A high-resolution map of human evolutionary constraint using 29 mammals

Autor: Kerstin, Lindblad-Toh, Manuel, Garber, Or, Zuk, Michael F, Lin, Brian J, Parker, Stefan, Washietl, Pouya, Kheradpour, Jason, Ernst, Gregory, Jordan, Evan, Mauceli, Lucas D, Ward, Craig B, Lowe, Alisha K, Holloway, Michele, Clamp, Sante, Gnerre, Jessica, Alföldi, Kathryn, Beal, Jean, Chang, Hiram, Clawson, James, Cuff, Federica, Di Palma, Stephen, Fitzgerald, Paul, Flicek, Mitchell, Guttman, Melissa J, Hubisz, David B, Jaffe, Irwin, Jungreis, W James, Kent, Dennis, Kostka, Marcia, Lara, Andre L, Martins, Tim, Massingham, Ida, Moltke, Brian J, Raney, Matthew D, Rasmussen, Jim, Robinson, Alexander, Stark, Albert J, Vilella, Jiayu, Wen, Xiaohui, Xie, Michael C, Zody, Jen, Baldwin, Toby, Bloom, Chee Whye, Chin, Dave, Heiman, Robert, Nicol, Chad, Nusbaum, Sarah, Young, Jane, Wilkinson, Kim C, Worley, Christie L, Kovar, Donna M, Muzny, Richard A, Gibbs, Andrew, Cree, Huyen H, Dihn, Gerald, Fowler, Shalili, Jhangiani, Vandita, Joshi, Sandra, Lee, Lora R, Lewis, Lynne V, Nazareth, Geoffrey, Okwuonu, Jireh, Santibanez, Wesley C, Warren, Elaine R, Mardis, George M, Weinstock, Richard K, Wilson, Kim, Delehaunty, David, Dooling, Catrina, Fronik, Lucinda, Fulton, Bob, Fulton, Tina, Graves, Patrick, Minx, Erica, Sodergren, Ewan, Birney, Elliott H, Margulies, Javier, Herrero, Eric D, Green, David, Haussler, Adam, Siepel, Nick, Goldman, Katherine S, Pollard, Jakob S, Pedersen, Eric S, Lander, Manolis, Kellis

Publikováno v: Nature
PubMed Central
Lindblad-Toh, K, Garber, M, Zuk, O, Lin, M F, Parker, B J, Washietl, S, Kheradpour, P, Ernst, J, Jordan, G, Mauceli, E, Ward, L D, Lowe, C B, Holloway, A K, Clamp, M, Gnerre, S, Alföldi, J, Beal, K, Chang, J, Clawson, H, Cuff, J, Di Palma, F, Fitzgerald, S, Flicek, P, Guttman, M, Hubisz, M J, Jaffe, D B, Jungreis, I, Kent, W J, Kostka, D, Lara, M, Martins, A L, Massingham, T, Moltke, I, Raney, B J, Rasmussen, M D, Robinson, J, Stark, A, Vilella, A J, Wen, J, Xie, X, Zody, M C, Baldwin, J, Bloom, T, Chin, C W, Heiman, D, Nicol, R, Nusbaum, C, Young, S, Wilkinson, J, Pedersen, J S & Broad Institute Sequencing Platform and Whole Genome Assembly Team 2011, ' A high-resolution map of human evolutionary constraint using 29 mammals ', Nature, vol. 478, no. 7370, pp. 476-82 . https://doi.org/10.1038/nature10530

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying sele

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::669061f2d8cec3d08d25af001dba00db
http://europepmc.org/articles/PMC3207357

The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures

Autor: Andreas Gruber, Stefan Washietl, Richard Neuböck, Ivo L. Hofacker

Publikováno v: University of Vienna-u:cris
Nucleic Acids Research

Many non-coding RNA genes and cis-acting regulatory elements of mRNAs contain RNA secondary structures that are critical for their function. Such functional RNAs can be predicted on the basis of thermodynamic stability and evolutionary conservation.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::068ff4e496a2ddf582e20d8f362c39e8
https://doi.org/10.1093/nar/gkm222

A benchmark of multiple sequence alignment programs upon structural RNAs

Autor: Andreas Wilm, Stefan Washietl, Paul P. Gardner

Publikováno v: Nucleic Acids Research

To date, few attempts have been made to benchmark the alignment algorithms upon nucleic acid sequences. Frequently, sophisticated PAM or BLOSUM like models are used to align proteins, yet equivalents are not considered for nucleic acids; instead, rat

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c55dd5e6e0a862f1d432f786b3c73eea
http://europepmc.org/articles/PMC1087786

Energy-based RNA consensus secondary structure prediction in multiple sequence alignments

Autor: Stefan, Washietl, Stephan H, Bernhart, Manolis, Kellis

Publikováno v: Methods in molecular biology (Clifton, N.J.). 1097

Many biologically important RNA structures are conserved in evolution leading to characteristic mutational patterns. RNAalifold is a widely used program to predict consensus secondary structures in multiple alignments by combining evolutionary inform

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::ac88939f85f1126f87cc3a86fec392e4
https://pubmed.ncbi.nlm.nih.gov/24639158

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction

Autor: Stefan Washietl, Peter F. Stadler, Manolis Kellis, Ivo L. Hofacker

Publikováno v: Nucleic Acids Research
Nucleic Acids Res.

Thermodynamic folding algorithms and structure probing experiments are commonly used to determine the secondary structure of RNAs. Here we propose a formal framework to reconcile information from both prediction algorithms and probing experiments. Th

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bb8212166af1e6d298d580a5fbcb6e68
https://pubmed.ncbi.nlm.nih.gov/22287623