Albert J. Vilella - Publications

Affiliations: 
European Bioinformatics Institute, Hinxton, England, United Kingdom 

28/32 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P. Ensembl comparative genomics resources. Database : the Journal of Biological Databases and Curation. 2016. PMID 27141089 DOI: 10.1093/database/baw053  1
2016 Pignatelli M, Vilella AJ, Muffato M, Gordon L, White S, Flicek P, Herrero J. ncRNA orthologies in the vertebrate lineage. Database : the Journal of Biological Databases and Curation. 2016. PMID 26980512 DOI: 10.1093/Database/Bav127  1
2016 Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P. Ensembl comparative genomics resources. Database : the Journal of Biological Databases and Curation. 2016. PMID 26896847 DOI: 10.1093/Database/Bav096  1
2016 Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SMJ, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P. Ensembl comparative genomics resources Database. 2016. DOI: 10.1093/database/bav096  1
2012 Löytynoja A, Vilella AJ, Goldman N. Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics (Oxford, England). 28: 1684-91. PMID 22531217 DOI: 10.1093/Bioinformatics/Bts198  1
2012 Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, ... ... Vilella AJ, et al. Insights into hominid evolution from the gorilla genome sequence. Nature. 483: 169-75. PMID 22398555 DOI: 10.1038/Nature10842  1
2012 Murchison EP, Schulz-Trieglaff OB, Ning Z, Alexandrov LB, Bauer MJ, Fu B, Hims M, Ding Z, Ivakhno S, Stewart C, Ng BL, Wong W, Aken B, White S, Alsop A, ... ... Vilella AJ, et al. Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer. Cell. 148: 780-91. PMID 22341448 DOI: 10.1016/J.Cell.2011.11.065  1
2012 Dessimoz C, Gabaldón T, Roos DS, Sonnhammer EL, Herrero J. Toward community standards in the quest for orthologs. Bioinformatics (Oxford, England). 28: 900-4. PMID 22332236 DOI: 10.1093/Bioinformatics/Bts050  1
2011 Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, ... ... Vilella AJ, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478: 476-82. PMID 21993624 DOI: 10.1038/Nature10530  1
2011 Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, ... ... Vilella AJ, et al. RNAcentral: A vision for an international database of RNA sequences. Rna (New York, N.Y.). 17: 1941-6. PMID 21940779 DOI: 10.1261/Rna.2750811  1
2011 Vilella AJ, Birney E, Flicek P, Herrero J. Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses. Genome Biology. 12: 401. PMID 21320298 DOI: 10.1186/Gb-2011-12-2-401  1
2011 Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, ... ... Vilella AJ, et al. Comparative and demographic analysis of orang-utan genomes. Nature. 469: 529-33. PMID 21270892 DOI: 10.1038/Nature09687  1
2011 Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, ... ... Vilella AJ, et al. Ensembl 2011. Nucleic Acids Research. 39: D800-6. PMID 21045057 DOI: 10.1093/nar/gkq1064  1
2010 Arensburger P, Megy K, Waterhouse RM, Abrudan J, Amedeo P, Antelo B, Bartholomay L, Bidwell S, Caler E, Camara F, Campbell CL, Campbell KS, Casola C, Castro MT, Chandramouliswaran I, ... ... Vilella AJ, et al. Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics. Science (New York, N.Y.). 330: 86-8. PMID 20929810 DOI: 10.1126/Science.1191864  1
2010 Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, ... ... Vilella AJ, et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. Plos Biology. 8. PMID 20838655 DOI: 10.1371/Journal.Pbio.1000475  1
