Alvis Brazma - Publications

European Bioinformatics Institute, Hinxton, England, United Kingdom 

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

Year Citation  Score
2017 Sarkans U, Gostev M, Athar A, Behrangi E, Melnichuk O, Ali A, Minguet J, Rada JC, Snow C, Tikhonov A, Brazma A, McEntyre J. The BioStudies database-one stop shop for all data supporting a life sciences study. Nucleic Acids Research. PMID 29069414 DOI: 10.1093/Nar/Gkx965  0.36
2016 Ferreira PG, Oti M, Barann M, Wieland T, Ezquina S, Friedländer MR, Rivas MA, Esteve-Codina A, Rosenstiel P, Strom TM, Lappalainen T, Guigó R, Sammeth M. Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing. Scientific Reports. 6: 32406. PMID 27617755 DOI: 10.1038/Srep32406  0.36
2016 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. Subtype-specific micro-RNA expression signatures in breast cancer progression. International Journal of Cancer. PMID 27082076 DOI: 10.1002/Ijc.30142  0.36
2015 McEntyre J, Sarkans U, Brazma A. The BioStudies database. Molecular Systems Biology. 11: 847. PMID 26700850 DOI: 10.15252/Msb.20156658  0.36
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  0.36
2015 Kirsanova C, Brazma A, Rustici G, Sarkans U. Cellular phenotype database: a repository for systems microscopy data. Bioinformatics (Oxford, England). PMID 25861964 DOI: 10.1093/Bioinformatics/Btv199  0.36
2015 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, ... ... Brazma A, et al. ArrayExpress update--simplifying data submissions. Nucleic Acids Research. 43: D1113-6. PMID 25361974 DOI: 10.1093/Nar/Gku1057  0.36
2015 Su J, Ekman C, Oskolkov N, Lahti L, Ström K, Brazma A, Groop L, Rung J, Hansson O. A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging Skeletal Muscle. 5. DOI: 10.1186/s13395-015-0059-1  0.36
2015 Brazma A, Cerans K, Ruklisa D, Schlitt T, Viksna J. Modeling and analysis of qualitative behavior of gene regulatory networks Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7699: 51-66. DOI: 10.1007/978-3-319-27656-4_3  0.36
2014 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, ... ... Brazma A, et al. Variation in genomic landscape of clear cell renal cell carcinoma across Europe. Nature Communications. 5: 5135. PMID 25351205 DOI: 10.1038/Ncomms6135  0.36
2014 Fonseca NA, Marioni J, Brazma A. RNA-Seq gene profiling--a systematic empirical comparison. Plos One. 9: e107026. PMID 25268973 DOI: 10.1371/Journal.Pone.0107026  0.36
2014 Greger L, Su J, Rung J, Ferreira PG, Lappalainen T, Dermitzakis ET, Brazma A. Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants. Plos One. 9: e104567. PMID 25133550 DOI: 10.1371/Journal.Pone.0104567  0.36
2014 Marguerat S, Lawler K, Brazma A, Bähler J. Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress. Rna Biology. 11: 702-14. PMID 25007214 DOI: 10.4161/Rna.29196  0.36
2014 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, ... ... Brazma A, et al. Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. Nucleic Acids Research. 42: D926-32. PMID 24304889 DOI: 10.1093/Nar/Gkt1270  0.36
2014 Faulconbridge A, Burdett T, Brandizi M, Gostev M, Pereira R, Vasant D, Sarkans U, Brazma A, Parkinson H. Updates to BioSamples database at European Bioinformatics Institute. Nucleic Acids Research. 42: D50-2. PMID 24265224 DOI: 10.1093/Nar/Gkt1081  0.36
2013 Milne R, La Vecchia C, Van Steen K, Hahn S, Buchholz M, Costello E, Esposito I, Hoheisel JD, Lange B, Lopez-Bigas N, Michalski CW, Real FX, Brand A, Malats N. EU Pancreas: an integrated European platform for pancreas cancer research--from basic science to clinical and public health interventions for a rare disease. Public Health Genomics. 16: 305-12. PMID 24503591 DOI: 10.1159/000355937  0.36
