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Phylogenomics illuminates the evolution of bobtail and bottletail squid (order Sepiolida).
Published in:
Communications Biology, 2021, v. 4, p. 1, doi. 10.1038/s42003-021-02348-y
By:
- Sanchez, Gustavo;
- Fernández-Álvarez, Fernando Á.;
- Taite, Morag;
- Sugimoto, Chikatoshi;
- Jolly, Jeffrey;
- Simakov, Oleg;
- Marlétaz, Ferdinand;
- Allcock, Louise;
- Rokhsar, Daniel S.
Publication type:
Article
Phytozome: a comparative platform for green plant genomics.
Published in:
Nucleic Acids Research, 2012, p. D1178, doi. 10.1093/nar/gkr944
By:
- Goodstein, David M.;
- Shu, Shengqiang;
- Howson, Russell;
- Neupane, Rochak;
- Hayes, Richard D.;
- Fazo, Joni;
- Mitros, Therese;
- Dirks, William;
- Hellsten, Uffe;
- Putnam, Nicholas ;
- Rokhsar, Daniel S.
Publication type:
Article
Genome and transcriptome mechanisms driving cephalopod evolution.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-29748-w
By:
- Albertin, Caroline B.;
- Medina-Ruiz, Sofia;
- Mitros, Therese;
- Schmidbaur, Hannah;
- Sanchez, Gustavo;
- Wang, Z. Yan;
- Grimwood, Jane;
- Rosenthal, Joshua J. C.;
- Ragsdale, Clifton W.;
- Simakov, Oleg;
- Rokhsar, Daniel S.
Publication type:
Article
Diversification of mandarin citrus by hybrid speciation and apomixis.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-24653-0
By:
- Wu, Guohong Albert;
- Sugimoto, Chikatoshi;
- Kinjo, Hideyasu;
- Azama, Chika;
- Mitsube, Fumimasa;
- Talon, Manuel;
- Gmitter, Frederick G.;
- Rokhsar, Daniel S.
Publication type:
Article
Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans.
Published in:
Nature Structural & Molecular Biology, 2010, v. 17, n. 8, p. 1030, doi. 10.1038/nsmb.1841
By:
- Taft, Ryan J.;
- Simons, Cas;
- Nahkuri, Satu;
- Oey, Harald;
- Korbie, Darren J.;
- Mercer, Timothy R.;
- Holst, Jeff;
- Ritchie, William;
- Wong, Justin J.-L.;
- Rasko, John E. J.;
- Rokhsar, Daniel S.;
- Degnan, Bernard M.;
- Mattick, John S.
Publication type:
Article
A chromosome‐scale reference genome of trifoliate orange (Poncirus trifoliata) provides insights into disease resistance, cold tolerance and genome evolution in Citrus.
Published in:
Plant Journal, 2020, v. 104, n. 5, p. 1215, doi. 10.1111/tpj.14993
By:
- Peng, Ze;
- Bredeson, Jessen V.;
- Wu, Guohong A.;
- Shu, Shengqiang;
- Rawat, Nidhi;
- Du, Dongliang;
- Parajuli, Saroj;
- Yu, Qibin;
- You, Qian;
- Rokhsar, Daniel S.;
- Gmitter, Frederick G.;
- Deng, Zhanao
Publication type:
Article
Anchoring and ordering NGS contig assemblies by population sequencing ( POPSEQ).
Published in:
Plant Journal, 2013, v. 76, n. 4, p. 718, doi. 10.1111/tpj.12319
By:
- Mascher, Martin;
- Muehlbauer, Gary J.;
- Rokhsar, Daniel S.;
- Chapman, Jarrod;
- Schmutz, Jeremy;
- Barry, Kerrie;
- Muñoz‐Amatriaín, María;
- Close, Timothy J.;
- Wise, Roger P.;
- Schulman, Alan H.;
- Himmelbach, Axel;
- Mayer, Klaus F.X.;
- Scholz, Uwe;
- Poland, Jesse A.;
- Stein, Nils;
- Waugh, Robbie
Publication type:
Article
Tracing cancer evolution and heterogeneity using Hi-C.
Published in:
Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-42651-2
By:
- Erdmann-Pham, Dan Daniel;
- Batra, Sanjit Singh;
- Turkalo, Timothy K.;
- Durbin, James;
- Blanchette, Marco;
- Yeh, Iwei;
- Shain, Hunter;
- Bastian, Boris C.;
- Song, Yun S.;
- Rokhsar, Daniel S.;
- Hockemeyer, Dirk
Publication type:
Article
Transposon signatures of allopolyploid genome evolution.
