Whole-genome analyses resolve early branches in the tree of life of modern birds

Autor: Bhanu Rekepalli, Jaime Huerta-Cepas, David Haussler, Beth Shapiro, Frank E. Rheindt, Bo Li, Per Alström, Oliver A. Ryder, Salvador Capella-Gutierrez, Jianwen Li, José Alfredo Samaniego, Binghang Liu, Paula F. Campos, David P. Mindell, Xiangjiang Zhan, An Pas, Yinhua Huang, Liang Liu, Scott V. Edwards, Dave Burt, David A. Ray, Andrew Dixon, Hui Li, Toni Gabaldón, Bastien Boussau, Cai Li, Hans Ellegren, Carsten Rahbek, Shengbin Li, Michael J. Braun, Peter Houde, Peter V. Lovell, Alexandros Stamatakis, Claudia C. Weber, Yong Zhang, Jian Wang, Thomas Sicheritz-Pontén, Volodymyr Zavidovych, Alexander Suh, Xiong Yinqi, Maria Paula Cruz Schneider, Stephen J. O'Brien, Ganesh Ganapathy, Shamsuzzoha Bayzid, Huanming Yang, Guojie Zhang, Alonzo Alfaro-Núñez, Claudio V. Mello, Michael Bunce, Amy C. Driskell, Francisco Prosdocimi, Zijun Xiong, Joel Cracraft, Long Zhou, Mikkel H. Schierup, Brant C. Faircloth, Gary R. Graves, F. Keith Barker, Jon Fjeldså, Benoit Nabholz, Bent E. K. Lindow, Frederick H. Sheldon, Robb T. Brumfield, Nitish Narula, Bent O. Petersen, Kasper Munch, Klaus-Peter Koepfli, Rute R. da Fonseca, Thomas L. Bailey, Kui Wu, Quiemei Zheng, Tandy Warnow, John E. McCormack, Elizabeth P. Derryberry, Linnéa Smeds, Simon Y. W. Ho, Polina L. Perelman, Siavash Mirarab, Qi Zhou, Michael William Bruford, Knud A. Jønsson, M. Thomas P. Gilbert, Ning Li, Richard E. Green, Edward L. Braun, R. Paul Scofield, Wesley C. Warren, Zhenyu Li, Fang Zhang Zhang, Warren E. Johnson, Morgan Wirthlin, Jason T. Howard, Travis C. Glenn, Ludovic Orlando, Mads F. Bertelsen, David M. Lambert, Andre J. Aberer, Erich D. Jarvis, Sankar Subramanian, Amhed Missael Vargas Velazquez, Yongli Zeng, Eske Willerslev, Jin Xiao, Shiping Liu, Wang Jun

