Publications based on calculations carried out on the servers of the UT HPC Center

2021

Articles

  1. Jurcek, Ondrej; Nonappa; Kalenius, Elina; Jurcek, Pia; Linnanto, Juha M.; Puttreddy, Rakesh; Valkenier, Hennie; Houbenov, Nikolay; Babiak, Michal; Peterek, Miroslav; Davis, Anthony P.; Marek, Radek; Rissanen, Kari (2021). Hexagonal Microparticles from Hierarchical Self-Organization of Chiral Trigonal Pd3L6 Macrotetracycles. Cell Reports Physical Science, 2, 100303-1−100303-19. DOI: 10.1016/j.xcrp.2020.100303.
  2. Lehti Saag, Sergey V. Vasilyev, Liivi Varul, Natalia V. Kosorukova, Dmitri V. Gerasimov, Svetlana V. Oshibkina, Samuel J. Griffith, Anu Solnik, Lauri Saag, Eugenia D’Atanasio, Ene Metspalu, Maere Reidla, Siiri Rootsi, Toomas Kivisild, Christiana Lyn Scheib, Kristiina Tambets, Aivar Kriiska, Mait Metspalu (2021). Genetic ancestry changes in Stone to Bronze Age transition in the East European plain. Science Advances doi: 10.1126/sciadv.abd6535

2020

Articles

  1. Arpan Kundu, Kaido Sillar, Joachim Sauer (2020). Predicting adsorption selectivities from pure gas isotherms for gas mixtures in metal–organic frameworks Chemical Science 3, 202
  2. Burk, Jaanus; Adamson, Aiko; Sikk, Lauri; Tämm, Kaido; Pupart, Anni; Burk, Peeter (2020). DFT study of 2,9-bis(1,2,4-triazin-3-yl)-1,10-phenanthroline (BTPhen) and its derivatives complexation with lanthanide series. Computational and Theoretical Chemistry, 1175, 112729.10.1016/j.comptc.2020.112729.
  3. Pankratov V, Montinaro F, Kushniarevich A, Hudjashov G, Jay F, Saag L, Flores R, Marnetto D, Seppel M, Kals M, Võsa U, Taccioli C, Möls M, Milani L, Aasa A, Lawson DJ, Esko T, Mägi R, Pagani L, Metspalu A, Metspalu M. Eur J Hum Genet. (2020).
    Differences in local population history at the finest level: the case of the Estonian populationEuropean journal of human genetics DOI: 10.1038/s41431-020-0699-4
  4. Örd T, Puurand T, Örd D, Annilo T, Möls M, Remm M and Örd T. (2020).A human-specific VNTR in the TRIB3 promoter causes gene expression variation between individuals. PLoS Genetics, 16(8):e1008981.
  5. Bücking R, Cox MP, Hudjashov G, Saag L, Sudoyo H, Stoneking M (2020).  Correction to: Archaic mitochondrial DNA inserts in modern day nuclear genomes. BMC Genomics. 2020 Jan 17;21(1):55. doi: 10.1186/s12864-020-6449-8.
  6. Natri HM, Bobowik KS, Kusuma P, Crenna Darusallam C, Jacobs GS, Hudjashov G, Lansing JS, Sudoyo H, Banovich NE, Cox MP, Gallego Romero I. (2020). Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago. PLoS Genetics 2020 May 26;16(5):e1008749. doi: 10.1371/journal.pgen.1008749. eCollection 2020 May.
  7. Elhi, Fred; Karu, Karl; Rinne, Pille; Nadel, Kadi-Anne; Jarvekulg, Martin; Aabloo, Alvo; Tamm, Tarmo; Ivanistsev, Vladislav; Pohako-Esko, Kaija (2020). Understanding the Behavior of Fully Non-Toxic Polypyrrole-Gelatin and Polypyrrole-PVdF Soft Actuators with Choline Ionic Liquids. Actuators, 9 (2).10.3390/act9020040.
  8. Lembinen, Meeri, Ergo Nõmmiste, Heigo Ers, Borja Docampo‐Álvarez, Jaanus Kruusma, Enn Lust, and Vladislav B. Ivaništšev (2020).Calculation of core‐level electron spectra of ionic liquids. International Journal of Quantum Chemistry (2020): e26247.
  9. Ers, Heigo; Lembinen, Meeri; Mišin, Maksim; Seitsonen, Ari P.; Fedorov, Maxim V.; Ivaništšev, Vladislav B. (2020). Graphene–Ionic Liquid Interfacial Potential Drop from Density Functional Theory-Based Molecular Dynamics Simulations. Journal of Physical Chemistry C, 124 (36), 19548−19555.
  10. K. Leiger, J. M. Linnanto, and A. Freiberg (2020).Establishment of the Qy Absorption Spectrum ofChlorophyll a Extending to Near-Infrared Molecules 25, 3796 (2020): doi:10.3390/molecules25173796
  11. A. Ghiami-Shomami*, M. Ashtari-Delivand, B. Ghalami-Choobar, I. Leito (2020). Computational  Studies of Acidities of Some Hydrodxycoumarins Computational & Theoretical Chemistry, 2020.
  12. Kolberg, L., Kerimov, N., Peterson, H., & Alasoo, K. (2020). Co-expression analysis reveals interpretable gene modules controlled by trans-acting genetic variants. eLife, 9, e58705. doi: 10.7554/eLife.58705
  13. Davide Marnetto, Katri Pärna, Kristi Läll, Ludovica Molinaro, Francesco Montinaro, Toomas Haller, Mait Metspalu, Reedik Mägi, Krista Fischer, Luca Pagani  (2020). Ancestry deconvolution and partial polygenic score can improve susceptibility predictions in recently admixed individuals Nature Communications volume 11, Article number: 1628 (2020)
  14. Aleksei Kuznetsov, Jaak Järv (2020) Mapping of ACE2 binding site on SARS-CoV-2 spike protein S1: docking study with peptides; pp. 228–234 Proceedings of the Estonian Academy of Sciences Vol 69, Issue 3, 2020 0.3176/proc.2020.3.06
  15. Karabulut, D.; Tertychnyi, P.; Arslan, H. S.; Ozcinar, C.; Nasrollahi, K.; Valls, J.; Vilaseca, J.; Moeslund, T. B.; Anbarjafari, G. (2020). Cycle-Consistent Adversarial Neural Networks Based Low Quality Fingerprint Enhancement. Multimedia Tools and Applications, 79, 1. DOI: 10.1007/s11042-020-08750-8.
  16. Ruoyun Hui, Eugenia D’Atanasio, Lara M. Cassidy, Christiana L. Scheib, Toomas Kivisild (2020). Evaluating genotype imputation pipeline for ultra low coverage ancient genomes. Scientific Reports 10, 18542 (2020) doi: 10.1038/s41598-020-75387-w
  17. Aslani F, Tedersoo L, Põlme S, Knox O, Bahram M. 2020. Global patterns and determinants of bacterial communities associated with ectomycorrhizal root tips of Alnus species. Soil Biology and Biochemistry 148: 107923. DOI: 10.1016/j.soilbio.2020.107923
  18. Sofja Tshepelevitsh, Sandip A. Kadam, Astrid Darnell, Johan Bobacka, Alo Rüütel, Tõiv Haljasorg, Ivo Leito (2020).
  19. Fomicheva, Marina; Sun, Shuo; Yankovskaya, Lisa; Blain, Frédéric; Guzmán, Francisco; Fishel, Mark; Aletras, Nikolaos; Chaudhary, Vishrav; Specia, Lucia (2020). Unsupervised Quality Estimation for Neural Machine Translation. Transactions of the Association for Computational Linguistics, 8, 539−555. DOI: 10.1162/tacl_a_00330.
  20. Gordevičius, Juozas; Narmontė, Milda; Gibas, Povilas; Kvederavičiūtė, Kotryna; Tomkutė, Vita; Paluoja, Priit; Krjutškov, Kaarel; Salumets, Andres; Kriukienė, Edita (2020). Identification of fetal unmodified and 5-hydroxymethylated CG sites in maternal cell-free DNA for non-invasive prenatal testing. Clinical Epigenetics, 12 (1). DOI: 10.1186/s13148-020-00938-x.
  21. Wedenoja, Satu; Yoshihara, Masahito; Teder, Hindrek; Sariola, Hannu; Gissler, Mika; Katayama, Shintaro; Wedenoja, Juho; Häkkinen, Inka M; Ezer, Sini; Linder, Nina; Lundin, Johan; Skoog, Tiina; Sahlin, Ellika; Iwarsson, Erik; Pettersson, Karin; Kajantie, Eero; Mokkonen, Mikael; Heinonen, Seppo; Laivuori, Hannele; Krjutškov, Kaarel … Kere, Juha (2020). Fetal HLA-G mediated immune tolerance and interferon response in preeclampsia. EBioMedicine, 102872−102872. DOI: 10.1016/j.ebiom.2020.102872.
  22. Oras E, Anderson J, Tõrv M, Vahur S, Rammo R, Remmer S, Mölder M, Malve M, Saag L, Saage R, Teearu-Ojakäär A, Peets P, Tambets K, Metspalu M, Lees DC, Barclay MVL, Hall MJR, Ikram S, Piombino-Mascali D. 2020. Multidisciplinary investigation of two Egyptian child mummies curated at the University of Tartu Art Museum, Estonia (Late/Graeco-Roman Periods). PLOS ONE 15(1): e0227446.
  23. Kittask, C., Milintsevich, K., & Sirts, K. (2020, September). Evaluating Multilingual BERT for Estonian. Baltic HLT (pp. 19-26).
  24. Milintsevich, K., & Sirts, K. (2020, September). Lexicon-Enhanced Neural Lemmatization for Estonian. Baltic HLT (pp. 158-165).
  25. Nicolas Perrot, Vincenza Valerio, Donato Moschetta, S Matthijs Boekholdt, Christian Dina, Hao Yu Chen, Erik Abner, Andreas Martinsson, Hasanga D Manikpurage, Sidwell Rigade, Romain Capoulade, Elvira Mass, Marie-Annick Clavel, Thierry Le Tourneau, David Messika-Zeitoun, Nicholas J Wareham, James C Engert, Gianluca Polvani, Philippe Pibarot, Tõnu Esko, J Gustav Smith, Patrick Mathieu, George Thanassoulis, Jean-Jacques Schott, Yohan Bossé, Marina Camera, Sébastien Thériault, Paolo Poggio, Benoit J Arsenault (2020). Genetic and in vitro inhibition of PCSK9 and calcific aortic valve stenosis JACC: Basic to Translational Science vol 5, issue 7

 

