| Year |
Citation |
Score |
| 2023 |
DeGorter MK, Goddard PC, Karakoc E, Kundu S, Yan SM, Nachun D, Abell N, Aguirre M, Carstensen T, Chen Z, Durrant M, Dwaracherla VR, Feng K, Gloudemans MJ, Hunter N, ... ... Flicek P, et al. Transcriptomics and chromatin accessibility in multiple African population samples. Biorxiv : the Preprint Server For Biology. PMID 37986808 DOI: 10.1101/2023.11.04.564839 |
0.399 |
|
| 2023 |
Contreras-Moreira B, Saraf S, Naamati G, Casas AM, Amberkar SS, Flicek P, Jones AR, Dyer S. GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation. Genome Biology. 24: 223. PMID 37798615 DOI: 10.1186/s13059-023-03071-z |
0.37 |
|
| 2023 |
Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, Hook PW, Koren S, Rautiainen M, Alexandrov IA, Allen J, Asri M, Bzikadze AV, Chen NC, Chin CS, ... ... Flicek P, et al. The complete sequence of a human Y chromosome. Nature. PMID 37612512 DOI: 10.1038/s41586-023-06457-y |
0.318 |
|
| 2023 |
Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ, Buonaiuto S, Chang XH, Cheng H, Chu J, Colonna V, ... ... Flicek P, et al. A draft human pangenome reference. Nature. 617: 312-324. PMID 37165242 DOI: 10.1038/s41586-023-05896-x |
0.319 |
|
| 2022 |
Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, Sisu C, Wright JC, Arnan C, Barnes I, Banerjee A, Bennett R, Berry A, Bignell A, Boix C, ... ... Flicek P, et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Research. PMID 36420896 DOI: 10.1093/nar/gkac1071 |
0.449 |
|
| 2022 |
Martin FJ, Amode MR, Aneja A, Austine-Orimoloye O, Azov AG, Barnes I, Becker A, Bennett R, Berry A, Bhai J, Bhurji SK, Bignell A, Boddu S, Branco Lins PR, Brooks L, ... ... Flicek P, et al. Ensembl 2023. Nucleic Acids Research. PMID 36318249 DOI: 10.1093/nar/gkac958 |
0.372 |
|
| 2022 |
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, ... ... Flicek P, et al. Author Correction: Comparative and demographic analysis of orang-utan genomes. Nature. PMID 35962045 DOI: 10.1038/s41586-022-04799-7 |
0.349 |
|
| 2022 |
Wang T, Antonacci-Fulton L, Howe K, Lawson HA, Lucas JK, Phillippy AM, Popejoy AB, Asri M, Carson C, Chaisson MJP, Chang X, Cook-Deegan R, Felsenfeld AL, Fulton RS, Garrison EP, ... ... Flicek P, et al. The Human Pangenome Project: a global resource to map genomic diversity. Nature. 604: 437-446. PMID 35444317 DOI: 10.1038/s41586-022-04601-8 |
0.42 |
|
| 2022 |
Morales J, Pujar S, Loveland JE, Astashyn A, Bennett R, Berry A, Cox E, Davidson C, Ermolaeva O, Farrell CM, Fatima R, Gil L, Goldfarb T, Gonzalez JM, Haddad D, ... ... Flicek P, et al. A joint NCBI and EMBL-EBI transcript set for clinical genomics and research. Nature. 604: 310-315. PMID 35388217 DOI: 10.1038/s41586-022-04558-8 |
0.364 |
|
| 2022 |
Contreras-Moreira B, Naamati G, Rosello M, Allen JE, Hunt SE, Muffato M, Gall A, Flicek P. Scripting Analyses of Genomes in Ensembl Plants. Methods in Molecular Biology (Clifton, N.J.). 2443: 27-55. PMID 35037199 DOI: 10.1007/978-1-0716-2067-0_2 |
0.333 |
|
| 2021 |
Rehm HL, Page AJH, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJS, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, ... ... Flicek P, et al. GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genomics. 1. PMID 35072136 DOI: 10.1016/j.xgen.2021.100029 |
0.378 |
|
| 2021 |
Hunt SE, Moore B, Amode RM, Armean IM, Lemos D, Mushtaq A, Parton A, Schuilenburg H, Szpak M, Thormann A, Perry E, Trevanion SJ, Flicek P, Yates AD, Cunningham F. Annotating and prioritising genomic variants using the Ensembl Variant Effect Predictor - a tutorial. Human Mutation. PMID 34816521 DOI: 10.1002/humu.24298 |
0.319 |
|
| 2021 |
Yates AD, Allen J, Amode RM, Azov AG, Barba M, Becerra A, Bhai J, Campbell LI, Carbajo Martinez M, Chakiachvili M, Chougule K, Christensen M, Contreras-Moreira B, Cuzick A, Da Rin Fioretto L, ... ... Flicek P, et al. Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. Nucleic Acids Research. PMID 34791415 DOI: 10.1093/nar/gkab1007 |
0.418 |
|
| 2021 |
Cunningham F, Allen JE, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Austine-Orimoloye O, Azov AG, Barnes I, Bennett R, Berry A, Bhai J, Bignell A, Billis K, Boddu S, ... ... Flicek P, et al. Ensembl 2022. Nucleic Acids Research. PMID 34791404 DOI: 10.1093/nar/gkab1049 |
0.397 |
|
| 2021 |
Cezard T, Cunningham F, Hunt SE, Koylass B, Kumar N, Saunders G, Shen A, Silva AF, Tsukanov K, Venkataraman S, Flicek P, Parkinson H, Keane TM. The European Variation Archive: a FAIR resource of genomic variation for all species. Nucleic Acids Research. PMID 34718739 DOI: 10.1093/nar/gkab960 |
0.348 |
|
| 2021 |
De Silva NH, Bhai J, Chakiachvili M, Contreras-Moreira B, Cummins C, Frankish A, Gall A, Genez T, Howe KL, Hunt SE, Martin FJ, Moore B, Ogeh D, Parker A, Parton A, ... ... Flicek P, et al. The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data. Nucleic Acids Research. PMID 34634797 DOI: 10.1093/nar/gkab889 |
0.327 |
|
| 2021 |
Korlević P, McAlister E, Mayho M, Makunin A, Flicek P, Lawniczak MKN. A Minimally Morphologically Destructive Approach for DNA Retrieval and Whole-Genome Shotgun Sequencing of Pinned Historic Dipteran Vector Species. Genome Biology and Evolution. 13. PMID 34599327 DOI: 10.1093/gbe/evab226 |
0.302 |
|
| 2021 |
Contreras-Moreira B, Filippi CV, Naamati G, García Girón C, Allen JE, Flicek P. K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes. The Plant Genome. e20143. PMID 34562304 DOI: 10.1002/tpg2.20143 |
0.344 |
|
| 2021 |
Harrison PW, Sokolov A, Nayak A, Fan J, Zerbino D, Cochrane G, Flicek P. The FAANG Data Portal: Global, Open-Access, "FAIR", and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes. Frontiers in Genetics. 12: 639238. PMID 34220930 DOI: 10.3389/fgene.2021.639238 |
0.341 |
|
| 2021 |
Martin FJ, Gall A, Szpak M, Flicek P. Accessing Livestock Resources in Ensembl. Frontiers in Genetics. 12: 650228. PMID 33995484 DOI: 10.3389/fgene.2021.650228 |
0.437 |
|
| 2021 |
Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, ... ... Flicek P, et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 592: 737-746. PMID 33911273 DOI: 10.1038/s41586-021-03451-0 |
0.415 |
|
| 2021 |
Kern C, Wang Y, Xu X, Pan Z, Halstead M, Chanthavixay G, Saelao P, Waters S, Xiang R, Chamberlain A, Korf I, Delany ME, Cheng HH, Medrano JF, Van Eenennaam AL, ... ... Flicek P, et al. Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research. Nature Communications. 12: 1821. PMID 33758196 DOI: 10.1038/s41467-021-22100-8 |
0.358 |
|
| 2021 |
Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, ... ... Flicek P, et al. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science (New York, N.Y.). PMID 33632895 DOI: 10.1126/science.abf7117 |
0.399 |
|
| 2020 |
Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I, Berry A, Bignell A, Boix C, Carbonell Sala S, Cunningham F, ... ... Flicek P, et al. GENCODE 2021. Nucleic Acids Research. PMID 33270111 DOI: 10.1093/nar/gkaa1087 |
0.44 |
|
| 2020 |
Tello-Ruiz MK, Naithani S, Gupta P, Olson A, Wei S, Preece J, Jiao Y, Wang B, Chougule K, Garg P, Elser J, Kumari S, Kumar V, Contreras-Moreira B, Naamati G, ... ... Flicek P, et al. Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Research. PMID 33170273 DOI: 10.1093/nar/gkaa979 |
0.316 |
|
| 2020 |
Howe KL, Achuthan P, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Charkhchi M, Cummins C, Da Rin Fioretto L, ... ... Flicek P, et al. Ensembl 2021. Nucleic Acids Research. PMID 33137190 DOI: 10.1093/nar/gkaa942 |
0.439 |
|
| 2020 |
Ordonez R, Kulis M, Russinol N, Chapaprieta V, Carrasco-Leon A, Garcia-Torre B, Charampopoulou S, Clot G, Beekman R, Meydan C, Duran-Ferrer M, Verdaguer-Dot N, Vilarrasa-Blasi R, Soler-Vila P, Garate L, ... ... Flicek PH, et al. Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma. Genome Research. PMID 32820006 DOI: 10.1101/Gr.265520.120 |
0.328 |
|
| 2020 |
Gemmell NJ, Rutherford K, Prost S, Tollis M, Winter D, Macey JR, Adelson DL, Suh A, Bertozzi T, Grau JH, Organ C, Gardner PP, Muffato M, Patricio M, Billis K, ... ... Flicek P, et al. Publisher Correction: The tuatara genome reveals ancient features of amniote evolution. Nature. PMID 32811988 DOI: 10.1038/S41586-020-2661-6 |
0.405 |
|
| 2020 |
Gemmell NJ, Rutherford K, Prost S, Tollis M, Winter D, Macey JR, Adelson DL, Suh A, Bertozzi T, Grau JH, Organ C, Gardner PP, Muffato M, Patricio M, Billis K, ... ... Flicek P, et al. The tuatara genome reveals ancient features of amniote evolution. Nature. PMID 32760000 DOI: 10.1038/S41586-020-2561-9 |
0.513 |
|
| 2020 |
Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, ... ... Flicek P, et al. Perspectives on ENCODE. Nature. 583: 693-698. PMID 32728248 DOI: 10.1038/S41586-020-2449-8 |
0.42 |
|
| 2020 |
