Publications

Publications by BIIT group

2021

  1. Martti Laan, Ahto Salumets, Annabel Klein, Kerli Reintamm, Rudolf Bichele, Hedi Peterson and Pärt Peterson “Post-Aire medullary thymic epithelial cells and Hassall’s corpuscles as inducers of tonic pro- inflammatory microenvironment” Frontiers in Immunology  (2021) https://doi/10.3389/fimmu.2021.635569
  2. Mohammed AS Ali, Oleg Misko, Sten-Oliver Salumaa, Mikhail Papkov, Kaupo Palo, Dmytro Fishman and Leopold Parts “Evaluating very deep convolutional neural networks for nucleus segmentation from brightfield cell microscopy images” SLAS DISCOVERY: Advancing the Science of Drug Discovery  (2021) https://doi.org/10.1177/24725552211023214
  3. Dmytro Fishman, Sten-Oliver Salumaa, Daniel Majoral, Samantha Peel, Jan Wildenhain, Alexander Schreiner, Kaupo Palo, Leopold Parts “Practical segmentation of nuclei in brightfield cell images with neural networks trained on fluorescently labelled samples” Journal of Microscopy https://doi.org/10.1111/jmi.13038
  4. Ian Walsh, Dmytro Fishman, Dario Garcia-Gasulla, Tiina Titma, Gianluca Pollastri, Jennifer Harrow, Fotis E Psomopoulos, Silvio CE Tosatto “DOME: Recommendations for supervised machine learning validation in biology” Nature Methods (2021) https://doi.org/10.1038/s41592-021-01205-4
  5. Mikhail Papkov, Kenny Roberts, Lee Ann Madissoon, Omer Bayraktar, Dmytro Fishman, Kaupo Palo, Leopold Parts “Noise2Stack: Improving Image Restoration by Learning from Volumetric Data” arXiv (2021)

