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

Maido Remm

https://www.etis.ee/CV/Maido_Remm/est
11.07.1965
737 5001
524 7725
maido.remm@ut.ee
http://bioinfo.ut.ee
AAI-8161-2021
https://github.com/bioinfo-ut

Teenistuskäik

Töökohad ja ametid
2003–...   
Tartu Ülikool, TÜ MRI, bioinformaatika õppetooli juhataja (1,00)
2001–2015   
Eesti Biokeskus, Vanemteadur (0,20)
1999–2000   
Karolinska Institute, Center for Genomics and Bioinformatics Research, Järeldoktor (1,00)
1997–1998   
Uppsala Ülikool, Molekulaarbioloogia osakond, Järeldoktor (1,00)
1990–1992   
Eesti Biokeskus, Teadur (1,00)
 
 
Haridustee
1992–1997   
doktorant, Tartu Ülikool
1983–1990   
Tartu Ülikool, bioloogia-geograafia teaduskond, biokeemia eriala.
 
 
Teadusorganisatsiooniline ja -administratiivne tegevus
2008−...   
Rahvusvahelise Arvutusliku Bioloogia Ühingu liige
2007−...   
TÜ LOTE Geenitehnoloogia ja Bioloogia õppekavade programmikomitee liige
2003−...   
Molekulaar- ja Rakubioloogia instituudi nõukogu liige
2015−2017   
ETAG ekspertkomisjoni liige
2008−2015   
Genoomika tippkeskuse juht
2008−2009   
TKN Hindamiskomisjoni liige
2005−2005   
Seitsmenda iga-aastase Põhjamaade Bioinformaatika konverentsi Bioinformatics2005 peakorraldaja (23 esinejat ja ca 200 osalejat, peamiselt välisriikidest).
2004−2007   
Bioloogia-Geograafia Teaduskonna nõukogu liige
2004−2005   
24 töökohaga Linux-põhise arvutiklassi loomine ja ühendamine Eesti GRIDiga
2004−2011   
Eesti HTM juures asuva Teaduskompetentsi nõukogu ekspertliige.
2004−2012   
Eesti esindaja Põhjamaade Bioinformaatika ühingu juhatuses.
2004−2007   
TÜ Bioloogia- Geograafia teaduskonna nõukogu liige
 
 
Loometöö
Õpik kõrgkoolidele "Bioinformaatika alused" (2015). http://www.tyk.ee/loodusteadused/00000011691.

Kvalifikatsioon

Teaduskraadid
Maido Remm, doktorikraad, 1997, (juh) Mart Ustav, Human papillomavirus type 18: replication, transformation and gene expression, Tartu Ülikool.
 
 
Teaduspreemiad ja tunnustused
2008, Maido Remm, Riigi teaduspreemia uurimuste tsükli “Inimgenoomi bioinformaatiline analüüs” eest
2001, Maido Remm, EC DG Research projekti Genemill repatrieerumise grant
 
 
Teadustöö põhisuunad
ETIS KLASSIFIKAATOR: 1. Bio- ja keskkonnateadused; 1.12. Bio- ja keskkonnateadustega seotud uuringud, näiteks biotehnoloogia, molekulaarbioloogia, rakubioloogia, biofüüsika, majandus- ja tehnoloogiauuringud; CERCS KLASSIFIKAATOR: B110 Bioinformaatika, meditsiiniinformaatika, biomatemaatika, biomeetrika
ETIS KLASSIFIKAATOR: 3. Terviseuuringud; 3.11. Terviseuuringutega seotud uuringud, näiteks biokeemia, geneetika, mikrobioloogia, biotehnoloogia, molekulaarbioloogia, rakubioloogia, biofüüsika ja bioinformaatika; CERCS KLASSIFIKAATOR: B110 Bioinformaatika, meditsiiniinformaatika, biomatemaatika, biomeetrika