Sisu C, Muir P, Frankish A, Fiddes I, Diekhans M, Thybert D, Odom DT, Flicek P, Keane TM, Hubbard T, Harrow J, Gerstein M. Transcriptional activity and strain-specific history of mouse pseudogenes. Nature Communications. 11: 3695. PMID 32728065 DOI: 10.1038/S41467-020-17157-W |
0.424 |
|
| 2020 |
Grassi L, Izuogu OG, Jorge NAN, Seyres D, Bustamante M, Burden F, Farrow S, Farahi N, Martin FJ, Frankish A, Mudge JM, Kostadima M, Petersen R, Lambourne JJ, Rowlston S, ... ... Flicek P, et al. Cell type specific novel lncRNAs and circRNAs in the BLUEPRINT haematopoietic transcriptomes atlas. Haematologica. PMID 32703790 DOI: 10.3324/Haematol.2019.238147 |
0.348 |
|
| 2020 |
Aitken SJ, Anderson CJ, Connor F, Pich O, Sundaram V, Feig C, Rayner TF, Lukk M, Aitken S, Luft J, Kentepozidou E, Arnedo-Pac C, Beentjes SV, Davies SE, Drews RM, ... ... Flicek P, et al. Pervasive lesion segregation shapes cancer genome evolution. Nature. PMID 32581361 DOI: 10.1038/S41586-020-2435-1 |
0.309 |
|
| 2020 |
Warr A, Affara N, Aken B, Beiki H, Bickhart DM, Billis K, Chow W, Eory L, Finlayson HA, Flicek P, Girón CG, Griffin DK, Hall R, Hannum G, Hourlier T, et al. An improved pig reference genome sequence to enable pig genetics and genomics research. Gigascience. 9. PMID 32543654 DOI: 10.1093/Gigascience/Giaa051 |
0.49 |
|
| 2020 |
Zerbino DR, Frankish A, Flicek P. Progress, Challenges, and Surprises in Annotating the Human Genome. Annual Review of Genomics and Human Genetics. PMID 32421357 DOI: 10.1146/Annurev-Genom-121119-083418 |
0.51 |
|
| 2020 |
Í Kongsstovu S, Dahl HA, Gislason H, Í Homrum E, Jacobsen JA, Flicek P, Mikalsen SO. Identification of male heterogametic sex determining regions on the Atlantic herring Clupea harengus genome. Journal of Fish Biology. PMID 32293027 DOI: 10.1111/Jfb.14349 |
0.382 |
|
| 2020 |
Lloyd KCK, Adams DJ, Baynam G, Beaudet AL, Bosch F, Boycott KM, Braun RE, Caulfield M, Cohn R, Dickinson ME, Dobbie MS, Flenniken AM, Flicek P, Galande S, Gao X, et al. The Deep Genome Project. Genome Biology. 21: 18. PMID 32008577 DOI: 10.1186/S13059-020-1931-9 |
0.506 |
|
| 2020 |
Kentepozidou E, Aitken SJ, Feig C, Stefflova K, Ibarra-Soria X, Odom DT, Roller M, Flicek P. Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains. Genome Biology. 21: 5. PMID 31910870 DOI: 10.1186/S13059-019-1894-X |
0.316 |
|
| 2019 |
Lowy-Gallego E, Fairley S, Zheng-Bradley X, Ruffier M, Clarke L, Flicek P. Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project. Wellcome Open Research. 4: 50. PMID 32175479 DOI: 10.12688/wellcomeopenres.15126.2 |
0.302 |
|
| 2019 |
Steward CA, Roovers J, Suner MM, Gonzalez JM, Uszczynska-Ratajczak B, Pervouchine D, Fitzgerald S, Viola M, Stamberger H, Hamdan FF, Ceulemans B, Leroy P, Nava C, Lepine A, Tapanari E, ... ... Flicek P, et al. Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in . Npj Genomic Medicine. 4: 31. PMID 31814998 DOI: 10.1038/S41525-019-0106-7 |
0.425 |
|
| 2019 |
Í Kongsstovu S, Mikalsen SO, Homrum EÍ, Jacobsen JA, Flicek P, Dahl HA. Using long and linked reads to improve an Atlantic herring (Clupea harengus) genome assembly. Scientific Reports. 9: 17716. PMID 31776409 DOI: 10.1038/S41598-019-54151-9 |
0.36 |
|
| 2019 |
Yates AD, Achuthan P, Akanni W, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Marugán JC, Cummins C, ... ... Flicek P, et al. Ensembl 2020. Nucleic Acids Research. PMID 31691826 DOI: 10.1093/nar/gkz966 |
0.438 |
|
| 2019 |
Robinson J, Barker DJ, Georgiou X, Cooper MA, Flicek P, Marsh SGE. IPD-IMGT/HLA Database. Nucleic Acids Research. PMID 31667505 DOI: 10.1093/Nar/Gkz950 |
0.459 |
|
| 2019 |
Pettersson ME, Rochus CM, Han F, Chen J, Hill J, Wallerman O, Fan G, Hong X, Xu Q, Zhang H, Liu S, Liu X, Haggerty L, Hunt T, Martin FJ, ... Flicek P, et al. A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection. Genome Research. PMID 31649060 DOI: 10.1101/Gr.253435.119 |
0.395 |
|
| 2019 |
Howe KL, Contreras-Moreira B, De Silva N, Maslen G, Akanni W, Allen J, Alvarez-Jarreta J, Barba M, Bolser DM, Cambell L, Carbajo M, Chakiachvili M, Christensen M, Cummins C, Cuzick A, ... ... Flicek P, et al. Ensembl Genomes 2020-enabling non-vertebrate genomic research. Nucleic Acids Research. PMID 31598706 DOI: 10.1093/Nar/Gkz890 |
0.54 |
|
| 2019 |
Fairley S, Lowy-Gallego E, Perry E, Flicek P. The International Genome Sample Resource (IGSR) collection of open human genomic variation resources. Nucleic Acids Research. PMID 31584097 DOI: 10.1093/Nar/Gkz836 |
0.48 |
|
| 2019 |
Saunders G, Baudis M, Becker R, Beltran S, Béroud C, Birney E, Brooksbank C, Brunak S, Van den Bulcke M, Drysdale R, Capella-Gutierrez S, Flicek P, Florindi F, Goodhand P, Gut I, et al. Author Correction: Leveraging European infrastructures to access 1 million human genomes by 2022. Nature Reviews. Genetics. PMID 31520075 DOI: 10.1038/S41576-019-0178-3 |
0.411 |
|
| 2019 |
Hardwick SA, Joglekar A, Flicek P, Frankish A, Tilgner HU. Getting the Entire Message: Progress in Isoform Sequencing. Frontiers in Genetics. 10: 709. PMID 31475029 DOI: 10.3389/Fgene.2019.00709 |
0.347 |
|
| 2019 |
Saunders G, Baudis M, Becker R, Beltran S, Béroud C, Birney E, Brooksbank C, Brunak S, Van den Bulcke M, Drysdale R, Capella-Gutierrez S, Flicek P, Florindi F, Goodhand P, Gut I, et al. Leveraging European infrastructures to access 1 million human genomes by 2022. Nature Reviews. Genetics. PMID 31455890 DOI: 10.1038/S41576-019-0156-9 |
0.473 |
|
| 2019 |
Benjelloun B, Boyer F, Streeter I, Zamani W, Engelen S, Alberti A, Alberto FJ, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Rezaei HR, Naderi S, Stella A, Chikhi A, ... ... Flicek P, et al. An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity. Molecular Ecology Resources. PMID 31359622 DOI: 10.1111/1755-0998.13070 |
0.447 |
|
| 2019 |
Cheung WA, Shao X, Morin A, Siroux V, Kwan T, Ge B, Aïssi D, Chen L, Vasquez L, Allum F, Guénard F, Bouzigon E, Simon MM, Boulier E, Redensek A, ... ... Flicek P, et al. Correction to: Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome. Genome Biology. 20: 89. PMID 31064398 DOI: 10.1186/S13059-019-1702-7 |
0.308 |
|
| 2019 |
Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, ... ... Flicek P, et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nature Communications. 10: 1784. PMID 30992455 DOI: 10.1038/S41467-018-08148-Z |
0.517 |
|
| 2019 |
Fiume M, Cupak M, Keenan S, Rambla J, de la Torre S, Dyke SOM, Brookes AJ, Carey K, Lloyd D, Goodhand P, Haeussler M, Baudis M, Stockinger H, Dolman L, Lappalainen I, ... ... Flicek P, et al. Publisher Correction: Federated discovery and sharing of genomic data using Beacons. Nature Biotechnology. PMID 30894680 DOI: 10.1038/S41587-019-0094-2 |
0.392 |
|
| 2019 |
Fiume M, Cupak M, Keenan S, Rambla J, de la Torre S, Dyke SOM, Brookes AJ, Carey K, Lloyd D, Goodhand P, Haeussler M, Baudis M, Stockinger H, Dolman L, Lappalainen I, ... ... Flicek P, et al. Federated discovery and sharing of genomic data using Beacons. Nature Biotechnology. 37: 220-224. PMID 30833764 DOI: 10.1038/S41587-019-0046-X |
0.465 |
|
| 2019 |
Yi G, Wierenga ATJ, Petraglia F, Narang P, Janssen-Megens EM, Mandoli A, Merkel A, Berentsen K, Kim B, Matarese F, Singh AA, Habibi E, Prange KHM, Mulder AB, Jansen JH, ... ... Flicek P, et al. Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes. Cell Reports. 26: 1059-1069.e6. PMID 30673601 DOI: 10.1016/J.Celrep.2018.12.098 |
0.337 |
|
| 2019 |
Sollis E, Buniello A, Cerezo M, Hall P, Harris L, Hayhurst J, Junkins H, Lewis E, Malangone C, McMahon A, Morales J, Suveges D, Vrousgou O, Whetzel PL, Flicek P, et al. User-focused development of the NHGRI-EBI Genome-Wide Association Studies Catalog F1000research. 8. DOI: 10.7490/F1000Research.1116621.1 |
0.412 |
|
| 2019 |
Muñoz-Fuentes V, Cacheiro P, Meehan TF, Aguilar-Pimentel JA, Beaudet AL, Brown SDM, Dickinson ME, Flenniken AM, Flicek P, Galli A, Mashhadi HH, Heaney JD, Angelis MHd, Kim JK, Lloyd KCK, et al. Correction to: The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation Conservation Genetics. 20: 135-136. DOI: 10.1007/S10592-019-01144-W |
0.445 |
|
| 2018 |
Hunt SE, McLaren W, Gil L, Thormann A, Schuilenburg H, Sheppard D, Parton A, Armean IM, Trevanion SJ, Flicek P, Cunningham F. Ensembl variation resources. Database : the Journal of Biological Databases and Curation. 2018. PMID 30576484 DOI: 10.1093/Database/Bay119 |
0.489 |
|
| 2018 |
Buniello A, MacArthur JAL, Cerezo M, Harris LW, Hayhurst J, Malangone C, McMahon A, Morales J, Mountjoy E, Sollis E, Suveges D, Vrousgou O, Whetzel PL, Amode R, Guillen JA, ... ... Flicek P, et al. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Research. PMID 30445434 DOI: 10.1093/Nar/Gky1120 |
0.425 |
|
| 2018 |
Cunningham F, Achuthan P, Akanni W, Allen J, Amode MR, Armean IM, Bennett R, Bhai J, Billis K, Boddu S, Cummins C, Davidson C, Dodiya KJ, Gall A, Girón CG, ... ... Flicek P, et al. Ensembl 2019. Nucleic Acids Research. PMID 30407521 DOI: 10.1093/nar/gky1113 |
