Publications by BIIT group

See also alist of Jaak Vilo's students completed MSc and BSc theses.
Links/searches: [PubMed] [ETIS] [Google Scholar, 2007+Google Scholar profile] [EXCS - Bioinformatics].

2014

  1. Kaie Lokk, Vijayachitra Modhukur, Balaji Rajashekar, Kaspar Märtens, Reedik Mägi, Raivo Kolde, Marina Koltšina, Torbjörn K Nilsson, Jaak Vilo, Andres Salumets, Neeme Tõnisson: DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns. Genome Biology. 2014, 15:r54. doi:10.1186/gb-2014-15-4-r54
  2. Ning Xuan, Xun Bu, Yan Yan Liu, Xue Yang, Guo Xia Liu, Zhong Xue Fan, Yu Ping Bi, Lian Qun Yang, Qi Nian Lou, Balaji Rajashekar, Getter Leppik,Sergo Kasvandik, Jean-François Picimbon: Molecular Evidence of RNA Editing in Bombyx Chemosensory Protein Family. PLOS One. 13 FEB 2014. DOI: 10.1371/journal.pone.0086932
  3. Guo Xia Liu, Ning Xuan, Dong Chu, Hong Yan Xie, Zhong Xue Fan, Yu Ping Bi, Jean‐François Picimbon, Yu Chuan Qin, Su Ting Zhong, Yao Fa Li, Zhan Lin Gao, Wen Liang Pan, Guo Ying Wang, Balaji Rajashekar: BIOTYPE EXPRESSION AND INSECTICIDE RESPONSE OF Bemisia tabaci CHEMOSENSORY PROTEIN-1. Archives of Insect Biochemistry and Physiology. 29 JAN 2014. DOI: 10.1002/arch.21148
  4. Sten Ilmjärv, Christian Ansgar Hundahl, Riin Reimets, Margus Niitsoo, Raivo Kolde, Jaak Vilo, Eero Vasar and Hendrik Luuk: Estimating differential expression from multiple indicators. Nucl. Acids Res., doi: 10.1093/nar/gku158 PMID:
  5. Waldmann T, Rempel E, Balmer NV, König A, Kolde R, Gaspar JA, Henry M, Hescheler J, Sachinidis A, Rahnenfuehrer J, Hengstler JG, Leist M.: Design principles of concentration dependent transcriptome deviations in drug-exposed differentiating stem cells. Chem Res Toxicol. 2014 Jan 2. [Epub ahead of print] PMID: 24383497

2013

  1. Leist M, Ringwald A, Kolde R, Bremer S, van Thriel C, Krause KH, Rahnenführer J, Sachinidis A, Hescheler J, Hengstler JG.: Test systems of developmental toxicity: state-of-the art and future perspectives. Arch Toxicol. 2013 Dec;87(12):2037-42.
    doi:10.1007/s00204-013-1154-x. PMID: 24190503
  2. H Peterson, R Abu Dawud, A Garg, Y Wang, J Vilo, I Xenarios, J Adjaye: Qualitative modeling identifies IL-11 as a novel regulator in maintaining self-renewal in human pluripotent stem cells
    Frontiers in physiology 4, 303
    [PUBMED] doi: 10.3389/fphys.2013.00303
  3. Konstantin Tretyakov, Tatyana Goldberg, Victor X Jin and Paul Horton. Summary of talks and papers at ISCB-Asia/SCCG 2012. BMC Genomics first published online February 14, 2013
  4. Liina Kamm, Dan Bogdanov, Sven Laur and Jaak Vilo: A new way to protect privacy in large-scale genome-wide association studies. Bioinformatics first published online February 14, 2013 doi:10.1093/bioinformatics/btt066 (link)
  5. Tretyakov, Konstantin; Laur, Sven; Smant, Geert; Vilo, Jaak; Prins, Pjotr (2012). Fast Probabilistic File Fingerprinting for Big Data. BMC Genomics 2013, 14(Suppl 2):S8
  6. K Tretjakov, L García-bañuelos, A Armas-cervantes, J Vilo, MG Dumas:
    Processing Search Queries Using A Data Structure
    US Patent 20,130,103,678 2013
  7. K Tretjakov, L Garcia-bañuelos, A Armas-cervantes, J Vilo, MG Dumas: Processing Search Queries In A Network Of Interconnected Nodes.
    US Patent 20,130,103,671
  8. Krug AK, Kolde R, Gaspar JA, Rempel E, Balmer NV, Meganathan K, Vojnits K, Baquié M, Waldmann T, Ensenat-Waser R, Jagtap S, Evans RM, Julien S, Peterson H, Zagoura D, Kadereit S, Gerhard D, Sotiriadou I, Heke M, Natarajan K, Henry M, Winkler J, Marchan R, Stoppini L, Bosgra S, Westerhout J, Verwei M, Vilo J, Kortenkamp A, Hescheler J, Hothorn L, Bremer S, van Thriel C, Krause KH, Hengstler JG, Rahnenführer J, Leist M, Sachinidis A. Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach.
    Arch. of Toxicol., v. 87, n. 1, pp. 123-143, 2013. doi:10.1007/s00204-012-0967-3
    PMID: 23179753
  9. Võsa U, Vooder T, Kolde R, Vilo J, Metspalu A, Annilo T. Meta-analysis of microrna expression in lung cancer. Int J Cancer. Volume 132, Issue 12, pages 2884–2893, 15 June 2013. doi:10.1002/ijc.27981. PMID: 23225545

