaro F, Zuccolo A, Rossini L, Jenkins J, Vendramin E, ... ... Rokhsar DS, et al. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nature Genetics. 45: 487-94. PMID 23525075 DOI: 10.1038/Ng.2586 |
0.491 |
|
| 2013 |
Simakov O, Marletaz F, Cho SJ, Edsinger-Gonzales E, Havlak P, Hellsten U, Kuo DH, Larsson T, Lv J, Arendt D, Savage R, Osoegawa K, de Jong P, Grimwood J, Chapman JA, ... ... Rokhsar DS, et al. Insights into bilaterian evolution from three spiralian genomes. Nature. 493: 526-31. PMID 23254933 DOI: 10.1038/Nature11696 |
0.83 |
|
| 2012 |
Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D, Llewellyn D, Showmaker KC, Shu S, Udall J, Yoo MJ, Byers R, Chen W, Doron-Faigenboim A, Duke MV, ... ... Rokhsar DS, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature. 492: 423-7. PMID 23257886 DOI: 10.1038/Nature11798 |
0.452 |
|
| 2012 |
Freeman R, Ikuta T, Wu M, Koyanagi R, Kawashima T, Tagawa K, Humphreys T, Fang GC, Fujiyama A, Saiga H, Lowe C, Worley K, Jenkins J, Schmutz J, Kirschner M, ... Rokhsar D, et al. Identical genomic organization of two hemichordate hox clusters. Current Biology : Cb. 22: 2053-8. PMID 23063438 DOI: 10.1016/J.Cub.2012.08.052 |
0.385 |
|
| 2012 |
Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio LA, Gunter LE, Ranjan P, Vining K, Pomraning KR, Wilhelm LJ, ... ... Rokhsar D, et al. Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. The New Phytologist. 196: 713-25. PMID 22861491 DOI: 10.1111/J.1469-8137.2012.04258.X |
0.442 |
|
| 2012 |
Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J, Jenkins J, Barry K, Lindquist E, Hellsten U, Deshpande S, ... ... Rokhsar D, et al. Reference genome sequence of the model plant Setaria. Nature Biotechnology. 30: 555-61. PMID 22580951 DOI: 10.1038/Nbt.2196 |
0.484 |
|
| 2012 |
Swaminathan K, Chae WB, Mitros T, Varala K, Xie L, Barling A, Glowacka K, Hall M, Jezowski S, Ming R, Hudson M, Juvik JA, Rokhsar DS, Moose SP. A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy. Bmc Genomics. 13: 142. PMID 22524439 DOI: 10.1186/1471-2164-13-142 |
0.336 |
|
| 2012 |
Prochnik S, Marri PR, Desany B, Rabinowicz PD, Kodira C, Mohiuddin M, Rodriguez F, Fauquet C, Tohme J, Harkins T, Rokhsar DS, Rounsley S. The Cassava Genome: Current Progress, Future Directions. Tropical Plant Biology. 5: 88-94. PMID 22523606 DOI: 10.1007/S12042-011-9088-Z |
0.418 |
|
| 2012 |
Sharma MK, Sharma R, Cao P, Jenkins J, Bartley LE, Qualls M, Grimwood J, Schmutz J, Rokhsar D, Ronald PC. A genome-wide survey of switchgrass genome structure and organization. Plos One. 7: e33892. PMID 22511929 DOI: 10.1371/Journal.Pone.0033892 |
0.49 |
|
| 2012 |
Jung S, Cestaro A, Troggio M, Main D, Zheng P, Cho I, Folta KM, Sosinski B, Abbott A, Celton JM, Arús P, Shulaev V, Verde I, Morgante M, Rokhsar D, et al. Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies. Bmc Genomics. 13: 129. PMID 22475018 DOI: 10.1186/1471-2164-13-129 |
0.429 |
|
| 2012 |
Grigoriev IV, Nordberg H, Shabalov I, Aerts A, Cantor M, Goodstein D, Kuo A, Minovitsky S, Nikitin R, Ohm RA, Otillar R, Poliakov A, Ratnere I, Riley R, Smirnova T, ... Rokhsar D, et al. The Genome Portal of the Department of Energy Joint Genome Institute Nucleic Acids Research. 40: D26-D32. PMID 22110030 DOI: 10.1093/Nar/Gkr947 |
0.459 |
|
| 2012 |
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research. 40: D1178-86. PMID 22110026 DOI: 10.1093/Nar/Gkr944 |
0.738 |
|
| 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, ... ... Rokhsar DS, 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 |
0.615 |
|
| 2011 |
Jiang Z, Michal JJ, Beckman KB, Lyons JB, Zhang M, Pan Z, Rokhsar DS, Harland RM. Development and initial characterization of a HAPPY panel for mapping the X. tropicalis genome. International Journal of Biological Sciences. 7: 1037-44. PMID 21912511 DOI: 10.7150/Ijbs.7.1037 |
0.361 |
|
| 2011 |
Hellsten U, Aspden JL, Rio DC, Rokhsar DS. A segmental genomic duplication generates a functional intron. Nature Communications. 2: 454. PMID 21878908 DOI: 10.1038/Ncomms1461 |
0.423 |
|
| 2011 |
Chapman JA, Ho I, Sunkara S, Luo S, Schroth GP, Rokhsar DS. Meraculous: de novo genome assembly with short paired-end reads. Plos One. 6: e23501. PMID 21876754 DOI: 10.1371/Journal.Pone.0023501 |
0.634 |
|