0.421 |
|
| 2018 |
Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, ... ... Flicek P, et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Research. PMID 30357393 DOI: 10.1093/Nar/Gky955 |
0.515 |
|
| 2018 |
Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane TM, Thybert D, Paten B, Pham S. Chromosome assembly of large and complex genomes using multiple references. Genome Research. PMID 30341161 DOI: 10.1101/Gr.236273.118 |
0.46 |
|
| 2018 |
Harrison PW, Fan J, Richardson D, Clarke L, Zerbino D, Cochrane G, Archibald AL, Schmidt CJ, Flicek P. FAANG, establishing metadata standards, validation and best practices for the farmed and companion animal community. Animal Genetics. PMID 30311252 DOI: 10.1111/Age.12736 |
0.38 |
|
| 2018 |
Spooner W, McLaren W, Slidel T, Finch DK, Butler R, Campbell J, Eghobamien L, Rider D, Kiefer CM, Robinson MJ, Hardman C, Cunningham F, Vaughan T, Flicek P, Huntington CC. Haplosaurus computes protein haplotypes for use in precision drug design. Nature Communications. 9: 4128. PMID 30297836 DOI: 10.1038/S41467-018-06542-1 |
0.375 |
|
| 2018 |
Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, ... ... Flicek P, et al. Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci. Nature Genetics. PMID 30275530 DOI: 10.1038/S41588-018-0223-8 |
0.495 |
|
| 2018 |
Muñoz-Fuentes V, Cacheiro P, Meehan TF, Aguilar-Pimentel JA, Brown SDM, Flenniken AM, Flicek P, Galli A, Mashhadi HH, Hrabě de Angelis M, Kim JK, Lloyd KCK, McKerlie C, Morgan H, Murray SA, et al. The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation. Conservation Genetics (Print). 19: 995-1005. PMID 30100824 DOI: 10.1007/S10592-018-1072-9 |
0.436 |
|
| 2018 |
Aitken SJ, Ibarra-Soria X, Kentepozidou E, Flicek P, Feig C, Marioni JC, Odom DT. CTCF maintains regulatory homeostasis of cancer pathways. Genome Biology. 19: 106. PMID 30086769 DOI: 10.1186/S13059-018-1484-3 |
0.445 |
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| 2018 |
Dyke SOM, Linden M, Lappalainen I, De Argila JR, Carey K, Lloyd D, Spalding JD, Cabili MN, Kerry G, Foreman J, Cutts T, Shabani M, Rodriguez LL, Haeussler M, Walsh B, ... ... Flicek P, et al. Registered access: authorizing data access. European Journal of Human Genetics : Ejhg. PMID 30069064 DOI: 10.1038/S41431-018-0219-Y |
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| 2018 |
Beekman R, Chapaprieta V, Russiñol N, Vilarrasa-Blasi R, Verdaguer-Dot N, Martens JHA, Duran-Ferrer M, Kulis M, Serra F, Javierre BM, Wingett SW, Clot G, Queirós AC, Castellano G, Blanc J, ... ... Flicek P, et al. The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia. Nature Medicine. PMID 29785028 DOI: 10.1038/S41591-018-0028-4 |
0.324 |
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| 2018 |
Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, ... ... Flicek P, et al. Repeat associated mechanisms of genome evolution and function revealed by theandgenomes. Genome Research. PMID 29563166 DOI: 10.1101/Gr.234096.117 |
0.488 |
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| 2018 |
Alberto FJ, Boyer F, Orozco-terWengel P, Streeter I, Servin B, de Villemereuil P, Benjelloun B, Librado P, Biscarini F, Colli L, Barbato M, Zamani W, Alberti A, Engelen S, Stella A, ... ... Flicek P, et al. Convergent genomic signatures of domestication in sheep and goats. Nature Communications. 9: 813. PMID 29511174 DOI: 10.1038/S41467-018-03206-Y |
0.485 |
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| 2018 |
Morales J, Welter D, Bowler EH, Cerezo M, Harris LW, McMahon AC, Hall P, Junkins HA, Milano A, Hastings E, Malangone C, Buniello A, Burdett T, Flicek P, Parkinson H, et al. A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog. Genome Biology. 19: 21. PMID 29448949 DOI: 10.1186/S13059-018-1396-2 |
0.47 |
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| 2018 |
Rozman J, Rathkolb B, Oestereicher MA, Schütt C, Ravindranath AC, Leuchtenberger S, Sharma S, Kistler M, Willershäuser M, Brommage R, Meehan TF, Mason J, Haselimashhadi H, Hough T, ... ... Flicek P, et al. Identification of genetic elements in metabolism by high-throughput mouse phenotyping. Nature Communications. 9: 288. PMID 29348434 DOI: 10.1038/S41467-017-01995-2 |
0.391 |
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| 2018 |
Berthelot C, Villar D, Horvath JE, Odom DT, Flicek P. Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression. Nature Ecology & Evolution. 2: 152-163. PMID 29180706 DOI: 10.1038/S41559-017-0377-2 |
0.354 |
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| 2018 |
Giroussens G, Muffato M, Flicek P. Inclusion of pseudogenes in the Ensembl comparative genomics resources F1000research. 7. DOI: 10.7490/F1000Research.1116155.1 |
0.473 |
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| 2018 |
Lowy-Gallego E, Fairley S, Zheng-Bradley H, Clarke L, Flicek P. Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes F1000research. 7. DOI: 10.7490/F1000Research.1116066.1 |
0.431 |
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| 2017 |
Martín-Gálvez D, Segonzac DDd, Ma MCJ, Kwitek AE, Thybert D, Flicek P. Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat. Bmc Genomics. 18: 986. PMID 29272997 DOI: 10.1186/S12864-017-4351-9 |
0.406 |
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| 2017 |
Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J, Billis K, Cummins C, Gall A, Girón CG, Gil L, Gordon L, Haggerty L, Haskell E, Hourlier T, ... ... Flicek P, et al. Ensembl 2018. Nucleic Acids Research. PMID 29155950 DOI: 10.1093/nar/gkx1098 |
0.418 |
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| 2017 |
Jasinska AJ, Zelaya I, Service SK, Peterson CB, Cantor RM, Choi OW, DeYoung J, Eskin E, Fairbanks LA, Fears S, Furterer AE, Huang YS, Ramensky V, Schmitt CA, Svardal H, ... ... Flicek P, et al. Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate. Nature Genetics. PMID 29083405 DOI: 10.1038/Ng.3959 |
0.431 |
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| 2017 |
Wong ES, Schmitt BM, Kazachenka A, Thybert D, Redmond A, Connor F, Rayner TF, Feig C, Ferguson-Smith AC, Marioni JC, Odom DT, Flicek P. Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution. Nature Communications. 8: 1092. PMID 29061983 DOI: 10.1038/S41467-017-01037-X |
0.328 |
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| 2017 |
Petersen R, Lambourne JJ, Javierre BM, Grassi L, Kreuzhuber R, Ruklisa D, Rosa IM, Tomé AR, Elding H, van Geffen JP, Jiang T, Farrow S, Cairns J, Al-Subaie AM, Ashford S, ... ... Flicek P, et al. Platelet function is modified by common sequence variation in megakaryocyte super enhancers. Nature Communications. 8: 16058. PMID 28703137 DOI: 10.1038/Ncomms16058 |
0.395 |
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| 2017 |
Meehan TF, Conte N, West DB, Jacobsen JO, Mason J, Warren J, Chen CK, Tudose I, Relac M, Matthews P, Karp N, Santos L, Fiegel T, Ring N, Westerberg H, ... ... Flicek P, et al. Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium. Nature Genetics. PMID 28650483 DOI: 10.1038/Ng.3901 |
0.445 |
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| 2017 |
Zheng-Bradley X, Streeter I, Fairley S, Richardson D, Clarke L, Flicek P. Alignment of 1000 Genomes Project Reads to Reference Assembly GRCh38. Gigascience. PMID 28531267 DOI: 10.1093/Gigascience/Gix038 |
0.438 |
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| 2017 |
Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, ... ... Flicek P, et al. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Research. PMID 28396521 DOI: 10.1101/Gr.213611.116 |
0.481 |
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| 2017 |
Ruffier M, Kähäri A, Komorowska M, Keenan S, Laird M, Longden I, Proctor G, Searle S, Staines D, Taylor K, Vullo A, Yates A, Zerbino D, Flicek P. Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation. Database : the Journal of Biological Databases and Curation. 2017. PMID 28365736 DOI: 10.1093/Database/Bax020 |
0.511 |
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| 2017 |
Raisaro JL, Tramèr F, Ji Z, Bu D, Zhao Y, Carey K, Lloyd D, Sofia H, Baker D, Flicek P, Shringarpure S, Bustamante C, Wang S, Jiang X, Ohno-Machado L, et al. Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks. Journal of the American Medical Informatics Association : Jamia. PMID 28339683 DOI: 10.1093/Jamia/Ocw167 |
0.444 |
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| 2017 |
Cummins C, Patricio M, Akanni W, Muffato M, Aken B, Flicek P. Moving towards comparative analysis of hundreds of vertebrate genomes F1000research. 6. DOI: 10.7490/F1000Research.1115012.1 |
0.483 |
