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

Raivo Kolde

https://etis.ee/CV/Raivo_Kolde/est
21.04.1983
5067961
rkolde@gmail.com

Teenistuskäik

Töökohad ja ametid
01.01.2021–...   
Tartu Ülikool, Loodus- ja täppisteaduste valdkond, arvutiteaduse instituut, terviseinformaatika kaasprofessor (1,00)
01.08.2019–...   
Tartu Ülikool, Terviseinformaatika (1,00)
09.01.2017–18.06.2019   
Philips Research North America, Teadur (1,00)
01.08.2014–08.01.2017   
Harvard Medical School, Järeldoktor (1,00)
01.08.2013–31.07.2014   
Tartu Ülikool, Matemaatika-informaatikateaduskond, Arvutiteaduse instituut, bioinformaatika teadur (1,00)
01.07.2012–31.07.2013   
Tartu Ülikool, Matemaatika-informaatikateaduskond, Arvutiteaduse instituut, programmeerija (0,20)
29.08.2008–08.09.2009   
Tartu Ülikool, Matemaatika-informaatikateaduskond, Arvutiteaduse instituut, erakorraline teadur (0,50)
2007–31.07.2014   
OÜ Quretec, Teadur (1,00)
01.01.2006–31.12.2007   
AS Egeen bioinformaatik
 
 
Haridustee
2009–2014   
Tartu Ülikool, Informaatika, PhD
2005–2008   
Tartu Ülikool, Matemaatiline statistika, Msc
2001–2005   
Tartu Ülikool, Matemaatiline statistika, Bsc
 
 
Teadusorganisatsiooniline ja -administratiivne tegevus
2007−...   
ISCB

Kvalifikatsioon

Teaduskraadid
Raivo Kolde, doktorikraad, 2014, (juh) Jaak Vilo, Methods for re-using public gene expression data (Meetodid avalike geeniekspressiooni andmete taaskasutamiseks), Tartu Ülikool, Matemaatika-informaatikateaduskond, Arvutiteaduse instituut.
Raivo Kolde, magistrikraad (teaduskraad), 2008, (juh) Jaak Vilo; Sven Laur; Jüri Lember, Co-expression queries across multiple experiments (Ko-ekspressiooni päringud üle mitmete eksperimentide), Tartu Ülikool, Matemaatika-informaatikateaduskond.
 
 
Teadustöö põhisuunad
ETIS KLASSIFIKAATOR: 4. Loodusteadused ja tehnika; 4.5. Statistika; TÄPSUSTUS: Bioinformaatika, geeniekspressiooniandmete analüüs

