Leopold Parts

9.03.1982
leopold.parts@gmail.com

Teenistuskäik

Töökohad ja ametid
02.03.2016–...    Tartu Ülikool, Loodus- ja täppisteaduste valdkond, Arvutiteaduse instituut, bioinformaatika vanemteadur (0,50)
01.01.2015–...    Wellcome Trust Sanger Institute, ruhmajuht
01.01.2016–01.03.2016    Tartu Ülikool, Loodus- ja täppisteaduste valdkond, Arvutiteaduse instituut, bioinformaatika vanemteadur (0,50)
01.08.2015–31.12.2015    Tartu Ülikool, Matemaatika-informaatikateaduskond, Arvutiteaduse instituut, bioinformaatika vanemteadur (0,50)
01.01.2015–31.12.2015    Stanfordi Ulikool, Kulalisteadlane
01.01.2013–31.12.2015    European Molecular Biology Laboratory; järeldoktor
01.01.2011–31.12.2014    University of Toronto; teadur
2006–2006    Tartu Ülikool, Matemaatika-informaatikateaduskond, Arvutiteaduse instituut, Jaak Vilo teadusruhma liige (1,00)
01.01.2005–31.12.2006    Massachusetts Institute of Technology Computational Biology Laboratory; teadustöötaja
01.01.2004–31.12.2004    EGeen AS, programmeerija (0,50)
01.01.2004–31.12.2005    European Bioinformatics Institute; teadustöötaja
01.01.2002–31.12.2003    WebMedia AS, programmeerija (0,50)
 
 
Haridustee
2006–2011    University of Cambridge
2004–2005    University of Cambridge
2003–2006    Massachusetts Institute of Technology
2001–2003    University of Tartu
 
 
Teadusorganisatsiooniline ja -administratiivne tegevus
2014−2015    Pacific Symposium for Biocomputing (PSB) session on Personalized Medicine. Conference chair
2012−2014    Toronto Bioinformatics User Group. Co-organizer
2008−2009    Sanger-EBI Ph.D student symposium session. Conference chair
2008−2009    Sanger-Cambridge Ph.D Symposium. Organising Committee, Program Committee
2007−2009    Wellcome Trust Sanger Institute Committee of Graduate Studies
2003−2003    Clobber Game Programming Contest. Head of Jury, main organizer
2003−2003    Baltic Olympiad in Informatics. Head of Social Committee
2002−2002    Baltic Way mathematical team contest. Head of Guides, Coordinator
2001−2005    High school students math tutor, Olympiad coach, Olympiad Jury member

Kvalifikatsioon

 
 
Teaduspreemiad ja tunnustused
2013, Leopold Parts, Marie Curie International Outgoing Fellow
2011, Leopold Parts, Canadian Institute for Advanced Research Global Fellow
2011, Leopold Parts, Grand Prix Estonian Life Science PhD theses
2011, Leopold Parts, 2nd place Estonian popular science writing competition
2011, Leopold Parts, Young Researcher at 61st Meeting of Nobel Laureates in Lindau
2006, Leopold Parts, Wellcome Trust PhD Studentship
2002, Leopold Parts, International Mathematics Competition 3rd prize
2001, Leopold Parts, Association for Computing Machinery International Collegiate Programming Contest semifinalist
2001, Leopold Parts, International Mathematics Olympiad Bronze Medal, Honorable Mention
2000, Leopold Parts, Estonian Mathematics Society Best Young Estonian Mathematician
2000, Leopold Parts, All-Estonian Mathematics Olympiad 1st place, Informatics Olympiad 2nd place
 
 
Teadustöö põhisuunad
VALDKOND: 1. Bio- ja keskkonnateadused; 1.3. Geneetika; CERCS ERIALA: B220 Geneetika, tsütogeneetika

Publikatsioonid

Klass
Aasta
Publikatsioon
 
1.2.
2017
1.2.
2017
1.1.
2016
1.1.
2016
1.1.
2016
1.1.
2015
1.2.
2015
3.1.
2015
5.1.
2015
5.2.
2015
1.1.
2014
1.1.
2014
1.1.
2014
1.1.
2014
5.2.
2014
1.1.
2013
1.1.
2013
1.1.
2013
1.1.
2013
1.1.
2013
1.1.
2012
1.1.
2012
1.1.
2012
1.1.
2012
1.1.
2012
1.1.
2012
1.1.
2011
1.1.
2011
1.1.
2011
1.1.
2011
1.1.
2010
1.1.
2010
1.1.
2010
1.1.
2009
1.1.
2009
1.1.
2009
1.1.
2007
1.1.
2007
1.1.
2007
6.3.
2002