2020

  1. Dmytro Fishman, Ivan Kuzmin, Priit Adler, Jaak Vilo, Hedi Peterson “PAWER: Protein Array Web ExploreR” BMC Bioinformatics 21, 411 (2020). https://doi.org/10.1186/s12859-020-03722-z
  2. Liis Kolberg, Nurlan Kerimov, Hedi Peterson, Kaur Alasoo “Co-expression analysis reveals interpretable gene modules controlled by trans-acting genetic variants” eLife 2020;9:e58705 https://doi.org/10.7554/eLife.58705
  3. Liis Kolberg, Uku Raudvere, Ivan Kuzmin, Jaak Vilo, Hedi Peterson gprofiler2– an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler F1000Research 2020, 9(ELIXIR):709 https://doi.org/10.12688/f1000research.24956.1
  4. Liis Haljasmägi, Ahto Salumets, Anna Pauliina Rumm, Meeri Jürgenson, Ekaterina Krassohhina, Anu Remm, Hanna Sein, Lauri Kareinen, Olli Vapalahti, Tarja Sironen, Hedi Peterson, Lili Milani, Anu Tamm, Adrian Hayday, Kai Kisand, Pärt Peterson “Longitudinal proteomic proling reveals increased early inammation and sustained apoptosis proteins in severe COVID-19” Scientific Reports volume 10, 20533 (2020)  https://doi.org/10.1038/s41598-020-77525-w
  5. Nurlan Kerimov, James D Hayhurst, Jonathan R Manning, Peter Walter, Liis Kolberg, Kateryna Peikova, Marija Samoviča, Tony Burdett, Simon Jupp, Helen Parkinson, Irene Papatheodorou, Daniel R Zerbino, Kaur Alasoo “eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs” bioRxiv https://doi.org/10.1101/2020.01.29.924266
  6. Kim T Gurwitz, Prakash Singh Gaur, Louisa J Bellis, Lee Larcombe, Eva Alloza, Balint Laszlo Balint, Alexander Botzki, Jure Dimec, Victoria Dominguez del Angel, Pedro L Fernandes, Eija Korpelainen, Roland Krause, Mateusz Kuzak, Loredana Le Pera, Brane Leskošek, Jessica M Lindvall, Diana Marek, Paula A Martinez, Tuur Muyldermans, Ståle Nygård, Patricia M Palagi, Hedi Peterson, Fotis Psomopoulos, Vojtech Spiwok, Celia WG van Gelder, Allegra Via, Marko Vidak, Daniel Wibberg, Sarah L Morgan, Gabriella Rustici “A framework to assess the quality and impact of bioinformatics training across ELIXIR” Plos Computational Biology 16/7 e1007976 https://doi.org/10.1371/journal.pcbi.1007976
  7. Steffen Möller, Nadine Saul, Alan A Cohen, Rüdiger Köhling, Sina Sender, Hugo Murua Escobar, Christian Junghanss, Francesca Cirulli, Alessandra Berry, Peter Antal, Priit Adler, Jaak Vilo, Michele Boiani, Ludger Jansen, Dirk Repsilber, Hans Jörgen Grabe, Stephan Struckmann, Israel Barrantes, Mohamed Hamed, Brecht Wouters, Liliane Schoofs, Walter Luyten, Georg Fuellen “Healthspan pathway maps in C. elegans and humans highlight transcription, proliferation/biosynthesis and lipids” Aging (Albany NY). 2020 Jul 15; 12(13): 12534–12581.10.18632/aging.103514
  8. Eleonora Porcu, Annique Claringbould, Kaido Lepik, BIOS Consortium, Tom G. Richardson, Federico A. Santoni, Lude Franke, Alexandre Reymond, Zoltán Kutalik  “The role of gene expression on human sexual dimorphism: too early to call” bioRxiv https://doi.org/10.1101/2020.04.15.042986
  9. Eleonora Porcu, Jennifer Sjaarda, Kaido Lepik, Cristian Carmeli, Liza Darrous, Jonathan Sulc, Ninon Mounier, and Zoltán Kutalik “Causal Inference Methods to Integrate Omics and Complex Traits” CSHL Perspectives in Medicine https://doi.org/10.1101/cshperspect.a040493
  10. Eran Segal, Feng Zhang, Xihong Lin, Gary King, Ophir Shalem, Smadar Shilo, William E Allen, Faisal Alquaddoomi, Han Altae-Tran, Simon Anders, Ran Balicer, Tal Bauman, Ximena Bonilla, Gisel Booman, Andrew T Chan, Ori Cohen, Silvano Coletti, Natalie Davidson, Yuval Dor, David A Drew, Olivier Elemento, Georgina Evans, Phil Ewels, Joshua Gale, Amir Gavrieli, Benjamin Geiger, Yonatan H Grad, Casey S Greene, Iman Hajirasouliha, Roman Jerala, Andre Kahles, Olli Kallioniemi, Ayya Keshet, Ljupco Kocarev, Gregory Landua, Tomer Meir, Aline Muller, Long H Nguyen, Matej Oresic, Svetlana Ovchinnikova, Hedi Peterson, Jana Prodanova, Jay Rajagopal, Gunnar Rätsch, Hagai Rossman, Johan Rung, Andrea Sboner, Alexandros Sigaras, Tim Spector, Ron Steinherz, Irene Stevens, Jaak Vilo, Paul Wilmes “Building an international consortium for tracking coronavirus health status” Nature Medicine 26, 1161–1165 (2020). https://doi.org/10.1038/s41591-020-0929-x

