Publications


Song, Q., J. Jenkins, G. Jia, D. L. Hyten, V. Pantalone, S. A. Jackson, J. Schmutz and P. B. Cregan (2016). "Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01." BMC Genomics 17(1): 33. (Link)

Shaw, A. J., J. Schmutz, N. Devos, S. Shu, A. A. Carrell and D. J. Weston (2016). "The Sphagnum Genome Project: A New Model for Ecological and Evolutionary Genomics." Advances in Botanical Research %@ 0065-2296. (Link)

Olsen, J. L., P. Rouze, B. Verhelst, Y. C. Lin, T. Bayer, J. Collen, E. Dattolo, E. De Paoli, S. Dittami, F. Maumus, G. Michel, A. Kersting, C. Lauritano, R. Lohaus, M. Topel, T. Tonon, K. Vanneste, M. Amirebrahimi, J. Brakel, C. Bostrom, M. Chovatia, J. Grimwood, J. W. Jenkins, A. Jueterbock, A. Mraz, W. T. Stam, H. Tice, E. Bornberg-Bauer, P. J. Green, G. A. Pearson, G. Procaccini, C. M. Duarte, J. Schmutz, T. B. Reusch and Y. Van de Peer (2016). "The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea." Nature 530(7590): 331-335. (Link)

Indjeian, V. B., G. A. Kingman, F. C. Jones, C. A. Guenther, J. Grimwood, J. Schmutz, R. M. Myers and D. M. Kingsley (2016). "Evolving New Skeletal Traits by cis-Regulatory Changes in Bone Morphogenetic Proteins." Cell 164(1-2): 45-56. (Link)

Yang, X., J. C. Cushman, A. M. Borland, E. J. Edwards, S. D. Wullschleger, G. A. Tuskan, N. A. Owen, H. Griffiths, J. A. Smith, H. C. De Paoli, D. J. Weston, R. Cottingham, J. Hartwell, S. C. Davis, K. Silvera, R. Ming, K. Schlauch, P. Abraham, J. R. Stewart, H. B. Guo, R. Albion, J. Ha, S. D. Lim, B. W. Wone, W. C. Yim, T. Garcia, J. A. Mayer, J. Petereit, S. S. Nair, E. Casey, R. L. Hettich, J. Ceusters, P. Ranjan, K. J. Palla, H. Yin, C. Reyes-Garcia, J. L. Andrade, L. Freschi, J. D. Beltran, L. V. Dever, S. F. Boxall, J. Waller, J. Davies, P. Bupphada, N. Kadu, K. Winter, R. F. Sage, C. N. Aguilar, J. Schmutz, J. Jenkins and J. A. Holtum (2015). "A roadmap for research on crassulacean acid metabolism (CAM) to enhance sustainable food and bioenergy production in a hotter, drier world." New Phytol 207(3): 491-504. (Link)

Weston, D. J., C. M. Timm, A. P. Walker, L. Gu, W. Muchero, J. Schmutz, A. J. Shaw, G. A. Tuskan, J. M. Warren and S. D. Wullschleger (2015). "Sphagnum physiology in the context of changing climate: emergent influences of genomics, modelling and host-microbiome interactions on understanding ecosystem function." Plant Cell Environ 38(9): 1737-1751. (Link)

Song, Q., G. Jia, D. Hyten, J. Jenkins, E.-Y. Hwang, S. Schroeder, J. Schmutz, S. Jackson, P. McClean and P. Cregan (2015). "SNP marker development for linkage map construction, anchoring of the common bean whole genome sequence and genetic research." G3, Genes/Genomes/Genetics 10: g3. (Link)

Simakov, O., T. Kawashima, F. Marletaz, J. Jenkins, R. Koyanagi, T. Mitros, K. Hisata, J. Bredeson, E. Shoguchi, F. Gyoja, J. X. Yue, Y. C. Chen, R. M. Freeman, Jr., A. Sasaki, T. Hikosaka-Katayama, A. Sato, M. Fujie, K. W. Baughman, J. Levine, P. Gonzalez, C. Cameron, J. H. Fritzenwanker, A. M. Pani, H. Goto, M. Kanda, N. Arakaki, S. Yamasaki, J. Qu, A. Cree, Y. Ding, H. H. Dinh, S. Dugan, M. Holder, S. N. Jhangiani, C. L. Kovar, S. L. Lee, L. R. Lewis, D. Morton, L. V. Nazareth, G. Okwuonu, J. Santibanez, R. Chen, S. Richards, D. M. Muzny, A. Gillis, L. Peshkin, M. Wu, T. Humphreys, Y. H. Su, N. H. Putnam, J. Schmutz, A. Fujiyama, J. K. Yu, K. Tagawa, K. C. Worley, R. A. Gibbs, M. W. Kirschner, C. J. Lowe, N. Satoh, D. S. Rokhsar and J. Gerhart (2015). "Hemichordate genomes and deuterostome origins." Nature 527(7579): 459-465. (Link)

Sharma, M. K., R. Sharma, P. Cao, M. Harkenrider, J. Jenkins, J. Grimwood, J. Zhang, M. K. Udvardi, J. Schmutz and P. C. Ronald (2015). "Targeted Switchgrass BAC Library Screening and Sequence Analysis Identifies Predicted Biomass and Stress Response-Related Genes." BioEnergy Research: 1-14 %@ 1939-1234. (Link)

Ševčíková, T., A. Horák, V. Klimeš, V. Zbránková, E. Demir-Hilton, S. Sudek, J. Jenkins, J. Schmutz, P. Přibyl and J. Fousek (2015). "Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endosymbiosis of an ochrophyte [quest]." Scientific reports 5. (Link)

Munoz-Amatriain, M., S. Lonardi, M. Luo, K. Madishetty, J. T. Svensson, M. J. Moscou, S. Wanamaker, T. Jiang, A. Kleinhofs, G. J. Muehlbauer, R. P. Wise, N. Stein, Y. Ma, E. Rodriguez, D. Kudrna, P. R. Bhat, S. Chao, P. Condamine, S. Heinen, J. Resnik, R. Wing, H. N. Witt, M. Alpert, M. Beccuti, S. Bozdag, F. Cordero, H. Mirebrahim, R. Ounit, Y. Wu, F. You, J. Zheng, H. Simkova, J. Dolezel, J. Grimwood, J. Schmutz, D. Duma, L. Altschmied, T. Blake, P. Bregitzer, L. Cooper, M. Dilbirligi, A. Falk, L. Feiz, A. Graner, P. Gustafson, P. M. Hayes, P. Lemaux, J. Mammadov and T. J. Close (2015). "Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome." Plant J 84(1): 216-227. (Link)

Lowry, D. B., K. Hernandez, S. H. Taylor, E. Meyer, T. L. Logan, K. W. Barry, J. A. Chapman, D. S. Rokhsar, J. Schmutz and T. E. Juenger (2015). "The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii." New Phytologist 205(1): 402-414. (Link)

Lao, J., M. K. Sharma, R. Sharma, S. M. Fernandez-Nino, J. Schmutz, P. C. Ronald, J. L. Heazlewood and B. Schwessinger (2015). "Proteome profile of the endomembrane of developing coleoptiles from switchgrass (Panicum virgatum)." Proteomics 15(13): 2286-2290. (Link)

Firrincieli, A., R. Otillar, A. Salamov, J. Schmutz, Z. Khan, R. S. Redman, N. D. Fleck, E. Lindquist, I. V. Grigoriev and S. L. Doty (2015). "Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1." Front Microbiol 6: 978. (Link)

Fiedler, J. D., C. Lanzatella, M. Okada, J. Jenkins, J. Schmutz and C. M. Tobias (2015). "High-Density Single Nucleotide Polymorphism Linkage Maps of Lowland Switchgrass using Genotyping-by-Sequencing." The Plant Genome 8(2 %@ 1940-3372). (Link)

Evans, J., E. Crisovan, K. Barry, C. Daum, J. Jenkins, G. Kunde‐Ramamoorthy, A. Nandety, C. Y. Ngan, B. Vaillancourt and C. L. Wei (2015). "Diversity and population structure of northern switchgrass as revealed through exome capture sequencing." The Plant Journal 84(4): 800-815 %@ 1365-1313X. (Link)

Chapman, J. A., M. Mascher, A. Buluc, K. Barry, E. Georganas, A. Session, V. Strnadova, J. Jenkins, S. Sehgal, L. Oliker, J. Schmutz, K. A. Yelick, U. Scholz, R. Waugh, J. A. Poland, G. J. Muehlbauer, N. Stein and D. S. Rokhsar (2015). "A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome." Genome Biol 16(1): 26. (Link)

Blouin, N., S. Prochnik, E. Gantt, S. Redmond, E. Lindquist, A. Grossman, J. W. Stiller, J. Schmutz, J. Jenkins and K. Barry (2015). THE PORPHYRA UMBILICALIS GENOME: STUDIES ON THE PATH FROM GENOME TO GROCERY STORE, TAYLOR & FRANCIS LTD 4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND.

