See veebileht kasutab küpsiseid kasutaja sessiooni andmete hoidmiseks. Veebilehe kasutamisega nõustute ETISe kasutustingimustega. Loe rohkem
Olen nõus

Hedi Peterson

https://www.etis.ee/CV/Hedi_Peterson/est
www.twitter.com/hedipeterson
hedi.peterson@ut.ee
F-4920-2017

Teenistuskäik

Töökohad ja ametid
01.01.2022–...   
Tartu Ülikool, Loodus- ja täppisteaduste valdkond, arvutiteaduse instituut, bioinformaatika professor (1,00)
01.01.2021–31.12.2021   
Tartu Ülikool, Loodus- ja täppisteaduste valdkond, arvutiteaduse instituut, bioinformaatika kaasprofessor (1,00)
01.01.2017–31.12.2020   
Tartu Ülikool, Loodus- ja täppisteaduste valdkond, arvutiteaduse instituut, bioinformaatika vanemteadur (1,00)
02.03.2016–31.12.2016   
Tartu Ülikool, Loodus- ja täppisteaduste valdkond, arvutiteaduse instituut, bioinformaatika teadur (0,80)
01.01.2016–01.03.2016   
Tartu Ülikool, Loodus- ja täppisteaduste valdkond, arvutiteaduse instituut, bioinformaatika teadur (0,80)
01.11.2015–31.12.2015   
Tartu Ülikool, Matemaatika-informaatikateaduskond, Arvutiteaduse instituut, bioinformaatika teadur (0,80)
01.09.2015–31.10.2015   
Tartu Ülikool, Matemaatika-informaatikateaduskond, Arvutiteaduse instituut, bioinformaatika teadur (1,00)
01.01.2014–31.08.2015   
Tartu Ülikool, Matemaatika-informaatikateaduskond, Arvutiteaduse instituut, bioinformaatika teadur (1,00)
01.01.2014–30.04.2020   
Quretec OÜ, Quretec, juhtivteadur (0,30)
01.07.2011–30.11.2013   
Genfi Ülikool, Genfi Ülikool, järeldoktor (1,00)
2007–2011   
OÜ Quretec, Teadur (1,00)
2006–2006   
Eesti Biokeskus, Erakorraline teadur (0,10)
01.01.2006–31.12.2007   
Egeen, teadur
2005–2005   
Eesti Biokeskus, programmeerija (0,10)
 
 
Haridustee
2006–2015   
Tartu Ülikool, bioinformaatika PhD
2005–2006   
Uppsala Ülikool, bioinformaatika M.Sc, vahetusüliõpilane
2004–2006   
Tartu Ülikool, bioinformaatika M.Sc
2000–2004   
Tartu Ülikool, bioinformaatika B.Sc
 
 
Teadusorganisatsiooniline ja -administratiivne tegevus
2021−...   
LUMI EuroHPC pre-exascale superarvuti teadusnõukoja liige (Eesti esindaja)
2021−...   
ETAG-i Euroopa Liidu partnerluse töörühma „Digilahendused igas eluvaldkonnas“ liige
2020−...   
EMBL-EBI "Bioinformatics Summer School" kaas-korraldaja
2020−...   
ELIXIR Belgia teadusnõukogu liige
2018−...   
ELIXIRi Recommended Interoperable Resources taotluste ja Node Services hindaja
2016−...   
Euroopa Komisjon, Horizon 2020 ja Horizon Europe teaduse- ja innovatsiooni programmi granditaotluste ekspert
2005−...   
SOCBIN
2020−2021   
NeIC PARI Reference Group liige
2018−2020   
Tryggve Reference Group liige
 
 
Lisainfo
Available in English

Kvalifikatsioon

Teaduskraadid
Hedi Peterson, doktorikraad, 2015, (juh) Jaak Vilo; Juhan Sedman, Exploiting high-throughput data for establishing relationships between genes (Suuremahuliste andmete kasutamine geenidevaheliste seoste leidmiseks), Tartu Ülikool, Loodus- ja tehnoloogiateaduskond, Tartu Ülikooli Molekulaar- ja Rakubioloogia Instituut.
Hedi Peterson, magistrikraad (teaduskraad), 2006, (juh) Jaak Vilo, The discovery and characterization of regulatory motifs in Saccharomyces cerevisiae, Tartu Ülikool, Bioloogia-geograafiateaduskond, Molekulaar- ja rakubioloogia instituut.
 
 
Teaduspreemiad ja tunnustused
2021, Hedi Peterson, Tartu Ülikooli aumärk
2017, Hedi Peterson, Researcher of the year 2017, Institute of Computer Science, University of Tartu
2010, Hedi Peterson, Haridus- ja Teadusminsiteeriumi tänukiri: Kaur Alasoo konkursitöö „Tugivektormasinate kombineerimine angiogeneesiga seotud geenide ennustamiseks” juhendamise eest loodusteaduste ja tehnika valdkonnas (I preemia)
2006, Hedi Peterson, Gertrud Thelins stipendium Tartu Ülikooli tudengitele õpinguteks Uppsala Ülikoolis, 2006/2007 õppeaasta kevadsemester
2005, Hedi Peterson, Human Research Potential & the Socio-economic Knowledge Base: Access to Research Infrastructures (ARI), 09.03-10.04.2005 Uppsala
2005, Hedi Peterson, Kristjan-Jaagu tasemeõppe stipendium, 2005/06 õppeaasta Uppsala Ülikoolis
2004, Hedi Peterson, Eesti olümpiakomitee kõrghariduse stipendium tippsportlastele, 2004/2005-2005/2006
 
 
Teadustöö põhisuunad
ETIS VALDKOND: 4. Loodusteadused ja tehnika; 4.6. Arvutiteadused; CERCS VALDKOND: P170 Arvutiteadus, arvutusmeetodid, süsteemid, juhtimine (automaatjuhtimisteooria)
ETIS VALDKOND: 1. Bio- ja keskkonnateadused; 1.12. Bio- ja keskkonnateadustega seotud uuringud, näiteks biotehnoloogia, molekulaarbioloogia, rakubioloogia, biofüüsika, majandus- ja tehnoloogiauuringud; TÄPSUSTUS: süsteemibioloogia geeniregulatsiooni bioinformaatika, süsteemibioloogia; geeniregulatsiooni bioinformaatika
ETIS VALDKOND: 3. Terviseuuringud; 3.11. Terviseuuringutega seotud uuringud, näiteks biokeemia, geneetika, mikrobioloogia, biotehnoloogia, molekulaarbioloogia, rakubioloogia, biofüüsika ja bioinformaatika; CERCS VALDKOND: B110 Bioinformaatika, meditsiiniinformaatika, biomatemaatika, biomeetrika

