Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 135

1.

Dynamics of gene regulatory networks and their dependence on network topology and quantitative parameters - the case of phage λ.

Ruklisa D, Brazma A, Cerans K, Schlitt T, Viksna J.

BMC Bioinformatics. 2019 May 31;20(1):296. doi: 10.1186/s12859-019-2909-z.

2.

The PRIDE database and related tools and resources in 2019: improving support for quantification data.

Perez-Riverol Y, Csordas A, Bai J, Bernal-Llinares M, Hewapathirana S, Kundu DJ, Inuganti A, Griss J, Mayer G, Eisenacher M, Pérez E, Uszkoreit J, Pfeuffer J, Sachsenberg T, Yilmaz S, Tiwary S, Cox J, Audain E, Walzer M, Jarnuczak AF, Ternent T, Brazma A, Vizcaíno JA.

Nucleic Acids Res. 2019 Jan 8;47(D1):D442-D450. doi: 10.1093/nar/gky1106.

3.

A call for public archives for biological image data.

Ellenberg J, Swedlow JR, Barlow M, Cook CE, Sarkans U, Patwardhan A, Brazma A, Birney E.

Nat Methods. 2018 Nov;15(11):849-854. doi: 10.1038/s41592-018-0195-8. No abstract available.

PMID:
30377375
4.

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.

5.

Publisher Correction: Image Data Resource: a bioimage data integration and publication platform.

Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Carazo Salas RE, Swedlow JR.

Nat Methods. 2018 Nov;15(11):984. doi: 10.1038/s41592-018-0169-x.

PMID:
30287931
6.

An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures.

Collord G, Tarpey P, Kurbatova N, Martincorena I, Moran S, Castro M, Nagy T, Bignell G, Maura F, Young MD, Berna J, Tubio JMC, McMurran CE, Young AMH, Sanders M, Noorani I, Price SJ, Watts C, Leipnitz E, Kirsch M, Schackert G, Pearson D, Devadass A, Ram Z, Collins VP, Allinson K, Jenkinson MD, Zakaria R, Syed K, Hanemann CO, Dunn J, McDermott MW, Kirollos RW, Vassiliou GS, Esteller M, Behjati S, Brazma A, Santarius T, McDermott U.

Sci Rep. 2018 Sep 10;8(1):13537. doi: 10.1038/s41598-018-31659-0.

7.

Aberration hubs in protein interaction networks highlight actionable targets in cancer.

Karimzadeh M, Jandaghi P, Papadakis AI, Trainor S, Rung J, Gonzàlez-Porta M, Scelo G, Vasudev NS, Brazma A, Huang S, Banks RE, Lathrop M, Najafabadi HS, Riazalhosseini Y.

Oncotarget. 2018 May 18;9(38):25166-25180. doi: 10.18632/oncotarget.25382. eCollection 2018 May 18.

8.

A General Framework for Interrogation of mRNA Stability Programs Identifies RNA-Binding Proteins that Govern Cancer Transcriptomes.

Perron G, Jandaghi P, Solanki S, Safisamghabadi M, Storoz C, Karimzadeh M, Papadakis AI, Arseneault M, Scelo G, Banks RE, Tost J, Lathrop M, Tanguay S, Brazma A, Huang S, Brimo F, Najafabadi HS, Riazalhosseini Y.

Cell Rep. 2018 May 8;23(6):1639-1650. doi: 10.1016/j.celrep.2018.04.031.

9.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.

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, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin AA, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Nachtweide S, Quail MA, Sisu C, Stanke M, Stefflova K, Van Oosterhout C, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams DJ, Brazma A, Gerstein M, Paten B, Pham S, Keane TM, Odom DT, Flicek P.

Genome Res. 2018 Apr;28(4):448-459. doi: 10.1101/gr.234096.117. Epub 2018 Mar 21.

10.

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.

11.

The BioStudies database-one stop shop for all data supporting a life sciences study.

Sarkans U, Gostev M, Athar A, Behrangi E, Melnichuk O, Ali A, Minguet J, Rada JC, Snow C, Tikhonov A, Brazma A, McEntyre J.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1266-D1270. doi: 10.1093/nar/gkx965.

12.

clustComp, a bioconductor package for the comparison of clustering results.