2019

Articles

  1. Zhurbas, V.; Väli, G.; Kostianoy, A.; Lavrova, O. (2019). Hindcast of the mesoscale eddy field in the Southeastern Baltic Sea: Model output vs satellite imagery. Russian Journal of Earth Sciences, 19 (4), 1−17.10.2205/2019ES000672.
  2. Zhurbas, V.; Väli, G.; Kuzmina, N. (2019). Rotation of floating particles in submesoscale cyclonic and anticyclonic eddies: a model study for the southeastern Baltic Sea. Ocean Science, 15 (6), 1691−1705.10.5194/os-15-1691-2019.
  3. Papathanasopoulou, Eleni; Simis, Stefan; Alikas, Krista; Ansper, Ave,  Anttila, Saku;  Attila, Jenni et al. (2019, September 30). Satellite-assisted monitoring of water quality to support the implementation of the Water Framework Directive (Version 1.2). Zenodo. DOI: 10.5281/zenodo.3903776
  4. Jacobs GS, Hudjashov G, Saag L, Kusuma P, Darusallam CC, Lawson DJ, Mondal M, Pagani L, Ricaut FX, Stoneking M, Metspalu M, Sudoyo H, Lansing JS, Cox MP. Cell. (2019 May 2); Multiple Deeply Divergent Denisovan Ancestries in Papuans. Cell 177(4):1010-1021.e32. doi: 10.1016/j.cell.2019.02.035. Epub 2019 Apr 11.
  5. Bücking R, Cox MP, Hudjashov G, Saag L, Sudoyo H, Stoneking M. (2019 Dec 26) Archaic mitochondrial DNA inserts in modern day nuclear genomes. BMC Genomics. 20(1):1017. DOI: 10.1186/s12864-019-6392-8.
  6. Karu, Karl; Elhi, Fred; Põhako-Esko, Kaija; Ivaništšev, Vladislav (2019). Predicting Melting Points of Biofriendly Choline-Based Ionic Liquids with Molecular Dynamics. Applied Sciences, 9 (24), 5367.10.3390/app9245367.
  7. Puurand T, Kukuškina V, Pajuste FD and Remm M. (2019). AluMine: alignment-free method for the discovery of polymorphic Alu element insertions. Mobile DNA, 10:31.
  8. Tamm, E., Di Cristofaro, J., Mazières, S. et al (2019). Genome-wide analysis of Corsican population reveals a close affinity with Northern and Central Italy. Sci Rep 9, 13581 DOI: 10.1038/s41598-019-49901-8
  9. Inskip, S., Scheib, C. L., Wohns, A. W., Ge, X., Kivisild, T., & Robb, J. (2019). Evaluating macroscopic sex estimation methods using genetically sexed archaeological material: The medieval skeletal collection from St John’s Divinity School, Cambridge. American Journal of Physical Anthropology (Vol. 168, Issue 2, pp. 340–351). DOI: 10.1002/ajpa.23753
  10. Järve M, Saag L, Scheib CL, Pathak AK, Montinaro F, Pagani L, Flores R, Guellil M, Saag L, Tambets K, Kushniarevich A, Solnik A, Varul L, Zadnikov S, Petrauskas O, Avramenko M, Magomedov B, Didenko S, Toshev G, Bruyako I, Grechko D, Okatenko V, Gorbenko K, Smyrnov O, Heiko A, Reida R, Sapiehin S, Sirotin S, Tairov A, Beisenov A, Starodubtsev M, Vasilev V, Nechvaloda A, Atabiev B, Litvinov S, Ekomasova N, Dzhaubermezov M, Voroniatov S, Utevska O, Shramko I, Khusnutdinova E, Metspalu M, Savelev N, Kriiska A, Kivisild T, Villems R. (2019). Shifts in the Genetic Landscape of the Western Eurasian Steppe Associated with the Beginning and End of the Scythian Dominance.Current Biology: CB, 29(14), 2430–2441.e10. DOI: 10.1016/j.cub.2019.06.019
  11. Saag L, Laneman M, Varul L, Malve M, Valk H, Razzak MA, Shirobokov IG, Khartanovich VI, Mikhaylova ER, Kushniarevich A, Scheib CL, Solnik A, Reisberg T, Parik J, Saag L, Metspalu E, Rootsi S, Montinaro F, Remm M, Mägi R, D’Atanasio E, Crema ER, Díez-Del-Molino D,
    Thomas MG, Kriiska A, Kivisild T, Villems R, Lang V, Metspalu M, Tambets K. (2019).The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East. Current Biology: CB, 29(10), 1701–1711.e16.
  12. Scheib, C. L., Hui, R., D’Atanasio, E., Wohns, A. W., Inskip, S. A., Rose, A., Cessford, C., O’Connell, T. C., Robb, J. E., Evans, C., Patten, R., & Kivisild, T. (2019). East Anglian early Neolithic monument burial linked to contemporary Megaliths. Annals of Human Biology, 46(2), 145–149. DOI: 10.1080/03014460.2019.1623912.
  13. M. Rätsep, J. M. Linnanto, R. Muru, M. Biczysko, J. R. Reimers, and A. Freiberg (2019) Absorption-emission symmetry breaking and the different origins of vibrational structures of the 1Qy and 1Qx electronic transitions of pheophytin aJ. Chem. Phys. 151, 165102 (2019): DOI: 10.1063/1.5116265
  14. Ongaro L, Scliar MO, Flores R, Raveane A, Marnetto D, Sarno S, Gnecchi-Ruscone GA, Alarcón-Riquelme ME, Patin E, Wangkumhang P, Hellenthal G, Gonzalez-Santos M, King RJ, Kouvatsi A, Balanovsky O, Balanovska E, Atramentova L, Turdikulova S, Mastana S, Marjanovic D, Mulahasanovic L, Leskovac A, Lima-Costa MF, Pereira AC, Barreto ML, Horta BL, Mabunda N, May CA, Moreno-Estrada A, Achilli A, Olivieri A, Semino O, Tambets K, Kivisild T, Luiselli D, Torroni A, Capelli C, Tarazona-Santos E, Metspalu M, Pagani L, Montinaro F. (2019) The genomic impact of European colonization of the Americas. Current Biology. 29(23):3974-3986.e4. DOI: 10.1016/j.cub.2019.09.076
  15. Natalia Balinova, Helen Post, Alena Kushniarevich, Rodrigo Flores, Richard Villems et al (2019). Y-chromosomal connection between Hungarians and geographically distant populations of the Ural Mountain region and West Siberia Scientific Reports ISSN 2045-2322 DOI: 10.1038/s41598-019-44272-6
  16. Natalia Balinova, Helen Post, Alena Kushniarevich, Rodrigo Flores (2019). Y-chromosomal analysis of clan structure of Kalmyks, the only European Mongol people, and their relationship to Oirat-Mongols of Inner Asia European Journal of Human Genetics ISSN 1476-5438 (online) DOI: 10.1038/s41431-019-0399-0
  17. Raudvere, U., Kolberg, L., Kuzmin, I., Arak, T., Adler, P., Peterson, H. and Vilo, J., (2019).g: Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic acids research, 47(W1), pp.W191-W198. DOI: 10.1093/nar/gkz369
  18. Molinaro, L., Montinaro, F., Yelmen, B., Marnetto, D., Behar, D. M., Kivisild, T., & Pagani, L. (2019). West Asian sources of the Eurasian component in Ethiopians: a reassessment. Scientific Reports 9(1):18811. DOI: 10.1038/s41598-019-55344-y.
  19. Haber M, Doumet-Serhal C, Scheib CL, Xue Y, Mikulski R, Martiniano R, Fischer-Genz B, Schutkowski H, Kivisild T, Tyler-Smith C. (2019). A Transient Pulse of Genetic Admixture from the Crusaders in the Near East Identified from Ancient Genome Sequences. American journal of Human Genetics 104(5):977-984. doi: 10.1016/j.ajhg.2019.03.015.
  20. Tätte K, Pagani L, Pathak AK, Kõks S, Ho Duy B, Ho XD, Sultana GNN, Sharif MI, Asaduzzaman M, Behar DM, Hadid Y, Villems R, Chaubey G, Kivisild T, Metspalu M. (2019).The genetic legacy of continental scale admixture in Indian Austroasiatic speakers. Scientific Reports. 9(1):3818. doi: 10.1038/s41598-019-40399-8. Erratum in: Sci Rep. 2019 Apr 10;9(1):6104.
  21. Pinotti T, Bergström A, Geppert M, Bawn M, Ohasi D, Shi W, Lacerda DR, Solli A, Norstedt J, Reed K, Dawtry K, González-Andrade F, Paz-Y-Miño C, Revollo S, Cuellar C, Jota MS, Santos JE Jr, Ayub Q, Kivisild T, Sandoval JR, Fujita R, Xue Y, Roewer L, Santos FR, Tyler-Smith C. (2019) Y Chromosome Sequences Reveal a Short Beringian Standstill, Rapid Expansion, and early Population structure of Native American Founders. Current Biology 29(1):149-157.e3. DOI: 10.1016/j.cub.2018.11.029. 
  22. I. Kuusik, M. Berholts, J. Kruusma, A. Tõnisoo, E. Lust, E. Nõmmiste, V. Kisanda  (2019). Valence electronic structure of [EMIM][B(CN)4]: ion-pair vs. bulk descriptionRSC Advances57, 2019
  23. Hasan Sait Arslan, Kairit Sirts, Mark Fishel, Gholamreza Anbarjafari Multimodal Sequential Fashion Attribute Prediction Information (ISSN 2078-2489) doi: 10.3390/info10100308
  24. Teder, Hindrek; Paluoja, Priit; Rekker, Kadri; Salumets, Andres; Krjutskov, Kaarel; Palta, Priit (2019). Computational framework for targeted high coverage sequencing based NIPT Computational framework for targeted high coverage sequencing based NIPT. PLOS ONE, 14 (7), ARTN e0209139.10.1371/journal.pone.0209139.
  25. Žilina, Olga; Rekker, Kadri; Kaplinski, Lauris; Sauk, Martin; Paluoja, Priit; Teder, Hindrek; Ustav, Eva-Liina; Tõnisson, Neeme; Reimand, Tiia; Ridnoi, Konstantin; Palta, Priit; Vermeesch, Joris Robert; Krjutškov, Kaarel; Kurg, Ants; Salumets, Andres (2019). Creating basis for introducing non-invasive prenatal testing in the Estonian public health setting.Prenatal Diagnosis, 39, 1262−1268.10.1002/pd.5578.
  26. Saare, Merli; Laisk, Triin; Teder, Hindrek; Paluoja, Priit; Palta, Priit; Koel, Mariann; Kirss, Fred; Karro, Helle; Sõritsa, Deniss; Salumets, Andres; Krjutškov, Kaarel; Peters, Maire (2019). A molecular tool for menstrual cycle phase dating of endometrial samples in endometriosis transcriptome studies. Biology of Reproduction, 101 (4), 868−868.10.1093/biolre/ioz092.
  27. Kaur Alasoo , Julia Rodrigues, John Danesh, Daniel F Freitag, Dirk S Paul, Daniel J Gaffney (2019). Genetic effects on promoter usage are highly context-specific and contribute to complex traits eLife Jan 8, 2019 DOI: 10.7554/eLife.41673.001
  28. Korotkova, Elizaveta; Luhtaru, Agnes; Del, Maksym; Liin, Krista; Deksne, Daiga; Fishel, Mark (2019). Grammatical Error Correction and Style Transfer via Zero-shot Monolingual Translation.  arXiv:1903.11283
  29. Tättar, Andre; Korotkova, Elizaveta; Fishel, Mark (2019). University of Tartu’s Multilingual Multi-domain WMT19 News Translation Shared Task Submission. In: Proceedings of the Fourth Conference on Machine Translation (Volume 2: Shared Task Papers, Day 1) (382−385). Association for Computational Linguistics. DOI: 10.18653/v1/W19-5342.
  30. M. Camargo, M. Dumas, O. González-Rojas (2019). Learning Accurate LSTM Models of Business Processes, Lect. Notes Bus. Inf. Process., 2019: pp. 286–302. doi:10.1007/978-3-030-26619-6_19.
  31. Loit Kaire et al (2019). Relative Performance of MinION (Oxford Nanopore Technologies) versus Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens. Applied and Environmental Microbiology 85.21 (2019): e01368-19.APA
  32. Sofja Tshepelevitsh, Agnes Kütt, Märt Lõkov, Ivari Kaljurand, Jaan Saame, Agnes Heering, Paul G. Plieger, Robert Vianello, Ivo Leito (2019). On the Basicity of Organic Bases in Different Media Chemistry Europe Volume2019, Issue40 DOI: 10.1002/ejoc.201900956
  33. Yakimenka, Y.; Skachek, V.; Bocharova, I.E.; Kudryashov, B.D. (2019). Stopping Redundancy Hierarchy Beyond the Minimum Distance. IEEE Transactions on Information Theory, 3724−3737. DOI: 10.1109/TIT.2018.2873140.
  34. Y Yakimenka, E Rosnes Failure analysis of the interval-passing algorithm for compressed sensing IEEE Transactions on Information Theory ( Volume: 66, Issue: 4, April 2020) DOI: 10.1109/TIT.2020.2969163
  35. Madli Jõks, Meelis Pärtel (2018). Plant diversity in Oceanic archipelagos: realistic patterns emulated by an agent‐based computer simulation Ecography Volume42, Issue4 DOI: 10.1111/ecog.03985.
  36. Tasa, T,; Krebs, K.; Kals, M.; Mägi, R.; Lauschke, V.M.; Haller, T.; Puurand, T.; Remm, M.; Esko, T.; Metspalu, A.; Vilo, J.; Milani, L. (2019). Genetic variation in the Estonian population: pharmacogenomics study of adverse drug effects using electronic health records. European Journal of Human Genetics, 442−454. DOI: 10.1038/s41431-018-0300-6.
  37. Andre Leesment, Ivari Kaljurand, Aleksander Trummal, Agnes Kütt, Thomas Netscher, Werner Bonrath, Ivo Leito (2019) Validation and extension of the gas‐phase superacidity scale DOI: 10.1002/rcm.8598
  38. Stark, C.W., Trummal, A., Uudsemaa, M. et al. Solute-solvent electronic interaction is responsible for initial charge separation in ruthenium complexes [Ru(bpy)3]2+ and [Ru(phen)3]2+. Commun Chem 2, 108 (2019). DOI: 10.1038/s42004-019-0213-5
  39. Anna Peterson, Mari-Liis Ludvig, Jevgenija Martõnova, Sandra Kaabel, Paul Kerner, Merle Uudsemaa, Aleksander Trummal, Maria Fomitšenko, Tõnis Pehk, Riina Aav & Jasper Adamson (2019). New oxacalix[4]arene carboxylate detects viologen in protic media DOI: 10.1080/10610278.2019.1659269
  40. Meelis Kull, Miquel Perello-Nieto, Markus Kängsepp, Telmo Silva Filho, Hao Song, Peter Flach (2019). Beyond temperature scaling: Obtaining well-calibrated multiclass probabilities with Dirichlet calibration. arXiv:1910.12656 [cs.LG]
  41. Shah, F.A., Sirts, K., and Pfahl, D. (2019), Simplifying the Classification of App Reviews Using Only Lexical Features, Springer book series on Communications in Computer and Information Science, 2019, vol. 1077, pp. 173
  42. Wei Q. Deng, Shihong Mao, Anette Kalnapenkis, Tõnu Esko, Reedik Mägi, Guillaume Paré, Lei Sun (2019). Analytical strategies to include the X‐chromosome in variance heterogeneity analyses: Evidence for trait‐specific polygenic variance structure Genetic Epidemiology volume43, Issue 7 DOI: 10.1002/gepi.22247
  43. Yankovskaya, Elizaveta; Tättar, Andre; Fishel, Mark (2019). Quality Estimation and Translation Metrics via Pre-trained Word and Sentence Embeddings. Proceedings of the Fourth Conference on Machine Translation (Volume 3: Shared Task Papers, Day 2) (101−105). Association for Computational Linguistics. DOI: 10.18653/v1/W19-5410.