Lõppenud projektid

Juhendatud väitekirjad

Publikatsioonid

Klass
Aasta
Publikatsioon
 
1.1.
2019
Vatanen, Tommi; Plichta, Damian R; Somani, Juhi; Münch, Philipp C; Arthur, Timothy D; Hall, Andrew Brantley; Rudolf, Sabine; Oakeley, Edward J; Ke, Xiaobo; Young, Rachel A; Haiser, Henry J; Kolde, Raivo; Yassour, Moran; Luopajärvi, Kristiina; Siljander, Heli; Virtanen, Suvi M; Ilonen, Jorma; Uibo, Raivo; Tillmann, Vallo; Mokurov, Sergei ... Xavier, Ramnik J (2019). Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life. Nature Microbiology, 4 (3), 470−479. DOI: 10.1038/s41564-018-0321-5.
1.1.
2019
Ward, Doyle V.; Hoss, Andrew G.; Kolde, Raivo; van Aggelen, Helen C.; Loving, Joshua; Smith, Stephen A.; Mack, Deborah A.; Kathirvel, Raja; Halperin, Jeffery A.; Buell, Douglas J.; Wong, Brian E.; Ashworth, Judy L.; Fortunato-Habib, Mary M.; Xu, Liyi; Barton, Bruce A.; Lazar, Peter; Carmona, Juan J.; Mathew, Jomol; Salgo, Ivan S.; Gross, Brian D. ... Ellison, Richard T., III (2019). Integration of genomic and clinical data augments surveillance of healthcare-acquired infections. Infection Control and Hospital Epidemiology, 40 (6), 649−655. DOI: 10.1017/ice.2019.75.
1.1.
2019
van Aggelen, Helen; Kolde, Raivo; Chamarthi, Hareesh; Loving, Joshua; Fan, Yu; Fallon, John T., III; Huang, Weihua; Wang, Guiqing; Fortunato-Habib, Mary M.; Carmona, Juan J.; Gross, Brian D. (2019). A core genome approach that enables prospective and dynamic monitoring of infectious outbreaks. Scientific Reports, 9, ARTN 7808. DOI: 10.1038/s41598-019-44189-0.
1.1.
2018
Graham, Daniel B.; Jasso, Guadalupe J.; Mok, Amanda; Goel, Gautam; Ng, Aylwin C. Y.; Kolde, Raivo; Varma, Mukund; Doench, John G.; Root, David E.; Clish, Clary B.; Carr, Steven A.; Xavier, Ramnik J. (2018). Nitric Oxide Engages an Anti-inflammatory Feedback Loop Mediated by Peroxiredoxin 5 in Phagocytes. Cell Reports, 24 (4), 838−850.10.1016/j.celrep.2018.06.081.
1.1.
2018
Kolde, Raivo; Franzosa, Eric A.; Rahnavard, Gholamali; Hall, Andrew Brantley; Vlamakis, Hera; Stevens, Christine; Daly, Mark J.; Xavier, Ramnik J.; Huttenhower, Curtis (2018). Host genetic variation and its microbiome interactions within the Human Microbiome Project. Genome Medicine, 10, ARTN 6.10.1186/s13073-018-0515-8.
6.8.
2018
Lai, Peggy S.; Kolde, Raivo; Franzosa, Eric A.; Gaffin, Jonathan M.; Baxi, Sachin N.; Sheehan, William J.; Gold, Diane R.; Gevers, Dirk; Xavier, Ramnik J.; Phipatanakul, Wanda (2018). The classroom microbiome and asthma morbidity in children attending 3 inner-city schools. The Journal of Allergy and Clinical Immunology, 141 (6), 2311−2313. DOI: 10.1016/j.jaci.2018.02.022.
1.1.
2017
Johannessen, Liv; Sundberg, Thomas B.; O'Connell, Daniel J.; Kolde, Raivo; Berstler, James; Billings, Katelyn J.; Khor, Bernard; Seashore-Ludlow, Brinton; Fassl, Anne; Russell, Caitlin N.; Latorre, Isabel J.; Jiang, Baishan; Graham, Daniel B.; Perez, Jose R.; Sicinski, Piotr; Phillips, Andrew J.; Schreiber, Stuart L.; Gray, Nathanael S.; Shamji, Alykhan F.; Xavier, Ramnik J. (2017). Small-molecule studies identify CDK8 as a regulator of IL-10 in myeloid cells. Nature Chemical Biology, 13 (10), 1102−1111.10.1038/NCHEMBIO.2458.
1.1.
2017
Wlodarska, Marta; Luo, Chengwei; Kolde, Raivo; d'Hennezel, Eva; Annand, John W.; Heim, Cortney E.; Krastel, Philipp; Schmitt, Esther K.; Omar, Abdifatah S.; Creasey, Elizabeth A.; Garner, Ashley L.; Mohammadi, Sina; O'Connell, Daniel J.; Abubucker, Sahar; Arthur, Timothy D.; Franzosa, Eric A.; Huttenhower, Curtis; Murphy, Leon O.; Haiser, Henry J.; Vlamakis, Hera ... Xavier, Ramnik J. (2017). Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation. Cell Host & Microbe, 22 (1), 25−44.10.1016/j.chom.2017.06.007.
1.1.
2017
Zhao, Qing; Harbour, Stacey N.; Kolde, Raivo; Latorre, Isabel J.; Tun, Hein M.; Schoeb, Trenton R.; Turner, Henrietta; Moon, James J.; Khafipour, Ehsan; Xavier, Ramnik J.; Weaver, Casey T.; Elson, Charles O. (2017). Selective Induction of Homeostatic Th17 Cells in the Murine Intestine by Cholera Toxin Interacting with the Microbiota. The Journal of Immunology, 199 (1), 312−322. DOI: 10.4049/jimmunol.1700171.
6.8.
2017
Lokk, Kaie; Vooder, Tonu; Kolde, Raivo; Valk, Kristjan; Vosa, Urmo; Roosipuu, Retlav; Milani, Lili; Fischer, Krista; Koltsina, Marina; Urgard, Egon; Annilo, Tarmo; Metspalu, Andres; Tonisson, Neeme (2017). Methylation Markers of Early-Stage Non-Small Cell Lung Cancer (vol 7, e39813, 2012). PLoS ONE, 1, ARTN e0170833. DOI: 10.1371/journal.pone.0170833.
1.1.
2016
Pettai, Kristi; Milani, Lili; Tammiste, Anu; Võsa, Urmo; Kolde, Raivo; Eller, Triin; Nutt, David; Metspalu, Andres; Maron, Eduard (2016). Whole-genome expression analysis reveals genes associated with treatment response to escitalopram in major depression. European Neuropsychopharmacology, 26 (9), 1475−1483. DOI: 10.1016/j.euroneuro.2016.06.007.
1.1.
2016
Kolde, R; Märtens, K; Lokk, K; Laur, S; Vilo, J (2016). seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data. Bioinformatics, btw304. DOI: 10.1093/bioinformatics/btw304.
1.1.
2016
O'Connell, Daniel J.; Kolde, Raivo; Sooknah, Matthew; Graham, Daniel B.; Sundberg, Thomas B.; Latorre, Isabel J.; Mikkelsen, Tarjei S.; Xavier, Ramnik J. (2016). Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing. Cell Systems, 2 (5), 323−334.10.1016/j.cels.2016.04.011.
1.1.
2016