Torrente A, Brazma A.

Bioinformatics. 2017 Dec 15;33(24):4001-4003. doi: 10.1093/bioinformatics/btx532.

13.

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

Roumeliotis TI, Williams SP, Gonçalves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S, Wright JC, Yu L, Yang M, Dienstmann R, Guinney J, Beltrao P, Brazma A, Pardo M, Stegle O, Adams DJ, Wessels L, Saez-Rodriguez J, McDermott U, Choudhary JS.

Cell Rep. 2017 Aug 29;20(9):2201-2214. doi: 10.1016/j.celrep.2017.08.010.

14.

The Image Data Resource: A Bioimage Data Integration and Publication Platform.

Williams E, Moore J, Li SW, Rustici G, Tarkowska A, Chessel A, Leo S, Antal B, Ferguson RK, Sarkans U, Brazma A, Salas REC, Swedlow JR.

Nat Methods. 2017 Aug;14(8):775-781. doi: 10.1038/nmeth.4326. Epub 2017 Jun 19. Erratum in: Nat Methods. 2018 Nov;15(11):984.

15.

Impact of Alternative Splicing on the Human Proteome.

Liu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO.

Cell Rep. 2017 Aug 1;20(5):1229-1241. doi: 10.1016/j.celrep.2017.07.025.

16.

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.

17.

Loss of chromosome Y leads to down regulation of KDM5D and KDM6C epigenetic modifiers in clear cell renal cell carcinoma.

Arseneault M, Monlong J, Vasudev NS, Laskar RS, Safisamghabadi M, Harnden P, Egevad L, Nourbehesht N, Panichnantakul P, Holcatova I, Brisuda A, Janout V, Kollarova H, Foretova L, Navratilova M, Mates D, Jinga V, Zaridze D, Mukeria A, Jandaghi P, Brennan P, Brazma A, Tost J, Scelo G, Banks RE, Lathrop M, Bourque G, Riazalhosseini Y.

Sci Rep. 2017 Mar 23;7:44876. doi: 10.1038/srep44876.

18.

Orchestrating differential data access for translational research: a pilot implementation.

Brandizi M, Melnichuk O, Bild R, Kohlmayer F, Rodriguez-Castro B, Spengler H, Kuhn KA, Kuchinke W, Ohmann C, Mustonen T, Linden M, Nyrönen T, Lappalainen I, Brazma A, Sarkans U.

BMC Med Inform Decis Mak. 2017 Mar 23;17(1):30. doi: 10.1186/s12911-017-0424-6.

19.

Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression.

Torrente A, Lukk M, Xue V, Parkinson H, Rung J, Brazma A.

PLoS One. 2016 Jun 20;11(6):e0157484. doi: 10.1371/journal.pone.0157484. eCollection 2016.

20.

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.

Wright JC, Mudge J, Weisser H, Barzine MP, Gonzalez JM, Brazma A, Choudhary JS, Harrow J.

Nat Commun. 2016 Jun 2;7:11778. doi: 10.1038/ncomms11778.

21.

Subtype-specific micro-RNA expression signatures in breast cancer progression.

Haakensen VD, Nygaard V, Greger L, Aure MR, Fromm B, Bukholm IR, Lüders T, Chin SF, Git A, Caldas C, Kristensen VN, Brazma A, Børresen-Dale AL, Hovig E, Helland Å.

Int J Cancer. 2016 Sep 1;139(5):1117-28. doi: 10.1002/ijc.30142. Epub 2016 May 9.

22.

HMGB1 binds to the rs7903146 locus in TCF7L2 in human pancreatic islets.

Zhou Y, Oskolkov N, Shcherbina L, Ratti J, Kock KH, Su J, Martin B, Oskolkova MZ, Göransson O, Bacon J, Li W, Bucciarelli S, Cilio C, Brazma A, Thatcher B, Rung J, Wierup N, Renström E, Groop L, Hansson O.

Mol Cell Endocrinol. 2016 Jul 15;430:138-45. doi: 10.1016/j.mce.2016.01.027. Epub 2016 Feb 1.

PMID:
26845344
23.

Modelling-based experiment retrieval: a case study with gene expression clustering.

