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Sequence Ontology terminology for gene regulation

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
2021-10 | Journal article
DOI: 10.1016/j.bbagrm.2021.194745
Contributors: David W. Sant; Michael Sinclair; Christopher J. Mungall; Stefan Schulz; Daniel Zerbino; Ruth C. Lovering; Colin Logie; Karen Eilbeck
Source: check_circle
Crossref

Ensembl 2021.

Nucleic acids research
2021-01 | Journal article
DOI: 10.1093/nar/gkaa942
PMID: 33137190
PMC: PMC7778975
Contributors: Howe KL; Achuthan P; Allen J; Allen J; Alvarez-Jarreta J; Amode MR; Armean IM; Azov AG; Bennett R; Bhai J et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

GENCODE 2021.

Nucleic acids research
2021-01 | Journal article
DOI: 10.1093/nar/gkaa1087
PMID: 33270111
PMC: PMC7778937
Contributors: Frankish A; Diekhans M; Jungreis I; Lagarde J; Loveland JE; Mudge JM; Sisu C; Wright JC; Armstrong J; Barnes I et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

eQTL Catalogue: a compendium of uniformly processed human expression and splicing QTLs

2020-12 | Other
DOI: 10.6019/tol.eqtlcatalogue-t.2020.00001.1
OTHER-ID:

C8048
Contributors: Zerbino D
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

The Ensembl COVID-19 resource: Ongoing integration of public SARS-CoV-2 data

2020-12 | Preprint
DOI: 10.1101/2020.12.18.422865
OTHER-ID:

PPR257173
Contributors: De Silva NH; Bhai J; Chakiachvili M; Contreras-Moreira B; Cummins C; Frankish A; Gall A; Genez T; Howe KL; Hunt SE et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

A Quantitative Proteome Map of the Human Body.

Cell
2020-09 | Journal article
DOI: 10.1016/j.cell.2020.08.036
PMID: 32916130
Contributors: Jiang L; Wang M; Lin S; Jian R; Li X; Chan J; Dong G; Fang H; Robinson AE; GTEx Consortium et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

A vast resource of allelic expression data spanning human tissues.

Genome biology
2020-09 | Journal article
DOI: 10.1186/s13059-020-02122-z
PMID: 32912332
PMC: PMC7488534
Contributors: Castel SE; Aguet F; Mohammadi P; GTEx Consortium; Ardlie KG; Lappalainen T
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Transcription and DNA Methylation Patterns of Blood-Derived CD8<sup>+</sup> T Cells Are Associated With Age and Inflammatory Bowel Disease But Do Not Predict Prognosis.

Gastroenterology
2020-08 | Journal article
DOI: 10.1053/j.gastro.2020.08.017
PMID: 32814113
PMC: PMC7428744
Contributors: Gasparetto M; Payne F; Nayak K; Kraiczy J; Glemas C; Philip-McKenzie Y; Ross A; Edgar RD; Zerbino DR; Salvestrini C et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Perspectives on ENCODE.

Nature
2020-07 | Journal article
DOI: 10.1038/s41586-020-2449-8
PMID: 32728248
PMC: PMC7410827
Contributors: ENCODE Project Consortium; Snyder MP; Gingeras TR; Moore JE; Weng Z; Gerstein MB; Ren B; Hardison RC; Stamatoyannopoulos JA; Graveley BR et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Progress, Challenges, and Surprises in Annotating the Human Genome.

Annual review of genomics and human genetics
2020-05 | Journal article
DOI: 10.1146/annurev-genom-121119-083418
PMID: 32421357
PMC: PMC7116059
Contributors: Zerbino DR; Frankish A; Flicek P
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

The open targets post-GWAS analysis pipeline.