2019

  1. Alasoo, Kaur, Julia Rodrigues, John Danesh, Daniel F. Freitag, Dirk S. Paul, and Daniel J. Gaffney. “Genetic effects on promoter usage are highly context-specific and contribute to complex traits.” eLife (2019): 319806. https://doi.org/10.7554/eLife.41673
  2. Jon Ison, Hans Ienasescu, Piotr Chmura, Emil Rydza, Hervé Ménager, Matúš Kalaš, Veit Schwämmle, Björn Grüning, Niall Beard, Rodrigo Lopez, Severine Duvaud, Heinz Stockinger, Bengt Persson, Radka Svobodová Vařeková, Tomáš Raček, Jiří Vondrášek, Hedi Peterson, Ahto Salumets, Inge Jonassen, Rob Hooft, Tommi Nyrönen, Alfonso Valencia, Salvador Capella, Josep Gelpí, Federico Zambelli, Babis Savakis, Brane Leskošek, Kristoffer Rapacki, Christophe Blanchet, Rafael Jimenez, Arlindo Oliveira, Gert Vriend, Olivier Collin, Jacques van Helden, Peter Løngreen, Søren Brunak “The bio.tools registry of software tools and data resources for the life sciences” Genome Biology (2019) https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1772-6
  3. Uku Raudvere, Liis Kolberg, Ivan Kuzmin, Tambet Arak, Priit Adler, Hedi Peterson, Jaak Vilo “g: Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)” Nucleic Acids Research (2019) https://doi.org/10.1093/nar/gkz369
  4. Elena Sügis, Jerome Dauvillier, Anna Leontjeva, Priit Adler, Valerie Hindie, Thomas Moncion, Vincent Collura, Rachel Daudin, Yann Loe-Mie, Yann Herault, Jean-Charles Lambert, Henning Hermjakob, Tal Pupko, Jean-Christophe Rain, Ioannis Xenarios, Jaak Vilo, Michel Simonneau, Hedi Peterson “HENA, heterogeneous network-based data set for Alzheimer’s disease” Scientific Data (2019) https://dx.doi.org/10.1038%2Fs41597-019-0152-0
  5. Katrin Männik, Thomas Arbogast, Maarja Lepamets, Kaido Lepik, Anna Pellaz, Herta Ademi, Zachary A Kupchinsky, Jacob Ellegood, Catia Attanasio, Andrea Messina, Samuel Rotman, Sandra Martin-Brevet, Estelle Dubruc, Jacqueline Chrast, Jason P Lerch, Lily R Qiu, Triin Laisk, Mark R Henkelman, Sebastien Jacquemont, Yann Herault, Cecilia M Lindgren, Hedi Peterson, Jean Christophe Stehle, Nicholas Katsanis, Zoltan Kutalik, Serge Nef, Bogdan Draganski, Erica E Davis, Reedik Mägi, Alexandre Reymond  “Leveraging biobank-scale rare and common variant analyses to identify ASPHD1 as the main driver of reproductive traits in the 16p11. 2 locus” BioRxiv https://doi.org/10.1101/716415
  6. Reisberg, Sulev; Krebs, Kristi; Lepamets, Maarja; Kals, Mart; Mägi, Reedik; Metsalu, Kristjan; Lauschke, Volker M.; Vilo, Jaak; Milani, Lili; (2019). “Translating genotype data of 44,000 biobank participants into clinical pharmacogenetic recommendations: challenges and solutions.” Genetics in medicine. https://doi.org/10.1038/s41436-018-0337-5
  7. Reisberg, Sulev; Galwey, Nicholas; Avillach, Paul; Sahlqvist, Anna-Stina; Kolberg, Liis; Mägi, Reedik; Esko, Tõnu; Vilo, Jaak; James, Glen (2019). “Comparison of variation in frequency for SNPs associated with asthma or liver disease between Estonia, HapMap populations and the 1000 genome project populations.” International Journal of Immunogenetics, 46 (1), https://doi.org/10.1111/iji.12413
  8. James, Glen; Reisberg, Sulev; Lepik, Kaido; Galwey, Nicholas; Avillach, Paul; Kolberg, Liis; Mägi, Reedik; Esko, Tõnu; Alexander, Myriam; Waterworth, Dawn; Loomis, A. Katrina; Vilo, Jaak (2019). “An exploratory phenome wide association study linking asthma and liver disease genetic variants to electronic health records from the Estonian Biobank.” PLOS ONE, 14 (4), https://doi.org/10.1371/journal.pone.0215026
  9. Liivlaid, Hedi; Eigo, Natalja; Reisberg, Sulev (2019). “Eriarstiabi haigestumusstatistika võrdlus Tervise Arengu Instituudi ja Eesti Haigekassa andmetel” “Comparing specialist care morbidity statistics on two datasets: National Institute for Health Development and Estonian Health Insurance Fund”. Eesti Arst, 1, 17−26. https://www.etis.ee/File/DownloadPublic/bf25c14a-5232-4337-ae6a-bae4c7fb5a42?name=EA1901lk17-26.pdf&type=application%2Fpdf
  10. Jon Ison, Hervé Ménager, Bryan Brancotte, Erik Jaaniso, Ahto Salumets, Tomáš Raček, Anna-Lena Lamprecht, Magnus Palmblad, Matúš Kalaš, Piotr Chmura, John M Hancock, Veit Schwämmle, Hans-Ioan Ienasescu “Community curation of bioinformatics software and data resources” Briefing in Bioinformatics https://doi.org/10.1093/bib/bbz075
  11. Tamara Knific, Dmytro Fishman, Andrej Vogler, Manuela Gstöttner, Rene Wenzl, Hedi Peterson, and Tea Lanisnik Rizner,  “Multiplex analysis of 40 cytokines do not allow separation between endometriosis patients and controls”. Sci Rep 9, 16738 (2019) doi:10.1038/s41598-019-52899-8
  12. Eleonora Porcu, Sina Rüeger, Kaido Lepik, eQTLGen Consortium, BIOS Consortium, Federico A. Santoni, Alexandre Reymond, and Zoltán Kutalik. “Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits.” Nature Communications (2019). https://doi.org/10.1038/s41467-019-10936-0
  13. Subhankar Mukhopadhyay, Eva Heinz, Immacolata Porreca, Kaur Alasoo, Amy Yeung, Huei-Ting Yang, Tobias Schwerd, Jessica L. Forbester, Christine Hale, Chukwuma A. Agu, Yoon Ha Choi, Julia Rodrigues, Melania Capitani, Luke Jostins-Dean, David C. Thomas , Simon Travis, Daniel Gaffney, William C. Skarnes, Nicholas Thomson, Holm H. Uhlig, Gordon Dougan, Fiona Powrie. “Loss of IL-10 signaling in macrophages limits bacterial killing driven by prostaglandin E2.” J Exp Med (2019). https://doi.org/10.1084/jem.20180649