Jooksvad projektid

Lõppenud projektid

Juhendamisel väitekirjad

Juhendatud väitekirjad

Publikatsioonid

Klass
Aasta
Publikatsioon
 
3.2.
2022
Bonturi, Nemailla; Pinheiro, Marina Julio; Monteiro de Oliveira, Paola; Rusadze, Eka; Eichinger, Tobias; Liudziute, Gintare; Sabedotti De Biaggi, Juliano; Brauer, Age; Remm, Maido; Miranda, Everson Alves; Ledesma-Amaro, Rodrigo; Lahtvee, Petri-Jaan (2022). Development of a dedicated Golden Gate Assembly platform (RtGGA) for Rhodotorula toruloides. bioRxiv. DOI: 10.1101/2022.03.02.482697.
1.1.
2021
Erki Aun, Veljo Kisand, Mailis Laht, Kaidi Telling, Piret Kalmus, Ülo Väli, Age Brauer, Maido Remm and Tanel Tenson (2021). Molecular Characterization of Enterococcus Isolates From Different Sources in Estonia Reveals Potential Transmission of Resistance Genes Among Different Reservoirs. Frontiers in Microbiology, 12, 1−13. DOI: 10.3389/fmicb.2021.601490.
1.1.
2021
Kaplinski, Lauris; Möls, Märt; Puurand, Tarmo; Pajuste, Fanny‐Dhelia; Remm, Maido (2021). KATK: fast genotyping of rare variants directly from unmapped sequencing reads. Human Mutation, 42 (6). DOI: 10.1002/humu.24197.
1.1.
2021
Modica, Maria Vittoria; Ahmad, Rafi; Ainsworth, Stuart; Anderluh, Gregor; Antunes, Agostinho; Beis, Dimitris; Caliskan, Figen; Serra, Mauro Dalla; Dutertre, Sebastien; Moran, Yehu; Nalbantsoy, Ayse; Oukkache, Naoual; Pekar, Stano; Remm, Maido; von Reumont, Bjoern Marcus; Sarigiannis, Yiannis; Tarallo, Andrea; Tytgat, Jan; Undheim, Eivind Andreas Baste; Utkin, Yuri ... Zancolli, Giulia (2021). The new COST Action European Venom Network (EUVEN)-synergy and future perspectives of modern venomics. GigaScience, 10 (3), ARTN giab019. DOI: 10.1093/gigascience/giab019.
1.1.
2021
Bellabarba, Agnese; Bacci, Giovanni; Decorosi, Francesca; Aun, Erki; Azzarello, Elisa; Remm, Maido; Giovannetti, Luciana; Viti, Carlo; Mengoni, Alessio; Pini, Francesco; Medema, Marnix (2021). Competitiveness for Nodule Colonization in Sinorhizobium meliloti: Combined In Vitro - Tagged Strain Competition and Genome-Wide Association Analysis. mSystems, 6 (4). DOI: 10.1128/mSystems.00550-21.
1.1.
2021
Mildenberger, J.; Remm, M.; Atanassova, M. (2021). Self-assembly potential of bioactive peptides from Norwegian sea cucumber Parastichopus tremulus for development of functional hydrogels. LWT - Food Science and Technology, 148, ARTN 111678. DOI: 10.1016/j.lwt.2021.111678.
1.1.
2020
Raime, Kairi; Krjutškov, Kaarel; Remm, Maido (2020). Method for the Identification of Plant DNA in Food Using Alignment-Free Analysis of Sequencing Reads: A Case Study on Lupin. Frontiers in Plant Science, 11, 646−646. DOI: 10.3389/fpls.2020.00646.
1.1.
2020
Örd, Tiit; Puurand, Tarmo; Örd, Daima; Annilo, Tarmo; Möls, Märt; Remm, Maido; Örd, Tõnis (2020). A human-specific VNTR in the TRIB3 promoter causes gene expression variation between individuals. PLoS Genetics, 16(8) e1008981. DOI: 10.1371/journal.pgen.1008981.
1.1.
2020
Telling, Kaidi; Brauer, Age; Laht, Mailis; Kalmus, Piret; Toompere, Karolin; Kisand, Veljo; Maimets, Matti; Remm, Maido; Tenson, Tanel; Lutsar, Irja (2020). Characteristics of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae and Contact to Animals in Estonia. Microorganisms, 8 (8), ARTN 1130. DOI: 10.3390/microorganisms8081130.
1.1.
2020
Rosendahl, Sirli; Tamman, Hedvig; Brauer, Age; Remm, Maido; Hõrak, Rita (2020). Chromosomal toxin-antitoxin systems in Pseudomonas putida are rather selfish than beneficial. Scientific Reports, 10 (1), 9230. DOI: 10.1038/s41598-020-65504-0.
1.1.
2019
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.
1.1.
2019
Saag, Lehti; Laneman, Margot; Varul, Liivi; Malve, Martin; Valk, Heiki; Razzak, Maria A.; Shirobokov, Ivan G.; Khartanovich, Valeri I.; Mikhaylova, Elena R.; Kushniarevich, Alena; Scheib, Christiana Lyn; Solnik, Anu; Reisberg, Tuuli; Parik, Juri; Saag, Lauri; Metspalu, Ene; Rootsi, Siiri; Montinaro, Francesco; Remm, Maido; Magi, Reedik ... Tambets, Kristiina (2019). The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East. Current Biology, 29 (10), 1701−1728. DOI: 10.1016/j.cub.2019.04.026.
1.1.
2019