2013 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, ... ... Brazma A, et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature. 501: 506-11. PMID 24037378 DOI: 10.1038/Nature12531  0.36
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  0.36
2013 Gonzàlez-Porta M, Frankish A, Rung J, Harrow J, Brazma A. Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene. Genome Biology. 14: R70. PMID 23815980 DOI: 10.1186/Gb-2013-14-7-R70  0.36
2013 Lawler K, Hammond-Kosack K, Brazma A, Coulson RM. Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum. Bmc Systems Biology. 7: 52. PMID 23805903 DOI: 10.1186/1752-0509-7-52  0.36
2013 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, ... ... Brazma A, et al. Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centred RNA sequencing. The Journal of Pathology. 230: 270-6. PMID 23661334 DOI: 10.1002/Path.4209  0.36
2013 Lahti L, Torrente A, Elo LL, Brazma A, Rung J. A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases. Nucleic Acids Research. 41: e110. PMID 23563154 DOI: 10.1093/Nar/Gkt229  0.36
2013 Rung J, Brazma A. Reuse of public genome-wide gene expression data. Nature Reviews. Genetics. 14: 89-99. PMID 23269463 DOI: 10.1038/Nrg3394  0.36
2013 Brazma A, Cerans K, Ruklisa D, Schlitt T, Viksna J. HSM - a hybrid system based approach for modelling intracellular networks. Gene. 518: 70-7. PMID 23266641 DOI: 10.1016/J.Gene.2012.11.084  0.36
2013 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, ... ... Brazma A, et al. ArrayExpress update--trends in database growth and links to data analysis tools. Nucleic Acids Research. 41: D987-90. PMID 23193272 DOI: 10.1093/Nar/Gks1174  0.36
2012 Fonseca NA, Rung J, Brazma A, Marioni JC. Tools for mapping high-throughput sequencing data. Bioinformatics (Oxford, England). 28: 3169-77. PMID 23060614 DOI: 10.1093/Bioinformatics/Bts605  0.36
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  0.36
2012 Xue V, Burdett T, Lukk M, Taylor J, Brazma A, Parkinson H. MageComet--web application for harmonizing existing large-scale experiment descriptions. Bioinformatics (Oxford, England). 28: 1402-3. PMID 22474121 DOI: 10.1093/Bioinformatics/Bts148  0.36
2012 Caldas J, Gehlenborg N, Kettunen E, Faisal A, Rönty M, Nicholson AG, Knuutila S, Brazma A, Kaski S. Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma. Bioinformatics (Oxford, England). 28: 246-53. PMID 22106335 DOI: 10.1093/Bioinformatics/Btr634  0.36
2012 Gostev M, Faulconbridge A, Brandizi M, Fernandez-Banet J, Sarkans U, Brazma A, Parkinson H. The BioSample Database (BioSD) at the European Bioinformatics Institute. Nucleic Acids Research. 40: D64-70. PMID 22096232 DOI: 10.1093/Nar/Gkr937  0.36
2012 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, ... ... Brazma A, et al. Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Research. 40: D1077-81. PMID 22064864 DOI: 10.1093/Nar/Gkr913  0.36
2011 Kutter C, Brown GD, Gonçalves A, Wilson MD, Watt S, Brazma A, White RJ, Odom DT. Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes. Nature Genetics. 43: 948-55. PMID 21873999 DOI: 10.1038/Ng.906  0.36
2011 Goncalves A, Tikhonov A, Brazma A, Kapushesky M. A pipeline for RNA-seq data processing and quality assessment. Bioinformatics (Oxford, England). 27: 867-9. PMID 21233166 DOI: 10.1093/Bioinformatics/Btr012  0.36
2011 Beisvåg V, Kauffmann A, Malone J, Foy C, Salit M, Schimmel H, Bongcam-Rudloff E, Landegren U, Parkinson H, Huber W, Brazma A, Sandvik AK, Kuiper M. Contributions of the EMERALD project to assessing and improving microarray data quality. Biotechniques. 50: 27-31. PMID 21231919 DOI: 10.2144/000113591  0.36
