Alvis Brazma

	2009
45		José Caldas, Nils Gehlenborg, Ali Faisal, Alvis Brazma, Samuel Kaski: Probabilistic retrieval and visualization of biologically relevant microarray experiments. Bioinformatics 25(12): (2009)
44		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)
43		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)
42		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)
	2008
41		Alvis Brazma, Satoru Miyano, Tatsuya Akutsu: Proceedings of the 6th Asia-Pacific Bioinformatics Conference, APBC 2008, 14-17 January 2008, Kyoto, Japan Imperial College Press 2008
40		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
39		Alvis Brazma, Satoru Miyano, Tatsuya Akutsu: Preface. APBC 2008
38		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)
37		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)
	2007
36		Thomas Schlitt, Alvis Brazma: Current approaches to gene regulatory network modelling. BMC Bioinformatics 8(S-6): (2007)
35		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)
34		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)
	2006
33		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)
32		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)
	2005
31		Walter R. Gilks, Brian D. M. Tom, Alvis Brazma: Fusing microarray experiments with multivariate regression. ECCB/JBI 2005: 143
30		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)
29		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)
28		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)
27		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)
	2004
26		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)
	2003
25		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)
24		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)
	2002
23		Kimmo Palin, Esko Ukkonen, Alvis Brazma, Jaak Vilo: Correlating gene promoters and expression in gene disruption experiments. ECCB 2002: 172-180
22		Johan Rung, Thomas Schlitt, Alvis Brazma, K. Freivalds, Jaak Vilo: Building and analysing genome-wide gene disruption networks. ECCB 2002: 202-210
21		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)
	2001
20		Alvis Brazma: On the Importance of Standardisation in Life Sciences. Bioinformatics 17(1): 113-114 (2001)
	2000
19		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
18		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
17		Alvis Brazma, Inge Jonassen, Jaak Vilo, Esko Ukkonen: Pattern Discovery in Biosequences. ICGI 1998: 257-270
16		Alvis Brazma, Inge Jonassen, Ingvar Eidhammer, David Gilbert: Approaches to the Automatic Discovery of Patterns in Biosequences. Journal of Computational Biology 5(2): 277-304 (1998)
	1997
15		Alvis Brazma, Tomas P. Flores, Peter Maccallum, Alan J. Robinson: Data Mining and Visualisation in Molecular Biology Databases. German Conference on Bioinformatics 1997: 127
14		Alvis Brazma, Jaak Vilo, Esko Ukkonen: Finding transcription factor binding site combinations in the yeast genome. German Conference on Bioinformatics 1997: 57-59
13		Alvis Brazma, Jaak Vilo, Esko Ukkonen, Kimmo Valtonen: Data Mining for Regulatory Elements in Yeast Genome. ISMB 1997: 65-74
12		Alvis Brazma, Karlis Cerans: Noise-Tolerant Efficient Inductive Synthesis of Regular Expressions from Good Examples. New Generation Comput. 15(1): 105-140 (1997)
	1996
11		Alvis Brazma, Esko Ukkonen, Jaak Vilo: Discovering Unbounded Unions of Regular Pattern Languages from Positive Examples (Extended Abstract). ISAAC 1996: 95-104
10		Alvis Brazma, Inge Jonassen, Esko Ukkonen, Jaak Vilo: Discovering Patterns and Subfamilies in Biosequences. ISMB 1996: 34-43
	1995
9		Alvis Brazma: Learning of regular expressions by pattern matching. EuroCOLT 1995: 392-403
	1994
8		Alvis Brazma: Efficient Algorithm for Learning Simple Regular Expressions from Noisy Examples. AII/ALT 1994: 260-271
7		Alvis Brazma, Karlis Cerans: Efficient Learning of Regular Expressions from Good Examples. AII/ALT 1994: 76-90
6		Karlis Kaugars, Juris Reinfelds, Alvis Brazma: A Simple Algorithm for Drawing Large Graphs on Small Screens. Graph Drawing 1994: 278-281
	1993
5		Alvis Brazma: Efficient Identification of Regular Expressions from Representative Examples. COLT 1993: 236-242
4		Alvis Brazma: Learning a Subclass of Regular Expressions by Recognizing Periodic Repetitions. SCAI 1993: 137-146
	1991
3		Alvis Brazma: Inductive Synthesis of Dot Expressions. Baltic Computer Science 1991: 156-212
	1990
2		Efim B. Kinber, Alvis Brazma: Models of Inductive Synthesis. J. Log. Program. 9(2&3): 221-233 (1990)
	1986
1		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)

