Genomes and Genes
Affiliation: Wellcome Trust Genome Campus
- Zepeda Mendoza C, Mukhopadhyay S, Wong E, Harder N, Splinter E, de Wit E, et al. Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2. BMC Genomics. 2015;16:982 pubmed publisher..Altogether, our PE-4Cseq analysis pipeline provides a comprehensive characterization of DNA deletion effects on chromatin structure and function. ..
- Rensch T, Villar D, Horvath J, Odom D, Flicek P. Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data. Genome Biol. 2016;17:139 pubmed publisher..Although largely consistent with previous studies in individual vertebrates, our integrated cross-species analysis provides valuable insights into the evolutionary dynamics of mitochondrial heteroplasmy. ..
- Flicek P, Birney E. Sense from sequence reads: methods for alignment and assembly. Nat Methods. 2009;6:S6-S12 pubmed publisher..We discuss the current algorithmic approaches and future directions of these fundamental tools and provide specific examples for some commonly used tools. ..
- Cunningham F, Amode M, Barrell D, Beal K, Billis K, Brent S, et al. Ensembl 2015. Nucleic Acids Res. 2015;43:D662-9 pubmed publisher..The Ensembl code base itself is more accessible: it is now hosted on our GitHub organization page (https://github.com/Ensembl) under an Apache 2.0 open source license. ..
- Clarke L, Fairley S, Zheng Bradley X, Streeter I, Perry E, Lowy E, et al. The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data. Nucleic Acids Res. 2017;45:D854-D859 pubmed publisher..We have also introduced a new data portal that increases discoverability of our data-previously only browseable through our FTP site-by focusing on particular samples, populations or data sets of interest. ..
- Chen Y, Cunningham F, Rios D, McLaren W, Smith J, Pritchard B, et al. Ensembl variation resources. BMC Genomics. 2010;11:293 pubmed publisher..All Ensembl data is freely available at http://www.ensembl.org and from the public MySQL database server at ensembldb.ensembl.org. ..
- Ballester B, Johnson N, Proctor G, Flicek P. Consistent annotation of gene expression arrays. BMC Genomics. 2010;11:294 pubmed publisher..Consistent, accurate and updated gene expression array annotations remain critical for biological research. Our annotations facilitate accurate biological interpretation of gene expression profiles. ..
- Nelson A, Cutty S, Niini M, Stemple D, Flicek P, Houart C, et al. Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression. BMC Biol. 2014;12:81 pubmed publisher..Eomesa therefore regulates the formation of all three germ layers in the early zebrafish embryo. ..
- Coghlan A, Fiedler T, McKay S, Flicek P, Harris T, Blasiar D, et al. nGASP--the nematode genome annotation assessment project. BMC Bioinformatics. 2008;9:549 pubmed publisher..We have created new gene sets for C. briggsae, C. remanei, C. brenneri, C. japonica, and Brugia malayi using some of the best-performing gene-finders. ..
- Flicek P, Amode M, Barrell D, Beal K, Brent S, Carvalho Silva D, et al. Ensembl 2012. Nucleic Acids Res. 2012;40:D84-90 pubmed publisher..ensembl.org) with preliminary support. The past year has also seen improvements across the project. ..
- Flicek P, Brent M. Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts. Genome Biol. 2006;7 Suppl 1:S8.1-9 pubmed..MARS is able to use an arbitrary number of informant sequences and predicts a number of alternative transcripts at each gene locus...
- Wong E, Schmitt B, Kazachenka A, Thybert D, Redmond A, Connor F, et al. Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution. Nat Commun. 2017;8:1092 pubmed publisher..Our results reveal the regulatory mechanisms that interplay to drive transcription factor occupancy, chromatin state, and gene expression in complex mammalian cell states. ..
- Berthelot C, Villar D, Horvath J, Odom D, Flicek P. Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression. Nat Ecol Evol. 2018;2:152-163 pubmed publisher..Using liver as a representative somatic tissue, our results illuminate how the evolutionary stability of gene expression is profoundly entwined with both the number and conservation of surrounding promoters and enhancers. ..