Publikováno v: Sicheritz-Pontén, T, Li, C, Li, B, Munch, K, Schierup, M H, Bertelsen, M F, Fjeldsa, J, Jønsson, K A, Wang, J, Willerslev, E & Petersen, B 2014, ' Whole-genome analyses resolve early branches in the tree of life of modern birds ', Science, vol. 346, no. 6215, pp. 1320-1331 . https://doi.org/10.1126/science.1253451
Science
Science, American Association for the Advancement of Science, 2014, 346 (6215), pp.1320-31. ⟨10.1126/science.1253451⟩
Science, 2014, 346 (6215), pp.1320-31. ⟨10.1126/science.1253451⟩
Jarvis, E D, Mirarab, S, Aberer, A J, Li, B, Houde, P, Li, C, Ho, S Y W, Faircloth, B C, Nabholz, B, Howard, J T, Suh, A, Weber, C C, da Fonseca, R R, Li, J, Zhang, F, Li, H, Zhou, L, Narula, N, Liu, L, Ganapathy, G, Boussau, B, Bayzid, M S, Zavidovych, V, Subramanian, S, Gabaldón, T, Capella-Gutiérrez, S, Huerta-Cepas, J, Rekepalli, B, Munch, K, Schierup, M, Lindow, B, Warren, W C, Ray, D, Green, R E, Bruford, M W, Zhan, X, Dixon, A, Li, S, Li, N, Huang, Y, Derryberry, E P, Bertelsen, M F, Sheldon, F H, Brumfield, R T, Mello, C V, Lovell, P V, Wirthlin, M, Schneider, M P C, Prosdocimi, F, Samaniego, J A, Vargas Velazquez, A M, Alfaro-Núñez, A, Campos, P F, Petersen, B, Sicheritz-Ponten, T, Pas, A, Bailey, T, Scofield, P, Bunce, M, Lambert, D M, Zhou, Q, Perelman, P, Driskell, A C, Shapiro, B, Xiong, Z, Zeng, Y, Liu, S, Li, Z, Liu, B, Wu, K, Xiao, J, Yinqi, X, Zheng, Q, Zhang, Y, Yang, H, Wang, J, Smeds, L, Rheindt, F E, Braun, M, Fjeldsa, J, Orlando, L, Barker, F K, Jønsson, K A, Johnson, W, Koepfli, K-P, O'Brien, S, Haussler, D, Ryder, O A, Rahbek, C, Willerslev, E, Graves, G R, Glenn, T C, McCormack, J, Burt, D, Ellegren, H, Alström, P, Edwards, S V, Stamatakis, A, Mindell, D P, Cracraft, J, Braun, E L, Warnow, T, Jun, W, Gilbert, M T P & Zhang, G 2014, ' Whole-genome analyses resolve early branches in the tree of life of modern birds ', Science, vol. 346, no. 6215, pp. 1320-31 . https://doi.org/10.1126/science.1253451

International audience; To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::dccb1b8bc34e5e4d44d26964386c4e02
https://doi.org/10.1126/science.1253451

HPC-BLAST

Autor: Bhanu Rekepalli, Shane Sawyer, Mitchel D. Horton, R. Glenn Brook

Publikováno v: BCB

The near exponential growth in sequence data available to bioinformaticists, and the emergence of new fields of biological research, continue to fuel an incessant need for increases in sequence alignment performance. Concurrently, the High Performanc

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::55010ccbf16c2ef1621c2b94d40380de
https://doi.org/10.1145/2808719.2811435

Big data - a 21st century science Maginot Line? No-boundary thinking: shifting from the big data paradigm

Autor: Donald C. Wunsch, Jennifer L. Specker, Yu Zhang, Pengyin Chen, Dong Hai Xiong, Bindu Nanduri, Zenglu Li, Jason H. Moore, Andy D. Perkins, Steven F. Jennings, Zhongming Zhao, Karl Walker, Alison Buchan, Donald F. McMullen, Saeed Salem, Barry D. Bruce, Gail McClure, Weihua Guan, Uwe Hilgert, Shuzhong Zhang, Hongmei Jiang, Carole L. Cramer, Liming Cai, Xiuzhen Huang, Bhanu Rekepalli

Publikováno v: BioData Mining

Whether your interests lie in scientific arenas, the corporate world, or in government, you have certainly heard the praises of big data: Big data will give you new insights, allow you to become more efficient, and/or will solve your problems. While

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9019c5cf2561fbcb85e44b1a0df9f1bd
https://pubmed.ncbi.nlm.nih.gov/25670967

Instrumenting Genomic Sequence Analysis Pipeline Mothur on Shared Memory Architecture

Autor: Pragneshkumar Patel, Chanda Drennen, Junqi Yin, Annette Summers Engel, Bhanu Rekepalli

Publikováno v: XSEDE

Mothur is an open source bioinformatics pipeline used for biological sequence analysis that has gained increasing attention in the microbial ecology community. Because a large set of functionalities in Mothur are memory bound, it is well suited for s

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::6abb8c82e0513ecdc7e3a25102dbc393
https://doi.org/10.1145/2616498.2616505