Doctorate Theses

  1. Eleri Aedmaa (2019). Detecting Compositionality of Estonian Particle Verbs with Statistical and Linguistic Methods (Eesti keele ühendverbide automaattuvastus lingvistiliste ja statistiliste meetoditega), Tartu Ülikool, Humanitaarteaduste ja kunstide valdkond, eesti ja üldkeeleteaduse instituut. Tartu Ülikooli Kirjastus

2018

Articles

  1. Pathak, Ajai K; Kadian, Anurag; Kushniarevich, Alena; Montinaro, Francesco; Mondal, Mayukh; Ongaro, Linda; Singh, Manvendra; Kumar, Pramod; Rai, Niraj; Parik, Jüri; Metspalu, Ene; Rootsi, Siiri; Pagani, Luca; Kivisild, Toomas; Metspalu, Mait; Chaubey, Gyaneshwer; Villems, Richard 2018 The genetic ancestry of modern Indus Valley populations from Northwest India The American Journal of Human Genetics 103 (6), 918-929
  2. Scheib, C. L., Li, H., Desai, T., Link, V., Kendall, C., Dewar, G., Griffith, P. W., Mörseburg, A., Johnson, J. R., Potter, A., Kerr, S. L., Endicott, P., Lindo, J., Haber, M., Xue, Y., Tyler-Smith, C., Sandhu, M. S., Lorenz, J. G., Randall, T. D., … Kivisild, T. (2018). Ancient human parallel lineages within North America contributed to a coastal expansion. Science, 360(6392), 1024–1027. DOI: 10.1126/science.aar6851.  
  3. Tshepelevitsh, S., Hernits, K. & Leito, I (2018). Prediction of partition and distribution coefficients in various solvent pairs with COSMO-RS. J Comput Aided Mol Des32, 711–722 (2018). doi: 10.1007/s10822-018-0125-y
  4.  Elizaveta Yankovskaya, Andre TättarMark Fishel (2018).

    Quality Estimation with Force-Decoded Attention and Cross-lingual Embeddings. WMT (shared task) 2018: 816-821

  5. Elizaveta Yankovskaya, Mark Fishel (2018). 

    Low-Resource Translation Quality Estimation for Estonian. Baltic HLT 2018: 175-182

  6. Maksym Del, Andre Tättar, Fishel (2018). Phrase-based Unsupervised Machine Translation withCompositional Phrase Embeddings Proceedings of the Third Conference on Machine Translation (WMT), Volume 2: Shared Task Papers DOI: 10.18653/v1/W18-64034
  7. Karu, Karl; Mišin, Maksim; Ers, Heigo; Sun, Jianwei; Ivaništšev, Vladislav; (2018). Performance of SCAN density functional for a set of ionic liquid ion pairs. International Journal of Quantum Chemistry, 118 (13), e25582.10.1002/qua.25582.
  8. Roos Nerut, Eva; Karu, Karl; Voroshylova, Iuliia; Kirchner, Kathleen; Kirchner, Tom; Fedorov, Maxim; Ivaništšev, Vladislav; (2018). NaRIBaS — A Scripting Framework for Computational Modeling of Nanomaterials and Room Temperature Ionic Liquids in Bulk and Slab. Computation, 6, 57.10.3390/computation6040057.
  9. Teder, Hindrek; Koel, Mariann; Paluoja, Priit; Jatsenko, Tatjana; Rekker, Kadri; Laisk-Podar, Triin; Kukuškina, Viktorija; Velthut-Meikas, Agne; Fjodorova, Olga; Peters, Maire; Kere, Juha; Salumets, Andres; Palta, Priit; Krjutškov, Kaarel (2018). TAC-seq: targeted DNA and RNA sequencing for precise biomarker molecule counting. npj Genomic Medicine, 3, ARTN 34. DOI: 10.1038/s41525-018-0072-5.
  10. Sõritsa, D.; Teder, H.; Roosipuu, R.; Tamm, H.; Laisk-Podar, T.; Soplepmann, P.; Altraja, A.; Salumets, A.; Peters, M. (2018). Whole exome sequencing of benign pulmonary metastasizing leiomyoma reveals mutation in the BMP8B gene. BMC Medical Genetics, 19 (1), 20. DOI: 10.1186/s12881-018-0537-5.
  11. Kolberg, L., Kuzmin, I., Adler, P., Vilo, J. and Peterson, H., 2018. funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data. BMC genomics19(1), pp.1-17. DOI: 10.1186/s12864-018-5176-x
  12. Triin Laisk, Viktorija Kukuškina, Duncan Palmer, Samantha Laber, Chia-Yen Chen, Teresa Ferreira, Nilufer Rahmioglu, Krina Zondervan, Christian Becker, Jordan W Smoller, Margaret Lippincott, Andres Salumets, Ingrid Granne, Stephanie Seminara, Benjamin Neale, Reedik Mägi, Cecilia M Lindgren, Large-scale meta-analysis highlights the hypothalamic–pituitary–gonadal axis in the genetic regulation of menstrual cycle length, Human Molecular Genetics, Volume 27, Issue 24, 15 December 2018, Pages 4323–4332, https://doi.org/10.1093/hmg/ddy317
  13. Tkachenko, A., & Sirts, K. (2018, September). Neural Morphological Tagging for Estonian. In Baltic HLT (pp. 166-174).
  14. Tkachenko, A., & Sirts, K. (2018, October). Modeling Composite Labels for Neural Morphological Tagging. In Proceedings of the 22nd Conference on Computational Natural Language Learning (pp. 368-379).
  15. Arslan, H. S., Sirts, K., Fishel, M., & Anbarjafari, G. (2019). Multimodal sequential fashion attribute prediction. Information10(10), 308.
  16. Shah, F.A., Sirts, K., and Pfahl, D. (2018). Simple App Review Classification with Only Lexical Features Proceedings of the 13th International Conference on Software Technologies, 2018, pp. 112-119.


2017

Articles

  1. Pajuste, Fanny-Dhelia; Kaplinski, Lauris; Möls, Märt; Puurand, Tarmo; Lepamets, Maarja; Remm, Maido (2017). FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads. Scientific Reports 7, Article number: 2537 (2017). doi:10.1038/s41598-017-02487-5.
  2. Kuzovkin, Ilya; Vicente, Raul; Petton, Mathilde; Lachaux, Jean-Philippe; Baciu, Monica; Kahane, Philippe; Rheims, Sylvain; Vidal, Juan R.; Aru, Jaan (2017). Activations of Deep Convolutional Neural Network are Aligned with Gamma Band Activity of Human Visual Cortex. doi: https://doi.org/10.1101/133694.
  3. Teinemaa, Irene; Dumas, Marlon; La Rosa, Marcello; Maggi, Fabrizio Maria (in spe). Outcome-Oriented Predictive Process Monitoring: Review and Benchmark. ArxivX CoRR abs/1707.06766, 2017.
  4. Haller, Toomas; Leitsalu, Liis; Fischer, Krista; Nuotio, Marja-Liisa; Esko, Tõnu; Boomsma, Dorothea Irene; Kyvik, Kirsten Ohm; Spector, Tim D.; Perola, Markus; Metspalu, Andres (2017). MixFit: Methodology for Computing Ancestry-Related Genetic Scores at the Individual Level and Its Application to the Estonian and Finnish Population Studies. PLoS One. 2017; 12(1): e0170325. doi: 10.1371/journal.pone.0170325.
  5. Haller, Toomas; Kals, Mart; Esko, Tõnu; Mägi, Reedik; Fischer, Krista. RegScan: a GWAS tool for quick estimation of allele effects on continuous traits and their combinations. Brief Bioinform. 2015 Jan; 16(1): 39–44. doi: 10.1093/bib/bbt066.
  6. Kasela, Silva; Kisand, Kai; Tserel, Liina; Kaleviste, Epp; Remm, Anu; Fischer, Krista; Esko, Tõnu; Westra, Harm-Jan; Fairfax, Benjamin P.; Makino, Seiko; Knight, Julian C.; Franke, Lude; Metspalu, Andres; Peterson, Pärt; Milani, Lili (2017). Pathogenic implications for autoimmune mechanisms derived by comparative eQTL analysis of CD4+ versus CD8+ T cells. https://doi.org/10.1371/journal.pgen.1006643
  7. Tshepelevitch, Sofja; Trummal, Aleksander; Haav, Kristjan; Martin, Kerli; Leito, Ivo (2017). Hydrogen-Bond Donicity in DMSO and Gas Phase and Its Dependence on Brønsted Acidity. J. Phys. Chem. A 2017, 121, 357–369; doi: 10.1021/acs.jpca.6b11115.
  8. Lõkov, Märt; Tshepelevitsh, Sofja; Heering, Agnes; Plieger, Paul G.; Vianello, Robert; Leito, Ivo (2017). On the Basicity of Conjugated Nitrogen Heterocycles in Different Media. Eur. J. Org. Chem. 2017, 30, 4475-4489; doi: 10.1002/ejoc.201700749.
  9. Teearu, A.; Vahur, S.; Rodima, T.; Herodes, K.; Bonrath, W.; Netscher, T.; Tshepelevitsh, S.; Trummal, A.; Lõkov, M.; Leito, I. (2017). Method development for the analysis of resinous materials with MALDI-FT-ICR-MS: novel internal standards and a new matrix material for negative ion mode. J. Mass Spectrom. 2017, 52, 603–617; doi: 10.1002/jms.3943
  10. Martin, Kerli; Nõges, Juuli; Haav, Kristjan; Kadam, Sandip A.; Pung, Astrid; Leito, Ivo (2017). Exploring Selectivity of 22 Acyclic Urea-, Carbazole- and Indolocarbazole-Based Receptors towards 11 Monocarboxylates. Eur. J. Org. Chem. 2017, 5231–5237.
  11. Pung, Astrid; Leito, Ivo (2017). Predicting Relative Stability of Conformers in Solution with COSMO-RS. J. Phys. Chem. A, 2017, 121, 6823 – 6829. doi: 10.1021/acs.jpca.7b05197.
  12. Kadam, Sandip A.; Haav, Kristjan; Toom, Lauri; Pung, Astrid; Mayeux, Charly; Leito, Ivo (2017). Multidentate Anion Receptors for Binding Glyphosate Dianion: Structure and Affinity. Eur. J. Org. Chem. 2017, 1396–1406. doi: 10.1002/ejoc.201601583.