Jooksvad projektid

Lõppenud projektid

Juhendamisel väitekirjad

Juhendatud väitekirjad

Publikatsioonid

Klass
Aasta
Publikatsioon
 
1.1.
2021
Laan, Martti; Salumets, Ahto; Klein, Annabel; Reintamm, Kerli; Bichele, Rudolf; Peterson, Hedi; Peterson, Pärt (2021). Post-Aire Medullary Thymic Epithelial Cells and Hassall’s Corpuscles as Inducers of Tonic Pro-Inflammatory Microenvironment. Frontiers in Immunology, 12 (12). DOI: 10.3389/fimmu.2021.635569.
1.1.
2020
Segal, Eran; Zhang, Feng; Lin, Xihong; King, Gary; Shalem, Ophir; Shilo, Smadar; Allen, William E.; Alquaddoomi, Faisal; Altae-Tran, Han; Anders, Simon; Balicer, Ran; Bauman, Tal; Bonilla, Ximena; Booman, Gisel; Chan, Andrew T.; Cohen, Ori; Coletti, Silvano; Davidson, Natalie; Dor, Yuval; Drew, David A. ... Wilmes, Paul (2020). Building an international consortium for tracking coronavirus health status. Nature Medicine, 1−4. DOI: 10.1038/s41591-020-0929-x.
1.1.
2020
Kolberg, Liis; Kerimov, Nurlan; Peterson, Hedi; Alasoo, Kaur (2020). Co-expression analysis reveals interpretable gene modules controlled by trans-acting genetic variants. eLife, 9. DOI: 10.7554/eLife.58705.
1.1.
2020
Fishman, Dmytro; Kuzmin, Ivan; Adler, Priit; Vilo, Jaak; Peterson, Hedi (2020). PAWER: protein array web exploreR. BMC Bioinformatics, 21 (1). DOI: 10.1186/s12859-020-03722-z.
1.1.
2020
Gurwitz, Kim T.; Gaur, Prakash Singh; Bellis, Louisa J.; Larcombe, Lee; Alloza, Eva; Balint, Balint Laszlo; Botzki, Alexander; Dimec, Jure; del Angel, Victoria Dominguez; Fernandes, Pedro L.; Korpelainen, Eija; Krause, Roland; Kuzak, Mateusz; Le Pera, Loredana; Leskosek, Brane; Lindvall, Jessica M.; Marek, Diana; Martinez, Paula A.; Muyldermans, Tuur; Nygard, Stale ... Rustici, Gabriella (2020). A framework to assess the quality and impact of bioinformatics training across ELIXIR. PLoS Computational Biology, 16 (7), ARTN e1007976. DOI: 10.1371/journal.pcbi.1007976.
1.1.
2020
Haljasmägi, Liis; Salumets, Ahto; Rumm, Anna Pauliina; Jürgenson, Meeri; Krassohhina, Ekaterina; Remm, Anu; Sein, Hanna; Kareinen, Lauri; Vapalahti, Olli; Sironen, Tarja; Peterson, Hedi; Milani, Lili; Tamm, Anu; Hayday, Adrian; Kisand, Kai; Peterson, Pärt (2020). Longitudinal proteomic profiling reveals increased early inflammation and sustained apoptosis proteins in severe COVID-19. Scientific Reports, 10 (1), 20533. DOI: 10.1038/s41598-020-77525-w.
1.1.
2020
Kolberg, Liis; Raudvere, Uku; Kuzmin, Ivan; Vilo, Jaak; Peterson, Hedi (2020). gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler. F1000Research, 9, 709. DOI: 10.12688/f1000research.24956.2.
1.1.
2019
Raudvere, Uku; Kolberg, Liis; Kuzmin, Ivan; Arak, Tambet; Adler, Priit; Peterson, Hedi; Vilo, Jaak (2019). g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic Acids Research. DOI: 10.1093/nar/gkz369.
1.1.
2019
Sügis, Elena; Dauvillier, Jerome; Leontjeva, Anna; Adler, Priit; Hindie, Valerie; Moncion, Thomas; Collura, Vincent; Daudin, Rachel; Loe-Mie, Yann; Herault, Yann; Lambert, Jean-Charles; Hermjakob, Henning; Pupko, Tal; Rain, Jean-Christophe; Xenarios, Ioannis; Vilo, Jaak; Simonneau, Michel; Peterson, Hedi (2019). HENA, heterogeneous network-based data set for Alzheimer's disease. Scientific Data, 6, ARTN 151. DOI: 10.1038/s41597-019-0152-0.
1.1.
2019
Ison, Jon; Ienasescu, Hans; Chmura, Piotr; Rydza, Emil; Menager, Herve; Kalas, Matus; Schwammle, Veit; Gruening, Bjoern; Beard, Niall; Lopez, Rodrigo; Duvaud, Severine; Stockinger, Heinz; Persson, Bengt; Varekova, Radka Svobodova; Racek, Tomas; Vondrasek, Jiri; Peterson, Hedi; Salumets, Ahto; Jonassen, Inge; Hooft, Rob ... Brunak, Soren (2019). The bio.tools registry of software tools and data resources for the life sciences. Genome Biology, 20 (1), ARTN 164. DOI: 10.1186/s13059-019-1772-6.
1.1.
2019
Knific, Tamara; Fishman, Dmytro; Vogler, Andrej; Gstöttner, Manuela; Wenzl, René; Peterson, Hedi; Lanišnik Rižner, Tea ; (2019). Multiplex analysis of 40 cytokines do not allow separation between endometriosis patients and controls. Scientific Reports, 9, 16738. DOI: 10.1038/s41598-019-52899-8.
6.7.
2019
Männik, Katrin; Arbogast, Thomas; Lepamets, Maarja; Lepik, Kaido; Pellaz, Anna; Ademi, Herta; Kupchinsky, Zachary A; Ellegood, Jacob; Attanasio, Catia; Messina, Andrea; Rotman, Samuel; Martin-Brevet, Sandra; Dubruc, Estelle; Chrast, Jacqueline; Lerch, Jason P; Qiu, Lily R; Laisk, Triin; The 16p11.2 European Consortium; The Simons VIP Consortium; The eQTLGen Consortium ... Reymond, Alexandre (2019). Leveraging biobank-scale rare and common variant analyses to identify ASPHD1 as the main driver of reproductive traits in the 16p11.2 locus. bioRxiv. DOI: 10.1101/716415.
1.1.
2018
Kolberg, Liis; Kuzmin, Ivan; Adler, Priit; Vilo, Jaak; Peterson, Hedi (2018). funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data. BMC Genomics, 19, ARTN 817. DOI: 10.1186/s12864-018-5176-x.
1.1.
2017
Colaianna, Marilena; Ilmjärv, Sten; Peterson, Hedi; Kern, Ilse; Julien, Stephanie; Baquié, Mathurin; Pallocca, Giorgia; Bosgra, Sieto; Sachinidis, Agapios; Hengstler, Jan G; Leist, Marcel; Krause, Karl-Heinz (2017). Fingerprinting of neurotoxic compounds using a mouse embryonic stem cell dual luminescence reporter assay. Archives of Toxicology, 365−391. DOI: 10.1007/s00204-016-1690-2.