Bioinformatics (Oxford, England)
2020-05 | Journal article
DOI: 10.1093/bioinformatics/btaa020
PMID: 31930349
PMC: PMC7203748
Contributors: Peat G; Jones W; Nuhn M; Marugán JC; Newell W; Dunham I; Zerbino D
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

CD8+T-cell transcription and DNA methylation show age specific differences and lack correlation with clinical outcome in pediatric Inflammatory Bowel Disease

2020-03-31 | Preprint
DOI: 10.1101/2020.03.30.015446
Contributors: M Gasparetto; F Payne; K Nayak; J Kraiczy; C Glemas; Y Philip-McKenzie; A Ross; RD Edgar; D Zerbino; C Salvestrini et al.
Source: check_circle
Crossref

eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs

2020-01 | Preprint
DOI: 10.1101/2020.01.29.924266
OTHER-ID:

PPR110850
Contributors: Kerimov N; Hayhurst JD; Peikova K; Manning JR; Walter P; Kolberg L; Samoviča M; Pandian Sakthivel M; Kuzmin I; Trevanion SJ et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Ensembl 2020.

Nucleic acids research
2019-11 | Journal article
DOI: 10.1093/nar/gkz966
PMID: 31691826
Contributors: Yates AD; Achuthan P; Akanni W; Allen J; Allen J; Alvarez-Jarreta J; Amode MR; Armean IM; Azov AG; Bennett R et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Sequence tube maps: making graph genomes intuitive to commuters.

Bioinformatics (Oxford, England)
2019-08 | Journal article
DOI: 10.1093/bioinformatics/btz597
PMID: 31368484
Contributors: Beyer W; Novak AM; Hickey G; Chan J; Tan V; Paten B; Zerbino DR
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Ensembl 2019.

Nucleic acids research
2018-11 | Journal article
DOI: 10.1093/nar/gky1113
PMID: 30407521
Contributors: Cunningham F; Achuthan P; Akanni W; Allen J; Amode MR; Armean IM; Bennett R; Bhai J; Billis K; Boddu S et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

FAANG, establishing metadata standards, validation and best practices for the farmed and companion animal community.

Animal genetics
2018-10 | Journal article
DOI: 10.1111/age.12736
PMID: 30311252
Contributors: Harrison PW; Fan J; Richardson D; Clarke L; Zerbino D; Cochrane G; Archibald AL; Schmidt CJ; Flicek P
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

GENCODE reference annotation for the human and mouse genomes.

Nucleic acids research
2018-10 | Journal article
DOI: 10.1093/nar/gky955
PMID: 30357393
Contributors: Frankish A; Diekhans M; Ferreira AM; Johnson R; Jungreis I; Loveland J; Mudge JM; Sisu C; Wright J; Armstrong J et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Ensembl 2018.

Nucleic acids research
2018-01 | Journal article
DOI: 10.1093/nar/gkx1098
PMID: 29155950
PMC: PMC5753206
Contributors: Zerbino DR; Achuthan P; Akanni W; Amode MR; Barrell D; Bhai J; Billis K; Cummins C; Gall A; Girón CG et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central
grade
Preferred source (of 2)‎

Comparative analysis of neutrophil and monocyte epigenomes

2017-12 | Other
DOI: 10.1101/237784
OTHER-ID:

PPR21045
Contributors: Rico D; Martens JH; Downes K; Carrillo-de-Santa-Pau E; Pancaldi V; Breschi A; Richardson D; Heath S; Saeed S; Frontini M et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Co-expression networks reveal the tissue-specific regulation of transcription and splicing.

Genome research
2017-11 | Journal article
DOI: 10.1101/gr.216721.116
PMID: 29021288
PMC: PMC5668942
Contributors: Saha A; Kim Y; Gewirtz ADH; Jo B; Gao C; McDowell IC; GTEx Consortium; Engelhardt BE; Battle A
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis.

Genome research
2017-11 | Journal article
DOI: 10.1101/gr.216754.116
PMID: 29021290
Contributors: Yang F; Wang J; GTEx Consortium; Pierce BL; Chen LS
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Dynamic landscape and regulation of RNA editing in mammals.

Nature
2017-10 | Journal article
DOI: 10.1038/nature24041
PMID: 29022589
PMC: PMC5723435
Contributors: Tan MH; Li Q; Shanmugam R; Piskol R; Kohler J; Young AN; Liu KI; Zhang R; Ramaswami G; Ariyoshi K et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Genetic effects on gene expression across human tissues.