2012

  1. Juri Reimand, Anu Aun, Jaak Vilo, Juan M Vaquerizas, Juhan Sedman and Nicholas M Luscombe: m:Explorer - multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence.  Genome Biology 2012, 13:R55 doi:10.1186/gb-2012-13-6-r55 

    [Web tool link] [PubMed] [Abstract]

  2. Nina V. Balmer, Matthias K. Weng, Bastian Zimmer, Violeta N. Ivanova, Stuart M. Chambers, Elena Nikolaeva, Smita Jagtap, Agapios Sachinidis, Jurgen Hescheler, Tanja Waldmann and Marcel Leist, Epigenetic changes and disturbed neural development in a human embryonic stem cell-based model relating to the fetal valproate syndrome, Human Molecular Genetics, 2012, June 20, doi:10.1093/hmg/dds239 

    [PubMed ][Abstract]

  3. Raivo Kolde, Sven Laur, Priit Adler, Jaak Vilo   Robust Rank Aggregation for gene list integration and meta-analysis.
    Bioinformatics 2012; doi:10.1093/bioinformatics/btr709

    [ PubMed ] [ MEM Web-tool ] [ RRA R Package]

  4. Rebane A, Zimmermann M, Aab A, Baurecht H, Koreck A, Karelson M, Abram K, Metsalu T, Pihlap M, Meyer N, Fölster-Holst R, Nagy N, Kemeny L, Kingo K, Vilo J, Illig T, Akdis M, Franke A, Novak N, Weidinger S, Akdis CA.
    Mechanisms of IFN-γ-induced apoptosis of human skin keratinocytes in patients with atopic dermatitis.
    J Allergy Clin Immunol. 2012 May;129(5):1297-306. Epub 2012 Mar 24.

    [Pubmed]

  5. Saare M, Rebane A,Rajashekar B, Vilo J, Peterson P. : Autoimmune regulator is acetylated by transcription coactivator CBP/p300.  Exp Cell Res. 2012 May 30. 

    [PubMed]   

  6. Agapios Sachinidis, John Antonydas Gaspar, Michael Xavier Doss, Johannes Winkler, Vilas Wagh, Raivo Kolde, Jaak Vilo, Juergen Hescheler, and Herbert Schulz. Gene Expression Signatures Defining Fundamental Biological Processes in Pluripotent, Early, and Late Differentiated Embryonic Stem Cells. Stem Cells and Development. 2012 Sep 1;21(13):2471-84. doi:10.1089/scd.2011.0637.

