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2020 – today
- 2021
- [j58]Ugis Sarkans
, Anja Füllgrabe
, Ahmed Ali, Awais Athar
, Ehsan Behrangi, Nestor Diaz, Silvie Fexova
, Nancy George, Haider Iqbal, Sandeep Kurri, Jhoan Munoz, Juan Camillo Rada, Irene Papatheodorou
, Alvis Brazma
:
From ArrayExpress to BioStudies. Nucleic Acids Res. 49(Database-Issue): D1502-D1506 (2021) - 2020
- [j57]Irene Papatheodorou
, Pablo Moreno
, Jonathan R. Manning
, Alfonso Muñoz-Pomer Fuentes, Nancy George, Silvie Fexova
, Nuno A. Fonseca
, Anja Füllgrabe
, Matthew Green, Ni Huang, Laura Huerta, Haider Iqbal
, Monica Jianu, Suhaib Mohammed
, Lingyun Zhao, Andrew F. Jarnuczak, Simon Jupp
, John C. Marioni
, Kerstin B. Meyer, Robert Petryszak, Cesar Augusto Prada Medina
, Carlos Talavera-López
, Sarah A. Teichmann, Juan Antonio Vizcaíno
, Alvis Brazma
:
Expression Atlas update: from tissues to single cells. Nucleic Acids Res. 48(Database-Issue): D77-D83 (2020) - [j56]Claudia Calabrese
, Natalie R. Davidson, Deniz Demircioglu, Nuno A. Fonseca
, Yao He, André Kahles, Kjong-Van Lehmann
, Fenglin Liu
, Yuichi Shiraishi, Cameron M. Soulette, Lara Urban
, Liliana Greger, Siliang Li, Dongbing Liu
, Marc D. Perry, Qian Xiang, Fan Zhang, Junjun Zhang, Peter Bailey
, Serap Erkek
, Katherine A. Hoadley, Yong Hou, Matthew R. Huska, Helena Kilpinen
, Jan O. Korbel, Maximillian G. Marin, Julia Markowski, Tannistha Nandi, Qiang Pan-Hammarström
, Chandra Sekhar Pedamallu, Reiner Siebert, Stefan G. Stark, Hong Su, Patrick Tan, Sebastian M. Waszak
, Christina K. Yung, Shida Zhu, Philip Awadalla, Matthew Meyerson
, B. F. Francis Ouellette
, Kui Wu
, Huanming Yang, Samirkumar B. Amin
, Aurélien Chateigner, Isidro Cortés-Ciriano
, Brian Craft, Milana Frenkel-Morgenstern
, Mary Goldman, Ekta Khurana, Fabien C. Lamaze
, Chang Li, Xiaobo Li
, Xinyue Li, Xingmin Liu, Morten Muhlig Nielsen, Akinyemi I. Ojesina, Peter J. Park, Jakob Skou Pedersen
, Bin Tean Teh, Jian Wang, Heng Xiong, Sergei Yakneen
, Chen Ye, Xiuqing Zhang, Liangtao Zheng, Jingchun Zhu, Chad Creighton, Jonathan Göke, Roland F. Schwarz
, Oliver Stegle
, Zemin Zhang, Alvis Brazma
, Gunnar Rätsch, Angela N. Brooks:
Genomic basis for RNA alterations in cancer. Nat. 578(7793): 129-136 (2020)
2010 – 2019
- 2019
- [j55]Dace Ruklisa
, Alvis Brazma
, Karlis Cerans, Thomas Schlitt
, Juris Viksna:
Dynamics of gene regulatory networks and their dependence on network topology and quantitative parameters - the case of phage λ. BMC Bioinform. 20(1): 296:1-296:14 (2019) - [j54]Yasset Pérez-Riverol
, Attila Csordas, Jingwen Bai, Manuel Bernal Llinares
, Suresh Hewapathirana
, Deepti Jaiswal Kundu
, Avinash Inuganti, Johannes Griss
, Gerhard Mayer
, Martin Eisenacher, Enrique Pérez
, Julian Uszkoreit
, Julianus Pfeuffer, Timo Sachsenberg, Sule Yilmaz
, Shivani Tiwary, Jürgen Cox, Enrique Audain
, Mathias Walzer, Andrew F. Jarnuczak
, Tobias Ternent, Alvis Brazma
, Juan Antonio Vizcaíno
:
The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 47(Database-Issue): D442-D450 (2019) - [j53]Awais Athar
, Anja Füllgrabe
, Nancy George, Haider Iqbal
, Laura Huerta
, Ahmed Ali, Catherine Snow, Nuno A. Fonseca
, Robert Petryszak, Irene Papatheodorou
, Ugis Sarkans
, Alvis Brazma
:
ArrayExpress update - from bulk to single-cell expression data. Nucleic Acids Res. 47(Database-Issue): D711-D715 (2019) - 2018
- [j52]Ugis Sarkans
, Mikhail Gostev, Awais Athar
, Ehsan Behrangi
, Olga Melnichuk, Ahmed Ali
, Jasmine Minguet, Juan Camillo Rada, Catherine Snow
, Andrew Tikhonov, Alvis Brazma
, Johanna R. McEntyre
:
The BioStudies database - one stop shop for all data supporting a life sciences study. Nucleic Acids Res. 46(Database-Issue): D1266-D1270 (2018) - [j51]Irene Papatheodorou
, Nuno A. Fonseca
, Maria Keays
, Y. Amy Tang
, Elisabet Barrera
, Wojciech Bazant, Melissa L. Burke
, Anja Füllgrabe
, Alfonso Muñoz-Pomer Fuentes, Nancy George, Laura Huerta
, Satu Koskinen, Suhaib Mohammed
, Matthew J. Geniza, Justin Preece, Pankaj Jaiswal
, Andrew F. Jarnuczak
, Wolfgang Huber
, Oliver Stegle
, Juan Antonio Vizcaíno
, Alvis Brazma
, Robert Petryszak
:
Expression Atlas: gene and protein expression across multiple studies and organisms. Nucleic Acids Res. 46(Database-Issue): D246-D251 (2018) - 2017
- [j50]Robert Petryszak
, Nuno A. Fonseca
, Anja Füllgrabe
, Laura Huerta
, Maria Keays
, Y. Amy Tang
, Alvis Brazma
:
The RNASeq-er API - a gateway to systematically updated analysis of public RNA-seq data. Bioinform. 33(14): 2218-2220 (2017) - [j49]Aurora Torrente
, Alvis Brazma
:
clustComp, a bioconductor package for the comparison of clustering results. Bioinform. 33(24): 4001-4003 (2017) - [j48]Marco Brandizi
, Olga Melnichuk, Raffael Bild, Florian Kohlmayer
, Benedicto Rodriguez-Castro, Helmut Spengler, Klaus A. Kuhn, Wolfgang Kuchinke
, Christian Ohmann, Timo Mustonen, Mikael Linden, Tommi H. Nyrönen
, Ilkka Lappalainen
, Alvis Brazma
, Ugis Sarkans
:
Orchestrating differential data access for translational research: a pilot implementation. BMC Medical Informatics Decis. Mak. 17(1): 30:1-30:14 (2017) - 2016
- [j47]Paul Blomstedt, Ritabrata Dutta
, Sohan Seth, Alvis Brazma
, Samuel Kaski:
Modelling-based experiment retrieval: a case study with gene expression clustering. Bioinform. 32(9): 1388-1394 (2016) - [j46]Robert Petryszak, Maria Keays
, Y. Amy Tang
, Nuno A. Fonseca
, Elisabet Barrera
, Tony Burdett
, Anja Füllgrabe
, Alfonso Muñoz-Pomer Fuentes
, Simon Jupp
, Satu Koskinen
, Oliver Mannion, Laura Huerta
, Karine Megy
, Catherine Snow, Eleanor Williams, Mitra Barzine, Emma Hastings
, Hendrik Weisser, James C. Wright
, Pankaj Jaiswal, Wolfgang Huber
, Jyoti Choudhary
, Helen E. Parkinson
, Alvis Brazma:
Expression Atlas update - an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Res. 44(Database-Issue): 746-752 (2016) - 2015
- [j45]Catherine Kirsanova, Alvis Brazma
, Gabriella Rustici, Ugis Sarkans
:
Cellular phenotype database: a repository for systems microscopy data. Bioinform. 31(16): 2736-2740 (2015) - [j44]Nikolay Kolesnikov, Emma Hastings
, Maria Keays
, Olga Melnichuk, Y. Amy Tang
, Eleanor Williams, Miroslaw Dylag, Natalja Kurbatova
, Marco Brandizi, Tony Burdett
, Karyn Megy
, Ekaterina Pilicheva, Gabriella Rustici
, Andrew Tikhonov, Helen E. Parkinson
, Robert Petryszak
, Ugis Sarkans
, Alvis Brazma
:
ArrayExpress update - simplifying data submissions. Nucleic Acids Res. 43(Database-Issue): 1113-1116 (2015) - [i2]Paul Blomstedt, Ritabrata Dutta, Sohan Seth, Alvis Brazma, Samuel Kaski:
Modelling-based experiment retrieval: A case study with gene expression clustering. CoRR abs/1505.05007 (2015) - 2014
- [j43]Adam Faulconbridge
, Tony Burdett
, Marco Brandizi, Mikhail Gostev, Rui Pedro Pereira, Drashtti Vasant, Ugis Sarkans
, Alvis Brazma
, Helen E. Parkinson
:
Updates to BioSamples database at European Bioinformatics Institute. Nucleic Acids Res. 42(Database-Issue): 50-52 (2014) - [j42]Robert Petryszak
, Tony Burdett
, Benedetto Fiorelli, Nuno A. Fonseca
, Mar Gonzalez-Porta, Emma Hastings
, Wolfgang Huber, Simon Jupp
, Maria Keays
, Nataliya Kryvych, Julie A. McMurry
, John C. Marioni
, James Malone, Karine Megy
, Gabriella Rustici
, Y. Amy Tang
, Jan Taubert, Eleanor Williams, Oliver Mannion, Helen E. Parkinson
, Alvis Brazma
:
Expression Atlas update - a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. Nucleic Acids Res. 42(Database-Issue): 926-932 (2014) - [c21]Alvis Brazma, Karlis Cerans, Dace Ruklisa, Thomas Schlitt
, Juris Viksna
:
Modeling and Analysis of Qualitative Behavior of Gene Regulatory Networks. HSB 2014: 51-66 - 2013
- [j41]Katherine Lawler, Kim E. Hammond-Kosack
, Alvis Brazma
, Richard M. R. Coulson:
Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum. BMC Syst. Biol. 7: 52 (2013) - [j40]Gabriella Rustici
, Nikolay Kolesnikov
, Marco Brandizi
, Tony Burdett
, Miroslaw Dylag, Ibrahim Emam
, Anna Farne, Emma Hastings
, Jon C. 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 Res. 41(Database-Issue): 987-990 (2013) - 2012
- [j39]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. Bioinform. 28(2): 246-253 (2012) - [j38]Vincent Xue, Tony Burdett
, Margus Lukk
, Julie Taylor, Alvis Brazma
, Helen E. Parkinson
:
MageComet - web application for harmonizing existing large-scale experiment descriptions. Bioinform. 28(10): 1402-1403 (2012) - [j37]Nuno A. Fonseca
, Johan Rung, Alvis Brazma
, John C. Marioni
:
Tools for mapping high-throughput sequencing data. Bioinform. 28(24): 3169-3177 (2012) - [j36]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 Res. 40(Database-Issue): 64-70 (2012) - [j35]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 Res. 40(Database-Issue): 1077-1081 (2012) - [i1]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) - 2011
- [j34]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. Bioinform. 27(4): 589-591 (2011) - [j33]Ângela Gonçalves, Andrew Tikhonov, Alvis Brazma
, Misha Kapushesky:
A pipeline for RNA-seq data processing and quality assessment. Bioinform. 27(6): 867-869 (2011) - [j32]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 Res. 39(Database-Issue): 1002-1004 (2011) - 2010
- [j31]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. Bioinform. 26(8): 1112-1118 (2010) - [j30]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. Bioinform. 26(19): 2470-2471 (2010) - [j29]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 Bioinform. 11: 112 (2010) - [j28]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 Res. 38(Database-Issue): 690-698 (2010) - [c20]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
2000 – 2009
- 2009
- [j27]José Caldas, Nils Gehlenborg
, Ali Faisal
, Alvis Brazma
, Samuel Kaski:
Probabilistic retrieval and visualization of biologically relevant microarray experiments. Bioinform. 25(12) (2009) - [j26]Audrey Kauffmann, Tim F. Rayner