Desch, A. Nicole; Gibbings, Sophie L.; Goyal, Rajni; Kolde, Raivo; Bednarek, Joe; Bruno, Tullia; Slansky, Jill E.; Jacobelli, Jordan; Mason, Robert; Ito, Yoko; Messier, Elise; Randolph, Gwendalyn J.; Prabagar, Miglena; Atif, Shaikh M.; Segura, Elodie; Xavier, Ramnik J.; Bratton, Donna L.; Janssen, William J.; Henson, Peter M.; Jakubzick, Claudia V. (2016). Flow Cytometric Analysis of Mononuclear Phagocytes in Nondiseased Human Lung and Lung-Draining Lymph Nodes. American Journal of Respiratory and Critical Care Medicine, 193 (6), 614−626.10.1164/rccm.201507-1376OC.
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
Vatanen, T.; Kostic, A. D.; d'Hennezel, E.; Siljander, H.; Franzosa, E. A.; Yassour, M.; Kolde, R.; Vlamakis, H.; Arthur, T. D.; Hamalainen, A. M.; Peet, A.; Tillmann, V.; Uibo, R.; Mokurov, S.; Dorshakova, N.; Ilonen, J.; Virtanen, S. M.; Szabo, S. J.; Porter, J. A.; Lahdesmaki, H. ... Xavier, R. J. (2016). Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Cell, 165, 842-53−853. DOI: 10.1016/j.cell.2016.04.007.
5.1.
2016
Peterson, P.; Tserel, L.; Kolde, R.; Limbach, M.; Tretyakov, K.; Kasela, S.; Kisand, K.; Saare, M.; Vilo, J.; Metspalu, A.; Milani, L. (2016). Age-related profiling of DNA methylation in CD8+T cells reveals changes in immune response and transcriptional regulator genes. European Journal of Immunology, 879−879.
1.1.
2015
Kolde, Raivo; Vilo, Jaak (2015). GOsummaries: an R Package for Visual Functional Annotation of Experimental Data. F1000Research, 4 (574), 1. DOI: 10.12688/f1000research.6925.1.
1.1.
2015
Tserel, Liina; Kolde, Raivo; Limbach, Maia; Tretyakov, Konstantin; Kasela, Silva; Kisand, Kai; Saare, Mario; Vilo, Jaak; Metspalu, Andres; Milani, Lili; Peterson, Pärt (2015). Age-related profiling of DNA methylation in CD8+ T cells reveals changes in immune response and transcriptional regulator genes. Scientific Reports, 5 (13107), 1−11. DOI: 10.1038/srep13107.
1.1.
2014
Waldmann, Tanja; Rempel, Eugen; Balmer, Nina V; König, Andre; Kolde, Raivo; Gaspar, John Antonydas; Henry, Margit; Hescheler, Jürgen; Sachinidis, Agapios; Rahnenführer, Jörg; Hengstler, Jan G; Leist, Marcel (2014). Design principles of concentration-dependent transcriptome deviations in drug-exposed differentiating stem cells. Chemical Research in Toxicology, 27 (3), 408−420.10.1021/tx400402j.
1.1.
2014
Lokk, Kaie; Modhukur, Vijayachitra; Rajashekar, Balaji; Märtens, Kaspar; Mägi, Reedik; Kolde, Raivo; Koltšina, Marina; Nilsson, Torbjörn K.; Vilo, Jaak; Salumets, Andres; Tõnisson, Neeme (2014). DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns. Genome Biology, 15 (4), R54. DOI: 10.1186/gb-2014-15-4-r54.
1.1.
2014
Ilmjärv, Sten; Hundahl, Christian Ansgar; Reimets, Riin; Niitsoo, Margus; Kolde, Raivo; Vilo, Jaak; Vasar, Eero; Luuk, Hendrik (2014). Estimating differential expression from multiple indicators. Nucleic Acids Research, 42 (8), e72. DOI: 10.1093/nar/gku158.
3.1.
2014
Võsa, Urmo; Kolde, Raivo; Vilo, Jaak; Metspalu, Andres; Tarmo, Annilo (2014). Comprehensive meta-analysis of microRNA expression using a robust rank aggregation approach. In: M. Lucrecia Alvarez, MS, PhD (Ed.). Structural and functional RNA mapping (361−373). . Springer. (Methods in Molecular Biology; 1182). DOI: 10.1007/978-1-4939-1062-5_28.
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.
5.2.
2013
Tõnisson, N.; Lokk, K; Modhukur, V.; Rajashekar, B; Martens, K; Koltšina, M; Mägi, R.; Kolde, R.; Salumets, A. (2013). DNA metylome comparison of various human tissues. European Journal of Human Genetics: European Human Genetics Conference; Pariis, Prantsusmaa; 8.–11. juuni, 2013. Nature Publishing Group, 373−373. (21; Suppl 2).
1.1.
2012
Gaspar, John Antonydas; Doss, Michael Xavier; Winkler, Johannes; Wagh, Vilas; Hescheler, Jürgen; Kolde, Raivo; Vilo, Jaak; Schulz, Herbert; Sachinidis, Agapios (2012). Gene expression signatures defining fundamental biological processes in pluripotent, early, and late differentiated embryonic stem cells. Stem Cells and Development, 21 (13), 2471−2484. DOI: 10.1089/scd.2011.0637.
1.1.
2012
Võsa, U; Vooder, T; Kolde, R; Vilo, J; Metspalu, A; Annilo, T (2012). Meta-analysis of microRNA expression in lung cancer. International Journal of Cancer, 132 (12), 2884−2893. DOI: 10.1002/ijc.27981.
1.1.
2012
Lokk, Kaie; Vooder, Tõnu; Kolde, Raivo; Välk, Kristjan; Võsa, Urmo; Roosipuu, Retlav; Milani, Lili; Fischer, Krista; Koltšina, Marina; Urgard, Egon; Annilo, Tarmo; Metspalu, Andres; Tõnisson, Neeme (2012). Methylation Markers of Early-Stage Non-Small Cell Lung Cancer. PLoS ONE, 7 (6), e39813− . DOI: 10.1371/journal.pone.0039813.
1.1.
2012
Kolde, Raivo; Laur, Sven ; Adler, Priit ; Vilo, Jaak (2012). Robust Rank Aggregation for gene list integration and meta-analysis. Bioinformatics, 28 (4), 573−580. DOI: 10.1093/bioinformatics/btr709.
5.2.
2012
Tõnisson, N.; Lokk, K.; Vooder, T.; Kolde, R.; Välk, K.; Roosipuu, R.; Võsa, U.; Milani, L.; Fischer, K.; Koltšina, M.; Urgard, E.; Annilo, T.; Metspalu, A. (2012). Altered DNA methylation in early-stage non-small-cell lung cancer. European Journal of Human Genetics: European Human Genetics Conference; Nürnberg, Saksamaa; 23.–26. juuni, 2012. Nature Publishing Group, 174−174. (20; Suppl 1).
1.1.
2011
Chen, Y; Jorgensen, M; Kolde, R; Zhao, X; Parker, B; Valen, E; Wen, J; Sandelin, A (2011). Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data. BMC Genomics, 12, 544. DOI: 10.1186/1471-2164-12-544.
1.1.
2011