Leopold Parts

9.03.1982
leopold.parts@gmail.com

Career

Institution and occupation
02.03.2016–...    University of Tartu, Faculty of Science and Technology, Institute of Computer Science, Senior Research Fellow in Bioinformatics (0,50)
01.01.2015–...    Wellcome Trust Sanger Institute, Faculty
01.01.2016–01.03.2016    University of Tartu, Faculty of Science and Technology, Institute of Computer Science, Senior Research Fellow in Bioinformatics (0,50)
01.08.2015–31.12.2015    University of Tartu, Faculty of Mathematics and Computer Science, Institute of Computer Science, Senior Research Fellow in Bioinformatics (0,50)
01.01.2015–31.12.2015    Stanford University, Visiting Scholar
01.01.2013–31.12.2015    European Molecular Biology Laboratory; postoctoral fellow
01.01.2011–31.12.2014    University of Toronto; research associate
2006–2006    University of Tartu, Faculty of Mathematics and Computer Science, Institute of Computer Science, Junior Researcher (1,00)
01.01.2005–31.12.2006    Massachusetts Institute of Technology Computational Biology Laboratory; research associate
01.01.2004–31.12.2004    EGeen, Inc, Other staff (0,50)
01.01.2004–31.12.2005    European Bioinformatics Institute; research associate
01.01.2002–31.12.2003    WebMedia AS, Other staff (0,50)
 
 
Education
2006–2011    University of Cambridge
2004–2005    University of Cambridge
2003–2006    Massachusetts Institute of Technology
2001–2003    University of Tartu
 
 
R&D related managerial and administrative work
2014−2015    Pacific Symposium for Biocomputing (PSB) session on Personalized Medicine. Conference chair
2012−2014    Toronto Bioinformatics User Group. Co-organizer
2008−2009    Sanger-EBI Ph.D student symposium session. Conference chair
2008−2009    Sanger-Cambridge Ph.D Symposium. Organising Committee, Program Committee
2007−2009    Wellcome Trust Sanger Institute Committee of Graduate Studies
2003−2003    Clobber Game Programming Contest. Head of Jury, main organizer
2003−2003    Baltic Olympiad in Informatics. Head of Social Committee
2002−2002    Baltic Way mathematical team contest. Head of Guides, Coordinator
2001−2005    High school students math tutor, Olympiad coach, Olympiad Jury member

Qualifications

 
 
Honours & awards
2013, Leopold Parts, Marie Curie International Outgoing Fellow
2011, Leopold Parts, Canadian Institute for Advanced Research Global Fellow
2011, Leopold Parts, Grand Prix Estonian Life Science PhD theses
2011, Leopold Parts, 2nd place Estonian popular science writing competition
2011, Leopold Parts, Young Researcher at 61st Meeting of Nobel Laureates in Lindau
2006, Leopold Parts, Wellcome Trust PhD Studentship
2002, Leopold Parts, International Mathematics Competition 3rd prize
2001, Leopold Parts, Association for Computing Machinery International Collegiate Programming Contest semifinalist
2001, Leopold Parts, International Mathematics Olympiad Bronze Medal, Honorable Mention
2000, Leopold Parts, Estonian Mathematics Society Best Young Estonian Mathematician
2000, Leopold Parts, All-Estonian Mathematics Olympiad 1st place, Informatics Olympiad 2nd place
 
 
Field of research
FIELD OF RESEARCH: 1. Biosciences and Environment; 1.3. Genetics; CERCS SPECIALTY: B220 Genetics, cytogenetics
 
 