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| 2017 |
Patricio M, Muffato M, Akanni W, Cummins C, Aken B, Flicek P. Ensembl comparative genomics update – HMMs and Orthology QC F1000research. 6. DOI: 10.7490/F1000Research.1114127.1 |
0.471 |
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| 2016 |
MacArthur J, Bowler E, Cerezo M, Gil L, Hall P, Hastings E, Junkins H, McMahon A, Milano A, Morales J, Pendlington ZM, Welter D, Burdett T, Hindorff L, Flicek P, et al. The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog). Nucleic Acids Research. PMID 27899670 DOI: 10.1093/Nar/Gkw1133 |
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| 2016 |
Maccari G, Robinson J, Ballingall K, Guethlein LA, Grimholt U, Kaufman J, Ho CS, de Groot NG, Flicek P, Bontrop RE, Hammond JA, Marsh SG. IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex. Nucleic Acids Research. PMID 27899604 DOI: 10.1093/Nar/Gkw1050 |
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| 2016 |
Aken BL, Achuthan P, Akanni W, Amode MR, Bernsdorff F, Bhai J, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, ... ... Flicek P, et al. Ensembl 2017. Nucleic Acids Research. PMID 27899575 DOI: 10.1093/nar/gkw1104 |
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| 2016 |
Fernández JM, de la Torre V, Richardson D, Royo R, Puiggròs M, Moncunill V, Fragkogianni S, Clarke L, Flicek P, Rico D, Torrents D, Carrillo de Santa Pau E, Valencia A. The BLUEPRINT Data Analysis Portal. Cell Systems. PMID 27863955 DOI: 10.1016/J.Cels.2016.10.021 |
0.426 |
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| 2016 |
Chen L, Ge B, Casale FP, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yan Y, Kundu K, Ecker S, Datta A, Richardson D, Burden F, Mead D, Mann AL, ... ... Flicek P, et al. Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells. Cell. 167: 1398-1414.e24. PMID 27863251 DOI: 10.1016/J.Cell.2016.10.026 |
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| 2016 |
Schuyler RP, Merkel A, Raineri E, Altucci L, Vellenga E, Martens JH, Pourfarzad F, Kuijpers TW, Burden F, Farrow S, Downes K, Ouwehand WH, Clarke L, Datta A, Lowy E, ... Flicek P, et al. Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems. Cell Reports. 17: 2101-2111. PMID 27851971 DOI: 10.1016/J.Celrep.2016.10.054 |
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| 2016 |
Streeter I, Harrison PW, Faulconbridge A, Flicek P, Parkinson H, Clarke L. The human-induced pluripotent stem cell initiative-data resources for cellular genetics. Nucleic Acids Research. PMID 27733501 DOI: 10.1093/Nar/Gkw928 |
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| 2016 |
Clarke L, Fairley S, Zheng-Bradley X, Streeter I, Perry E, Lowy E, Tassé AM, Flicek P. The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data. Nucleic Acids Research. PMID 27638885 DOI: 10.1093/Nar/Gkw829 |
0.499 |
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| 2016 |
Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, Meehan TF, Weninger WJ, Westerberg H, Adissu H, Baker CN, Bower L, Brown JM, Caddle LB, Chiani F, ... ... Flicek P, et al. High-throughput discovery of novel developmental phenotypes. Nature. PMID 27626380 DOI: 10.1038/Nature19356 |
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| 2016 |
Zheng-Bradley X, Flicek P. Applications of the 1000 Genomes Project resources Briefings in Functional Genomics. 16: 163-170. PMID 27436001 DOI: 10.1093/Bfgp/Elw027 |
0.503 |
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| 2016 |
Morgan AP, Holt JM, McMullan RC, Bell TA, Clayshulte AM, Didion JP, Yadgary L, Thybert D, Odom DT, Flicek P, McMillan L, Pardo-Manuel de Villena F. The Evolutionary Fates of a Large Segmental Duplication in Mouse. Genetics. PMID 27371833 DOI: 10.1534/Genetics.116.191007 |
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| 2016 |
Rensch T, Villar D, Horvath J, Odom DT, Flicek P. Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data. Genome Biology. 17: 139. PMID 27349964 DOI: 10.1186/S13059-016-0996-Y |
0.307 |
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| 2016 |
Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, ... Flicek P, et al. Making sense of big data in health research: Towards an EU action plan. Genome Medicine. 8: 71. PMID 27338147 DOI: 10.1186/S13073-016-0323-Y |
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| 2016 |
Aken BL, Ayling S, Barrell D, Clarke L, Curwen V, Fairley S, Fernandez Banet J, Billis K, García Girón C, Hourlier T, Howe K, Kähäri A, Kokocinski F, Martin FJ, Murphy DN, ... ... Flicek P, et al. The Ensembl gene annotation system. Database : the Journal of Biological Databases and Curation. 2016. PMID 27337980 DOI: 10.1093/Database/Baw093 |
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| 2016 |
Page A, Baker D, Bobrow M, Boycott K, Burn J, Chanock S, Donnelly S, Dove E, Durbin R, Dyke S, Fiume M, Flicek P, Glazer D, Goodhand P, Haussler D, et al. A federated ecosystem for sharing genomic, clinical data Science. PMID 27284183 DOI: 10.1126/Science.Aaf6162 |
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| 2016 |
McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. The Ensembl Variant Effect Predictor. Genome Biology. 17: 122. PMID 27268795 DOI: 10.1186/S13059-016-0974-4 |
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| 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 |
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| 2016 |
Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, Ayub Q, McCarthy SA, Narechania A, Kashin S, Chen Y, Banerjee R, Rodriguez-Flores JL, Cerezo M, Shao H, ... ... Flicek P, et al. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nature Genetics. PMID 27111036 DOI: 10.1038/Ng.3559 |
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| 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 |
0.458 |
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| 2016 |
Uebbing S, Künstner A, Mäkinen H, Backström N, Bolivar P, Burri R, Dutoit L, Mugal CF, Nater A, Aken B, Flicek P, Martin FJ, Searle SM, Ellegren H. Divergence in gene expression within and between two closely related flycatcher species. Molecular Ecology. PMID 26928872 DOI: 10.1111/Mec.13596 |
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| 2016 |
Fontanesi L, Di Palma F, Flicek P, Smith AT, Thulin CG, Alves PC. LaGomiCs - Lagomorph Genomics Consortium: an international collaborative effort for sequencing the genomes of an entire mammalian order. The Journal of Heredity. PMID 26921276 DOI: 10.1093/Jhered/Esw010 |
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| 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 |
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| 2016 |
Zerbino DR, Johnson N, Juetteman T, Sheppard D, Wilder SP, Lavidas I, Nuhn M, Perry E, Raffaillac-Desfosses Q, Sobral D, Keefe D, Gräf S, Ahmed I, Kinsella R, Pritchard B, ... ... Flicek P, et al. Ensembl regulation resources. Database : the Journal of Biological Databases and Curation. 2016. PMID 26888907 DOI: 10.1093/Database/Bav119 |
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| 2016 |
Vilarrasa-Blasi R, Queirós AC, Beekman R, Russiñol N, Castellano G, Blanc J, Serra F, Beà S, Kulis M, Verdaguer-Dot N, Enjuanes A, Bergmann A, Salaverria I, Werken HJGvd, Datta A, ... Flicek P, et al. Aberrant Expression of the SOX11 Oncogene in Mantle Cell Lymphoma Is Associated with Activation and De Novo 3D Looping of a Distant Enhancer Element Blood. 128: 459-459. DOI: 10.1182/Blood.V128.22.459.459 |
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| 2016 |
Kaloff C, Anastassiadis K, Ayadi A, Baldock R, Beig J, Birling M, Bradley A, Brown S, Bürger A, Bushell W, Chiani F, Collins F, Doe B, Eppig J, Finnell R, ... ... Flicek P, et al. Genome wide conditional mouse knockout resources Drug Discovery Today: Disease Models. 20: 3-12. DOI: 10.1016/J.Ddmod.2017.08.002 |
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| 2015 |
Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, ... ... Flicek P, et al. Ensembl 2016. Nucleic Acids Research. PMID 26687719 DOI: 10.1093/nar/gkv1157 |
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| 2015 |
Zepeda-Mendoza CJ, Mukhopadhyay S, Wong ES, Harder N, Splinter E, de Wit E, Eckersley-Maslin MA, Ried T, Eils R, Rohr K, Mills A, de Laat W, Flicek P, Sengupta AM, Spector DL. Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2. Bmc Genomics. 16: 982. PMID 26589460 DOI: 10.1186/S12864-015-2137-5 |
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| 2015 |
Kretzmer H, Bernhart SH, Wang W, Haake A, Weniger MA, Bergmann AK, Betts MJ, Carrillo-de-Santa-Pau E, Doose G, Gutwein J, Richter J, Hovestadt V, Huang B, Rico D, Jühling F, ... ... Flicek P, et al. DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control. Nature Genetics. PMID 26437030 DOI: 10.1038/Ng.3413 |
