2013

ENCODE Data in the UCSC Genome Browser: year 5 update.
Rosenbloom, Kate R., Sloan Cricket A., Malladi Venkat S., Dreszer Timothy R., Learned Katrina, Kirkup Vanessa M., Wong Matthew C., Maddren Morgan, Fang Ruihua, Heitner Steven G., et al.
Nucleic Acids Res. 1, Volume 41, Number D1, (2013), England, p.D56-63 doi: 10.1093/nar/gks1172
dbVar and DGVa: public archives for genomic structural variation.
Lappalainen, Ilkka, Lopez John, Skipper Lisa, Hefferon Timothy, Spalding Dylan J., Garner John, Chen Chao, Maguire Michael, Corbett Matt, Zhou George, et al.
Nucleic Acids Res. 1, Volume 41, Number D1, (2013), England, p.D936-41 doi: 10.1093/nar/gks1213
Ensembl 2013.
Flicek, Paul, Ahmed Ikhlak, Amode Ridwan M., Barrell Daniel, Beal Kathryn, Brent Simon, Carvalho-Silva Denise, Clapham Peter, Coates Guy, Fairley Susan, et al.
Nucleic Acids Res. 1, Volume 41, Number D1, (2013), England, p.D48-55 doi: 10.1093/nar/gks1236
Latent Regulatory Potential of Human-Specific Repetitive Elements
Ward, Michelle C, Wilson Michael D, Barbosa-Morais Nuno L, Schmidt Dominic, Stark Rory, Pan Qun, Schwalie Petra C, Menon Suraj, Lukk Margus, Watt Stephen, et al.
Molecular Cell. Volume 49, Number 2, (2013), p.262 - 272 doi: 10.1016/j.molcel.2012.11.013
Genomicus: five genome browsers for comparative genomics in eukaryota.
Louis, Alexandra, Muffato Matthieu, and Roest Crollius Hugues
Nucleic Acids Res. 1, Volume 41, Number D1, (2013), England, p.D700-5 doi: 10.1093/nar/gks1156