1.1.
2017
Šahmatova, Liisi; Sügis, Elena; Šunina, Marina; Hermann, Helen; Prans, Ele; Pihlap, Maire; Abram, Kristi; Rebane, Ana; Peterson, Hedi; Peterson, Pärt; Kingo, Külli; Kisand, Kai (2017). Signs of innate immune activation and premature immunosenescence in psoriasis patients. Scientific Reports, 7 (1), 7553−7553. DOI: 10.1038/s41598-017-07975-2.
1.1.
2017
Fishman, Dmytro; Kisand, Kai; Hertel, Christina; Rothe, Mike; Remm, Anu; Pihlap, Maire; Adler, Priit; Vilo, Jaak; Peet, Aleksandr; Meloni, Antonella; Podkrajsek, Katarina Trebusak; Battelino, Tadej; Bruserud, Øyvind; Wolff, Anette S B; Husebye, Eystein S; Kluger, Nicolas; Krohn, Kai; Ranki, Annamari; Peterson, Hedi; Hayday, Adrian ... Peterson, Pärt (2017). Autoantibody Repertoire in APECED Patients Targets Two Distinct Subgroups of Proteins. Frontiers in Immunology, 8, 976−976. DOI: 10.3389/fimmu.2017.00976.
1.1.
2017
Lepik, Kaido; Annilo, Tarmo; Kukuškina, Viktorija; eQTLGen Consortium; Kisand, Kai; Kutalik, Zoltán; Peterson, Pärt; Peterson, Hedi (2017). C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis. PLoS Computational Biology, 13 (9), ARTN e1005766. DOI: 10.1371/journal.pcbi.1005766.
1.1.
2017
Hillion, Kenzo-Hugo; Kuzmin, Ivan; Khodak, Anton; Rasche, Eric; Crusoe, Michael; Peterson, Hedi; Ison, Jon; Ménager, Hervé (2017). Using bio.tools to generate and annotate workbench tool descriptions. F1000Research, 6. DOI: 10.12688/f1000research.12974.1.
1.1.
2016
Reimand Jüri; Arak Tambet; Adler Priit; Kolberg Liis; Reisberg Sulev; Peterson Hedi; Vilo Jaak (2016). g:Profiler-a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Research, gkw199. DOI: 10.1093/nar/gkw199.
1.1.
2016
Altmäe, S; Tamm-Rosenstein, K; Esteban, F.J.; Simm, J; Kolberg, L; Peterson, H; Metsis, M; Haldre, K; Horcajadas, J.A.; Salumets, A; Stavreus-Evers, A. (2016). Natural cycle is superior to artificial cycle in endometrial preparation for frozen embryo transfer in women with recurrent implantation failure: endometrial transcriptome analysis. Reproductive BioMedicine Online, x−x [ilmumas].
1.1.
2016
Fernando, Ruani N; Chaudhari, Umesh; Escher, Sylvia E; Hengstler, Jan G; Hescheler, Jürgen; Jennings, Paul; Keun, Hector C; Kleinjans, Jos C S; Kolde, Raivo; Kollipara, Laxmikanth; Kopp-Schneider, Annette; Limonciel, Alice; Nemade, Harshal; Nguemo, Filomain; Peterson, Hedi; Prieto, Pilar; Rodrigues, Robim M; Sachinidis, Agapios; Schäfer, Christoph; Sickmann, Albert ... Rogiers, Vera (2016). "Watching the Detectives" report of the general assembly of the EU project DETECTIVE Brussels, 24-25 November 2015. Archives of Toxicology, 90 (6), 1529−1539. DOI: 10.1007/s00204-016-1719-6.
1.1.
2016
Altmäe, Signe; Tamm-Rosenstein, Karin; Esteban Francisco J.; Simm, Jaak; Kolberg, Liis; Peterson, Hedi; Metsis, Madis; Haldre, Kai; Horcajadas, Jose A.; Salumets, Andres; Stavreus-Evers, Anneli (2016). Endometrial transcriptome analysis indicates superiority of natural over artificial cycles in recurrent implantation failure patients undergoing frozen embryo transfer. Reproductive BioMedicine Online, 32 (6), 597−613. DOI: 10.1016/j.rbmo.2016.03.004.
1.1.
2016
Meyer, Steffen; Woodward, Martin; Hertel, Christina; Vlaicu, Philip; Haque, Yasmin; Kärner, Jaanika; Macagno, Annalisa; Onuoha, Shimobi C; Fishman, Dmytro; Peterson, Hedi; Metsküla, Kaja; Uibo, Raivo; Jäntti, Kirsi; Hokynar, Kati; Wolff, Anette S B; ,; Krohn, Kai; Ranki, Annamari; Peterson, Pärt; Kisand, Kai ... Hayday, Adrian (2016). AIRE-Deficient Patients Harbor Unique High-Affinity Disease-Ameliorating Autoantibodies. Cell, 166 (3), 582−595. DOI: 10.1016/j.cell.2016.06.024.
1.1.
2015
Jon Ison,*, Kristoffer Rapacki, Hervé Ménager, Matúš Kalaš, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael Jimenez, Nick Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Mičetić, Rune Møllegaard Friborg, Sebastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vařeková, Silvio C.E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen Parkinson, Peter Løngreen1 and Søren Brunak (2015). Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research, 44 (D1), D38−D47. DOI: 10.1093/nar/gkv1116.
1.1.
2015
Cosset, É., Martinez, Y., Preynat-Seauve, O., Lobrinus, J.A., Tapparel, C., Cordey, S., Peterson, H., Petty, T.J., Colaianna, M., Tieng, V. and Tirefort, D. (2015). Human three-dimensional engineered neural tissue reveals cellular and molecular events following cytomegalovirus infection. Biomaterials, 296−308. DOI: 10.1016/j.biomaterials.2015.02.094.
1.1.
2013
Peterson, Hedi; Abu Dawud, Raed; Garg, Abishek; Wang, Ying; Vilo, Jaak; Xenarios, Ioannis; Adjaye, James (2013). Qualitative modeling identifies IL-11 as a novel regulator in maintaining self-renewal in human pluripotent stem cells. Frontiers in Physiology, 4 (303), 303.
1.1.
2013
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 ... Sachinidis, A (2013). Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach. Archives of Toxicology, 87 (1), 123−143. DOI: 10.1007/s00204-012-0967-3.
1.1.
2013