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| 2015 |
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, ... ... Flicek P, et al. An integrated map of structural variation in 2,504 human genomes. Nature. 526: 75-81. PMID 26432246 DOI: 10.1038/Nature15394 |
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| 2015 |
Leigh-Brown S, Goncalves A, Thybert D, Stefflova K, Watt S, Flicek P, Brazma A, Marioni JC, Odom DT. Regulatory Divergence of Transcript Isoforms in a Mammalian Model System. Plos One. 10: e0137367. PMID 26339903 DOI: 10.1371/Journal.Pone.0137367 |
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| 2015 |
Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, ... ... Flicek P, et al. Third Report on Chicken Genes and Chromosomes 2015. Prepared by. Cytogenetic and Genome Research. 145: 78-179. PMID 26282327 DOI: 10.1159/000430927 |
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| 2015 |
Dyke SO, Cheung WA, Joly Y, Ammerpohl O, Lutsik P, Rothstein MA, Caron M, Busche S, Bourque G, Rönnblom L, Flicek P, Beck S, Hirst M, Stunnenberg H, Siebert R, et al. Epigenome data release: a participant-centered approach to privacy protection. Genome Biology. 16: 142. PMID 26185018 DOI: 10.1186/S13059-015-0723-0 |
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| 2015 |
Lappalainen I, Almeida-King J, Kumanduri V, Senf A, Spalding JD, Ur-Rehman S, Saunders G, Kandasamy J, Caccamo M, Leinonen R, Vaughan B, Laurent T, Rowland F, Marin-Garcia P, Barker J, ... ... Flicek P, et al. The European Genome-phenome Archive of human data consented for biomedical research. Nature Genetics. 47: 692-5. PMID 26111507 DOI: 10.1038/Ng.3312 |
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| 2015 |
Kulis M, Merkel A, Heath S, Queirós AC, Schuyler RP, Castellano G, Beekman R, Raineri E, Esteve A, Clot G, Verdaguer-Dot N, Duran-Ferrer M, Russiñol N, Vilarrasa-Blasi R, Ecker S, ... ... Flicek P, et al. Whole-genome fingerprint of the DNA methylome during human B cell differentiation. Nature Genetics. PMID 26053498 DOI: 10.1038/Ng.3291 |
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| 2015 |
Benjelloun B, Alberto FJ, Streeter I, Boyer F, Coissac E, Stucki S, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Leempoel K, Alberti A, Engelen S, Chikhi A, Clarke L, ... Flicek P, et al. Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data. Frontiers in Genetics. 6: 107. PMID 25904931 DOI: 10.3389/Fgene.2015.00107 |
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| 2015 |
Zerbino DR, Wilder SP, Johnson N, Juettemann T, Flicek PR. The ensembl regulatory build. Genome Biology. 16: 56. PMID 25887522 DOI: 10.1186/S13059-015-0621-5 |
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| 2015 |
Raposo AA, Vasconcelos FF, Drechsel D, Marie C, Johnston C, Dolle D, Bithell A, Gillotin S, van den Berg DL, Ettwiller L, Flicek P, Crawford GE, Parras CM, Berninger B, Buckley NJ, et al. Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis. Cell Reports. PMID 25753420 DOI: 10.1016/J.Celrep.2015.02.025 |
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| 2015 |
Eöry L, Gilbert MT, Li C, Li B, Archibald A, Aken BL, Zhang G, Jarvis E, Flicek P, Burt DW. Avianbase: a community resource for bird genomics. Genome Biology. 16: 21. PMID 25723810 DOI: 10.1186/S13059-015-0588-2 |
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| 2015 |
Church DM, Schneider VA, Steinberg KM, Schatz MC, Quinlan AR, Chin CS, Kitts PA, Aken B, Marth GT, Hoffman MM, Herrero J, Mendoza ML, Durbin R, Flicek P. Extending reference assembly models. Genome Biology. 16: 13. PMID 25651527 DOI: 10.1186/S13059-015-0587-3 |
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| 2015 |
Agirre X, Castellano G, Pascual M, Heath S, Kulis M, Segura V, Bergmann A, Esteve A, Merkel A, Raineri E, Agueda L, Blanc J, Richardson D, Clarke L, Datta A, ... ... Flicek P, et al. Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers. Genome Research. 25: 478-87. PMID 25644835 DOI: 10.1016/J.Clml.2015.07.243 |
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| 2015 |
Villar D, Berthelot C, Aldridge S, Rayner TF, Lukk M, Pignatelli M, Park TJ, Deaville R, Erichsen JT, Jasinska AJ, Turner JM, Bertelsen MF, Murchison EP, Flicek P, Odom DT. Enhancer evolution across 20 mammalian species. Cell. 160: 554-66. PMID 25635462 DOI: 10.1016/J.Cell.2015.01.006 |
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| 2015 |
Robinson J, Halliwell JA, Hayhurst JD, Flicek P, Parham P, Marsh SG. The IPD and IMGT/HLA database: allele variant databases. Nucleic Acids Research. 43: D423-31. PMID 25414341 DOI: 10.1093/Nar/Gku1161 |
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| 2015 |
Wong ES, Thybert D, Schmitt BM, Stefflova K, Odom DT, Flicek P. Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals. Genome Research. 25: 167-78. PMID 25394363 DOI: 10.1101/Gr.177840.114 |
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| 2015 |
Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, ... ... Flicek P, et al. Ensembl 2015. Nucleic Acids Research. 43: D662-9. PMID 25352552 DOI: 10.1093/nar/gku1010 |
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| 2015 |
Mateo JL, van den Berg DL, Haeussler M, Drechsel D, Gaber ZB, Castro DS, Robson P, Crawford GE, Flicek P, Ettwiller L, Wittbrodt J, Guillemot F, Martynoga B. Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal. Genome Research. 25: 41-56. PMID 25294244 DOI: 10.1101/Gr.173435.114 |
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| 2015 |
Ritchie GRS, Flicek P. Functional annotation of rare genetic variants Assessing Rare Variation in Complex Traits: Design and Analysis of Genetic Studies. 57-70. DOI: 10.1007/978-1-4939-2824-8_5 |
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| 2014 |
Ritchie GR, Flicek P. Computational approaches to interpreting genomic sequence variation. Genome Medicine. 6: 87. PMID 25473426 DOI: 10.1186/S13073-014-0087-1 |
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| 2014 |
Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, ... ... Flicek P, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 515: 355-64. PMID 25409824 DOI: 10.1038/Nature13992 |
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|
| 2014 |
Nelson AC, Cutty SJ, Niini M, Stemple DL, Flicek P, Houart C, Bruce AE, Wardle FC. 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 Biology. 12: 81. PMID 25277163 DOI: 10.1186/S12915-014-0081-5 |
0.362 |
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| 2014 |
Chen L, Kostadima M, Martens JH, Canu G, Garcia SP, Turro E, Downes K, Macaulay IC, Bielczyk-Maczynska E, Coe S, Farrow S, Poudel P, Burden F, Jansen SB, Astle WJ, ... ... Flicek P, et al. Transcriptional diversity during lineage commitment of human blood progenitors. Science (New York, N.Y.). 345: 1251033. PMID 25258084 DOI: 10.1126/Science.1251033 |
0.35 |
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| 2014 |
Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, ... ... Flicek P, et al. Gibbon genome and the fast karyotype evolution of small apes. Nature. 513: 195-201. PMID 25209798 DOI: 10.1038/Nature13679 |
0.459 |
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| 2014 |
Jiang Y, Xie M, Chen W, Talbot R, Maddox JF, Faraut T, Wu C, Muzny DM, Li Y, Zhang W, Stanton JA, Brauning R, Barris WC, Hourlier T, Aken BL, ... ... Flicek P, et al. The sheep genome illuminates biology of the rumen and lipid metabolism. Science (New York, N.Y.). 344: 1168-73. PMID 24904168 DOI: 10.1126/Science.1252806 |
0.355 |
|
| 2014 |
Ramos EM, Din-Lovinescu C, Berg JS, Brooks LD, Duncanson A, Dunn M, Good P, Hubbard TJ, Jarvik GP, O'Donnell C, Sherry ST, Aronson N, Biesecker LG, Blumberg B, Calonge N, ... ... Flicek P, et al. Characterizing genetic variants for clinical action. American Journal of Medical Genetics. Part C, Seminars in Medical Genetics. 166: 93-104. PMID 24634402 DOI: 10.1002/Ajmg.C.31386 |
0.414 |
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| 2014 |
Villar D, Flicek P, Odom DT. Evolution of transcription factor binding in metazoans - mechanisms and functional implications. Nature Reviews. Genetics. 15: 221-33. PMID 24590227 DOI: 10.1038/Nrg3481 |
0.396 |
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| 2014 |
Eckersley-Maslin MA, Thybert D, Bergmann JH, Marioni JC, Flicek P, Spector DL. Random monoallelic gene expression increases upon embryonic stem cell differentiation. Developmental Cell. 28: 351-65. PMID 24576421 DOI: 10.1016/J.Devcel.2014.01.017 |
0.347 |
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| 2014 |