Võsa, Urmo; Vooder, Tõnu; Kolde, Raivo; Fischer, Krista; Välk, Kristjan; Tõnisson, Neeme; Roosipuu, Retlav; Vilo, Jaak; Metspalu, Andres; Annilo, Tarmo (2011). Identification of miR-374a as a prognostic marker for survival in patients with early-stage nonsmall cell lung cancer. Genes Chromosomes and Cancer, 50 (10), 812−822. DOI: 10.1002/gcc.20902.
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.
5.1.
2011
Peters, Maire; Altmäe, Signe; Reimand, Jüri; Laisk, Triin; Saare, Merli; Hovatta, Outti; Kolde, Raivo; Vilo, Jaak; Stavreus-Evers, Anneli; Salumets, Andres. (2011). Human embryo-endometrium interactions at the time of implantation. 26: 27th Annual Meeting of the European Society of Human Reproduction and Embryology, 3-6 juuli, Stockholm, Rootsi. Oxford University Press, 216−216. (1).
5.1.
2011
Valk, K.; Vooder, T.; Kolde, R.; Roosipuu, R.; Vilo, J.; Metspalu, A. (2011). GENE EXPRESSION-BASED APPROACHES IN DIFFERENTIATION OF METASTASES AND SECOND PRIMARY TUMOUR. 6. , s1055−s1056.
5.2.
2011
Välk, K.; Vooder, T.; Kolde, R.; Roosipuu, R.; Vilo, J.; Metspalu, A. (2011). Whole genome gene expression profiling of two control and three subsequent lung cancer samples of the same patient. World Conference on Lung Cancer, Amsterdam, 2011.
5.2.
2011
Kirotar, K.; Vooder, T., Kolde R.; Välk, K.; Solovjova, M.; Roosipuu, R.; Annilo, T.; Metspalu, A.; Tõnisson, N. (2011). Genome-wide methylation profiling of non-small cell lung cancer. European Journal of Human Genetics, Suppl 2: European Human Genetics Conference; Amsterdam, Holland; 28.–31. mai, 2011. Nature Publishing Group, 378−378. (19).
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
Välk, Kristjan; Vooder, Tõnu; Kolde, Raivo; Reintam, Mari-Ann; Petzold, Cathleen; Vilo, Jaak; Metspalu, Andres (2010). Gene Expression Profiles of Non-Small Cell Lung Cancer: Survival Prediction and New Biomarkers. Oncology, 79, 283−292. DOI: 10.1159/000322116.
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
Doss, Michael Xavier ; Wagh, Vilas ; Schulz, Herbert ; Kull, Meelis ; Kolde, Raivo ; Pfannkuche, Kurt ; Nolden, Tobias ; Himmelbauer, Heinz; Vilo, Jaak ; Hescheler, Jürgen ; Sachinidis, Agapios (2010). Global transcriptomic analysis of murine embryonic stem cell-derived brachyury+ (T) cells. Genes to Cells, 15 (3), 209−228. DOI: 10.1111/j.1365-2443.2010.01390.x.
1.1.
2010
Maron, E.; Kallassalu, K.; Tammiste, A.; Kolde, R.; Vilo, J.; Tõru, I.; Vasar, V.; Shlik, J.; Metspalu, A. (2010). Peripheral Gene Expression Profiling of CCK-4-Induced Panic in Healthy Subjects. American Journal of Medical Genetics Part B Neuropsychiatric Genetics, 153B (1), 269−274. DOI: 10.1002/ajmg.b.30898.
1.2.
2010
Vooder, Tõnu; Välk, Kristjan; Kolde, Raivo; Roosipuu, Retlav; Vilo, Jaak; Metspalu, Andres (2010). Gene Expression-Based Approaches in Differentiation of metastases and Second Primary Tumour. Case Reports in Oncology, 3 (2), 255−261. DOI: 10.1159/000318010.
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.
5.2.
2010
Kirotar, K.; Vooder, T.; Kolde, R.; Välk, K.; Solovjova, M.; Roosipuu, R.; Annilo, T.; Metspalu, A.; Tõnisson, N. (2010). Methylation markers of early-stage non-small cell lung cancer. European Journal of Human Genetics, Suppl 1: European Human Genetics Conference, Göteborg, Rootsi; 12.-15. juuni, 2010. Nature Publishing Group, 276−276. (15).
5.2.
2010
Annilo, Tarmo; Võsa, Urmo; Kolde, Raivo; Välk, Kristjan; Roosipuu, Retlav; Vooder, Tõnu; Metspalu, Andres (2010). Aberrantly expressed microRNAs indicate the pathways potentially associated with non-small cell lung cancer development. European Journal of Human Genetics: European Human Genetics Conference, Gothenburg, Sweden; June 12-15, 2010. Nature Publishing Group, 182−183. (18; Suppl 1).
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
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 ... Functional Genomics in Embryonic Stem Cells Consortium, x (2009). The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation. PLoS ONE, 4 (9), e6804−e6804. DOI: 10.1371/journal.pone.0006804.
1.1.
2009
Storm, M.l P.; Kumpfmueller, B.; Thompson, B. ; Kolde, R.; Vilo, J. ; Hummel, O.; Schulz, H.; Welham, M. J. (2009). Characterization of the Phosphoinositide 3-Kinase-Dependent Transcriptome in Murine Embryonic Stem Cells: Identification of Novel Regulators of Pluripotency. Stem Cells, 27 (4), 764−775. DOI: 10.1002/stem.3.
1.1.
2009
Trouillas, M.; Saucourt, C.; Guillotin, B.; Gauthereau, X.; Ding, L.; Buchholz, F.; Doss, M.-X.; Sachinidis, A.; Hescheler, J.; Hummel, O.; Huebner, N.; Kolde, R.; Vilo, J.; Schultz, H.; Boeuf, H. (2009). Three LIF-dependent signatures and gene clusters with atypical expression profiles, identified by transcriptome studies in mouse ES cells and early derivatives. BMC Genomics, 10 (73), 1. DOI: 10.1186/1471-2164-10-73.
5.1.
2009
Vooder, T., Välk, K., Palta ,P., Kolde, R., Metspalu, A. (2009). Parallel comparison of NSCLC CNV, survival and gene expression profiles in Estonian population. Journal of Thoracic Oncology: 13 th World Conference on Lung Cancer; San Francisco, USA; 31.07-04.08.2009. Lippincott Williams & Wilkins, 932−932. (Supplement: Suppl. 1).
5.2.
2009
Kirotar, K.; Kolde, R.; Bure, I.; Solvjova, M.; Vooder, T.; Välk, K.; Metspalu, A.; Tõnisson, N. (2009). Methylation changes in p53 pathway in non-small cell lung cancer and their potential association with TP53 mutations. European Journal of Human Genetics: European Human Genetics Conference, Wienna, Austria; 23.-26. mai, 2009. Nature Publishing Group, 301−301, P11.090. (17; Suppl. 2).
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.
23.03.2021