2018

  1.  Kerli Mooses, Marek Oja, Sulev Reisberg, Jaak Vilo and Merike Kull. Validating Fitbit Zip for monitoring physical activity of children in school: a cross-sectional study. BMC public health, 18(1), 858. https://doi.org/10.1186/s12889-018-5752-7
  2. Vijayachitra Modhukur, Tatjana Iljasenko, Tauno Metsalu, Kaie Lokk, Triin Laisk-Podar, and Jaak Vilo. “MethSurv: a web tool to perform multivariable survival analysis using DNA methylation data.” Epigenomics 10, no. 3 (2018): 277-288. DOI: 10.2217/epi-2017-0118
  3. Sadam, Helle, Arno Pihlak, Anri Kivil, Susan Pihelgas, Mariliis Jaago, Priit Adler, Jaak Vilo et al. “Prostaglandin D2 Receptor DP1 Antibodies Predict Vaccine-induced and Spontaneous Narcolepsy Type 1: Large-scale Study of Antibody Profiling.” EBioMedicine 29 (2018): 47-59.
  4. Reisberg, Sulev, Kristi Krebs, Mart Kals, Reedik Magi, Kristjan Metsalu, Volker M. Lauschke, Jaak Vilo, and Lili Milani. “Translating genotype data of 44,000 biobank participants into clinical pharmacogenetic recommendations: challenges and solutions.” bioRxiv (2018): 356204.
  5. Moeller Steffen, Nadine Saul, Alan A. Cohen, Ruediger Koehling, Sina Sender,
    Hugo Murua Escobar, Christian Junghanss, Francesca Cirulli, Alessandra Berry,
    Peter Antal, Priit Adler, Jaak Vilo, Michele Boiani, Ludger Jansen,
    Stephan Struckmann, Israel Barrantes, Mohamed Hamed, Walter Luyten,
    Georg Fuellen “Healthspan pathway maps in C. elegans and humans highlight transcription, proliferation/biosynthesis and lipids.” bioRxiv (2018): 355131.
  6. Alasoo, Kaur, Julia Rodrigues, Subhankar Mukhopadhyay, Andrew J. Knights, Alice L. Mann, Kousik Kundu, Christine Hale, Gordon Dougan, and Daniel J. Gaffney. “Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response.” Nature genetics 50, no. 3 (2018): 424.
  7. Madrigal, Pedro, and Kaur Alasoo. “AP-1 Takes Centre Stage in Enhancer Chromatin Dynamics.” Trends in cell biology 28, no. 7 (2018): 509-511.
  8. Schwartzentruber, Jeremy, Stefanie Foskolou, Helena Kilpinen, Julia Rodrigues, Kaur Alasoo, Andrew J. Knights, Minal Patel et al. “Molecular and functional variation in iPSC-derived sensory neurons.” Nature genetics 50, no. 1 (2018): 54.
  9. Liis Kolberg, Ivan Kuzmin, Priit Adler, Jaak Vilo, Hedi Peterson “funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data” BMC Genomics (2018) https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5176-x