2016

Articles

  1. Yakimenka, Yauhen, and Eirik Rosnes (2016). “On Failing Sets of the Interval-Passing Algorithm for
    Compressed Sensing
    .” 54th Annual Allerton Conference on Communication, Control, and Computing (Allerton). IEEE, 2016.
  2. Läll, Kristi; Mägi, Reedik; Morris, Andrew; Metspalu, Andres; Fischer, Krista (2016). Personalized risk prediction for type 2 diabetes: the potential of genetic risk scores. Genetics in medicine : official journal of the American College of Medical Genetics, 1−10, 10.1038/gim.2016.103
  3. Mark, Kristiina; Saag, Lauri; Leavitt, Steven D.; Will-Wolf, Susan; Nelsen, Matthew P.; Tõrra, Tiiu; Saag, Andres; Randlane, Tiina; Lumbsch, H. Thorsten (2016). Evaluation of traditionally circumscribed species in the lichen-forming genus Usnea, section Usnea (Parmeliaceae, Ascomycota) using a six-locus dataset. Organisms Diversity & Evolution, x (x), 1−28, 10.1007/s13127-016-0273-7.
  4. Ilumäe, Anne-Mai; Reidla, Maere; Chukhryaeva, Marina; Järve, Mari; Post, Helen; Karmin, Monika; Saag, Lauri; Agdzhoyan, Anastasiya; Kushniarevich, Alena; Litvinov, Sergey; Ekomasova, Natalya; Tambets, Kristiina; Metspalu, Ene; Khusainova, Rita; Yunusbayev, Bayazit; Khusnutdinova, Elza K; Osipova, Ludmila P; Fedorova, Sardana; Utevska, Olga; Koshel, Sergey … Rootsi, Siiri (2016). Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families. American Journal of Human Genetics, 163−173, 10.1016/j.ajhg.2016.05.025.
  5. Karmin, M.; Saag, L.; Vicente, M.; Wilson Sayres, M.A.; Järve, M.; Gerst Talas, U.; Rootsi, S.; Ilumäe, A.-M.; Mägi, R.; Mitt, M.; Pagani, L.; Puurand, T.; Faltyskova, Z.; Clemente, F.; Cardona, A.; Metspalu, E.; Sahakyan, H.; Yunusbayev, B.; Hudjashov, G.; DeGiorgio, M. … Kivisild, T. (2015). A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Research, 459−66, gr.186684.114.
  6. Kuznetsov, Aleksei; Kivi, Rait; Järv, Jaak (2016). Computational modeling of acrylodan-labeled cAMP dependent protein kinase catalytic subunit unfolding. Computational Biology and Chemistry, 197−201.
  7. Salmar, Siim; Vaalma, Morten; Vider, Henry; Tenno, Tiina; Kuznetsov, Aleksei; Järv, Jaak; Tuulmets, Ants (2016). Reaction kinetics and solubility in water-organic binary solutions are governed by similar solvation equilibria. Journal of Physical Organic Chemistry, 29 (3), 118−126, 10.1002/poc.3507.
  8. Limbach, Maia; Saare, Mario; Tserel, Liina; Kisand, Kai; Eglit, Triin; Sauer, Sacha; Axelsson, Tomas; Syvänen, Ann-Christine; Metspalu, Andrus; Milani, Lili; Peterson, Pärt. (2016). Epigenetic profiling in CD4+ and CD8+ T cells from Graves’ disease patients reveals changes in genes associated with T cell receptor signaling. Journal of Autoimmunity, 1, j.jaut.2015.09.006
  9. C. Siimenson, M. Lembinen, O. Oll, L. Läll, M. Tarkanovskaja, V. Ivaništšev, L. Siinor, T. Thomberg, K. Lust, E. Lust, Electrochemical Investigation of 1-Ethyl-3-methylimidazolium Bromide and Tetrafluoroborate Mixture at Bi (111) Electrode Interface, J. Electrochem. Soc. 163 (2016) H723–H730. doi: 10.1149/2.0111609jes
  10. A. Ruzanov, K. Karu, V. Ivaništšev, R.R. Nazmutdinov, E. Lust, Interplay between the hydrophilicity of metal electrodes and their interfacial capacitance, Electrochim. Acta. 210 (2016) 615–621. doi:10.1016/j.electacta.2016.05.110.
  11. Lage-Estebanez, A. Ruzanov, J.M.G. de la Vega, M.V. Fedorov, V.B. Ivaništšev, Self-interaction error in DFT-based modelling of ionic liquids, Phys. Chem. Chem. Phys. 18 (2016) 2175–2182. doi:10.1039/C5CP05922D.
  12. K. Karu, A. Ruzanov, H. Ers, V. Ivaništšev, I. Lage-Estebanez, J.M. García de la Vega, Predictions of Physicochemical Properties of Ionic Liquids with DFT, Computation. 4 (2016) 25. doi:10.3390/computation4030025.
  13. >Haring L, Müürsepp A, Mõttus R, Ilves P, Koch K, Uppin K, Tarnovskaja J, Maron E, Zharkovsky A, Vasar E, Vasar V. Cortical thickness and surface area correlates with cognitive dysfunction among first-episode psychosis patients. 2016 Jul;46(10):2145-55. doi: 10.1017/S0033291716000684. Epub 2016 Jun 7
  14. Kaljurand, Ivari; Saame, Jaan; Rodima, Toomas; Koppel, Ivar; Koppel, Ilmar A.; Ko?gel, Julius F.; Sundermeyer, Jörg; Ko?hn, Uwe; Coles, Martyn P.; Leito, Ivo (2016). Experimental Basicities of Phosphazene, Guanidinophosphazene, and Proton Sponge Superbases in the Gas Phase and Solution. Journal of Physical Chemistry A, 120 (16), 2591−2604, 10.1021/acs.jpca.6b01552.
  15. A. Tamm, G. Samolyuk, A. A. Correa, M. Klintenberg, A. Aabloo, and A. Caro, (2016) The electron-phonon interaction within classical molecular dynamicsPhys. Rev. B94, 024305.
  16. Priit Priimägi, Daniel Brandell, Shruti Srivastav, Alvo Aabloo, Heiki Kasemägi, Vahur Zadin (2016) Optimizing the design of 3D-pillar microbatteries using finite element modelling, Electrochimica Acta 209(10), 138–148.
  17. Kalvet, I.; Tammiku-Taul, J.; Mäeorg, U.; Tämm, K.; Burk, P.; Sikk, L. (2016). NMR and DFT Study of the Copper(I)-Catalyzed Cycloaddition Reaction: H/D Scrambling of Alkynes and Variable Reaction Order of the Catalyst. ChemCatChem, 8 (10), 1804−1808, 10.1002/cctc.201600176.
  18. Tämm, K.; Sikk, L.; Burk, J.; Rallo, R.; Pokhrel, S.; Mädler, L.; Scott-Fordsmand, J.J.; Burk, P.; Tamm, T. (2016). Parametrization of nanoparticles: development of full-particle nanodescriptors. Nanoscale, 0000−0000, C6NR04376C.
  19. Adamson, Aiko; Kaljurand, Ivari; Guillemin, Jean-Claude; Burk, Peeter (2016). Relative stability and proton transfer reactions of unsaturated isocyanides and cyanides. Journal of Physical Organic Chemistry, xx−xx, 10.1002/poc.3562.
  20. Pillai, G.G.; Mederos, L.; Panda, C.S.; Gronski, A.; Burk, P.; Hall, C.D.; Katritzky, A.R.; Tämm, K.; Karelson, M. (2016). Robust Modeling and Scaffold Hopping: Case Study based on HIV Reverse Transcriptase Inhibitors Type-1 Data. Medicinal Chemistry, x−x, 1573406411666151005110141
  21. Negi N, Tamang R, Pande V, Sharma A, Shah A, Reddy AG, Vishnupriya S, Singh L, Chaubey G, Thangaraj K. The paternal ancestry of Uttarakhand does not imitate the classical caste system of India. J Hum Genet. 2016. 61(2):167:72.
  22. Mörseburg A, Pagani L, Ricaut FX, Yngvadottir B, Harney E, Castillo C, Hoogervorst T, Antao T, Kusuma P, Brucato N, Cardona A, Pierron D, Letellier T, Wee J, Abdullah S, Metspalu M, Kivisild T. Multi-layered population structure in Island Southeast Asians. Eur J Hum Genet. 2016.
  23. Brucato N, Kusuma P, Cox MP, Pierron D, Purnomo GA, Adelaar A, Kivisild T, Letellier T, Sudoyo H, Ricaut FX. Malagasy Genetic Ancestry Comes from an Historical Malay Trading Post in Southeast Borneo. Mol Biol Evol. 2016. 33(9):2396-400.
  24. Kivi G, Teesalu K, Parik J, Kontkar E, Ustav M Jr, Noodla L, Ustav M, Männik A. HybriFree: a robust and rapid method for the development of monoclonal antibodies from different host species. BMC Biotechnol. 2016. 16:2.
  25. Šarac J, Šari? T, Havaš Auguštin D, Novokmet N, Vekari? N, Musta? M, Grahovac B, Kapovi? M, Nevajda B, Glasnovi? A, Missoni S, Rootsi S, Rudan P. Genetic heritage of Croatians in the Southeastern European gene pool-Y chromosome analysis of the Croatian continental and Island population. Am J Hum Biol. 2016.
  26. Chaubey G, Singh M, Rai N, Kariappa M, Singh K, Singh A, Pratap Singh D, Tamang R, Selvi Rani D, Reddy AG, Kumar Singh V, Singh L, Thangaraj K. Genetic affinities of the Jewish populations of India. Sci Rep. 2016. 6:19166.
  27. Pankratov V, Litvinov S, Kassian A, Shulhin D, Tchebotarev L, Yunusbayev B, Möls M, Sahakyan H, Yepiskoposyan L, Rootsi S, Metspalu E, Golubenko M, Ekomasova N, Akhatova F, Khusnutdinova E, Heyer E, Endicott P, Derenko M, Malyarchuk B, Metspalu M, Davydenko O, Villems R, Kushniarevich A. East Eurasian ancestry in the middle of Europe: genetic footprints of Steppe nomads in the genomes of Belarusian Lipka Tatars. Sci Rep. 2016. 6:30197.
  28. Singh S, Singh A, Rajkumar R, Sampath Kumar K, Kadarkarai Samy S, Nizamuddin S, Singh A, Ahmed Sheikh S, Peddada V, Khanna V, Veeraiah P, Pandit A, Chaubey G, Singh L, Thangaraj K. Dissecting the influence of Neolithic demic diffusion on Indian Y-chromosome pool through J2-M172 haplogroup. Sci Rep. 2016. 6:19157.
  29. Tšuiko O, Nõukas M, Žilina O, Hensen K, Tapanainen JS, Mägi R, Kals M, Kivistik PA, Haller-Kikkatalo K, Salumets A, Kurg A. Copy number variation analysis detects novel candidate genes involved in follicular growth and oocyte maturation in a cohort of premature ovarian failure cases.  Hum Reprod. 2016 Aug;31(8):1913-25. doi: 10.1093/humrep/dew142. Epub 2016 Jun 14.
  30. Ivanov M, Kals M, Lauschke V, Barragan I, Ewels P, Käller M, Axelsson T, Lehtiö J, Milani L, Ingelman-Sundberg M. Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression. Nucleic Acids Res. 2016 Aug 19;44(14):6756-69. doi: 10.1093/nar/gkw316. Epub 2016 Apr 29.
  31. Mihailov E, Nikopensius T, Reigo A, Nikkolo C, Kals M, Aruaas K, Milani L, Seepter H, Metspalu A. Whole-exome sequencing identifies a potential TTN mutation in a multiplex family with inguinal hernia. Hernia. Epub 2016 Apr 26.
  32. Pervjakova N, Kasela S, Morris AP, Kals M, Metspalu A, Lindgren CM, Salumets A, Mägi R. Imprinted genes and imprinting control regions show predominant intermediate methylation in adult somatic tissues. 2016 Jun;8(6):789-99. doi: 10.2217/epi.16.8. Epub 2016 Mar 23.
  33. Ivask M, Hugill A, Kõks S. 2016. RNA-sequencing of WFS1-deficient pancreatic islets. Physiol Rep 4(7): e12750
  34. Ronk, A., de Bello, F., Fibich, P., & Pärtel, M. (2016). Large-scale dark diversity estimates: new perspectives with combined methods. Ecology and Evolution, n/a-n/a. doi:10.1002/ece3.2371 
  35. Juurmaa, J., Menke, R. A. L., Vila, P., Müürsepp, A., Tomberg, T., Ilves, P., Nigul, M., Johansen-Berg, H., Donaghy, M., Stagg, C. J., Stepens, A. and Taba, P. (2016), Grey matter abnormalities in methcathinone abusers with a Parkinsonian syndrome. Brain and Behavior, 00:1–8. e00539, doi: 10.1002/brb3.539
  36. Abboud, Jose-Luis M; Alkorta, Ibon; Davalos, Juan Z; Koppel, Ilmar A; Koppel, Ivar; Lenoir, Dieter; Martinez, Sonia; Mishima, Masaaki; The Thermodynamic Stability of Adamantylideneadamantane and Its Proton-and Electron-Exchanges. Comparison with Simple Alkenes, Bulletin of the Chemical Society of Japan,,0,,2016.
  37. Trummal, Aleksander; Lipping, Lauri; Kaljurand, Ivari; Koppel, Ilmar; Leito, Ivo (2016). Acidity of Strong Acids in Water and Dimethyl Sulfoxide. The Journal of Physical Chemistry A, 120 (20), 3663−3669, 10.1021/acs.jpca.6b02253.
  38. Pagani, Luca; Lawson, Daniel John; Jagoda, Evelyn; Mörseburg, Alexander; Eriksson, Anders; Mitt, Mario; Clemente, Florian; Hudjashov, Georgi; DeGiorgio, Michael; Saag, Lauri; Wall, Jeffrey D; Cardona, Alexia; Mägi, Reedik; Sayres, Melissa A Wilson; Kaewert, Sarah; Inchley, Charlotte; Scheib, Christiana L; Järve, Mari; Karmin, Monika; Jacobs, Guy S … Metspalu, Mait (2016). Genomic analyses inform on migration events during the peopling of Eurasia. Nature, 1−5, 10.1038/nature19792.
  39. Andrea Ganna, Giulio Genovese, Daniel P. Howrigan, Andrea Byrnes, Mitja Kurki, Seyedeh M. Zekavat, Christopher W. Whelan, Mart Kals, et al. Ultra-rare disruptive and damaging mutations influence educational attainment in the general population Nature Neuroscience, 19 (12), 1563−1565, 10.1038/nn.4404.
  40. Michael Guoa, Satish K. Nandakumar, Jacob C. Ulirsch, Seyedeh Maryam Zekavat, Jason D. Buenrostro, Pradeep Natarajan, Rany Salem, Roberto Chiarle, Mario Mitt, Mart Kals, Kalle Pärn, Krista Fischer, Lili Milani, Reedik Mägi, Priit Palta, Stacey B. Gabriel, Andres Metspalu, Eric S. Lander, Sekar Kathiresan, Joel N. Hirschhorn, Tõnu Esko, & Vijay G. Sankarana Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms, MH Guo et al. Proc Natl Acad Sci U S A 114 (3), E327-E336.