Raivo Kolde

https://etis.ee/CV/Raivo_Kolde/eng
21.04.1983
5067961
rkolde@gmail.com

Career

Institutions and positions
01.01.2021–...   
University of Tartu, Faculty of Science and Technology, Institute of Computer Science, Associate Professor of Health Informatics (1,00)
01.08.2019–...   
University of Tartu, Health Informatics (1,00)
09.01.2017–18.06.2019   
Philips Research North America, Research Scientist (1,00)
01.08.2014–08.01.2017   
Harvard Medical School, Postdoctoral fellow (1,00)
01.08.2013–31.07.2014   
University of Tartu, Faculty of Mathematics and Computer Science, Institute of Computer Science, Research Fellow of Bioinformatics (1,00)
01.07.2012–31.07.2013   
University of Tartu, Faculty of Mathematics and Computer Science, Institute of Computer Science, Programmer (0,20)
29.08.2008–08.09.2009   
University of Tartu, Faculty of Mathematics and Computer Science, Institute of Computer Science, Research Fellow extraordinarius (0,50)
2007–31.07.2014   
Quretec Ltd, Researcher (1,00)
01.01.2006–31.12.2007   
AS Egeen bioinformatician
 
 
Education
2009–2014   
University of Tartu, Computer Science, Phd
2005–2008   
University of Tartu, Mathematical statistics, Msc
2001–2005   
University of Tartu, Mathematical statistics, Bsc
 
 
R&D related managerial and administrative work
2007−...   
ISCB

Qualifications

Academic degrees
Raivo Kolde, Doctor's Degree, 2014, (sup) Jaak Vilo, Methods for re-using public gene expression data, University of Tartu, Faculty of Mathematics and Computer Science, Institute of Computer Science.
Raivo Kolde, Research Master's Degree, 2008, (sup) Jaak Vilo; Sven Laur; Jüri Lember, Co-expression queries across multiple experiments, University of Tartu, Faculty of Mathematics and Computer Science.
 
 
Fields of research
ETIS CLASSIFICATION: 4. Natural Sciences and Engineering; 4.5. Statistics; SPECIFICATION: Bioinformatics, gene aexpression data analysis
 
 