Ritchie GR, Dunham I, Zeggini E, Flicek P. Functional annotation of noncoding sequence variants. Nature Methods. 11: 294-6. PMID 24487584 DOI: 10.1038/Nmeth.2832 |
0.474 |
|
| 2014 |
Zerbino DR, Johnson N, Juettemann T, Wilder SP, Flicek P. WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis. Bioinformatics (Oxford, England). 30: 1008-9. PMID 24363377 DOI: 10.1093/Bioinformatics/Btt737 |
0.475 |
|
| 2014 |
Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, Klemm A, Flicek P, Manolio T, Hindorff L, Parkinson H. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Research. 42: D1001-6. PMID 24316577 DOI: 10.1093/Nar/Gkt1229 |
0.363 |
|
| 2014 |
Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt S, et al. Ensembl 2014. Nucleic Acids Research. 42: D749-55. PMID 24316576 DOI: 10.1093/nar/gkt1196 |
0.355 |
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| 2014 |
MacArthur JA, Morales J, Tully RE, Astashyn A, Gil L, Bruford EA, Larsson P, Flicek P, Dalgleish R, Maglott DR, Cunningham F. Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants. Nucleic Acids Research. 42: D873-8. PMID 24285302 DOI: 10.1093/Nar/Gkt1198 |
0.515 |
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| 2014 |
Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, Blake A, Chen CK, Easty R, Di Fenza A, Fiegel T, Grifiths M, Horne A, Karp NA, Kurbatova N, ... ... Flicek P, et al. The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data. Nucleic Acids Research. 42: D802-9. PMID 24194600 DOI: 10.1093/Nar/Gkt977 |
0.372 |
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| 2014 |
Kulis M, Heath S, Castellano G, Beekman R, Merkel A, Raineri E, Esteve A, Queirós AC, Clot G, Schuyler R, Ecker S, Pancaldi V, Rico D, Agueda L, Blanc J, ... ... Flicek P, et al. Characterization of the DNA Methylome during Human B-Cell Differentiation Blood. 124: 4346-4346. DOI: 10.1182/Blood.V124.21.4346.4346 |
0.331 |
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| 2014 |
Agirre X, Castellano G, Pascual M, Kulis M, Segura V, Bergmann A, Esteve A, Merkel A, Raineri E, Agueda L, Blanc J, Richardson D, Clarke L, Russiñol N, Queirós AC, ... ... Flicek P, et al. Whole-genome epigenomic analysis in multiple myeloma reveals DNA hypermethylation of b-cell specific enhancers Blood. 124: 2032-2032. DOI: 10.1182/Blood.V124.21.2032.2032 |
0.358 |
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| 2013 |
Schwalie PC, Ward MC, Cain CE, Faure AJ, Gilad Y, Odom DT, Flicek P. Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes. Genome Biology. 14: R148. PMID 24380390 DOI: 10.1186/Gb-2013-14-12-R148 |
0.381 |
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| 2013 |
Schauer T, Schwalie PC, Handley A, Margulies CE, Flicek P, Ladurner AG. CAST-ChIP maps cell-type-specific chromatin states in the Drosophila central nervous system. Cell Reports. 5: 271-82. PMID 24095734 DOI: 10.1016/J.Celrep.2013.09.001 |
0.305 |
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| 2013 |
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, ... ... Flicek P, et al. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science (New York, N.Y.). 342: 1235587. PMID 24092746 DOI: 10.1126/Science.1235587 |
0.46 |
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| 2013 |
Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PA, Monlong J, Rivas MA, Gonzà lez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, ... ... Flicek P, et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature. 501: 506-11. PMID 24037378 DOI: 10.1038/Nature12531 |
0.507 |
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| 2013 |
Seitan VC, Faure AJ, Zhan Y, McCord RP, Lajoie BR, Ing-Simmons E, Lenhard B, Giorgetti L, Heard E, Fisher AG, Flicek P, Dekker J, Merkenschlager M. Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments. Genome Research. 23: 2066-77. PMID 24002784 DOI: 10.1101/Gr.161620.113 |
0.385 |
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| 2013 |
Flicek P. Evolutionary biology: The handiwork of tinkering. Nature. 500: 158-9. PMID 23925235 DOI: 10.1038/500158A |
0.359 |
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| 2013 |
Stefflova K, Thybert D, Wilson MD, Streeter I, Aleksic J, Karagianni P, Brazma A, Adams DJ, Talianidis I, Marioni JC, Flicek P, Odom DT. Cooperativity and rapid evolution of cobound transcription factors in closely related mammals. Cell. 154: 530-40. PMID 23911320 DOI: 10.1016/J.Cell.2013.07.007 |
0.415 |
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| 2013 |
Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, ... ... Flicek P, et al. Computational approaches to identify functional genetic variants in cancer genomes. Nature Methods. 10: 723-9. PMID 23900255 DOI: 10.1038/Nmeth.2562 |
0.403 |
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| 2013 |
Atanur SS, Diaz AG, Maratou K, Sarkis A, Rotival M, Game L, Tschannen MR, Kaisaki PJ, Otto GW, Ma MC, Keane TM, Hummel O, Saar K, Chen W, Guryev V, ... ... Flicek P, et al. Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat. Cell. 154: 691-703. PMID 23890820 DOI: 10.1016/J.Cell.2013.06.040 |
0.371 |
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| 2013 |
Baud A, Hermsen R, Guryev V, Stridh P, Graham D, McBride MW, Foroud T, Calderari S, Diez M, Ockinger J, Beyeen AD, Gillett A, Abdelmagid N, Guerreiro-Cacais AO, ... ... Flicek P, et al. Combined sequence-based and genetic mapping analysis of complex traits in outbred rats. Nature Genetics. 45: 767-75. PMID 23708188 DOI: 10.1038/Ng.2644 |
0.372 |
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| 2013 |
Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, Huang Z, Li C, White S, Xiong Z, Fang D, Wang B, Ming Y, Chen Y, Zheng Y, Kuraku S, ... ... Flicek P, et al. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nature Genetics. 45: 701-6. PMID 23624526 DOI: 10.1038/Ng.2615 |
0.405 |
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| 2013 |
Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, ... ... Flicek P, et al. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nature Genetics. 45: 415-21, 421e1-2. PMID 23435085 DOI: 10.1038/Ng.2568 |
0.507 |
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| 2013 |
Ward MC, Wilson MD, Barbosa-Morais NL, Schmidt D, Stark R, Pan Q, Schwalie PC, Menon S, Lukk M, Watt S, Thybert D, Kutter C, Kirschner K, Flicek P, Blencowe BJ, et al. Latent regulatory potential of human-specific repetitive elements. Molecular Cell. 49: 262-72. PMID 23246434 DOI: 10.1016/J.Molcel.2012.11.013 |
0.423 |
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| 2013 |
Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, GarcÃa-Girón C, Gordon L, Hourlier T, et al. Ensembl 2013. Nucleic Acids Research. 41: D48-55. PMID 23203987 DOI: 10.1093/nar/gks1236 |
0.418 |
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| 2013 |
Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M, Zhou G, Paschall J, Ananiev V, Flicek P, Church DM. DbVar and DGVa: public archives for genomic structural variation. Nucleic Acids Research. 41: D936-41. PMID 23193291 DOI: 10.1093/Nar/Gks1213 |
0.355 |
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| 2012 |
Mallon AM, Iyer V, Melvin D, Morgan H, Parkinson H, Brown SD, Flicek P, Skarnes WC. Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 23: 641-52. PMID 22991088 DOI: 10.1007/S00335-012-9428-9 |
0.387 |
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| 2012 |
Goncalves A, Leigh-Brown S, Thybert D, Stefflova K, Turro E, Flicek P, Brazma A, Odom DT, Marioni JC. Extensive compensatory cis-trans regulation in the evolution of mouse gene expression. Genome Research. 22: 2376-84. PMID 22919075 DOI: 10.1101/Gr.142281.112 |
0.351 |
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| 2012 |
Nelson AC, Pillay N, Henderson S, Presneau N, Tirabosco R, Halai D, Berisha F, Flicek P, Stemple DL, Stern CD, Wardle FC, Flanagan AM. An integrated functional genomics approach identifies the regulatory network directed by brachyury (T) in chordoma. The Journal of Pathology. 228: 274-85. PMID 22847733 DOI: 10.1002/Path.4082 |
0.418 |
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| 2012 |
Faure AJ, Schmidt D, Watt S, Schwalie PC, Wilson MD, Xu H, Ramsay RG, Odom DT, Flicek P. Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules. Genome Research. 22: 2163-75. PMID 22780989 DOI: 10.1101/Gr.136507.111 |
0.346 |
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| 2012 |
Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P. The 1000 Genomes Project: data management and community access. Nature Methods. 9: 459-62. PMID 22543379 DOI: 10.1038/Nmeth.1974 |
0.402 |
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| 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, ... ... Flicek P, et al. Insights into hominid evolution from the gorilla genome sequence. Nature. 483: 169-75. PMID 22398555 DOI: 10.1038/Nature10842 |