Nayernia, Z.; Turchi, L.; Cosset, E.; Peterson, H.; Dutoit, V.; Dietrich, P.; Tirefort, D.; Chneiweiss, H.; Lobrinus, J.; Krause, K-H.; Virolle, T.; Preynat-Seauve, O. (2013). The relationship between brain tumor cell invasion of engineered neural tissues and in vivo features of glioblastoma. Biomaterials, 34 (33), 8279−8290. DOI: 10.1016/j.biomaterials.2013.07.006.
3.5.
2013
Adler, Priit; Peterson, Hedi; Vilo, Jaak (2013). Prioritization of protein-protein interactions associated with Alzheimer’s disease using data mining. Info- ja kommunikatsioonitehnoloogia doktorikooli IKTDK VII aastakonverentsi artiklite kogumik: Info- ja kommunikatsioonitehnoloogia doktorikooli VII aastakonverents 15.-16.11.2013.
3.5.
2012
Nikolaeva, Elena; Peterson, Hedi; Vilo, Jaak (2012). In silico modeling of histone modification dynamics associated with pluripotency in human embryonic stem cells. Bioinformatics Research and Education Workshop 2012; University of Bergen, Bergen, Norway; May 3rd-6th, 2012.
1.1.
2011
Tserel, L.; Runnel, T.; Kisand, K.; Pihlap, M.; Bakhoff, L.; Kolde, R.; Peterson, H.; Vilo, J.; Peterson, P.; Rebane, A. (2011). MicroRNA Expression Profiles of Human Blood Monocyte-derived Dendritic Cells and Macrophages Reveal miR-511 as Putative Positive Regulator of Toll-like Receptor 4. Journal of Biological Chemistry, 286 (30), 26487−26495. DOI: 10.1074/jbc.M110.213561.
3.5.
2011
Nikolaeva, Elena; Peterson, Hedi; Vilo, Jaak (2011). Visualization of ChiP data for ESCD. Bioinformatics Research and Education Workshop 2011; University of Tartu, Tartu, Estonia; May 20-22, 2011.
3.5.
2011
Nikolaeva, Elena; Peterson, Hedi; Vilo, Jaak (2011). Visualization of ChiP data for Embryonic Stem Cell Database. Info- ja kommunikatsioonitehnoloogia doktorikooli IKTDK viienda aastakonverents; Eesti; 25.-26. novembril 2011.
1.1.
2010
Tserel, Liina; Kolde, Raivo; Rebane, Ana; Kisand, Kai; Org, Tõnis; Peterson, Hedi; Vilo, Jaak; Peterson, Pärt (2010). Genome-wide promoter analysis of histone modifications in human monocyte-derived antigen presenting cells. BMC Genomics, 11, 642. DOI: 10.1186/1471-2164-11-642.
1.1.
2010
Billon, Nathalie; Kolde, Raivo; Reimand, Juri; Monteiro, Miguel C; Kull, Meelis; Peterson, Hedi; Tretyakov, Konstantin; Adler, Priit; Wdziekonski, Brigitte; Vilo, Jaak; Dani, Christian (2010). Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development. Genome Biology, 11 (8), R80. DOI: 10.1186/gb-2010-11-8-r80.
1.1.
2010
Jung, Marc; Peterson, Hedi ; Chavez, Lukas; Kahlem, Pascal; Lehrach, Hans ; Vilo, Jaak ; Adjaye, James (2010). A Data Integration Approach to Mapping OCT4 Gene Regulatory Networks Operative in Embryonic Stem Cells and Embryonal Carcinoma Cells. PLoS ONE, 5 (5), e10709. DOI: 10.1371/journal.pone.0010709.
5.1.
2010
Tserel, Liina; Kolde, Raivo; Rebane, Ana; Kisand, Kai; Org, Tonis; Peterson, Hedi; Vilo, Jaak; Peterson, Pärt (2010). Gene Expression and Epigenetic Changes in Differentiation of Human Macrophages and Dendritic Cells. Scandinavian Journal of Immunology, 71 (6), 526−526.
5.1.
2010
Rebane, Ana; Tserel, Liina; Kisand, Kai; Backhoff, Lairi; Runnel, Toomas; Kolde, Raivo; Peterson, Hedi; Vilo, Jaak; Peterson, Pärt (2010). Balanced Expression of miRNA-S Secures Differentiation and Maturation of Human Blood Monocyte Derived Dendritic Cells. Scandinavian Journal of Immunology, 71 (6), 512−513.
1.1.
2009
Adler, P.; Kolde, R.; Kull, M.; Tkachenko, A.; Peterson, H.; Reimand, J.; Vilo, J. (2009). Mining for coexpression across hundreds of datasets using novel rank aggregation and visualisation methods. Genome Biology, 10 (12), R139. DOI: 10.1186/gb-2009-10-12-r139.
1.1.
2009
Krushevskaya, D.; Peterson, H.; Reimand, J.; Kull, M.; Vilo, J. (2009). VisHiC—hierarchical functional enrichment analysis of microarray data. Nucleic Acids Research, 37, W587−W592. DOI: 10.1093/nar/gkp435.
3.1.
2009
Adler, P.; Peterson, H.; Agius, P.; Reimand, J.; Vilo, J. (2009). Ranking genes by their co-expression to subsets of pathway members. In: Annals of the New York Academy of Sciences (1−13). . Oxford: Blackwell Publishing. (Challenges of Systems Biology: Community Effort to Harness Biological Complexity). DOI: 10.1111/j.1749-6632.2008.03747.x.
1.1.
2008
Reimand, J. ; Tooming, L. ; Peterson, H.; Adler, P.; Vilo, J. (2008). GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. Nucleic Acids Research, 36, W452−W459. DOI: 10.1093/nar/gkn230.
1.1.
2008
Adler, P.; Reimand, J.; Jänes, J.; Kolde, R.; Peterson, H.; Vilo, J. (2008). KEGGanim: pathway animations for high-throughput data. Bioinformatics, 24 (4), 588−590. DOI: 10.1093/bioinformatics/btm581.
1.1.
2007
Reimand, J.; Kull, M.; Peterson, H.; Hansen, J., Vilo, J. (2007). g:Profiler – a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Research, 35, W193−W200. DOI: 10.1093/nar/gkm226.
3.5.
2007
Pavlidis, P.; Uri, J.; Kuzmitshov, I.; Peterson, H.; Vilo, J. (2007). Incremental use of homologies to infer cis-regulatory motifs in gene clusters. Info- ja kommunikatsioonitehnoloogia doktorikooli IKTDK teise aastakonverentsi artiklite kogumik : 11.-12. mai 2007, Viinistu Kunstimuuseum. , 121−124.
10.06.2022