2011 Gostev M, Fernandez-Banet J, Rung J, Dietrich J, Prokopenko I, Ripatti S, McCarthy MI, Brazma A, Krestyaninova M. SAIL--a software system for sample and phenotype availability across biobanks and cohorts. Bioinformatics (Oxford, England). 27: 589-91. PMID 21169373 DOI: 10.1093/Bioinformatics/Btq693  0.36
2011 Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, ... ... Brazma A, et al. ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Research. 39: D1002-4. PMID 21071405 DOI: 10.1093/Nar/Gkq1040  0.36
2010 Zheng-Bradley X, Rung J, Parkinson H, Brazma A. Large scale comparison of global gene expression patterns in human and mouse. Genome Biology. 11: R124. PMID 21182765 DOI: 10.1186/Gb-2010-11-12-R124  0.36
2010 Shankar R, Parkinson H, Burdett T, Hastings E, Liu J, Miller M, Srinivasa R, White J, Brazma A, Sherlock G, Stoeckert CJ, Ball CA. Annotare--a tool for annotating high-throughput biomedical investigations and resulting data. Bioinformatics (Oxford, England). 26: 2470-1. PMID 20733062 DOI: 10.1093/Bioinformatics/Btq462  0.36
2010 McKinney EF, Lyons PA, Carr EJ, Hollis JL, Jayne DR, Willcocks LC, Koukoulaki M, Brazma A, Jovanovic V, Kemeny DM, Pollard AJ, Macary PA, Chaudhry AN, Smith KG. A CD8+ T cell transcription signature predicts prognosis in autoimmune disease. Nature Medicine. 16: 586-91, 1p following. PMID 20400961 DOI: 10.1038/Nm.2130  0.36
2010 Lukk M, Kapushesky M, Nikkilä J, Parkinson H, Goncalves A, Huber W, Ukkonen E, Brazma A. A global map of human gene expression. Nature Biotechnology. 28: 322-4. PMID 20379172 DOI: 10.1038/Nbt0410-322  0.36
2010 Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H. Modeling sample variables with an Experimental Factor Ontology. Bioinformatics (Oxford, England). 26: 1112-8. PMID 20200009 DOI: 10.1093/Bioinformatics/Btq099  0.36
2010 Vainshtein Y, Sanchez M, Brazma A, Hentze MW, Dandekar T, Muckenthaler MU. The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays. Bmc Bioinformatics. 11: 112. PMID 20193060 DOI: 10.1186/1471-2105-11-112  0.36
2010 Kapushesky M, Emam I, Holloway E, Kurnosov P, Zorin A, Malone J, Rustici G, Williams E, Parkinson H, Brazma A. Gene expression atlas at the European bioinformatics institute. Nucleic Acids Research. 38: D690-8. PMID 19906730 DOI: 10.1093/Nar/Gkp936  0.36
2010 Kapushesky M, Tikhonov A, Aulchenko YS, Gonçalves A, Rung J, Santamaria R, Brazma A. EBI R CLOUD – Cloud computing for functional genomics at the EBI F1000research. 1. DOI: 10.7490/F1000Research.328.1  0.36
2010 Peltonen J, Aidos H, Gehlenborg N, Brazma A, Kaski S. An information retrieval perspective on visualization of gene expression data with ontological annotation Icassp, Ieee International Conference On Acoustics, Speech and Signal Processing - Proceedings. 2178-2181. DOI: 10.1109/ICASSP.2010.5495665  0.36
2009 Aligianni S, Lackner DH, Klier S, Rustici G, Wilhelm BT, Marguerat S, Codlin S, Brazma A, de Bruin RA, Bähler J. The fission yeast homeodomain protein Yox1p binds to MBF and confines MBF-dependent cell-cycle transcription to G1-S via negative feedback. Plos Genetics. 5: e1000626. PMID 19714215 DOI: 10.1371/Journal.Pgen.1000626  0.36
2009 Krestyaninova M, Zarins A, Viksna J, Kurbatova N, Rucevskis P, Neogi SG, Gostev M, Perheentupa T, Knuuttila J, Barrett A, Lappalainen I, Rung J, Podnieks K, Sarkans U, McCarthy MI, ... Brazma A, et al. A System for Information Management in BioMedical Studies--SIMBioMS. Bioinformatics (Oxford, England). 25: 2768-9. PMID 19633095 DOI: 10.1093/Bioinformatics/Btp420  0.36
2009 Kauffmann A, Rayner TF, Parkinson H, Kapushesky M, Lukk M, Brazma A, Huber W. Importing ArrayExpress datasets into R/Bioconductor. Bioinformatics (Oxford, England). 25: 2092-4. PMID 19505942 DOI: 10.1093/Bioinformatics/Btp354  0.36