Jõers, Arvi; Vind, Kristiina; Hernández, Sara B; Maruste, Regina; Pereira, Marta D; Brauer, Age; Remm, Maido; Cava, Felipe; Tenson, Tanel (2019). Muropeptides Stimulate Growth Resumption from Stationary Phase in Escherichia coli. Scientific Reports, 9, 18043. DOI: 10.1038/s41598-019-54646-5.
1.1.
2019
Kõiv, Viia; Arbo, Krõõt; Maiväli, Ülo; Kisand, Veljo; Roosaare, Mart; Remm, Maido; Tenson, Tanel (2019). Endophytic bacterial communities in peels and pulp of five root vegetables. PLoS ONE, 14 (1), ARTN e0210542. DOI: 10.1371/journal.pone.0210542.
1.1.
2019
Bilozor, Anastasia; Balode, Arta; Chakhunashvili, Giorgi; Chumachenko, Tetyana; Egorova, Svetlana; Ivanova, Marina; Kaftyreva, Liidia; Kõljalg, Siiri; Kõressaar, Triinu; Lysenko, Olga; Miciuleviciene, Jolanta; Mändar, Reet; Lis, Danuta O.; Wesolowska, Monika Pomorska; Ratnik, Kaspar; Remm, Maido; Rudzko, Jelena; Rööp, Tiiu; Saule, Mara; Sepp, Epp ... Naaber, Paul (2019). Application of Molecular Methods for Carbapenemase Detection. Frontiers in Microbiology, 10, ARTN 1755. DOI: 10.3389/fmicb.2019.01755.
1.1.
2019
Sepp, Epp; Andreson, Reidar; Balode, Arta; Bilozor, Anastasia; Brauer, Age; Egorova, Svetlana; Huik, Kristi; Ivanova, Marina; Kaftyreva, Lidia; Kõljalg, Siiri; Koressaar, Triinu; Makarova, Maria; Miciuleviciene, Jolanta; Pai, Kristiine; Remm, Maido; Rööp, Tiiu; Naaber, Paul (2019). Phenotypic and Molecular Epidemiology of ESBL-, AmpC-, and Carbapenemase-Producing Escherichia coli in Northern and Eastern Europe. Frontiers in Microbiology, 10, ARTN 2465. DOI: 10.3389/fmicb.2019.02465.
1.1.
2019
Puurand, Tarmo; Kukuškina, Viktoria; Pajuste, Fanny-Dhelia; Remm, Maido (2019). AluMine: alignment-free method for the discovery of polymorphic Alu element insertions. Mobile DNA, 10, 31−31. DOI: 10.1186/s13100-019-0174-3.
1.1.
2018
Raime, Kairi; Remm, Maido (2018). Method for the Identification of Taxon-Specific k-mers from Chloroplast Genome: A Case Study on Tomato Plant (Solanum lycopersicum). Frontiers in Plant Science, 9, 6. DOI: 10.3389/fpls.2018.00006.
1.1.
2018
Roosaare, Märt; Puustusmaa, Mikk; Möls, Märt; Vaher, Mihkel; Remm, Maido (2018). PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads. PeerJ. DOI: 10.7717/peerj.4588.
1.1.
2018
Kõressaar, Triinu; Lepamets, Maarja; Kaplinski, Lauris; Raime, Kairi; Andreson, Reidar; Remm, Maido (2018). Primer3_masker: integrating masking of template sequence with primer design software. Bioinformatics, 34 (11), 1937−1938. DOI: 10.1093/bioinformatics/bty036.
1.1.
2018
Aun, Erki; Brauer, Age; Kisand, Veljo; Tenson, Tanel; Remm, Maido (2018). A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria. PLoS Computational Biology, 14 (10), ARTN e1006434. DOI: 10.1371/journal.pcbi.1006434.
1.1.
2018
Telling, Kaidi; Laht, Mailis; Brauer, Age; Remm, Maido; Kisand, Veljo; Maimets, Matti; Tenson, Tanel; Lutsar, Irja (2018). Multidrug resistant Pseudomonas aeruginosa in Estonian hospitals. BMC Infectious Diseases, 18 (1), ARTN 513. DOI: 10.1186/s12879-018-3421-1.
1.1.
2017
Vasar, Martti; Andreson, Reidar; Davison, John; Jairus, Teele; Moora, Mari; Remm, Maido; Young, J. Peter W.; Zobel, Martin; Öpik, Maarja (2017). Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi. Mycorrhiza, 27 (8), 761−773. DOI: 10.1007/s00572-017-0791-y.
1.1.
2017
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 (1), 2537−2537. DOI: 10.1038/s41598-017-02487-5.
1.1.
2017
Roosaare, Märt; Vaher, Mihkel; Kaplinski, Lauris; Möls, Märt; Andreson, Reidar; Lepamets, Maarja; Kõressaar, Triinu; Naaber, Paul; Kõljalg, Siiri; Remm, Maido (2017). StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees. PeerJ, 5, ARTN e3353−e3353. DOI: 10.7717/peerj.3353.
1.1.
2016
Jakobson, Liina1; Vaahtera, Lauri; Tõldsepp, Kadri; Nuhkat, Maris; Wang, Cun; Wang, Yuh-Shuh; Hõrak, Hanna; Valk, Ervin; Pechter, Priit; Sindarovska, Yana; Tang, Jing; Xiao, Chuanlei; Xu, Yang; Gerst Talas, Ulvi; Garcia-Sosa, Alfonso T.; Kangasjärvi, Saijaliisa; Maran, Uko; Remm, Maido; Roelfsema, M. Rob G.; Hu, Honghong ... Brosche, Mikael (2016). Natural Variation in Arabidopsis Cvi-0 Accession Reveals an Important Role of MPK12 in Guard Cell CO2 Signaling. PLoS Biology, 1/25−25/25. DOI: 10.1371/journal.pbio.2000322.
1.1.
2016