0.506 |
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| 2012 |
Zheng-Bradley X, Flicek P. Maps for the world of genomic medicine: the 2011 CSHL Personal Genomes meeting. Human Mutation. 33: 1016-9. PMID 22253119 DOI: 10.1002/Humu.22024 |
0.495 |
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| 2012 |
Schmidt D, Schwalie PC, Wilson MD, Ballester B, Gonçalves A, Kutter C, Brown GD, Marshall A, Flicek P, Odom DT. Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell. 148: 335-48. PMID 22244452 DOI: 10.1016/J.Cell.2011.11.058 |
0.426 |
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| 2012 |
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Gordon L, Hendrix M, Hourlier T, Johnson N, et al. Ensembl 2012. Nucleic Acids Research. 40: D84-90. PMID 22086963 DOI: 10.1093/nar/gkr991 |
0.32 |
|
| 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, ... ... Flicek P, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478: 476-82. PMID 21993624 DOI: 10.1038/Nature10530 |
0.467 |
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| 2011 |
Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge M, Blackwell T, Zheng-Bradley X, Chen Y, Challis D, Clarke L, Ball EV, Cibulskis K, ... ... Flicek P, et al. The functional spectrum of low-frequency coding variation. Genome Biology. 12: R84. PMID 21917140 DOI: 10.1186/Gb-2011-12-9-R84 |
0.395 |
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| 2011 |
Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ES, Lefèvre CM, Nicholas KR, Kuroki Y, Wakefield MJ, ... ... Flicek P, et al. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biology. 12: R81. PMID 21854559 DOI: 10.1186/Gb-2011-12-8-R81 |
0.486 |
|
| 2011 |
Kinsella RJ, Kähäri A, Haider S, Zamora J, Proctor G, Spudich G, Almeida-King J, Staines D, Derwent P, Kerhornou A, Kersey P, Flicek P. Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database : the Journal of Biological Databases and Curation. 2011: bar030. PMID 21785142 DOI: 10.1093/Database/Bar030 |
0.479 |
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| 2011 |
Church DM, Schneider VA, Graves T, Auger K, Cunningham F, Bouk N, Chen HC, Agarwala R, McLaren WM, Ritchie GR, Albracht D, Kremitzki M, Rock S, Kotkiewicz H, Kremitzki C, ... ... Flicek P, et al. Modernizing reference genome assemblies. Plos Biology. 9: e1001091. PMID 21750661 DOI: 10.1371/Journal.Pbio.1001091 |
0.332 |
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| 2011 |
Lipman D, Flicek P, Salzberg S, Gerstein M, Knight R. Closure of the NCBI SRA and implications for the long-term future of genomics data storage. Genome Biology. 12: 402. PMID 21418618 DOI: 10.1186/Gb-2011-12-3-402 |
0.4 |
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| 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 |
0.391 |
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| 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, ... ... Flicek P, et al. Comparative and demographic analysis of orang-utan genomes. Nature. 469: 529-33. PMID 21270892 DOI: 10.1038/Nature09687 |
0.494 |
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| 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, et al. Ensembl 2011. Nucleic Acids Research. 39: D800-6. PMID 21045057 DOI: 10.1093/nar/gkq1064 |
0.377 |
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| 2011 |
Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ESW, Lefèvre CM, Nicholas KR, Kuroki Y, Wakefield MJ, ... ... Flicek P, et al. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development Genome Biology. 12. DOI: 10.1186/Gb-2011-12-12-414 |
0.486 |
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| 2010 |
Ye K, Jia Z, Wang Y, Flicek P, Apweiler R. Mining Unique- Substrings from Genomes. Journal of Proteomics & Bioinformatics. 3: 099-103. PMID 29657484 DOI: 10.4172/Jpb.1000127 |
0.5 |
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| 2010 |
Church DM, Lappalainen I, Sneddon TP, Hinton J, Maguire M, Lopez J, Garner J, Paschall J, DiCuccio M, Yaschenko E, Scherer SW, Feuk L, Flicek P. Public data archives for genomic structural variation. Nature Genetics. 42: 813-4. PMID 20877315 DOI: 10.1038/Ng1010-813 |
0.443 |
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| 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, ... ... Flicek P, 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 |
0.538 |
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| 2010 |
Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K. A standard variation file format for human genome sequences. Genome Biology. 11: R88. PMID 20796305 DOI: 10.1186/Gb-2010-11-8-R88 |
0.501 |
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| 2010 |
Schnetz MP, Handoko L, Akhtar-Zaidi B, Bartels CF, Pereira CF, Fisher AG, Adams DJ, Flicek P, Crawford GE, Laframboise T, Tesar P, Wei CL, Scacheri PC. CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. Plos Genetics. 6: e1001023. PMID 20657823 DOI: 10.1371/Journal.Pgen.1001023 |
0.358 |
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| 2010 |
Smedley D, Schofield P, Chen CK, Aidinis V, Ainali C, Bard J, Balling R, Birney E, Blake A, Bongcam-Rudloff E, Brookes AJ, Cesareni G, Chandras C, Eppig J, Flicek P, et al. Finding and sharing: new approaches to registries of databases and services for the biomedical sciences. Database : the Journal of Biological Databases and Curation. 2010: baq014. PMID 20627863 DOI: 10.1093/Database/Baq014 |
0.32 |
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| 2010 |
McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics (Oxford, England). 26: 2069-70. PMID 20562413 DOI: 10.1093/Bioinformatics/Btq330 |
0.455 |
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| 2010 |
Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Gräf S, Flicek P, Kerkhoven RM, van Lohuizen M, Reinders M, Wessels L, van Steensel B. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Molecular Cell. 38: 603-13. PMID 20513434 DOI: 10.1016/J.Molcel.2010.03.016 |
0.409 |
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| 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 |
0.426 |
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| 2010 |
Rios D, McLaren WM, Chen Y, Birney E, Stabenau A, Flicek P, Cunningham F. A database and API for variation, dense genotyping and resequencing data. Bmc Bioinformatics. 11: 238. PMID 20459810 DOI: 10.1186/1471-2105-11-238 |
0.48 |
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| 2010 |
Ballester B, Johnson N, Proctor G, Flicek P. Consistent annotation of gene expression arrays. Bmc Genomics. 11: 294. PMID 20459806 DOI: 10.1186/1471-2164-11-294 |
0.439 |
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| 2010 |
Chen Y, Cunningham F, Rios D, McLaren WM, Smith J, Pritchard B, Spudich GM, Brent S, Kulesha E, Marin-Garcia P, Smedley D, Birney E, Flicek P. Ensembl variation resources. Bmc Genomics. 11: 293. PMID 20459805 DOI: 10.1186/1471-2164-11-293 |
0.514 |
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| 2010 |
Atanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, Behmoaras J, Fernandez-Suarez XM, Johnson MD, McLaren WM, Patone G, Petretto E, Plessy C, Rockland KS, Rockland C, ... ... Flicek P, et al. The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Genome Research. 20: 791-803. PMID 20430781 DOI: 10.1101/Gr.103499.109 |
0.497 |
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| 2010 |
Dalgleish R, Flicek P, Cunningham F, Astashyn A, Tully RE, Proctor G, Chen Y, McLaren WM, Larsson P, Vaughan BW, Béroud C, Dobson G, Lehväslaiho H, Taschner PE, den Dunnen JT, et al. Locus Reference Genomic sequences: an improved basis for describing human DNA variants. Genome Medicine. 2: 24. PMID 20398331 DOI: 10.1186/Gm145 |
0.506 |
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| 2010 |
Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, Bernabé RR, Bhan MK, Calvo F, Eerola I, Gerhard DS, Guttmacher A, Guyer M, Hemsley FM, Jennings JL, ... ... Flicek P, et al. International network of cancer genome projects. Nature. 464: 993-8. PMID 20393554 DOI: 10.1038/Nature08987 |
0.398 |
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| 2010 |
Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, Talianidis I, Flicek P, Odom DT. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science (New York, N.Y.). 328: 1036-40. PMID 20378774 DOI: 10.1126/Science.1186176 |
0.376 |
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| 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, ... ... Flicek P, et al. The genome of a songbird. Nature. 464: 757-62. PMID 20360741 DOI: 10.1038/Nature08819 |
0.52 |
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| 2010 |