Hedi Peterson

https://www.etis.ee/CV/Hedi_Peterson/eng
www.twitter.com/hedipeterson
hedi.peterson@ut.ee
F-4920-2017

Career

Institutions and positions
01.01.2022–...   
University of Tartu, Faculty of Science and Technology, Institute of Computer Science, Professor of Bioinformatics (1,00)
01.01.2021–31.12.2021   
University of Tartu, Faculty of Science and Technology, Institute of Computer Science, Associate Professor of Bioinformatics (1,00)
01.01.2017–31.12.2020   
University of Tartu, Faculty of Science and Technology, Institute of Computer Science, Senior Researcher (1,00)
02.03.2016–31.12.2016   
University of Tartu, Faculty of Science and Technology, Institute of Computer Science, Research Fellow of Bioinformatics (0,80)
01.01.2016–01.03.2016   
University of Tartu, Faculty of Science and Technology, Institute of Computer Science, Research Fellow of Bioinformatics (0,80)
01.11.2015–31.12.2015   
University of Tartu, Faculty of Mathematics and Computer Science, Institute of Computer Science, Research Fellow of Bioinformatics (0,80)
01.09.2015–31.10.2015   
University of Tartu, Faculty of Mathematics and Computer Science, Institute of Computer Science, Research Fellow of Bioinformatics (1,00)
01.01.2014–31.08.2015   
University of Tartu, Faculty of Mathematics and Computer Science, Institute of Computer Science, Research Fellow of Bioinformatics (1,00)
01.01.2014–30.04.2020   
Quretec OÜ, Quretec, Lead researcher (0,30)
01.07.2011–30.11.2013   
Genfi Ülikool, University of Geneva, Postdoctoral researcher (1,00)
2007–2011   
Quretec Ltd, Researcher (1,00)
2006–2006   
Estonian Biocentre, Extraordinary Researcher (0,10)
01.01.2006–31.12.2007   
Egeen, scientist
2005–2005   
Estonian Biocentre, Other staff (0,10)
 
 
Education
2006–2015   
University of Tartu, PhD bioinformatics
2005–2006   
University of Uppsala, M.Sc bioinformatics
2004–2006   
University of Tartu, M.Sc bioinformatics
2000–2004   
University of Tartu, B.Sc bioinformatics
 
 
R&D related managerial and administrative work
2021−...   
LUMI EuroHPC pre-exascale super computer Scientific Advisory Board member (Estonian representative)
2021−...   
Estonian Research Council European Union partnership workgroup "Digital solutions for every walk of life" member
2020−...   
Co-organiser of "Bioinformatics Summer School" at EMBL-EBI
2020−...   
Member of ELIXIR Belgium Scientific Advisory Board
2018−...   
Evaluator for ELIXIR Recommended Interoperable Resources and Node Services
2016−...   
European Commission, Horizon 2020 and Horizon Europe research and innovation program; expert-evaluator
2005−...   
SOCBIN
2020−2021   
Member of NeIC PARI Reference Group
2018−2020   
Member of Tryggve Reference Group
 
 
Additional information
Teaching activities:

1. Lecturing bioinformatics in “Bioinformatics for bioengineering" course, University of Tartu, 2017/2018, 2018/2019, 2019/2020
2. ELIXIR-Estonia course “Web-based tools to analyse and interpret high-throughput biological data”,
Institute Pasteur, France 18.10.2016
3. ELIXIR-Estonia course “Web-based tools to analyse and interpret high-throughput biological data”,
University of Oxford, UK, 12.01.2016
4. ELIXIR Linux Command Line course, Tartu, 15.05.2015
5. ELIXIR g:Profiler course, Tartu, 05.12.2014
6. Lectures of Bioinformatics course, Tartu, autumnt 2010
7. BIIT service workshop City of Hope, USA, 23.11.2010
8. EMBO Practical course for microarray analysis, Hinxton, UK 20.10.2010
9. EMBO Practical course for microarray analysis, Hinxton, UK 15.10.2009
10. 9th BioSapiens European Bioinformatics School, Brussels, Belgium 30.01.2009
11. EBI Roadshow 2009, Tartu 07.-10.09.2009 (main local organiser)
12. ENFIN-EMBRACE workshop, Helsinki, Finland 06.10.2009

Undergraduate supervising activities:
1. Joanna Niklus, bachelor thesis "Modern bioinformatics methods in Alzheimer's disease research” (2017)
2. Andreas Ellervee, bachelor thesis “Automatic detection of intermediate genes responsible for signal mediation from high-throughput data” (2015)
3. Henry Mägi, bachelor thesis “RNA-seq pipeline” (2014)
4. Kaur Alasoo, bachelor thesis „Combining Support Vector Machines to Predict Novel Angiogenesis Genes“ (2010) (The thesis got the First prizes from the Estonian Ministry of Education and Science from the Estonian Academy of Sciences in 2010)
5. Priidik Vaikla, bachelor thesis „Project management system by the example of BIIT scientific group“ (2008)
6. Sten Ilmjärv, bachelor thesis„Describing transcription start sites in Saccharomyces cerevisiae“ (2007)
7. Marten Teino, bachelor thesis „Scientific literature database for a research group“ (2007)

Qualifications

Academic degrees
Hedi Peterson, Doctor's Degree, 2015, (sup) Jaak Vilo; Juhan Sedman, Exploiting high-throughput data for establishing relationships between genes, University of Tartu, Faculty of Science and Technology (old), Institute of Molecular and Cell Biology, University of Tartu.
Hedi Peterson, Research Master's Degree, 2006, (sup) Jaak Vilo, The discovery and characterization of regulatory motifs in Saccharomyces cerevisiae (The discovery and characterization of regulatory motifs in Saccharomyces cerevisiae), University of Tartu, Faculty of Biology and Geography, Institute of Molecular and Cell Biology.
 
 
Honours & awards
2021, Hedi Peterson, University of Tartu Badge of Distinction
2017, Hedi Peterson, Researcher of the year 2017, Institute of Computer Science, University of Tartu
2010, Hedi Peterson, Minister of Science and Education: letter of thanks for successful supervision of Kaur Alasoo's bachelor thesis " Combining Support Vector Machines to Predict Novel Angiogenesis Genes" in Natural Sciences and Engineering (1st prize)
2006, Hedi Peterson, Gertrud Thelin's scholarship for University of Tartu students for studing at University of Uppsala, spring semester 2006/2007
2005, Hedi Peterson, Human Research Potential & the Socio-economic Knowledge Base: Access to Research Infrastructures (ARI), 09.03-10.04.2005 Uppsala
2005, Hedi Peterson, Kristjan-Jaak fellowship for studying at the University of Uppsala, 2005/06 academic year
2004, Hedi Peterson, Estonian Olympic Committee scholarship for Higher Education studies for National Level athletes, 2004/2005-2005/2006
 
 
Fields of research
ETIS RESEARCH FIELD: 4. Natural Sciences and Engineering; 4.6. Computer Sciences; CERCS RESEARCH FIELD: P170 Computer science, numerical analysis, systems, control
ETIS RESEARCH FIELD: 1. Biosciences and Environment; 1.12. Biotechnology, Molecular Biology, Cell Biology, Biophysics and Economic and Technological Research relating to Bio- and Environmental Sciences; SPECIFICATION: systems biology, bioinformatics of gene regulation
ETIS RESEARCH FIELD: 3. Health; 3.11. Biochemistry, Genetics, Microbiology, Biotechnology, Molecular Biology, Cell Biology, Biophysics and Bioinformatics relating to Health Studies; CERCS RESEARCH FIELD: B110 Bioinformatics, medical informatics, biomathematics, biometrics
 