    [ PubMed ] [Abstract ]

  7. Jaan Aru, Kristjan Korjus, Carolina Murd, and Talis Bachmann. Journal of Caffeine Research. March 2012, 2(1): 23-30. doi:10.1089/jcr.2011.0028.

2011

  1. Hundahl CA, Luuk H, Ilmjärv S, Falktoft B, Raida Z, et al. 2011 Neuroglobin-Deficiency Exacerbates Hif1A and c-FOS Response, but Does Not Affect Neuronal Survival during Severe Hypoxia In Vivo. PLoS ONE 6(12): e28160. doi:10.1371/journal.pone.0028160 
  2. Konstantin Tretyakov, Abel Armas-Cervantes, Luciano García-Bañuelos, Jaak Vilo, Marlon Dumas. Fast fully dynamic landmark-based estimation of shortest path distances in very large graphs. (2011) In Proceedings of the 20th ACM international conference on Information and knowledge management (CIKM '11). ACM, New York, NY, USA, 1785-1794.

    doi:10.1145/2063576.2063834  [Abstract]

  3. Signe Altmäe, Jüri Reimand, Outi Hovatta, Pu Zhang, Juha Kere, Triin Laisk, Merli Saare, Maire Peters, Jaak Vilo, Anneli Stavreus-Evers and Andres Salumets. Research Resource: Interactome of Human Embryo Implantation: Identification of Gene Expression Pathways, Regulation, and Integrated Regulatory Networks. Molecular Endocrinology November 10, 2011 me.2011-1196 doi:10.1210/me.2011-1196 
  4. Jüri Reimand, Tambet Arak, Jaak Vilo: g:Profiler—a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Research 2011 Jul;39 Suppl 2:W307-15. (Advance online access June 6, 2011)

    doi:10.1093/nar/gkr378

    [ PubMed]   

  5. Võsa U, Vooder T, Kolde R, Fischer K, Välk K, Tõnisson N, Roosipuu R, Vilo J, Metspalu A, Annilo T. Identification of miR-374a as a prognostic marker for survival in patients with early-stage nonsmall cell lung cancer. Genes Chromosomes Cancer. 2011 Jul 11. doi: 10.1002/gcc.20902

    [PubMed]

  6. Tserel L, Runnel T, Kisand K, Pihlap M, Bakhoff L, Kolde R, Peterson H, Vilo J, Peterson P, Rebane A. :  microRNA expression profiles of human blood monocyte derived dendritic cells and macrophages reveal miR-511 as putative positive regulator of TLR4. J Biol Chem 2011 Jun 6.
    [ Pubmed]
  7. Välk, K; Vooder, T; Kolde, R; Reintam, MA; Petzold, C; Vilo, J; Metspalu, A (2011). Gene Expression Profiles of Non-Small Cell Lung Cancer: Survival Prediction and New Biomarkers. Oncology, 79(3-4), 283 - 292.
    doi:10.1159/000322116

    [PubMed]

  8. Tretyakov K, Laur S, Vilo J, G = MAT: Linking Transcription Factor Expression and DNA Binding Data. PLoS ONE 2011 6(1): e14559.
    doi:10.1371/journal.pone.0014559

    [ PubMed ] [G=MAT web tool ]