Bartholome, J., E. Mandrou, A. Mabiala, J. Jenkins, I. Nabihoudine, C. Klopp, J. Schmutz, C. Plomion and J. M. Gion (2015). "High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly." New Phytol 206(4): 1283-1296. (Link)

Wu, G. A., S. Prochnik, J. Jenkins, J. Salse, U. Hellsten, F. Murat, X. Perrier, M. Ruiz, S. Scalabrin, J. Terol, M. A. Takita, K. Labadie, J. Poulain, A. Couloux, K. Jabbari, F. Cattonaro, C. Del Fabbro, S. Pinosio, A. Zuccolo, J. Chapman, J. Grimwood, F. R. Tadeo, L. H. Estornell, J. V. Munoz-Sanz, V. Ibanez, A. Herrero-Ortega, P. Aleza, J. Perez-Perez, D. Ramon, D. Brunel, F. Luro, C. Chen, W. G. Farmerie, B. Desany, C. Kodira, M. Mohiuddin, T. Harkins, K. Fredrikson, P. Burns, A. Lomsadze, M. Borodovsky, G. Reforgiato, J. Freitas-Astua, F. Quetier, L. Navarro, M. Roose, P. Wincker, J. Schmutz, M. Morgante, M. A. Machado, M. Talon, O. Jaillon, P. Ollitrault, F. Gmitter and D. Rokhsar (2014). "Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication." Nat Biotechnol 32(7): 656-662. (Link)

Wang, W., G. Haberer, H. Gundlach, C. Gläßer, T. Nussbaumer, M. C. Luo, A. Lomsadze, M. Borodovsky, R. A. Kerstetter, J. Shanklin, D. W. Byrant, T. C. Mockler, K. J. Appenroth, J. Grimwood, J. Jenkins, J. Chow, C. Choi, C. Adam, X. H. Cao, J. Fuchs, I. Schubert, D. Rokhsar, J. Schmutz, T. P. Michael, K. F. X. Mayer and J. Messing (2014). "The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle." Nat Commun 5. (Link)

Sherman-Broyles, S., A. Bombarely, J. Grimwood, J. Schmutz and J. Doyle (2014). "Complete plastome sequences from Glycine syndetika and six additional perennial wild relatives of soybean." G3 (Bethesda) 4(10): 2023-2033. (Link)

Schmutz, J., P. E. McClean, S. Mamidi, G. A. Wu, S. B. Cannon, J. Grimwood, J. Jenkins, S. Shu, Q. Song, C. Chavarro, M. Torres-Torres, V. Geffroy, S. M. Moghaddam, D. Gao, B. Abernathy, K. Barry, M. Blair, M. A. Brick, M. Chovatia, P. Gepts, D. M. Goodstein, M. Gonzales, U. Hellsten, D. L. Hyten, G. Jia, J. D. Kelly, D. Kudrna, R. Lee, M. M. Richard, P. N. Miklas, J. M. Osorno, J. Rodrigues, V. Thareau, C. A. Urrea, M. Wang, Y. Yu, M. Zhang, R. A. Wing, P. B. Cregan, D. S. Rokhsar and S. A. Jackson (2014). "A reference genome for common bean and genome-wide analysis of dual domestications." Nat Genet 46(7): 707-713. (Link)

Myburg, A. A., D. Grattapaglia, G. A. Tuskan, U. Hellsten, R. D. Hayes, J. Grimwood, J. Jenkins, E. Lindquist, H. Tice, D. Bauer, D. M. Goodstein, I. Dubchak, A. Poliakov, E. Mizrachi, A. R. Kullan, S. G. Hussey, D. Pinard, K. van der Merwe, P. Singh, I. van Jaarsveld, O. B. Silva-Junior, R. C. Togawa, M. R. Pappas, D. A. Faria, C. P. Sansaloni, C. D. Petroli, X. Yang, P. Ranjan, T. J. Tschaplinski, C. Y. Ye, T. Li, L. Sterck, K. Vanneste, F. Murat, M. Soler, H. S. Clemente, N. Saidi, H. Cassan-Wang, C. Dunand, C. A. Hefer, E. Bornberg-Bauer, A. R. Kersting, K. Vining, V. Amarasinghe, M. Ranik, S. Naithani, J. Elser, A. E. Boyd, A. Liston, J. W. Spatafora, P. Dharmwardhana, R. Raja, C. Sullivan, E. Romanel, M. Alves-Ferreira, C. Kulheim, W. Foley, V. Carocha, J. Paiva, D. Kudrna, S. H. Brommonschenkel, G. Pasquali, M. Byrne, P. Rigault, J. Tibbits, A. Spokevicius, R. C. Jones, D. A. Steane, R. E. Vaillancourt, B. M. Potts, F. Joubert, K. Barry, G. J. Pappas, S. H. Strauss, P. Jaiswal, J. Grima-Pettenati, J. Salse, Y. Van de Peer, D. S. Rokhsar and J. Schmutz (2014). "The genome of Eucalyptus grandis." Nature 510(7505): 356-362. (Link)

Moghaddam, S. M., Q. Song, S. Mamidi, J. Schmutz, R. Lee, P. Cregan, J. M. Osorno and P. E. McClean (2014). "Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L." Front Plant Sci 5(185): 185. (Link)

Gao, D., B. Abernathy, D. Rohksar, J. Schmutz and S. A. Jackson (2014). "Annotation and sequence diversity of transposable elements in common bean (Phaseolus vulgaris)." Front Plant Sci 5: 339. (Link)

International Peach Genome Initiative. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nature Gen. [2013/03/24]. (Link)

BJ Condon, Y Leng, D Wu, KE Bushley, RA Ohm, R Otillar, J Martin, W Schackwitz, J Grimwood, N MohdZainudin, C Xue, R Wang, VA Manning, B Dhillon, ZJ Tu, BJ Steffenson, A Salamov, H Sun, S Lowry, K LaButti, J Han, A Copeland, E Lindquist, K Barry, J Schmutz, SE Baker, LM Ciuffetti, IV Grigoriev, S Zhong, BG Turgeon. Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens. PLoS Genet 9(1):e1003233 [2013/01/24]. (Link)

J Zhang, Y Lee, I Torres-Jerez, M Wang, Y Yin, W Chou, J He, H Shen, AC Srivastava, C Pennacchio, E Lindquist, J Grimwood, J Schmutz, Y Xu, M Sharma, R Sharma, LE Bartley, PC Ronald, MC Saha, RA Dixon, Y Tang, MK Udvardi. Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.). Plant J. [2013/01/01]. (Link)

Yang, R., D. E. Jarvis, H. Chen, M. A. Beilstein, J. Grimwood, J. Jenkins, S. Shu, S. Prochnik, M. Xin, C. Ma, J. Schmutz, R. A. Wing, T. Mitchell-Olds, K. S. Schumaker and X. Wang (2013). "The Reference Genome of the Halophytic Plant Eutrema salsugineum." Front Plant Sci 4: 46. (Link)

Slotte, T., K. M. Hazzouri, J. A. Agren, D. Koenig, F. Maumus, Y. L. Guo, K. Steige, A. E. Platts, J. S. Escobar, L. K. Newman, W. Wang, T. Mandakova, E. Vello, L. M. Smith, S. R. Henz, J. Steffen, S. Takuno, Y. Brandvain, G. Coop, P. Andolfatto, T. T. Hu, M. Blanchette, R. M. Clark, H. Quesneville, M. Nordborg, B. S. Gaut, M. A. Lysak, J. Jenkins, J. Grimwood, J. Chapman, S. Prochnik, S. Shu, D. Rokhsar, J. Schmutz, D. Weigel and S. I. Wright (2013). "The Capsella rubella genome and the genomic consequences of rapid mating system evolution." Nat Genet 45(7): 831-835. (Link)

Read, B. A., J. Kegel, M. J. Klute, A. Kuo, S. C. Lefebvre, F. Maumus, C. Mayer, J. Miller, A. Monier, A. Salamov, J. Young, M. Aguilar, J. M. Claverie, S. Frickenhaus, K. Gonzalez, E. K. Herman, Y. C. Lin, J. Napier, H. Ogata, A. F. Sarno, J. Schmutz, D. Schroeder, C. de Vargas, F. Verret, P. von Dassow, K. Valentin, Y. Van de Peer, G. Wheeler, C. Emiliania huxleyi Annotation, J. B. Dacks, C. F. Delwiche, S. T. Dyhrman, G. Glockner, U. John, T. Richards, A. Z. Worden, X. Zhang and I. V. Grigoriev (2013). "Pan genome of the phytoplankton Emiliania underpins its global distribution." Nature 499(7457): 209-213. (Link)

O'Rourke, J. A., L. P. Iniguez, B. Bucciarelli, J. Roessler, J. Schmutz, P. E. McClean, S. A. Jackson, G. Hernandez, M. A. Graham, R. M. Stupar and C. P. Vance (2013). "A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar." Front Plant Sci 4: 210. (Link)

Motamayor, J. C., K. Mockaitis, J. Schmutz, N. Haiminen, D. Livingstone, O. Cornejo, S. D. Findley, P. Zheng, F. Utro and S. Royaert (2013). "The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color." Genome biology 14(6): R53. (Link)

International Peach Genome, I., I. Verde, A. G. Abbott, S. Scalabrin, S. Jung, S. Shu, F. Marroni, T. Zhebentyayeva, M. T. Dettori, J. Grimwood, F. Cattonaro, A. Zuccolo, L. Rossini, J. Jenkins, E. Vendramin, L. A. Meisel, V. Decroocq, B. Sosinski, S. Prochnik, T. Mitros, A. Policriti, G. Cipriani, L. Dondini, S. Ficklin, D. M. Goodstein, P. Xuan, C. Del Fabbro, V. Aramini, D. Copetti, S. Gonzalez, D. S. Horner, R. Falchi, S. Lucas, E. Mica, J. Maldonado, B. Lazzari, D. Bielenberg, R. Pirona, M. Miculan, A. Barakat, R. Testolin, A. Stella, S. Tartarini, P. Tonutti, P. Arus, A. Orellana, C. Wells, D. Main, G. Vizzotto, H. Silva, F. Salamini, J. Schmutz, M. Morgante and D. S. Rokhsar (2013). "The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution." Nat Genet 45(5): 487-494. (Link)

Hellsten, U., K. M. Wright, J. Jenkins, S. Shu, Y. Yuan, S. R. Wessler, J. Schmutz, J. H. Willis and D. S. Rokhsar (2013). "Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing." Proc Natl Acad Sci U S A 110(48): 19478-19482. (Link)

Haudry, A., A. E. Platts, E. Vello, D. R. Hoen, M. Leclercq, R. J. Williamson, E. Forczek, Z. Joly-Lopez, J. G. Steffen, K. M. Hazzouri, K. Dewar, J. R. Stinchcombe, D. J. Schoen, X. Wang, J. Schmutz, C. D. Town, P. P. Edger, J. C. Pires, K. S. Schumaker, D. E. Jarvis, T. Mandakova, M. A. Lysak, E. van den Bergh, M. E. Schranz, P. M. Harrison, A. M. Moses, T. E. Bureau, S. I. Wright and M. Blanchette (2013). "An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions." Nat Genet 45(8): 891-898. (Link)