2012

MouseFinder: candidate disease genes from mouse phenotype data.
Chen, Chao-Kung K., Mungall Christopher J., Gkoutos Georgios V., Doelken Sandra C., Köhler Sebastian, Ruef Barbara J., Smith Cynthia, Westerfield Monte, Robinson Peter N., Lewis Suzanna E., et al.
Hum Mutat. 2, Volume 33, Number 5, (2012), p.858-866 doi: 10.1002/humu.22051
Toward community standards in the quest for orthologs.
Dessimoz, Christophe, Gabaldón Toni, Roos David S., Sonnhammer Erik L. L., Herrero Javier, and the for Consortium Quest Orthologs
Bioinformatics. 3, Volume 28, Number 6, (2012), p.900-904 doi: 10.1093/bioinformatics/bts050
Paralogous annotation of disease-causing variants in long QT syndrome genes.
Ware, James S., Walsh Roddy, Cunningham Fiona, Birney Ewan, and Cook Stuart A.
Hum Mutat. 5, Volume 33, Number 8, (2012), p.1188-1191 doi: 10.1002/humu.22114
Integrative annotation of chromatin elements from ENCODE data.
Hoffman, Michael M., Ernst Jason, Wilder Steven P., Kundaje Anshul, Harris Robert S., Libbrecht Max, Giardine Belinda, Ellenbogen Paul M., Bilmes Jeffrey A., Birney Ewan, et al.
Nucleic Acids Res. 12, (2012), doi: 10.1093/nar/gks1284
Genome sequencing and analysis of the tasmanian devil and its transmissible cancer.
Murchison, Elizabeth P., Schulz-Trieglaff Ole B., Ning Zemin, Alexandrov Ludmil B., Bauer Markus J., Fu Beiyuan, Hims Matthew, Ding Zhihao, Ivakhno Sergii, Stewart Caitlin, et al.
Cell. 2, Volume 148, Number 4, (2012), United States, p.780-91 doi: 10.1016/j.cell.2011.11.065
Insights into Negative Regulation by the Glucocorticoid Receptor from Genome-wide Profiling of Inflammatory Cistromes.
Uhlenhaut, Henriette N., Barish Grant D., Yu Ruth T., Downes Michael, Karunasiri Malith, Liddle Christopher, Schwalie Petra, Hübner Norbert, and Evans Ronald M.
Mol Cell. 11, (2012), doi: 10.1016/j.molcel.2012.10.013
Rare copy number variants contribute to congenital left-sided heart disease.
Hitz, Marc-Phillip P., Lemieux-Perreault Louis-Philippe P., Marshall Christian, Feroz-Zada Yassamin, Davies Robbie, Yang Shi Wei, Lionel Anath Christopher, D'Amours Guylaine, Lemyre Emmanuelle, Cullum Rebecca, et al.
PLoS Genet. 9, Volume 8, Number 9, (2012), United States, p.e1002903 doi: 10.1371/journal.pgen.1002903
A systematic survey of loss-of-function variants in human protein-coding genes.
MacArthur, Daniel G., Balasubramanian Suganthi, Frankish Adam, Huang Ni, Morris James, Walter Klaudia, Jostins Luke, Habegger Lukas, Pickrell Joseph K., Montgomery Stephen B., et al.
Science. 2, Volume 335, Number 6070, (2012), United States, p.823-8 doi: 10.1126/science.1215040
Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules.
Faure, Andre J., Schmidt Dominic, Watt Stephen, Schwalie Petra C., Wilson Michael D., Xu Huiling, Ramsay Robert G., Odom Duncan T., and Flicek Paul
Genome Res. 10, Volume 22, Number 11, (2012), United States, p.2163-75 doi: 10.1101/gr.136507.111
Insights into hominid evolution from the gorilla genome sequence.
Scally, Aylwyn, Dutheil Julien Y., Hillier LaDeana W., Jordan Gregory E., Goodhead Ian, Herrero Javier, Hobolth Asger, Lappalainen Tuuli, Mailund Thomas, Marques-Bonet Tomas, et al.
Nature. 3, Volume 483, Number 7388, (2012), England, p.169-75 doi: 10.1038/nature10842
Analyses of pig genomes provide insight into porcine demography and evolution.
Groenen, Martien A. M., Archibald Alan L., Uenishi Hirohide, Tuggle Christopher K., Takeuchi Yasuhiro, Rothschild Max F., Rogel-Gaillard Claire, Park Chankyu, Milan Denis, Megens Hendrik-Jan J., et al.
Nature. 11, Volume 491, Number 7424, (2012), England, p.393-8 doi: 10.1038/nature11622
Deleterious- and Disease-Allele Prevalence in Healthy Individuals: Insights from Current Predictions, Mutation Databases, and Population-Scale Resequencing.
Xue, Yali, Chen Yuan, Ayub Qasim, Huang Ni, Ball Edward V., Mort Matthew, Phillips Andrew D., Shaw Katy, Stenson Peter D., Cooper David N., et al.
Am J Hum Genet. 12, Volume 91, Number 6, (2012), p.1022-1032 doi: 10.1016/j.ajhg.2012.10.015
Genome-wide meta-analysis of common variant differences between men and women.
Boraska, Vesna, Jerončić Ana, Colonna Vincenza, Southam Lorraine, Nyholt Dale R., Rayner Nigel William, Perry John R. B., Toniolo Daniela, Albrecht Eva, Ang Wei, et al.
Hum Mol Genet. 11, Volume 21, Number 21, (2012), England, p.4805-15 doi: 10.1093/hmg/dds304
Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans.
Mallon, Ann-Marie M., Iyer Vivek, Melvin David, Morgan Hugh, Parkinson Helen, Brown Steve D. M., Flicek Paul, and Skarnes William C.
Mamm Genome. 10, Volume 23, Number 9-10, (2012), United States, p.641-52 doi: 10.1007/s00335-012-9428-9
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.
Kersey, Paul J., Staines Daniel M., Lawson Daniel, Kulesha Eugene, Derwent Paul, Humphrey Jay C., Hughes Daniel S. T., Keenan Stephan, Kerhornou Arnaud, Koscielny Gautier, et al.
Nucleic Acids Res. 1, Volume 40, Number Database issue, (2012), England, p.D91-7 doi: 10.1093/nar/gkr895
Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages.
Schmidt, Dominic, Schwalie Petra C., Wilson Michael D., Ballester Benoit, Gonçalves Angela, Kutter Claudia, Brown Gordon D., Marshall Aileen, Flicek Paul, and Odom Duncan T.
Cell. 1, Volume 148, Number 1-2, (2012), United States, p.335-48 doi: 10.1016/j.cell.2011.11.058
Analysis of variation at transcription factor binding sites in Drosophila and humans.
Spivakov, Mikhail, Akhtar Junaid, Kheradpour Pouya, Beal Kathryn, Girardot Charles, Koscielny Gautier, Herrero Javier, Kellis Manolis, Furlong Eileen Em, and Birney Ewan
Genome Biol. Volume 13, Number 9, (2012), England, p.R49 doi: 10.1186/gb-2012-13-9-r49
The 1000 Genomes Project: data management and community access.
Clarke, Laura, Zheng-Bradley Xiangqun, Smith Richard, Kulesha Eugene, Xiao Chunlin, Toneva Iliana, Vaughan Brendan, Preuss Don, Leinonen Rasko, Shumway Martin, et al.
Nat Methods. Volume 9, Number 5, (2012), p.459-462 doi: 10.1038/nmeth.1974
De novo assembly and genotyping of variants using colored de Bruijn graphs.
Iqbal, Zamin, Caccamo Mario, Turner Isaac, Flicek Paul, and McVean Gil
Nat Genet. Volume 44, Number 2, (2012), United States, p.226-32 doi: 10.1038/ng.1028
Large-Scale Identification of MicroRNA Targets in Murine Dgcr8-Deficient Embryonic Stem Cell Lines.
Davis, Matthew P. A., Abreu-Goodger Cei, van Dongen Stijn, Lu Dong, Tate Peri H., Bartonicek Nenad, Kutter Claudia, Liu Pentao, Skarnes William C., Enright Anton J., et al.
PLoS One. Volume 7, Number 8, (2012), United States, p.e41762 doi: 10.1371/journal.pone.0041762
A Combined Functional Annotation Score for Non-Synonymous Variants.
Lopes, Margarida C., Joyce Chris, Ritchie Graham R. S., John Sally L., Cunningham Fiona, Asimit Jennifer, and Zeggini Eleftheria
Hum Hered. 1, Volume 73, Number 1, (2012), p.47-51 doi: 10.1159/000334984
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm.
Löytynoja, Ari, Vilella Albert J., and Goldman Nick
Bioinformatics. 7, Volume 28, Number 13, (2012), England, p.1684-91 doi: 10.1093/bioinformatics/bts198
An integrated map of genetic variation from 1,092 human genomes.
Consortium, Genomes Project 1000
Nature. 11, Volume 491, Number 7422, (2012), England, p.56-65 doi: 10.1038/nature11632
Maps for the world of genomic medicine: The 2011 CSHL Personal Genomes Meeting.
Zheng-Bradley, Xiangqun, and Flicek Paul
Hum Mutat. 1, Volume 33, Number 6, (2012), p.1016-1019 doi: 10.1002/humu.22024
An integrated functional genomics approach identifies the regulatory network directed by brachyury (T) in chordoma.
Nelson, Andrew C., Pillay Nischalan, Henderson Stephen, Presneau Nadège, Tirabosco Roberto, Halai Dina, Berisha Fitim, Flicek Paul, Stemple Derek L., Stern Claudio, et al.
J Pathol. 7, Volume 228, Number 3, (2012), England, p.274-85 doi: 10.1002/path.4082
Ensembl 2012.
Flicek, Paul, Amode Ridwan M., Barrell Daniel, Beal Kathryn, Brent Simon, Carvalho-Silva Denise, Clapham Peter, Coates Guy, Fairley Susan, Fitzgerald Stephen, et al.
Nucleic Acids Res. 1, Volume 40, Number 1, (2012), England, p.D84-90 doi: 10.1093/nar/gkr991
BLUEPRINT to decode the epigenetic signature written in blood.
Adams, David, Altucci Lucia, Antonarakis Stylianos E., Ballesteros Juan, Beck Stephan, Bird Adrian, Bock Christoph, Boehm Bernhard, Campo Elias, Caricasole Andrea, et al.
Nat Biotechnol. Volume 30, Number 3, (2012), United States, p.224-6 doi: 10.1038/nbt.2153
MiR-25 Regulates Wwp2 and Fbxw7 and Promotes Reprogramming of Mouse Fibroblast Cells to iPSCs.
Lu, Dong, Davis Matthew P. A., Abreu-Goodger Cei, Wang Wei, Campos Lia S., Siede Julia, Vigorito Elena, Skarnes William C., Dunham Ian, Enright Anton J., et al.
PLoS One. Volume 7, Number 8, (2012), United States, p.e40938 doi: 10.1371/journal.pone.0040938
CreZOO–the European virtual repository of Cre and other targeted conditional driver strains.
Chandras, Christina, Zouberakis Michael, Salimova Ekaterina, Smedley Damian, Rosenthal Nadia, and Aidinis Vassilis
Database (Oxford). 1, Volume 2012, (2012), England, p.bas029 doi: 10.1093/database/bas029
An integrated encyclopedia of DNA elements in the human genome.
Consortium, ENCODE Project
Nature. 9, Volume 489, Number 7414, (2012), England, p.57-74 doi: 10.1038/nature11247
Analyzing genomic data: understanding the genome
Fernández-Suárez, X. M.
Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery. 3, Volume 2, Number 2, (2012), p.116-137 doi: 10.1002/widm.54
Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.
Goncalves, Angela, Leigh-Brown Sarah, Thybert David, Stefflova Klara, Turro Ernest, Flicek Paul, Brazma Alvis, Odom Duncan T., and Marioni John C.
Genome Res. 8, Volume 22, Number 12, (2012), United States, p.2376-84 doi: 10.1101/gr.142281.112