Published in:
Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-38560-z
By:
- Session, Adam M.;
- Rokhsar, Daniel S.
Publication type:
Article
Meraculous: de novo genome assembly with short paired-end reads.
Published in:
PLoS ONE, 2011, v. 6, n. 8, p. 1, doi. 10.1371/journal.pone.0023501
By:
- Chapman, Jarrod A.;
- Ho, Isaac;
- Sirisha Sunkara;
- Shujun Luo;
- Schroth, Gary P.;
- Rokhsar, Daniel S.
Publication type:
Article
Correction to: Current status and impending progress for cassava structural genomics.
Published in:
2022
By:
- Lyons, Jessica B.;
- Bredeson, Jessen V.;
- Mansfeld, Ben N.;
- Bauchet, Guillaume Jean;
- Berry, Jeffrey;
- Boyher, Adam;
- Mueller, Lukas A.;
- Rokhsar, Daniel S.;
- Bart, Rebecca S.
Publication type:
Correction Notice
Current status and impending progress for cassava structural genomics.
Published in:
Plant Molecular Biology, 2022, v. 109, n. 3, p. 177, doi. 10.1007/s11103-020-01104-w
By:
- Lyons, Jessica B.;
- Bredeson, Jessen V.;
- Mansfeld, Ben N.;
- Bauchet, Guillaume Jean;
- Berry, Jeffrey;
- Boyher, Adam;
- Mueller, Lukas A.;
- Rokhsar, Daniel S.;
- Bart, Rebecca S.
Publication type:
Article
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.
Published in:
Development Genes & Evolution, 2008, v. 218, n. 11/12, p. 613, doi. 10.1007/s00427-008-0249-5
By:
- Horton, Amy C.;
- Mahadevan, Navin R.;
- Minguillon, Carolina;
- Osoegawa, Kazutoyo;
- Rokhsar, Daniel S.;
- Ruvinsky, Ilya;
- de Jong, Pieter J.;
- Logan, Malcolm P.;
- Gibson-Brown, Jeremy J.
Publication type:
Article
Analysis of meiosis in Pristionchus pacificus reveals plasticity in homolog pairing and synapsis in the nematode lineage.
Published in:
eLife, 2021, p. 1, doi. 10.7554/eLife.70990
By:
- Rillo-Bohn, Regina;
- Adilardi, Renzo;
- Mitros, Therese;
- Avşaroğlu, Barış;
- Stevens, Lewis;
- Köhler, Simone;
- Bayes, Joshua;
- Wang, Clara;
- Lin, Sabrina;
- Baskevitch, K. Alienor;
- Rokhsar, Daniel S.;
- Dernburg, Abby F.
Publication type:
Article
Chromosome-level genome assemblies of 2 hemichordates provide new insights into deuterostome origin and chromosome evolution.
Published in:
PLoS Biology, 2024, v. 22, n. 6, p. 1, doi. 10.1371/journal.pbio.3002661
By:
- Lin, Che-Yi;
- Marlétaz, Ferdinand;
- Pérez-Posada, Alberto;
- Martínez-García, Pedro Manuel;
- Schloissnig, Siegfried;
- Peluso, Paul;
- Conception, Greg T.;
- Bump, Paul;
- Chen, Yi-Chih;
- Chou, Cindy;
- Lin, Ching-Yi;
- Fan, Tzu-Pei;
- Tsai, Chang-Tai;
- Gómez Skarmeta, José Luis;
- Tena, Juan J.;
- Lowe, Christopher J.;
- Rank, David R.;
- Rokhsar, Daniel S.;
- Yu Jr, Kai;
- Su, Yi-Hsien
Publication type:
Article
Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals.
Published in:
Nature, 2008, v. 455, n. 7217, p. 1193, doi. 10.1038/nature07415
By:
- Grimson, Andrew;
- Srivastava, Mansi;
- Fahey, Bryony;
- Woodcroft, Ben J.;
- Chiang, H. Rosaria;
- King, Nicole;
- Degnan, Bernard M.;
- Rokhsar, Daniel S.;
- Bartel, David P.
Publication type:
Article
Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution.