AH Paterson, JF Wendel, H Gundlach, H Guo, J Jenkins, D Jin, D Llewellyn, KC Showmaker, S Shu, J Udall, M Yoo, R Byers, W Chen, A Doron-Faigenboim, MV Duke, L Gong, J Grimwood, C Grover, K Grupp, G Hu, T Lee, J Li, L Lin, T Liu, BS Marler, JT Page, AW Roberts, E Romanel, WS Sanders, E Szadkowski, X Tan, H Tang, C Xu, J Wang, Z Wang, D Zhang, L Zhang, H Ashrafi, F Bedon, JE Bowers, CL Brubaker, PW Chee, S Das, AR Gingle, CH Haigler, D Harker, LV Hoffmann, R Hovav, DC Jones, C Lemke, S Mansoor, Mu Rahman, LN Rainville, A Rambani, UK Reddy, J Rong, Y Saranga, BE Scheffler, JA Scheffler, DM Stelly, BA Triplett, A Van Deynze, MFS Vaslin, VN Waghmare, SA Walford, RJ Wright, EA Zaki, T Zhang, ES Dennis, KFX Mayer, DG Peterson, DS Rokhsar, X Wang, J Schmutz. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492(7429):423-427 [2012/12/20]. (Link)

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, Shapiro H, Aerts A, Otillar RP, Terry AY, Boore JL, Grigoriev IV, Lindberg DR, Seaver EC, Weisblat DA, Putnam NH, Rokhsar DS. Insights into bilaterian evolution from three spiralian genomes. Nature. 2013 Jan 24;493(7433):526-31. doi: 10.1038/nature11696. Epub 2012 Dec 19. PubMed PMID: 23254933. (Link)

BA Curtis, G Tanifuji, F Burki, A Gruber, M Irimia, S Maruyama, MC Arias, SG Ball, GH Gile, Y Hirakawa, JF Hopkins, A Kuo, SA Rensing, J Schmutz, A Symeonidi, M Elias, RJM Eveleigh, EK Herman, MJ Klute, T Nakayama, M Obornik, A Reyes-Prieto, EV Armbrust, SJ Aves, RG Beiko, P Coutinho, JB Dacks, DG Durnford, NM Fast, BR Green, CJ Grisdale, F Hempel, B Henrissat, MP Hoppner, K Ishida, E Kim, L Koreny, PG Kroth, Y Liu, S Malik, UG Maier, D McRose, T Mock, JAD Neilson, NT Onodera, AM Poole, EJ Pritham, TA Richards, G Rocap, SW Roy, C Sarai, S Schaack, S Shirato, CH Slamovits, DF Spencer, S Suzuki, AZ Worden, S Zauner, K Barry, C Bell, AK Bharti, JA Crow, J Grimwood, R Kramer, E Lindquist, S Lucas, A Salamov, GI McFadden, CE Lane, PJ Keeling, MW Gray, IV Grigoriev, JM Archibald. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature 492(7427):59-65 [2012/12/06]. (Link)

E Morin, A Kohler, AR Baker, M Foulongne-Oriol, V Lombard, LG Nagy, RA Ohm, A Patyshakuliyeva, A Brun, AL Aerts, AM Bailey, C Billette, PM Coutinho, G Deakin, H Doddapaneni, D Floudas, J Grimwood, K Hildén, U Kües, KM LaButti, A Lapidus, EA Lindquist, SM Lucas, C Murat, RW Riley, AA Salamov, J Schmutz, V Subramanian, HAB Wösten, J Xu, DC Eastwood, GD Foster, ASM Sonnenberg, D Cullen, RP de Vries, T Lundell, DS Hibbett, B Henrissat, KS Burton, RW Kerrigan, MP Challen, IV Grigoriev, F Martin. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. PNAS 109(43):17501-17506 [2012/10/23]. (Link)

Mascher, M., G. J. Muehlbauer, D. S. Rokhsar, J. Chapman, J. Schmutz, K. Barry, M. Munoz-Amatriain, T. J. Close, R. P. Wise, A. H. Schulman, A. Himmelbach, K. F. Mayer, U. Scholz, J. A. Poland, N. Stein and R. Waugh (2013). "Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)." Plant J 76(4): 718-727. (Link)

Jenkins, J., B. Wilson, J. Grimwood, J. Schmutz and L. Grauke (2013). "Towards a reference pecan genome sequence." I International Symposium on Pecans and Other Carya in Indigenous and Managed Systems 1070: 101-108. (Link)

Iwata, A., A. L. Tek, M. M. Richard, B. Abernathy, A. Fonseca, J. Schmutz, N. W. Chen, V. Thareau, G. Magdelenat, Y. Li, M. Murata, A. Pedrosa-Harand, V. Geffroy, K. Nagaki and S. A. Jackson (2013). "Identification and characterization of functional centromeres of the common bean." Plant J 76(1): 47-60. (Link)

R Freeman, T Ikuta, M Wu, R Koyanagi, T Kawashima, K Tagawa, T Humphreys, G Fang, A Fujiyama, H Saiga, C Lowe, K Worley, J Jenkins, J Schmutz, M Kirschner, D Rokhsar, N Satoh, J Gerhart. Identical Genomic Organization of Two Hemichordate Hox Clusters. Curr Biol 22(21):2053-2058 [2012/11/06]. (Link)

KH Lamour, J Mudge, D Gobena, OP Hurtado-Gonzales, J Schmutz, A Kuo, NA Miller, BJ Rice, S Raffaele, LM Cano, AK Bharti, RS Donahoo, S Finley, E Huitema, J Hulvey, D Platt, A Salamov, A Savidor, R Sharma, R Stam, D Storey, M Thines, J Win, BJ Haas, DL Dinwiddie, J Jenkins, JR Knight, JP Affourtit, CS Han, O Chertkov, EA Lindquist, C Detter, IV Grigoriev, S Kamoun, SF Kingsmore. Genome Sequencing and Mapping Reveal Loss of Heterozygosity as a Mechanism for Rapid Adaptation in the Vegetable Pathogen Phytophthora capsici. MPMI 25(10):1350-1360 [2012/10]. (Link)

K Sumiyama, T Miyake, J Grimwood, A Stuart, M Dickson, J Schmutz, FH Ruddle, RM Myers, CT Amemiya. Theria-Specific Homeodomain and cis-Regulatory Element Evolution of the Dlx3-4 Bigene Cluster in 12 Different Mammalian Species. J. Exp. Zool. (Mol. Dev. Evol.) 318(8):639-650 [2012/12/01]. (Link)

AR Wark, MG Mills, L Dang, YF Chan, FC Jones, SD Brady, DM Absher, J Grimwood, J Schmutz, RM Myers, DM Kingsley, CL Peichel. Genetic Architecture of Variation in the Lateral Line Sensory System of Threespine Sticklebacks. G3: Genes|Genomes|Genetics 2(9):1047-1056 [2012/09/01]. (Link)

D Floudas, M Binder, R Riley, K Barry, RA Blanchette, B Henrissat, AT Martínez, R Otillar, JW Spatafora, JS Yadav, A Aerts, I Benoit, A Boyd, A Carlson, A Copeland, PM Coutinho, RP de Vries, P Ferreira, K Findley, B Foster, J Gaskell, D Glotzer, P Górecki, J Heitman, C Hesse, C Hori, K Igarashi, JA Jurgens, N Kallen, P Kersten, A Kohler, U Kües, TKA Kumar, A Kuo, K LaButti, LF Larrondo, E Lindquist, A Ling, V Lombard, S Lucas, T Lundell, R Martin, DJ McLaughlin, I Morgenstern, E Morin, C Murat, LG Nagy, M Nolan, RA Ohm, A Patyshakuliyeva, A Rokas, FJ Ruiz-Dueñas, G Sabat, A Salamov, M Samejima, J Schmutz, JC Slot, F St. John, J Stenlid, H Sun, S Sun, K Syed, A Tsang, A Wiebenga, D Young, A Pisabarro, DC Eastwood, F Martin, D Cullen, IV Grigoriev, DS Hibbett. The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes. Science 336(6089):1715-1719 [2012/06/29]. (Link)

Å Olson, A Aerts, F Asiegbu, L Belbahri, O Bouzid, A Broberg, B Canbäck, PM Coutinho, D Cullen, K Dalman, G Deflorio, LT van Diepen, C Dunand, S Duplessis, M Durling, P Gonthier, J Grimwood, CG Fossdal, D Hansson, B Henrissat, A Hietala, K Himmelstrand, D Hoffmeister, N Högberg, TY James, M Karlsson, A Kohler, U Kües, Y Lee, Y Lin, M Lind, E Lindquist, V Lombard, S Lucas, K Lundén, E Morin, C Murat, J Park, T Raffaello, P Rouzé, A Salamov, J Schmutz, H Solheim, J StÅhlberg, H Vélëz, RP de Vries, A Wiebenga, S Woodward, I Yakovlev, M Garbelotto, F Martin, IV Grigoriev, J Stenlid. Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen. New Phytologist 194(4):1001-1013 [2012/06/01]. (Link)

G Blanc, I Agarkova, J Grimwood, A Kuo, A Brueggeman, D Dunigan, J Gurnon, I Ladunga, E Lindquist, S Lucas, J Pangilinan, T Pröschold, A Salamov, J Schmutz, D Weeks, T Yamada, A Lomsadze, M Borodovsky, J Claverie, I Grigoriev, J Van Etten. The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation. Genome Biology 13(5):1-12 (2012/5/25). (Link)

J Bennetzen, J Schmutz, H Wang, R Percifield, J Hawkins, A Pontaroli, M Estep, L Feng, J Vaughn, J Grimwood, J Jenkins, K Barry, E Lindquist, U Hellsten, S Deshpande, X Wang, X Wu, T Mitros, J Triplett, X Yang, C Ye, M Mauro-Herrera, L Wang, P Li, M Sharma, R Sharma, P Ronald, O Panaud, E Kellogg, T Brutnell, A Doust, G Tuskan, D Rokhsar, K Devos. Reference genome sequence of the model plant Setaria. Nat Biotech 30(6):555-561 [2012/05/13]. (Link)