| 2011 |
Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, ... ... Rokhsar D, et al. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science (New York, N.Y.). 332: 960-3. PMID 21551031 DOI: 10.1126/Science.1203810 |
0.392 |
|
| 2011 |
Tuskan G, Slavov G, DiFazio S, Muchero W, Pryia R, Schackwitz W, Martin J, Rokhsar D, Sykes R, Davis M, Studer M, Wyman C. Populus resequencing: towards genome-wide association studies Bmc Proceedings. 5. DOI: 10.1186/1753-6561-5-S7-I21 |
0.377 |
|
| 2011 |
Myburg A, Grattapaglia D, Tuskan G, Jenkins J, Schmutz J, Mizrachi E, Hefer C, Pappas G, Sterck L, Van De Peer Y, Hayes R, Rokhsar D. The Eucalyptus grandisGenome Project: Genome and transcriptome resources for comparative analysis of woody plant biology Bmc Proceedings. 5. DOI: 10.1186/1753-6561-5-S7-I20 |
0.48 |
|
| 2010 |
Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier ME, Mitros T, Richards GS, Conaco C, Dacre M, Hellsten U, Larroux C, Putnam NH, Stanke M, Adamska M, Darling A, ... ... Rokhsar DS, et al. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature. 466: 720-6. PMID 20686567 DOI: 10.1038/Nature09201 |
0.832 |
|
| 2010 |
Prochnik SE, Umen J, Nedelcu AM, Hallmann A, Miller SM, Nishii I, Ferris P, Kuo A, Mitros T, Fritz-Laylin LK, Hellsten U, Chapman J, Simakov O, Rensing SA, Terry A, ... ... Rokhsar DS, et al. Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri. Science (New York, N.Y.). 329: 223-6. PMID 20616280 DOI: 10.1126/Science.1188800 |
0.603 |
|
| 2010 |
Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, ... ... Rokhsar DS, et al. The genome of the Western clawed frog Xenopus tropicalis. Science (New York, N.Y.). 328: 633-6. PMID 20431018 DOI: 10.1126/Science.1183670 |
0.83 |
|
| 2010 |
Wang J, Roe B, Macmil S, Yu Q, Murray JE, Tang H, Chen C, Najar F, Wiley G, Bowers J, Van Sluys MA, Rokhsar DS, Hudson ME, Moose SP, Paterson AH, et al. Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes. Bmc Genomics. 11: 261. PMID 20416060 DOI: 10.1186/1471-2164-11-261 |
0.396 |
|
| 2010 |
Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T, Weinmaier T, Rattei T, Balasubramanian PG, Borman J, Busam D, Disbennett K, Pfannkoch C, Sumin N, Sutton GG, Viswanathan LD, ... ... Rokhsar DS, et al. The dynamic genome of Hydra. Nature. 464: 592-6. PMID 20228792 DOI: 10.1038/Nature08830 |
0.805 |
|
| 2010 |
Fritz-Laylin LK, Prochnik SE, Ginger ML, Dacks JB, Carpenter ML, Field MC, Kuo A, Paredez A, Chapman J, Pham J, Shu S, Neupane R, Cipriano M, Mancuso J, Tu H, ... ... Rokhsar DS, et al. The genome of Naegleria gruberi illuminates early eukaryotic versatility. Cell. 140: 631-42. PMID 20211133 DOI: 10.1016/J.Cell.2010.01.032 |
0.676 |
|
| 2010 |
Vogel JP, Garvin DF, Mockler TC, Schmutz J, Rokhsar D, Bevan MW, Barry K, Lucas S, Harmon-Smith M, Lail K, Tice H, Grimwood J, McKenzie N, Huo N, Gu YQ, et al. Genome sequencing and analysis of the model grass Brachypodium distachyon Nature. 463: 763-768. PMID 20148030 DOI: 10.1038/Nature08747 |
0.467 |
|
| 2010 |
Swaminathan K, Alabady MS, Varala K, De Paoli E, Ho I, Rokhsar DS, Arumuganathan AK, Ming R, Green PJ, Meyers BC, Moose SP, Hudson ME. Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses. Genome Biology. 11: R12. PMID 20128909 DOI: 10.1186/Gb-2010-11-2-R12 |
0.415 |
|
| 2010 |
Wang S, Peatman E, Abernathy J, Waldbieser G, Lindquist E, Richardson P, Lucas S, Wang M, Li P, Thimmapuram J, Liu L, Vullaganti D, Kucuktas H, Murdock C, Small BC, ... ... Rokhsar D, et al. Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biology. 11: R8. PMID 20096101 DOI: 10.1186/Gb-2010-11-1-R8 |
0.453 |
|
| 2010 |
Srivastava M, Larroux C, Lu DR, Mohanty K, Chapman J, Degnan BM, Rokhsar DS. Early evolution of the LIM homeobox gene family. Bmc Biology. 8: 4. PMID 20082688 DOI: 10.1186/1741-7007-8-4 |
0.66 |
|
| 2010 |
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, ... ... Rokhsar D, et al. Genome sequence of the palaeopolyploid soybean. Nature. 463: 178-83. PMID 20075913 DOI: 10.1038/Nature08670 |
0.498 |
|
| 2010 |
Jackson DJ, McDougall C, Woodcroft B, Moase P, Rose RA, Kube M, Reinhardt R, Rokhsar DS, Montagnani C, Joubert C, Piquemal D, Degnan BM. Parallel evolution of nacre building gene sets in molluscs. Molecular Biology and Evolution. 27: 591-608. PMID 19915030 DOI: 10.1093/molbev/msp278 |