Completed projects

Supervised dissertations

Publications

Category
Year
Publication
 
1.1.
2019
Vatanen, Tommi; Plichta, Damian R; Somani, Juhi; Münch, Philipp C; Arthur, Timothy D; Hall, Andrew Brantley; Rudolf, Sabine; Oakeley, Edward J; Ke, Xiaobo; Young, Rachel A; Haiser, Henry J; Kolde, Raivo; Yassour, Moran; Luopajärvi, Kristiina; Siljander, Heli; Virtanen, Suvi M; Ilonen, Jorma; Uibo, Raivo; Tillmann, Vallo; Mokurov, Sergei ... Xavier, Ramnik J (2019). Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life. Nature Microbiology, 4 (3), 470−479. DOI: 10.1038/s41564-018-0321-5.
1.1.
2019
Ward, Doyle V.; Hoss, Andrew G.; Kolde, Raivo; van Aggelen, Helen C.; Loving, Joshua; Smith, Stephen A.; Mack, Deborah A.; Kathirvel, Raja; Halperin, Jeffery A.; Buell, Douglas J.; Wong, Brian E.; Ashworth, Judy L.; Fortunato-Habib, Mary M.; Xu, Liyi; Barton, Bruce A.; Lazar, Peter; Carmona, Juan J.; Mathew, Jomol; Salgo, Ivan S.; Gross, Brian D. ... Ellison, Richard T., III (2019). Integration of genomic and clinical data augments surveillance of healthcare-acquired infections. Infection Control and Hospital Epidemiology, 40 (6), 649−655. DOI: 10.1017/ice.2019.75.
1.1.
2019
van Aggelen, Helen; Kolde, Raivo; Chamarthi, Hareesh; Loving, Joshua; Fan, Yu; Fallon, John T., III; Huang, Weihua; Wang, Guiqing; Fortunato-Habib, Mary M.; Carmona, Juan J.; Gross, Brian D. (2019). A core genome approach that enables prospective and dynamic monitoring of infectious outbreaks. Scientific Reports, 9, ARTN 7808. DOI: 10.1038/s41598-019-44189-0.
1.1.
2018
Graham, Daniel B.; Jasso, Guadalupe J.; Mok, Amanda; Goel, Gautam; Ng, Aylwin C. Y.; Kolde, Raivo; Varma, Mukund; Doench, John G.; Root, David E.; Clish, Clary B.; Carr, Steven A.; Xavier, Ramnik J. (2018). Nitric Oxide Engages an Anti-inflammatory Feedback Loop Mediated by Peroxiredoxin 5 in Phagocytes. Cell Reports, 24 (4), 838−850.10.1016/j.celrep.2018.06.081.
1.1.
2018
Kolde, Raivo; Franzosa, Eric A.; Rahnavard, Gholamali; Hall, Andrew Brantley; Vlamakis, Hera; Stevens, Christine; Daly, Mark J.; Xavier, Ramnik J.; Huttenhower, Curtis (2018). Host genetic variation and its microbiome interactions within the Human Microbiome Project. Genome Medicine, 10, ARTN 6.10.1186/s13073-018-0515-8.
6.8.
2018
Lai, Peggy S.; Kolde, Raivo; Franzosa, Eric A.; Gaffin, Jonathan M.; Baxi, Sachin N.; Sheehan, William J.; Gold, Diane R.; Gevers, Dirk; Xavier, Ramnik J.; Phipatanakul, Wanda (2018). The classroom microbiome and asthma morbidity in children attending 3 inner-city schools. The Journal of Allergy and Clinical Immunology, 141 (6), 2311−2313. DOI: 10.1016/j.jaci.2018.02.022.
1.1.
2017
Johannessen, Liv; Sundberg, Thomas B.; O'Connell, Daniel J.; Kolde, Raivo; Berstler, James; Billings, Katelyn J.; Khor, Bernard; Seashore-Ludlow, Brinton; Fassl, Anne; Russell, Caitlin N.; Latorre, Isabel J.; Jiang, Baishan; Graham, Daniel B.; Perez, Jose R.; Sicinski, Piotr; Phillips, Andrew J.; Schreiber, Stuart L.; Gray, Nathanael S.; Shamji, Alykhan F.; Xavier, Ramnik J. (2017). Small-molecule studies identify CDK8 as a regulator of IL-10 in myeloid cells. Nature Chemical Biology, 13 (10), 1102−1111.10.1038/NCHEMBIO.2458.
1.1.
2017
Wlodarska, Marta; Luo, Chengwei; Kolde, Raivo; d'Hennezel, Eva; Annand, John W.; Heim, Cortney E.; Krastel, Philipp; Schmitt, Esther K.; Omar, Abdifatah S.; Creasey, Elizabeth A.; Garner, Ashley L.; Mohammadi, Sina; O'Connell, Daniel J.; Abubucker, Sahar; Arthur, Timothy D.; Franzosa, Eric A.; Huttenhower, Curtis; Murphy, Leon O.; Haiser, Henry J.; Vlamakis, Hera ... Xavier, Ramnik J. (2017). Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation. Cell Host & Microbe, 22 (1), 25−44.10.1016/j.chom.2017.06.007.
1.1.
2017
Zhao, Qing; Harbour, Stacey N.; Kolde, Raivo; Latorre, Isabel J.; Tun, Hein M.; Schoeb, Trenton R.; Turner, Henrietta; Moon, James J.; Khafipour, Ehsan; Xavier, Ramnik J.; Weaver, Casey T.; Elson, Charles O. (2017). Selective Induction of Homeostatic Th17 Cells in the Murine Intestine by Cholera Toxin Interacting with the Microbiota. The Journal of Immunology, 199 (1), 312−322. DOI: 10.4049/jimmunol.1700171.
6.8.
2017
Lokk, Kaie; Vooder, Tonu; Kolde, Raivo; Valk, Kristjan; Vosa, Urmo; Roosipuu, Retlav; Milani, Lili; Fischer, Krista; Koltsina, Marina; Urgard, Egon; Annilo, Tarmo; Metspalu, Andres; Tonisson, Neeme (2017). Methylation Markers of Early-Stage Non-Small Cell Lung Cancer (vol 7, e39813, 2012). PLoS ONE, 1, ARTN e0170833. DOI: 10.1371/journal.pone.0170833.
1.1.
2016
Pettai, Kristi; Milani, Lili; Tammiste, Anu; Võsa, Urmo; Kolde, Raivo; Eller, Triin; Nutt, David; Metspalu, Andres; Maron, Eduard (2016). Whole-genome expression analysis reveals genes associated with treatment response to escitalopram in major depression. European Neuropsychopharmacology, 26 (9), 1475−1483. DOI: 10.1016/j.euroneuro.2016.06.007.
1.1.
2016
Kolde, R; Märtens, K; Lokk, K; Laur, S; Vilo, J (2016). seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data. Bioinformatics, btw304. DOI: 10.1093/bioinformatics/btw304.
1.1.
2016
O'Connell, Daniel J.; Kolde, Raivo; Sooknah, Matthew; Graham, Daniel B.; Sundberg, Thomas B.; Latorre, Isabel J.; Mikkelsen, Tarjei S.; Xavier, Ramnik J. (2016). Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing. Cell Systems, 2 (5), 323−334.10.1016/j.cels.2016.04.011.
1.1.
2016
Desch, A. Nicole; Gibbings, Sophie L.; Goyal, Rajni; Kolde, Raivo; Bednarek, Joe; Bruno, Tullia; Slansky, Jill E.; Jacobelli, Jordan; Mason, Robert; Ito, Yoko; Messier, Elise; Randolph, Gwendalyn J.; Prabagar, Miglena; Atif, Shaikh M.; Segura, Elodie; Xavier, Ramnik J.; Bratton, Donna L.; Janssen, William J.; Henson, Peter M.; Jakubzick, Claudia V. (2016). Flow Cytometric Analysis of Mononuclear Phagocytes in Nondiseased Human Lung and Lung-Draining Lymph Nodes. American Journal of Respiratory and Critical Care Medicine, 193 (6), 614−626.10.1164/rccm.201507-1376OC.
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
Vatanen, T.; Kostic, A. D.; d'Hennezel, E.; Siljander, H.; Franzosa, E. A.; Yassour, M.; Kolde, R.; Vlamakis, H.; Arthur, T. D.; Hamalainen, A. M.; Peet, A.; Tillmann, V.; Uibo, R.; Mokurov, S.; Dorshakova, N.; Ilonen, J.; Virtanen, S. M.; Szabo, S. J.; Porter, J. A.; Lahdesmaki, H. ... Xavier, R. J. (2016). Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Cell, 165, 842-53−853. DOI: 10.1016/j.cell.2016.04.007.
5.1.
2016
Peterson, P.; Tserel, L.; Kolde, R.; Limbach, M.; Tretyakov, K.; Kasela, S.; Kisand, K.; Saare, M.; Vilo, J.; Metspalu, A.; Milani, L. (2016). Age-related profiling of DNA methylation in CD8+T cells reveals changes in immune response and transcriptional regulator genes. European Journal of Immunology, 879−879.
1.1.
2015
Kolde, Raivo; Vilo, Jaak (2015). GOsummaries: an R Package for Visual Functional Annotation of Experimental Data. F1000Research, 4 (574), 1. DOI: 10.12688/f1000research.6925.1.
1.1.
2015
Tserel, Liina; Kolde, Raivo; Limbach, Maia; Tretyakov, Konstantin; Kasela, Silva; Kisand, Kai; Saare, Mario; Vilo, Jaak; Metspalu, Andres; Milani, Lili; Peterson, Pärt (2015). Age-related profiling of DNA methylation in CD8+ T cells reveals changes in immune response and transcriptional regulator genes. Scientific Reports, 5 (13107), 1−11. DOI: 10.1038/srep13107.
1.1.
2014
Waldmann, Tanja; Rempel, Eugen; Balmer, Nina V; König, Andre; Kolde, Raivo; Gaspar, John Antonydas; Henry, Margit; Hescheler, Jürgen; Sachinidis, Agapios; Rahnenführer, Jörg; Hengstler, Jan G; Leist, Marcel (2014). Design principles of concentration-dependent transcriptome deviations in drug-exposed differentiating stem cells. Chemical Research in Toxicology, 27 (3), 408−420.10.1021/tx400402j.
1.1.
2014
Lokk, Kaie; Modhukur, Vijayachitra; Rajashekar, Balaji; Märtens, Kaspar; Mägi, Reedik; Kolde, Raivo; Koltšina, Marina; Nilsson, Torbjörn K.; Vilo, Jaak; Salumets, Andres; Tõnisson, Neeme (2014). DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns. Genome Biology, 15 (4), R54. DOI: 10.1186/gb-2014-15-4-r54.
1.1.
2014
Ilmjärv, Sten; Hundahl, Christian Ansgar; Reimets, Riin; Niitsoo, Margus; Kolde, Raivo; Vilo, Jaak; Vasar, Eero; Luuk, Hendrik (2014). Estimating differential expression from multiple indicators. Nucleic Acids Research, 42 (8), e72. DOI: 10.1093/nar/gku158.