2010 Severin J, Beal K, Vilella AJ, Fitzgerald S, Schuster M, Gordon L, Ureta-Vidal A, Flicek P, Herrero J. eHive: an artificial intelligence workflow system for genomic analysis. Bmc Bioinformatics. 11: 240. PMID 20459813 DOI: 10.1186/1471-2105-11-240  1
2010 Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, et al. The genome of a songbird. Nature. 464: 757-62. PMID 20360741 DOI: 10.1038/Nature08819  1
2010 Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Gräf S, Haider S, ... ... Vilella A, et al. Ensembl's 10th year. Nucleic Acids Research. 38: D557-62. PMID 19906699 DOI: 10.1093/Nar/Gkp972  1
2010 Kersey PJ, Lawson D, Birney E, Derwent PS, Haimel M, Herrero J, Keenan S, Kerhornou A, Koscielny G, Kähäri A, Kinsella RJ, Kulesha E, Maheswari U, Megy K, Nuhn M, ... ... Vilella AJ, et al. Ensembl Genomes: extending Ensembl across the taxonomic space. Nucleic Acids Research. 38: D563-9. PMID 19884133 DOI: 10.1093/Nar/Gkp871  1
2009 Gabaldón T, Dessimoz C, Huxley-Jones J, Vilella AJ, Sonnhammer EL, Lewis S. Joining forces in the quest for orthologs. Genome Biology. 10: 403. PMID 19785718 DOI: 10.1186/Gb-2009-10-9-403  1
2009 Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, ... ... Vilella A, et al. Ensembl 2009. Nucleic Acids Research. 37: D690-7. PMID 19033362 DOI: 10.1093/nar/gkn828  1
2009 Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E. EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Research. 19: 327-35. PMID 19029536 DOI: 10.1101/Gr.073585.107  1
2008 Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, Guo Y, Hériché JK, Hu Y, Kristiansen K, Li R, Liu T, Moses A, Qin J, Vang S, Vilella AJ, et al. TreeFam: 2008 Update. Nucleic Acids Research. 36: D735-40. PMID 18056084 DOI: 10.1093/Nar/Gkm1005  1
2008 Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, ... ... Vilella AJ, et al. Ensembl 2008. Nucleic Acids Research. 36: D707-14. PMID 18000006 DOI: 10.1093/nar/gkm988  1
2007 Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, ... ... Vilella A, et al. Ensembl 2007. Nucleic Acids Research. 35: D610-7. PMID 17148474 DOI: 10.1093/nar/gkl996  1
2007 Lapp H, Bala S, Balhoff JP, Bouck A, Goto N, Holder M, Holland R, Holloway A, Katayama T, Lewis PO, Mackey AJ, Osborne BI, Piel WH, Pond SLK, Poon AFY, ... ... Vilella AJ, et al. The 2006 NESCent phyloinformatics hackathon: A field report Evolutionary Bioinformatics. 3: 287-296. DOI: 10.4137/Ebo.S0  1
2006 Hutter S, Vilella AJ, Rozas J. Genome-wide DNA polymorphism analyses using VariScan. Bmc Bioinformatics. 7: 409. PMID 16968531 DOI: 10.1186/1471-2105-7-409  1
2005 Vilella AJ, Blanco-Garcia A, Hutter S, Rozas J. VariScan: Analysis of evolutionary patterns from large-scale DNA sequence polymorphism data. Bioinformatics (Oxford, England). 21: 2791-3. PMID 15814564 DOI: 10.1093/Bioinformatics/Bti403  1
Low-probability matches
2017 Bowes O, Coutts S, Ismailjee A, Trocme E, Vilella AJ, Perry H, Barsam A. Pulsed Light Accelerated Corneal Collagen Cross-Linking: 1-Year Results. Cornea. 36: e15-e16. PMID 28476054 DOI: 10.1097/ICO.0000000000001187  0.01
2015 Tarasov A, Vilella AJ, Cuppen E, Nijman IJ, Prins P. Sambamba: fast processing of NGS alignment formats. Bioinformatics (Oxford, England). 31: 2032-4. PMID 25697820 DOI: 10.1093/Bioinformatics/Btv098  0.01
2014 . The common marmoset genome provides insight into primate biology and evolution. Nature Genetics. 46: 850-7. PMID 25038751 DOI: 10.1038/Ng.3042  0.01
2007 Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, ... ... Vilella AJ, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341  0.01
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