2015

Articles

  1. Karmin et al. A recent bottleneck of Y chromosome diversity coincides with a global change in culture, Cold Spring Harbor Laboratory Press, March 13, 2015, doi:10.1101/gr.186684.114
  2. Leito, Ivo; Koppel, Ilmar; Koppel, Ivar; Kaupmees, Karl; Tshepelevitsh, Sofja; Saame, Jaan (2015). Basicity Limits of Neutral Organic Superbases. Angewandte Chemie-International Edition in English, 54(32), 9262 – 9265.
  3. Abboud, Jose-Luis M.; Koppel, Ilmar A.; Uggerud, Einar; Leito, Ivo; Koppel, Ivar; Sekiguchi, Osamu; Kaupmees, Karl; Saame, Jaan; Kütt, Karl; Mishima, Masaaki (2015). Solution and Gas-Phase Acidities of all-trans (all-E) Retinoic Acid: An Experimental and Computational Study. Chemistry – A European Journal, 21, 11238 – 11243.
  4. Lipping, l.; Leito, I; Koppel , I.; Krossing , I.; Himmel , H.; Koppel , I.A. (2015). Superacidity of Closo-Dodecaborate-Based Brönsted Acids:a DFT Study. Journal of Physical Chemistry A, 119(4), 735 – 743.
  5. Reimann, E.; Kingo, K.; Karelson, M.; Silm, H.; Aunin, E.; Raud, K.; Vasar, E.; Kõks, S.. Gene expression study of CRH-POMC system including endogenous opioids in vitiligo skin biopsies and peripheral blood mononuclear cells.
  6. Kasvandik, Sergo; Sillaste, Gerly; Velthut-Meikas, Agne; Mikelsaar, Aavo-Valdur; Hallap, Triin; Padrik, Peeter; Tenson, Tanel; Jaakma, Ülle; Kõks, Sulev; Salumets, Andres (2015). Bovine sperm plasma membrane proteomics through biotinylation and subcellular enrichment. Proteomics, 15(11), 1906 – 1920.
  7. Nomm, Monika; Mark, Elina; Kilk, Kalle; Koks, Sulev; Jaakma, Ulle (2014). LOW-MOLECULAR-WEIGHT METABOLITES IN BOVINE IN VITRO PRODUCTION CULTURE MEDIA AS EMBRYO QUALITY MARKERS. In: Reproduction, fertility, and development: IETS, Versailles, France, 2015. CSIRO PUBLISHING, 135 – 136.
  8. Klavan, Jane; Pilvik, Maarja-Liisa; Uiboaed, Kristel (2015). The Use of Multivariate Statistical Classification Models for Predicting Constructional Choice in Spoken, Non-Standard Varieties of Estonian. SKY Journal of Linguistics, 28, 187−224.
  9. Kuusik, Ivar; Tarkanovskaja, Marta; Kruusma, Jaanus; Reedo, Valter; Välbe, Raul; Lõhmus, Ants; Kisand, Vambola; Lust, Enn; Kukk, Edwin; Nõmmiste, Ergo (2015). Near threshold photodissociation study of EMIMBF4 vapor. RSC Advances, 5, 6834−6842, C4RA12775G.
  10. Yunusbayev B, Metspalu M, Metspalu E, Valeev A, Litvinov S, Valiev R, et al. (2015) The Genetic Legacy of the Expansion of Turkic-Speaking Nomads across Eurasia. PLoS Genet 11(4): e1005068. doi:10.1371/journal.pgen.1005068
  11. Pliss L, Timša L, Rootsi S, Tambets K, Pelnena I, Zole E, Puzuka A, Sabule A, Rozane S, Lace B, Kucinskas V, Krumina A, Ranka R, Baumanis V. Y-Chromosomal Lineages of Latvians in the Context of the Genetic Variation of the Eastern-Baltic Region. Ann Hum Genet. 2015. 79(6):418-30.
  12. Underhill PA, Poznik GD, Rootsi S, Järve M, et al. The phylogenetic and geographic structure of Y-chromosome haplogroup R1a. Eur J Hum Genet. 2015. 23(1):124-31.
  13. Negi N, Tamang R, Pande V, Sharma A, Shah A, Reddy AG, Vishnupriya S, Singh L, Chaubey G, Thangaraj K. The paternal ancestry of Uttarakhand does not imitate the classical caste system of India. J Hum Genet. 2015.
  14. Allentoft ME, Sikora M, Sjögren KG, Rasmussen S, Rasmussen M, Metspalu M,  Saag L, et al. Population genomics of Bronze Age Eurasia. Nature. 2015. 522(7555):167-72.
  15. Raghavan M, Metspalu M, Metspalu E, Karmin M, Tambets K, et al. POPULATION GENETICS. Genomic evidence for he Pleistocene and recent population history of NativAmericans. Science. 2015. 349(6250): aab3884.
  16. Babu Gurramkonda V, Hussain Syed A, Murthy J, Chaubey G, Bhaskar Lakkakula VK. Polymorphic variants near 1p22 and 20q11.2 loci and the risk of non-syndromic cleft lip and palate inSouth Indian population. Int J Pediatr Otorhinolaryngol. 2015. 79(12):2389-93.
  17. Sudmant PH, Sahakyan H, Kivisild T, Metspalu E, Parik J, Villems R, Metspalu M, et al. Global diversity, population stratification, and selection of human copy number variation. Science. 2015.
  18. Kushniarevich A, Metspalu E, Reidla M, Tambets K, Tamm E, Metspalu M, Kivisild T, Villems R, et al. Genetic Heritage of the Balto-Slavic Speaking Populations: A Synthesis of Autosomal, Mitochondrial and Y-Chromosomal Data. PLoS One. 2015. 10(9):e0135820.
  19. Chaubey G, Kadian A, Bala S, Rao VR. Genetic Affinity of the Bhil, Kol and Gond Mentioned in Epic Ramayana. PLoS One. 2015. 10(6):e0127655.
  20. Utevska OM, Pshenichnov AS, Dibirova KhD, Rootsi S, Agdzhoyan AT, Churnosov MI, Balanovska EV, Atramentova LA, Balanovsky OP. Gene Pool Similarities and Differences between Ukrainians and Russians of Slobozhanshchina Based on YChromosome Data. Cytology and Genetics. 2015. 49(4):245-53.
  21. De Fanti S, Barbieri C, Sarno S, Sevini F, Vianello D, Tamm E, Metspalu E, van Oven M, Hübner A, Sazzini M, Franceschi C, Pettener D, Luiselli D. Fine Dissection of Human Mitochondrial DNA Haplogroup HV Lineages Reveals Paleolithic Signatures from European Glacial Refugia. PLoS One. 2015. 10(12):e0144391
  22. Sultana GN, Sharif MI, Asaduzzaman M, Chaubey G. Evaluating the genetic impact of South and Southeast Asia on the peopling of Bangladesh. Leg Med (Tokyo). 2015. 17(6):446-50.
  23. Rasmussen S, Allentoft ME, Nielsen K, Orlando L, Sikora M, Sjögren KG, Pedersen AG, Schubert M, Van Dam A, Kapel CM, Nielsen HB, Brunak S, Avetisyan P, Epimakhov A, Khalyapin MV, Gnuni A, Kriiska A, Lasak I, Metspalu M, Moiseyev V, Gromov A, Pokutta D, Saag L, Varul L, Yepiskoposyan L, Sicheritz-Pontén T, Foley RA, Lahr MM, Nielsen R, Kristiansen K, Willerslev E. Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago. Cell. 2015. 163(3):571-82.
  24. Keermann M, Kõks S, Reimann E, Prans E, Abram K, Kingo K. 2015. Transcriptional landscape of psoriasis identifies the involvement of IL36 and IL36RN. BMC Genomics 16:322
  25. Keermann M, Kõks S, Reimann E, Abram K, Erm T, Silm H, Kingo K. 2015. Expression of IL-36 family cytokines and IL-37 but not IL-38 is altered in psoriatic skin. J Dermatol Sci 80(2):150-2
  26. Kõks G, Uudelepp ML, Limbach M, Peterson P, Reimann E, Kõks S. 2015. Smoking-induced expression of the GPR15 gene indicates its potential role in chronic inflammatory pathologies. Am J Pathol 187(11):2898-906
  27. Ronk, A., Szava-Kovats, R., & Pärtel, M. (2015). Applying the dark diversity concept to plants at the European scale. Ecography, 38(10), 1015-1025. doi:10.1111/ecog.01236
  28. Ploom, A.; Tuulmets, A.; Panov, D.; Burk, P. (2015). A kinetic view of the mechanism of the Grignard reaction with alkoxysilanes. Phosphorus, sulfur, and silicon and the related elements, 190 (4), 509−519, 10426507.2014.952002.
  29. Kekišev, Ott; Kaljurand, Ivari; Toom, Lauri; Lenoir, Dieter; Burk, Peeter; Järv, Jaak (2015). Effect of strain on gas-phase basicity of (E)-1- methyl-2-(1-methyl-2-adamantylidene) adamantane. Journal of Physical Organic Chemistry, 28 (7), 447−451, poc.3435.
  30. Adamson, Aiko; Guillemin, Jean-Claude; Burk, Peeter (2015). Proton transfer reactions of hydrazine-boranes. Journal of Physical Organic Chemistry, 28 (4), 244−249, poc.3401.
  31. Pillai, Girinath G.; Sikk, Lauri; Tamm, Tarmo; Karelson, Mati; Burk, Peeter; Tamm, Kaido. (2015). Theoretical Modeling of HPV: QSAR and Novodesign with Fragment Approach. Current Computer Aided-Drug Design, 10 (4), 303−314, 1574886309666141126145756 .
  32. Kadam, Sandip A.; Martin, Kerli; Haav, Kristjan; Toom, Lauri; Mayeux, Charly; Pung, Astrid; Gale, Philip, A.; Hiscock, Jennifer R.; Brooks, Simon J.; Kirby, Isabelle L.; Busschaert, Nathalie; Leito, Ivo (2015). Towards the Discrimination of Carboxylates by Hydrogen-Bond Donor Anion Receptors. Chemistry – A European Journal, 21 (13), 5145−5160, chem.201405858.
  33. Brioche, Julien; Pike, Sarah; Tshepelevitsh, Sofa; Leito, Ivo; Morris, Gareth A.; Webb, Simon J.; Clayden, Jonathan (2015). Conformational Switching of a Foldamer in a Multicomponent System by pH-Filtered Selection between Competing Noncovalent Interactions. Journal of the American Chemical Society, 137 (20), 6680−6691, 10.1021/jacs.5b03284.