Brauer, Age; Telling, Kaidi; Laht, Mailis; Kalmus, Piret; Lutsar, Irja; Remm, Maido; Kisand, Veljo; Tenson, Tanel (2016). Plasmid with colistin resistance gene mcr-1 in ESBL-producing Escherichia coli strains isolated from pig slurry in Estonia. Antimicrobial Agents and Chemotherapy, 60 (11), 6933−36. DOI: 10.1128/AAC.00443-16.
1.1.
2016
Toubiana, Julie; Okada, Satoshi; Hiller, Julia; Oleastro, Matias; Lagos Gomez, Macarena; Aldave Becerra, Juan Carlos; Ouachée-Chardin, Marie; Fouyssac, Fanny; Girisha, Katta Mohan; Etzioni, Amos; Van Montfrans, Joris; Camcioglu, Yildiz; Kerns, Leigh Ann; Belohradsky, Bernd; Blanche, Stéphane; Bousfiha, Aziz; Rodriguez-Gallego, Carlos; Meyts, Isabelle; Kisand, Kai; Reichenbach, Janine ... , (2016). Heterozygous STAT1 gain-of-function mutations underlie an unexpectedly broad clinical phenotype. Blood, 127 (25), 3154−3164. DOI: 10.1182/blood-2015-11-679902.
1.1.
2015
Kõiv, V.; Roosaare, M.; Vedler, E; Kivistik., P A; Toppi, K.; Schryer, DW.; Remm, M.; Tenson, T; Mäe, A. (2015). Microbial population dynamics in response to Pectobacterium atrosepticum infection in potato tubers. Scientific Reports, 5 (11606), 1−18. DOI: 10.1038/srep11606.
1.1.
2015
Palta, Priit; Kaplinski, Lauris; Nagirnaja, Liina; Veidenberg, Andres; Möls, Märt; Nelis, Mari; Esko, Tõnu; Metspalu, Andres; Laan, Maris; Remm, Maido (2015). Haplotype phasing and inheritance of copy number variants in nuclear families. PLoS ONE, 10 (4), UNSP e0122713. DOI: 10.1371/journal.pone.0122713.
1.1.
2015
Kaplinski, Lauris; Lepamets, Maarja; Remm, Maido (2015). GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists. GigaScience, 4 (58), 1−8. DOI: 10.1186/s13742-015-0097-y.
1.1.
2015
Karmin, Monika; Saag, Lauri; Vicente, Mário; Wilson Sayres, Melissa A; Järve, Mari; Talas, Ulvi Gerst; Rootsi, Siiri; Ilumäe, Anne-Mai; Mägi, Reedik; Mitt, Mario; Pagani, Luca; Puurand, Tarmo; Faltyskova, Zuzana; Clemente, Florian; Cardona, Alexia; Metspalu, Ene; Sahakyan, Hovhannes; Yunusbayev, Bayazit; Hudjashov, Georgi; DeGiorgio, Michael ... Kivisild, Toomas (2015). A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Research, 25 (4), 459−466. DOI: 10.1101/gr.186684.114.
3.1.
2015
Andreson, Reidar; Kaplinski, Lauris; Remm Maido (2015). Fast masking of repeated primer binding sites in eukaryotic genomes. In: Basu, Chhandak (Ed.). PCR Primer Design (1−16). New York: Springer. (Methods in Molecular Biology). DOI: 10.1007/978-1-59745-528-2_10.
3.1.
2015
Kaplinski, Lauris; Remm, Maido (2015). MultiPLX: automatic grouping and evaluation of PCR primers. In: Basu, Chhadank (Ed.). PCR Primer Design (127−142). New York: Springer. (Methods in Molecular Biology). DOI: 10.1007/978-1-59745-528-2_14.
5.2.
2015
Naaber, Paul; Balode, Arta; Egorova, Svetlana; Huik, Kristi; Ivanova, Marina; Kaftyreva, Lidia; Kõljalg, Siiri; Kõressaar, Triinu; Lillo, Jana; Löhr, Iren; Miciuleviciene, Jolanta; Pai, Kristiine; Pavelkovich, Anastassia; Remm, Maido; Sepp, Epp (2015). The epidemiology of CTX-M group genes among clinical Escherichia coli strains in Estonia, Latvia, Lithuania, Norway and Russia.
1.1.
2014
van den Brand, Marre; Peters, Remco P. H.; Catsburg, Arnold; Rubenjan, Anna; Broeke, Ferdi J.; van den Dungen, Frank A. M.; van Weissenbruch, Mirjam M.; van Furth, A. Marceline; Kõressaar, Triinu; Remm, Maido; Savelkoul, Paul H. M.; Bos, Martine P. (2014). Development of a multiplex real-time PCR assay for the rapid diagnosis of neonatal late onset sepsis. Journal of Microbiological Methods, 106, 8−15. DOI: 10.1016/j.mimet.2014.07.034.
1.1.
2014
Sothiselvam, S; Liu, B; Han, W; Ramu, H; Klepacki, D; Atkinson, GC; Brauer, A; Remm, M; Tenson, T; Schulten, K; Vázquez-Laslop, N; Mankin, AS. (2014). Macrolide antibiotics allosterically predispose the ribosome for translation arrest. Proceedings of the National Academy of Sciences, 111 (27), 9804−9809. DOI: 10.1073/pnas.1403586111.
1.1.
2014
Nagirnaja, Liina; Palta, Priit; Kasak, Laura; Rull, Kristiina; Christiansen, Ole B.; Nielsen, Henriette S.; Steffensen, Rudi; Esko, Tõnu; Remm, Maido; Laan, Maris (2014). Structural genomic variation as risk factor for idiopathic recurrent miscarriage. Human Mutation, 35 (8), 972−982. DOI: 10.1002/humu.22589.
1.1.
2013
Vedler, Eve; Heinaru, Eeva; Jutkina, Jekaterina; Viggor, Signe; Kõressaar, Triinu; Remm, Maido; Heinaru, Ain (2013). Limnobacter spp. as newly detected phenol-degraders among Baltic Sea surface water bacteria characterized by comparative analysis of catabolic genes. Systematic and Applied Microbiology, 36 (8), 525−532. DOI: 10.1016/j.syapm.2013.07.004.
