Implementing Attribute Grammars by Computational Models. - Jaak Vilo (PLILP, 1992)

An ALgorithm for Learning Hierarchical Classifiers. - Jyrki Kivinen; Heikki Mannila; Esko Ukkonen; Jaak Vilo (ECML, 1994)

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

Discovering Patterns and Subfamilies in Biosequences. - Alvis Brazma; Inge Jonassen; Esko Ukkonen; Jaak Vilo (ISMB, 1996)

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

Data Mining for Regulatory Elements in Yeast Genome. - Alvis Brazma; Jaak Vilo; Esko Ukkonen; Kimmo Valtonen (ISMB, 1997)

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

Pattern Discovery in Biosequences. - Alvis Brazma; Inge Jonassen; Jaak Vilo; Esko Ukkonen (ICGI, 1998)

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

Prediction of the coupling specificity of G protein coupled receptors to their G proteins. - Steffen Möller; Jaak Vilo; Michael D. R. Croning (ISMB (Supplement of Bioinformatics), 2001)

Correlating gene promoters and expression in gene disruption experiments. - Kimmo Palin; Esko Ukkonen; Alvis Brazma; Jaak Vilo (ECCB, 2002)

Building and analysing genome-wide gene disruption networks. - Johan Rung; Thomas Schlitt; Alvis Brazma; K. Freivalds; Jaak Vilo (ECCB, 2002)

ArrayExpress - a public repository for microarray gene expression data at the EBI. - 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; et al. (Nucleic Acids Res., 2003)

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

g: Profiler - a web-based toolset for functional profiling of gene lists from large-scale experiments. - Jüri Reimand; Meelis Kull; Hedi Peterson; Jaanus Hansen; Jaak Vilo (Nucleic Acids Res., 2007)

Flexible Database Platform for Biomedical Research with Multiple User Interfaces and a Universal Query Engine. - Margus Jäger; Liina Kamm; Darja Krushevskaja; Harry-Anton Talvik; Janno Veldemann; Andres Vilgota; Jaak Vilo (DB&IS, 2008)

Strengthening the Estonian Language Technology. - Einar Meister; Jaak Vilo (LREC, 2008)

Fast approximate hierarchical clustering using similarity heuristics. - Meelis Kull; Jaak Vilo (BioData Min., 2008)

KEGGanim: pathway animations for high-throughput data. - Priit Adler; Jüri Reimand; Jürgen Jänes; Raivo Kolde; Hedi Peterson; Jaak Vilo (Bioinform., 2008)

GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. - Jüri Reimand; Laur Tooming; Hedi Peterson; Priit Adler; Jaak Vilo (Nucleic Acids Res., 2008)

VisHiC - hierarchical functional enrichment analysis of microarray data. - Darya Krushevskaya; Hedi Peterson; Jüri Reimand; Meelis Kull; Jaak Vilo (Nucleic Acids Res., 2009)

An Evolutionary Model of DNA Substring Distribution. - Meelis Kull; Konstantin Tretyakov; Jaak Vilo (Algorithms and Applications, 2010)

National Programme for Estonian Language Technology: a Pre-final Summary. - Einar Meister; Jaak Vilo; Neeme Kahusk (Baltic HLT, 2010)

Information Retrieval of Word Form Variants in Spoken Language Corpora Using Generalized Edit Distance. - Siim Orasmaa; Reina Käärik; Jaak Vilo; Tiit Hennoste (LREC, 2010)

Fast fully dynamic landmark-based estimation of shortest path distances in very large graphs. - Konstantin Tretyakov; Abel Armas-Cervantes; Luciano García-Bañuelos; Jaak Vilo; Marlon Dumas (CIKM, 2011)

g: Profiler - a web server for functional interpretation of gene lists (2011 update). - Jüri Reimand; Tambet Arak; Jaak Vilo (Nucleic Acids Res., 2011)

Fraud Detection: Methods of Analysis for Hypergraph Data. - Anna Leontjeva; Konstantin Tretyakov; Jaak Vilo; Taavi Tamkivi (ASONAM, 2012)

Robust rank aggregation for gene list integration and meta-analysis. - Raivo Kolde; Sven Laur; Priit Adler; Jaak Vilo (Bioinform., 2012)

A new way to protect privacy in large-scale genome-wide association studies. - Liina Kamm; Dan Bogdanov; Sven Laur; Jaak Vilo (Bioinform., 2013)

FUN-L: gene prioritization for RNAi screens. - Jonathan G. Lees; Jean-Karim Hériché; Ian Morilla; José María Fernández 001; Priit Adler; Martin Krallinger; Jaak Vilo; Alfonso Valencia; Jan Ellenberg; Juan A. G. Ranea; Christine A. Orengo (Bioinform., 2015)

GOsummaries: an R Package for Visual Functional Annotation of Experimental Data. - Raivo Kolde; Jaak Vilo (F1000Research, 2015)

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap. - Tauno Metsalu; Jaak Vilo (Nucleic Acids Res., 2015)

seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data. - Raivo Kolde; Kaspar Märtens; Kaie Lokk; Sven Laur; Jaak Vilo (Bioinform., 2016)

g: Profiler - a web server for functional interpretation of gene lists (2016 update). - Jüri Reimand; Tambet Arak; Priit Adler; Liis Kolberg; Sulev Reisberg; Hedi Peterson; Jaak Vilo (Nucleic Acids Res., 2016)

g: Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). - Uku Raudvere; Liis Kolberg; Ivan Kuzmin; Tambet Arak; Priit Adler; Hedi Peterson; Jaak Vilo (Nucleic Acids Res., 2019)

PAWER: protein array web exploreR. - Dmytro Fishman; Ivan Kuzmin; Priit Adler; Jaak Vilo; Hedi Peterson (BMC Bioinform., 2020)

gprofiler2 - an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler. - Liis Kolberg; Uku Raudvere; Ivan Kuzmin; Jaak Vilo; Hedi Peterson (F1000Research, 2020)

g:Profiler - interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update). - Liis Kolberg; Uku Raudvere; Ivan Kuzmin; Priit Adler; Jaak Vilo; Hedi Peterson (Nucleic Acids Res., 2023)

Markov modeling for cost-effectiveness using federated health data network. - Markus Haug; Marek Oja; Maarja Pajusalu; Kerli Mooses; Sulev Reisberg; Jaak Vilo; Antonio Fernández Giménez; Thomas Falconer; Ana Danilovic; Filip Maljkovic; Dalia Dawoud; Raivo Kolde (J. Am. Medical Informatics Assoc., 2024)

Repeatable process for extracting health data from HL7 CDA documents. - Harry-Anton Talvik; Marek Oja; Sirli Tamm; Kerli Mooses; Dage Särg; Marcus Lõo; Õie Renata Siimon; Hendrik Suvalov; Raivo Kolde; Jaak Vilo; Sulev Reisberg; Sven Laur (J. Biomed. Informatics, 2025)