2010

  1. Tserel, L. , Kolde, R. , Rebane, A. , Kisand, K. , Org, T. , Peterson, H. , Vilo, J. , Peterson, P. .  Genome-wide promoter analysis of histone modifications in human monocyte-derived antigen presenting cells.  BMC Genomics, v. 11, article 642, 2010.
    doi:10.1186/1471-2164-11-642 [ Pubmed ]
  2. Tarkade Klubi: okt. 2010: Arvutite abil looduse saladusi muukimas: Intervjuu Jaak Viloga
  3. Tarkade Klubi: okt. 2010: Tehisintellekt tuleb tasa ja targu (Intervjuu Jaak Vilo ja Sven Lauriga)
  4. Marko Lõoke, Jüri Reimand, Tiina Sedman, Juhan Sedman, Lari Järvinen, Signe Värv, Kadri Peil, Kersti Kristjuhan, Jaak Vilo and Arnold Kristjuhan: Relicensing of transcriptionally inactivated replication origins in budding yeast J. Biol. Chem. jbc.M110.148924First Published on October 20, 2010,
    doi:10.1074/jbc.M110.148924 [Article @JBC]
  5. Vooder T, Välk K, Kolde R, Roosipuu R, Vilo J, Metspalu A. Gene Expression-Based Approaches in Differentiation of Metastases and Second Primary Tumour.Case Rep Oncol. 2010 Jul 21;3(2):255-261.
    doi:10.1159/000318010 [Article @Karger] [EID] [PubMed] [Abstract] [PDF]
  6. Nathalie Billon, Raivo Kolde, Juri Reimand, Miguel C Monteiro, Meelis Kull, Hedi Peterson, Konstantin Tretyakov, Priit Adler, Brigitte Wdziekonski, Jaak Vilo and Christian Dani. Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development. Genome Biology 2010, 11:R80
    doi:10.1186/gb-2010-11-8-r80 [Abstract] [PubMed] [PDF]
  7. Siim Orasmaa, Reina Käärik, Jaak Vilo, Tiit Hennoste. Information Retrieval of Word Form Variants in Spoken Language Corpora Using Generalized Edit Distance. Proceedings of the Seventh conference on International Language
    Resources and Evaluation (LREC'10). pages:623-629. Editors: Nicoletta Calzolari (Conference Chair), Khalid Choukri, Bente Maegaard, Joseph Mariani, Jan Odjik, Stelios Piperidis, Mike Rosner, Daniel Tapias. (European Language Resources Association
    (ELRA), ISBN:2-9517408-6-7)
    [PDF] [Abstract]
  8. Marc Jung, Hedi Peterson, Lukas Chavez, Pascal Kahlem, Hans Lehrach, Jaak Vilo, James Adjaye. A Data Integration Approach to Mapping OCT4 Gene Regulatory Networks Operative in Embryonic Stem Cells and Embryonal Carcinoma Cells. PLoS ONE 2010, 5(5): e10709.
    doi:10.1371/journal.pone.0010709 [Article download] [PubMed]
  9. Meelis Kull, Konstantin Tretyakov, Jaak Vilo An Evolutionary Model of DNA Substring Distribution. In Algorithms and Applications. 2010 Springer, Lecture Notes in Computer Science, Vol. 6060, pages:147-157
    doi:10.1007/978-3-642-12476-1_10
  10. Kuegler PB, Zimmer B, Waldmann T, Baudis B, Ilmjärv S, Hescheler J, Gaughwin P, Brundin P, Mundy W, Bal-Price AK, Schrattenholz A, Krause KH, van Thriel C, Rao MS, Kadereit S, Leist M. Markers of murine embryonic and neural stem cells, neurons and astrocytes: reference points for developmental neurotoxicity testing. Altex 2010, 27 (16-42)
    [PubMed] [Abstract]
  11. Francisco, Roque; Laura, Slaughter; Aleksandr, Tkatšenko (2010). A Comparison of Several Key Information Visualization Systems for Secondary Use of Electronic Health Record Content. Proceedings of the NAACL HLT 2010 Second Louhi Workshop on Text and Data Mining of Health Documents, Los Angeles, California, USA. , 2010, 76 - 83.   
  12. Jüri Reimand, Juan M Vaquerizas, Annabel E Todd, Jaak Vilo and Nicholas
    M Luscombe.  Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets, Nucleic Acids Research, 2010.
    doi:10.1093/nar/gkq232 [Abstract] [PubMed] [PDF]
  13. Michael Xavier Doss, Vilas Wagh, Herbert Schulz, Meelis Kull, Raivo Kolde, Kurt Pfannkuche, Tobias Nolden, Heinz Himmelbauer, Jaak Vilo, Jürgen Hescheler and Agapios Sachinidis. Global transcriptomic analysis of murine embryonic stem cell-derived brachyury+ (T) cells. Genes to Cells. 2010, 15(3),(p 209-228) 
    10.1111/j.1365-2443.2010.01390.x [PubMed] [PDF]
  14. Maron E, Kallassalu K, Tammiste A, Kolde R, Vilo J, Tõru I, Vasar V, Shlik J, Metspalu A. Peripheral gene expression profiling of CCK-4-induced panic in healthy subjects.Am J Med Genet B Neuropsychiatr Genet. Volume 153B Issue 1, Pages 269 - 274 (Published Online:2008 Dec 2).
    [doi:10.1002/ajmg.b.30898] [PubMed]
  15. Kahlem P., Adjaye J., Vilo J., Xenarios X.(2010) Enabling systems biology. Research Media 19-21.     