 

Projects in progress

Completed projects

Dissertations under supervision

Supervised dissertations

Publications

Category
Year
Publication
 
1.1.
2021
Laan, Martti; Salumets, Ahto; Klein, Annabel; Reintamm, Kerli; Bichele, Rudolf; Peterson, Hedi; Peterson, Pärt (2021). Post-Aire Medullary Thymic Epithelial Cells and Hassall’s Corpuscles as Inducers of Tonic Pro-Inflammatory Microenvironment. Frontiers in Immunology, 12 (12). DOI: 10.3389/fimmu.2021.635569.
1.1.
2020
Segal, Eran; Zhang, Feng; Lin, Xihong; King, Gary; Shalem, Ophir; Shilo, Smadar; Allen, William E.; Alquaddoomi, Faisal; Altae-Tran, Han; Anders, Simon; Balicer, Ran; Bauman, Tal; Bonilla, Ximena; Booman, Gisel; Chan, Andrew T.; Cohen, Ori; Coletti, Silvano; Davidson, Natalie; Dor, Yuval; Drew, David A. ... Wilmes, Paul (2020). Building an international consortium for tracking coronavirus health status. Nature Medicine, 1−4. DOI: 10.1038/s41591-020-0929-x.
1.1.
2020
Kolberg, Liis; Kerimov, Nurlan; Peterson, Hedi; Alasoo, Kaur (2020). Co-expression analysis reveals interpretable gene modules controlled by trans-acting genetic variants. eLife, 9. DOI: 10.7554/eLife.58705.
1.1.
2020
Fishman, Dmytro; Kuzmin, Ivan; Adler, Priit; Vilo, Jaak; Peterson, Hedi (2020). PAWER: protein array web exploreR. BMC Bioinformatics, 21 (1). DOI: 10.1186/s12859-020-03722-z.
1.1.
2020
Gurwitz, Kim T.; Gaur, Prakash Singh; Bellis, Louisa J.; Larcombe, Lee; Alloza, Eva; Balint, Balint Laszlo; Botzki, Alexander; Dimec, Jure; del Angel, Victoria Dominguez; Fernandes, Pedro L.; Korpelainen, Eija; Krause, Roland; Kuzak, Mateusz; Le Pera, Loredana; Leskosek, Brane; Lindvall, Jessica M.; Marek, Diana; Martinez, Paula A.; Muyldermans, Tuur; Nygard, Stale ... Rustici, Gabriella (2020). A framework to assess the quality and impact of bioinformatics training across ELIXIR. PLoS Computational Biology, 16 (7), ARTN e1007976. DOI: 10.1371/journal.pcbi.1007976.
1.1.
2020
Haljasmägi, Liis; Salumets, Ahto; Rumm, Anna Pauliina; Jürgenson, Meeri; Krassohhina, Ekaterina; Remm, Anu; Sein, Hanna; Kareinen, Lauri; Vapalahti, Olli; Sironen, Tarja; Peterson, Hedi; Milani, Lili; Tamm, Anu; Hayday, Adrian; Kisand, Kai; Peterson, Pärt (2020). Longitudinal proteomic profiling reveals increased early inflammation and sustained apoptosis proteins in severe COVID-19. Scientific Reports, 10 (1), 20533. DOI: 10.1038/s41598-020-77525-w.
1.1.
2020
Kolberg, Liis; Raudvere, Uku; Kuzmin, Ivan; Vilo, Jaak; Peterson, Hedi (2020). gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler. F1000Research, 9, 709. DOI: 10.12688/f1000research.24956.2.
1.1.
2019
Raudvere, Uku; Kolberg, Liis; Kuzmin, Ivan; Arak, Tambet; Adler, Priit; Peterson, Hedi; Vilo, Jaak (2019). g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic Acids Research. DOI: 10.1093/nar/gkz369.
1.1.
2019
Sügis, Elena; Dauvillier, Jerome; Leontjeva, Anna; Adler, Priit; Hindie, Valerie; Moncion, Thomas; Collura, Vincent; Daudin, Rachel; Loe-Mie, Yann; Herault, Yann; Lambert, Jean-Charles; Hermjakob, Henning; Pupko, Tal; Rain, Jean-Christophe; Xenarios, Ioannis; Vilo, Jaak; Simonneau, Michel; Peterson, Hedi (2019). HENA, heterogeneous network-based data set for Alzheimer's disease. Scientific Data, 6, ARTN 151. DOI: 10.1038/s41597-019-0152-0.
1.1.
2019
Ison, Jon; Ienasescu, Hans; Chmura, Piotr; Rydza, Emil; Menager, Herve; Kalas, Matus; Schwammle, Veit; Gruening, Bjoern; Beard, Niall; Lopez, Rodrigo; Duvaud, Severine; Stockinger, Heinz; Persson, Bengt; Varekova, Radka Svobodova; Racek, Tomas; Vondrasek, Jiri; Peterson, Hedi; Salumets, Ahto; Jonassen, Inge; Hooft, Rob ... Brunak, Soren (2019). The bio.tools registry of software tools and data resources for the life sciences. Genome Biology, 20 (1), ARTN 164. DOI: 10.1186/s13059-019-1772-6.
1.1.
2019
Knific, Tamara; Fishman, Dmytro; Vogler, Andrej; Gstöttner, Manuela; Wenzl, René; Peterson, Hedi; Lanišnik Rižner, Tea ; (2019). Multiplex analysis of 40 cytokines do not allow separation between endometriosis patients and controls. Scientific Reports, 9, 16738. DOI: 10.1038/s41598-019-52899-8.
6.7.
2019
Männik, Katrin; Arbogast, Thomas; Lepamets, Maarja; Lepik, Kaido; Pellaz, Anna; Ademi, Herta; Kupchinsky, Zachary A; Ellegood, Jacob; Attanasio, Catia; Messina, Andrea; Rotman, Samuel; Martin-Brevet, Sandra; Dubruc, Estelle; Chrast, Jacqueline; Lerch, Jason P; Qiu, Lily R; Laisk, Triin; The 16p11.2 European Consortium; The Simons VIP Consortium; The eQTLGen Consortium ... Reymond, Alexandre (2019). Leveraging biobank-scale rare and common variant analyses to identify ASPHD1 as the main driver of reproductive traits in the 16p11.2 locus. bioRxiv. DOI: 10.1101/716415.
1.1.
2018
Kolberg, Liis; Kuzmin, Ivan; Adler, Priit; Vilo, Jaak; Peterson, Hedi (2018). funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data. BMC Genomics, 19, ARTN 817. DOI: 10.1186/s12864-018-5176-x.
1.1.
2017
Colaianna, Marilena; Ilmjärv, Sten; Peterson, Hedi; Kern, Ilse; Julien, Stephanie; Baquié, Mathurin; Pallocca, Giorgia; Bosgra, Sieto; Sachinidis, Agapios; Hengstler, Jan G; Leist, Marcel; Krause, Karl-Heinz (2017). Fingerprinting of neurotoxic compounds using a mouse embryonic stem cell dual luminescence reporter assay. Archives of Toxicology, 365−391. DOI: 10.1007/s00204-016-1690-2.