1.1.
2013
Koua, D; Laht, S; Kaplinski, L; Stöcklin, R; Remm, M; Favreau, P; Lisacek, F (2013). Position-specific scoring matrix and hidden Markov model complement each other for the prediction of conopeptide superfamilies. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1834 (4), 717−724. DOI: 10.1016/j.bbapap.2012.12.015.
1.1.
2013
Nikopensius, T; Annilo, T; Jagomägi, T; Gilissen, C; Kals, M; Krjutškov, K; Mägi, R; Eelmets, M; Gerst-Talas, U; Remm, M; Saag, M; Hoischen, A; Metspalu, A (2013). Non-syndromic Tooth Agenesis Associated with a Nonsense Mutation in Ectodysplasin-A (EDA). Journal of Dental Research, 92 (6), 507−511. DOI: 10.1177/0022034513487210.
3.1.
2013
Remm, Maido; Krjutškov, Kaarel; Metspalu, Andres (2013). Primer Design for Large-Scale Multiplex PCR and Arrayed Primer Extension (APEX). In: Tania Nolan; Stephen A. Bustin (Ed.). PCR Technology: Current Innovation - 3rd Edition (199−207). CRC PRESS.
1.1.
2012
Võsa, L; Sudakov, A; Remm, M; Ustav, M; Kurg, R. (2012). Identification and analysis of papillomavirus E2 protein binding sites in the human genome. Journal of Virology, 86 (1), 348−357. DOI: 10.1128/JVI.05606-11.
1.1.
2012
Brauer, A.; Kurz, A.; Stockwell, T.; Baden-Tillson, H.; Heidler, J.; Wittig, I.; Kauferstein, S.; Mebs, D.; Stöcklin, R.; Remm, M. (2012). The Mitochondrial Genome of the Venomous Cone Snail Conus consors. PLoS ONE, 7 (12), e51528 .
1.1.
2012
Untergasser, Andreas; Cutcutache, Ioana; Koressaar, Triinu; Ye, Jian; Faircloth, Brant C; Remm, Maido; Rozen, Steve. (2012). Primer3 - new capabilities and interfaces. Nucleic Acids Research, 40 (15), e115. DOI: 10.1093/nar/gks596.
1.1.
2012
Laht S, Koua D, Kaplinski L, Lisacek F, Stöcklin R, Remm M (2012). Identification and classification of conopeptides using profile Hidden Markov Models. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1824, 488−492. DOI: 10.1016/j.bbapap.2011.12.004.
1.1.
2012
Terrat Y, Biass D, Dutertre S, Favreau P, Remm M, Stöcklin R, Piquemal D, Ducancel F. (2012). High-resolution picture of a venom gland transcriptome: Case study with the marine snail Conus consors. Toxicon, 59, 34−46.
1.1.
2012
Koressaar, Triinu; Remm, Maido (2012). Characterization of Species-Specific Repeats in 613 Prokaryotic Species. DNA Research, 19 (3), 219−230. DOI: 10.1093/dnares/dss006.
1.1.
2012
Koua, D.; Brauer, A.; Laht, S.; Kaplinksi, L.; Favreau, P.; Remm, M.; Lisacek, F.; Stöcklin, R. (2012). ConoDictor: a tool for prediction of conopeptide superfamilies. Nucleic Acids Research, 40, W238−W241. DOI: 10.1093/nar/gks337.
1.1.
2012
Saare, Merli; Sõritsa, Deniss; Vaidla, Kadri; Palta, Priit; Remm, Maido; Laan, Martti; Karro, Helle; Sõritsa, Andrei; Salumets, Andres; D'Hooghe, Thomas; Peters, Maire (2012). No evidence of somatic DNA copy number alterations in eutopic and ectopic endometrial tissue in endometriosis. Human Reproduction, 27 (6), 1857−1864. DOI: 10.1093/humrep/des125.
1.1.
2011
Scheler, O.; Kaplinski, L.; Glynn, B.; Palta, P.; Parkel, S.; Toome, K.; Maher, M.; Barry, T.; Remm, M.; Kurg, A. (2011). Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes. BMC Biotechnology, 11, 11−17. DOI: 10.1186/1472-6750-11-17.
1.1.
2011
Knapp, D.C.; Serva, S.; D'Onofrio, J.; Keller, A.; Lubys, A.; Kurg, A.; Remm, M.; Engels, JW. (2011). Fluoride-Cleavable, Fluorescently Labelled Reversible Terminators: Synthesis and Use in Primer Extension. Chemistry - A European Journal, 17 (10), 2903−2915. DOI: 10.1002/chem.201001952.
1.1.
2011
Siibak, Triinu; Peil, Lauri; Doenhoefer, Alexandra; Tats, Age; Remm, Maido; Wilson, Daniel N.; Tenson, Tanel; Remme, Jaanus (2011). Antibiotic-induced ribosomal assembly defects result from changes in the synthesis of ribosomal proteins. Molecular Microbiology, 80 (1), 54−67. DOI: 10.1111/j.1365-2958.2011.07555.x.
1.1.
2011
Männik, K; Parkel, S; Palta, P; Zilina, O; Puusepp, H; Esko, T; Mägi, R; Nõukas, M; Veidenberg, A; Nelis, M; Metspalu, A; Remm, M; Ounap, K; Kurg, A. (2011). A parallel SNP array study of genomic aberrations associated with mental retardation in patients and general population in Estonia. European Journal of Medical Genetics, 54 (2), 136−143.