2011

SORGOdb: Superoxide Reductase Gene Ontology curated DataBase.
Lucchetti-Miganeh, Céline, Goudenège David, Thybert David, Salbert Gilles, and Barloy-Hubler Frédérique
BMC Microbiol. Volume 11, (2011), England, p.105 doi: 10.1186/1471-2180-11-105
The functional spectrum of low-frequency coding variation.
Marth, Gabor T., Yu Fuli, Indap Amit R., Garimella Kiran, Gravel Simon, Leong Wen Fung, Tyler-Smith Chris, Bainbridge Matthew, Blackwell Thomas, Zheng-Bradley Xiangqun, et al.
Genome Biol. 9, Volume 12, Number 9, (2011), p.R84 doi: 10.1186/gb-2011-12-9-r84
Deciphering the colon cancer genes–report of the InSiGHT-Human Variome Project Workshop, UNESCO, Paris 2010.
Kohonen-Corish, Maija R. J., Macrae Finlay, Genuardi Maurizio, Aretz Stefan, Bapat Bharati, Bernstein Inge T., Burn John, Cotton Richard G. H., den Dunnen Johan T., Frebourg Thierry, et al.
Hum Mutat. 4, Volume 32, Number 4, (2011), United States, p.491-4 doi: 10.1002/humu.21450
Variation in genome-wide mutation rates within and between human families.
Conrad, Donald F., Keebler Jonathan E. M., Depristo Mark A., Lindsay Sarah J., Zhang Yujun, Casals Ferran, Idaghdour Youssef, Hartl Chris L., Torroja Carlos, Garimella Kiran V., et al.
Nat Genet. 7, Volume 43, Number 7, (2011), United States, p.712-4 doi: 10.1038/ng.862
BioMart as an integration solution for the International Knockout Mouse Consortium.
Oakley, Darren J., Iyer Vivek, Skarnes William C., and Smedley Damian
Database (Oxford). Volume 2011, (2011), England, p.bar028 doi: 10.1093/database/bar028
A high-resolution map of human evolutionary constraint using 29 mammals.
Lindblad-Toh, Kerstin, Garber Manuel, Zuk Or, Lin Michael F., Parker Brian J., Washietl Stefan, Kheradpour Pouya, Ernst Jason, Jordan Gregory, Mauceli Evan, et al.
Nature. 10, Volume 478, Number 7370, (2011), England, p.476-82 doi: 10.1038/nature10530
The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium.
Ringwald, Martin, Iyer Vivek, Mason Jeremy C., Stone Kevin R., Tadepally Hamsa D., Kadin James A., Bult Carol J., Eppig Janan T., Oakley Darren J., Briois Sebastien, et al.
Nucleic Acids Res. 1, Volume 39, Number Database issue, (2011), England, p.D849-55 doi: 10.1093/nar/gkq879
Hes6 is required for actin cytoskeletal organization in differentiating C2C12 myoblasts.
Malone, Caroline M. P., Domaschenz Renae, Amagase Yoko, Dunham Ian, Murai Kasumi, and Jones Philip H.
Exp Cell Res. 7, Volume 317, Number 11, (2011), United States, p.1590-602 doi: 10.1016/j.yexcr.2011.03.023
Evaluating the fidelity of de novo short read metagenomic assembly using simulated data.
Pignatelli, Miguel, and Moya Andrés
PLoS One. Volume 6, Number 5, (2011), United States, p.e19984 doi: 10.1371/journal.pone.0019984
Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.
Renfree, Marilyn B., Papenfuss Anthony T., Deakin Janine E., Lindsay James, Heider Thomas, Belov Katherine, Rens Willem, Waters Paul D., Pharo Elizabeth A., Shaw Geoff, et al.
Genome Biol. 8, Volume 12, Number 8, (2011), p.R81 doi: 10.1186/gb-2011-12-8-r81
Investigating the effect of paralogs on microarray gene-set analysis.
Faure, Andre J., Seoighe Cathal, and Mulder Nicola J.
BMC Bioinformatics. 1, Volume 12, Number 1, (2011), p.29 doi: 10.1186/1471-2105-12-29
Towards BioDBcore: a community-defined information specification for biological databases.
Gaudet, Pascale, Bairoch Amos, Field Dawn, Sansone Susanna-Assunta A., Taylor Chris, Attwood Teresa K., Bateman Alex, Blake Judith A., Bult Carol J., Cherry Michael J., et al.
Database (Oxford). Volume 2011, (2011), England, p.baq027 doi: 10.1093/database/baq027
Cre recombinase resources for conditional mouse mutagenesis.
Smedley, Damian, Salimova Ekaterina, and Rosenthal Nadia
Methods. 4, Volume 53, Number 4, (2011), United States, p.411-6 doi: 10.1016/j.ymeth.2010.12.027
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.
Song, Lingyun, Zhang Zhancheng, Grasfeder Linda L., Boyle Alan P., Giresi Paul G., Lee Bum-Kyu K., Sheffield Nathan C., Gräf Stefan, Huss Mikael, Keefe Damian, et al.
Genome Res. 7, Volume 21, Number 10, (2011), United States, p.1757-67 doi: 10.1101/gr.121541.111
Mapping copy number variation by population-scale genome sequencing.
Mills, Ryan E., Walter Klaudia, Stewart Chip, Handsaker Robert E., Chen Ken, Alkan Can, Abyzov Alexej, Yoon Seungtai Chris, Ye Kai, Cheetham Keira R., et al.
Nature. 2, Volume 470, Number 7332, (2011), England, p.59-65 doi: 10.1038/nature09708
BioMart Central Portal: an open database network for the biological community.
Guberman, Jonathan M., Ai J., Arnaiz O., Baran Joachim, Blake Andrew, Baldock Richard, Chelala Claude, Croft David, Cros Anthony, Cutts Rosalind J., et al.
Database (Oxford). Volume 2011, (2011), England, p.bar041 doi: 10.1093/database/bar041
Ensembl 2011.
Flicek, Paul, Amode Ridwan M., Barrell Daniel, Beal Kathryn, Brent Simon, Chen Yuan, Clapham Peter, Coates Guy, Fairley Susan, Fitzgerald Stephen, et al.
Nucleic Acids Res. 1, Volume 39, Number Database issue, (2011), England, p.D800-6 doi: 10.1093/nar/gkq1064
The Variant Call Format and VCFtools.
Danecek, Petr, Auton Adam, Abecasis Goncalo, Albers Cornelis A., Banks Eric, Depristo Mark A., Handsaker Robert, Lunter Gerton, Marth Gabor, Sherry Stephen T., et al.
Bioinformatics. 6, Volume 27, Number 15, (2011), p.2156-8 doi: 10.1093/bioinformatics/btr330
Modernizing reference genome assemblies.
Church, Deanna M., Schneider Valerie A., Graves Tina, Auger Katherine, Cunningham Fiona, Bouk Nathan, Chen Hsiu-Chuan C., Agarwala Richa, McLaren William M., Ritchie Graham R. S., et al.
PLoS Biol. 7, Volume 9, Number 7, (2011), United States, p.e1001091 doi: 10.1371/journal.pbio.1001091
Closure of the NCBI SRA and implications for the long-term future of genomics data storage.
Lipman, David, Flicek Paul, Salzberg Steven, Gerstein Mark, and Knight Rob
Genome Biol. Volume 12, Number 3, (2011), England, p.402 doi: 10.1186/gb-2011-12-3-402
RNAcentral: A vision for an international database of RNA sequences.
Bateman, Alex, Agrawal Shipra, Birney Ewan, Bruford Elspeth A., Bujnicki Janusz M., Cochrane Guy, Cole James R., Dinger Marcel E., Enright Anton J., Gardner Paul P., et al.
RNA. 11, Volume 17, Number 11, (2011), United States, p.1941-6 doi: 10.1261/rna.2750811
Comparative and demographic analysis of orang-utan genomes.
Locke, Devin P., Hillier LaDeana W., Warren Wesley C., Worley Kim C., Nazareth Lynne V., Muzny Donna M., Yang Shiaw-Pyng P., Wang Zhengyuan, Chinwalla Asif T., Minx Pat, et al.
Nature. 1, Volume 469, Number 7331, (2011), England, p.529-33 doi: 10.1038/nature09687
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.
Boyle, Alan P., Song Lingyun, Lee Bum-Kyu K., London Darin, Keefe Damian, Birney Ewan, Iyer Vishwanath R., Crawford Gregory E., and Furey Terrence S.
Genome Res. 3, Volume 21, Number 3, (2011), United States, p.456-64 doi: 10.1101/gr.112656.110
Disease and phenotype data at ensembl.
Spudich, Giulietta M., and Fernández-Suárez Xosé M.
Curr Protoc Hum Genet. 2, Volume Chapter 6, (2011), United States, p.Unit6.11 doi: 10.1002/0471142905.hg0611s69
Genome sequence of Lactococcus garvieae UNIUD074, isolated in Italy from a lactococcosis outbreak.
Reimundo, Pilar, Pignatelli Miguel, Alcaraz Luis David, D'Auria Giuseppe, Moya Andrés, and Guijarro José A.
J Bacteriol. 7, Volume 193, Number 14, (2011), United States, p.3684-5 doi: 10.1128/JB.05210-11
Towards BioDBcore: a community-defined information specification for biological databases.
Gaudet, Pascale, Bairoch Amos, Field Dawn, Sansone Susanna-Assunta A., Taylor Chris, Attwood Teresa K., Bateman Alex, Blake Judith A., Bult Carol J., Cherry Michael J., et al.
Nucleic Acids Res. 1, Volume 39, Number Database issue, (2011), England, p.D7-10 doi: 10.1093/nar/gkq1173
Ensembl BioMarts: a hub for data retrieval across taxonomic space.
Kinsella, Rhoda J., Kähäri Andreas, Haider Syed, Zamora Jorge, Proctor Glenn, Spudich Giulietta, Almeida-King Jeff, Staines Daniel, Derwent Paul, Kerhornou Arnaud, et al.
Database (Oxford). Volume 2011, (2011), England, p.bar030 doi: 10.1093/database/bar030
Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses.
Vilella, Albert J., Birney Ewan, Flicek Paul, and Herrero Javier
Genome Biol. 2, Volume 12, Number 2, (2011), p.401 doi: 10.1186/gb-2011-12-2-401
A User's Guide to the Encyclopedia of DNA Elements (ENCODE).
Consortium, ENCODE Project
PLoS Biol. 4, Volume 9, Number 4, (2011), United States, p.e1001046 doi: 10.1371/journal.pbio.1001046
Demographic history and rare allele sharing among human populations.
Gravel, Simon, Henn Brenna M., Gutenkunst Ryan N., Indap Amit R., Marth Gabor T., Clark Andrew G., Yu Fuli, Gibbs Richard A., and Bustamante Carlos D.
Proc Natl Acad Sci U S A. 7, Volume 108, Number 29, (2011), United States, p.11983-8 doi: 10.1073/pnas.1019276108