Nature
2017-10 | Journal article
DOI: 10.1038/nature24277
PMID: 29022597
Contributors: GTEx Consortium; Laboratory; Data Analysis &Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group; Montgomery SB
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Landscape of X chromosome inactivation across human tissues.

Nature
2017-10 | Journal article
DOI: 10.1038/nature24265
PMID: 29022598
Contributors: Tukiainen T; Villani AC; Yen A; Rivas MA; Marshall JL; Satija R; Aguirre M; Gauthier L; Fleharty M; Kirby A et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

The impact of rare variation on gene expression across tissues.

Nature
2017-10 | Journal article
DOI: 10.1038/nature24267
PMID: 29022581
Contributors: Li X; Kim Y; Tsang EK; Davis JR; Damani FN; Chiang C; Hess GT; Zappala Z; Strober BJ; Scott AJ et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Ensembl 2017.

2017-01 | Journal article
DOI: 10.1093/nar/gkw1104
PMID: 27899575
PMC: PMC5210575
Contributors: Aken BL; Achuthan P; Akanni W; Amode MR; Bernsdorff F; Bhai J; Billis K; Carvalho-Silva D; Cummins C; Clapham P et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.

Database : the journal of biological databases and curation
2017-01 | Journal article
DOI: 10.1093/database/bax020
PMID: 28365736
PMC: PMC5467575
Contributors: Ruffier M; Kähäri A; Komorowska M; Keenan S; Laird M; Longden I; Proctor G; Searle S; Staines D; Taylor K et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data.

2016 | Journal article
DOI: 10.1186/s13059-016-0992-2
PMID: 27306882
PMC: PMC4908757
Contributors: Cairns J; Freire-Pritchett P; Wingett SW; Várnai C; Dimond A; Plagnol V; Zerbino D; Schoenfelder S; Javierre BM; Osborne C et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Ensembl regulation resources.

2016 | Journal article
DOI: 10.1093/database/bav119
PMID: 26888907
PMC: PMC4756621
Contributors: Zerbino DR; Johnson N; Juetteman T; Sheppard D; Wilder SP; Lavidas I; Nuhn M; Perry E; Raffaillac-Desfosses Q; Sobral D et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Ensembl Core Software Resources: storage and programmatic access for DNA sequence and genome annotation

2016-11 | Other
DOI: 10.1101/087239
OTHER-ID:

PPR7007
Contributors: Ruffier M; Kähäri A; Komorowska M; Keenan S; Laird MR; Longden I; Proctor G; Steve S; Staines D; Taylor K et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.

2016-11 | Journal article
DOI: 10.1016/j.cell.2016.09.037
PMID: 27863249
PMC: PMC5123897
Contributors: Javierre BM; Burren OS; Wilder SP; Kreuzhuber R; Hill SM; Sewitz S; Cairns J; Wingett SW; Várnai C; Thiecke MJ et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery.

2016-11 | Journal article
DOI: 10.1016/j.cell.2016.11.007
PMID: 27863232
Contributors: Stunnenberg HG; International Human Epigenome Consortium; Hirst M
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs.

2016-09 | Journal article
PMID: 27687569
PMC: PMC5043639
Contributors: Zerbino DR; Ballinger T; Paten B; Hickey G; Haussler D
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.

2016-06 | Journal article
DOI: 10.1038/ng.3559
PMID: 27111036
PMC: PMC4884158
Contributors: Poznik GD; Xue Y; Mendez FL; Willems TF; Massaia A; Wilson Sayres MA; Ayub Q; McCarthy SA; Narechania A; Kashin S et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Ensembl 2016.

2016-01 | Journal article
DOI: 10.1093/nar/gkv1157
PMID: 26687719
PMC: PMC4702834
Contributors: Yates A; Akanni W; Amode MR; Barrell D; Billis K; Carvalho-Silva D; Cummins C; Clapham P; Fitzgerald S; Gil L et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

The ensembl regulatory build.