2009 Brazma A. Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges. Thescientificworldjournal. 9: 420-3. PMID 19484163 DOI: 10.1100/Tsw.2009.57  0.36
2009 Caldas J, Gehlenborg N, Faisal A, Brazma A, Kaski S. Probabilistic retrieval and visualization of biologically relevant microarray experiments. Bioinformatics (Oxford, England). 25: i145-53. PMID 19477980 DOI: 10.1186/1471-2105-10-S13-P1  0.36
2009 Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, et al. Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Molecular Oncology. 3: 9-17. PMID 19383362 DOI: 10.1016/J.Molonc.2008.11.003  0.36
2009 Vingron M, Brazma A, Coulson R, van Helden J, Manke T, Palin K, Sand O, Ukkonen E. Integrating sequence, evolution and functional genomics in regulatory genomics. Genome Biology. 10: 202. PMID 19226437 DOI: 10.1186/Gb-2009-10-1-202  0.36
2009 Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, ... ... Brazma A, et al. ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Research. 37: D868-72. PMID 19015125 DOI: 10.1093/Nar/Gkn889  0.36
2009 Caldas J, Gehlenborg N, Faisal A, Brazma A, Kaski S. Probabilistic retrieval and visualization of biologically relevant microarray experiments Bmc Bioinformatics. 10: P1. DOI: 10.1186/1471-2105-10-S13-P1  0.36
2009 Gehlenborg N, Brazma A. Visualization of large microarray experiments with space maps Bmc Bioinformatics. 10: O7. DOI: 10.1186/1471-2105-10-S13-O7  0.36
2009 Brazma A, Hwang MJ, Mamitsuka H, Sheu PCY. Message from the program chairs Proceedings of the 2009 9th Ieee International Conference On Bioinformatics and Bioengineering, Bibe 2009. xiv.  0.36
2009 Brazma A, Miyano S, Akutsu T. Introduction Journal of Bioinformatics and Computational Biology. 7: v.  0.36
2008 Rustici G, Kapushesky M, Kolesnikov N, Parkinson H, Sarkans U, Brazma A. Data storage and analysis in ArrayExpress and Expression Profiler. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 7.13. PMID 18819076 DOI: 10.1002/0471250953.Bi0713S23  0.36
2008 Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, et al. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnology. 26: 889-96. PMID 18688244 DOI: 10.1038/Nbt.1411  0.36
2008 Sansone SA, Rocca-Serra P, Brandizi M, Brazma A, Field D, Fostel J, Garrow AG, Gilbert J, Goodsaid F, Hardy N, Jones P, Lister A, Miller M, Morrison N, Rayner T, et al. The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?". Omics : a Journal of Integrative Biology. 12: 143-9. PMID 18447634 DOI: 10.1089/Omi.2008.0019  0.36
2008 Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen JH, Daian F, Dauga D, Davidson DR, Gimenez G, Goo YA, Grimmond S, et al. Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nature Biotechnology. 26: 305-12. PMID 18327244 DOI: 10.1038/Nbt1391  0.36
2008 Giegerich R, Brazma A, Jonassen I, Ukkonen E, Vingron M. The BREW workshop series: a stimulating experience in PhD education. Briefings in Bioinformatics. 9: 250-3. PMID 18216087 DOI: 10.1093/Bib/Bbn002  0.36
2008 Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T. 4DXpress: a database for cross-species expression pattern comparisons. Nucleic Acids Research. 36: D847-53. PMID 17916571 DOI: 10.1093/Nar/Gkm797  0.36
2008 Coulson R, Manke T, Palin K, Roider H, Sand O, Van Helden J, Ukkonen E, Vingron M, Brazma A. From gene expression profiling to gene regulation Modern Genome Annotation: the Biosapiens Network. 105-119. DOI: 10.1007/978-3-211-75123-7_6  0.36
2008 Haudry Y, Ong CK, Ettwiller L, Berube H, Letunic I, Kapushesky M, Weeber PD, Wang X, Gagneur J, Girardot C, Arendt D, Bork P, Brazma A, Furlong E, Wittbrodt J, et al. Comparing and analysing gene expression patterns across animal species using 4DXpress Series On Advances in Bioinformatics and Computational Biology. 6: 373-382.  0.36