2017

  1. Ottas, Aigar; Fishman, Dmytro; Okas, Tiia-Linda; Püssa, Tõnu; Toomik, Peeter; Märtson, Aare; Kingo, Külli; Soomets, Ursel. Blood serum metabolome of atopic dermatitis: Altered energy cycle and the markers of systemic inflammation. PLOS one. Nov 27, 2017 doi: https://doi.org/10.1371/journal.pone.0188580
  2. Jones, William; Alasoo, Kaur; Fishman, Dmytro; Parts, Leopold. Computational Biology – Deep Learning. Emerging Topics in Life Sciences. Nov 14, 2017 doi: 10.1042/ETLS20160025
  3. Kukushkina V, Modhukur V , Suhorutshenko M, Peters M, Mägi R, Rahmioglu N, Velthut-Meikas A, Altmäe S, Francisco J. Esteban, Vilo J, Zondervan K, Salumets A, Laisk-Podar T. DNA methylation changes in endometrium and correlation with gene expression during the transition from pre-receptive to receptive phase. Scientific Reports. 2017 June 20. doi: 10.1038/s41598-017-03682-0
  4. Rekker K, Saare, M, Eriste E, Tasa T, Kukuškina V, Roost AM, Anderson K, Samuel K, Karro H, Salumets A, Peters M. High-throughput mRNA sequencing of stromal cells from endometriomas and endometrium. Reproduction. 2017 May 17.
    doi: 10.1530/REP-17-0092
  5. Guha M, Saare M, Maslovskaja J, Kisand K, Liiv I, Haljasorg U, Tasa TMetspalu A, Milani L, Peterson P. DNA breaks and chromatin structural changes enhance the transcription of autoimmune regulator target genes. Journal of Biological Chemistry. 2017 Apr 21;292:6542-6554.
    doi: 10.1074/jbc.M116.764704
  6. Dmytro Fishman, Kai Kisand, Christina Hertel, Mike Rothe, Anu Remm, Maire Pihlap, Priit Adler, Jaak Vilo, Aleksandr Peet, Antonella Meloni, Tadej Battelino, Katarina Trebusak, Øyvind Bruserud, Anette SB Wolff, Eystein Husebye, Nicolas Kluger, Kai Krohn, Annamari Ranki, Hedi Peterson, Adrian Hayday, Pärt Peterson. Autoantibody repertoire in APECED patients targets two distinct subgroups of proteins Frontiers in Immunology 16 August 2017
    https://doi.org/10.3389/fimmu.2017.00976
  7. Liisi Šahmatova, Elena Sügis, Marina Šunina, Helen Hermann, Ele Prans, Maire Pihlap, Kristi Abram, Ana Rebane, Hedi Peterson, Pärt Peterson, Külli Kingo, Kai Kisand. Signs of innate immune activation and premature immunosenescence in psoriasis patients Scientific Reports2017; 7: 7553.
    https://dx.doi.org/10.1038%2Fs41598-017-07975-2
  8. Sulev Reisberg, Tatjana Iljasenko, Kristi Läll, Krista Fischer, Jaak Vilo. Comparing distributions of polygenic risk scores of type 2 diabetes and coronary heart disease within different populationsPloS One e0179238.
    https://doi.org/10.1371/journal.pone.0179238
  9. Aigar Ottas, Dmytro Fishman, Tiia-Linda Okas, Külli Kingo, Ursel Soomets. The metabolic analysis of psoriasis identifies the associated metabolites while providing computational models for the monitoring of the disease Archives of Dermatological Research
    https://link.springer.com/article/10.1007/s00403-017-1760-1
  10. Kaido Lepik, Tarmo Annilo, Viktorija Kukuškina, eQTLGen Consortium , Kai Kisand, Zoltán Kutalik , Pärt Peterson, Hedi Peterson C-reactive protein upregulates the whole blood expression of CD59 – an integrative analysis PLOS Computational Biologyhttp://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005766