MK Sharma, R Sharma, P Cao, J Jenkins, LE Bartley, M Qualls, J Grimwood, J Schmutz, D Rokhsar, PC Ronald. A Genome-Wide Survey of Switchgrass Genome Structure and Organization. PLoS ONE 7(4):e33892 [2012/04/12]. (Link)

FC Jones, MG Grabherr, YF Chan, P Russell, E Mauceli, J Johnson, R Swofford, M Pirun, MC Zody, S White, E Birney, S Searle, J Schmutz, J Grimwood, MC Dickson, RM Myers, CT Miller, BR Summers, AK Knecht, SD Brady, H Zhang, AA Pollen, T Howes, C Amemiya, ES Lander, F Di Palma, K Lindblad-Toh, DM Kingsley. The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484(7392):55-61 [2012/04/05]. (Link)

F Jones, Y Chan, J Schmutz, J Grimwood, S Brady, A Southwick, D Absher, R Myers, T Reimchen, B Deagle, D Schluter, D Kingsley. A Genome-wide SNP Genotyping Array Reveals Patterns of Global and Repeated Species-Pair Divergence in Sticklebacks. Curr Biol 22(1):83-90 [2012/01/10]. (Link)

M Grbic, T Van Leeuwen, RM Clark, S Rombauts, P Rouze, V Grbic, EJ Osborne, W Dermauw, PC Thi Ngoc, F Ortego, P Hernandez-Crespo, I Diaz, M Martinez, M Navajas, E Sucena, S Magalhaes, L Nagy, RM Pace, S Djuranovic, G Smagghe, M Iga, O Christiaens, JA Veenstra, J Ewer, RM Villalobos, JL Hutter, SD Hudson, M Velez, SV Yi, J Zeng, A Pires-daSilva, F Roch, M Cazaux, M Navarro, V Zhurov, G Acevedo, A Bjelica, JA Fawcett, E Bonnet, C Martens, G Baele, L Wissler, A Sanchez-Rodriguez, L Tirry, C Blais, K Demeestere, SR Henz, TR Gregory, J Mathieu, L Verdon, L Farinelli, J Schmutz, E Lindquist, R Feyereisen, Y Van de Peer. The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature 479(7374):487-492 [2011/11/24] (Link)

MD Casler, CM Tobias, SM Kaeppler, CR Buell, Z Wang, P Cao, J Schmutz, P Ronald. The Switchgrass Genome: Tools and Strategies. Plant Gen. 4(3):273-282 [2011/11/01]. (Link)

R Berka, I Grigoriev, R Otillar, A Salamov, J Grimwood, I Reid, N Ishmael, T John, C Darmond, M Moisan, B Henrissat, P Coutinho, V Lombard, D Natvig, E Lindquist, J Schmutz, S Lucas, P Harris, J Powlowski, A Bellemare, D Taylor, G Butler, R de Vries, I Allijn, J van den Brink, S Ushinsky, R Storms, A Powell, I Paulsen, L Elbourne, S Baker, J Magnuson, S LaBoissiere, J Clutterbuck, D Martinez, M Wogulis, AL de Leon, M Rey, A Tsang. Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. Nat Biotech 29(10):922-927 [2011/10/02]. (Link)

DC Eastwood, D Floudas, M Binder, A Majcherczyk, P Schneider, A Aerts, FO Asiegbu, SE Baker, K Barry, M Bendiksby, M Blumentritt, PM Coutinho, D Cullen, RP de Vries, A Gathman, B Goodell, B Henrissat, K Ihrmark, H Kauserud, A Kohler, K LaButti, A Lapidus, JL Lavin, Y Lee, E Lindquist, W Lilly, S Lucas, E Morin, C Murat, JA Oguiza, J Park, AG Pisabarro, R Riley, A Rosling, A Salamov, O Schmidt, J Schmutz, I Skrede, J Stenlid, A Wiebenga, X Xie, U Kües, DS Hibbett, D Hoffmeister, N Högberg, F Martin, IV Grigoriev, SC Watkinson. The Plant Cell Wall-Decomposing Machinery Underlies the Functional Diversity of Forest Fungi. Science 333(6043):762-765 [2011/08/05]. (Link)

SA Jackson, A Iwata, S Lee, J Schmutz, R Shoemaker. Sequencing crop genomes: approaches and applications. New Phytologist 191(4):915-925 [2011/09/01]. (Link)

A Bresson, V Jorge, A Dowkiw, V Guerin, I Bourgait, GA Tuskan, J Schmutz, B Chalhoub, C Bastien, P Faivre Rampant. Qualitative and quantitative resistances to leaf rust finely mapped within two nucleotide-binding site leucine-rich repeat (NBS-LRR)-rich genomic regions of chromosome 19 in poplar. New Phytologist 192(1):151-163 [2011/10/01]. (Link)

Smith DR, Burki F, Yamada T, Grimwood J, Grigoriev IV, Van Etten JL, Keeling PJ. The GC-rich mitochondrial and plastid genomes of the green alga Coccomyxa give insight into the evolution of organelle DNA nucleotide landscape. PLoS One. 2011;6(8):e23624. doi: 10.1371/journal.pone.0023624. Epub 2011 Aug 26. PubMed PMID: 21887287; PubMed Central PMCID: PMC3162594. (Link)

SB Goodwin, S Ben M'Barek, B Dhillon, AHJ Wittenberg, CF Crane, JK Hane, AJ Foster, TAJ Van der Lee, J Grimwood, A Aerts, J Antoniw, A Bailey, B Bluhm, J Bowler, J Bristow, A van der Burgt, B Canto-Canché, ACL Churchill, L Conde-Ferràez, HJ Cools, PM Coutinho, M Csukai, P Dehal, P De Wit, B Donzelli, HC van de Geest, RCH van Ham, KE Hammond-Kosack, B Henrissat, A Kilian, AK Kobayashi, E Koopmann, Y Kourmpetis, A Kuzniar, E Lindquist, V Lombard, C Maliepaard, N Martins, R Mehrabi, JPH Nap, A Ponomarenko, JJ Rudd, A Salamov, J Schmutz, HJ Schouten, H Shapiro, I Stergiopoulos, SFF Torriani, H Tu, RP de Vries, C Waalwijk, SB Ware, A Wiebenga, L Zwiers, RP Oliver, IV Grigoriev, GHJ Kema. Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis. PLoS Genet 7(6):e1002070 [2011/06/09]. (Link)

S Duplessis, CA Cuomo, Y Lin, A Aerts, E Tisserant, C Veneault-Fourrey, DL Joly, S Hacquard, J Amselem, BL Cantarel, R Chiu, PM Coutinho, N Feau, M Field, P Frey, E Gelhaye, J Goldberg, MG Grabherr, CD Kodira, A Kohler, U Kües, EA Lindquist, SM Lucas, R Mago, E Mauceli, E Morin, C Murat, JL Pangilinan, R Park, M Pearson, H Quesneville, N Rouhier, S Sakthikumar, AA Salamov, J Schmutz, B Selles, H Shapiro, P Tanguay, GA Tuskan, B Henrissat, Y Van de Peer, P Rouzé, JG Ellis, PN Dodds, JE Schein, S Zhong, RC Hamelin, IV Grigoriev, LJ Szabo, F Martin. Obligate biotrophy features unraveled by the genomic analysis of rust fungi. PNAS 108(22):9166-9171 [2011/05/31]. (Link)

JA Banks, T Nishiyama, M Hasebe, JL Bowman, M Gribskov, C dePamphilis, VA Albert, N Aono, T Aoyama, BA Ambrose, NW Ashton, MJ Axtell, E Barker, MS Barker, JL Bennetzen, ND Bonawitz, C Chapple, C Cheng, LGG Correa, M Dacre, J DeBarry, I Dreyer, M Elias, EM Engstrom, M Estelle, L Feng, C Finet, SK Floyd, WB Frommer, T Fujita, L Gramzow, M Gutensohn, J Harholt, M Hattori, A Heyl, T Hirai, Y Hiwatashi, M Ishikawa, M Iwata, KG Karol, B Koehler, U Kolukisaoglu, M Kubo, T Kurata, S Lalonde, K Li, Y Li, A Litt, E Lyons, G Manning, T Maruyama, TP Michael, K Mikami, S Miyazaki, S Morinaga, T Murata, B Mueller-Roeber, DR Nelson, M Obara, Y Oguri, RG Olmstead, N Onodera, BL Petersen, B Pils, M Prigge, SA Rensing, DM Riaño-Pachón, AW Roberts, Y Sato, HV Scheller, B Schulz, C Schulz, EV Shakirov, N Shibagaki, N Shinohara, DE Shippen, I Sørensen, R Sotooka, N Sugimoto, M Sugita, N Sumikawa, M Tanurdzic, G Theißen, P Ulvskov, S Wakazuki, J Weng, WW Willats, D Wipf, PG Wolf, L Yang, AD Zimmer, Q Zhu, T Mitros, U Hellsten, D Loqué, R Otillar, A Salamov, J Schmutz, H Shapiro, E Lindquist, S Lucas, D Rokhsar, IV Grigoriev. The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants. Science 332 (6032):960-963 [2011/05/20]. (Link)

Andersen MR, Salazar MP, Schaap PJ, van de Vondervoort PJ, Culley D, Thykaer J, Frisvad JC, Nielsen KF, Albang R, Albermann K, Berka RM, Braus GH, Braus-Stromeyer SA, Corrochano LM, Dai Z, van Dijck PW, Hofmann G, Lasure LL, Magnuson JK, Menke H, Meijer M, Meijer SL, Nielsen JB, Nielsen ML, van Ooyen AJ, Pel HJ, Poulsen L, Samson RA, Stam H, Tsang A, van den Brink JM, Atkins A, Aerts A, Shapiro H, Pangilinan J, Salamov A, Lou Y, Lindquist E, Lucas S, Grimwood J,Grigoriev IV, Kubicek CP, Martinez D, van Peij NN, Roubos JA, Nielsen J, Baker SE. Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. Genome Res. 2011 Jun;21(6):885-97. doi: 10.1101/gr.112169.110. Epub 2011 May 4. PubMed PMID: 21543515; PubMed Central PMCID: PMC3106321. (Link)