2008 Brazma A, Miyano S, Akutsu T. Preface Series On Advances in Bioinformatics and Computational Biology. 6: v-vi.  0.36
2007 Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK, Laursen K, et al. The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nature Biotechnology. 25: 1127-33. PMID 17921998 DOI: 10.1038/Nbt1347  0.36
2007 Schlitt T, Brazma A. Current approaches to gene regulatory network modelling. Bmc Bioinformatics. 8: S9. PMID 17903290 DOI: 10.1186/1471-2105-8-S6-S9  0.36
2007 Samsonova AA, Niranjan M, Russell S, Brazma A. Prediction of gene expression in embryonic structures of Drosophila melanogaster. Plos Computational Biology. 3: e144. PMID 17658945 DOI: 10.1371/Journal.Pcbi.0030144  0.36
2007 Rustici G, van Bakel H, Lackner DH, Holstege FC, Wijmenga C, Bähler J, Brazma A. Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study. Genome Biology. 8: R73. PMID 17477863 DOI: 10.1186/Gb-2007-8-5-R73  0.36
2007 Viksna J, Celms E, Opmanis M, Podnieks K, Rucevskis P, Zarins A, Barrett A, Neogi SG, Krestyaninova M, McCarthy MI, Brazma A, Sarkans U. PASSIM--an open source software system for managing information in biomedical studies. Bmc Bioinformatics. 8: 52. PMID 17291344 DOI: 10.1186/1471-2105-8-52  0.36
2007 Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, ... Brazma A, et al. ArrayExpress--a public database of microarray experiments and gene expression profiles. Nucleic Acids Research. 35: D747-50. PMID 17132828 DOI: 10.1093/Nar/Gkl995  0.36
2006 Brazma A, Parkinson H. ArrayExpress service for reviewers/editors of DNA microarray papers. Nature Biotechnology. 24: 1321-2. PMID 17093465 DOI: 10.1038/Nbt1106-1321  0.36
2006 Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ, White J, ... ... Brazma A, et al. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. Bmc Bioinformatics. 7: 489. PMID 17087822 DOI: 10.1186/1471-2105-7-489  0.36
2006 Brazma A, Kapushesky M, Parkinson H, Sarkans U, Shojatalab M. Data storage and analysis in ArrayExpress. Methods in Enzymology. 411: 370-86. PMID 16939801 DOI: 10.1016/S0076-6879(06)11020-4  0.36
2006 Deutsch EW, Ball CA, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen J, Davidson D, Eichner LJ, Goo YA, Grimmond S, Henrich T, Johnson MH, Korb M, et al. Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). Omics : a Journal of Integrative Biology. 10: 205-8. PMID 16901227 DOI: 10.1089/Omi.2006.10.205  0.36
2006 Ball CA, Brazma A. MGED standards: work in progress. Omics : a Journal of Integrative Biology. 10: 138-44. PMID 16901218 DOI: 10.1089/Omi.2006.10.138  0.36
2006 Brazma A, Krestyaninova M, Sarkans U. Standards for systems biology. Nature Reviews. Genetics. 7: 593-605. PMID 16847461 DOI: 10.1038/Nrg1922  0.36
2006 Schlitt T, Brazma A. Modelling in molecular biology: describing transcription regulatory networks at different scales. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361: 483-94. PMID 16524837 DOI: 10.1098/Rstb.2005.1806  0.36
2006 Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden N. Top-down standards will not serve systems biology. Nature. 440: 24. PMID 16511469 DOI: 10.1038/440024A  0.36
2006 Blake J, Schwager C, Kapushesky M, Brazma A. ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression. Bioinformatics (Oxford, England). 22: 765-7. PMID 16377611 DOI: 10.1093/Bioinformatics/Btk022  0.36
2006 Freeman T, Brazma A. Editorial Briefings in Functional Genomics and Proteomics. 5: 1-3. DOI: 10.1093/bfgp/ell016  0.36