Published in:
Communications Biology, 2020, v. 3, n. 1, p. N.PAG, doi. 10.1038/s42003-020-1096-9
By:
- Mudd, Austin B.;
- Bredeson, Jessen V.;
- Baum, Rachel;
- Hockemeyer, Dirk;
- Rokhsar, Daniel S.
Publication type:
Article
New bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu islands revealed by molecular and morphological analysis.
Published in:
Communications Biology, 2019, v. 2, n. 1, p. 1, doi. 10.1038/s42003-019-0661-6
By:
- Sanchez, Gustavo;
- Jolly, Jeffrey;
- Reid, Amanda;
- Sugimoto, Chikatoshi;
- Azama, Chika;
- Marlétaz, Ferdinand;
- Simakov, Oleg;
- Rokhsar, Daniel S.
Publication type:
Article
Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing.
Published in:
G3: Genes | Genomes | Genetics, 2015, v. 5, n. 7, p. 1463, doi. 10.1534/g3.115.017905
By:
- Glazer, Andrew M.;
- Killingbeck, Emily E.;
- Mitros, Therese;
- Rokhsar, Daniel S.;
- Miller, Craig T.
Publication type:
Article
Candidate genes for field resistance to cassava brown streak disease revealed through the analysis of multiple data sources.
Published in:
Frontiers in Plant Science, 2023, v. 14, p. 1, doi. 10.3389/fpls.2023.1270963
By:
- Ferguson, Morag E.;
- Eyles, Rodney P.;
- Garcia-Oliveira, Ana Luísa;
- Kapinga, Fortunus;
- Masumba, Esther A.;
- Amuge, Teddy;
- Bredeson, Jessen V.;
- Rokhsar, Daniel S.;
- Lyons, Jessica B.;
- Shah, Trushar;
- Rounsley, Steve;
- Mkamilo, Geoffrey
Publication type:
Article
CRISPR-Cas9-mediated knockout of CYP79D1 and CYP79D2 in cassava attenuates toxic cyanogen production.
Published in:
Frontiers in Plant Science, 2023, v. 14, p. 1, doi. 10.3389/fpls.2022.1079254
By:
- Gomez, Michael A.;
- Berkoff, Kodiak C.;
- Gill, Baljeet K.;
- Iavarone, Anthony T.;
- Lieberman, Samantha E.;
- Ma, Jessica M.;
- Schultink, Alex;
- Karavolias, Nicholas G.;
- Wyman, Stacia K.;
- Chauhan, Raj Deepika;
- Taylor, Nigel J.;
- Staskawicz, Brian J.;
- Myeong-Je Cho;
- Rokhsar, Daniel S.;
- Lyons, Jessica B.
Publication type:
Article
QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from Manihot glaziovii.
Published in:
Frontiers in Plant Science, 2017, p. 1, doi. 10.3389/fpls.2017.01168
By:
- Nzuki, Inosters;
- Katari, Manpreet S.;
- Bredeson, Jessen V.;
- Masumba, Esther;
- Kapinga, Fortunus;
- Salum, Kasele;
- Mkamilo, Geoffrey S.;
- Shah, Trushar;
- Lyons, Jessica B.;
- Rokhsar, Daniel S.;
- Rounsley, Steve;
- Myburg, Alexander A.;
- Ferguson, Morag E.
Publication type:
Article
A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome.
Published in:
Genome Biology, 2015, v. 16, n. 1, p. 281, doi. 10.1186/s13059-015-0582-8
By:
- Chapman, Jarrod A.;
- Mascher, Martin;
- Buluç, Aydın;
- Barry, Kerrie;
- Georganas, Evangelos;
- Session, Adam;
- Strnadova, Veronika;
- Jenkins, Jerry;
- Sehgal, Sunish;
- Oliker, Leonid;
- Schmutz, Jeremy;
- Yelick, Katherine A.;
- Scholz, Uwe;
- Waugh, Robbie;
- Poland, Jesse A.;
- Muehlbauer, Gary J.;
- Stein, Nils;
- Rokhsar, Daniel S.
Publication type:
Article
Early evolution of the LIM homeobox gene family.
Published in:
BMC Biology, 2010, v. 8, p. 1, doi. 10.1186/1741-7007-8-4
By:
- Srivastava, Mansi;
- Larroux, Claire;
- Lu, Daniel R.;
- Mohanty, Kareshma;
- Chapman, Jarrod;
- Degnan, Bernard M.;
- Rokhsar, Daniel S.