Schmidt D, Schwalie PC, Ross-Innes CS, Hurtado A, Brown GD, Carroll JS, Flicek P, Odom DT. A CTCF-independent role for cohesin in tissue-specific transcription. Genome Research. 20: 578-88. PMID 20219941 DOI: 10.1101/Gr.100479.109 |
0.379 |
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| 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, et al. Ensembl's 10th year. Nucleic Acids Research. 38: D557-62. PMID 19906699 DOI: 10.1093/Nar/Gkp972 |
0.527 |
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| 2010 |
Flicek P. Discovery and annotation human variation New Biotechnology. 27. DOI: 10.1016/J.Nbt.2010.01.319 |
0.333 |
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| 2009 |
Flicek P, Birney E. Sense from sequence reads: methods for alignment and assembly. Nature Methods. 6: S6-S12. PMID 19844229 DOI: 10.1038/Nmeth.1376 |
0.353 |
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| 2009 |
Bruce AW, López-Contreras AJ, Flicek P, Down TA, Dhami P, Dillon SC, Koch CM, Langford CF, Dunham I, Andrews RM, Vetrie D. Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level. Genome Research. 19: 994-1005. PMID 19401398 DOI: 10.1101/Gr.089086.108 |
0.368 |
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| 2009 |
Flicek P. The need for speed. Genome Biology. 10: 212. PMID 19344490 DOI: 10.1186/Gb-2009-10-3-212 |
0.338 |
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| 2009 |
Kaput J, Cotton RG, Hardman L, Watson M, Al Aqeel AI, Al-Aama JY, Al-Mulla F, Alonso S, Aretz S, Auerbach AD, Bapat B, Bernstein IT, Bhak J, Bleoo SL, Blöcker H, ... ... Flicek P, et al. Planning the human variome project: the Spain report. Human Mutation. 30: 496-510. PMID 19306394 DOI: 10.1002/Humu.20972 |
0.436 |
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| 2009 |
Carlile M, Swan D, Jackson K, Preston-Fayers K, Ballester B, Flicek P, Werner A. Strand selective generation of endo-siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues. Nucleic Acids Research. 37: 2274-82. PMID 19237395 DOI: 10.1093/Nar/Gkp088 |
0.355 |
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| 2009 |
Morley RH, Lachani K, Keefe D, Gilchrist MJ, Flicek P, Smith JC, Wardle FC. A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation. Proceedings of the National Academy of Sciences of the United States of America. 106: 3829-34. PMID 19225104 DOI: 10.1073/Pnas.0808382106 |
0.41 |
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| 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, ... ... Flicek P, et al. Ensembl 2009. Nucleic Acids Research. 37: D690-7. PMID 19033362 DOI: 10.1093/nar/gkn828 |
0.393 |
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| 2008 |
Coghlan A, Fiedler TJ, McKay SJ, Flicek P, Harris TW, Blasiar D, Stein LD. nGASP--the nematode genome annotation assessment project. Bmc Bioinformatics. 9: 549. PMID 19099578 DOI: 10.1186/1471-2105-9-549 |
0.469 |
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| 2008 |
Paten B, Herrero J, Fitzgerald S, Beal K, Flicek P, Holmes I, Birney E. Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Research. 18: 1829-43. PMID 18849525 DOI: 10.1101/Gr.076521.108 |
0.434 |
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| 2008 |
Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nature Biotechnology. 26: 779-85. PMID 18612301 DOI: 10.1038/Nbt1414 |
0.393 |
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| 2008 |
Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Gräf S, Tomazou EM, Bäckdahl L, Johnson N, Herberth M, Howe KL, Jackson DK, Miretti MM, Fiegler H, Marioni JC, et al. An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Research. 18: 1518-29. PMID 18577705 DOI: 10.1101/Gr.077479.108 |
0.451 |
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| 2008 |
Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, ... ... Flicek P, et al. Genome analysis of the platypus reveals unique signatures of evolution. Nature. 453: 175-83. PMID 18464734 DOI: 10.1038/Nature06936 |
0.474 |
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| 2008 |
Saar K, Beck A, Bihoreau MT, Birney E, Brocklebank D, Chen Y, Cuppen E, Demonchy S, Dopazo J, Flicek P, Foglio M, Fujiyama A, Gut IG, Gauguier D, et al. SNP and haplotype mapping for genetic analysis in the rat. Nature Genetics. 40: 560-6. PMID 18443594 DOI: 10.1038/Ng.124 |
0.304 |
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| 2008 |
Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, et al. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Research. 18: 393-403. PMID 18258921 DOI: 10.1101/Gr.7080508 |
0.372 |
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| 2007 |
Flicek P. Gene prediction: Compare and CONTRAST Genome Biology. 8. PMID 18096089 DOI: 10.1186/Gb-2007-8-12-233 |
0.346 |
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| 2007 |
Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, Beazley C, Ingle CE, Dunning M, Flicek P, Koller D, Montgomery S, Tavaré S, Deloukas P, Dermitzakis ET. Population genomics of human gene expression. Nature Genetics. 39: 1217-24. PMID 17873874 DOI: 10.1038/Ng2142 |
0.423 |
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| 2007 |
Gräf S, Nielsen FG, Kurtz S, Huynen MA, Birney E, Stunnenberg H, Flicek P. Optimized design and assessment of whole genome tiling arrays. Bioinformatics (Oxford, England). 23: i195-204. PMID 17646297 DOI: 10.1093/bioinformatics/btm200 |
0.342 |
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| 2007 |
Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Flicek P, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874 |
0.52 |
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| 2007 |
Koch CM, Andrews RM, Flicek P, Dillon SC, Karaöz U, Clelland GK, Wilcox S, Beare DM, Fowler JC, Couttet P, James KD, Lefebvre GC, Bruce AW, Dovey OM, Ellis PD, et al. The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Research. 17: 691-707. PMID 17567990 DOI: 10.1101/Gr.5704207 |
0.357 |
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| 2007 |
Cotton RG, Appelbe W, Auerbach AD, Becker K, Bodmer W, Boone DJ, Boulyjenkov V, Brahmachari S, Brody L, Brookes A, Brown AF, Byers P, Cantu JM, Cassiman JJ, ... ... Flicek P, et al. Recommendations of the 2006 Human Variome Project meeting. Nature Genetics. 39: 433-6. PMID 17392799 DOI: 10.1038/Ng2024 |
0.417 |
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| 2007 |
Nielsen F, Graef S, Zhang X, Kurtz S, Denissov S, Green R, Birney E, Flicek P, Huynen M, Stunnenberg H. Optimising oligonucleotide array design for ChIP-on-chip Bmc Bioinformatics. 8. DOI: 10.1186/1471-2105-8-S8-P4 |
0.436 |
|
| 2006 |
Flicek P, Brent MR. Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts. Genome Biology. 7: S8.1-9. PMID 16925842 DOI: 10.1186/Gb-2006-7-S1-S8 |
0.423 |
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| 2006 |
Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, et al. EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biology. 7: S2.1-31. PMID 16925836 DOI: 10.1186/Gb-2006-7-S1-S2 |
0.462 |
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| 2006 |
Cunningham F, Rios D, Griffiths M, Smith J, Ning Z, Cox T, Flicek P, Marin-Garcin P, Herrero J, Rogers J, Van Der Weyden L, Bradley A, Birney E, Adams DJ. TranscriptSNPView: A genome-wide catalog of mouse coding variation [1] Nature Genetics. 38: 853. PMID 16874317 DOI: 10.1038/Ng0806-853A |
0.493 |
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| 2005 |
Eyras E, Reymond A, Castelo R, Bye JM, Camara F, Flicek P, Huckle EJ, Parra G, Shteynberg DD, Wyss C, Rogers J, Antonarakis SE, Birney E, Guigo R, Brent MR. Gene finding in the chicken genome. Bmc Bioinformatics. 6: 131. PMID 15924626 DOI: 10.1186/1471-2105-6-131 |
0.502 |
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| 2003 |
Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, ... ... Flicek P, et al. The DNA sequence of human chromosome 7. Nature. 424: 157-64. PMID 12853948 DOI: 10.1038/Nature01782 |
0.41 |
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| 2003 |
Flicek P, Keibler E, Hu P, Korf I, Brent MR. Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. Genome Research. 13: 46-54. PMID 12529305 DOI: 10.1101/Gr.830003 |
0.51 |
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| 2002 |
Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, ... ... Flicek P, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/Nature01262 |
0.529 |
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| 2001 |
Korf I, Flicek P, Duan D, Brent MR. Integrating genomic homology into gene structure prediction. Bioinformatics (Oxford, England). 17: S140-8. PMID 11473003 DOI: 10.1093/Bioinformatics/17.Suppl_1.S140 |
0.509 |
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