0.351 |
|
| 2010 |
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, ... ... Rokhsar D, et al. Erratum: Genome sequence of the palaeopolyploid soybean Nature. 465: 120-120. DOI: 10.1038/Nature08957 |
0.43 |
|
| 2009 |
Kawashima T, Kawashima S, Tanaka C, Murai M, Yoneda M, Putnam NH, Rokhsar DS, Kanehisa M, Satoh N, Wada H. Domain shuffling and the evolution of vertebrates. Genome Research. 19: 1393-403. PMID 19443856 DOI: 10.1101/Gr.087072.108 |
0.667 |
|
| 2009 |
Jiang Z, Rokhsar DS, Harland RM. Old can be new again: HAPPY whole genome sequencing, mapping and assembly. International Journal of Biological Sciences. 5: 298-303. PMID 19381348 DOI: 10.7150/Ijbs.5.298 |
0.443 |
|
| 2009 |
Martinez D, Challacombe J, Morgenstern I, Hibbett D, Schmoll M, Kubicek CP, Ferreira P, Ruiz-Duenas FJ, Martinez AT, Kersten P, Hammel KE, Vanden Wymelenberg A, Gaskell J, Lindquist E, Sabat G, ... ... Rokhsar D, et al. Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proceedings of the National Academy of Sciences of the United States of America. 106: 1954-9. PMID 19193860 DOI: 10.1073/Pnas.0809575106 |
0.376 |
|
| 2009 |
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, ... ... Rokhsar DS, et al. The Sorghum bicolor genome and the diversification of grasses. Nature. 457: 551-6. PMID 19189423 DOI: 10.1038/Nature07723 |
0.675 |
|
| 2009 |
Marlow HQ, Srivastava M, Matus DQ, Rokhsar D, Martindale MQ. Anatomy and development of the nervous system of Nematostella vectensis, an anthozoan cnidarian. Developmental Neurobiology. 69: 235-54. PMID 19170043 DOI: 10.1002/Dneu.20698 |
0.541 |
|
| 2008 |
Sela DA, Chapman J, Adeuya A, Kim JH, Chen F, Whitehead TR, Lapidus A, Rokhsar DS, Lebrilla CB, German JB, Price NP, Richardson PM, Mills DA. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. Proceedings of the National Academy of Sciences of the United States of America. 105: 18964-9. PMID 19033196 DOI: 10.1073/Pnas.0809584105 |
0.603 |
|
| 2008 |
Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar RP, Rayko E, Salamov A, Vandepoele K, Beszteri B, Gruber A, ... ... Rokhsar DS, et al. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature. 456: 239-44. PMID 18923393 DOI: 10.1038/Nature07410 |
0.5 |
|
| 2008 |
Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, King N, Degnan BM, Rokhsar DS, Bartel DP. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature. 455: 1193-7. PMID 18830242 DOI: 10.1038/Nature07415 |
0.51 |
|
| 2008 |
Horton AC, Mahadevan NR, Minguillon C, Osoegawa K, Rokhsar DS, Ruvinsky I, de Jong PJ, Logan MP, Gibson-Brown JJ. Conservation of linkage and evolution of developmental function within the Tbx2/3/4/5 subfamily of T-box genes: implications for the origin of vertebrate limbs. Development Genes and Evolution. 218: 613-28. PMID 18815807 DOI: 10.1007/S00427-008-0249-5 |
0.422 |
|
| 2008 |
Opperman CH, Bird DM, Williamson VM, Rokhsar DS, Burke M, Cohn J, Cromer J, Diener S, Gajan J, Graham S, Houfek TD, Liu Q, Mitros T, Schaff J, Schaffer R, et al. Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism. Proceedings of the National Academy of Sciences of the United States of America. 105: 14802-7. PMID 18809916 DOI: 10.1073/Pnas.0805946105 |
0.438 |
|
| 2008 |
Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, Shen L, Donahue WF, Tusneem N, Stromberg MP, Stewart DA, Zhang L, Ranade SS, Warner JB, Lee CC, ... ... Rokhsar DS, et al. Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Research. 18: 1638-42. PMID 18775913 DOI: 10.1101/Gr.077776.108 |
0.584 |
|
| 2008 |
Srivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U, Kawashima T, Kuo A, Mitros T, Salamov A, Carpenter ML, Signorovitch AY, Moreno MA, Kamm K, Grimwood J, Schmutz J, ... ... Rokhsar DS, et al. The Trichoplax genome and the nature of placozoans. Nature. 454: 955-60. PMID 18719581 DOI: 10.1038/Nature07191 |
0.838 |
|
| 2008 |
Schierwater B, Kamm K, Srivastava M, Rokhsar D, Rosengarten RD, Dellaporta SL. The early ANTP gene repertoire: insights from the placozoan genome. Plos One. 3: e2457. PMID 18716659 DOI: 10.1371/Journal.Pone.0002457 |
0.661 |
|
| 2008 |
Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutiérrez EL, Dubchak I, Garcia-Fernà ndez J, Gibson-Brown JJ, Grigoriev IV, ... ... Rokhsar DS, et al. The amphioxus genome and the evolution of the chordate karyotype. Nature. 453: 1064-71. PMID 18563158 DOI: 10.1038/Nature06967 |
0.835 |
|
| 2008 |
Holland LZ, Albalat R, Azumi K, Benito-Gutiérrez E, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DE, Garcia-Fernà ndez J, Gibson-Brown JJ, Gissi C, Godzik A, ... ... Rokhsar DS, et al. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Research. 18: 1100-11. PMID 18562680 DOI: 10.1101/Gr.073676.107 |
0.796 |
|
| 2008 |
Hendrix DA, Hong JW, Zeitlinger J, Rokhsar DS, Levine MS. Promoter elements associated with RNA Pol II stalling in the Drosophila embryo. Proceedings of the National Academy of Sciences of the United States of America. 105: 7762-7. PMID 18505835 DOI: 10.1073/Pnas.0802406105 |
0.721 |
|
| 2008 |
Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EG, Grigoriev IV, Harris P, Jackson M, Kubicek CP, ... ... Rokhsar DS, et al. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nature Biotechnology. 26: 553-60. PMID 18454138 DOI: 10.1038/Nbt1403 |
0.737 |
|
| 2008 |
Larroux C, Luke GN, Koopman P, Rokhsar DS, Shimeld SM, Degnan BM. Genesis and expansion of metazoan transcription factor gene classes. Molecular Biology and Evolution. 25: 980-96. PMID 18296413 DOI: 10.1093/molbev/msn047 |
0.418 |
|
| 2008 |
King N, Westbrook MJ, Young SL, Kuo A, Abedin M, Chapman J, Fairclough S, Hellsten U, Isogai Y, Letunic I, Marr M, Pincus D, Putnam N, Rokas A, Wright KJ, ... ... Rokhsar D, et al. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature. 451: 783-8. PMID 18273011 DOI: 10.1038/Nature06617 |
0.801 |
|
| 2008 |
Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EGJ, Grigoriev IV, Harris P, Jackson M, Kubicek CP, ... ... Rokhsar DS, et al. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina) (Nature Biotechnology (2008) 26, (553-560)) Nature Biotechnology. 26: 1193. DOI: 10.1038/Nbt1008-1193A |
0.741 |
|
| 2008 |
Baker SE, Thykaer J, Adney WS, Brettin TS, Brockman FJ, D'haeseleer P, Martinez AD, Miller RM, Rokhsar DS, Schadt CW, Torok T, Tuskan G, Bennett J, Berka RM, Briggs SP, et al. Fungal genome sequencing and bioenergy Fungal Biology Reviews. 22: 1-5. DOI: 10.1016/J.Fbr.2008.03.001 |
0.446 |
|
| 2008 |
Holland LZ, Albalat R, Azumi K, Benito-Gutiérrez E, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DEK, Garcia-Fernàndez J, Gibson-Brown JJ, Gissi C, Godzik A, ... ... Rokhsar DS, et al. The amphioxus genome illuminates vertebrate origins and cephalochordate biology (Genome Research (2008) 18, (1100-1111)) Genome Research. 18: 1380. |
0.724 |
|
| 2007 |
Kawashima S, Kawashima T, Putnam NH, Rokhsar DS, Wada H, Kanehisa M. Comparative pair-wise domain-combinations for screening the clade specific domain-architectures in metazoan genomes. Genome Informatics. International Conference On Genome Informatics. 19: 50-60. PMID 18546504 DOI: 10.11234/Gi1990.19.50 |
0.701 |
|
| 2007 |
Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Maréchal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, ... ... Rokhsar DS, et al. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science (New York, N.Y.). 318: 245-50. PMID 17932292 DOI: 10.1126/Science.1143609 |
0.42 |
|
| 2007 |
Hellsten U, Khokha MK, Grammer TC, Harland RM, Richardson P, Rokhsar DS. Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis. Bmc Biology. 5: 31. PMID 17651506 DOI: 10.1186/1741-7007-5-31 |
0.498 |
|
| 2007 |
Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV, Jurka J, Genikhovich G, Grigoriev IV, Lucas SM, Steele RE, ... ... Rokhsar DS, et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science (New York, N.Y.). 317: 86-94. PMID 17615350 DOI: 10.1126/Science.1139158 |
0.83 |
|
| 2007 |
Kelleher CT, Chiu R, Shin H, Bosdet IE, Krzywinski MI, Fjell CD, Wilkin J, Yin T, DiFazio SP, Ali J, Asano JK, Chan S, Cloutier A, Girn N, Leach S, ... ... Rokhsar D, et al. A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. The Plant Journal : For Cell and Molecular Biology. 50: 1063-78. PMID 17488239 DOI: 10.1111/J.1365-313X.2007.03112.X |
0.729 |
|
| 2007 |