2010

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.
McLaren, William, Pritchard Bethan, Rios Daniel, Chen Yuan, Flicek Paul, and Cunningham Fiona
Bioinformatics. 6, Volume 26, Number 16, (2010), p.2069-70 doi: 10.1093/bioinformatics/btq330
XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments.
Swertz, Morris A., van der Velde Joeri K., Tesson Bruno M., Scheltema Richard A., Arends Danny, Vera Gonzalo, Alberts Rudi, Dijkstra Martijn, Schofield Paul, Schughart Klaus, et al.
Genome Biol. 3, Volume 11, Number 3, (2010), p.R27 doi: 10.1186/gb-2010-11-3-r27
Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene.
Gheldof, Nele, Smith Emily M., Tabuchi Tomoko M., Koch Christoph M., Dunham Ian, Stamatoyannopoulos John A., and Dekker Job
Nucleic Acids Res. 7, Volume 38, Number 13, (2010), England, p.4325-36 doi: 10.1093/nar/gkq175
EMMA–mouse mutant resources for the international scientific community.
Wilkinson, Phil, Sengerova Jitka, Matteoni Raffaele, Chen Chao-Kung K., Soulat Gaetan, Ureta-Vidal Abel, Fessele Sabine, Hagn Michael, Massimi Marzia, Pickford Karen, et al.
Nucleic Acids Res. 1, Volume 38, Number Database issue, (2010), England, p.D570-6 doi: 10.1093/nar/gkp799
High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta.
Daelemans, Caroline, Ritchie Matthew E., Smits Guillaume, Abu-Amero Sayeda, Sudbery Ian M., Forrest Matthew S., Campino Susana, Clark Taane G., Stanier Philip, Kwiatkowski Dominic, et al.
BMC Genet. 4, Volume 11, Number 1, (2010), p.25 doi: 10.1186/1471-2156-11-25
A CTCF-independent role for cohesin in tissue-specific transcription.
Schmidt, Dominic, Schwalie Petra C., Ross-Innes Caryn S., Hurtado Antoni, Brown Gordon D., Carroll Jason S., Flicek Paul, and Odom Duncan T.
Genome Res. 4, Volume 20, Number 5, (2010), p.578-88 doi: 10.1101/gr.100479.109
Heritable individual-specific and allele-specific chromatin signatures in humans.
McDaniell, Ryan, Lee Bum-Kyu K., Song Lingyun, Liu Zheng, Boyle Alan P., Erdos Michael R., Scott Laura J., Morken Mario A., Kucera Katerina S., Battenhouse Anna, et al.
Science. 4, Volume 328, Number 5975, (2010), United States, p.235-9 doi: 10.1126/science.1184655
Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics.
Gruenberger, Michael, Alberts Rudi, Smedley Damian, Swertz Morris, Schofield Paul, consortium The CASIMIR, and Schughart Klaus
BMC Res Notes. Volume 3, Number 1, (2010), p.16 doi: 10.1186/1756-0500-3-16
Journal club. A computational geneticist looks at mechanisms of chromosomal evolution.
Flicek, Paul
Nature. 2, Volume 463, Number 7282, (2010), England, p.713 doi: 10.1038/463713e
Research funding. Sustaining the data and bioresource commons.
Schofield, Paul N., Eppig Janan, Huala Eva, Hrabe de Angelis Martin, Harvey Mark, Davidson Duncan, Weaver Tom, Brown Steve, Smedley Damian, Rosenthal Nadia, et al.
Science. 10, Volume 330, Number 6004, (2010), United States, p.592-3 doi: 10.1126/science.1191506
Touring Ensembl: a practical guide to genome browsing.
Spudich, Giulietta M., and Fernández-Suárez Xosé M.
BMC Genomics. Volume 11, (2010), England, p.295 doi: 10.1186/1471-2164-11-295
Mining Unique-m Substrings from Genomes
Ye, Kai, Jia Zhenyu, Wang Yipeng, Flicek Paul, and Apweiler Rolf
J Proteomics Bioinform. 3, Volume 3, (2010), p.099-100 doi: 10.4172/jpb.1000127
Finding and sharing: new approaches to registries of databases and services for the biomedical sciences.
Smedley, Damian, Schofield Paul, Chen Chao-Kung K., Aidinis Vassilis, Ainali Chrysanthi, Bard Jonathan, Balling Rudi, Birney Ewan, Blake Andrew, Bongcam-Rudloff Erik, et al.
Database (Oxford). Volume 2010, (2010), England, p.baq014 doi: 10.1093/database/baq014
A map of human genome variation from population-scale sequencing.
Consortium, Genomes Project 1000
Nature. 10, Volume 467, Number 7319, (2010), England, p.1061-73 doi: 10.1038/nature09534
eHive: An Artificial Intelligence workflow system for genomic analysis.
Severin, Jessica, Beal Kathryn, Vilella Albert J., Fitzgerald Stephen, Schuster Michael, Gordon Leo, Ureta-Vidal Abel, Flicek Paul, and Herrero Javier
BMC Bioinformatics. 5, Volume 11, Number 1, (2010), p.240 doi: 10.1186/1471-2105-11-240
Locus Reference Genomic sequences: an improved basis for describing human DNA variants.
Dalgleish, Raymond, Flicek Paul, Cunningham Fiona, Astashyn Alex, Tully Raymond E., Proctor Glenn, Chen Yuan, McLaren William M., Larsson Pontus, Vaughan Brendan W., et al.
Genome Med. 4, Volume 2, Number 4, (2010), p.24 doi: 10.1186/gm145
Ensembl Genomes: extending Ensembl across the taxonomic space.
Kersey, P. J., Lawson D., Birney E., Derwent PS, Haimel M., Herrero J., Keenan S., Kerhornou A., Koscielny G., Kähäri A., et al.
Nucleic Acids Res. 1, Volume 38, Number Database issue, (2010), England, p.D563-9 doi: 10.1093/nar/gkp871
CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression.
Schnetz, Michael P., Handoko Lusy, Akhtar-Zaidi Batool, Bartels Cynthia F., Pereira Filipe C., Fisher Amanda G., Adams David J., Flicek Paul, Crawford Gregory E., Laframboise Thomas, et al.
PLoS Genet. Volume 6, Number 7, (2010), United States, p.e1001023 doi: 10.1371/journal.pgen.1001023
How to catch all those mutations–the report of the third Human Variome Project Meeting, UNESCO Paris, May 2010.