T Hu, P Pattyn, E Bakker, J Cao, J Cheng, R Clark, N Fahlgren, J Fawcett, J Grimwood, H Gundlach, G Haberer, J Hollister, S Ossowski, R Ottilar, A Salamov, K Schneeberger, M Spannagl, X Wang, L Yang, M Nasrallah, J Bergelson, J Carrington, B Gaut, J Schmutz, K Mayer, Y Van de Peer, I Grigoriev, M Nordborg, D Weigel, Y Guo. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet 43(5):476-481 [2011/04/10]. (Link)

R Sucgang, A Kuo, X Tian, W Salerno, A Parikh, C Feasley, E Dalin, H Tu, E Huang, K Barry, E Lindquist, H Shapiro, D Bruce, J Schmutz, A Salamov, P Fey, P Gaudet, C Anjard, M Babu, S Basu, Y Bushmanova, H van der Wel, M Katoh-Kurasawa, C Dinh, P Coutinho, T Saito, M Elias, P Schaap, R Kay, B Henrissat, L Eichinger, F Rivero, N Putnam, C West, W Loomis, R Chisholm, G Shaulsky, J Strassmann, D Queller, A Kuspa, I Grigoriev. Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biology 12(2):R20 [2011/2/28]. (Link)

AK Greenwood, FC Jones, YF Chan, SD Brady, DM Absher, J Grimwood, J Schmutz, RM Myers, D Kingsley, KPeichel. The genetic basis of divergent pigment patterns in juvenile threespine sticklebacks. Heredity 107(2):155-166 [2011/09/02]. (Link)

MY Kim, S Lee, K Van, T Kim, S Jeong, I Choi, D Kim, Y Lee, D Park, J Ma, W Kim, B Kim, S Park, K Lee, DH Kim, KH Kim, JH Shin, YE Jang, KD Kim, WX Liu, T Chaisan, YJ Kang, Y Lee, K Kim, J Moon, J Schmutz, SA Jackson, J Bhak, S Lee. Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. And Zucc.) genome. PNAS 107(51):22032-22037 [2010/12/21]. (Link)

RA Ohm, JF de Jong, LG Lugones, A Aerts, E Kothe, JE Stajich, RP de Vries, E Record, A Levasseur, SE Baker, KA Bartholomew, PM Coutinho, S Erdmann, TJ Fowler, AC Gathman, V Lombard, B Henrissat, N Knabe, U Kues, WW Lilly, E Lindquist, S Lucas, JK Magnuson, F Piumi, M Raudaskoski, A Salamov, J Schmutz, F Schwarze, PA vanKuyk, JS Horton, IV Grigoriev, H Wosten. Genome sequence of the model mushroom Schizophyllum commune. Nat Biotech 28(9):957-963 [2010/7/11]. (Link)

SE Prochnik, J Umen, AM Nedelcu, A Hallmann, SM Miller, I Nishii, P Ferris, A Kuo, T Mitros, LK Fritz-Laylin, U Hellsten, J Chapman, O Simakov, SA Rensing, A Terry, J Pangilinan, V Kapitonov, J Jurka, A Salamov, H Shapiro, J Schmutz, J Grimwood, E Lindquist, S Lucas, IV Grigoriev, R Schmitt, D Kirk, DS Rokhsar. Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri. Science 329 (5988):223-226 [2010/07/09]. (Link)

J Schmutz, SB Cannon, T Mitros, W Nelson, S Shu, D Goodstein, and D Rokhsar. The Draft Soybean Genome Sequence. Genetics, Genomics, and Breeding of Soybean. 223 [2010/6/3]. (Link)

Rosa SF, Powell AE, Rosengarten RD, Nicotra ML, Moreno MA, Grimwood J, Lakkis FG, Dellaporta SL, Buss LW. Hydractinia allodeterminant alr1 resides in an immunoglobulin superfamily-like gene complex. Curr Biol. 2010 Jun 22;20(12):1122-7. doi: 10.1016/j.cub.2010.04.050. Epub 2010 May 27. PubMed PMID: 20537535; PubMed Central PMCID: PMC2921677. (Link)

U Hellsten, RM Harland, MJ Gilchrist, D Hendrix, J Jurka, V Kapitonov, I Ovcharenko, NH Putnam, S Shu, L Taher, IL Blitz, B Blumberg, DS Dichmann, I Dubchak, E Amaya, JC Detter, R Fletcher, DS Gerhard, D Goodstein, T Graves, IV Grigoriev, J Grimwood, T Kawashima, E Lindquist, SM Lucas, PE Mead, T Mitros, H Ogino, Y Ohta, AV Poliakov, N Pollet, J Robert, A Salamov, AK Sater, J Schmutz, A Terry, PD Vize, WC Warren, D Wells, A Wills, RK Wilson, LB Zimmerman, AM Zorn, R Grainger, T Grammer, MK Khokha, PM Richardson, DS Rokhsar. The Genome of the Western Clawed Frog tropicalis. Science 328 (5978):633-636 [2010/04/30]. (Link)

P Ferris, BJS Olson, PL De Hoff, S Douglass, D Casero, S Prochnik, S Geng, R Rai, J Grimwood, J Schmutz, I Nishii, T Hamaji, H Nozaki, M Pellegrini, JG Umen. Evolution of an Expanded Sex-Determining Locus in Volvox. Science 328 (5976):351-354 [2010/04/16]. (Link)

DL Goode, GM Cooper, J Schmutz, M Dickson, E Gonzales, M Tsai, K Karra, E Davydov, S Batzoglou, RM Myers, A Sidow. Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes. Genome Research 20(3):301-310 [2010/03/01]. (Link)

CT Amemiya, TP Powers, SJ Prohaska, J Grimwood, J Schmutz, M Dickson, T Miyake, MA Schoenborn, RM Myers, FH Ruddle, PF Stadler. Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome. PNAS 107(8):3622-3627 [2010/02/23]. (Link)

International Brachypodium Sequencing Consortium. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463(7282):763-768 [2010/02/11]. (Link)

YF Chan, ME Marks, FC Jones, G Villarreal, MD Shapiro, SD Brady, AM Southwick, DM Absher, J Grimwood, J Schmutz, RM Myers, D Petrov, B Jónsson, D Schluter, MA Bell, DM Kingsley. Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer. Science 327(5963):302-305 [2010/01/15]. (Link)

J Schmutz, SB Cannon, J Schlueter, J Ma, T Mitros, W Nelson, DL Hyten, Q Song, JJ Thelen, J Cheng, D Xu, U Hellsten, GD May, Y Yu, T Sakurai, T Umezawa, MK Bhattacharyya, D Sandhu, B Valliyodan, E Lindquist, M Peto, D Grant, S Shu, D Goodstein, K Barry, M Futrell-Griggs, B Abernathy, J Du, Z Tian, L Zhu, N Gill, T Joshi, M Libault, A Sethuraman, X Zhang, K Shinozaki, HT Nguyen, RA Wing, P Cregan, J Specht, J Grimwood, D Rokhsar, G Stacey, RC Shoemaker, SA Jackson. Genome sequence of the palaeopolyploid soybean. Nature 463 (7278):178-183 [2010/01/14]. (Link)

J Du, Z Tian, NJ Bowen, J Schmutz, RC Shoemaker, J Ma. Bifurcation and enhancement of autonomous-nonautonomous retrotransposon partnership through LTR swapping in soybean. The Plant Cell Online 22(1):48-61 [2010]. (Link)

The MGC Project Team, G Temple, DS Gerhard, R Rasooly, EA Feingold, PJ Good, C Robinson, A Mandich, JG Derge, J Lewis, D Shoaf, FS Collins, W Jang, L Wagner, CM Shenmen, L Misquitta, CF Schaefer, KH Buetow, TI Bonner, L Yankie, M Ward, L Phan, A Astashyn, G Brown, C Farrell, J Hart, M Landrum, BL Maidak, M Murphy, T Murphy, B Rajput, L Riddick, D Webb, J Weber, W Wu, KD Pruitt, D Maglott, A Siepel, B Brejova, M Diekhans, R Harte, R Baertsch, J Kent, D Haussler, M Brent, L Langton, CL Comstock, M Stevens, C Wei, MJ van Baren, K Salehi-Ashtiani, RR Murray, L Ghamsari, E Mello, C Lin, C Pennacchio, K Schreiber, N Shapiro, A Marsh, E Pardes, T Moore, A Lebeau, M Muratet, B Simmons, D Kloske, S Sieja, J Hudson, P Sethupathy, M Brownstein, N Bhat, J Lazar, H Jacob, CE Gruber, MR Smith, J McPherson, AM Garcia, PH Gunaratne, J Wu, D Muzny, RA Gibbs, AC Young, GG Bouffard, RW Blakesley, J Mullikin, ED Green, MC Dickson, AC Rodriguez, J Grimwood, J Schmutz, RM Myers, M Hirst, T Zeng, K Tse, M Moksa, M Deng, K Ma, D Mah, J Pang, G Taylor, E Chuah, A Deng, K Fichter, A Go, S Lee, J Wang, M Griffith, R Morin, RA Moore, M Mayo, S Munro, S Wagner, SJ Jones, RA Holt, MA Marra, S Lu, S Yang, J Hartigan, M Graf, R Wagner, S Letovksy, JC Pulido, K Robison, D Esposito, J Hartley, VE Wall, RF Hopkins, O Ohara, S Wiemann. The completion of the Mammalian Gene Collection (MGC). Genome Research 19 (12):2324-2333 [2009/12/01]. (Link)