3.1.
2014
Võsa, Urmo; Kolde, Raivo; Vilo, Jaak; Metspalu, Andres; Tarmo, Annilo (2014). Comprehensive meta-analysis of microRNA expression using a robust rank aggregation approach. In: M. Lucrecia Alvarez, MS, PhD (Ed.). Structural and functional RNA mapping (361−373). . Springer. (Methods in Molecular Biology; 1182). DOI: 10.1007/978-1-4939-1062-5_28.
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.
5.2.
2013
Tõnisson, N.; Lokk, K; Modhukur, V.; Rajashekar, B; Martens, K; Koltšina, M; Mägi, R.; Kolde, R.; Salumets, A. (2013). DNA metylome comparison of various human tissues. European Journal of Human Genetics: European Human Genetics Conference; Pariis, Prantsusmaa; 8.–11. juuni, 2013. Nature Publishing Group, 373−373. (21; Suppl 2).
1.1.
2012
Gaspar, John Antonydas; Doss, Michael Xavier; Winkler, Johannes; Wagh, Vilas; Hescheler, Jürgen; Kolde, Raivo; Vilo, Jaak; Schulz, Herbert; Sachinidis, Agapios (2012). Gene expression signatures defining fundamental biological processes in pluripotent, early, and late differentiated embryonic stem cells. Stem Cells and Development, 21 (13), 2471−2484. DOI: 10.1089/scd.2011.0637.
1.1.
2012
Võsa, U; Vooder, T; Kolde, R; Vilo, J; Metspalu, A; Annilo, T (2012). Meta-analysis of microRNA expression in lung cancer. International Journal of Cancer, 132 (12), 2884−2893. DOI: 10.1002/ijc.27981.
1.1.
2012
Lokk, Kaie; Vooder, Tõnu; Kolde, Raivo; Välk, Kristjan; Võsa, Urmo; Roosipuu, Retlav; Milani, Lili; Fischer, Krista; Koltšina, Marina; Urgard, Egon; Annilo, Tarmo; Metspalu, Andres; Tõnisson, Neeme (2012). Methylation Markers of Early-Stage Non-Small Cell Lung Cancer. PLoS ONE, 7 (6), e39813− . DOI: 10.1371/journal.pone.0039813.
1.1.
2012
Kolde, Raivo; Laur, Sven ; Adler, Priit ; Vilo, Jaak (2012). Robust Rank Aggregation for gene list integration and meta-analysis. Bioinformatics, 28 (4), 573−580. DOI: 10.1093/bioinformatics/btr709.
5.2.
2012
Tõnisson, N.; Lokk, K.; Vooder, T.; Kolde, R.; Välk, K.; Roosipuu, R.; Võsa, U.; Milani, L.; Fischer, K.; Koltšina, M.; Urgard, E.; Annilo, T.; Metspalu, A. (2012). Altered DNA methylation in early-stage non-small-cell lung cancer. European Journal of Human Genetics: European Human Genetics Conference; Nürnberg, Saksamaa; 23.–26. juuni, 2012. Nature Publishing Group, 174−174. (20; Suppl 1).
1.1.
2011
Chen, Y; Jorgensen, M; Kolde, R; Zhao, X; Parker, B; Valen, E; Wen, J; Sandelin, A (2011). Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data. BMC Genomics, 12, 544. DOI: 10.1186/1471-2164-12-544.
1.1.
2011
Võsa, Urmo; Vooder, Tõnu; Kolde, Raivo; Fischer, Krista; Välk, Kristjan; Tõnisson, Neeme; Roosipuu, Retlav; Vilo, Jaak; Metspalu, Andres; Annilo, Tarmo (2011). Identification of miR-374a as a prognostic marker for survival in patients with early-stage nonsmall cell lung cancer. Genes Chromosomes and Cancer, 50 (10), 812−822. DOI: 10.1002/gcc.20902.
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.
5.1.
2011
Peters, Maire; Altmäe, Signe; Reimand, Jüri; Laisk, Triin; Saare, Merli; Hovatta, Outti; Kolde, Raivo; Vilo, Jaak; Stavreus-Evers, Anneli; Salumets, Andres. (2011). Human embryo-endometrium interactions at the time of implantation. 26: 27th Annual Meeting of the European Society of Human Reproduction and Embryology, 3-6 juuli, Stockholm, Rootsi. Oxford University Press, 216−216. (1).
5.1.
2011
Valk, K.; Vooder, T.; Kolde, R.; Roosipuu, R.; Vilo, J.; Metspalu, A. (2011). GENE EXPRESSION-BASED APPROACHES IN DIFFERENTIATION OF METASTASES AND SECOND PRIMARY TUMOUR. 6. , s1055−s1056.
5.2.
2011
Välk, K.; Vooder, T.; Kolde, R.; Roosipuu, R.; Vilo, J.; Metspalu, A. (2011). Whole genome gene expression profiling of two control and three subsequent lung cancer samples of the same patient. World Conference on Lung Cancer, Amsterdam, 2011.
5.2.
2011
Kirotar, K.; Vooder, T., Kolde R.; Välk, K.; Solovjova, M.; Roosipuu, R.; Annilo, T.; Metspalu, A.; Tõnisson, N. (2011). Genome-wide methylation profiling of non-small cell lung cancer. European Journal of Human Genetics, Suppl 2: European Human Genetics Conference; Amsterdam, Holland; 28.–31. mai, 2011. Nature Publishing Group, 378−378. (19).
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
Välk, Kristjan; Vooder, Tõnu; Kolde, Raivo; Reintam, Mari-Ann; Petzold, Cathleen; Vilo, Jaak; Metspalu, Andres (2010). Gene Expression Profiles of Non-Small Cell Lung Cancer: Survival Prediction and New Biomarkers. Oncology, 79, 283−292. DOI: 10.1159/000322116.
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
Doss, Michael Xavier ; Wagh, Vilas ; Schulz, Herbert ; Kull, Meelis ; Kolde, Raivo ; Pfannkuche, Kurt ; Nolden, Tobias ; Himmelbauer, Heinz; Vilo, Jaak ; Hescheler, Jürgen ; Sachinidis, Agapios (2010). Global transcriptomic analysis of murine embryonic stem cell-derived brachyury+ (T) cells. Genes to Cells, 15 (3), 209−228. DOI: 10.1111/j.1365-2443.2010.01390.x.
1.1.
2010
Maron, E.; Kallassalu, K.; Tammiste, A.; Kolde, R.; Vilo, J.; Tõru, I.; Vasar, V.; Shlik, J.; Metspalu, A. (2010). Peripheral Gene Expression Profiling of CCK-4-Induced Panic in Healthy Subjects. American Journal of Medical Genetics Part B Neuropsychiatric Genetics, 153B (1), 269−274. DOI: 10.1002/ajmg.b.30898.
1.2.
2010
Vooder, Tõnu; Välk, Kristjan; Kolde, Raivo; Roosipuu, Retlav; Vilo, Jaak; Metspalu, Andres (2010). Gene Expression-Based Approaches in Differentiation of metastases and Second Primary Tumour. Case Reports in Oncology, 3 (2), 255−261. DOI: 10.1159/000318010.
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.
5.2.
2010
Kirotar, K.; Vooder, T.; Kolde, R.; Välk, K.; Solovjova, M.; Roosipuu, R.; Annilo, T.; Metspalu, A.; Tõnisson, N. (2010). Methylation markers of early-stage non-small cell lung cancer. European Journal of Human Genetics, Suppl 1: European Human Genetics Conference, Göteborg, Rootsi; 12.-15. juuni, 2010. Nature Publishing Group, 276−276. (15).
5.2.
2010
Annilo, Tarmo; Võsa, Urmo; Kolde, Raivo; Välk, Kristjan; Roosipuu, Retlav; Vooder, Tõnu; Metspalu, Andres (2010). Aberrantly expressed microRNAs indicate the pathways potentially associated with non-small cell lung cancer development. European Journal of Human Genetics: European Human Genetics Conference, Gothenburg, Sweden; June 12-15, 2010. Nature Publishing Group, 182−183. (18; Suppl 1).
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
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 ... Functional Genomics in Embryonic Stem Cells Consortium, x (2009). The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation. PLoS ONE, 4 (9), e6804−e6804. DOI: 10.1371/journal.pone.0006804.
1.1.
2009
Storm, M.l P.; Kumpfmueller, B.; Thompson, B. ; Kolde, R.; Vilo, J. ; Hummel, O.; Schulz, H.; Welham, M. J. (2009). Characterization of the Phosphoinositide 3-Kinase-Dependent Transcriptome in Murine Embryonic Stem Cells: Identification of Novel Regulators of Pluripotency. Stem Cells, 27 (4), 764−775. DOI: 10.1002/stem.3.
1.1.
2009
Trouillas, M.; Saucourt, C.; Guillotin, B.; Gauthereau, X.; Ding, L.; Buchholz, F.; Doss, M.-X.; Sachinidis, A.; Hescheler, J.; Hummel, O.; Huebner, N.; Kolde, R.; Vilo, J.; Schultz, H.; Boeuf, H. (2009). Three LIF-dependent signatures and gene clusters with atypical expression profiles, identified by transcriptome studies in mouse ES cells and early derivatives. BMC Genomics, 10 (73), 1. DOI: 10.1186/1471-2164-10-73.
5.1.
2009
Vooder, T., Välk, K., Palta ,P., Kolde, R., Metspalu, A. (2009). Parallel comparison of NSCLC CNV, survival and gene expression profiles in Estonian population. Journal of Thoracic Oncology: 13 th World Conference on Lung Cancer; San Francisco, USA; 31.07-04.08.2009. Lippincott Williams & Wilkins, 932−932. (Supplement: Suppl. 1).
5.2.
2009
Kirotar, K.; Kolde, R.; Bure, I.; Solvjova, M.; Vooder, T.; Välk, K.; Metspalu, A.; Tõnisson, N. (2009). Methylation changes in p53 pathway in non-small cell lung cancer and their potential association with TP53 mutations. European Journal of Human Genetics: European Human Genetics Conference, Wienna, Austria; 23.-26. mai, 2009. Nature Publishing Group, 301−301, P11.090. (17; Suppl. 2).
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.
23.03.2021