Kohonen-Corish, Maija R. J., Al-Aama Jumana Y., Auerbach Arleen D., Axton Myles, Barash Carol Isaacson, Bernstein Inge, Béroud Christophe, Burn John, Cunningham Fiona, Cutting Garry R., et al.
Hum Mutat. 12, Volume 31, Number 12, (2010), United States, p.1374-81 doi: 10.1002/humu.21379
Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.
Arensburger, Peter, Megy Karine, Waterhouse Robert M., Abrudan Jenica, Amedeo Paolo, Antelo Beatriz, Bartholomay Lyric, Bidwell Shelby, Caler Elisabet, Camara Francisco, et al.
Science. 10, Volume 330, Number 6000, (2010), United States, p.86-8 doi: 10.1126/science.1191864
International network of cancer genome projects.
Consortium, International Cancer Genome
Nature. 4, Volume 464, Number 7291, (2010), England, p.993-8 doi: 10.1038/nature08987
Consistent annotation of gene expression arrays.
Ballester, Benoit, Johnson Nathan, Proctor Glenn, and Flicek Paul
BMC Genomics. 5, Volume 11, Number 1, (2010), p.294 doi: 10.1186/1471-2164-11-294
Public data archives for genomic structural variation.
Church, Deanna M., Lappalainen Ilkka, Sneddon Tam P., Hinton Jonathan, Maguire Michael, Lopez John, Garner John, Paschall Justin, Dicuccio Michael, Yaschenko Eugene, et al.
Nat Genet. 10, Volume 42, Number 10, (2010), United States, p.813-4 doi: 10.1038/ng1010-813
Mouse Resource Browser–a database of mouse databases.
Zouberakis, Michael, Chandras Christina, Swertz Morris, Smedley Damian, Gruenberger Michael, Bard Jonathan, Schughart Klaus, Rosenthal Nadia, Hancock John M., Schofield Paul N., et al.
Database (Oxford). Volume 2010, (2010), England, p.baq010 doi: 10.1093/database/baq010
A standard variation file format for human genome sequences.
Reese, Martin G., Moore Barry, Batchelor Colin, Salas Fidel, Cunningham Fiona, Marth Gabor, Stein Lincoln, Flicek Paul, Yandell Mark, and Eilbeck Karen
Genome Biol. 8, Volume 11, Number 8, (2010), p.R88 doi: 10.1186/gb-2010-11-8-r88
Ensembl's 10th year.
Flicek, Paul, Aken Bronwen L., Ballester Benoit, Beal Kathryn, Bragin Eugene, Brent Simon, Chen Yuan, Clapham Peter, Coates Guy, Fairley Susan, et al.
Nucleic Acids Res. 1, Volume 38, Number Database issue, (2010), England, p.D557-62 doi: 10.1093/nar/gkp972
A database and API for variation, dense genotyping and resequencing data.
Rios, Daniel, McLaren William M., Chen Yuan, Birney Ewan, Stabenau Arne, Flicek Paul, and Cunningham Fiona
BMC Bioinformatics. 5, Volume 11, Number 1, (2010), p.238 doi: 10.1186/1471-2105-11-238
Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis.
Sudbery, Ian, Enright Anton J., Fraser Andrew G., and Dunham Ian
BMC Genomics. Volume 11, (2010), England, p.175 doi: 10.1186/1471-2164-11-175
Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis.
Dalloul, Rami A., Long Julie A., Zimin Aleksey V., Aslam Luqman, Beal Kathryn, Ann Blomberg Le, Bouffard Pascal, Burt David W., Crasta Oswald, Crooijmans Richard P. M. A., et al.
PLoS Biol. 9, Volume 8, Number 9, (2010), United States, p.e1000475 doi: 10.1371/journal.pbio.1000475
Ensembl Variation Resources.
Chen, Yuan, Cunningham Fiona, Rios Daniel, McLaren William M., Smith James, Pritchard Bethan, Spudich Giulietta M., Brent Simon, Kulesha Eugene, Marin-Garcia Pablo, et al.
BMC Genomics. 5, Volume 11, Number 1, (2010), p.293 doi: 10.1186/1471-2164-11-293
Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding.
Schmidt, Dominic, Wilson Michael D., Ballester Benoit, Schwalie Petra C., Brown Gordon D., Marshall Aileen, Kutter Claudia, Watt Stephen, Martinez-Jimenez Celia P., Mackay Sarah, et al.
Science. 4, Volume 328, Number 5981, (2010), p.1036-40 doi: 10.1126/science.1186176
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
Atanur, Santosh S., Birol Inanç, Guryev Victor, Hirst Martin, Hummel Oliver, Morrissey Catherine, Behmoaras Jacques, Fernandez-Suarez Xose M., Johnson Michelle D., McLaren William M., et al.
Genome Res. 4, Volume 20, Number 6, (2010), p.791-803 doi: 10.1101/gr.103499.109
Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation.
Peric-Hupkes, Daan, Meuleman Wouter, Pagie Ludo, Bruggeman Sophia W. M., Solovei Irina, Brugman Wim, Gräf Stefan, Flicek Paul, Kerkhoven Ron M., van Lohuizen Maarten, et al.
Mol Cell. 5, Volume 38, Number 4, (2010), United States, p.603-13 doi: 10.1016/j.molcel.2010.03.016
Diversity of human copy number variation and multicopy genes.
Sudmant, Peter H., Kitzman Jacob O., Antonacci Francesca, Alkan Can, Malig Maika, Tsalenko Anya, Sampas Nick, Bruhn Laurakay, Shendure Jay, Project Genomes 1000, et al.
Science. 10, Volume 330, Number 6004, (2010), United States, p.641-6 doi: 10.1126/science.1197005
ATR-X syndrome protein targets tandem repeats and influences allele-specific expression in a size-dependent manner.
Law, Martin J., Lower Karen M., Voon Hsiao P. J., Hughes Jim R., Garrick David, Viprakasit Vip, Mitson Matthew, De Gobbi Marco, Marra Marco, Morris Andrew, et al.
Cell. 10, Volume 143, Number 3, (2010), United States, p.367-78 doi: 10.1016/j.cell.2010.09.023
The genome of a songbird.
Warren, Wesley C., Clayton David F., Ellegren Hans, Arnold Arthur P., Hillier LaDeana W., Künstner Axel, Searle Steve, White Simon, Vilella Albert J., Fairley Susan, et al.
Nature. 4, Volume 464, Number 7289, (2010), England, p.757-62 doi: 10.1038/nature08819