PSG Chain, DV Grafham, RS Fulton, MG FitzGerald, J Hostetler, D Muzny, J Ali, B Birren, DC Bruce, C Buhay, JR Cole, Y Ding, S Dugan, D Field, GM Garrity, R Gibbs, T Graves, CS Han, SH Harrison, S Highlander, P Hugenholtz, HM Khouri, CD Kodira, E Kolker, NC Kyrpides, D Lang, A Lapidus, SA Malfatti, V Markowitz, T Metha, KE Nelson, J Parkhill, S Pitluck, X Qin, TD Read, J Schmutz, S Sozhamannan, P Sterk, RL Strausberg, G Sutton, NR Thomson, JM Tiedje, G Weinstock, A Wollam, Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium, JC Detter. Genome Project .Standards in a New Era of Sequencing. Science 326 (5950):236-237 [2009/10/09]. (Link)

J Kitano, JA Ross, S Mori, M Kume, FC Jones, YF Chan, DM Absher, J Grimwood, J Schmutz, RM Myers, DM Kingsley, CL Peichel. A role for a neo-sex chromosome in stickleback speciation. Nature 461(7267):1079-1083 [2009/10/22]. (Link)

JJ Coleman, SD Rounsley, M Rodriguez-Carres, A Kuo, CC Wasmann, J Grimwood, J Schmutz, M Taga, GJ White, S Zhou, DC Schwartz, M Freitag, L Ma, EGJ Danchin, B Henrissat, PM Coutinho, DR Nelson, D Straney, CA Napoli, BM Barker, M Gribskov, M Rep, S Kroken, I Molnár, C Rensing, JC Kennell, J Zamora, ML Farman, EU Selker, A Salamov, H Shapiro, J Pangilinan, E Lindquist, C Lamers, IV Grigoriev, DM Geiser, SF Covert, E Temporini, HD VanEtten. The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion. PLoS Genet 5(8):e1000618 [2009/08/28]. (Link)

J O'Rourke, R Nelson, D Grant, J Schmutz, J Grimwood, S Cannon, C Vance, M Graham, R Shoemaker. Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response. BMC Genomics 10(1):376 [2009/8/13]. (Link)

Nicotra ML, Powell AE, Rosengarten RD, Moreno M, Grimwood J, Lakkis FG, Dellaporta SL, Buss LW. A hypervariable invertebrate allodeterminant. Curr Biol. 2009 Apr 14;19(7):583-9. doi: 10.1016/j.cub.2009.02.040. Epub 2009 Mar 19. PubMed PMID: 19303297; PubMed Central PMCID: PMC2681180. (Link)

AZ Worden, J Lee, T Mock, P Rouzé, MP Simmons, AL Aerts, AE Allen, ML Cuvelier, E Derelle, MV Everett, E Foulon, J Grimwood, H Gundlach, B Henrissat, C Napoli, SM McDonald, MS Parker, S Rombauts, A Salamov, P Von Dassow, JH Badger, PM Coutinho, E Demir, I Dubchak, C Gentemann, W Eikrem, JE Gready, U John, W Lanier, EA Lindquist, S Lucas, KFX Mayer, H Moreau, F Not, R Otillar, O Panaud, J Pangilinan, I Paulsen, B Piegu, A Poliakov, S Robbens, J Schmutz, E Toulza, T Wyss, A Zelensky, K Zhou, EV Armbrust, D Bhattacharya, UW Goodenough, Y Van de Peer, IV Grigoriev. Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas. Science 324(5924):268-272 [2009/04/10]. (Link)

AH Paterson, JE Bowers, R Bruggmann, I Dubchak, J Grimwood, H Gundlach, G Haberer, U Hellsten, T Mitros, A Poliakov, J Schmutz, M Spannagl, H Tang, X Wang, T Wicker, AK Bharti, J Chapman, FA Feltus, U Gowik, IV Grigoriev, E Lyons, CA Maher, M Martis, A Narechania, RP Otillar, BW Penning, AA Salamov, Y Wang, L Zhang, NC Carpita, M Freeling, AR Gingle, CT Hash, B Keller, P Klein, S Kresovich, MC McCann, R Ming, DG Peterson, Mehboob-ur-Rahman, D Ware, P Westhoff, KFX Mayer, J Messing, DS Rokhsar. The Sorghum bicolor genome and the diversification of grasses. Nature 457(7229):551-556 [2009/01/29]. (Link)

C Bowler, AE Allen, JH Badger, J Grimwood, K Jabbari, A Kuo, U Maheswari, C Martens, F Maumus, RP Otillar, E Rayko, A Salamov, K Vandepoele, B Beszteri, A Gruber, M Heijde, M Katinka, T Mock, K Valentin, F Verret, JA Berges, C Brownlee, J Cadoret, A Chiovitti, CJ Choi, S Coesel, A De Martino, JC Detter, C Durkin, A Falciatore, J Fournet, M Haruta, MJJ Huysman, BD Jenkins, K Jiroutova, RE Jorgensen, Y Joubert, A Kaplan, N Kroger, PG Kroth, J La Roche, E Lindquist, M Lommer, V Martin-Jezequel, PJ Lopez, S Lucas, M Mangogna, K McGinnis, LK Medlin, A Montsant, MO Secq, C Napoli, M Obornik, MS Parker, J Petit, BM Porcel, N Poulsen, M Robison, L Rychlewski, TA Rynearson, J Schmutz, H Shapiro, M Siaut, M Stanley, MR Sussman, AR Taylor, A Vardi, P von Dassow, W Vyverman, A Willis, LS Wyrwicz, DS Rokhsar, J Weissenbach, EV Armbrust, BR Green, Y Van de Peer, IV Grigoriev. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456(7219):239-244 [2008/11/13]. (Link)

J Labbé, X Zhang, T Yin, J Schmutz, J Grimwood, F Martin, GA Tuskan, F Le Tacon. A genetic linkage map for the ectomycorrhizal fungus Laccaria bicolor and its alignment to the whole-genome sequence assemblies. New Phytologist 180(2):316-328 [2008/10/01]. (Link)

M Srivastava, E Begovic, J Chapman, NH Putnam, U Hellsten, T Kawashima, A Kuo, T Mitros, A Salamov, ML Carpenter, AY Signorovitch, MA Moreno, K Kamm, J Grimwood, J Schmutz, H Shapiro, IV Grigoriev, LW Buss, B Schierwater, SL Dellaporta, DS Rokhsar. The Trichoplax genome and the nature of placozoans. Nature 454(7207):955-960 [2008/08/21]. (Link)

NH Putnam, T Butts, DEK Ferrier, RF Furlong, U Hellsten, T Kawashima, M Robinson-Rechavi, E Shoguchi, A Terry, J Yu, E Benito-Gutierrez, I Dubchak, J Garcia-Fernandez, JJ Gibson-Brown, IV Grigoriev, AC Horton, PJ de Jong, J Jurka, VV Kapitonov, Y Kohara, Y Kuroki, E Lindquist, S Lucas, K Osoegawa, LA Pennacchio, AA Salamov, Y Satou, T Sauka-Spengler, J Schmutz, T Shin-I, A Toyoda, M Bronner-Fraser, A Fujiyama, LZ Holland, PWH Holland, N Satoh, DS Rokhsar. The amphioxus genome and the evolution of the chordate karyotype. Nature 453(7198):1064-1071 [2008/06/19]. (Link)

RC Shoemaker, D Grant, T Olson, WC Warren, R Wing, Y Yu, H Kim, P Cregan, B Joseph, M Futrell-Griggs, W Nelson, J Davito, J Walker, J Wallis, C Kremitski, D Scheer, SW Clifton, T Graves, H Nguyen, X Wu, M Luo, J Dvorak, R Nelson, S Cannon, J Tomkins, J Schmutz, G Stacey, S Jackson. Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps. Genome 51(4):294-302 [2008/3/18]. (Link)

F Martin, A Aerts, D Ahren, A Brun, EGJ Danchin, F Duchaussoy, J Gibon, A Kohler, E Lindquist, V Pereda, A Salamov, HJ Shapiro, J Wuyts, D Blaudez, M Buee, P Brokstein, B Canback, D Cohen, PE Courty, PM Coutinho, C Delaruelle, JC Detter, A Deveau, S DiFazio, S Duplessis, L Fraissinet-Tachet, E Lucic, P Frey-Klett, C Fourrey, I Feussner, G Gay, J Grimwood, PJ Hoegger, P Jain, S Kilaru, J Labbe, YC Lin, V Legue, F Le Tacon, R Marmeisse, D Melayah, B Montanini, M Muratet, U Nehls, H Niculita-Hirzel, MPO Secq, M Peter, H Quesneville, B Rajashekar, M Reich, N Rouhier, J Schmutz, T Yin, M Chalot, B Henrissat, U Kues, S Lucas, Y Van de Peer, GK Podila, A Polle, PJ Pukkila, PM Richardson, P Rouze, IR Sanders, JE Stajich, A Tunlid, G Tuskan, IV Grigoriev. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452(7183):88-92 [2008/03/06]. (Link)

SS Merchant, SE Prochnik, O Vallon, EH Harris, SJ Karpowicz, GB Witman, A Terry, A Salamov, LK Fritz-Laylin, L Maréchal-Drouard, WF Marshall, L Qu, DR Nelson, AA Sanderfoot, MH Spalding, VV Kapitonov, Q Ren, P Ferris, E Lindquist, H Shapiro, SM Lucas, J Grimwood, J Schmutz, P Cardol, H Cerutti, G Chanfreau, C Chen, V Cognat, MT Croft, R Dent, S Dutcher, E Fernández, H Fukuzawa, D González-Ballester, D González-Halphen, A Hallmann, M Hanikenne, M Hippler, W Inwood, K Jabbari, M Kalanon, R Kuras, PA Lefebvre, SD Lemaire, AV Lobanov, M Lohr, A Manuell, I Meier, L Mets, M Mittag, T Mittelmeier, JV Moroney, J Moseley, C Napoli, AM Nedelcu, K Niyogi, SV Novoselov, IT Paulsen, G Pazour, S Purton, J Ral, DM Riaño-Pachón, W Riekhof, L Rymarquis, M Schroda, D Stern, J Umen, R Willows, N Wilson, SL Zimmer, J Allmer, J Balk, K Bisova, C Chen, M Elias, K Gendler, C Hauser, MR Lamb, H Ledford, JC Long, J Minagawa, MD Page, J Pan, W Pootakham, S Roje, A Rose, E Stahlberg, AM Terauchi, P Yang, S Ball, C Bowler, CL Dieckmann, VN Gladyshev, P Green, R Jorgensen, S Mayfield, B Mueller-Roeber, S Rajamani, RT Sayre, P Brokstein, I Dubchak, D Goodstein, L Hornick, YW Huang, J Jhaveri, Y Luo, D Martínez, WCA Ngau, B Otillar, A Poliakov, A Porter, L Szajkowski, G Werner, K Zhou, IV Grigoriev, DS Rokhsar, AR Grossman. The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions. Science 318(5848):245-250 [2007/10/12]. (Link)