Otsi projekti

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Asutus on projekti finantseerija   Asutus on projekti teostaja  
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Kõik   Tavaprojektid   Ülemprojektid   Alamprojektid  
Uus Frascati (2015)
Uus ja vana Frascati (otsing uue järgi väljastab ka seotud vanad)
Kõik
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Lõppenud
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Hajus
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  • Leitud 10 kirjet
ProgrammLiikNumberNimiProjekti algusProjekti lõppVastutav täitjaAsutusFinantseerijapoolne rahastamine
1.2.3.3.DETECTIVE (266838)Biomarkerite tuvastamine korduvate toksilisuse mõõtmiste jaoks in vitro süsteemides01.01.201131.12.2015Jaak ViloOÜ Quretec145 372,80 EUR
MUUMMTAT07037RCOBRED - Colon and Breast Cancer Diagnostic (Projekti COBRED) andmebaasi ning andmete analüüsi meetodite ja tööriistade loomine).01.03.200728.02.2010Jaak ViloTartu Ülikool396 891,34 EUR
RITA1AlamprojektRITA1/02-120-03COVID-19 haigusjuhtumite analüüs ja riskirühmade väljaselgitamine Eestis14.09.202021.03.2022Raivo KoldeTartu Ülikool, Loodus- ja täppisteaduste valdkond, arvutiteaduse instituut74 240,00 EUR
MUUESNATSEmbrüonaalsete tüvirakkude põhised alternatiivsed testimisstrateegiad01.04.200831.03.2013Jaak ViloOÜ Quretec447 381,54 EUR
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