Publications

Category
Year
Publication
 
1.2.
2017
1.2.
2017
1.1.
2016
1.1.
2016
1.1.
2016
1.1.
2015
1.2.
2015
3.1.
2015
5.1.
2015
5.2.
2015
1.1.
2014
1.1.
2014
1.1.
2014
1.1.
2014
5.2.
2014
1.1.
2013
1.1.
2013
1.1.
2013
1.1.
2013
1.1.
2013
1.1.
2012
1.1.
2012
1.1.
2012
1.1.
2012
1.1.
2012
1.1.
2012
1.1.
2011
1.1.
2011
1.1.
2011
1.1.
2011
1.1.
2010
1.1.
2010
1.1.
2010
1.1.
2009
1.1.
2009
1.1.
2009
1.1.
2007
1.1.
2007
1.1.
2007
6.3.
2002
  • Leitud 4 kirjet
ProgrammNumberNimiProjekti algusProjekti lõppVastutav täitjaAsutusRahastamine kokku
IUTIUT34-4Andmeteaduse meetodid ja rakendused (DSMA)01.01.201531.12.2020Jaak ViloTartu Ülikool, Loodus- ja täppisteaduste valdkond, Arvutiteaduse instituut349 800,00 EUR
TKTAR16013 (EXCITE) (TK148)IT Tippkeskus EXCITE01.09.201631.08.2023Maarja KruusmaaTallinna Tehnikaülikool, Infotehnoloogia teaduskond, Biorobootika keskus; Tartu Ülikool, Loodus- ja täppisteaduste valdkond, Arvutiteaduse instituut; Tartu Ülikool, Loodus- ja täppisteaduste valdkond, Tehnoloogiainstituut; Cybernetica AS2 642 075,15 EUR
MOBJDMOBJD67Mittekodeerivate haruldaste geneetiliste variantide mõju ennustamine01.06.201731.05.2019Kaur AlasooTartu Ülikool, Loodus- ja täppisteaduste valdkond, Arvutiteaduse instituut75 800,00 EUR
2.2.1.VLTAT17348Süvaneurovõrkude kasutamine rakupiltide analüüsis15.06.201715.06.2018Leopold PartsTartu Ülikool, Loodus- ja täppisteaduste valdkond, Arvutiteaduse instituut100 000,00 EUR
  • Leitud 41 kirjet
PublikatsioonKlassifikaatorFail
Jones, William; Alasoo, Kaur; Fishman, Dmytro; Parts, Leopold (2017). Computational Biology - Deep Learning. Emerging Topics in Life Sciences [ilmumas].1.1.
Pärnamaa, Tanel; Parts, Leopold (2017). Accurate classification of protein subcellular localization from high throughput microscopy images using deep learning. bioRxiv [ilmumas].1.2.
Angermueller, Christof; Pärnamaa, Tanel; Parts, Leopold; Stegle, Oliver (2016). Deep learning for computational biology. Molecular systems biology, 12 (7), 878−878.10.15252/msb.20156651.1.1.
Hallin, Johan; Märtens, Kaspar; Young, Alexander I; Zackrisson, Martin; Salinas, Francisco; Parts, Leopold; Warringer, Jonas; Liti, Gianni (2016). Powerful decomposition of complex traits in a diploid model. Nature communications, 7, 13311−13311.10.1038/ncomms13311.1.1.
Märtens, Kaspar; Hallin, Johan; Warringer, Jonas; Liti, Gianni; Parts, Leopold (2016). Predicting quantitative traits from genome and phenome with near perfect accuracy. Nature communications, 7, 11512−11512.10.1038/ncomms11512.1.1.
Smith, Justin D; Suresh, Sundari; Schlecht, Ulrich; Wu, Manhong; Wagih, Omar; Peltz, Gary; Davis, Ronald W; Steinmetz, Lars M; Parts, Leopold; Onge, Robert P St (2016). Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design. Genome Biology, 17 (1), 1−16.10.1186/s13059-016-0900-9.1.1.
Brown, Andrew; Ding, Zhihao; Viñuela, Ana; Glass, Dan; Parts, Leopold; Spector, Tim; Winn, John; Durbin, Richard (2015). Pathway Based Factor Analysis of Gene Expression Data Produces Highly Heritable Phenotypes that Associate with Age. G3: Genes/Genomes/Genetics, 3 (9), 1−35.10.1534/g3.114.011411.1.1.
Märtens, Kaspar; Hallin, Johan; Warringer, Jonas; Liti, Gianni; Parts, Leopold (2015). Predicting quantitative traits from genome and phenome with near perfect accuracy. bioRxiv, 1−12.10.1101/029868 [ilmumas].1.2.
Wagih, Omar; Parts, Leopold (2015). Genetic Interaction Scoring Procedure for Bacterial Species. In: Prokaryotic Systems Biology (169−185). Springer International Publishing.10.1007/978-3-319-23603-2_10.3.1.
Garcia-Rios, Estefani; Parts, Leopold; Liti, Gianni; Navarro, Jose Manuel Guillamon (2015). Polygenic analysis of low temperature adaptation in wine yeast. Yeast, 32 (1), 235−235.5.1.