CT Kelleher, R Chiu, H Shin, IE Bosdet, MI Krzywinski, CD Fjell, J Wilkin, T Yin, SP DiFazio, J Ali, JK Asano, S Chan, A Cloutier, N Girn, S Leach, D Lee, CA Mathewson, T Olson, K O'Connor, A Prabhu, DE Smailus, JM Stott, M Tsai, NH Wye, GS Yang, J Zhuang, RA Holt, NH Putnam, J Vrebalov, JJ Giovannoni, J Grimwood, J Schmutz, D Rokhsar, SJ Jones, MA Marra, GA Tuskan, J Bohlmann, BE Ellis, K Ritland, CJ Douglas, JE Schein. 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 50(6):1063-1078 [2007/06/01]. (Link)

B Palenik, J Grimwood, A Aerts, P Rouzé, A Salamov, N Putnam, C Dupont, R Jorgensen, E Derelle, S Rombauts, K Zhou, R Otillar, SS Merchant, S Podell, T Gaasterland, C Napoli, K Gendler, A Manuell, V Tai, O Vallon, G Piganeau, S Jancek, M Heijde, K Jabbari, C Bowler, M Lohr, S Robbens, G Werner, I Dubchak, GJ Pazour, Q Ren, I Paulsen, C Delwiche, J Schmutz, D Rokhsar, Y Van de Peer, H Moreau, IV Grigoriev. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. PNAS 104(18):7705-7710 [2007/05/01]. (Link)

Oudot-Le Secq MP, Grimwood J, Shapiro H, Armbrust EV, Bowler C, Green BR. Chloroplast genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana: comparison with other plastid genomes of the red lineage. Mol Genet Genomics. 2007 Apr;277(4):427-39. Epub 2007 Jan 25. PubMed PMID: 17252281. (Link)

T Jeffries, I Grigoriev, J Grimwood, J Laplaza, A Aerts, A Salamov, J Schmutz, E Lindquist, P Dehal, H Shapiro, Y Jin, V Passoth, P Richardson. Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis. Nat Biotech 25(3):319-326 [2007/03/04]. (Link)

SA Jackson, D Rokhsar, G Stacey, RC Shoemaker, J Schmutz, J Grimwood. Toward a Reference Sequence of the Soybean Genome: A Multiagency Effort. Crop Sci. 46(Supplement_1):S-55-S-61 [2006/11/01]. (Link)

GA Tuskan, S DiFazio, S Jansson, J Bohlmann, I Grigoriev, U Hellsten, N Putnam, S Ralph, S Rombauts, A Salamov, J Schein, L Sterck, A Aerts, RR Bhalerao, RP Bhalerao, D Blaudez, W Boerjan, A Brun, A Brunner, V Busov, M Campbell, J Carlson, M Chalot, J Chapman, G Chen, D Cooper, PM Coutinho, J Couturier, S Covert, Q Cronk, R Cunningham, J Davis, S Degroeve, A Déjardin, C dePamphilis, J Detter, B Dirks, I Dubchak, S Duplessis, J Ehlting, B Ellis, K Gendler, D Goodstein, M Gribskov, J Grimwood, A Groover, L Gunter, B Hamberger, B Heinze, Y Helariutta, B Henrissat, D Holligan, R Holt, W Huang, N Islam-Faridi, S Jones, M Jones-Rhoades, R Jorgensen, C Joshi, J Kangasjärvi, J Karlsson, C Kelleher, R Kirkpatrick, M Kirst, A Kohler, U Kalluri, F Larimer, J Leebens-Mack, J Leplé, P Locascio, Y Lou, S Lucas, F Martin, B Montanini, C Napoli, DR Nelson, C Nelson, K Nieminen, O Nilsson, V Pereda, G Peter, R Philippe, G Pilate, A Poliakov, J Razumovskaya, P Richardson, C Rinaldi, K Ritland, P Rouzé, D Ryaboy, J Schmutz, J Schrader, B Segerman, H Shin, A Siddiqui, F Sterky, A Terry, C Tsai, E Uberbacher, P Unneberg, J Vahala, K Wall, S Wessler, G Yang, T Yin, C Douglas, M Marra, G Sandberg, Y Van de Peer, D Rokhsar. The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray). Science 313(5793):1596-1604 [2006/09/15]. (Link)

RD Morin, E Chang, A Petrescu, N Liao, M Griffith, R Kirkpatrick, YS Butterfield, AC Young, J Stott, S Barber, R Babakaiff, MC Dickson, C Matsuo, D Wong, GS Yang, DE Smailus, KD Wetherby, PN Kwong, J Grimwood, CP Brinkley, M Brown-John, ND Reddix-Dugue, M Mayo, J Schmutz, J Beland, M Park, S Gibson, T Olson, GG Bouffard, M Tsai, R Featherstone, S Chand, AS Siddiqui, W Jang, E Lee, SL Klein, RW Blakesley, BR Zeeberg, S Narasimhan, JN Weinstein, CP Pennacchio, RM Myers, ED Green, L Wagner, DS Gerhard, MA Marra, SJ Jones, RA Holt. Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling. Genome Research 16(6):796-803 [2006/06/01]. (Link)

LW Hillier, TA Graves, RS Fulton, LA Fulton, KH Pepin, P Minx, C Wagner-McPherson, D Layman, K Wylie, M Sekhon, MC Becker, GA Fewell, KD Delehaunty, TL Miner, WE Nash, C Kremitzki, L Oddy, H Du, H Sun, H Bradshaw-Cordum, J Ali, J Carter, M Cordes, A Harris, A Isak, A van Brunt, C Nguyen, F Du, L Courtney, J Kalicki, P Ozersky, S Abbott, J Armstrong, EA Belter, L Caruso, M Cedroni, M Cotton, T Davidson, A Desai, G Elliott, T Erb, C Fronick, T Gaige, W Haakenson, K Haglund, A Holmes, R Harkins, K Kim, SS Kruchowski, CM Strong, N Grewal, E Goyea, S Hou, A Levy, S Martinka, K Mead, MD McLellan, R Meyer, J Randall-Maher, C Tomlinson, S Dauphin-Kohlberg, A Kozlowicz-Reilly, N Shah, S Swearengen-Shahid, J Snider, JT Strong, J Thompson, M Yoakum, S Leonard, C Pearman, L Trani, M Radionenko, JE Waligorski, C Wang, SM Rock, A Tin-Wollam, R Maupin, P Latreille, MC Wendl, S Yang, C Pohl, JW Wallis, J Spieth, TA Bieri, N Berkowicz, JO Nelson, J Osborne, L Ding, R Meyer, A Sabo, Y Shotland, P Sinha, PE Wohldmann, LL Cook, MT Hickenbotham, J Eldred, D Williams, TA Jones, X She, FD Ciccarelli, E Izaurralde, J Taylor, J Schmutz, RM Myers, DR Cox, X Huang, JD McPherson, ER Mardis, SW Clifton, WC Warren, AT Chinwalla, SR Eddy, MA Marra, I Ovcharenko, TS Furey, W Miller, EE Eichler, P Bork, M Suyama, D Torrents, RH Waterston, RK Wilson. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature 434(7034):724-731 [2005/04/07]. (Link)

PF Colosimo, KE Hosemann, S Balabhadra, G Villarreal, M Dickson, J Grimwood, J Schmutz, RM Myers, D Schluter, DM Kingsley. Widespread Parallel Evolution in Sticklebacks by Repeated Fixation of Ectodysplasin Alleles. Science 307(5717):1928-1933 [2005/03/25]. (Link)

J Martin, C Han, LA Gordon, A Terry, S Prabhakar, X She, G Xie, U Hellsten, YM Chan, M Altherr, O Couronne, A Aerts, E Bajorek, S Black, H Blumer, E Branscomb, NC Brown, WJ Bruno, JM Buckingham, DF Callen, CS Campbell, ML Campbell, EW Campbell, C Caoile, JF Challacombe, LA Chasteen, O Chertkov, HC Chi, M Christensen, LM Clark, JD Cohn, M Denys, JC Detter, M Dickson, M Dimitrijevic-Bussod, J Escobar, JJ Fawcett, D Flowers, D Fotopulos, T Glavina, M Gomez, E Gonzales, D Goodstein, LA Goodwin, DL Grady, I Grigoriev, M Groza, N Hammon, T Hawkins, L Haydu, CE Hildebrand, W Huang, S Israni, J Jett, PB Jewett, K Kadner, H Kimball, A Kobayashi, M Krawczyk, T Leyba, JL Longmire, F Lopez, Y Lou, S Lowry, T Ludeman, CF Manohar, GA Mark, KL McMurray, LJ Meincke, J Morgan, RK Moyzis, MO Mundt, AC Munk, RD Nandkeshwar, S Pitluck, M Pollard, P Predki, B Parson-Quintana, L Ramirez, S Rash, J Retterer, DO Ricke, DL Robinson, A Rodriguez, A Salamov, EH Saunders, D Scott, T Shough, RL Stallings, M Stalvey, RD Sutherland, R Tapia, JG Tesmer, N Thayer, LS Thompson, H Tice, DC Torney, M Tran-Gyamfi, M Tsai, LE Ulanovsky, A Ustaszewska, N Vo, P Scott White, AL Williams, PL Wills, J Wu, K Wu, J Yang, P DeJong, D Bruce, NA Doggett, L Deaven, J Schmutz, J Grimwood, P Richardson, DS Rokhsar, EE Eichler, P Gilna, SM Lucas, RM Myers, EM Rubin, LA Pennacchio. The sequence and analysis of duplication-rich human chromosome 16. Nature 432(7020):988-994 [2004/12/23]. (Link)

