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Items: 20

1.

Quantifying the impact of public omics data.

Perez-Riverol Y, Zorin A, Dass G, Vu MT, Xu P, Glont M, Vizcaíno JA, Jarnuczak AF, Petryszak R, Ping P, Hermjakob H.

Nat Commun. 2019 Aug 5;10(1):3512. doi: 10.1038/s41467-019-11461-w.

2.

ArrayExpress update - from bulk to single-cell expression data.

Athar A, Füllgrabe A, George N, Iqbal H, Huerta L, Ali A, Snow C, Fonseca NA, Petryszak R, Papatheodorou I, Sarkans U, Brazma A.

Nucleic Acids Res. 2019 Jan 8;47(D1):D711-D715. doi: 10.1093/nar/gky964.

3.

Expression Atlas: gene and protein expression across multiple studies and organisms.

Papatheodorou I, Fonseca NA, Keays M, Tang YA, Barrera E, Bazant W, Burke M, Füllgrabe A, Fuentes AM, George N, Huerta L, Koskinen S, Mohammed S, Geniza M, Preece J, Jaiswal P, Jarnuczak AF, Huber W, Stegle O, Vizcaino JA, Brazma A, Petryszak R.

Nucleic Acids Res. 2018 Jan 4;46(D1):D246-D251. doi: 10.1093/nar/gkx1158.

4.

Gramene 2018: unifying comparative genomics and pathway resources for plant research.

Tello-Ruiz MK, Naithani S, Stein JC, Gupta P, Campbell M, Olson A, Wei S, Preece J, Geniza MJ, Jiao Y, Lee YK, Wang B, Mulvaney J, Chougule K, Elser J, Al-Bader N, Kumari S, Thomason J, Kumar V, Bolser DM, Naamati G, Tapanari E, Fonseca N, Huerta L, Iqbal H, Keays M, Munoz-Pomer Fuentes A, Tang A, Fabregat A, D'Eustachio P, Weiser J, Stein LD, Petryszak R, Papatheodorou I, Kersey PJ, Lockhart P, Taylor C, Jaiswal P, Ware D.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1181-D1189. doi: 10.1093/nar/gkx1111.

5.

Gramene Database: Navigating Plant Comparative Genomics Resources.

Gupta P, Naithani S, Tello-Ruiz MK, Chougule K, D'Eustachio P, Fabregat A, Jiao Y, Keays M, Lee YK, Kumari S, Mulvaney J, Olson A, Preece J, Stein J, Wei S, Weiser J, Huerta L, Petryszak R, Kersey P, Stein LD, Ware D, Jaiswal P.

Curr Plant Biol. 2016 Nov;7-8:10-15. doi: 10.1016/j.cpb.2016.12.005.

6.

Discovering and linking public omics data sets using the Omics Discovery Index.

Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H.

Nat Biotechnol. 2017 May 9;35(5):406-409. doi: 10.1038/nbt.3790. No abstract available.

7.

The RNASeq-er API-a gateway to systematically updated analysis of public RNA-seq data.

Petryszak R, Fonseca NA, Füllgrabe A, Huerta L, Keays M, Tang YA, Brazma A.

Bioinformatics. 2017 Jul 15;33(14):2218-2220. doi: 10.1093/bioinformatics/btx143.

8.

Open Targets: a platform for therapeutic target identification and validation.

Koscielny G, An P, Carvalho-Silva D, Cham JA, Fumis L, Gasparyan R, Hasan S, Karamanis N, Maguire M, Papa E, Pierleoni A, Pignatelli M, Platt T, Rowland F, Wankar P, Bento AP, Burdett T, Fabregat A, Forbes S, Gaulton A, Gonzalez CY, Hermjakob H, Hersey A, Jupe S, Kafkas Ş, Keays M, Leroy C, Lopez FJ, Magarinos MP, Malone J, McEntyre J, Munoz-Pomer Fuentes A, O'Donovan C, Papatheodorou I, Parkinson H, Palka B, Paschall J, Petryszak R, Pratanwanich N, Sarntivijal S, Saunders G, Sidiropoulos K, Smith T, Sondka Z, Stegle O, Tang YA, Turner E, Vaughan B, Vrousgou O, Watkins X, Martin MJ, Sanseau P, Vamathevan J, Birney E, Barrett J, Dunham I.

Nucleic Acids Res. 2017 Jan 4;45(D1):D985-D994. doi: 10.1093/nar/gkw1055. Epub 2016 Nov 29.