Palenik B, Grimwood J, Aerts A, Rouzé P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S, Zhou K, Otillar R, Merchant SS, Podell S, Gaasterland T, ... ... Rokhsar D, et al. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proceedings of the National Academy of Sciences of the United States of America. 104: 7705-10. PMID 17460045 DOI: 10.1073/Pnas.0611046104 |
0.727 |
|
| 2007 |
Larroux C, Fahey B, Degnan SM, Adamski M, Rokhsar DS, Degnan BM. The NK homeobox gene cluster predates the origin of Hox genes. Current Biology : Cb. 17: 706-10. PMID 17379523 DOI: 10.1016/j.cub.2007.03.008 |
0.365 |
|
| 2007 |
Montsant A, Allen AE, Coesel S, Martino AD, Falciatore A, Mangogna M, Siaut M, Heijde M, Jabbari K, Maheswari U, Rayko E, Vardi A, Apt KE, Berges JA, Chiovitti A, ... ... Rokhsar DS, et al. Identification and comparative genomic analysis of signaling and regulatory components in the diatom Thalassiosira pseudonana Journal of Phycology. 43: 585-604. DOI: 10.1111/J.1529-8817.2007.00342.X |
0.427 |
|
| 2006 |
Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CM, Dorrance AE, Dou D, Dickerman AW, ... ... Rokhsar DS, et al. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science (New York, N.Y.). 313: 1261-6. PMID 16946064 DOI: 10.1126/Science.1128796 |
0.795 |
|
| 2006 |
Sullivan JC, Ryan JF, Watson JA, Webb J, Mullikin JC, Rokhsar D, Finnerty JR. StellaBase: the Nematostella vectensis Genomics Database. Nucleic Acids Research. 34: D495-9. PMID 16381919 DOI: 10.1093/Nar/Gkj020 |
0.486 |
|
| 2006 |
Shoguchi E, Kawashima T, Satou Y, Hamaguchi M, Sin-I T, Kohara Y, Putnam N, Rokhsar DS, Satoh N. Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis. Genome Research. 16: 297-303. PMID 16354750 DOI: 10.1101/gr.4156606 |
0.424 |
|
| 2006 |
Jackson SA, Rokhsar D, Stacey G, Shoemaker RC, Schmutz J, Grimwood J. Toward a reference sequence of the soybean genome: A multiagency effort Crop Science. 46: S-55-S-61. DOI: 10.2135/Cropsci2006.08.0514Tpg |
0.445 |
|
| 2005 |
Keys DN, Lee BI, Di Gregorio A, Harafuji N, Detter JC, Wang M, Kahsai O, Ahn S, Zhang C, Doyle SA, Satoh N, Satou Y, Saiga H, Christian AT, Rokhsar DS, et al. A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis. Proceedings of the National Academy of Sciences of the United States of America. 102: 679-83. PMID 15647365 DOI: 10.1073/Pnas.0408952102 |
0.572 |
|
| 2005 |
Mahony S, Hendrix D, Golden A, Smith TJ, Rokhsar DS. Transcription factor binding site identification using the self-organizing map. Bioinformatics (Oxford, England). 21: 1807-14. PMID 15647296 DOI: 10.1093/Bioinformatics/Bti256 |
0.628 |
|
| 2004 |
Martin J, Han C, Gordon LA, Terry A, Prabhakar S, She X, Xie G, Hellsten U, Chan YM, Altherr M, Couronne O, Aerts A, Bajorek E, Black S, Blumer H, ... ... Rokhsar DS, et al. The sequence and analysis of duplication-rich human chromosome 16. Nature. 432: 988-94. PMID 15616553 DOI: 10.1038/Nature03187 |
0.375 |
|
| 2004 |
Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, ... ... Rokhsar DS, et al. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science (New York, N.Y.). 306: 79-86. PMID 15459382 DOI: 10.1126/Science.1101156 |
0.734 |
|
| 2004 |
Schmutz J, Martin J, Terry A, Couronne O, Grimwood J, Lowry S, Gordon LA, Scott D, Xie G, Huang W, Hellsten U, Tran-Gyamfi M, She X, Prabhakar S, Aerts A, ... ... Rokhsar DS, et al. The DNA sequence and comparative analysis of human chromosome 5. Nature. 431: 268-74. PMID 15372022 DOI: 10.1038/Nature02919 |
0.393 |
|
| 2004 |
Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D, Richardson PM, DeLong EF. Reverse methanogenesis: testing the hypothesis with environmental genomics. Science (New York, N.Y.). 305: 1457-62. PMID 15353801 DOI: 10.1126/Science.1100025 |
0.367 |
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| 2004 |
Martinez D, Larrondo LF, Putnam N, Gelpke MD, Huang K, Chapman J, Helfenbein KG, Ramaiya P, Detter JC, Larimer F, Coutinho PM, Henrissat B, Berka R, Cullen D, Rokhsar D. Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nature Biotechnology. 22: 695-700. PMID 15122302 DOI: 10.1038/Nbt967 |
0.656 |
|
| 2004 |
Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O, Tran-Gyamfi M, Aerts A, Altherr M, Ashworth L, Bajorek E, Black S, ... ... Rokhsar DS, et al. The DNA sequence and biology of human chromosome 19. Nature. 428: 529-35. PMID 15057824 DOI: 10.1038/Nature02399 |
0.392 |
|
| 2004 |
