Alvis Brazma

Gabriella Rustici, Nikolay Kolesnikov, Marco Brandizi, Tony Burdett, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Emma Hastings, Jon Ison, Maria Keays, Natalja Kurbatova, James Malone, Roby Mani, Annalisa Mupo, Rui Pedro Pereira, Ekaterina Pilicheva, Johan Rung, Anjan Sharma, Y. Amy Tang, Tobias Ternent, Andrew Tikhonov, Danielle Welter, Eleanor Williams, Alvis Brazma, Helen E. Parkinson, Ugis Sarkans: ArrayExpress update - trends in database growth and links to data analysis tools. Nucleic Acids Research 41(Database-Issue): 987-990 (2013)

José Caldas, Nils Gehlenborg, Eeva Kettunen, Ali Faisal, Mikko Rönty, Andrew G. Nicholson, Sakari Knuutila, Alvis Brazma, Samuel Kaski: Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma. Bioinformatics 28(2): 246-253 (2012)

Vincent Xue, Tony Burdett, Margus Lukk, Julie Taylor, Alvis Brazma, Helen E. Parkinson: MageComet - web application for harmonizing existing large-scale experiment descriptions. Bioinformatics 28(10): 1402-1403 (2012)

Nuno A. Fonseca, Johan Rung, Alvis Brazma, John C. Marioni: Tools for mapping high-throughput sequencing data. Bioinformatics 28(24): 3169-3177 (2012)

Mikhail Gostev, Adam Faulconbridge, Marco Brandizi, Julio Fernandez-Banet, Ugis Sarkans, Alvis Brazma, Helen E. Parkinson: The BioSample Database (BioSD) at the European Bioinformatics Institute. Nucleic Acids Research 40(Database-Issue): 64-70 (2012)

Misha Kapushesky, Tomasz Adamusiak, Tony Burdett, Aedín C. Culhane, Anna Farne, Alexey Filippov, Ele Holloway, Andrey Klebanov, Nataliya Kryvych, Natalja Kurbatova, Pavel Kurnosov, James Malone, Olga Melnichuk, Robert Petryszak, Nikolay Pultsin, Gabriella Rustici, Andrew Tikhonov, Ravensara S. Travillian, Eleanor Williams, Andrey Zorin, Helen E. Parkinson, Alvis Brazma: Gene Expression Atlas update - a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Research 40(Database-Issue): 1077-1081 (2012)

Leo Lahti, Aurora Torrente, Laura Elo, Alvis Brazma, Johan Rung: Fully scalable online-preprocessing algorithm for short oligonucleotide microarray atlases. CoRR abs/1212.5932 (2012)

Mikhail Gostev, Julio Fernandez-Banet, Johan Rung, Joern Dietrich, Inga Prokopenko, Samuli Ripatti, Mark I. McCarthy, Alvis Brazma, Maria Krestyaninova: SAIL - a software system for sample and phenotype availability across biobanks and cohorts. Bioinformatics 27(4): 589-591 (2011)

Angela Goncalves, Andrew Tikhonov, Alvis Brazma, Misha Kapushesky: A pipeline for RNA-seq data processing and quality assessment. Bioinformatics 27(6): 867-869 (2011)

Helen E. Parkinson, Ugis Sarkans, Nikolay Kolesnikov, Niran Abeygunawardena, Tony Burdett, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Emma Hastings, Ele Holloway, Natalja Kurbatova, Margus Lukk, James Malone, Roby Mani, Ekaterina Pilicheva, Gabriella Rustici, Anjan Sharma, Eleanor Williams, Tomasz Adamusiak, Marco Brandizi, Nataliya Sklyar, Alvis Brazma: ArrayExpress update - an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Research 39(Database-Issue): 1002-1004 (2011)

James Malone, Ele Holloway, Tomasz Adamusiak, Misha Kapushesky, Jie Zheng, Nikolay Kolesnikov, Anna Zhukova, Alvis Brazma, Helen E. Parkinson: Modeling sample variables with an Experimental Factor Ontology. Bioinformatics 26(8): 1112-1118 (2010)

Ravi Shankar, Helen E. Parkinson, Tony Burdett, Emma Hastings, Junmin Liu, Michael Miller, Rashmi Srinivasa, Joseph White, Alvis Brazma, Gavin Sherlock, Christian J. Stoeckert Jr., Catherine A. Ball: Annotare - a tool for annotating high-throughput biomedical investigations and resulting data. Bioinformatics 26(19): 2470-2471 (2010)

Yevhen Vainshtein, Mayka Sanchez, Alvis Brazma, Matthias W. Hentze, Thomas Dandekar, Martina U. Muckenthaler: The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays. BMC Bioinformatics 11: 112 (2010)