2009

  1. Priit Adler, Raivo Kolde, Meelis Kull, Aleksandr Tkachenko, Hedi Peterson, Jüri Reimand and Jaak Vilo. Mining for coexpression across hundreds of datasets using novel rank aggregation and visualisation methods. Genome Biology 2009, 10:R139. doi:10.1186/gb-2009-10-12-r139


    [MEM Web tool] [PubMed] [Abstract@GB] [PDF]

    MEM article has been nominated for the annual Genome Biology best research paper award!

  2. Schulz H, Kolde R, Adler P, Aksoy I, Anastassiadis K, Bader M, Billon N, Boeuf H, Bourillot PY, Buchholz F, Dani C, Doss MX, Forrester L, Gitton M, Henrique D, Hescheler J, Himmelbauer H, Hübner N, Karantzali E, Kretsovali A, Lubitz S, Pradier L, Rai M, Reimand J, Rolletschek A, Sachinidis A, Savatier P, Stewart F, Storm MP, Trouillas M, Vilo J, Welham MJ, Winkler J, Wobus AM, Hatzopoulos AK, Functional Genomics in Embryonic Stem Cells Consortium: The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation. PLoS One 2009, 4:e6804 doi:10.1371/journal.pone.0006804

    [FunGenES Database] [PubMed] [PLOS One]

  3. Darya Krushevskaya, Hedi Peterson, Jüri Reimand, Meelis Kull and Jaak Vilo: VisHiC—hierarchical functional enrichment analysis of microarray data. Nucleic Acids Research, 2009, doi:10.1093/nar/gkp435

    [VisHiC web tool]  [abstract] [PDF]

  4. Storm MP, Kumpfmueller B, Thompson B, Kolde R, Vilo J, Hummel O, Schulz H, Welham MJ: Characterization of the Phosphoinositide 3-Kinase-Dependent Transcriptome in Murine Embryonic Stem Cells: Identification of Novel Regulators of Pluripotency. Stem Cells. 2009 Jan 15;27(4):764-775.

    [Pubmed] [Article]

  5. Priit Adler, Hedi Peterson, Phaedra Agius, Jüri Reimand, Jaak Vilo. Ranking genes by their co-expression to subsets of pathway members. Annals of the New York Academy of Sciences Vol 1158, Issue 1, start page 1 (Issue published online 31 Mar) 2009.

    For reprints please send email request. (publisher policy does not allow personal web posts)
  6. Marina Trouillas, Claire Saucourt, Bertrand Guillotin, Xavier Gauthereau, Li Ding, Frank Buchholz, Michael-Xavier Doss, Agapios Sachinidis, Jurgen Hescheler, Oliver Hummel, Norbert Huebner, Raivo Kolde, Jaak Vilo, Herbert Schultz, Helene Boeuf:
    Three LIF-dependent signatures and gene clusters with atypical expression profiles, identified by transcriptome studies in mouse ES cells and early derivatives BMC Genomics 2009, 10:73 (9 February 2009)

    [BMC[PubMed] [PDF] doi:10.1186/1471-2164-10-73

  7. Margus Jäger, Liina Kamm, Darja Krushevskaja, Harry-Anton Talvik, Janno Veldemann, Andres Vilgota, Jaak Vilo. Flexible Database Platform for Biomedical Research with Multiple User Interfaces and a Universal Query Engine. in Frontiers in Artificial Intelligence and Applications, Volume 187, 2009. Databases and Information Systems V. - Selected Papers from the Eighth International Baltic Conference, DB&IS 2008. Edited by Hele-Mai Haav, Ahto Kalja IOS Press 2009. ISBN 978-1-58603-939-4.