Dudley, Joel; Listgarten, Jennifer; Stegkle, Oliver; Brenner, Steven; Parts, Leopold (2015). Personalized medicine: from genotypes, molecular phenotypes, and the quantified self, towards improved medicine. Pacific Symposium on Biocomputing 2015, 07.09.2015, University of California. California: Sage Publications Ltd, 342−346.5.2.
Bergström, A.; Simpson, J. T; Salinas, F.; Barré, B.; Parts, L.; Zia, A.; Nguyen Ba, A. N.; Moses, A. M.; Louis, E. J.; Mustonen, V.; Warringer, J.; Durbin, R.; Liti, G. (2014). A high-definition view of functional genetic variation from natural yeast genomes. Molecular Biology and Evolution, 31 (4), 872−888.10.1093/molbev/msu037.1.1.
Parts, L. (2014). Genome‐wide mapping of cellular traits using yeast. Yeast, 31 (6), 197−205.10.1002/yea.3010.1.1.
Wagih, O.; Parts, L. (2014). gitter: A Robust and Accurate Method for Quantification of Colony Sizes from Plate Images. G3: Genes/Genomes/Genetics, 4 (3), 547−552.10.1534/g3.113.009431.1.1.
Parts,L.; Liu,Y.-C.; Tekkedil, M. M.; Steinmetz, L. M.; Caudy, A. A.; Fraser, A. G.; Boone, C.; Andrews, B. J.; Rosebrock, A. P. (2014). Heritability and genetic basis of protein level variation in an outbred population. Genome Research, 24 (8), 1363−1370.1.1.
Listgarten, J.; Stegle, O.; Morris, Q.; Brenner, S. E.; Parts, L. (2014). Personalized medicine: from genotypes and molecular phenotypes towards therapy-session introduction. Pacific Symposium on Biocomputing, 19. 224−228.5.2.
Glass, D.; Viñuela, A.; Davies, M.N.; Ramasamy, A.; Parts, L. etc (2013). Gene expression changes with age in skin, adipose tissue, blood and brain. Genome Biology, 14 (7), R75−R75.10.1186/gb-2013-14-7-r75.1.1.
Cubillos, F. A.; Parts, L.; Salinas, F.; Bergström, A.; Scovacricchi, E.; Zia, A.; Illingworth, C. JR; Mustonen, V.; Ibstedt, S.; Warringer, J.; Louis, E. J; Durbin, R.; Liti, G. (2013). High resolution mapping of complex traits with a four-parent advanced intercross yeast population. Genetics, 195 (3), 1141−1155.10.1534/genetics.113.155515.1.1.
Illingworth, C. JR.; Parts, L.; Bergström, A.; Liti, G.; Mustonen, V. (2013). Inferring genome-wide recombination landscapes from advanced intercross lines: application to yeast crosses. PLoS ONE, 8 (5), e62266−e62266.10.1371/journal.pone.0062266.1.1.
Wagih, O.; Usaj, M.; Baryshnikova, A.; VanderSluis, B.; Kuzmin, E.; Costanzo, M.; Myers, C. L.; Andrews, B. J.; Boone, C. M.; Parts, L. (2013). SGAtools: one-stop analysis and visualization of array-based genetic interaction screens. Nucleic Acids Research, 41, 591−596.10.1093/nar/gkt400.1.1.
Bunt, M. van de; Gaulton, K. J.; Parts, L. etc (2013). The miRNA profile of human pancreatic islets and beta-cells and relationship to type 2 diabetes pathogenesis. PLoS ONE, 8 (1), e55272−e55272.10.1371/journal.pone.0055272.g003.1.1.
Tullus, Arvo; Kupper, Priit; Sellin, Arne; Parts, Leopold; Sõber, Jaak; Tullus, Tea; Lõhmus, Krista; Sõber, Anu; Tullus, Hardi (2012). Climate Change at Northern Latitudes: Rising Atmospheric Humidity Decreases Transpiration, N-uptake and Growth Rate of Hybrid Aspen. PLoS ONE, 7 (8), e42648.10.1371/journal.pone.0042648.1.1.
Parts, L.; Hedman, AK.; Keildson, S.; Knights, AJ.; Abreu-Goodger, C.; van de Bunt, M.; Guerra-Assuncao, JA.; Bartonicek, N.; van Dongen, S.; Mägi, R.; Nisbet, J.; Barrett, A.; Rantalainen, M.; Nica, AC.; Quail, MA.; Small, KS.; Glass, D.; Enright, AJ.; Winn, J.; Deloukas, P. ... Lindgren, CM. (2012). Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose Tissue. Plos Genetics, 8 (5), e1002704−e1002704.10.1371/journal.pgen.1002704.1.1.
Grundberg, E.; Small, K. S.; Parts, L. etc (2012). Mapping cis-and trans-regulatory effects across multiple tissues in twins. Nature Genetics, 44 (10), 1084−1089.10.1038/ng.2394.1.1.
Stranger, B. E.; Montgomery, S. B.; Dimas, A. S.; Parts, L. etc (2012). Patterns of cis regulatory variation in diverse human populations. Plos Genetics, 8 (4), 272−284.10.1371/journal.pgen.1002639.1.1.