1.1.
2011
Metspalu, M.; Romero, IG.; Yunusbayev, B.; Chaubey, G.; Mallick, CB.; Hudjashov, G.; Nelis, M.; Mägi, R.; Metspalu, E.; Remm, M.; Pitchappan, R.; Singh, L.; Thangaraj, K.; Villems, R.; Kivisild, T. (2011). Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia. The American Journal of Human Genetics, 89 (6), 731−44. DOI: 10.1016/j.ajhg.2011.11.010.
1.1.
2011
Chaubey, Gyaneshwer; Metspalu, Mait; Choi, Ying; Mägi, Reedik; Gallego Romero, Irene; Soares, Pedro; van Oven, Mannis; Behar, Doron M; Rootsi, Siiri; Hudjashov, Georgi; Basu Mallick, Chandana; Karmin, Monika; Nelis, Mari; Parik, Jüri; Goverdhana Reddy, Alla; Metspalu, Ene; vanDriem, George; Xue, Yali; Tyler-Smith, Chris; Thangaraj, Kumarasamy ... Kivisild, Toomas. (2011). Population Genetic Structure in Indian Austroasiatic speakers: The Role of Landscape Barriers and Sex-specific Admixture. Molecular Biology and Evolution, 28(2), 1013−24.
1.1.
2011
Margus, T.; Remm, M.; Tenson, T. (2011). A Computational Study of Elongation Factor G (EFG) Duplicated Genes: Diverged Nature Underlying the Innovation on the Same Structural Template. PLoS ONE, 6, e22789.
5.1.
2011
Nagirnaja, L.; Kasak, L.; Palta, P.; Rull, K.; Christiansen, O.B.; Esko, T.; Remm, M.; Metspalu, A.; Laan, M. (2011). Role of DNA copy number variations in genetic predisposition to recurrent pregnancy loss. Journal of Reproductive Immunology, 90: 9th Congress of the European Society for Reproductive Immunology and European Society for Human Reproduction and Embryology Early Pregnancy Special Interest Group; Copenhagen, Denmark; August 23-26, 2011. UK: Elsevier Ireland Ltd, 145. (2). DOI: 10.1016/j.jri.2011.06.028.
5.1.
2011
Nagirnaja, L.; Kasak, L.; Palta, P.; Rull, K.; Christiansen, OB.; Esko, T.; Remm, M.; Metspalu, A.; Laan, M. (2011). DNA copy number variations in recurrent miscarriage. Placenta: International Federation of Placenta Associations - 14th European Placenta Group Meeting 2011 14.-17. 09.2011 Geilo, Norra. Elsevier Ireland Ltd, A140−A140. (32; 9).
1.1.
2010
Kaplinski, L.; Scheler, O.; Parkel, S.; Palta, P.; Toome, K.; Kurg, A.; Remm, M. (2010). Detection of tmRNA molecules on microarrays at low temperatures using helper oligonucleotides. BMC Biotechnology, 10 (34), 1−10. DOI: 10.1186/1472-6750-10-34.
1.1.
2010
Oitmaa, E.; Peters, M.; Vaidla, K.; Andreson, R.; Mägi, R.; Slavin, G.; Velthut, .; Tõnisson, N.; Reimand, T.; Remm, M.; Schneider, M.; Õunap, K.; Salumets, A.; Metspalu, A. (2010). Molecular diagnosis of Down Syndrome using Quantitative APEX-2 microarrays. Prenatal Diagnosis, 30, 1170−1177. DOI: 10.1002/pd.2639.
1.1.
2009
Scheler, O.; Glynn, B.; Parkel, S.; Palta, P.; Toome, K.; Kaplinski, L.; Remm, M.; Maher, M.; Kurg, A. (2009). Fluorescent labeling of NASBA amplified tmRNA molecules for microarray applications. BMC Biotechnology, 15 (9), 45−50. DOI: 10.1186/1472-6750-9-45.
1.1.
2009
Koressaar, T.; Jõers, K.; Remm, M. (2009). Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms. Bioinformatics, 25 (11), 1349−1355.
1.1.
2009
Nelis, M.; Esko, T.; Mägi, R.; Zimprich, F.; Zimprich, A.; Toncheva, D.; Karachanak, S.; Piskácková, T.; Balascák, I.; Peltonen, L.; Jakkula, E.; Rehnström, K.; Lathrop, M.; Heath, S.; Galan, P.; Schreiber, S.; Meitinger, T.; Pfeufer, A.; Wichmann, HE.; Melegh, B. ... Metspalu, A. (2009). Genetic structure of Europeans: a view from the North-East. PLoS ONE, 4(5), e5472.
1.1.
2008
Tats, A.; Tenson, T.; Remm, M. (2008). Preferred and avoided codon pairs in three domains of life. BMC Genomics, 9, 463.
1.1.
2008
Krjutskov, K.; Andreson, R.; Mägi, R.; Nikopensius, T.; Khrunin, A.; Mihailov, E.; Tammekivi, V.; Sork, H.; Remm, M.; Metspalu, A. (2008). Development of a single tube 640-plex genotyping method for detection of nucleic acid variations on microarrays. Nucleic Acids Research, 36 (12), e75.
1.1.
2008
Kousoulidou, L.; Männik, K.; Zilina, O.; Parkel, S.; Palta, P.; Remm, M.; Kurg, A.; Patsalis, P.C. (2008). Application of two different microarray-based copy-number detection methodologies - array-comparative genomic hybridization and array-multiplex amplifiable probe hybridization - with identical amplifiable target sequences. Clinical Chemistry and Laboratory Medicine (CCLM), 46 (5), 722−724.