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 428: 37-43. PMID 14961025 DOI: 10.1038/Nature02340 |
0.658 |
|
| 2003 |
Gibson-Brown JJ, Osoegawa K, McPherson JD, Waterston RH, De Jong PJ, Rokhsar DS, Holland LZ. A proposal to sequence the amphioxus genome submitted to the Joint Genome Institute of the US Department of Energy. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 300: 5-22. PMID 14984031 DOI: 10.1002/Jez.B.42 |
0.437 |
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| 2003 |
Grossman AR, Harris EE, Hauser C, Lefebvre PA, Martinez D, Rokhsar D, Shrager J, Silflow CD, Stern D, Vallon O, Zhang Z. Chlamydomonas reinhardtii at the crossroads of genomics. Eukaryotic Cell. 2: 1137-50. PMID 14665449 DOI: 10.1128/Ec.2.6.1137-1150.2003 |
0.356 |
|
| 2003 |
Azumi K, De Santis R, De Tomaso A, Rigoutsos I, Yoshizaki F, Pinto MR, Marino R, Shida K, Ikeda M, Ikeda M, Arai M, Inoue Y, Shimizu T, Satoh N, Rokhsar DS, et al. Genomic analysis of immunity in a Urochordate and the emergence of the vertebrate immune system: "waiting for Godot". Immunogenetics. 55: 570-81. PMID 14530883 DOI: 10.1007/s00251-003-0606-5 |
0.399 |
|
| 2003 |
Yagi K, Satou Y, Mazet F, Shimeld SM, Degnan B, Rokhsar D, Levine M, Kohara Y, Satoh N. A genomewide survey of developmentally relevant genes in Ciona intestinalis. III. Genes for Fox, ETS, nuclear receptors and NFkappaB. Development Genes and Evolution. 213: 235-44. PMID 12743820 DOI: 10.1007/S00427-003-0322-Z |
0.63 |
|
| 2003 |
Wada S, Tokuoka M, Shoguchi E, Kobayashi K, Di Gregorio A, Spagnuolo A, Branno M, Kohara Y, Rokhsar D, Levine M, Saiga H, Satoh N, Satou Y. A genomewide survey of developmentally relevant genes in Ciona intestinalis. II. Genes for homeobox transcription factors. Development Genes and Evolution. 213: 222-34. PMID 12736825 DOI: 10.1007/S00427-003-0321-0 |
0.606 |
|
| 2003 |
Satou Y, Imai KS, Levine M, Kohara Y, Rokhsar D, Satoh N. A genomewide survey of developmentally relevant genes in Ciona intestinalis. I. Genes for bHLH transcription factors. Development Genes and Evolution. 213: 213-21. PMID 12736824 DOI: 10.1007/S00427-003-0319-7 |
0.659 |
|
| 2002 |
Detter JC, Jett JM, Lucas SM, Dalin E, Arellano AR, Wang M, Nelson JR, Chapman J, Lou Y, Rokhsar D, Hawkins TL, Richardson PM. Isothermal strand-displacement amplification applications for high-throughput genomics Genomics. 80: 691-698. PMID 12523365 DOI: 10.1006/Geno.2002.7020 |
0.62 |
|
| 2002 |
Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, Harafuji N, Hastings KE, Ho I, Hotta K, Huang W, ... ... Rokhsar DS, et al. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science (New York, N.Y.). 298: 2157-67. PMID 12481130 DOI: 10.1126/Science.1080049 |
0.756 |
|
| 2002 |
Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MD, Roach J, Oh T, Ho IY, Wong M, ... ... Rokhsar D, et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science (New York, N.Y.). 297: 1301-10. PMID 12142439 DOI: 10.1126/Science.1072104 |
0.684 |
|
| 2001 |
Dehal P, Predki P, Olsen AS, Kobayashi A, Folta P, Lucas S, Land M, Terry A, Ecale Zhou CL, Rash S, Zhang Q, Gordon L, Kim J, Elkin C, Pollard MJ, ... ... Rokhsar D, et al. Human chromosome 19 and related regions in mouse: conservative and lineage-specific evolution. Science (New York, N.Y.). 293: 104-11. PMID 11441184 DOI: 10.1126/Science.1060310 |
0.427 |
|
| 2001 |
Butts DA, Rokhsar DS. The information content of spontaneous retinal waves. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 21: 961-73. PMID 11157082 DOI: 10.1523/Jneurosci.21-03-00961.2001 |
0.613 |
|
| 1999 |
Butts DA, Feller MB, Shatz CJ, Rokhsar DS. Retinal waves are governed by collective network properties. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 19: 3580-93. PMID 10212317 DOI: 10.1523/Jneurosci.19-09-03580.1999 |
0.701 |
|
| 1999 |
Butts DA, Rokhsar DS. Predicted signatures of rotating Bose-Einstein condensates Nature. 397: 327-329. DOI: 10.1038/16865 |
0.611 |
|
| 1997 |
Feller MB, Butts DA, Aaron HL, Rokhsar DS, Shatz CJ. Dynamic processes shape spatiotemporal properties of retinal waves. Neuron. 19: 293-306. PMID 9292720 DOI: 10.1016/S0896-6273(00)80940-X |
0.701 |
|
| 1997 |
Butts DA, Rokhsar DS. Trapped Fermi gases Physical Review a - Atomic, Molecular, and Optical Physics. 55: 4346-4350. DOI: 10.1103/Physreva.55.4346 |