, Helen E. Parkinson
, Misha Kapushesky, Margus Lukk
, Alvis Brazma
, Wolfgang Huber
:
Importing ArrayExpress datasets into R/Bioconductor. Bioinform. 25(16): 2092-2094 (2009) - [j25]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. Bioinform. 25(20): 2768-2769 (2009) - [j24]José Caldas, Nils Gehlenborg, Ali Faisal, Alvis Brazma, Samuel Kaski:
Probabilistic retrieval and visualization of biologically relevant microarray experiments. BMC Bioinform. 10(S-13): 0 (2009) - [j23]Nils Gehlenborg, Alvis Brazma:
Visualization of large microarray experiments with space maps. BMC Bioinform. 10(S-13): 0 (2009) - [j22]Helen E. Parkinson
, Misha Kapushesky, Nikolay Kolesnikov
, Gabriella Rustici
, Mohammadreza Shojatalab, Niran Abeygunawardena, Hugo Bérubé, 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 Res. 37(Database-Issue): 868-872 (2009) - 2008
- [j21]Robert Giegerich, Alvis Brazma
, Inge Jonassen
, Esko Ukkonen
, Martin Vingron:
The BREW workshop series: a stimulating experience in PhD education. Briefings Bioinform. 9(3): 250-253 (2008) - [j20]Yannick Haudry, Hugo Bérubé, 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 Res. 36(Database-Issue): 847-853 (2008) - [c19]Alvis Brazma, Satoru Miyano, Tatsuya Akutsu:
Preface. APBC 2008 - [c18]Yannick Haudry, Chuang Kee Ong, Laurence Ettwiller, Hugo Bérubé, 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 - [e1]Alvis Brazma, Satoru Miyano, Tatsuya Akutsu:
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 [contents] - 2007
- [j19]Thomas Schlitt
, Alvis Brazma
:
Current approaches to gene regulatory network modelling. BMC Bioinform. 8(S-6) (2007) - [j18]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 Bioinform. 8 (2007) - [j17]Helen E. Parkinson
, Misha Kapushesky, Mohammadreza Shojatalab, Niran Abeygunawardena, Richard Coulson, Anna Farne, Ele Holloway, Nikolay 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 Res. 35(Database-Issue): 747-750 (2007) - [j16]Anastasia Samsonova
, Mahesan Niranjan, Steven Russell
, Alvis Brazma
:
Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster. PLoS Comput. Biol. 3(7) (2007) - 2006
- [j15]Jonathon Blake, Christian Schwager, Misha Kapushesky, Alvis Brazma
:
ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression. Bioinform. 22(6): 765-767 (2006) - [j14]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 Bioinform. 7: 489 (2006) - 2005
- [j13]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. Bioinform. 21(8): 1495-1501 (2005) - [j12]Steffen Durinck, Yves Moreau
, Arek Kasprzyk, Sean R. Davis
, Bart De Moor, Alvis Brazma
, Wolfgang Huber
:
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinform. 21(16): 3439-3440 (2005) - [j11]Aurora Torrente
, Misha Kapushesky, Alvis Brazma
:
A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings. Bioinform. 21(21): 3993-3999 (2005) - [j10]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 Res. 33(Database-Issue): 553-555 (2005) - [c17]Walter R. Gilks, Brian D. M. Tom, Alvis Brazma
:
Fusing microarray experiments with multivariate regression. ECCB/JBI 2005: 143 - 2004
- [j9]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 Res. 32(Web-Server-Issue): 465-470 (2004) - 2003