2014

Articles

  1. Gyaneshwer Chaubey, et al. Unravelling the distinct strains of Tharu ancestry, European Journal of Human Genetics advance online publication, 26 March 2014; doi:10.1038/ejhg.2014.36
  2. Raul Laasner. G0W0 band structure of CdWO4, 2014 J. Phys.: Condens. Matter 26 125503 doi:10.1088/0953-8984/26/12/125503
  3. Lejla Kovacevic, Kristiina Tambets et al. Standing at the Gateway to Europe – The Genetic Structure of Western Balkan Populations Based on Autosomal and Haploid Markers, August 22, 2014, DOI: 10.1371/journal.pone.0105090
  4. Morten Rasmussen, Sarah L. Anzick et al. The genome of a Late Pleistocene human from a Clovis burial site in western Montana, Nature 506, 225–229 (13 February 2014), doi:10.1038/nature13025
  5. Behar, Doron M.; Metspalu, Mait et al. No Evidence from Genome-Wide Data of a Khazar Origin for the Ashkenazi Jews, Human Biology Open Access Pre-Prints. Paper 41
  6. Mencacci, NE; Isaias, IU; Reich, MM; Ganos, C; Plagnol, V; Polke, JM; Bras, J; Hersheson, J; Stamelou, M; Pittman, AM; Noyce, AJ; Mok, KY; Opladen, T; Kunstmann, E; Hodecker, S; Münchau, A; Volkmann, J; Samnick, S; Sidle, K; Nanji, T; Sweeney, MG; Houlden, H; Balta, A; Zecchinelli, AL; Pezzoli, G; Marotta, G; Lees, A; Alegria, P; Krack, P; Cormier-Dequaire, F; Lesage, S; Brice, A; Heutink, P; Gasser, T; Lubbe, SJ; Morris, HR; Taba, P; Koks, S; Majounie, E; Raphael Gibbs, J; Singleton, A; Hardy, J; Klebe, S; Bhatia, KP; Wood, NW. (2014). Parkinson’s disease in GTP cyclohydrolase 1 mutation carries. Brain, 137, 2480 – 2492.
  7. Reemann, P.; Reimann, E.; Ilmjärv, S.; Porosaar, O.; Silm, H.; Jaks, V.; Vasar, E.; Kingo, K.; Kõks, S. (2014). Melanocytes in the skin – comparative whole transcriptome analysis of main skin cell types. PLoS ONE, 9(12), e115717
  8. Karask, Anti; Eimre, Margus; Ivask, Marilin; Kõks, Sulev (2014). Energeetilise metabolismi muutused wolframiindefitsiitsete hiirte lihastes. In: Eesti Arst: Tartu Ülikooli arstiteaduskonna aastapäeva teaduskonverents 2014. Tartu:, 27
  9. Koks, S; Reimann, E; Lilleoja, R; Lättekivi, F; Salumets, A; Reemann, P; Jaakma, Ü. (2014). Sequencing and annotated analysis of full genome of Holstein breed bull. Mammalian genome, 25(7-8), 363 – 373.
  10. Reimann, Ene; Kõks, Sulev; Ho, Xuan; Maasalu, Katre; Märtson, Aare (2014). Whole exome sequencing of a single osteosarcoma case – integrative analysis with whole transcriptome RNA-seq data. Human Genomics, 8(20), 20
  11. Rakitin, A; Eglit, T; Kõks, S; Lember, M; Haldre, S. (2014). Comparison of the metabolic syndrome risk in valproate-treated patients with epilepsy and the general population in Estonia. PLoS ONE, 9(7), e103856
  12. Metsalu, Tauno; Viltrop, Triin; Tiirats, Airi; Rajashekar, Balaji; Reimann, Ene; Kõks, Sulev; Rull, Kristiina; Milani, Lili; Acharya, Ganesh; Basnet, Purusotam; Vilo, Jaak; Mägi, Reedik; Metspalu, Andres; Peters, Maire; Haller-Kikkatalo, Kadri; Salumets, Andres (2014). Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta. Epigenetics, 9(10), 1397 – 1409.
  13. Noormets, Klari; Kõks, Sulev; Ivask, Marilin; Aunapuu, Marina; Arend, Andres; Vasar, Eero; Tillmann, Vallo (2014). Energy metabolism and thyroid function of mice with deleted wolfram in (Wfs1) gene. Experimental and Clinical Endocrinology of Diabetes, 122(5), 281 – 286.
  14. Punapart, Marite; Eltermaa, Mall; Oflijan, Julia; Sütt, Silva; Must, Anne; Kõks, Sulev; Schalkwyk, Leonard C.; Fernandes, Catherine; Vasar, Eero; Soomets, Ursel; Terasmaa, Anton (2014). Effect of Chronic Valproic Acid Treatment on Hepatic Gene Expression Profile in Wfs1 Knockout Mouse. PPAR Research, 2014, 349525
  15. Örd, Tiit; Innos, Jürgen; Lilleväli, Kersti; Tekko, Triin; Sütt, Silva; Örd, Daima; Kõks, Sulev; Vasar, Eero; Örd, Tõnis (2014). Trib3 is developmentally and nutritionally regulated in the brain but is dispensable for spatial memory, fear conditioning and sensing of amino acid-imbalanced diet. PLoS ONE, 9(4), e94691
  16. Reimann, Ene; Kingo, Külli; Karelson, Maire; Reemann, Paula; Vasar, Eero; Silm, Helgi; Kõks, Sulev (2014). Whole Transcriptome Analysis (RNA Sequencing) of Peripheral Blood Mononuclear Cells of Vitiligo Patients. Dermatopathology, 1(1), 11 – 23.
  17. Reemann, P; Reimann, E.; Suutre, S.; Paavo, M.; Loite, U.; Porosaar, O.; Abram, K.; Silm, H; Vasar, E.; Kõks, S.; Kingo, K. (2014). Expression of Class II Cytokine Genes in Children’s Skin. Acta Dermato-Venereologica, 94(4), 386 – 392.
  18. Reimann E, Kõks S, Ho XD, Maasalu K, Märtson A. (2014). Whole exome sequencing of a single osteosarcoma case–integrative analysis with whole transcriptome RNA-seq data. Hum Genomics 11;8:20

2013

Articles

  1. T. Haller, M. Kals, T. Esko, R. Mägi, K. Fischer. RegScan: a GWAS tool for quick estimation of allele effects on continuous traits and their combinations. Brief Bioinform (2013) doi: 10.1093/bib/bbt066
  2. Chaubey, Gyaneshwer and Endicott, Phillip (2013) “The Andaman Islanders in a Regional Genetic Context: Reexamining the Evidence for an Early Peopling of the Archipelago from South Asia,” Human Biology: Vol. 85: Iss. 1, Article 7.
  3. Basu Mallick C, Iliescu FM, Möls M, Hill S, Tamang R, et al. The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent. (2013) PLoS Genet 9(11): e1003912. doi:10.1371/journal.pgen.1003912
  4. Maanasa Raghavan, Pontus Skoglund, Kelly E. Graf, Mait Metspalu et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans, Nature (20 November 2013) | doi:10.1038/nature12736
  5. Alfonso T. Garcia-Sosa, Hydration Properties of Ligands and Drugs in Protein Binding Sites: Tightly-Bound, Bridging Water Molecules and Their Effects and Consequences on Molecular Design Strategies, Journal of Chemical Information and Modeling, 2013, DOI: 10.1021/ci3005786
  6. E. Tempel, R. S. Stoica, E. Saar, Evidence for spin alignment of spiral and elliptical/S0 galaxies in filaments, Monthly Notices of the Royal Astronomical Society, 2013, 428, 1827
  7. Veryan Codd et al. Identification of seven loci affecting mean telomere length and their association with disease, Nature Genetics 45, 422–427 (2013) doi:10.1038/ng.2528
  8. C.-G. Ma and M. G. Brik, First-principles calculations of structural and electronic properties of pure and Tm^2+ -doped SrCl2, Phys. Status Solidi B 250, No. 4, 858–863 (2013) / DOI 10.1002/pssb.201200741
  9. Marcel den Hoed et al. Identification of heart rate–associated loci and their effects on cardiac conduction and rhythm disorders, Nature Genetics (2013) – doi:10.1038/ng.2610
  10. Salmar S., Kuznetsov A., Tuulmets A., Järv J., Piiskop S.: Kinetic sonication effects in
    light of molecular dynamics simulation of the reaction medium
    , Ultrasonics Sonochemistry, Volume 20, Issue 2, March 2013, Pages 703–707, doi:10.1016/j.ultsonch.2012.10.010
  11. Sander Piiskop, Siim Salmar, Ants Tuulmets, Aleksei Kuznetsov, Jaak Järv. Kinetic sonication effects in aqueous acetonitrile solutions. Reaction rate levelling by ultrasound. Ultrasonics Sonochemistry Volume 20, Issue 6, November 2013, Pages 1414–1418, doi:/10.1016/j.ultsonch.2013.03.014
  12. Koppel, I.A.; Burk, P.; Kasemets, K.; Koppel, I. (2013). Relativistic Effects on Acidities and Basicities of Brönsted Acids and Bases Containing Gold. Physical Chemistry Chemical Physics, 15(41), 17971 – 17975.
  13. Kaljurand, Ivari; Rodima, Toomas; Koppel, Ivar; Koppel, Ilmar A.; Saame, Jaan; Leito, Ivo; Kögel, Julius; Sundermeyer, Jörg (2013). Choosing superbases for extending the experimental gas-phase basicity scaleIn: Book of Abstracts: 14th European Symposium on Organic Reactivity, Prague, Czech Republic, September 1-6, 2013. Praha:, 37.
  14. Abboud, J-L.; Koppel, I.A.; Koppel, I. (2013). Additivity of substituent effects on the acidity of alcohols. Journal of Physical Organic Chemistry, 26(6), 467 – 472.
  15. Raamat, E.; Kaupmees, K.; Ovsjannikov, G.; Trummal, A.; Kütt, A.; Saame, J.; Koppel, I.; Kaljurand, I.; Lipping, L. Rodima, T.; Pihl, V.; Koppel, I. A.; Leito, I. (2013). Acidities of strong neutral Brønsted acids in different media. Journal of Physical Organic Chemistry, 26(2), 162 – 170.
  16. Kaljurand, Ivari; Lilleorg, Roman; Murumaa, Algis; Mishima, Masaaki; Burk, Peeter; Koppel, Ivar; Koppel, Ilmar A.; Leito, Ivo (2013). The basicity of substituted N,N-dimethylanilines in solution and in the gas phase. Journal of Physical Organic Chemistry, 26(2), 171 – 181.
  17. Parn, Pille; Plaas, Mario; Nomm, Monika; Jaakma, Ulle; Kõks, Sulev. (2013). EFFECTS OF CULTURE CONDITIONS AND GENE TRANSFECTION ON THE DEVELOPMENT OF BOVINE SOMATIC CELL NUCLEAR TRANSFER EMBRYOS. In: REPRODUCTION FERTILITY AND DEVELOPMENT: IETS, Hannover, Germany, January 19-22, 2013. CSIRO PUBLISHING, 172 – 172.
  18. Planken, Anu; Kadastik-Eerme, Liis; Kurvits, Lille; Rinken, Siim; Pilv, Jaagup; Reimann, Ene; Kingo, Külli; Kõks, Sulev; Taba, Pille. (2013). Gene expression in skin of Parkinson´s Disease patients. The Movement Disorder Society’s 17th International Congress of Parkinson’s Disease and Movement Disorders, June 16-20, 2013.
  19. Nõmm, Monika; Pärn, Pille; Kavak, Ants; Jaakma, Ülle; Kõks, Sulev (2013). Veise embrüote kasvatamine laboris. Konverentsi “Terve loom ja tervislik toit 2013” kogumik (25 – 29). Tartu: Eesti Maaülikool
  20. Planken, Anu; Kadastik-Eerme, Liis; Kurvits, Lille; Reimann, Ene; Kõks, Sulev; Taba, Pille. (2013). Transcriptomic profiling of skin from Parkinson´s Disease patients. XX World Congress on Parkinson’s Disease and Related Disorders; Geneva, Swizerland; 8-11 december2013. .
  21. Märtson, Aare; Kõks, Sulev; Reimann, Ene; Prans, Ele; Erm, Triin; Maasalu, Katre (2013). Transcriptome analysis of osteosarcoma identifies suppression of wnt pathway and up-regulation of adiponectin as potential biomarker. Genomics Discovery, 1 – 9.
  22. Visnapuu, T.; Raud, S.; Loomets, M.; Reimets, R.: Sütt, S.; Luuk, H.; Plaas, M.; Kõks, S.; Volke, V.; Alttoa, A.; Harro, J.; Vasar, E. (2013). Wfs1-deficient mice display altered function of serotonergic system and increased behavioural response to antidepressants. Frontiers in Neuroscience, 7(132), 1 – 8.
  23. Plass, Dietrich; Mangen, Marie-Josée; Havelaar, Arie H; Gibbons, Cheryl; Haagsma, Juanita; Jahn, Beate; Lai, Taavi; van Lier, Alies; Longhi, Silvia; McDonald, Scott A; Kraemer, Alexander; Kramarz, Piotr; Cassini, Alessandro; Kretzschmar, Mirjam E. (2013). The incidence-based and pathogen-based disability-adjusted life-years approach for measuring infectious disease burden in Europe: the Burden of Communicable Diseases in Europe (BCoDE) projectIn: LANCET: 3rd Global Health Metrics and Evaluation Conference, Seattle, WA, JUN 17-19, 2013 . Elsevier, S114.
  24. Reemann, Paula; Kangur, Triin; Pook, Martin; Paalo, Madis; Nurmis, Liis; Kink, Ilmar; Porosaar, Orm; Kingo, Külli; Vasar, Eero; Kõks, Sulev; Jaks, Viljar; Järvekülg, Martin (2013). Fibroblast growth on micro- and nanopatterned surfaces prepared by a novel sol-gel phase separation method. Journal of Materials Science: Materials in Medicine, 24(3), 783 – 792.
  25. Rull, Kristiina; Tomberg, Kärt; Kõks, Sulev; Männik, Jaana; Möls, Märt; Sirotkina, Meeli; Värv, Signe; Laan, Maris (2013). Increased placental expression and maternal serum levels of apoptosis-inducing TRAIL in recurrent miscarriage. Placenta, 34(2), 141 – 148.
  26. Lill, M.; Kõks, S.; Soomets, U.; Schalkwyk, LC.; Fernandes, C.; Lutsar, I.; Taba, P. (2013). Peripheral blood RNA gene expression profiling in patients with bacterial meningitis. Frontiers in Neuroscience, 7, 33
  27. Visnapuu, T.; Plaas, M.; Reimets, R.; Raud, S.; Terasmaa, A.; Kõks, S.; Sütt, S.; Luuk, H.; Hundahl, C.A.; Eskla, K.-L.; Altpere, A.; Alttoa, A.; Harro, J.; Vasar, E. (2013). Evidence for impaired function of dopaminergic system in Wfs1-deficient mice. Behavioural Brain Research, 244, 90 – 99.
  28. Kõks, S.; Overall, R.W.; Ivask, M.; Soomets, U.; Guha, M.; Vasar, E.; Fernandes, C.; Schalkwyk, L.C. (2013). Silencing of the WFS1 gene in HEK cells induces pathways related to neurodegeneration and mitochondrial damage. Physiological genomics, 45(5), 182 – 190.
  29. Loite, U; Kingo, K; Reimann, E; Reemann, P; Vasar, E; Silm, H; Kõks, S. (2013). Gene Expression Analysis of the Corticotrophin-releasing Hormone-proopiomelanocortin System in Psoriasis Skin Biopsies. Acta Dermato-Venereologica, 93(4), 400 – 405.
  30. Asser, A.; Raki, M.; Juurmaa, J.; Krispin, V.; Muldmaa, M.; Põldsepp, S.; Rätsep, H.; Männistö, P.; Kõks, S.; Bergström, K.; Taba, P. (2013). Metkatinoon ja mangaan vähendavad dopamiin-D2 retseptorite funktsiooni – in vivo SPECT uuring hiirtel. Eesti Arst, 91(lisa 1), 23
  31. Prans, Ele; Kingo, Külli; Traks, Tanel; Silm, Helgi; Vasar, Eero; Kõks, Sulev (2013). Copy number variations in IL22 gene are associated with psoriasis vulgaris. Human Immunology, 74(6), 792 – 795.
  32. Innos, Jürgen; Leidmaa, Este; Philips, Mari-Anne; Sütt, Silva; Alttoa, Aet; Harro, Jaanus; Kõks, Sulev; Vasar, Eero (2013). Lsamp(-/-) mice display lower sensitivity to amphetamine and have elevated 5-HT turnover. Biochemical and Biophysical Research Communications, 430(1), 413 – 418.