Publication type:
Article
Parallel Evolution of Nacre Building Gene Sets in Molluscs.
Published in:
Molecular Biology & Evolution, 2010, v. 27, n. 3, p. 591, doi. 10.1093/molbev/msp278
By:
- Jackson, Daniel J.;
- McDougall, Carmel;
- Woodcroft, Ben;
- Moase, Patrick;
- Rose, Robert A.;
- Kube, Michael;
- Reinhardt, Richard;
- Rokhsar, Daniel S.;
- Montagnani, Caroline;
- Joubert, Caroline;
- Piquemal, David;
- Degnan, Bernard M.
Publication type:
Article
Genesis and Expansion of Metazoan Transcription Factor Gene Classes.
Published in:
Molecular Biology & Evolution, 2008, v. 25, n. 5, p. 980, doi. 10.1093/molbev/msn047
By:
- Larroux, Claire;
- Luke, Graham N.;
- Koopman, Peter;
- Rokhsar, Daniel S.;
- Shimeld, Sebastian M.;
- Degnan, Bernard M.
Publication type:
Article
Community structure and metabolism through reconstruction of microbial genomes from the environment.
Published in:
Nature, 2004, v. 428, n. 6978, p. 37, doi. 10.1038/nature02340
By:
- Tyson, Gene W.;
- Chapman, Jarrod;
- Hugenholtz, Philip;
- Allen, Eric E.;
- Ram, Rachna J.;
- Richardson, Paul M.;
- Solovyev, Victor V.;
- Rubin, Edward M.;
- Rokhsar, Daniel S.;
- Banfield, Jillian F.
Publication type:
Article
The octopus genome and the evolution of cephalopod neural and morphological novelties.
Published in:
Nature, 2015, v. 524, n. 7564, p. 220, doi. 10.1038/nature14668
By:
- Albertin, Caroline B.;
- Simakov, Oleg;
- Mitros, Therese;
- Wang, Z. Yan;
- Pungor, Judit R.;
- Edsinger-Gonzales, Eric;
- Brenner, Sydney;
- Ragsdale, Clifton W.;
- Rokhsar, Daniel S.
Publication type:
Article
The deuterostome context of chordate origins.
Published in:
Nature, 2015, v. 520, n. 7548, p. 456, doi. 10.1038/nature14434
By:
- Lowe, Christopher J.;
- Clarke, D. Nathaniel;
- Medeiros, Daniel M.;
- Rokhsar, Daniel S.;
- Gerhart, John
Publication type:
Article
Transcription factor binding site identification using the self-organizing map.
Published in:
Bioinformatics, 2005, v. 21, n. 9, p. 1807, doi. 10.1093/bioinformatics/bti256
By:
- Shaun Mahony;
- David Hendrix;
- Aaron Golden;
- Terry J. Smith;
- Daniel S. Rokhsar
Publication type:
Article
A large CRISPR-induced bystander mutation causes immune dysregulation.
Published in:
Communications Biology, 2019, v. 2, n. 1, p. N.PAG, doi. 10.1038/s42003-019-0321-x
By:
- Simeonov, Dimitre R.;
- Brandt, Alexander J.;
- Chan, Alice Y.;
- Cortez, Jessica T.;
- Li, Zhongmei;
- Woo, Jonathan M.;
- Lee, Youjin;
- Carvalho, Claudia M. B.;
- Indart, Alyssa C.;
- Roth, Theodore L.;
- Zou, James;
- May, Andrew P.;
- Lupski, James R.;
- Anderson, Mark S.;
- Buaas, F. William;
- Rokhsar, Daniel S.;
- Marson, Alexander
Publication type:
Article
Genomic analysis of immunity in a Urochordate and the emergence of the vertebrate immune system: “waiting for Godot”.
Published in:
Immunogenetics, 2003, v. 55, n. 8, p. 570, doi. 10.1007/s00251-003-0606-5
By:
- Azumi, Kaoru;
- De Santis, Rosaria;
- De Tomaso, Anthony;
- Rigoutsos, Isidore;
- Yoshizaki, Fumiko;
- Pinto, Maria Rosaria;
- Marino, Rita;
- Shida, Kazuhito;
- Ikeda, Makoto;
- Ikeda, Masami;
- Arai, Masafumi;
- Inoue, Yasuhito;
- Shimizu, Toshio;
- Satoh, Nori;
- Rokhsar, Daniel S.;
- Du Pasquier, Louis;
- Kasahara, Masanori;
- Satake, Masanobu;
- Nonaka, Masaru
Publication type:
Article
The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii.