J Schmutz, J Grimwood. Genomes: Fowl sequence. Nature 432(7018):679-680 [2004/12/09]. (Link)

JP Noonan, J Grimwood, J Danke, J Schmutz, M Dickson, CT Amemiya, RM Myers. Coelacanth genome sequence reveals the evolutionary history of vertebrate genes. Genome Research 14(12):2397-2405 [2004/12/01]. (Link)

DS Gerhard, L Wagner, EA Feingold, CM Shenmen, LH Grouse, G Schuler, SL Klein, S Old, R Rasooly, P Good, M Guyer, AM Peck, JG Derge, D Lipman, FS Collins, W Jang, S Sherry, M Feolo, L Misquitta, E Lee, K Rotmistrovsky, SF Greenhut, CF Schaefer, K Buetow, TI Bonner, D Haussler, J Kent, M Kiekhaus, T Furey, M Brent, C Prange, K Schreiber, N Shapiro, NK Bhat, RF Hopkins, F Hsie, T Driscoll, MB Soares, TL Casavant, TE Scheetz, Brown-stein MJ, TB Usdin, S Toshiyuki, P Carninci, Y Piao, DB Dudekula, MS Ko, K Kawakami, Y Suzuki, S Sugano, CE Gruber, MR Smith, B Simmons, T Moore, R Waterman, SL Johnson, Y Ruan, CL Wei, S Mathavan, PH Gunaratne, J Wu, AM Garcia, SW Hulyk, E Fuh, Y Yuan, A Sneed, C Kowis, A Hodgson, DM Muzny, J McPherson, RA Gibbs, J Fahey, E Helton, M Ketteman, A Madan, S Rodrigues, A Sanchez, M Whiting, A Madari, AC Young, KD Wetherby, SJ Granite, PN Kwong, CP Brinkley, RL Pearson, GG Bouffard, RW Blakesly, ED Green, MC Dickson, AC Rodriguez, J Grimwood, J Schmutz, RM Myers, YS Butterfield, M Griffith, OL Griffith, MI Krzywinski, N Liao, R Morin, R Morrin, D Palmquist, AS Petrescu, U Skalska, DE Smailus, JM Stott, A Schnerch, JE Schein, SJ Jones, RA Holt, A Baross, MA Marra, S Clifton, KA Makowski, S Bosak, J Malek. The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC). Genome Research 14(10b):2121-2127 [2004/10/15]. (Link)

CL Peichel, JA Ross, CK Matson, M Dickson, J Grimwood, J Schmutz, RM Myers, S Mori, D Schluter, DM Kingsley. The Master Sex-Determination Locus in Threespine Sticklebacks Is on a Nascent Y Chromosome. Curr Biol 14(16):1416-1424 [2004/08/24]. (Link)

J Schmutz, J Martin, A Terry, O Couronne, J Grimwood, S Lowry, LA Gordon, D Scott, G Xie, W Huang, U Hellsten, M Tran-Gyamfi, X She, S Prabhakar, A Aerts, M Altherr, E Bajorek, S Black, E Branscomb, C Caoile, JF Challacombe, Y Man Chan, M Denys, JC Detter, J Escobar, D Flowers, D Fotopulos, T Glavina, M Gomez, E Gonzales, D Goodstein, I Grigoriev, M Groza, N Hammon, T Hawkins, L Haydu, S Israni, J Jett, K Kadner, H Kimball, A Kobayashi, F Lopez, Y Lou, D Martinez, C Medina, J Morgan, R Nandkeshwar, JP Noonan, S Pitluck, M Pollard, P Predki, J Priest, L Ramirez, J Retterer, A Rodriguez, S Rogers, A Salamov, A Salazar, N Thayer, H Tice, M Tsai, A Ustaszewska, N Vo, J Wheeler, K Wu, J Yang, M Dickson, J Cheng, EE Eichler, A Olsen, LA Pennacchio, DS Rokhsar, P Richardson, SM Lucas, RM Myers, EM Rubin. The DNA sequence and comparative analysis of human chromosome 5. Nature 431(7006):268-274 [2004/09/16]. (Link)

J Schmutz, J Wheeler, J Grimwood, M Dickson, J Yang, C Caoile, E Bajorek, S Black, YM Chan, M Denys, J Escobar, D Flowers, D Fotopulos, C Garcia, M Gomez, E Gonzales, L Haydu, F Lopez, L Ramirez, J Retterer, A Rodriguez, S Rogers, A Salazar, M Tsai, RM Myers. Quality assessment of the human genome sequence. Nature 429(6990):365-368 [2004/05/27]. (Link)

J Grimwood, LA Gordon, A Olsen, A Terry, J Schmutz, J Lamerdin, U Hellsten, D Goodstein, O Couronne, M Tran-Gyamfi, A Aerts, M Altherr, L Ashworth, E Bajorek, S Black, E Branscomb, S Caenepeel, A Carrano, C Caoile, Y Man Chan, M Christensen, CA Cleland, A Copeland, E Dalin, P Dehal, M Denys, JC Detter, J Escobar, D Flowers, D Fotopulos, C Garcia, AM Georgescu, T Glavina, M Gomez, E Gonzales, M Groza, N Hammon, T Hawkins, L Haydu, I Ho, W Huang, S Israni, J Jett, K Kadner, H Kimball, A Kobayashi, V Larionov, S Leem, F Lopez, Y Lou, S Lowry, S Malfatti, D Martinez, P McCready, C Medina, J Morgan, K Nelson, M Nolan, I Ovcharenko, S Pitluck, M Pollard, AP Popkie, P Predki, G Quan, L Ramirez, S Rash, J Retterer, A Rodriguez, S Rogers, A Salamov, A Salazar, X She, D Smith, T Slezak, V Solovyev, N Thayer, H Tice, M Tsai, A Ustaszewska, N Vo, M Wagner, J Wheeler, K Wu, G Xie, J Yang, I Dubchak, TS Furey, P DeJong, M Dickson, D Gordon, EE Eichler, LA Pennacchio, P Richardson, L Stubbs, DS Rokhsar, RM Myers, EM Rubin, SM Lucas. The DNA sequence and biology of human chromosome 19. Nature 428(6982):529-535 [2004/04/01/print]. (Link)

JP Noonan, J Grimwood, J Schmutz, M Dickson, RM Myers. Gene Conversion and the Evolution of Protocadherin Gene Cluster Diversity. Genome Research 14(3):354-366 [2004/03/01]. (Link)

International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431(7011):931-945 [2004/10/21]. (Link)

J Schmutz, J Grimwood, R Myers. Assembly of DNA Sequencing Data. Bacterial Artificial Chromosomes. 255:319-332 [2004]. (Link)

J Schmutz, J Grimwood, R Myers. Sequence Finishing. Bacterial Artificial Chromosomes. 255:333-342 [2004]. (Link)

J Schmutz, J Grimwood, R Myers. Quality Assessment of Finished BAC Sequences. Bacterial Artificial Chromosomes. 255:343-349 [2004]. (Link)

DM Kingsley, B Zhu, K Osoegawa, PJ de Jong, J Schein, M Marra, C Peichel, C Amemiya, D Schluter, S Balabhadra, B Friedlander, YM Cha, M Dickson, J Grimwood, J Schmutz, WS Talbot, R Myers. New Genomic Tools for Molecular Studies of Evolutionary Change in Threespine Sticklebacks. Behaviour 141(11-12):1331-1344 [2004]. (Link)

E Murphy, D Yu, J Grimwood, J Schmutz, M Dickson, MA Jarvis, G Hahn, JA Nelson, RM Myers, TE Shenk. Coding potential of laboratory and clinical strains of human megalovirus. PNAS 100(25):14976-14981 [2003/12/09]. (Link)

JP Noonan, J Li, L Nguyen, C Caoile, M Dickson, J Grimwood, J Schmutz, MW Feldman, RM Myers. Extensive Linkage Disequilibrium, a Common 16.7-Kilobase Deletion, and Evidence of Balancing Selection in the Human Protocadherin Cluster. Am J Hum Genet 72(3):621-635 [2003/03/01]. (Link)

J Schmutz, J Wheeler, J Grimwood, M Dickson, R Myers. Assessing the Quality of Finished Genomic Sequence. Cold Spring Harbor Symposia on Quantitative Biology 68: 31 -38 [2003/01/01]. (Link)

J Grimwood, J Schmutz. Genomics: Six is seventh. Nature 425(6960):775-776 [2003/10/23]. (Link)

Mammalian Gene Collection (MGC) Program Team. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. PNAS 99 (26):16899 -16903 [2002/12/24]. (Link)

HL Stickney, J Schmutz, IG Woods, CC Holtzer, MC Dickson, PD Kelly, RM Myers, WS Talbot. Rapid Mapping of Zebrafish Mutations With SNPs and Oligonucleotide Microarrays. Genome Research 12 (12):1929-1934 [2002/12/01]. (Link)

Q Wu, T Zhang, J Cheng, Y Kim, J Grimwood, J Schmutz, M Dickson, JP Noonan, MQ Zhang, RM Myers, T Maniatis. Comparative DNA Sequence Analysis of Mouse and Human Protocadherin Gene Clusters. Genome Research 11(3):389-404 [2001/03/01]. (Link)

The International Human Genome Mapping Consortium. A physical map of the human genome. Nature 409 (6822):934-941 [2001/02/15]. (Link)

International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409 (6822):860-921 [2001/02/15]. (Link)