2012

Doctorate Theses

  1. Marko Prous, Taxonomy and phylogeny of the sawfly genus Empria (Hymenoptera, Tenthredinidae), Loodus- ja tehnoloogiateaduskond, Tartu Ülikool
  2. Tõnu Esko, Novel applications of SNP array data in the analysis of the genetic structure of Europeans and in genetic association studies, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool
  3. Vahur Zadin, Modelling the 3D-microbattery, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool

Articles

  1. Prous, M., Heidemaa, M. 2012. Empria formosana sp. n. from Taiwan with notes on E. wui species group (Hymenoptera, Tenthredinidae). Deutsche Entomologische Zeitschrift 59: 249-257. doi: 10.1002/mmnd.201200021
  2. Alfonso T. García-Sosa, Mare Oja, Csaba Hetényi, and Uko Maran. DrugLogit: Logistic Discrimination between Drugs and Nondrugs Including Disease-Specificity by Assigning Probabilities Based on Molecular Properties. J. Chem. Inf. Model., 2012, 52 (8), pp 2165–2180 DOI: 10.1021/ci200587h
  3. Kisand V, Valente A, Lahm A, Tanet G, Lettieri T. Phylogenetic and Functional Metagenomic Profiling for Assessing Microbial Biodiversity in Environmental Monitoring. PLoS ONE 7(8): e43630. 2012.  doi:10.1371/journal.pone.0043630
  4. V. Krasnenko, M.G. Brik. First-principles calculations of hydrostatic pressure effects on the structural, elastic and thermodynamic properties of cubic monocarbides XC (X = Ti, V, Cr, Nb, Mo, Hf). Solid State Sciences, Volume 14, Issue 10, October 2012, Pages 1431-1444. doi:10.1016/j.solidstatesciences.2012.08.007
  5. Vesna Boraska et al. Genome-wide meta-analysis of common variant differences between men and women. Hum. Mol. Genet. (2012). doi: 10.1093/hmg/dds304
  6. Daniel I. Chasman et al. Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function.  Hum. Mol. Genet. 2012. doi: 10.1093/hmg/dds369
  7.  McQuillan R, Eklund N, Pirastu N, Kuningas M, McEvoy BP, et al. (2012) Evidence of Inbreeding Depression on Human Height. PLoS Genet 8(7): e1002655. doi:10.1371/journal.pgen.1002655
  8.  Pattaro C, Köttgen A, Teumer A, Garnaas M, Böger CA, et al. (2012) Genome-Wide Association and Functional Follow-Up Reveals New Loci for Kidney Function. PLoS Genet 8(3): e1002584. doi:10.1371/journal.pgen.1002584
  9. Robert A Scott et al. Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways. Nature Genetics 44, 991–1005 (2012). doi:10.1038/ng.2385
  10. Lisette Stolk et al. Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways.  Nature Genetics 44, 260–268 (2012). doi:10.1038/ng.1051
  11. Verhoeven VJ et al. Large scale international replication and meta-analysis study confirms association of the 15q14 locus with myopia. The CREAM consortium. Hum Genet. 2012 Sep;131(9):1467-80. Epub 2012 Jun 5.
  12. Jian Yang et al. FTO genotype is associated with phenotypic variability of body mass index. Nature (2012). doi:10.1038/nature11401
  13. arcOGEN Consortium and arcOGEN Collaborators. Identification of new susceptibility loci for osteoarthritis (arcOGEN): a genome-wide association study. Lancet. 2012 Sep 1;380(9844):815-23. Epub 2012 Jul 3.
  14. de Moor MH et al. Meta-analysis of genome-wide association studies for personality. Mol Psychiatry. 2012 Mar;17(3):337-49. doi: 10.1038/mp.2010.128. Epub 2010 Dec 21.
  15. Andrew P Morris et al. Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nature Genetics 44, 981–990 (2012). doi:10.1038/ng.2383
  16. Juri Reimand, Anu Aun, Jaak Vilo, Juan M Vaquerizas, Juhan Sedman and Nicholas M Luscombe: m:Explorer – multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence. Genome Biology 2012, 13:R55 doi:10.1186/gb-2012-13-6-r55
  17. Veera Krasnenko, Jaak Kikas, Mikhail G. Brik: Modification of the structural and electronic properties of graphene by the benzene molecule adsorption, Physica B: Condensed Matter, Volume 407, Issue 23, doi:10.1016/j.physb.2012.08.019
  18. L. J. Liivamägi, E. Tempel, E. Saar SDSS DR7 superclusters. The catalogues, Astronomy & Astrophysics, 2012, Volume 539, A80, DOI: 10.1051/0000-6361/201016288
  19. Kunetskiy, R.A.;Polyakova, S.M.;Vavrik, J.;Cisarova, I.;Saame, J.;Nerut, E.R.;Koppel, I.;Koppel, I.A.;Kütt, A.;Leito, I.;Lyapkalo, I.M. (2012). A New Class of Organosuperbases,N-Alkyl-and N-Aryl-1,3-dialkyl-,4,5-dimethylimidazol-2-ylidene Amines:Synthesis,Structure,pKBH+ Measurements,and Properties. Chemistry – A European Journal, 18(12), 3621 – 3630.

2011

Doctorate theses (09. November 2011)

  1. Kessy Abarenkov, PlutoF – cloud database and computing services supporting biological research, Loodus- ja tehnoloogiateaduskond, Tartu Ülikool