Misha Kapushesky, Ibrahim Emam, Ele Holloway, Pavel Kurnosov, Andrey Zorin, James Malone, Gabriella Rustici, Eleanor Williams, Helen E. Parkinson, Alvis Brazma: Gene Expression Atlas at the European Bioinformatics Institute. Nucleic Acids Research 38(Database-Issue): 690-698 (2010)

Jaakko Peltonen, Helena Aidos, Nils Gehlenborg, Alvis Brazma, Samuel Kaski: An information retrieval perspective on visualization of gene expression data with ontological annotation. ICASSP 2010: 2178-2181

José Caldas, Nils Gehlenborg, Ali Faisal, Alvis Brazma, Samuel Kaski: Probabilistic retrieval and visualization of biologically relevant microarray experiments. Bioinformatics 25(12) (2009)

Audrey Kauffmann, Tim F. Rayner, Helen E. Parkinson, Misha Kapushesky, Margus Lukk, Alvis Brazma, Wolfgang Huber: Importing ArrayExpress datasets into R/Bioconductor. Bioinformatics 25(16): 2092-2094 (2009)

Maria Krestyaninova, Andris Zarins, Juris Viksna, Natalja Kurbatova, Peteris Rucevskis, Sudeshna Guha Neogi, Mike Gostev, Teemu Perheentupa, Juha Knuuttila, Amy Barrett, Ilkka Lappalainen, Johan Rung, Karlis Podnieks, Ugis Sarkans, Mark I. McCarthy, Alvis Brazma: A System for Information Management in BioMedical Studies - SIMBioMS. Bioinformatics 25(20): 2768-2769 (2009)

José Caldas, Nils Gehlenborg, Ali Faisal, Alvis Brazma, Samuel Kaski: Probabilistic retrieval and visualization of biologically relevant microarray experiments. BMC Bioinformatics 10(S-13): 0 (2009)

Nils Gehlenborg, Alvis Brazma: Visualization of large microarray experiments with space maps. BMC Bioinformatics 10(S-13): 0 (2009)

Helen E. Parkinson, Misha Kapushesky, Nikolay Kolesnikov, Gabriella Rustici, Mohammadreza Shojatalab, Niran Abeygunawardena, Hugo Berube, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Ele Holloway, Margus Lukk, James Malone, Roby Mani, Ekaterina Pilicheva, Tim F. Rayner, Faisal Ibne Rezwan, Anjan Sharma, Eleanor Williams, Xiangqun Zheng Bradley, Tomasz Adamusiak, Marco Brandizi, Tony Burdett, Richard Coulson, Maria Krestyaninova, Pavel Kurnosov, Eamonn Maguire, Sudeshna Guha Neogi, Philippe Rocca-Serra, Susanna-Assunta Sansone, Nataliya Sklyar, Mengyao Zhao, Ugis Sarkans, Alvis Brazma: ArrayExpress update - from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Research 37(Database-Issue): 868-872 (2009)

Robert Giegerich, Alvis Brazma, Inge Jonassen, Esko Ukkonen, Martin Vingron: The BREW workshop series: a stimulating experience in PhD education. Briefings in Bioinformatics 9(3): 250-253 (2008)

Yannick Haudry, Hugo Berube, Ivica Letunic, Paul-Daniel Weeber, Julien Gagneur, Charles Girardot, Misha Kapushesky, Detlev Arendt, Peer Bork, Alvis Brazma, Eileen E. M. Furlong, Joachim Wittbrodt, Thorsten Henrich: 4DXpress: a database for cross-species expression pattern comparisons. Nucleic Acids Research 36(Database-Issue): 847-853 (2008)

Alvis Brazma, Satoru Miyano, Tatsuya Akutsu: Preface. APBC 2008

Yannick Haudry, Chuang Kee Ong, Laurence Ettwiller, Hugo Berube, Ivica Letunic, Misha Kapushesky, Paul-Daniel Weeber, Xi Wang, Julien Gagneur, Charles Girardot, Detlev Arendt, Peer Bork, Alvis Brazma, Eileen E. M. Furlong, Joachim Wittbrodt, Thorsten Henrich: Comparing and Analysing Gene Expression Patterns Across Animal Species Using 4DXpress. APBC 2008: 373-382

Alvis Brazma, Satoru Miyano, Tatsuya Akutsu (Eds.): Proceedings of the 6th Asia-Pacific Bioinformatics Conference, APBC 2008, 14-17 January 2008, Kyoto, Japan. Advances in Bioinformatics and Computational Biology 6, Imperial College Press 2008, isbn 978-1-84816-108-5