1.1.
2008
Tamm, R.; Oselin, K.; Kallassalu, K.; Magi, R.; Anier, K.; Remm, M.; Metspalu, A. (2008). Thiopurine S-methyltransferase (TPMT) pharmacogenetics: three new mutations and haplotype analysis in the Estonian population. Clinical Chemistry and Laboratory Medicine (CCLM), 46 (7), 974−979.
1.1.
2008
Andreson, R.; Möls, T.; Remm, M. (2008). Predicting failure rate of PCR in large genomes. Nucleic Acids Research, 36 (11), e66. DOI: 10.1093/nar/gkn290.
1.1.
2008
Kousoulidou, L.; Männik, K.; Sismani, C.; Zilina, O.; Parkel, S.; Puusepp, H.; Tõnisson, N.; Palta, P.; Remm, M.; Kurg, A.; Patsalis, P. C. (2008). Array-MAPH: a methodology for the detection of locus copy-number changes in complex genomes. Nature Protocols, 3 (5), 849−865. DOI: 10.1038/nprot.2008.49.
5.1.
2008
Knapp, D.C.; Keller, A.; D'Onofrio, J.; Lubys, A.; Serva, S.; Kurg, A.; Remm, M.; Kwiatkowski, M.; Engels, J.W. (2008). Synthesis of four colors fluorescently labelled 3'-O-blocked nucleotides with fluoride cleavable blocking group and linker for array based Sequencing-by-Synthesis applications. Nucleic Acids Symposium Series, 52, 345−346.
5.1.
2008
Glynn, B.; Lacey, K.; Palta, P.; Kaplinski, L.; Remm, M.; Barry, T.; Smith, T.; Maher, M. (2008). Demonstration of the application of the tmRNA transcript of the bacterial ssrA gene as a molecular diagnostic target using a combination of NASBA and BiaCore technologies. International Journal of Antimicrobial Agents, 29, S392.
5.1.
2008
Palta, P.; Parkel, S.; Veidenberg, A.; Mannik, K.; Puusepp, H.; Zilina, O.; Kurg, A.; Remm, M. (2008). Web-based database platform for large-scale copy number variation studies. Cellular Oncology, 30 (3), 270.
5.2.
2008
Oitmaa, Eneli; Krjutskov, Kaarel; Mägi, Reedik ; Andreson, Reidar ; Raukas, Elve; Remm, Maido; Tõnisson, Neeme; Schneider, Marion; Metspalu, Andres (2008). Molecular diagnostics of Down syndrome using quantitative APEX microarrays. RBM online, vol.16-suppl. 3: Eighth International Symposium of Preimplantation Genetic Diagnosis, Barcelona, April 23-26, 2008. , S17.
1.1.
2007
Magi, R.; Pfeufer, A.; Nelis, M.; Montpetit, A.; Metspalu, A.; Remm, M. (2007). Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation. BMC Genomics, 8 (159), x.
1.1.
2007
Kousoulidou, L.; Parkel, S.; Zilina, O.; Palta, P.; Puusepp, H.; Remm, M.; Turner, G.; Boyle, J.; van Bokhoven, H.; de Brouwer, A.; Van Esch, H.; Froyen, G.; Ropers, H.-H.; Chelly, J.; Moraine, C.; Gecz, J.; Kurg, A.; Patsalis, P. (2007). Screening of 20 patients with X-linked mental retardation using chromosome X–specific array-MAPH. European Journal of Medical Genetics, 50 (6), 399−410.
1.1.
2007
Koressaar, T.; Remm, M. (2007). Enhancements and modifications of primer design program Primer3. Bioinformatics, 23 (10), 1289−1291.
1.1.
2007
Kuningas, M.; Mägi, R.; Westendorp, R.G.; Slagboom, P.E.; Remm, M.; van Heemst, D. (2007). Haplotypes in the human Foxo1a and Foxo3a genes; impact on disease and mortality at old age. European Journal of Human Genetics, 15 (3), 294−301. DOI: 10.1038/sj.ejhg.5201766.
1.1.
2007
Margus, T.; Remm, M.; Tenson, T. (2007). Phylogenetic distribution of translational GTPases in bacteria. BMC Genomics, 8, 15. DOI: 10.1186/1471-2164-8-15.
1.1.
2007
Patsalis, P.C.; Kousoulidou, L.; Männik, K.; Sismani, C.; Žilina, O.; Parkel, S.; Puusepp, H.; Tõnisson, N.; Palta, P.; Remm, M.; Kurg, A. (2007). Detection of small genomic imbalances using microarray-based multiplex amplifiable probe hybridization. European Journal of Human Genetics, 15 (2), 162−172. DOI: 10.1038/sj.ejhg.5201738.
3.1.
2007
Kaplinski, L.; Remm, M. (2007). MultiPLX: Automatic Grouping and Evaluation of PCR Primers. In: A.Yuryev (Ed.). PCR Primer Design (367). . Humana Press.
3.1.
2007
Andreson, R.; Kaplinski, L.; Remm, M. (2007). Fast Masking of Repeated Primer Binding Sites in Eukaryotic Genomes. In: Yuryev, A. (Ed.). PCR Primer Design (367). . Humana Press. (July 2007 ).
1.1.
2006
Andreson, R.; Puurand, T.; Remm, M. (2006). SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes. Nucleic Acids Research, 34, W651−W656.
1.1.
2006