2009

DNA methylation-histone modification relationships across the desmin locus in human primary cells.
Allen, Marianne Lindahl, Koch Christoph M., Clelland Gayle K., Dunham Ian, and Antoniou Michael
BMC Mol Biol. Volume 10, (2009), England, p.51 doi: 10.1186/1471-2199-10-51
Mosaic 22q13 deletions: evidence for concurrent mosaic segmental isodisomy and gene conversion.
Bonaglia, Maria Clara, Giorda Roberto, Beri Silvana, Bigoni Stefania, Sensi Alberto, Baroncini Anna, Capucci Antonella, De Agostini Cristina, Gwilliam Rhian, Deloukas Panos, et al.
Eur J Hum Genet. 4, Volume 17, Number 4, (2009), England, p.426-33 doi: 10.1038/ejhg.2008.195
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.
Vilella, Albert J., Severin Jessica, Ureta-Vidal Abel, Heng Li, Durbin Richard, and Birney Ewan
Genome Res. 1, Volume 19, Number 2, (2009), p.327-35 doi: 10.1101/gr.073585.107
Planning the Human Variome Project: The Spain Report
Kaput, Jim, Cotton Richard G. H., Hardman Lauren, Watson Michael, Al Aqeel Aida I., Al-Aama Jumana Y., Al-Mulla Fahd, Alonso Santos, Aretz Stefan, Auerbach Arleen D., et al.
Human Mutation. 1, Volume 30, Number 4, (2009), p.496-510 doi: 10.1002/humu.20972
Strand selective generation of endo-siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues.
Carlile, Mark, Swan Daniel, Jackson Kelly, Preston-Fayers Keziah, Ballester Benoit, Flicek Paul, and Werner Andreas
Nucleic Acids Res. 2, Volume 37, Number 7, (2009), p.2274-82 doi: 10.1093/nar/gkp088
A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation.
Morley, Rosalind H., Lachani Kim, Keefe Damian, Gilchrist Michael J., Flicek Paul, Smith James C., and Wardle Fiona C.
Proc Natl Acad Sci U S A. 3, Volume 106, Number 10, (2009), United States, p.3829-34 doi: 10.1073/pnas.0808382106
BioMart–biological queries made easy.
Smedley, Damian, Haider Syed, Ballester Benoit, Holland Richard, London Darin, Thorisson Gudmundur, and Kasprzyk Arek
BMC Genomics. Volume 10, (2009), England, p.22 doi: 10.1186/1471-2164-10-22
Joining forces in the quest for orthologs.
Gabaldón, Toni, Dessimoz Christophe, Huxley-Jones Julie, Vilella Albert J., Sonnhammer Erik LL L., and Lewis Suzanna
Genome Biol. 9, Volume 10, Number 9, (2009), p.403 doi: 10.1186/gb-2009-10-9-403
Visualising the Epigenome
Flicek, Paul, and Birney Ewan
Epigenomics. (2009), p.55-66
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.
Pruitt, Kim D., Harrow Jennifer, Harte Rachel A., Wallin Craig, Diekhans Mark, Maglott Donna R., Searle Steve, Farrell Catherine M., Loveland Jane E., Ruef Barbara J., et al.
Genome Res. 7, Volume 19, Number 7, (2009), United States, p.1316-23 doi: 10.1101/gr.080531.108
Post-publication sharing of data and tools.
Schofield, Paul N., Bubela Tania, Weaver Thomas, Portilla Lili, Brown Stephen D., Hancock John M., Einhorn David, Tocchini-Valentini Glauco, Hrabe de Angelis Martin, Rosenthal Nadia, et al.
Nature. 9, Volume 461, Number 7261, (2009), England, p.171-3 doi: 10.1038/461171a
BioMart Central Portal–unified access to biological data.
Haider, Syed, Ballester Benoit, Smedley Damian, Zhang Junjun, Rice Peter, and Kasprzyk Arek
Nucleic Acids Res. 5, Volume 37, Number Web Server issue, (2009), p.W23-7 doi: 10.1093/nar/gkp265
A System for Information Management in BioMedical Studies -SIMBioMS.
Krestyaninova, Maria, Zarins Andris, Viksna Juris, Kurbatova Natalja, Rucevskis Peteris, Neogi Sudeshna Guha, Gostev Mike, Perheentupa Teemu, Knuuttila Juha, Barrett Amy, et al.
Bioinformatics. 7, Volume 25, Number 20, (2009), p.2768-9 doi: 10.1093/bioinformatics/btp420
Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level.
Bruce, Alexander W., López-Contreras Andrés J., Flicek Paul, Down Thomas A., Dhami Pawandeep, Dillon Shane C., Koch Christoph M., Langford Cordelia F., Dunham Ian, Andrews Robert M., et al.
Genome Res. 4, Volume 19, Number 6, (2009), p.994-1005 doi: 10.1101/gr.089086.108
Models for financial sustainability of biological databases and resources.
Chandras, Christina, Weaver Thomas, Zouberakis Michael, Smedley Damian, Schughart Klaus, Rosenthal Nadia, Hancock John M., Kollias George, Schofield Paul N., and Aidinis Vassilis
Database (Oxford). Volume 2009, (2009), p.bap017 doi: 10.1093/database/bap017
The need for speed.
Flicek, Paul
Genome Biol. 3, Volume 10, Number 3, (2009), p.212 doi: 10.1186/gb-2009-10-3-212
Sense from sequence reads: methods for alignment and assembly.
Flicek, Paul, and Birney Ewan
Nat Methods. 11, Volume 6, Number 11 Suppl, (2009), United States, p.S6-S12 doi: 10.1038/nmeth.1376
Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.
Paten, Benedict, Herrero Javier, Beal Kathryn, and Birney Ewan
Bioinformatics. 2, Volume 25, Number 3, (2009), England, p.295-301 doi: 10.1093/bioinformatics/btn630
Ensembl 2009.
Hubbard, T. J. P., Aken BL, Ayling S., Ballester B., Beal K., Bragin E., Brent S., Chen Y., Clapham P., Clarke L., et al.
Nucleic Acids Res. 1, Volume 37, Number Database issue, (2009), England, p.D690-7 doi: 10.1093/nar/gkn828