2016

  1. Padari H, Oselin K, Tasa T, Metsvaht T, Lõivukene K, Lutsar I. Coagulase negative staphylococcal sepsis in neonates: do we need to adapt vancomycin dose or target?. BMC pediatrics. 2016 Dec 8;16(1):206.
    doi: 10.1186/s12887-016-0753-0
  2. Hallik M, Tasa T, Starkopf J, Metsvaht T. Dosing of Milrinone in Preterm Neonates to Prevent Postligation Cardiac Syndrome: Simulation Study Suggests Need for Bolus Infusion. Neonatology. 2016 Aug 5;111(1):8-11.
    doi:10.1159/000447049
  3. Tamme K, Oselin K, Kipper K, Tasa T, Metsvaht T, Karjagin J, Herodes K, Kern H, Starkopf J. Pharmacokinetics and pharmacodynamics of piperacillin/tazobactam during high volume haemodiafiltration in patients with septic shock. Acta Anaesthesiologica Scandinavica. 2016 Feb 1;60(2):230-40.
    doi:10.1111/aas.12629
  4. Raivo Kolde; Kaspar Märtens; Kaie Lokk; Sven Laur; Jaak Vilo: seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data. Bioinformatics 2016;
    doi:10.1093/bioinformatics/btw304
  5. P Peterson, L Tserel, R Kolde, M Limbach, K Tretyakov, S Kasela, K Kisand, M Saare, J Vilo, A Metspalu, L Milani: Age-related profiling of DNA methylation in CD8+ T cells reveals changes in immune response and transcriptional regulator genes. European Journal of Immunology46, 879-879
  6. Pappu P, Chandrasekharan M, Modhukur V , Nallapeta, S, Suravajhala, P. (2016) Next Generation Sequencing Analysis of Lung Cancer Datasets: A Functional Genomics Perspective. Indian Journal of Cancer , 53 (1), 1−7. Jan-Mar;53(1):1-7. doi: 10.4103/0019-509X.180832
  7. Jüri Reimand, Tambet Arak, Priit Adler, Liis Kolberg, Sulev Reisberg, Hedi Peterson, and Jaak Vilo: g:Profiler—a web server for functional interpretation of gene lists (2016 update) Nucl. Acids Res. first published online April 20, 2016 doi:10.1093/nar/gkw199
  8. Sflomos G, Dormoy V, Metsalu T, Jeitziner R, Battista L, Scabia V, Raffoul W, Delaloye JF, Treboux A, Fiche M, Vilo J, Ayyanan A, Brisken C.: A Preclinical Model for ERα-Positive Breast Cancer Points to the Epithelial Microenvironment as Determinant of Luminal Phenotype and Hormone Response. Cancer Cell. 2016 Mar 14;29(3):407-22. doi:10.1016/j.ccell.2016.02.002. Epub 2016 Mar 3.
    PMID: 26947176
  9. Saare M, Modhukur V , Suhorutshenko M, Rajasekar B , Rekker K, Sõritsa D, Karro H, Soplepmann P, Sõritsa A, Lindgren CM, Rahmioglu N, Drong A, Becker CM, Zondervan KT, Salumets A, Peters M. (2016) The influence of menstrual cycle and endometriosis on endometrial methylome. Clinical Epigenetics ,2Jan 12;8:2. doi: 10.1186/s13148-015-0168-z. eCollection 2016
  10. Steffen Meyer; Martin Woodward; Christina Hertel; Philip Vlaicu; Yasmin Haque; Jaanika Kärner; Annalisa Macagno; Shimobi C Onuoha; Dmytro Fishman; Hedi Peterson; Kaja Metsküla; Raivo Uibo; Kirsi Jäntti; Kati Hokynar; Anette SB Wolff; Kai Krohn; Annamari Ranki; Pärt Peterson; Kai Kisand; Adrian Hayday: AIRE-Deficient Patients Harbor Unique High-Affinity Disease-Ameliorating Autoantibodies Cell 2016;
    doi:http://dx.doi.org/10.1016/j.cell.2016.06.024
  11. Ruani N Fernando, Umesh Chaudhari, Sylvia E Escher, Jan G Hengstler, Jürgen Hescheler, Paul Jennings, Hector C Keun, Jos CS Kleinjans, Raivo Kolde, Laxmikanth Kollipara, Annette Kopp-Schneider, Alice Limonciel, Harshal Nemade, Filomain Nguemo, Hedi Peterson, Pilar Prieto, Robim M Rodrigues, Agapios Sachinidis, Christoph Schäfer, Albert Sickmann, Dimitry Spitkovsky, Regina Stöber, Simone GJ van Breda, Bob van de Water, Manon Vivier, René P Zahedi, Mathieu Vinken, Vera Rogiers: “Watching the Detectives” report of the general assembly of the EU project DETECTIVE Brussels, 24–25 November 2015 Archives of toxicology 2016; doi:10.1007/s00204-016-1719-6
  12. Signe Altmäea, Karin Tamm-Rosenstein, Francisco J. Esteban, Jaak Simm, Liis Kolberg, Hedi Peterson, Madis Metsis, Kai Haldre, José A. Horcajadas, Andres Salumets, Anneli Stavreus-Evers: Endometrial transcriptome analysis indicates superiority of natural over artificial cycles in recurrent implantation failure patients undergoing frozen embryo transferReproductive BioMedicine Onlinedoi:10.1016/j.rbmo.2016.03.004