Blomstedt P, Dutta R, Seth S, Brazma A, Kaski S.

Bioinformatics. 2016 May 1;32(9):1388-94. doi: 10.1093/bioinformatics/btv762. Epub 2016 Jan 6.

PMID:
26740526
24.

The BioStudies database.

McEntyre J, Sarkans U, Brazma A.

Mol Syst Biol. 2015 Dec 23;11(12):847. doi: 10.15252/msb.20156658. No abstract available.

25.

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.

26.

A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging.

Su J, Ekman C, Oskolkov N, Lahti L, Ström K, Brazma A, Groop L, Rung J, Hansson O.

Skelet Muscle. 2015 Oct 9;5:35. doi: 10.1186/s13395-015-0059-1. eCollection 2015.

27.

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.

Leigh-Brown S, Goncalves A, Thybert D, Stefflova K, Watt S, Flicek P, Brazma A, Marioni JC, Odom DT.

PLoS One. 2015 Sep 4;10(9):e0137367. doi: 10.1371/journal.pone.0137367. eCollection 2015.

28.

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.

29.

Cellular phenotype database: a repository for systems microscopy data.

Kirsanova C, Brazma A, Rustici G, Sarkans U.

Bioinformatics. 2015 Aug 15;31(16):2736-40. doi: 10.1093/bioinformatics/btv199. Epub 2015 Apr 9.

30.

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.

31.

Variation in genomic landscape of clear cell renal cell carcinoma across Europe.

Scelo G, Riazalhosseini Y, Greger L, Letourneau L, Gonzàlez-Porta M, Wozniak MB, Bourgey M, Harnden P, Egevad L, Jackson SM, Karimzadeh M, Arseneault M, Lepage P, How-Kit A, Daunay A, Renault V, Blanché H, Tubacher E, Sehmoun J, Viksna J, Celms E, Opmanis M, Zarins A, Vasudev NS, Seywright M, Abedi-Ardekani B, Carreira C, Selby PJ, Cartledge JJ, Byrnes G, Zavadil J, Su J, Holcatova I, Brisuda A, Zaridze D, Moukeria A, Foretova L, Navratilova M, Mates D, Jinga V, Artemov A, Nedoluzhko A, Mazur A, Rastorguev S, Boulygina E, Heath S, Gut M, Bihoreau MT, Lechner D, Foglio M, Gut IG, Skryabin K, Prokhortchouk E, Cambon-Thomsen A, Rung J, Bourque G, Brennan P, Tost J, Banks RE, Brazma A, Lathrop GM.

Nat Commun. 2014 Oct 29;5:5135. doi: 10.1038/ncomms6135.

PMID:
25351205
32.

RNA-Seq gene profiling--a systematic empirical comparison.

Fonseca NA, Marioni J, Brazma A.

PLoS One. 2014 Sep 30;9(9):e107026. doi: 10.1371/journal.pone.0107026. eCollection 2014.

33.

Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants.

Greger L, Su J, Rung J, Ferreira PG; Geuvadis consortium, Lappalainen T, Dermitzakis ET, Brazma A.

PLoS One. 2014 Aug 18;9(8):e104567. doi: 10.1371/journal.pone.0104567. eCollection 2014.

34.

Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress.

Marguerat S, Lawler K, Brazma A, Bähler J.

RNA Biol. 2014;11(6):702-14. Epub 2014 Jul 9.

35.

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.

36.

Updates to BioSamples database at European Bioinformatics Institute.

Faulconbridge A, Burdett T, Brandizi M, Gostev M, Pereira R, Vasant D, Sarkans U, Brazma A, Parkinson H.

Nucleic Acids Res. 2014 Jan;42(Database issue):D50-2. doi: 10.1093/nar/gkt1081. Epub 2013 Nov 21.

37.

Transcriptome and genome sequencing uncovers functional variation in humans.

Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HP, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM; Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, Häsler R, Syvänen AC, van Ommen GJ, Brazma A, Meitinger T, Rosenstiel P, Guigó R, Gut IG, Estivill X, Dermitzakis ET.

Nature. 2013 Sep 26;501(7468):506-11. doi: 10.1038/nature12531. Epub 2013 Sep 15.

38.

Cooperativity and rapid evolution of cobound transcription factors in closely related mammals.