2008

SNP and haplotype mapping for genetic analysis in the rat.
Consortium, STAR, Saar Kathrin, Beck Alfred, Bihoreau Marie-Thérèse T., Birney Ewan, Brocklebank Denise, Chen Yuan, Cuppen Edwin, Demonchy Stephanie, Dopazo Joaquin, et al.
Nat Genet. 5, Volume 40, Number 5, (2008), United States, p.560-6 doi: 10.1038/ng.124
nGASP - the nematode genome annotation assessment project.
Coghlan, Avril, Fiedler Tristan J., McKay Sheldon J., Flicek Paul, Harris Todd W., Blasiar Darin, Consortium The Ngasp, and Stein Lincoln D.
BMC Bioinformatics. 12, Volume 9, Number 1, (2008), p.549 doi: 10.1186/1471-2105-9-549
Ensembl 2008.
Flicek, P., Aken BL, Beal K., Ballester B., Caccamo M., Chen Y., Clarke L., Coates G., Cunningham F., Cutts T., et al.
Nucleic Acids Res. 1, Volume 36, Number Database issue, (2008), England, p.D707-14 doi: 10.1093/nar/gkm988
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
Johnson, David S., Li Wei, Gordon Benjamin D., Bhattacharjee Arindam, Curry Bo, Ghosh Jayati, Brizuela Leonardo, Carroll Jason S., Brown Myles, Flicek Paul, et al.
Genome Res. 3, Volume 18, Number 3, (2008), United States, p.393-403 doi: 10.1101/gr.7080508
Genome-wide nucleotide-level mammalian ancestor reconstruction.
Paten, Benedict, Herrero Javier, Fitzgerald Stephen, Beal Kathryn, Flicek Paul, Holmes Ian, and Birney Ewan
Genome Res. 10, Volume 18, Number 11, (2008), p.1829-43 doi: 10.1101/gr.076521.108
GENETICS. The Human Variome Project.
Cotton, Richard G. H., Auerbach Arleen D., Axton Myles, Barash Carol Isaacson, Berkovic Samuel F., Brookes Anthony J., Burn John, Cutting Garry, den Dunnen Johan T., Flicek Paul, et al.
Science. 11, Volume 322, Number 5903, (2008), United States, p.861-2 doi: 10.1126/science.1167363
What everybody should know about the rat genome and its online resources.
Twigger, Simon N., Pruitt Kim D., Fernández-Suárez Xosé M., Karolchik Donna, Worley Kim C., Maglott Donna R., Brown Garth, Weinstock George, Gibbs Richard A., Kent Jim, et al.
Nat Genet. 5, Volume 40, Number 5, (2008), United States, p.523-7 doi: 10.1038/ng0508-523
Genome analysis of the platypus reveals unique signatures of evolution.
Warren, Wesley C., Hillier LaDeana W., Marshall Graves Jennifer A., Birney Ewan, Ponting Chris P., Grützner Frank, Belov Katherine, Miller Webb, Clarke Laura, Chinwalla Asif T., et al.
Nature. 5, Volume 453, Number 7192, (2008), England, p.175-83 doi: 10.1038/nature06936
Integrating biological data - the Distributed Annotation System.
Jenkinson, Andrew M., Albrecht Mario, Birney Ewan, Blankenburg Hagen, Down Thomas, Finn Robert D., Hermjakob Henning, Hubbard Tim Jp, Jimenez Rafael C., Jones Philip, et al.
BMC Bioinformatics. 7, Volume 9 Suppl 8, (2008), p.S3 doi: 10.1186/1471-2105-9-S8-S3
Finishing the finished human chromosome 22 sequence.
Cole, Charlotte G., McCann Owen T., Collins John E., Oliver Karen, Willey David, Gribble Susan M., Yang Fengtang, McLaren Karen, Rogers Jane, Ning Zemin, et al.
Genome Biol. Volume 9, Number 5, (2008), England, p.R78 doi: 10.1186/gb-2008-9-5-r78
Epigenomics at the tipping point. Foreword.
Stamatoyannopoulos, John A., and Dunham Ian
Pharmacogenomics. 12, Volume 9, Number 12, (2008), England, p.1781-3 doi: 10.2217/14622416.9.12.1781
Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs.
Paten, Benedict, Herrero Javier, Beal Kathryn, Fitzgerald Stephen, and Birney Ewan
Genome Res. 11, Volume 18, Number 11, (2008), United States, p.1814-28 doi: 10.1101/gr.076554.108
Progress and prospects in rat genetics: a community view.
Aitman, Timothy J., Critser John K., Cuppen Edwin, Dominiczak Anna, Fernandez-Suarez Xose M., Flint Jonathan, Gauguier Dominique, Geurts Aron M., Gould Michael, Harris Peter C., et al.
Nat Genet. 5, Volume 40, Number 5, (2008), United States, p.516-22 doi: 10.1038/ng.147
Control of T(reg) and T(H)17 cell differentiation by the aryl hydrocarbon receptor.
Quintana, Francisco J., Basso Alexandre S., Iglesias Antonio H., Korn Thomas, Farez Mauricio F., Bettelli Estelle, Caccamo Mario, Oukka Mohamed, and Weiner Howard L.
Nature. 5, Volume 453, Number 7191, (2008), England, p.65-71 doi: 10.1038/nature06880
Solutions for data integration in functional genomics: a critical assessment and case study.
Smedley, Damian, Swertz Morris A., Wolstencroft Katy, Proctor Glenn, Zouberakis Michael, Bard Jonathan, Hancock John M., and Schofield Paul
Brief Bioinform. 11, Volume 9, Number 6, (2008), England, p.532-44 doi: 10.1093/bib/bbn040
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs).
Rakyan, Vardhman K., Down Thomas A., Thorne Natalie P., Flicek Paul, Kulesha Eugene, Gräf Stefan, Tomazou Eleni M., Bäckdahl Liselotte, Johnson Nathan, Herberth Marlis, et al.
Genome Res. 8, Volume 18, Number 9, (2008), p.1518-29 doi: 10.1101/gr.077479.108
TreeFam: 2008 Update.
Ruan, Jue, Li Heng, Chen Zhongzhong, Coghlan Avril, Coin Lachlan James M., Guo Yiran, Hériché Jean-Karim K., Hu Yafeng, Kristiansen Karsten, Li Ruiqiang, et al.
Nucleic Acids Res. 1, Volume 36, Number Database issue, (2008), England, p.D735-40 doi: 10.1093/nar/gkm1005
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.
Down, Thomas A., Rakyan Vardhman K., Turner Daniel J., Flicek Paul, Li Heng, Kulesha Eugene, Gräf Stefan, Johnson Nathan, Herrero Javier, Tomazou Eleni M., et al.
Nat Biotechnol. 7, Volume 26, Number 7, (2008), United States, p.779-85 doi: 10.1038/nbt1414