2006 Stoeckert C, Ball C, Brazma A, Brinkman R, Causton H, Fan L, Fostel J, Fragoso G, Heiskanen M, Holstege F, Morrison N, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, et al. To the editor [2] Nature Biotechnology. 24: 21-22. DOI: 10.1038/nbt0106-21b  0.36
2006 Parkinson H, Sansone SA, Sarkans U, Rocca-Serra P, Brazma A. ArrayExpress: A Public Repository for Microarray Data Cell Biology, Four-Volume Set. 4: 95-102. DOI: 10.1016/B978-012164730-8/50198-2  0.36
2005 Ruklisa D, Brazma A, Viksna J. Reconstruction of gene regulatory networks under the finite state linear model. Genome Informatics. International Conference On Genome Informatics. 16: 225-36. PMID 16901105 DOI: 10.11234/Gi1990.16.2_225  0.36
2005 Mukherjee G, Abeygunawardena N, Parkinson H, Contrino S, Durinck S, Farne A, Holloway E, Lilja P, Moreau Y, Oezcimen A, Rayner T, Sharma A, Brazma A, Sarkans U, Shojatalab M. Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress. Plant Physiology. 139: 632-6. PMID 16219923 DOI: 10.1104/Pp.105.063156  0.36
2005 Gilks WR, Tom BD, Brazma A. Fusing microarray experiments with multivariate regression. Bioinformatics (Oxford, England). 21: ii137-43. PMID 16204093 DOI: 10.1093/Bioinformatics/Bti1123  0.36
2005 Torrente A, Kapushesky M, Brazma A. A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings. Bioinformatics (Oxford, England). 21: 3993-9. PMID 16141251 DOI: 10.1093/Bioinformatics/Bti644  0.36
2005 Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, Huber W. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics (Oxford, England). 21: 3439-40. PMID 16082012 DOI: 10.1093/Bioinformatics/Bti525  0.36
2005 Schlitt T, Brazma A. Modelling gene networks at different organisational levels. Febs Letters. 579: 1859-66. PMID 15763564 DOI: 10.1016/J.Febslet.2005.01.073  0.36
2005 Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, Coulson R, Farne A, Lara GG, Holloway E, Kapushesky M, Lilja P, Mukherjee G, Oezcimen A, Rayner T, Rocca-Serra P, ... ... Brazma A, et al. ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Research. 33: D553-5. PMID 15608260 DOI: 10.1093/Nar/Gki056  0.36
2005 Sarkans U, Parkinson H, Lara GG, Oezcimen A, Sharma A, Abeygunawardena N, Contrino S, Holloway E, Rocca-Serra P, Mukherjee G, Shojatalab M, Kapushesky M, Sansone SA, Farne A, Rayner T, ... Brazma A, et al. The ArrayExpress gene expression database: a software engineering and implementation perspective. Bioinformatics (Oxford, England). 21: 1495-501. PMID 15564302 DOI: 10.1093/Bioinformatics/Bti157  0.36
2004 Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Icahn C, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, et al. An open letter on microarray data from the MGED Society. Microbiology (Reading, England). 150: 3522-4. PMID 15528642 DOI: 10.1099/mic.0.27637-0  0.36
2004 Ball C, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, et al. Standards for microarray data: an open letter. Environmental Health Perspectives. 112: A666-7. PMID 15345376 DOI: 10.1289/Ehp.112-1277123  0.36
2004 Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, et al. Submission of microarray data to public repositories. Plos Biology. 2: E317. PMID 15340489 DOI: 10.1371/Journal.Pbio.0020317  0.36
2004 Ball CA, Sherlock G, Brazma A. Funding high-throughput data sharing. Nature Biotechnology. 22: 1179-83. PMID 15340487 DOI: 10.1038/Nbt0904-1179  0.36
2004 Brazma A, Freeman T, Gardiner K, Weissman S, Werner T, Korn B. Report on the thirteenth international workshop on the identification and functional, evolutionary and expression analysis of transcribed sequences: comparative and functional genomics workshop. Cytogenetic and Genome Research. 105: 11-7. PMID 15218252 DOI: 10.1159/000078003  0.36