2015

  1. Örd, T., Örd, D., Adler, P., Vilo, J., & Örd, T. (2015). TRIB3 enhances cell viability during glucose deprivation in HEK293-derived cells by upregulating IGFBP2, a novel nutrient deficiency survival factor. Biochimica et Biophysica Acta (BBA)-Molecular Cell Research, 1853(10), 2492-2505
  2. Liina Tserel, Raivo Kolde, Maia Limbach, Konstantin Tretyakov, Silva Kasela, Kai Kisand, Mario Saare, Jaak Vilo, Andres Metspalu, Lili Milani, Pärt Peterson: Age-related profiling of DNA methylation in CD8+ T cells reveals changes in immune response and transcriptional regulator genes. Scientific Reports. 2015 Aug 19;5:13107.
    doi:10.1038/srep13107
  3. Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S. (2015) Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research, gkv1116
  4. Lees, J. G., Hériché, J.-K., Morilla, I., Fernández, J. M., Adler, P., Krallinger, M., Vilo J., Valencia A., Ellenberg J., Ranea J. A., & Orengo C. (2015). FUN-L: Gene prioritization for RNAi screens. Bioinformatics, btv073.
  5. R Kolde, J Vilo: GOsummaries: an R Package for Visual Functional Annotation of Experimental Data F1000Research, 2015, 4:574,doi:10.12688/f1000research.6925.1
  6. Metsalu, Tauno and Vilo, Jaak. ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap. Nucleic Acids Research Advance Access published May 12, 2015, doi:10.1093/nar/gkv468
  7. Dreser, N., Zimmer, B., Dietz, C., Sügis, E., Pallocca, G., Nyffeler, J., Meisig, J., Blüthgen, N., Berthold, M.R., Waldmann, T. and Leist, M., 2015. Grouping of histone deacetylase inhibitors and other toxicants disturbing neural crest migration by transcriptional profiling. Neurotoxicology, 50, pp.56-70, https://doi.org/10.1016/j.neuro.2015.07.008

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
  6. Saare, M.; Rekker, K.; Laisk-Podar, T.; Sõritsa, D.; Roost, AM.; Simm, J.; Velthut-Meikas, A.; Samuel, K.; Metsalu, T.; Karro, H.; Sõritsa, A.; Salumets, A.; Peters, M. (2014). High-Throughput Sequencing Approach Uncovers the miRNome of Peritoneal Endometriotic Lesions and Adjacent Healthy Tissues. PLoS ONE, 9(11), e112630
  7. Metsalu, Tauno; Viltrop, Triin; Tiirats, Airi; Rajashekar, Balaji; Reimann, Ene; Kõks, Sulev; Rull, Kristiina; Milani, Lili; Acharya, Ganesh; Basnet, Purusotam; Vilo, Jaak; Mägi, Reedik; Metspalu, Andres; Peters, Maire; Haller-Kikkatalo, Kadri; Salumets, Andres (2014). Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta. Epigenetics, 9(10), 1397 – 1409.
  8. Hériché, J.-K., Lees, J. G., Morilla, I., Walter, T., Petrova, B., Roberti, M. J., Hossain M. J., Adler P., Fernández J. M., Krallinger M., Haering C. H., Vilo J., Valencia A., Ranea J. A., Orengo C., & Ellenberg J. (2014). Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation. Molecular Biology of the Cell, 25(16), 2522–2536.

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. 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]
  3. 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]
  4. 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 Biology2010, 11:R80
    doi:10.1186/gb-2010-11-8-r80 [Abstract] [PubMed] [PDF]
  5. 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]
  6. 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]
  7. 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
  8. 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]
  9. 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.
  10. 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]
  11. 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]
  12. 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]
  13. 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: https://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: https://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.