- [b1]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 - [j8]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 Res. 31(1): 43-50 (2003) - [j7]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 Res. 31(1): 68-71 (2003) - 2002
- [j6]Catherine A. Ball, Gavin Sherlock
, Helen E. Parkinson
, Philippe Rocca-Serra, Catherine Brooksbank
, Helen C. Causton, Duccio Cavalieri, Terry Gaasterland, Pascal Hingamp
, Frank C. P. 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. Bioinform. 18(11): 1409 (2002) - [c16]Kimmo Palin, Esko Ukkonen, Alvis Brazma, Jaak Vilo:
Correlating gene promoters and expression in gene disruption experiments. ECCB 2002: 172-180 - [c15]Johan Rung, Thomas Schlitt, Alvis Brazma, K. Freivalds, Jaak Vilo:
Building and analysing genome-wide gene disruption networks. ECCB 2002: 202-210 - 2001
- [j5]Alvis Brazma
:
On the Importance of Standardisation in Life Sciences. Bioinform. 17(1): 113-114 (2001) - 2000
- [c14]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
1990 – 1999
- 1998
- [j4]Alvis Brazma
, Inge Jonassen
, Ingvar Eidhammer, David R. Gilbert:
Approaches to the Automatic Discovery of Patterns in Biosequences. J. Comput. Biol. 5(2): 279-305 (1998) - [c13]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 - [c12]Alvis Brazma
, Inge Jonassen
, Jaak Vilo, Esko Ukkonen:
Pattern Discovery in Biosequences. ICGI 1998: 257-270 - 1997
- [j3]Alvis Brazma, Karlis Cerans:
Noise-Tolerant Efficient Inductive Synthesis of Regular Expressions from Good Examples. New Gener. Comput. 15(1): 105-140 (1997) - [c11]Alvis Brazma, Jaak Vilo, Esko Ukkonen:
Finding transcription factor binding site combinations in the yeast genome. German Conference on Bioinformatics 1997: 57-59 - [c10]Alvis Brazma, Tomas P. Flores, Peter Maccallum, Alan J. Robinson:
Data Mining and Visualisation in Molecular Biology Databases. German Conference on Bioinformatics 1997: 127 - [c9]Alvis Brazma, Jaak Vilo, Esko Ukkonen, Kimmo Valtonen:
Data Mining for Regulatory Elements in Yeast Genome. ISMB 1997: 65-74 - 1996
- [c8]Alvis Brazma
, Esko Ukkonen, Jaak Vilo:
Discovering Unbounded Unions of Regular Pattern Languages from Positive Examples (Extended Abstract). ISAAC 1996: 95-104 - [c7]Alvis Brazma, Inge Jonassen, Esko Ukkonen, Jaak Vilo:
Discovering Patterns and Subfamilies in Biosequences. ISMB 1996: 34-43 - 1995
- [c6]Alvis Brazma
:
Learning of regular expressions by pattern matching. EuroCOLT 1995: 392-403 - 1994
- [c5]Alvis Brazma
, Karlis Cerans:
Efficient Learning of Regular Expressions from Good Examples. AII/ALT 1994: 76-90 - [c4]Alvis Brazma
:
Efficient Algorithm for Learning Simple Regular Expressions from Noisy Examples. AII/ALT 1994: 260-271 - [c3]Karlis Kaugars, Juris Reinfelds, Alvis Brazma:
A Simple Algorithm for Drawing Large Graphs on Small Screens. Graph Drawing 1994: 278-281 - 1993
- [c2]Alvis Brazma:
Efficient Identification of Regular Expressions from Representative Examples. COLT 1993: 236-242 - [c1]Alvis Brazma:
Learning a Subclass of Regular Expressions by Recognizing Periodic Repetitions. SCAI 1993: 137-146 - 1991
- [p1]Alvis Brazma
:
Inductive Synthesis of Dot Expressions. Baltic Computer Science 1991: 156-212 - 1990
- [j2]Efim B. Kinber, Alvis Brazma:
Models of Inductive Synthesis. J. Log. Program. 9(2&3): 221-233 (1990)
1980 – 1989
- 1986
- [j1]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)