    DOI:10.3233/978-1-58603-939-4-301

  8. Koscielny G, Texier VL, Gopalakrishnan C, Kumanduri V, Riethoven JJ,
    Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M, Harrington E, Boué
    S, Eyras E, Plass M, Lopez F, Ritchie W, Moucadel V, Ara T, Pospisil H, Herrmann A, G Reich J, Guigó R, Bork P, Doeberitz MV, Vilo J, Hide W,
    Apweiler R, Thanaraj TA, Gautheret D. ASTD: The Alternative Splicing and Transcript Diversity database.
    Genomics. 2009 Mar;93(3):213-20.

    [PubMed]

2008

  1. Meelis Kull, Jaak Vilo. Fast Approximate Hierarchical Clustering using Similarity Heuristics. BioData Mining, 1:9 2008.
    [HappieClust website] [URL, doi:10.1186/1756-0381-1-9][Pubmed]
  2. Jüri Reimand, Laur Tooming, Hedi Peterson, Priit Adler, Jaak Vilo. GraphWeb: mining heterogeneous biological networks for gene modules with functional significance, Nucleic Acids Research, 2008 doi:10.1093/nar/gkn230.
    [NAR] [GraphWeb] [PubMed]

  3. Einar Meister and Jaak Vilo. Strengthening the Estonian Language Technology.
    Proceedings of the Sixth International Language Resources and Evaluation (LREC'08), 2008.
    European Language Resources Association (ELRA), Marrakech, Morocco, May 28-30. [PDF, Summary]
  4. Margus Jäger, Liina Kamm, Darja Krushevskaja, Harry-Anton Talvik, Janno Veldemann, Andres Vilgota, Jaak Vilo:
    Flexible Database Platform for Biomedical Research with Multiple User Interfaces and a Universal Query Engine. 2008 8th International Baltic Conference on Databases and Information Systems (Baltic DB & IS) p. 279-287. ISBN: 978-9985-59-789-7 [PDF]
  5. Aleksandr Tkachenko, Konstantin Tretjakov, Priit Adler and
    Jaak Vilo:
    Text mining for automatic annotation of
    microarray experiment clusters. 8th International Baltic Conference on Databases and Information Systems. Jun 02-05, 2008 Tallinn, ESTONIA Pages: 423-426   Published: 2008


  6. Obi L. Griffith, Stephen B. Montgomery, .... and The Open Regulatory Annotation Consortium: ORegAnno: an open-access community-driven resource for regulatory annotation Nucleic Acids Research, doi:10.1093/nar/gkm967
    (Hedi Peterson and Priit Adler are part of the consortium)
    [NAR]
  7. Priit Adler*, Jüri Reimand*, Jürgen Jänes, Raivo Kolde, Hedi Peterson, Jaak Vilo. KEGGanim: pathway animations for high-throughput data. Bioinformatics, 2008.
    Bioinformatics Volume 24, Number 4, Pp. 588-590. doi:10.1093/bioinformatics/btm581
    Advance Access published online on December 1, 2007.
    [Abstract; PubMed ; PDF ] [URL: http://biit.cs.ut.ee/KEGGanim/]

2007

  1. Jüri Reimand, Meelis Kull, Hedi Peterson, Jaanus Hansen and Jaak Vilo.
    g:Profiler—a web-based toolset for functional profiling of gene lists
    from large-scale experiments Nucleic Acids Research, 2007 Jul 1;35(Web Server issue):W193-200.
    doi:10.1093/nar/gkm226

    [g:Profiler] [Abstract [URL: http://biit.cs.ut.ee/gprofiler/]
  2. Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny.
    Nature 450, 203-218 (8 November 2007) | doi:10.1038/nature06341