0.596 |
|
| 1996 |
Singh KG, Rokhsar DS. Collective Excitations of a Confined Bose Condensate. Physical Review Letters. 77: 1667-1670. PMID 10063141 DOI: 10.1103/Physrevlett.77.1667 |
0.619 |
|
| 1996 |
Deaven DM, Rokhsar DS. Variational evidence for spin liquids in frustrated lattices. Physical Review. B, Condensed Matter. 53: 14966-14970. PMID 9983290 DOI: 10.1103/Physrevb.53.14966 |
0.708 |
|
| 1996 |
Butts DA, Rokhsar DS. Trapped Fermi gases Phys. Rev. a 55 (1997) 4346. DOI: 10.1103/PhysRevA.55.4346 |
0.552 |
|
| 1996 |
Deaven DM, Rokhsar DS. Variational evidence for spin liquids in frustrated lattices Physical Review B - Condensed Matter and Materials Physics. 53: 14966-14970. |
0.682 |
|
| 1995 |
Lammert PE, Rokhsar DS, Chakravarty S, Kivelson S, Salkola MI. Metallic screening and correlation effects in superconducting fullerenes. Physical Review Letters. 74: 996-999. PMID 10058901 DOI: 10.1103/Physrevlett.74.996 |
0.571 |
|
| 1995 |
Deaven DM, Lammert PE, Rokhsar DS. Pairing in alkaline-earth-metal-doped fullerenes. Physical Review. B, Condensed Matter. 52: 16377-16380. PMID 9981034 |
0.752 |
|
| 1995 |
Toner J, Lammert PE, Rokhsar DS. Topology and nematic ordering. II. Observable critical behavior. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 52: 1801-1810. PMID 9963599 DOI: 10.1103/Physreve.52.1801 |
0.571 |
|
| 1995 |
Lammert PE, Rokhsar DS, Toner J. Topology and nematic ordering. I. A gauge theory. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 52: 1778-1800. PMID 9963598 DOI: 10.1103/Physreve.52.1778 |
0.582 |
|
| 1995 |
Lammert PE, Rokhsar DS, Chakravarty S, Kivelson S, Salkola MI. Metallic screening and correlation effects in superconducting fullerenes Physical Review Letters. 74: 996-999. DOI: 10.1103/PhysRevLett.74.996 |
0.521 |
|
| 1995 |
Toner J, Lammert PE, Rokhsar DS. Topology and nematic ordering. II. Observable critical behavior Physical Review E. 52: 1801-1810. DOI: 10.1103/PhysRevE.52.1801 |
0.519 |
|
| 1995 |
Lammert PE, Rokhsar DS, Toner J. Topology and nematic ordering. I. A gauge theory Physical Review E. 52: 1778-1800. DOI: 10.1103/PhysRevE.52.1778 |
0.519 |
|
| 1995 |
Deaven DM, Lammert PE, Rokhsar DS. Pairing in alkaline-earth-metal-doped fullerenes Physical Review B. 52: 16377-16380. DOI: 10.1103/PhysRevB.52.16377 |
0.752 |
|
| 1994 |
Singh KG, Rokhsar DS. Disordered bosons: Condensate and excitations. Physical Review. B, Condensed Matter. 49: 9013-9023. PMID 10009681 DOI: 10.1103/Physrevb.49.9013 |
0.631 |
|
| 1993 |
Lammert PE, Rokhsar DS, Toner J. Topology and nematic ordering. Physical Review Letters. 70: 1650-1653. PMID 10053349 DOI: 10.1103/Physrevlett.70.1650 |
0.58 |
|
| 1993 |
Deaven DM, Rokhsar DS. Isotopic disorder in superconducting fullerenes. Physical Review. B, Condensed Matter. 48: 4114-4118. PMID 10008863 DOI: 10.1103/Physrevb.48.4114 |
0.703 |
|
| 1993 |
Lammert PE, Rokhsar DS. Electronic pairing mechanism in fullerenes: Interactions and correlations. Physical Review. B, Condensed Matter. 48: 4103-4113. PMID 10008862 DOI: 10.1103/Physrevb.48.4103 |
0.58 |
|
| 1993 |
Lammert PE, Rokhsar DS. Isotopic disorder and the electronic pairing mechanism in superconducting fullerenes. Physical Review. B, Condensed Matter. 48: 1310-1313. PMID 10008001 DOI: 10.1103/Physrevb.48.1310 |
0.569 |
|
| 1993 |
Deaven DM, Rokhsar DS. Isotopic disorder in superconducting fullerenes Physical Review B. 48: 4114-4118. DOI: 10.1103/PhysRevB.48.4114 |
0.679 |
|
| 1993 |
Lammert PE, Rokhsar DS. Electronic pairing mechanism in fullerenes: Interactions and correlations Physical Review B. 48: 4103-4113. DOI: 10.1103/PhysRevB.48.4103 |
0.522 |
|
| 1993 |
Lammert PE, Rokhsar DS. Isotopic disorder and the electronic pairing mechanism in superconducting fullerenes Physical Review B. 48: 1310-1313. DOI: 10.1103/PhysRevB.48.1310 |
0.525 |
|
| 1992 |
Singh KG, Rokhsar DS. Real-space renormalization study of disordered interacting bosons. Physical Review. B, Condensed Matter. 46: 3002-3008. PMID 10003994 DOI: 10.1103/Physrevb.46.3002 |
0.637 |
|
| 1992 |
Barbieri A, Deaven DM, Rokhsar DS. Gutzwiller projection with embedded clusters. Physical Review. B, Condensed Matter. 45: 8288-8299. PMID 10000660 |
0.674 |