1.1.
2017
Šahmatova, Liisi; Sügis, Elena; Šunina, Marina; Hermann, Helen; Prans, Ele; Pihlap, Maire; Abram, Kristi; Rebane, Ana; Peterson, Hedi; Peterson, Pärt; Kingo, Külli; Kisand, Kai (2017). Signs of innate immune activation and premature immunosenescence in psoriasis patients. Scientific Reports, 7 (1), 7553−7553. DOI: 10.1038/s41598-017-07975-2.
1.1.
2017
Fishman, Dmytro; Kisand, Kai; Hertel, Christina; Rothe, Mike; Remm, Anu; Pihlap, Maire; Adler, Priit; Vilo, Jaak; Peet, Aleksandr; Meloni, Antonella; Podkrajsek, Katarina Trebusak; Battelino, Tadej; Bruserud, Øyvind; Wolff, Anette S B; Husebye, Eystein S; Kluger, Nicolas; Krohn, Kai; Ranki, Annamari; Peterson, Hedi; Hayday, Adrian ... Peterson, Pärt (2017). Autoantibody Repertoire in APECED Patients Targets Two Distinct Subgroups of Proteins. Frontiers in Immunology, 8, 976−976. DOI: 10.3389/fimmu.2017.00976.
1.1.
2017
Lepik, Kaido; Annilo, Tarmo; Kukuškina, Viktorija; eQTLGen Consortium; Kisand, Kai; Kutalik, Zoltán; Peterson, Pärt; Peterson, Hedi (2017). C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis. PLoS Computational Biology, 13 (9), ARTN e1005766. DOI: 10.1371/journal.pcbi.1005766.
1.1.
2017
Hillion, Kenzo-Hugo; Kuzmin, Ivan; Khodak, Anton; Rasche, Eric; Crusoe, Michael; Peterson, Hedi; Ison, Jon; Ménager, Hervé (2017). Using bio.tools to generate and annotate workbench tool descriptions. F1000Research, 6. DOI: 10.12688/f1000research.12974.1.
1.1.
2016
Reimand Jüri; Arak Tambet; Adler Priit; Kolberg Liis; Reisberg Sulev; Peterson Hedi; Vilo Jaak (2016). g:Profiler-a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Research, gkw199. DOI: 10.1093/nar/gkw199.
1.1.
2016
Altmäe, S; Tamm-Rosenstein, K; Esteban, F.J.; Simm, J; Kolberg, L; Peterson, H; Metsis, M; Haldre, K; Horcajadas, J.A.; Salumets, A; Stavreus-Evers, A. (2016). Natural cycle is superior to artificial cycle in endometrial preparation for frozen embryo transfer in women with recurrent implantation failure: endometrial transcriptome analysis. Reproductive BioMedicine Online, x−x [forthcoming].
1.1.
2016
Fernando, Ruani N; Chaudhari, Umesh; Escher, Sylvia E; Hengstler, Jan G; Hescheler, Jürgen; Jennings, Paul; Keun, Hector C; Kleinjans, Jos C S; Kolde, Raivo; Kollipara, Laxmikanth; Kopp-Schneider, Annette; Limonciel, Alice; Nemade, Harshal; Nguemo, Filomain; Peterson, Hedi; Prieto, Pilar; Rodrigues, Robim M; Sachinidis, Agapios; Schäfer, Christoph; Sickmann, Albert ... Rogiers, Vera (2016). "Watching the Detectives" report of the general assembly of the EU project DETECTIVE Brussels, 24-25 November 2015. Archives of Toxicology, 90 (6), 1529−1539. DOI: 10.1007/s00204-016-1719-6.
1.1.
2016
Altmäe, Signe; Tamm-Rosenstein, Karin; Esteban Francisco J.; Simm, Jaak; Kolberg, Liis; Peterson, Hedi; Metsis, Madis; Haldre, Kai; Horcajadas, Jose A.; Salumets, Andres; Stavreus-Evers, Anneli (2016). Endometrial transcriptome analysis indicates superiority of natural over artificial cycles in recurrent implantation failure patients undergoing frozen embryo transfer. Reproductive BioMedicine Online, 32 (6), 597−613. DOI: 10.1016/j.rbmo.2016.03.004.
1.1.
2016
Meyer, Steffen; Woodward, Martin; Hertel, Christina; Vlaicu, Philip; Haque, Yasmin; Kärner, Jaanika; Macagno, Annalisa; Onuoha, Shimobi C; Fishman, Dmytro; Peterson, Hedi; Metsküla, Kaja; Uibo, Raivo; Jäntti, Kirsi; Hokynar, Kati; Wolff, Anette S B; ,; Krohn, Kai; Ranki, Annamari; Peterson, Pärt; Kisand, Kai ... Hayday, Adrian (2016). AIRE-Deficient Patients Harbor Unique High-Affinity Disease-Ameliorating Autoantibodies. Cell, 166 (3), 582−595. DOI: 10.1016/j.cell.2016.06.024.
1.1.
2015
Jon Ison,*, Kristoffer Rapacki, Hervé Ménager, Matúš Kalaš, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael Jimenez, Nick Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Mičetić, Rune Møllegaard Friborg, Sebastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vařeková, Silvio C.E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen Parkinson, Peter Løngreen1 and Søren Brunak (2015). Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research, 44 (D1), D38−D47. DOI: 10.1093/nar/gkv1116.
1.1.
2015
Cosset, É., Martinez, Y., Preynat-Seauve, O., Lobrinus, J.A., Tapparel, C., Cordey, S., Peterson, H., Petty, T.J., Colaianna, M., Tieng, V. and Tirefort, D. (2015). Human three-dimensional engineered neural tissue reveals cellular and molecular events following cytomegalovirus infection. Biomaterials, 296−308. DOI: 10.1016/j.biomaterials.2015.02.094.
1.1.
2013
Peterson, Hedi; Abu Dawud, Raed; Garg, Abishek; Wang, Ying; Vilo, Jaak; Xenarios, Ioannis; Adjaye, James (2013). Qualitative modeling identifies IL-11 as a novel regulator in maintaining self-renewal in human pluripotent stem cells. Frontiers in Physiology, 4 (303), 303.
1.1.
2013
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 ... Sachinidis, A (2013). Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach. Archives of Toxicology, 87 (1), 123−143. DOI: 10.1007/s00204-012-0967-3.
1.1.