    [Nature, PubMed]
  3. Alexander Stark, Michael F. Lin, Pouya Kheradpour, Jakob S. Pedersen, Leopold Parts, et. al. Discovery of functional elements in 12 fly genomes using evolutionary signatures. Nature 450, 219-232 (8 November 2007) | doi:10.1038/nature06340;

    [Nature, PubMed]
  4. Alexander Stark, Pouya Kheradpour, Leopold Parts, Julius Brennecke, Emily Hodges,Gregory J. Hannon, and Manolis Kellis. Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Research, 2007
    doi:10.1101/gr.6593807
    [PubMed,Genom. Res]
  5. Mattias Ellert, M. Grønager, Aleksandr Konstantinov, Balázs Kónya, J. Lindemann, I. Livenson, Jakob Langgaard Nielsen, Marko Niinimäki, Oxana Smirnova, Anders Wäänänen: Advanced Resource Connector middleware for lightweight computational Grids. Future Generation Computer Systems. Volume 23, Issue 2, February 2007, Pages 219-240.
    doi:10.1016/j.future.2006.05.008

2006

  1. Pavlos Pavlidis and Panayiota Poirazi.
    Individualized markers optimize class prediction of microarray data
    BMC Bioinformatics 2006, 7:345 doi:10.1186/1471-2105-7-345
    [Abstract] [Pubmed] [PDF]
  2. Konstantin Tretyakov.
    Machine Learning Techniques in Spam Filtering.
    In Satish, D. & Prabhakar, K. R. (eds.). Combating Spam. The ICFAI University Press, 2006. pp 6-33.
    [Text]

2005

  1. Aron Jalakas, Terje Vellemaa, Asko Tiidumaa. What do you want to manage today? Leadership & Strategy in a Cyber-Infrastructure World, Proceedings of the 11th International Conference of European University Information Systems, 2005
  2. Asko Tiidumaa. A Data Mart approach to analysing exam data. Leadership & Strategy in a Cyber-Infrastructure World, Proceedings of the 11th International Conference of European University Information Systems, 2005
  3. Tiia Lillemaa, Asko Tiidumaa. Implementation of the Document Management System as an audit for sustainability of procedures within the university. Leadership & Strategy in a Cyber-Infrastructure World, Proceedings of the 11th International Conference of European University Information Systems, 2005

2004

  1. 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, 2004, Vol. 32, Web Server issue W465 W470

    [NAR:Web] [PubMed:Abstract] [DOI:10.1093/nar/gkh470] [PDF copy]

  2. Asko Tiidumaa. Knowledge Discovery in the Studies Information System of the University of Tartu. IT Innovation in a Changing World, Proceedings of the 10th International Conference of European University Information Systems (pp 179-187). Viljan Mahnič, Boštjan Vilfan (ed). University of Ljubljana, Faculty of Computer and Information Science. 2004.

2003

  1. Jaak Vilo, Misha Kapushesky, Patrick Kemmeren, Ugis Sarkans, Alvis Brazma.
    Expression Profiler. In Parmigiani,G., Garrett,E.S., Irizarry,R. and Zeger,S.L. (eds), The Analysis of Gene Expression Data: Methods and Software, Springer Verlag, 2003, New York, NY.

    [Accompanying web page] [Amazon UK] [Amazon.com]

  2. A. Brazma, H. Parkinson, U. Sarkans, M. Shojatalab, J. Vilo, N. Abeygunawardena, E. Holloway, M. Kapushesky, P. Kemmeren, G.G. Lara, A. Oezcimen, P. Rocca-Serra and S. Sansone: ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Research, 2003, 31: 68-71.

    [Abstract] [PDF]

  3. Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M, Contrino S, Vilo J, Abeygunawardena N, Mukherjee G, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Sansone SA.
    ArrayExpress: a public database of gene expression data at EBI. Comptes Rendus Biologies Volume 326, Issues 10-11 , 2003 Oct-Nov;326(10-11):1075-8. PMID:14744115

2002 and before

See Publications by Jaak Vilo.