Published in:
New Phytologist, 2015, v. 205, n. 1, p. 402, doi. 10.1111/nph.13027
By:
- Lowry, David B.;
- Hernandez, Kyle;
- Taylor, Samuel H.;
- Meyer, Eli;
- Logan, Tierney L.;
- Barry, Kerrie W.;
- Chapman, Jarrod A.;
- Rokhsar, Daniel S.;
- Schmutz, Jeremy;
- Juenger, Thomas E.
Publication type:
Article
Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes.
Published in:
Genes, 2018, v. 9, n. 4, p. 185, doi. 10.3390/genes9040185
By:
- Kliver, Sergei;
- Rayko, Mike;
- Komissarov, Alexey;
- Bakin, Evgeny;
- Zhernakova, Daria;
- Prasad, Kasavajhala;
- Rushworth, Catherine;
- Baskar, R.;
- Smetanin, Dmitry;
- Schmutz, Jeremy;
- Rokhsar, Daniel S.;
- Mitchell-Olds, Thomas;
- Grossniklaus, Ueli;
- Brukhin, Vladimir
Publication type:
Article
Correction to: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta.
Published in:
2019
By:
- Wang, Baosheng;
- Mojica, Julius P.;
- Perera, Nadeesha;
- Lee, Cheng-Ruei;
- Lovell, John T.;
- Sharma, Aditi;
- Adam, Catherine;
- Lipzen, Anna;
- Barry, Kerrie;
- Rokhsar, Daniel S.;
- Schmutz, Jeremy;
- Mitchell-Olds, Thomas
Publication type:
Correction Notice
Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta.
Published in:
Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1729-9
By:
- Wang, Baosheng;
- Mojica, Julius P.;
- Perera, Nadeesha;
- Lee, Cheng-Ruei;
- Lovell, John T.;
- Sharma, Aditi;
- Adam, Catherine;
- Lipzen, Anna;
- Barry, Kerrie;
- Rokhsar, Daniel S.;
- Schmutz, Jeremy;
- Mitchell-Olds, Thomas
Publication type:
Article
Beyond "living fossils": Can comparative genomics finally reveal novelty?
Published in:
Molecular Ecology Resources, 2022, v. 22, n. 1, p. 9, doi. 10.1111/1755-0998.13488
By:
- Sanchez, Gustavo;
- Simakov, Oleg;
- S. Rokhsar, Daniel
Publication type:
Article
A detailed gene expression study of the Miscanthus genus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes.
Published in:
BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-864
By:
- Barling, Adam;
- Swaminathan, Kankshita;
- Mitros, Therese;
- James, Brandon T.;
- Morris, Juliette;
- Ngamboma, Ornella;
- Hall, Megan C.;
- Kirkpatrick, Jessica;
- Alabady, Magdy;
- Spence, Ashley K.;
- Hudson, Matthew E.;
- Rokhsar, Daniel S.;
- Moose, Stephen P.
Publication type:
Article
Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes.
Published in:
BMC Genomics, 2010, v. 11, p. 261, doi. 10.1186/1471-2164-11-261
By:
- Jianping Wang;
- Roe, Bruce;
- Macmil, Simone;
- Qingyi Yu;
- Murray, Jan E.;
- Tang, Haibao;
- Cuixia Chen;
- Najar, Fares;
- Wiley, Graham;
- Bowers, John;
- Van Sluys, Marie-Anne;
- Rokhsar, Daniel S.;
- Hudson, Matthew E.;
- Moose, Stephen P.;
- Paterson, Andrew H.;
- Ming, Ray
Publication type:
Article
A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis.
Published in:
Cytogenetic & Genome Research, 2015, v. 145, n. 3/4, p. 187, doi. 10.1159/000381292
By:
- Matsuda, Yoichi;
- Uno, Yoshinobu;
- Kondo, Mariko;
- Gilchrist, Michael J.;
- Zorn, aaron M.;
- Rokhsar, Daniel S.;
- Schmid, Michael;
- Taira, Masanori
Publication type:
Article
Condensates in a twist.
Published in:
Nature, 1999, v. 401, n. 6753, p. 533, doi. 10.1038/44024
By:
- Rokhsar, Daniel S.
Publication type:
Article

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