Thomas Schlitt, Alvis Brazma: Current approaches to gene regulatory network modelling. BMC Bioinformatics 8(S-6) (2007)

Juris Viksna, Edgars Celms, Martins Opmanis, Karlis Podnieks, Peteris Rucevskis, Andris Zarins, Amy Barrett, Sudeshna Guha Neogi, Maria Krestyaninova, Mark I. McCarthy, Alvis Brazma, Ugis Sarkans: PASSIM - an open source software system for managing information in biomedical studies. BMC Bioinformatics 8 (2007)

Helen E. Parkinson, Misha Kapushesky, Mohammadreza Shojatalab, Niran Abeygunawardena, Richard Coulson, Anna Farne, Ele Holloway, N. Kolesnykov, P. Lilja, Margus Lukk, Roby Mani, Tim F. Rayner, Anjan Sharma, E. William, Ugis Sarkans, Alvis Brazma: ArrayExpress - a public database of microarray experiments and gene expression profiles. Nucleic Acids Research 35(Database-Issue): 747-750 (2007)

Anastasia Samsonova, Mahesan Niranjan, Steven Russell, Alvis Brazma: Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster. PLoS Computational Biology 3(7) (2007)

Jonathon Blake, Christian Schwager, Misha Kapushesky, Alvis Brazma: ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression. Bioinformatics 22(6): 765-767 (2006)

Tim F. Rayner, Philippe Rocca-Serra, Paul T. Spellman, Helen C. Causton, Anna Farne, Ele Holloway, Rafael A. Irizarry, Junmin Liu, Donald Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J. Stoeckert Jr., Joseph White, Patricia L. Whetzel, Farrell Wymore, Helen E. Parkinson, Ugis Sarkans, Catherine A. Ball, Alvis Brazma: A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics 7: 489 (2006)

Ugis Sarkans, Helen E. Parkinson, Gonzalo Garcia Lara, Ahmet Oezcimen, Anjan Sharma, Niran Abeygunawardena, Sergio Contrino, Ele Holloway, Philippe Rocca-Serra, Gaurab Mukherjee, Mohammadreza Shojatalab, Misha Kapushesky, Susanna-Assunta Sansone, Anna Farne, Tim F. Rayner, Alvis Brazma: The ArrayExpress gene expression database: a software engineering and implementation perspective. Bioinformatics 21(8): 1495-1501 (2005)

Steffen Durinck, Yves Moreau, Arek Kasprzyk, Sean Davis, Bart De Moor, Alvis Brazma, Wolfgang Huber: BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21(16): 3439-3440 (2005)

Aurora Torrente, Misha Kapushesky, Alvis Brazma: A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings. Bioinformatics 21(21): 3993-3999 (2005)

Helen E. Parkinson, Ugis Sarkans, Mohammadreza Shojatalab, Niran Abeygunawardena, Sergio Contrino, Richard Coulson, Anna Farne, Gonzalo Garcia Lara, Ele Holloway, Misha Kapushesky, P. Lilja, Gaurab Mukherjee, Ahmet Oezcimen, Tim F. Rayner, Philippe Rocca-Serra, Anjan Sharma, Susanna-Assunta Sansone, Alvis Brazma: ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Research 33(Database-Issue): 553-555 (2005)

Walter R. Gilks, Brian D. M. Tom, Alvis Brazma: Fusing microarray experiments with multivariate regression. ECCB/JBI 2005: 143

Misha Kapushesky, Patrick Kemmeren, Aedín C. Culhane, Steffen Durinck, Jan Ihmels, Christine Körner, Meelis Kull, Aurora Torrente, Ugis Sarkans, Jaak Vilo, Alvis Brazma: Expression Profiler: next generation - an online platform for analysis of microarray data. Nucleic Acids Research 32(Web-Server-Issue): 465-470 (2004)

Helen C. Causton, John Quackenbush, Alvis Brazma: Microarray gene expression data analysis - a beginner's guide. Blackwell 2003, isbn 978-1-40510-682-5, pp. I-VIII, 1-160

Catherine Brooksbank, Evelyn Camon, Midori A. Harris, Michele Magrane, Maria Jesus Martin, Nicola J. Mulder, Claire O'Donovan, Helen E. Parkinson, Mary Ann Tuli, Rolf Apweiler, Ewan Birney, Alvis Brazma, Kim Henrick, Rodrigo Lopez, Guenter Stoesser, Peter Stoehr, Graham Cameron: The European Bioinformatics Institute's data resources. Nucleic Acids Research 31(1): 43-50 (2003)