2007

Recommendations of the 2006 Human Variome Project meeting.
Cotton, Richard G. H., Project Human Variome 2006, Appelbe William, Auerbach Arleen D., Becker Kevin, Bodmer Walter, Boone Joe D., Boulyjenkov Victor, Brahmachari Samir, Brody Lawrence, et al.
Nat Genet. 4, Volume 39, Number 4, (2007), United States, p.433-6 doi: 10.1038/ng2024
Evolution of genes and genomes on the Drosophila phylogeny.
Consortium, Drosophila Genomes 12, Clark Andrew G., Eisen Michael B., Smith Douglas R., Bergman Casey M., Oliver Brian, Markow Therese A., Kaufman Thomas C., Kellis Manolis, Gelbart William, et al.
Nature. 11, Volume 450, Number 7167, (2007), England, p.203-18 doi: 10.1038/nature06341
The landscape of histone modifications across 1% of the human genome in five human cell lines.
Koch, Christoph M., Andrews Robert M., Flicek Paul, Dillon Shane C., Karaöz Ulaş, Clelland Gayle K., Wilcox Sarah, Beare David M., Fowler Joanna C., Couttet Phillippe, et al.
Genome Res. 6, Volume 17, Number 6, (2007), United States, p.691-707 doi: 10.1101/gr.5704207
Optimized design and assessment of whole genome tiling arrays.
Gräf, Stefan, Nielsen Fiona G. G., Kurtz Stefan, Huynen Martijn A., Birney Ewan, Stunnenberg Henk, and Flicek Paul
Bioinformatics. 7, Volume 23, Number 13, (2007), England, p.i195-204 doi: 10.1093/bioinformatics/btm200
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Consortium, ENCODE Project, Birney Ewan, Stamatoyannopoulos John A., Dutta Anindya, Guigó Roderic, Gingeras Thomas R., Margulies Elliott H., Weng Zhiping, Snyder Michael, Dermitzakis Emmanouil T., et al.
Nature. 6, Volume 447, Number 7146, (2007), England, p.799-816
Population genomics of human gene expression.
Stranger, Barbara E., Nica Alexandra C., Forrest Matthew S., Dimas Antigone, Bird Christine P., Beazley Claude, Ingle Catherine E., Dunning Mark, Flicek Paul, Koller Daphne, et al.
Nat Genet. 10, Volume 39, Number 10, (2007), United States, p.1217-24 doi: 10.1038/ng2142
Gene prediction: compare and CONTRAST.
Flicek, Paul
Genome Biol. Volume 8, Number 12, (2007), England, p.233 doi: 10.1186/gb-2007-8-12-233
Ensembl 2007.
Hubbard, T. J. P., Aken BL, Beal K., Ballester B., Caccamo M., Chen Y., Clarke L., Coates G., Cunningham F., Cutts T., et al.
Nucleic Acids Res. 1, Volume 35, Number Database issue, (2007), England, p.D610-7 doi: 10.1093/nar/gkl996
Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets.
Oeder, Sebastian, Mages Joerg, Flicek Paul, and Lang Roland
BMC Genomics. Volume 8, (2007), England, p.200 doi: 10.1186/1471-2164-8-200

2006

Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.
Flicek, Paul, and Brent Michael R.
Genome Biol. Volume 7 Suppl 1, (2006), England, p.S8.1-9 doi: 10.1186/gb-2006-7-s1-s8
EGASP: the human ENCODE Genome Annotation Assessment Project.
Guigó, Roderic, Flicek Paul, Abril Josep F., Reymond Alexandre, Lagarde Julien, Denoeud France, Antonarakis Stylianos, Ashburner Michael, Bajic Vladimir B., Birney Ewan, et al.
Genome Biol. Volume 7 Suppl 1, (2006), England, p.S2.1-31 doi: 10.1186/gb-2006-7-s1-s2
Ensembl 2006.
Birney, E., Andrews D., Caccamo M., Chen Y., Clarke L., Coates G., Cox T., Cunningham F., Curwen V., Cutts T., et al.
Nucleic Acids Res. 1, Volume 34, Number Database issue, (2006), England, p.D556-61 doi: 10.1093/nar/gkj133
TranscriptSNPView: a genome-wide catalog of mouse coding variation.
Cunningham, Fiona, Rios Daniel, Griffiths Mark, Smith James, Ning Zemin, Cox Tony, Flicek Paul, Marin-Garcin Pablo, Herrero Javier, Rogers Jane, et al.
Nat Genet. 8, Volume 38, Number 8, (2006), United States, p.853 doi: 10.1038/ng0806-853a

2005

Gene finding in the chicken genome.
Eyras, Eduardo, Reymond Alexandre, Castelo Robert, Bye Jacqueline M., Camara Francisco, Flicek Paul, Huckle Elizabeth J., Parra Genis, Shteynberg David D., Wyss Carine, et al.
BMC Bioinformatics. Volume 6, (2005), England, p.131 doi: 10.1186/1471-2105-6-131

2004

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
Consortium, International Chicken Genome Sequencing
Nature. 12, Volume 432, Number 7018, (2004), England, p.695-716 doi: 10.1038/nature03154

2003

The DNA sequence of human chromosome 7.
Hillier, LaDeana W., Fulton Robert S., Fulton Lucinda A., Graves Tina A., Pepin Kymberlie H., Wagner-McPherson Caryn, Layman Dan, Maas Jason, Jaeger Sara, Walker Rebecca, et al.
Nature. 7, Volume 424, Number 6945, (2003), England, p.157-64 doi: 10.1038/nature01782
Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map.
Flicek, Paul, Keibler Evan, Hu Ping, Korf Ian, and Brent Michael R.
Genome Res. 1, Volume 13, Number 1, (2003), United States, p.46-54 doi: 10.1101/gr.830003

2002

Initial sequencing and comparative analysis of the mouse genome.
Consortium, Mouse Genome Sequencing, Waterston Robert H., Lindblad-Toh Kerstin, Birney Ewan, Rogers Jane, Abril Josep F., Agarwal Pankaj, Agarwala Richa, Ainscough Rachel, Alexandersson Marina, et al.
Nature. 12, Volume 420, Number 6915, (2002), England, p.520-62 doi: 10.1038/nature01262

2001

Integrating genomic homology into gene structure prediction.
Korf, I., Flicek P., Duan D., and Brent M. R.
Bioinformatics. Volume 17 Suppl 1, (2001), England, p.S140-8

1999

Guidelines for the safe use of radioactive materials during localization and resection of the sentinel lymph node.
Miner, T. J., Shriver C. D., Flicek P. R., Miner F. C., Jaques D. P., Maniscalco-Theberge M. E., and Krag D. N.
Ann Surg Oncol. Volume 6, Number 1, (1999), UNITED STATES, p.75-82

1993

Core potentials for quasi-one electron systems
Albright, Brian J., Bartschat Klaus, and Flicek Paul R.
J Phys B: At Mol Opt Phys. Volume 26, (1993), p.337-44