2004 Kapushesky M, Kemmeren P, Culhane AC, Durinck S, Ihmels J, Körner C, Kull M, Torrente A, Sarkans U, Vilo J, Brazma A. Expression Profiler: next generation--an online platform for analysis of microarray data. Nucleic Acids Research. 32: W465-70. PMID 15215431 DOI: 10.1093/Nar/Gkh470  0.36
2004 Rustici G, Mata J, Kivinen K, Lió P, Penkett CJ, Burns G, Hayles J, Brazma A, Nurse P, Bähler J. Periodic gene expression program of the fission yeast cell cycle. Nature Genetics. 36: 809-17. PMID 15195092 DOI: 10.1038/Ng1377  0.36
2004 Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, ... ... Brazma A, et al. The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nature Biotechnology. 22: 177-83. PMID 14755292 DOI: 10.1038/Nbt926  0.36
2004 Stoeckert CJ, Quackenbush J, Brazma A, Ball CA. Minimum information about a functional genomics experiment: The state of microarray standards and their extension to other technologies Drug Discovery Today: Targets. 3: 159-164. DOI: 10.1016/S1741-8372(04)02435-1  0.36
2003 Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M, Contrino S, Vilo J, Abeygunawardena N, Mukherjee G, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Sansone SA. ArrayExpress: a public database of gene expression data at EBI. Comptes Rendus Biologies. 326: 1075-8. PMID 14744115 DOI: 10.1016/J.Crvi.2003.09.026  0.36
2003 Schlitt T, Palin K, Rung J, Dietmann S, Lappe M, Ukkonen E, Brazma A. From gene networks to gene function. Genome Research. 13: 2568-76. PMID 14656964 DOI: 10.1101/Gr.1111403  0.36
2003 Brazma A, Ikeo K, Tateno Y. [Standardization of microarray experiment data]. Tanpakushitsu Kakusan Koso. Protein, Nucleic Acid, Enzyme. 48: 280-5. PMID 12652749  0.36
2003 Soinov LA, Krestyaninova MA, Brazma A. Towards reconstruction of gene networks from expression data by supervised learning. Genome Biology. 4: R6. PMID 12540298 DOI: 10.1186/Gb-2003-4-1-R6  0.36
2003 Chen D, Toone WM, Mata J, Lyne R, Burns G, Kivinen K, Brazma A, Jones N, Bähler J. Global transcriptional responses of fission yeast to environmental stress. Molecular Biology of the Cell. 14: 214-29. PMID 12529438 DOI: 10.1091/Mbc.E02-08-0499  0.36
2003 Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA. ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Research. 31: 68-71. PMID 12519949 DOI: 10.1093/nar/gkg091  0.36
2003 Brooksbank C, Camon E, Harris MA, Magrane M, Martin MJ, Mulder N, O'Donovan C, Parkinson H, Tuli MA, Apweiler R, Birney E, Brazma A, Henrick K, Lopez R, Stoesser G, et al. The European Bioinformatics Institute's data resources. Nucleic Acids Research. 31: 43-50. PMID 12519944 DOI: 10.1093/nar/gkg066  0.36
2002 Schlitt T, Brazma A. Learning about gene regulatory networks from gene deletion experiments. Comparative and Functional Genomics. 3: 499-503. PMID 18629255 DOI: 10.1002/Cfg.220  0.36
2002 Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Stewart JE, Taylor R, ... Brazma A, et al. The underlying principles of scientific publication. Bioinformatics (Oxford, England). 18: 1409. PMID 12424109 DOI: 10.1093/Bioinformatics/18.11.1409  0.36
2002 Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Stewart JE, Taylor R, ... Brazma A, et al. Standards for microarray data. Science (New York, N.Y.). 298: 539. PMID 12387284 DOI: 10.1126/Science.298.5593.539B  0.36
2002 Rung J, Schlitt T, Brazma A, Freivalds K, Vilo J. Building and analysing genome-wide gene disruption networks. Bioinformatics (Oxford, England). 18: S202-10. PMID 12386004  0.36
2002 Palin K, Ukkonen E, Brazma A, Vilo J. Correlating gene promoters and expression in gene disruption experiments. Bioinformatics (Oxford, England). 18: S172-80. PMID 12386000  0.36