2013
Nayernia, Z.; Turchi, L.; Cosset, E.; Peterson, H.; Dutoit, V.; Dietrich, P.; Tirefort, D.; Chneiweiss, H.; Lobrinus, J.; Krause, K-H.; Virolle, T.; Preynat-Seauve, O. (2013). The relationship between brain tumor cell invasion of engineered neural tissues and in vivo features of glioblastoma. Biomaterials, 34 (33), 8279−8290. DOI: 10.1016/j.biomaterials.2013.07.006.
3.5.
2013
Adler, Priit; Peterson, Hedi; Vilo, Jaak (2013). Prioritization of protein-protein interactions associated with Alzheimer’s disease using data mining. Info- ja kommunikatsioonitehnoloogia doktorikooli IKTDK VII aastakonverentsi artiklite kogumik: Info- ja kommunikatsioonitehnoloogia doktorikooli VII aastakonverents 15.-16.11.2013.
3.5.
2012
Nikolaeva, Elena; Peterson, Hedi; Vilo, Jaak (2012). In silico modeling of histone modification dynamics associated with pluripotency in human embryonic stem cells. Bioinformatics Research and Education Workshop 2012; University of Bergen, Bergen, Norway; May 3rd-6th, 2012.
1.1.
2011
Tserel, L.; Runnel, T.; Kisand, K.; Pihlap, M.; Bakhoff, L.; Kolde, R.; Peterson, H.; Vilo, J.; Peterson, P.; Rebane, A. (2011). MicroRNA Expression Profiles of Human Blood Monocyte-derived Dendritic Cells and Macrophages Reveal miR-511 as Putative Positive Regulator of Toll-like Receptor 4. Journal of Biological Chemistry, 286 (30), 26487−26495. DOI: 10.1074/jbc.M110.213561.
3.5.
2011
Nikolaeva, Elena; Peterson, Hedi; Vilo, Jaak (2011). Visualization of ChiP data for ESCD. Bioinformatics Research and Education Workshop 2011; University of Tartu, Tartu, Estonia; May 20-22, 2011.
3.5.
2011
Nikolaeva, Elena; Peterson, Hedi; Vilo, Jaak (2011). Visualization of ChiP data for Embryonic Stem Cell Database. Info- ja kommunikatsioonitehnoloogia doktorikooli IKTDK viienda aastakonverents; Eesti; 25.-26. novembril 2011.
1.1.
2010
Tserel, Liina; Kolde, Raivo; Rebane, Ana; Kisand, Kai; Org, Tõnis; Peterson, Hedi; Vilo, Jaak; Peterson, Pärt (2010). Genome-wide promoter analysis of histone modifications in human monocyte-derived antigen presenting cells. BMC Genomics, 11, 642. DOI: 10.1186/1471-2164-11-642.
1.1.
2010
Billon, Nathalie; Kolde, Raivo; Reimand, Juri; Monteiro, Miguel C; Kull, Meelis; Peterson, Hedi; Tretyakov, Konstantin; Adler, Priit; Wdziekonski, Brigitte; Vilo, Jaak; Dani, Christian (2010). Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development. Genome Biology, 11 (8), R80. DOI: 10.1186/gb-2010-11-8-r80.
1.1.
2010
Jung, Marc; Peterson, Hedi ; Chavez, Lukas; Kahlem, Pascal; Lehrach, Hans ; Vilo, Jaak ; Adjaye, James (2010). A Data Integration Approach to Mapping OCT4 Gene Regulatory Networks Operative in Embryonic Stem Cells and Embryonal Carcinoma Cells. PLoS ONE, 5 (5), e10709. DOI: 10.1371/journal.pone.0010709.
5.1.
2010
Tserel, Liina; Kolde, Raivo; Rebane, Ana; Kisand, Kai; Org, Tonis; Peterson, Hedi; Vilo, Jaak; Peterson, Pärt (2010). Gene Expression and Epigenetic Changes in Differentiation of Human Macrophages and Dendritic Cells. Scandinavian Journal of Immunology, 71 (6), 526−526.
5.1.
2010
Rebane, Ana; Tserel, Liina; Kisand, Kai; Backhoff, Lairi; Runnel, Toomas; Kolde, Raivo; Peterson, Hedi; Vilo, Jaak; Peterson, Pärt (2010). Balanced Expression of miRNA-S Secures Differentiation and Maturation of Human Blood Monocyte Derived Dendritic Cells. Scandinavian Journal of Immunology, 71 (6), 512−513.
1.1.
2009
Adler, P.; Kolde, R.; Kull, M.; Tkachenko, A.; Peterson, H.; Reimand, J.; Vilo, J. (2009). Mining for coexpression across hundreds of datasets using novel rank aggregation and visualisation methods. Genome Biology, 10 (12), R139. DOI: 10.1186/gb-2009-10-12-r139.
1.1.
2009
Krushevskaya, D.; Peterson, H.; Reimand, J.; Kull, M.; Vilo, J. (2009). VisHiC—hierarchical functional enrichment analysis of microarray data. Nucleic Acids Research, 37, W587−W592. DOI: 10.1093/nar/gkp435.
3.1.
2009
Adler, P.; Peterson, H.; Agius, P.; Reimand, J.; Vilo, J. (2009). Ranking genes by their co-expression to subsets of pathway members. In: Annals of the New York Academy of Sciences (1−13). . Oxford: Blackwell Publishing. (Challenges of Systems Biology: Community Effort to Harness Biological Complexity). DOI: 10.1111/j.1749-6632.2008.03747.x.
1.1.
2008
Reimand, J. ; Tooming, L. ; Peterson, H.; Adler, P.; Vilo, J. (2008). GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. Nucleic Acids Research, 36, W452−W459. DOI: 10.1093/nar/gkn230.
1.1.
2008
Adler, P.; Reimand, J.; Jänes, J.; Kolde, R.; Peterson, H.; Vilo, J. (2008). KEGGanim: pathway animations for high-throughput data. Bioinformatics, 24 (4), 588−590. DOI: 10.1093/bioinformatics/btm581.
1.1.
2007
Reimand, J.; Kull, M.; Peterson, H.; Hansen, J., Vilo, J. (2007). g:Profiler – a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Research, 35, W193−W200. DOI: 10.1093/nar/gkm226.
3.5.
2007
Pavlidis, P.; Uri, J.; Kuzmitshov, I.; Peterson, H.; Vilo, J. (2007). Incremental use of homologies to infer cis-regulatory motifs in gene clusters. Info- ja kommunikatsioonitehnoloogia doktorikooli IKTDK teise aastakonverentsi artiklite kogumik : 11.-12. mai 2007, Viinistu Kunstimuuseum. , 121−124.
10.06.2022