9.

Plant Reactome: a resource for plant pathways and comparative analysis.

Naithani S, Preece J, D'Eustachio P, Gupta P, Amarasinghe V, Dharmawardhana PD, Wu G, Fabregat A, Elser JL, Weiser J, Keays M, Fuentes AM, Petryszak R, Stein LD, Ware D, Jaiswal P.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1029-D1039. doi: 10.1093/nar/gkw932. Epub 2016 Oct 30.

10.

Gramene 2016: comparative plant genomics and pathway resources.

Tello-Ruiz MK, Stein J, Wei S, Preece J, Olson A, Naithani S, Amarasinghe V, Dharmawardhana P, Jiao Y, Mulvaney J, Kumari S, Chougule K, Elser J, Wang B, Thomason J, Bolser DM, Kerhornou A, Walts B, Fonseca NA, Huerta L, Keays M, Tang YA, Parkinson H, Fabregat A, McKay S, Weiser J, D'Eustachio P, Stein L, Petryszak R, Kersey PJ, Jaiswal P, Ware D.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1133-40. doi: 10.1093/nar/gkv1179. Epub 2015 Nov 8.

11.

Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.

Petryszak R, Keays M, Tang YA, Fonseca NA, Barrera E, Burdett T, Füllgrabe A, Fuentes AM, Jupp S, Koskinen S, Mannion O, Huerta L, Megy K, Snow C, Williams E, Barzine M, Hastings E, Weisser H, Wright J, Jaiswal P, Huber W, Choudhary J, Parkinson HE, Brazma A.

Nucleic Acids Res. 2016 Jan 4;44(D1):D746-52. doi: 10.1093/nar/gkv1045. Epub 2015 Oct 19.

12.

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.

Frankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D, Petryszak R, Mudge JM, Fonseca N, Brazma A, Guigo R, Harrow J.

BMC Genomics. 2015;16 Suppl 8:S2. doi: 10.1186/1471-2164-16-S8-S2. Epub 2015 Jun 18.

13.

ArrayExpress update--simplifying data submissions.

Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, Dylag M, Kurbatova N, Brandizi M, Burdett T, Megy K, Pilicheva E, Rustici G, Tikhonov A, Parkinson H, Petryszak R, Sarkans U, Brazma A.

Nucleic Acids Res. 2015 Jan;43(Database issue):D1113-6. doi: 10.1093/nar/gku1057. Epub 2014 Oct 31.

14.

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A.

Nucleic Acids Res. 2014 Jan;42(Database issue):D926-32. doi: 10.1093/nar/gkt1270. Epub 2013 Dec 4.

15.

UniChem: a unified chemical structure cross-referencing and identifier tracking system.

Chambers J, Davies M, Gaulton A, Hersey A, Velankar S, Petryszak R, Hastings J, Bellis L, McGlinchey S, Overington JP.

J Cheminform. 2013 Jan 14;5(1):3. doi: 10.1186/1758-2946-5-3.

16.

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

Kapushesky M, Adamusiak T, Burdett T, Culhane A, Farne A, Filippov A, Holloway E, Klebanov A, Kryvych N, Kurbatova N, Kurnosov P, Malone J, Melnichuk O, Petryszak R, Pultsin N, Rustici G, Tikhonov A, Travillian RS, Williams E, Zorin A, Parkinson H, Brazma A.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1077-81. doi: 10.1093/nar/gkr913. Epub 2011 Nov 7.

17.

Building a biological space based on protein sequence similarities and biological ontologies.

Kersey P, Lonsdale D, Mulder NJ, Petryszak R, Apweiler R.

Comb Chem High Throughput Screen. 2008 Sep;11(8):653-60. Review.

PMID:
18795884
18.

New developments in the InterPro database.

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.

Nucleic Acids Res. 2007 Jan;35(Database issue):D224-8.

19.

The predictive power of the CluSTr database.

Petryszak R, Kretschmann E, Wieser D, Apweiler R.

Bioinformatics. 2005 Sep 15;21(18):3604-9. Epub 2005 Jun 16.

PMID:
15961444
20.

Integr8 and Genome Reviews: integrated views of complete genomes and proteomes.

Kersey P, Bower L, Morris L, Horne A, Petryszak R, Kanz C, Kanapin A, Das U, Michoud K, Phan I, Gattiker A, Kulikova T, Faruque N, Duggan K, Mclaren P, Reimholz B, Duret L, Penel S, Reuter I, Apweiler R.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D297-302.

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