Coauthor Index

1	Niran Abeygunawardena	[24] [27] [28] [34] [42]
2	Tomasz Adamusiak	[42]
3	Tatsuya Akutsu	[39] [41]
4	Rolf Apweiler	[25]
5	Detlev Arendt	[37] [40]
6	Catherine A. Ball	[21] [33]
7	Amy Barrett	[35] [43]
8	Hugo Berube	[37] [40] [42]
9	Ewan Birney	[25]
10	Jonathon Blake	[32]
11	Peer Bork	[37] [40]
12	Xiangqun Zheng Bradley	[42]
13	Marco Brandizi	[42]
14	Catherine Brooksbank	[21] [25]
15	Tony Burdett	[42]
16	José Caldas	[45]
17	Graham Cameron	[25]
18	Evelyn Camon	[25]
19	Helen C. Causton	[21] [33]
20	Duccio Cavalieri	[21]
21	Edgars Celms	[35]
22	Karlis Cerans	[7] [12]
23	Sergio Contrino	[27] [28]
24	Richard Coulson	[27] [34] [42]
25	Aedín C. Culhane	[26]
26	Sean Davis	[30]
27	Steffen Durinck	[26] [30]
28	Miroslaw Dylag	[42]
29	Ingvar Eidhammer	[16]
30	Ibrahim Emam	[42]
31	Laurence Ettwiller	[40]
32	Ali Faisal	[45]
33	Anna Farne	[27] [28] [33] [34] [42]
34	Tomas P. Flores	[15]
35	K. Freivalds	[22]
36	Eileen E. M. Furlong	[37] [40]
37	Terry Gaasterland	[21]
38	Julien Gagneur	[37] [40]
39	Nils Gehlenborg	[45]
40	Robert Giegerich	[38]
41	David Gilbert (David R. Gilbert)	[16]
42	Walter R. Gilks	[31]
43	Charles Girardot	[37] [40]
44	Mike Gostev	[43]
45	Midori A. Harris	[25]
46	Yannick Haudry	[37] [40]
47	Thorsten Henrich	[37] [40]
48	Kim Henrick	[25]
49	Pascal Hingamp	[21]
50	Ele Holloway	[24] [27] [28] [33] [34] [42]
51	Frank Holstege	[21]
52	Wolfgang Huber	[30] [44]
53	Jan Ihmels	[26]
54	Rafael A. Irizarry	[33]
55	Inge Jonassen	[10] [16] [17] [18] [19] [38]
56	Misha Kapushesky	[24] [26] [27] [28] [29] [32] [34] [37] [40] [42] [44]
57	Samuel Kaski	[45]
58	Arek Kasprzyk	[30]
59	Audrey Kauffmann	[44]
60	Karlis Kaugars	[6]
61	Patrick Kemmeren	[24] [26]
62	Efim B. Kinber	[1] [2]
63	Juha Knuuttila	[43]
64	Nikolay Kolesnikov	[42]
65	N. Kolesnykov	[34]
66	Christine Körner	[26]
67	Maria Krestyaninova	[35] [42] [43]
68	Meelis Kull	[26]
69	Natalja Kurbatova	[43]
70	Pavel Kurnosov	[42]
71	Ilkka Lappalainen	[43]
72	Gonzalo Garcia Lara	[24] [27] [28]
73	Ivica Letunic	[37] [40]
74	P. Lilja	[27] [34]
75	Junmin Liu	[33]
76	Rodrigo Lopez	[25]
77	Margus Lukk	[34] [42] [44]
78	Peter Maccallum	[15]
79	Michele Magrane	[25]
80	Eamonn Maguire	[42]
81	Donald Maier	[33]
82	James Malone	[42]
83	Roby Mani	[34] [42]
84	Maria Jesus Martin	[25]
85	Mark I. McCarthy	[35] [43]
86	Michael Miller	[33]
87	Satoru Miyano	[39] [41]
88	Bart De Moor	[30]
89	Yves Moreau	[30]
90	Gaurab Mukherjee	[27] [28]
91	Nicola J. Mulder	[25]
92	Sudeshna Guha Neogi	[35] [42] [43]
93	Claire O'Donovan	[25]
94	Ahmet Oezcimen	[24] [27] [28]
95	Chuang Kee Ong	[40]
96	Martins Opmanis	[35]
97	Kimmo Palin	[23]
98	Helen E. Parkinson	[21] [24] [25] [27] [28] [33] [34] [42] [44]
99	Teemu Perheentupa	[43]
100	Kjell Petersen	[33]
101	Ekaterina Pilicheva	[42]
102	Karlis Podnieks	[35] [43]
103	John Quackenbush	[21] [33]
104	Tim F. Rayner	[27] [28] [33] [34] [42] [44]
105	Juris Reinfelds	[6]
106	Faisal Ibne Rezwan	[42]
107	Martin Ringwald	[21]
108	Alan J. Robinson	[15] [19]
109	Philippe Rocca-Serra	[21] [24] [27] [28] [33] [42]
110	Peteris Rucevskis	[35] [43]
111	Johan Rung	[22] [43]
112	Gabriella Rustici	[42]
113	Susanna-Assunta Sansone	[24] [27] [28] [42]
114	Ugis Sarkans	[24] [26] [27] [28] [33] [34] [35] [42] [43]
115	Thomas Schlitt	[22] [36]
116	Christian Schwager	[32]
117	Anjan Sharma	[27] [28] [34] [42]
118	Gavin Sherlock	[21] [33]
119	Mohammadreza Shojatalab	[24] [27] [28] [34] [42]
120	Nataliya Sklyar	[42]
121	Paul T. Spellman	[21] [33]
122	Jason E. Stewart	[21]
123	Christian J. Stoeckert Jr.	[21] [33]
124	Peter Stoehr	[25]
125	Guenter Stoesser	[25]
126	Ronald Taylor	[21]
127	Brian D. M. Tom	[31]
128	Aurora Torrente	[26] [29]
129	Mary Ann Tuli	[25]
130	Esko Ukkonen	[10] [11] [13] [14] [17] [18] [19] [23] [38]
131	Kimmo Valtonen	[13]
132	Juris Viksna	[35] [43]
133	Jaak Vilo	[10] [11] [13] [14] [17] [18] [19] [22] [23] [24] [26]
134	Martin Vingron	[38]
135	Xi Wang	[40]
136	Paul-Daniel Weeber	[37] [40]
137	Patricia L. Whetzel	[33]
138	Joseph White	[33]
139	E. William	[34]
140	Eleanor Williams	[42]
141	Joachim Wittbrodt	[37] [40]
142	Farrell Wymore	[33]
143	Andris Zarins	[35] [43]
144	Mengyao Zhao	[42]

Colors in the list of coauthors