Articles

  1. Mait Metspalu et al. Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia, The American Journal of Human Genetics – 9 December 2011 (Vol. 89, Issue 6, pp. 731-744)
  2. Hundahl CA , Luuk H , Ilmjärv S , Falktoft B , Raida Z , et al. 2011 Neuroglobin-Deficiency Exacerbates Hif1A and c-FOS Response, but Does Not Affect Neuronal Survival during Severe Hypoxia In Vivo, PLoS ONE 6(12): e28160. doi:10.1371/journal.pone.0028160
  3. Kõljalg Urmas; Abarenkov Kessy. Elurikkuse informaatika, Teadusmõte Eestis (VI). Elu ja Maateadused. Eesti Teaduste Akadeemia. Tallinn 2011
  4. Bayazit Yunusbayev et al. The Caucasus as an asymmetric semipermeable barrier to ancient human migrations, Mol Biol Evol, September 13, 2011, doi:10.1093/molbev/msr221
  5. Endel Soolo, Daniel Brandell, Anti Liivat, Heiki Kasemägi, Tarmo Tamm and Alvo Aabloo. Molecular Dynamics simulations of EMI-BF4 in nanoporous carbon actuators, Journal of Molecular Modeling (2011), doi:10.1007/s00894-011-1182-5
  6. Daniel Brandell, Priit Priimägi, Heiki Kasemägi, Alvo Aabloo. Branched polyethylene/poly(ethylene oxide) as a host matrix for Li-ion battery electrolytes: an MD study, Electrochimica Acta, doi:10.1016/j.electacta.2011.03.022.
  7. Vahur Zadin; Daniel Brandell. Modelling Polymer Electrolytes for 3D-Microbatteries using Finite Element Analysis, Electrochimica Acta, doi:10.1016/j.electacta.2011.03.026.
  8. Vahur Zadin, Heiki Kasemägi, Alvo Aabloo, Josh Thomas, Daniel Brandell. Finite element modelling of ion transport in the electrolyte of a 3D-microbattery, Solid State Ionics, doi:10.1016/j.ssi.2010.02.007.
  9. Gyaneshwer Chaubey, Mait Metspalu et al. Population Genetic Structure in Indian Austroasiatic Speakers: The Role of Landscape Barriers and Sex-Specific Admixture, Mol Biol Evol (2011) 28 (2): 1013-1024. doi:10.1093/molbev/msq288
  10. Alfonso T. García-Sosa, Sulev Sild, Kalev Takkis, and Uko Maran. Combined Approach using Ligand Efficiency, Cross-Docking, and Anti-Target Hits for Wild-Type and Drug-Resistant Y181C HIV-1 Reverse Transcriptase, Journal of Chemical Information and Modeling, 2011, 51 (10), pp 2595–2611, doi:10.1021/ci200203h
  11. Speliotes EK et al. Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits, PLoS Genet. 2011 Mar;7(3):e1001324. Epub 2011 Mar 10
  12. Schumann G et al. Genome-wide association and genetic functional studies identify autism susceptibility candidate 2 gene (AUTS2) in the regulation of alcohol consumption, Proc Natl Acad Sci U S A. 2011 Apr 26;108(17):7119-24. Epub 2011 Apr 6
  13. Day-Williams AG et al. A Variant in MCF2L Is Associated with Osteoarthritis, Am J Hum Genet. 2011 Sep 9;89(3):446-50. Epub 2011 Aug 25.
  14. The International Consortium for Blood Pressure Genome-Wide Association Studies, Ehret GB et al. Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk, Nature. 2011 Sep 11. doi:10.1038/nature10405
  15. Wain LV, Verwoert GC et al. Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure, Nat Genet. 2011 Sep 11. doi:10.1038/ng.922
  16. Suhhonenko, I.; Einasto, J.; Liivamägi, L. J.; Saar, E.; Einasto, M.; Hütsi, G.; Müller, V.; Starobinsky, A. A.; Tago, E.; Tempel, E. The cosmic web for density perturbations of various scales, Astronomy & Astrophysics, 2011, Volume 531, id.A149
  17. Einasto, J.; Hütsi, G.; Saar, E.; Suhhonenko, I.; Liivamägi, L. J.; Einasto, M.; Müller, V.; Starobinsky, A. A.; Tago, E.; Tempel, E. Wavelet analysis of the cosmic web formation, Astronomy & Astrophysics, 2011, Volume 531, id.A75
  18. Einasto, J.; Suhhonenko, I.; Hütsi, G.; Saar, E.; Einasto, M.; Liivamägi, L. J.; Müller, V.; Starobinsky, A. A.; Tago, E.; Tempel, E. Toward understanding the void phenomenon, Astronomy & Astrophysics, 2011, 534, A128
  19. Kütt, A.; Rodima, T.; Trummal, A.; Saame, J.; Kaljurand, I.; Koppel, I.A.; Yagupolskii, Y.I.; Leito, I. (2011). Acidities of Superacids in 1,2-Dichloroethane. In: Book of Abstracts ESOR XIII: The 13th European Symposium on Organic Reactivity,Tartu,Estonia,11-16 September,2011. (Toim.) Burk, Peeter. Tartu :, P18 – P18.
  20. Lipping, L.; Kütt, A.; Kaupmees, K.; Koppel, I.; Burk, P.; Leito, I.; Koppel, I. A. (2011). Acidity of Anilines: Calculations vs Experiment. Journal of Physical Chemistry A, 115, 10335 – 10344.
  21. Leito, I.; Kütt, A.; Rodima, T.; Lipping, L.; Kaljurand, I.; Saame, J.; Koppel, I.; Koppel, I.A. (2011). Design and Acidity Measurements of Superacidic Molecules. In: Book of Abstracts ESOR XIII: The 13th European Symposium on Organic Reactivity,Tartu,Estonia,11-16 September,2011;invited lecture. , IL3 – IL3.
  22. Koppel, I.A.; Kütt, A.; Leito, I.; Koppel, I.; Rodima, T.; Kaljurand, I; Saame, J; Kolomeitsev, A.A. (2011). Superbasicity of Neutral Molecules-Quo Vadis Plenary lecture. In: Book of Abstracts ESOR: The 13th European Symposium on Organic Reactivity Tartu,Estonia,11-16 September 2011. Tartu:, O19 – O19.
  23. Trummal, A.; Rummel, A.; Lippmaa, E.; Koppel, I.; Koppel, I.A. (2011). Calculation of pKa of Superacids in 1,2-Dichloroethane. In: Abstracts of Papers: Ninth triennial congress of the World Association of Theoretical and Computational Chemists(WATOC),Santiago de Compostela,Spain;July 17-22,2011. Spain,Santiago de Compostela:, 094 – 094.
  24. Trummal, A.; Rummel, A.; Lippmaa, E.; Koppel, I.; Koppel, I.A. (2011). Calculations of pKa of Superacids in 1,2-Dichloroethane. Journal of Physical Chemistry A, 115, 6641 – 6645.
  25. Lipping, L.; Koppel, I.; Koppel, I. A.; Kolomeitsev, A.; Röschenthaler, G.-V.; Leito, I. (2010). Polytrifluoromethylation versus Polyfluorination of the Isomers of Kekule Benzene and Phenol: A Theoretical Study. Journal of Organic Chemistry, 75(19), 6436 – 6444.

2010

Doctorate Thesis

  1. Jüri Reimand, Functional Analysis of Gene Lists, Networks and Regulatory Systems, Tartu Ülikool, Matemaatika-informaatikateaduskond

Articles

  1. K. Panoutsopoulou et al. Insights into the genetic architecture of osteoarthritis from stage 1 of the arcOGEN study, Ann Rheum Dis, doi:10.1136/ard.2010.141473
  2. de Moor MH et al. Meta-analysis of genome-wide association studies for personality, Molecular Psychiatry advance online publication 21 December 2010, doi:10.1038/mp.2010.128
  3. Karl Kruusamäe, Paola Brunetto, Salvatore Graziani, Andres Punning, Giovanna Di Pasquale, Alvo Aabloo (2010) Self-sensing ionic polymer-metal composite actuating device with patterned surface electrodes, Polymer International, 59(3), 300-304.
  4. Pugal, David; Jung, Kwangmok; Aabloo, Alvo; Kim, Kwang (2010) Ionic polymer-metal composite mechanoelectrical transduction: review and perspectives, Polymer International, 59(3), 279-289.
  5. Daniel Brandell, Heiki Kasemägi, Alvo Aabloo (2010), Poly(ethylene oxide)-poly(butadiene) interpenetrated networks as electroactive polymers for actuators: a molecular dynamics study, Electrochimica Acta, 55, n 4, p 1333-1337.
  6. Soolo, E.; Brandell, D.; Liivat, A.; Tamm, T.; Kasemägi, A.; Aabloo, A. (2010) Force Field Generation and Molecular Dynamics Simulations of Li+ – Nafion, Electrochimica Acta, 55, n 4, p 2587-2591.
  7. Vahur Zadin, Heiki Kasemägi, Alvo Aabloo, Josh Thomas, Daniel Brandell (2010), Finite element modelling of ion transport in the electrolyte of a 3D-microbattery, Solid State Ionics, accepted.
  8. Vahur Zadin; Heiki Kasemägi, Alvo Aabloo, Daniel Brandell (2010), Modelling electrode material utilization in the trench-model 3D-microbattery by finite element analysis, Journal of Power Sources, 195,18,6218-6224.
  9. Brandell, Daniel, Karo, Jaanus and Thomas, John O. (2010) Modelling the Nafion (R) diffraction profile by molecular dynamics simulation, Journal of Power Sources, 195, 18, 5962-5965.
  10. Jaanus Karo, Alvo Aabloo, John O. Thomas and Daniel Brandell (2010) Molecular Dynamics Modeling of Proton Transport in Nafion and Hyflon Nanostructures, Journal of Chemical Physics B, 114, 6056–6064.
  11. Cathy E Elks et al. Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies, Nature Genetics 42, 1077–1085 (2010), doi:10.1038/ng.714
  12. Lango Allen H et al. Hundreds of variants clustered in genomic loci and biological pathways affect human height, Nature 467, 832–838 (14 October 2010), doi:10.1038/nature09410
  13. Iris M Heid et al. Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution, Nature Genetics (2010), doi:10.1038/ng.685
  14. Elizabeth K Speliotes et al. Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index, Nature Genetics (2010), doi:10.1038/ng.686
  15. Alfonso T. Garcia-Sosa, Ricardo L. Mancera; Free Energy Calculations of Mutations Involving a Tightly Bound Water Molecule and Ligand Substitutions in a Ligand-Protein Complex, Molecular Informatics, 29: 589–600. doi: 10.1002/minf.201000007
  16. Doron M. Behar, Bayazit Yunusbayev, Mait Metspalu et al.; The genome-wide structure of the Jewish people; Nature 466, 238–242 (08 July 2010), doi:10.1038/nature09103
  17. Morten Rasmussen et al; Ancient human genome sequence of an extinct Palaeo-Eskimo; Nature 463, 757-762 (11 February 2010), doi:10.1038/nature08835
  18. R. G. Walters et al.; A new highly penetrant form of obesity due to deletions on chromosome 16p11.2; Nature 463, 671-675 (4 February 2010) doi:10.1038/nature08727
  19. Tempel, E.; Tamm, A.; Tenjes, P. (2010); Dust-corrected surface photometry of M31 from Spitzer far-infrared observations; Astronomy & Astrophysics
  20. Kessy Abarenkov et al. PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences, Evol Bioinform Online. 2010; 6: 189–196. doi:10.4137/EBO.S6271

2009

Doctorate Thesis

  1. Karo, Jaanus; The Role of Side-Chains in Polymer Electrolytes for Batteries and Fuel Cells, Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology

Articles

  1. Daniel Brandell, Heiki Kasemägi, Alvo Aabloo (2009), Poly(ethylene oxide)-poly(butadiene) interpenetrated networks as electroactive polymers for actuators: a molecular dynamics study, Electrochimica Acta, accepted.
  2. Soolo, E.; Brandell, D.; Liivat, A.; Tamm, T.; Kasemägi, A.; Aabloo, A. (2009) Force Field Generation and Molecular Dynamics Simulations of Li+ – Nafion, Electrochimica Acta, accepted.
  3. Nelis M, Esko T, Mägi R, Zimprich F, Zimprich A, et al. (2009) Genetic Structure of Europeans: A View from the North–East. PLoS ONE 4(5): e5472. doi:10.1371/journal.pone.0005472
  4. Pugal, David; Jung, Kwangmok; Aabloo, Alvo; Kim, Kwang (2009) IPMC Mechanoelectrical Transduction Review and Perspectives, Polymer International, accepted.
  5. Andres Punning, Urmas Johanson, Mart Anton, Alvo Aabloo, and Maarja Kruusmaa (2009) A Distributed Model of Ionomeric Polymer Metal Composite, Journal of Intelligent Material Systems and Structures, 20, 14, 1711-1724.
  6. Pugal, D.; Aabloo, A.; Kim, Kwang J (2009) Dynamic surface resistance model of IPMC, Proc. SPIE, Vol. 7289, 72891E
  7. Jaanus Karo, Daniel Brandell (2009), A Molecular dynamics study of the influence of side-chain length and spacing on lithium mobility in non-crystalline LiPF6-PEO; x10 and 20, Solid State Ionics, 180,1272-1284.
  8. Tamm, T.;  Raudsepp, T.; Visk, U.; Marandi, M.;  Tamm, J.  Importance of the initial stage: a comparative study of the development of polypyrrole properties    
  9. Karelson, M.; Karelson, G.; Tamm, T.; Tulp, I.; Jänes, J.; Tämm, K.; Lomaka, A.; Savchenko, D.; Dobchev, D. QSAR study of pharmacological permeabilities  Arkivoc
  10. Tamm, T.; Visk, U.; Raudsepp, T.  Overoxidation of Polypyrrole, Role of Dopants: An Electrochemical, Theoretical, and FTIR Study
  11. Raudsepp, T.; Marandi, M.; Sammelselg, V.; Tamm, T.; Tamm, J.   Influence of Redoping on Electrochemical Properties of the Polypyrrole films    
  12. Tamm, J.; Marandi, M.; Raudsepp, T.; Sammelselg, V.; Tamm, T.   Formation of the Electrochemical Properties of the Polypyrrole Films