2002 Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Stewart JE, Taylor R, ... Brazma A, et al. A guide to microarray experiments - An open letter to the scientific journals [1] Lancet. 360: 1019. PMID 12383684  0.36
2002 Brazma A, Sarkans U, Robinson A, Vilo J, Vingron M, Hoheisel J, Fellenberg K. Microarray data representation, annotation and storage. Advances in Biochemical Engineering/Biotechnology. 77: 113-39. PMID 12227734 DOI: 10.1007/3-540-45713-5_7  0.36
2002 Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M, Swiatek M, Marks WL, Goncalves J, Markel S, Iordan D, ... ... Brazma A, et al. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biology. 3: RESEARCH0046. PMID 12225585 DOI: 10.1186/Gb-2002-3-9-Research0046  0.36
2002 Kemmeren P, van Berkum NL, Vilo J, Bijma T, Donders R, Brazma A, Holstege FC. Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Molecular Cell. 9: 1133-43. PMID 12049748 DOI: 10.1016/S1097-2765(02)00531-2  0.36
2002 Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Stewart JE, Taylor R, ... Brazma A, et al. An open letter to the scientific journals Bioinformatics. 18: 1409.  0.36
2001 Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature Genetics. 29: 365-71. PMID 11726920 DOI: 10.1038/Ng1201-365  0.36
2001 Brazma A, Vilo J. Gene expression data analysis. Microbes and Infection / Institut Pasteur. 3: 823-9. PMID 11580977 DOI: 10.1016/S1286-4579(01)01440-X  0.36
2001 Brazma A. On the importance of standardisation in life sciences. Bioinformatics (Oxford, England). 17: 113-4. PMID 11238066 DOI: 10.1093/Bioinformatics/17.2.113  0.36
2001 Brazma A. Microarrays - Challenges and opportunities Comments On Toxicology. 7: 347-359.  0.36
2000 Vilo J, Brazma A, Jonassen I, Robinson A, Ukkonen E. Mining for putative regulatory elements in the yeast genome using gene expression data. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 8: 384-94. PMID 10977099  0.36
2000 Brazma A, Vilo J. Gene expression data analysis. Febs Letters. 480: 17-24. PMID 10967323 DOI: 10.1016/S0014-5793(00)01772-5  0.36
2000 Brazma A, Robinson A, Cameron G, Ashburner M. One-stop shop for microarray data. Nature. 403: 699-700. PMID 10693778 DOI: 10.1038/35001676  0.36
1998 Brazma A, Jonassen I, Vilo J, Ukkonen E. Predicting gene regulatory elements in silico on a genomic scale Genome Research. 8: 1202-1215. PMID 9847082  0.36
1998 Brazma A, Jonassen I, Eidhammer I, Gilbert D. Approaches to the automatic discovery of patterns in biosequences Journal of Computational Biology. 5: 279-305. PMID 9672833 DOI: 10.1089/Cmb.1998.5.279  0.36
1997 Brazma A, Vilo J, Ukkonen E, Valtonen K. Data mining for regulatory elements in yeast genome Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 5: 65-74. PMID 9322017  0.36
1996 Brazma A, Jonassen I, Ukkonen E, Vilo J. Discovering patterns and subfamilies in biosequences Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 4: 34-43. PMID 8877502  0.36
1995 Kaugars K, Reinfelds J, Brazma A. A simple algorithm for drawing large graphs on small screens Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 894: 278-281. DOI: 10.1007/3-540-58950-3_382  0.36
1990 Kinber EB, Brazma AN. Models of inductive synthesis The Journal of Logic Programming. 9: 221-233. DOI: 10.1016/0743-1066(90)90041-3  0.36
1987 Barzdin' YM, Brazma AN, Kinber EB. Inductive synthesis of programs: State of the art, problems, prospects Cybernetics. 23: 818-826. DOI: 10.1007/BF01070244  0.36
1986 Brazma A, Kinber E. Generalized regular expressions-A language for synthesis of programs with branching in loops Theoretical Computer Science. 46: 175-195. DOI: 10.1016/0304-3975(86)90029-0  0.36
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