Alvis Brazma, Helen E. Parkinson, Ugis Sarkans, Mohammadreza Shojatalab, Jaak Vilo, Niran Abeygunawardena, Ele Holloway, Misha Kapushesky, Patrick Kemmeren, Gonzalo Garcia Lara, Ahmet Oezcimen, Philippe Rocca-Serra, Susanna-Assunta Sansone: ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Research 31(1): 68-71 (2003)

Catherine A. Ball, Gavin Sherlock, Helen E. Parkinson, Philippe Rocca-Serra, Catherine Brooksbank, Helen C. Causton, Duccio Cavalieri, Terry Gaasterland, Pascal Hingamp, Frank Holstege, Martin Ringwald, Paul T. Spellman, Christian J. Stoeckert Jr., Jason E. Stewart, Ronald Taylor, Alvis Brazma, John Quackenbush: An open letter to the scientific journals. Bioinformatics 18(11): 1409 (2002)

Kimmo Palin, Esko Ukkonen, Alvis Brazma, Jaak Vilo: Correlating gene promoters and expression in gene disruption experiments. ECCB 2002: 172-180

Johan Rung, Thomas Schlitt, Alvis Brazma, K. Freivalds, Jaak Vilo: Building and analysing genome-wide gene disruption networks. ECCB 2002: 202-210

Alvis Brazma: On the Importance of Standardisation in Life Sciences. Bioinformatics 17(1): 113-114 (2001)

Jaak Vilo, Alvis Brazma, Inge Jonassen, Alan J. Robinson, Esko Ukkonen: Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data. ISMB 2000: 384-394

Alvis Brazma, Inge Jonassen, Ingvar Eidhammer, David Gilbert: Approaches to the Automatic Discovery of Patterns in Biosequences. Journal of Computational Biology 5(2): 279-305 (1998)

Alvis Brazma, Inge Jonassen, Jaak Vilo, Esko Ukkonen: Predicting gene regulatory elements from their expression data in the complete yeast genome. German Conference on Bioinformatics 1998

Alvis Brazma, Inge Jonassen, Jaak Vilo, Esko Ukkonen: Pattern Discovery in Biosequences. ICGI 1998: 257-270

Alvis Brazma, Karlis Cerans: Noise-Tolerant Efficient Inductive Synthesis of Regular Expressions from Good Examples. New Generation Comput. 15(1): 105-140 (1997)

Alvis Brazma, Jaak Vilo, Esko Ukkonen: Finding transcription factor binding site combinations in the yeast genome. German Conference on Bioinformatics 1997: 57-59

Alvis Brazma, Tomas P. Flores, Peter Maccallum, Alan J. Robinson: Data Mining and Visualisation in Molecular Biology Databases. German Conference on Bioinformatics 1997: 127

Alvis Brazma, Jaak Vilo, Esko Ukkonen, Kimmo Valtonen: Data Mining for Regulatory Elements in Yeast Genome. ISMB 1997: 65-74

Alvis Brazma, Esko Ukkonen, Jaak Vilo: Discovering Unbounded Unions of Regular Pattern Languages from Positive Examples (Extended Abstract). ISAAC 1996: 95-104

Alvis Brazma, Inge Jonassen, Esko Ukkonen, Jaak Vilo: Discovering Patterns and Subfamilies in Biosequences. ISMB 1996: 34-43

Alvis Brazma: Learning of regular expressions by pattern matching. EuroCOLT 1995: 392-403

Alvis Brazma, Karlis Cerans: Efficient Learning of Regular Expressions from Good Examples. AII/ALT 1994: 76-90

Alvis Brazma: Efficient Algorithm for Learning Simple Regular Expressions from Noisy Examples. AII/ALT 1994: 260-271

Karlis Kaugars, Juris Reinfelds, Alvis Brazma: A Simple Algorithm for Drawing Large Graphs on Small Screens. Graph Drawing 1994: 278-281

Alvis Brazma: Efficient Identification of Regular Expressions from Representative Examples. COLT 1993: 236-242

Alvis Brazma: Learning a Subclass of Regular Expressions by Recognizing Periodic Repetitions. SCAI 1993: 137-146

Alvis Brazma: Inductive Synthesis of Dot Expressions. Baltic Computer Science 1991: 156-212

Efim B. Kinber, Alvis Brazma: Models of Inductive Synthesis. J. Log. Program. 9(2&3): 221-233 (1990)

Alvis Brazma, Efim B. Kinber: Generalized Regular Expressions-A Language for Synthesis of Programs with Braching in Loops. Theor. Comput. Sci. 46(3): 175-195 (1986)