2015 | Journal article
DOI:

10.1186/s13059-015-0621-5

PMID:

25887522

PMC:

PMC4407537
Contributors: Zerbino DR; Wilder SP; Johnson N; Juettemann T; Flicek PR
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

A global reference for human genetic variation.

2015-10 | Journal article
DOI: 10.1038/nature15393
PMID: 26432245
PMC: PMC4750478
Contributors: 1000 Genomes Project Consortium; Auton A; Brooks LD; Durbin RM; Garrison EP; Kang HM; Korbel JO; Marchini JL; McCarthy S; McVean GA et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Building a pan-genome reference for a population.

2015-05 | Journal article
DOI:

10.1089/cmb.2014.0146

PMID:

25565268
Contributors: Nguyen N; Hickey G; Zerbino DR; Raney B; Earl D; Armstrong J; Kent WJ; Haussler D; Paten B
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Ensembl 2015.

2015-01 | Journal article
DOI:

10.1093/nar/gku1010

PMID:

25352552

PMC:

PMC4383879
Contributors: Cunningham F; Amode MR; Barrell D; Beal K; Billis K; Brent S; Carvalho-Silva D; Clapham P; Coates G; Fitzgerald S et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

A unifying model of genome evolution under parsimony.

2014 | Journal article
DOI:

10.1186/1471-2105-15-206

PMID:

24946830

PMC:

PMC4082375
Contributors: Paten B; Zerbino DR; Hickey G; Haussler D
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis.

2014-04 | Journal article
DOI:

10.1093/bioinformatics/btt737

PMID:

24363377

PMC:

PMC3967112
Contributors: Zerbino DR; Johnson N; Juettemann T; Wilder SP; Flicek P
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Assessment of transcript reconstruction methods for RNA-seq.

2013-12 | Journal article
DOI:

10.1038/nmeth.2714

PMID:

24185837
Contributors: Steijger T; Abril JF; Engström PG; Kokocinski F; RGASP Consortium; Abril JF; Akerman M; Alioto T; Ambrosini G; Antonarakis SE et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Ensembl 2014.

2013-12 | Journal article
PMID:

24316576
Contributors: Flicek P; Amode MR; Barrell D; Beal K; Billis K; Brent S; Carvalho-Silva D; Clapham P; Coates G; Fitzgerald S et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability.

2013-09 | Journal article
DOI:

10.1093/bib/bbt045

PMID:

23793381

PMC:

PMC3771235
Contributors: Li JW; Bolser D; Manske M; Giorgi FM; Vyahhi N; Usadel B; Clavijo BJ; Chan TF; Wong N; Zerbino D et al.
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

HAL: a hierarchical format for storing and analyzing multiple genome alignments.

2013-05 | Journal article
DOI:

10.1093/bioinformatics/btt128

PMID:

23505295

PMC:

PMC3654707
Contributors: Hickey G; Paten B; Earl D; Zerbino D; Haussler D
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Comprehensive genomic characterization of squamous cell lung cancers.

2012-09 | Journal article
DOI:

10.1038/nature11404

PMID:

22960745

PMC:

PMC3466113
Contributors: Cancer Genome Atlas Research Network
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Comprehensive molecular characterization of human colon and rectal cancer.

2012-07 | Journal article
DOI:

10.1038/nature11252

PMID:

22810696

PMC:

PMC3401966
Contributors: Cancer Genome Atlas Network
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Integrating genomes.

2012-04 | Journal article
DOI:

10.1126/science.1216830

PMID:

22499938
Contributors: Zerbino DR; Paten B; Haussler D
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.

2012-04 | Journal article
DOI:

10.1093/bioinformatics/bts094

PMID:

22368243

PMC:

PMC3324515
Contributors: Schulz MH; Zerbino DR; Vingron M; Birney E
Source: Self-asserted source
Daniel Zerbino via Europe PubMed Central
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Peer review (6 reviews for 4 publications/grants)

Review activity for European journal of human genetics (1)
Review activity for Genome biology. (3)
Review activity for Nature communications (1)
Review activity for PLoS computational biology. (1)
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