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Books and Theses
- 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
Journal Articles
- 2023
- [j62]Sean Upchurch
, Emilio Palumbo, Jeremy Adams, David Bujold, Guillaume Bourque, Jared Nedzel, Keenan Graham, Meenakshi S. Kagda, Pedro Assis, Benjamin C. Hitz, Emilio Righi, Roderic Guigó, Barbara J. Wold, Alvis Brazma, Julia Burchard, Joe Capka, Michael Cherry, Laura Clarke, Brian Craft, Manolis Dermitzakis, Mark Diekhans, John Dursi, Michael Sean Fitzsimons, Zac Flaming, Romina Garrido, Alfred Gil, Paul Godden, Matt Green, Mitch Guttman, Brian Haas, Max Haeussler, Bo Li, Sten Linnarsson, Adam Lipski, David Liu, Simonne Longerich, David Lougheed, Jonathan Manning, John C. Marioni, Christopher Meyer, Stephen B. Montgomery, Alyssa Morrow, Alfonso Muñoz-Pomer Fuentes, Jared L. Nedzel, David Nguyen, Kevin Osborn, Francis Ouellette, Irene Papatheodorou, Dmitri D. Pervouchine, Arun K. Ramani, Jordi Rambla, Bashir Sadjad, David Steinberg, Jeremiah Talkar, Timothy Tickle, Kathy Tzeng, Saman Vaisipour, Sean Watford, Barbara Wold, Zhenyu Zhang, Jing Zhu:
RNAget: an API to securely retrieve RNA quantifications. Bioinform. 39(4) (2023) - [j61]Maria Theiss, Jean-Karim Hériché, Craig Russell, David Helekal, Alisdair Soppitt, Jonas Ries, Jan Ellenberg, Alvis Brazma, Virginie Uhlmann:
Simulating structurally variable nuclear pore complexes for microscopy. Bioinform. 39(10) (2023) - 2022
- [j60]Pablo A. Moreno, Silvie Fexova, Nancy George, Jonathan R. Manning, Zhichao Miao, Suhaib Mohammed, Alfonso Muñoz-Pomer Fuentes, Anja Füllgrabe, Yalan Bi, Natassja Bush, Haider Iqbal, Upendra Kumbham, Andrey Solovyev, Lingyun Zhao, Ananth Prakash, David García-Seisdedos, Deepti Jaiswal Kundu, Shengbo Wang, Mathias Walzer, Laura Clarke, David Osumi-Sutherland, Marcela Karey Tello-Ruiz, Sunita Kumari, Doreen Ware, Jana Eliasova, Mark J. Arends, Martijn C. Nawijn, Kerstin B. Meyer, Tony Burdett, John C. Marioni, Sarah A. Teichmann, Juan Antonio Vizcaíno, Alvis Brazma, Irene Papatheodorou:
Expression Atlas update: gene and protein expression in multiple species. Nucleic Acids Res. 50(D1): 129-140 (2022) - [j59]Yasset Pérez-Riverol, Jingwen Bai, Chakradhar Bandla, David García-Seisdedos, Suresh Hewapathirana, Selvakumar Kamatchinathan, Deepti Jaiswal Kundu, Ananth Prakash, Anika Frericks-Zipper, Martin Eisenacher, Mathias Walzer, Shengbo Wang, Alvis Brazma, Juan Antonio Vizcaíno:
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. 50(D1): 543-552 (2022) - 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 A. 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) - 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) - 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) - 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) - 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) - 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) - 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) - 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
- [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 C. Taylor, Alvis Brazma, John Quackenbush:
An open letter to the scientific journals. Bioinform. 18(11): 1409 (2002) - 2001
- [j5]Alvis Brazma:
On the Importance of Standardisation in Life Sciences. Bioinform. 17(1): 113-114 (2001) - 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) - 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) - 1990
- [j2]Efim B. Kinber, Alvis Brazma:
Models of Inductive Synthesis. J. Log. Program. 9(2&3): 221-233 (1990) - 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)
Conference and Workshop Papers
- 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 - 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 - 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 - 2005
- [c17]Walter R. Gilks, Brian D. M. Tom, Alvis Brazma:
Fusing microarray experiments with multivariate regression. ECCB/JBI 2005: 143 - 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 - 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 - 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
- [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. GD 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
Parts in Books or Collections
- 1991
- [p1]Alvis Brazma:
Inductive Synthesis of Dot Expressions. Baltic Computer Science 1991: 156-212
Editorship
- 2008
- [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]
Informal and Other Publications
- 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) - 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)
Coauthor Index
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