Stefflova K, Thybert D, Wilson MD, Streeter I, Aleksic J, Karagianni P, Brazma A, Adams DJ, Talianidis I, Marioni JC, Flicek P, Odom DT.

Cell. 2013 Aug 1;154(3):530-40. doi: 10.1016/j.cell.2013.07.007.

39.

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene.

Gonzàlez-Porta M, Frankish A, Rung J, Harrow J, Brazma A.

Genome Biol. 2013 Jul 1;14(7):R70. doi: 10.1186/gb-2013-14-7-r70.

40.

Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum.

Lawler K, Hammond-Kosack K, Brazma A, Coulson RM.

BMC Syst Biol. 2013 Jun 27;7:52. doi: 10.1186/1752-0509-7-52.

41.

Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centred RNA sequencing.

Majewski IJ, Mittempergher L, Davidson NM, Bosma A, Willems SM, Horlings HM, de Rink I, Greger L, Hooijer GK, Peters D, Nederlof PM, Hofland I, de Jong J, Wesseling J, Kluin RJ, Brugman W, Kerkhoven R, Nieboer F, Roepman P, Broeks A, Muley TR, Jassem J, Niklinski J, van Zandwijk N, Brazma A, Oshlack A, van den Heuvel M, Bernards R.

J Pathol. 2013 Jul;230(3):270-6. doi: 10.1002/path.4209.

PMID:
23661334
42.

A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.

Lahti L, Torrente A, Elo LL, Brazma A, Rung J.

Nucleic Acids Res. 2013 May 1;41(10):e110. doi: 10.1093/nar/gkt229. Epub 2013 Apr 5.

43.

Reuse of public genome-wide gene expression data.

Rung J, Brazma A.

Nat Rev Genet. 2013 Feb;14(2):89-99. doi: 10.1038/nrg3394. Epub 2012 Dec 27. Review.

PMID:
23269463
44.

HSM - a hybrid system based approach for modelling intracellular networks.

Brazma A, Cerans K, Ruklisa D, Schlitt T, Viksna J.

Gene. 2013 Apr 10;518(1):70-7. doi: 10.1016/j.gene.2012.11.084. Epub 2012 Dec 21.

PMID:
23266641
45.

ArrayExpress update--trends in database growth and links to data analysis tools.

Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, Tikhonov A, Welter D, Williams E, Brazma A, Parkinson H, Sarkans U.

Nucleic Acids Res. 2013 Jan;41(Database issue):D987-90. doi: 10.1093/nar/gks1174. Epub 2012 Nov 27.

46.

Tools for mapping high-throughput sequencing data.

Fonseca NA, Rung J, Brazma A, Marioni JC.

Bioinformatics. 2012 Dec 15;28(24):3169-77. doi: 10.1093/bioinformatics/bts605. Epub 2012 Oct 11.

PMID:
23060614
47.

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.

Goncalves A, Leigh-Brown S, Thybert D, Stefflova K, Turro E, Flicek P, Brazma A, Odom DT, Marioni JC.

Genome Res. 2012 Dec;22(12):2376-84. doi: 10.1101/gr.142281.112. Epub 2012 Aug 23.

48.

MageComet--web application for harmonizing existing large-scale experiment descriptions.

Xue V, Burdett T, Lukk M, Taylor J, Brazma A, Parkinson H.

Bioinformatics. 2012 May 15;28(10):1402-3. doi: 10.1093/bioinformatics/bts148. Epub 2012 Apr 2.

49.

Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma.

Caldas J, Gehlenborg N, Kettunen E, Faisal A, Rönty M, Nicholson AG, Knuutila S, Brazma A, Kaski S.

Bioinformatics. 2012 Jan 15;28(2):246-53. doi: 10.1093/bioinformatics/btr634. Epub 2011 Nov 20.

50.

The BioSample Database (BioSD) at the European Bioinformatics Institute.

Gostev M, Faulconbridge A, Brandizi M, Fernandez-Banet J, Sarkans U, Brazma A, Parkinson H.

Nucleic Acids Res. 2012 Jan;40(Database issue):D64-70. doi: 10.1093/nar/gkr937. Epub 2011 Nov 16.

Supplemental Content

Loading ...
Support Center