|
| 1992 |
Barbieri A, Deaven DM, Rokhsar DS. Gutzwiller projection with embedded clusters Physical Review B. 45: 8288-8299. DOI: 10.1103/PhysRevB.45.8288 |
0.674 |
|
| 1991 |
Deaven DM, Rokhsar DS, Johnson M. Simple theory of exchange coupling in transition-metal magnetic multilayers. Physical Review. B, Condensed Matter. 44: 5977-5980. PMID 9998459 |
0.687 |
|
| 1991 |
Rabson DA, Mermin ND, Rokhsar DS, Wright DC. The space groups of axial crystals and quasicrystals Reviews of Modern Physics. 63: 699-733. DOI: 10.1103/Revmodphys.63.699 |
0.478 |
|
| 1991 |
Deaven DM, Rokhsar DS, Johnson M. Simple theory of exchange coupling in transition-metal magnetic multilayers Physical Review B. 44: 5977-5980. DOI: 10.1103/PhysRevB.44.5977 |
0.687 |
|
| 1990 |
Gronlund LD, Wright DC, Sethna JP, Rokhsar DS. Constrained spin model of phason dynamics in quasicrystals. Physical Review. B, Condensed Matter. 42: 8517-8536. PMID 9995028 DOI: 10.1103/PhysRevB.42.8517 |
0.493 |
|
| 1990 |
Mermin ND, Rabson DA, Rokhsar DS, Wright DC. Stacking quasicrystallographic lattices. Physical Review. B, Condensed Matter. 41: 10498-10502. PMID 9993457 DOI: 10.1103/Physrevb.41.10498 |
0.483 |
|
| 1990 |
Mermin ND, Rabson DA, Rokhsar DS, Wright DC. Stacking quasicrystallographic lattices Physical Review B. 41: 10498-10502. DOI: 10.1103/PhysRevB.41.10498 |
0.421 |
|
| 1989 |
Kivelson SA, Rokhsar DS, Sethna JP, Shore JD. Reply to "Neutral-fermion-soliton statistics in the short-range resonating-valence-bond state: A reevaluation" Physical Review. B, Condensed Matter. 40: 7343-7344. PMID 9991137 |
0.447 |
|
| 1989 |
Kivelson SA, Rokhsar DS, Sethna JP, Shore JD. Reply to Neutral-fermion-soliton statistics in the short-range resonating-valence-bond state: A reevaluation Physical Review B. 40: 7343-7344. DOI: 10.1103/PhysRevB.40.7343 |
0.447 |
|
| 1988 |
Rokhsar DS, Wright DC, Mermin ND. Scale equivalence of quasicrystallographic space groups. Physical Review. B, Condensed Matter. 37: 8145-8149. PMID 9944146 DOI: 10.1103/Physrevb.37.8145 |
0.476 |
|
| 1988 |
Kivelson SA, Rokhsar DS, Sethna JP. 2e or not 2e: Flux quantization in the resonating valence bond state Epl. 6: 353-358. DOI: 10.1209/0295-5075/6/4/013 |
0.511 |
|
| 1988 |
Rokhsar DS, Wright DC, Mermin ND. The two‐dimensional quasicrystallographic space groups with rotational symmetries less than 23‐fold Acta Crystallographica Section A. 44: 197-211. DOI: 10.1107/S0108767387010511 |
0.48 |
|
| 1988 |
Rokhsar DS, Wright DC, Mermin ND. Scale equivalence of quasicrystallographic space groups Physical Review B. 37: 8145-8149. DOI: 10.1103/PhysRevB.37.8145 |
0.413 |
|
| 1987 |
Mermin ND, Rokhsar DS, Wright DC. Beware of 46-fold symmetry: The classification of two-dimensional quasicrystallographic lattices. Physical Review Letters. 58: 2099-2101. PMID 10034648 DOI: 10.1103/Physrevlett.58.2099 |
0.475 |
|
| 1987 |
Kivelson SA, Rokhsar DS, Sethna JP. Topology of the resonating valence-bond state: Solitons and high-Tc superconductivity. Physical Review. B, Condensed Matter. 35: 8865-8868. PMID 9941277 DOI: 10.1103/Physrevb.35.8865 |
0.519 |
|
| 1987 |
Rokhsar DS, Mermin ND, Wright DC. Rudimentary quasicrystallography: The icosahedral and decagonal reciprocal lattices. Physical Review. B, Condensed Matter. 35: 5487-5495. PMID 9940757 DOI: 10.1103/Physrevb.35.5487 |
0.488 |
|
| 1987 |
Mermin ND, Rokhsar DS, Wright DC. Beware of 46-Fold symmetry: The classification of two-dimensional quasicrystallographic lattices Physical Review Letters. 58: 2099-2101. DOI: 10.1103/PhysRevLett.58.2099 |
0.412 |
|
| 1987 |
Rokhsar DS, Mermin ND, Wright DC. Rudimentary quasicrystallography: The icosahedral and decagonal reciprocal lattices Physical Review B. 35: 5487-5495. DOI: 10.1103/PhysRevB.35.5487 |
0.426 |
|
| 1986 |
Rokhsar DS, Sethna JP. Quasicrystalline textures of cholesteric liquid crystals: Blue phase III? Physical Review Letters. 56: 1727-1730. PMID 10032753 DOI: 10.1103/PhysRevLett.56.1727 |
0.49 |
|
| 1986 |
Rokhsar DS, Anderson PW, Stein DL. Self-organization in prebiological systems: simulations of a model for the origin of genetic information. Journal of Molecular Evolution. 23: 119-26. PMID 3091843 DOI: 10.1007/BF02099906 |
0.658 |
|
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