Montpetit, A.; Nelis, M.; Laflamme, P.; Magi, R.; Ke, X.Y.; Remm, M.; Cardon, L.; Hudson, T.J.; Metspalu, A. (2006). An evaluation of the performance of tag SNPs derived from HapMap in a Caucasian population. PLoS Genetics, 2 (3), 282−290.
1.1.
2006
Andreson, R; Reppo, E; Kaplinski, L; Remm, M (2006). GENOMEMASKER package for designing unique genomic PCR primers. BMC Bioinformatics, 7, 172.
1.1.
2006
Tats, A.; Remm, M.; Tenson, T. (2006). Highly expressed proteins have an increased frequency of alanine in the second amino acid position. BMC Genomics, 7, 28.
3.2.
2006
Mägi, R.; Kaplinski, L.; Remm, M. (2006). The Whole Genome TagSNP Selection and Transferability Among HapMap Populations. Pacific Symposium on Biocomputing 2006: 2006. World Scientific Publ Co Pte Ltd, 535−543.
1.1.
2005
Mueller, J. C.; Lõhmussaar, E.; Mägi, R.; Remm, M.; Bettecken, T.; Lichtner, P.; Huber, S.; Illig, T; Luedemann, J.; Schreiber, S.; Wichmann, H. E.; Pramstaller, P.; Romeo, G.; Testa, A.; Metspalu, A.; Meitinger, T. (2005). Linkage Disequilibrium Patterns and tagSNP Transferability among European Populations. The American Journal of Human Genetics, 76 (3), 387−398.
1.1.
2005
Laan, M.; Wiebe, V.; Khusnutdinova, E.; Remm, M.; Paabo, S. (2005). X-chromosome as a marker for population history: linkage disequilibrium and haplotype study in Eurasian populations. European Journal of Human Genetics, 13 (4), 452−462.
1.1.
2005
Kaplinski, L.; Andreson, R.; Puurand, T.; Remm, M. (2005). MultiPLX: automatic grouping and evaluation of PCR primers. Bioinformatics, 21 (8), 1701−1702.
1.1.
2005
O'Brien, KP.; Remm, M.; Sonnhammer, ELL. (2005). Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Research, 33, D476−D480.
5.2.
2005
Andreson, R.; Reppo, E.; Kaplinski, L.; Möls, T.; Remm, M. (2005). GENOMEMASKER package: tools for design of high quality genomic PCR primers. ECCB 2005, Spain, Madrid (28 sep. - 01 oct., 2005): European conference on computational biology, Madrid, 2005.
3.1.
2004
Remm, M.; Kurg, A.; Metspalu, A. (2004). Primer Design for Large-Scale Multiplex PCR and Arrayed Primer Extension (APEX). In: Weissensteiner, T.; Griffin, H.G.; Griffin, A. (Ed.). PCR Technology, Current Innovations, 2nd Edition (131−139). . Boca Raton: CRC PRESS.
5.2.
2003
Reppo, E.; Andreson, R.; Remm, M. (2003). GenomeMasker and GenomeTester: tools for design of high quality genomic PCR primers. Bioinformatics 2003, Helsinki, Finland, May 22-24, 2003: Bioinformatics 2003, Helsinki.
1.1.
2002
Remm, M.; Metspalu, A. (2002). High-density genotyping and linkage disequilibrium in the human genome using chromosome 22 as a model. Current Opinion in Chemical Biology, 6 (1), 24−30.
1.1.
2002
Dawson, E.; Abecasis, GR.; Bumpstead, S.; Chen, Y.; Hunt, S.; Beare, DM.; Pabial, J.; Dibling, T.; Tinsley, E.; Kirby, S.; Carter, D.; Papaspyridonos, M.; Livingstone, S.; Ganske, R.; Lohmmussaar, E.; Zernant, J.; Tonisson, N.; Remm, M.; Magi, R.; Puurand, T. ... Dunham, I. (2002). A first-generation linkage disequilibrium map of human chromosome 22. Nature, 418 (6897), 544−548.
5.1.
2002
Kepp, K.; Remm, M.; Lohmussaar, E.; Gerst-Talas, U. (2002). APEX scaling up. Optimisation of the high throughput Arrayed Primer Extension based DNA variation analysis for accurate and affordable large-scale projects. 10. , 297.
5.1.
2002
Lohmussaar, E.; Zernant, J.; Magi, R.; Kepp, K.; Puurand, T.; Tonisson, N.; Valvas, I.; Slavin, G.; Andreson, R.; Kurg, A.; Remm, M.; Metspalu, A. (2002). SNP analysis and linkage disequilibrium map of the human chromosome 22 using APEX arrays. European Journal of Human Genetics, 10, 299−299.
5.1.
2002
Lohmussaar, E.; Zernant, J.; Magi, R.; Puurano, T.; Tonisson, N.; Valvas, I.; Slavin, G.; Kurg, A.; Remm, M.; Metspalu, A. (2002). SNP analysis and linkage disequilibrium map of the human chromosome 22 using Arrayed Primer EXtension (APEX) technology. The American Journal of Human Genetics, 71 (4), 449−449.
5.2.
2002
Andreson, R.; Lukk, M.; Remm, M.; Vilo, J.; Metspalu, A. (2002). A comparison of different methods to find PCR primer binding sites in the human genome. Bioinformatics 2002, Bergen, Norway (aprill 4-7, 2002): Bioinformatics 2002, Bergen, 2002.
1.1.
2001
Remm, M.; Storm, CEV.; Sonnhammer, ELL. (2001). Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. Journal of Molecular Biology, 314 (5), 1041−1052.
5.1.
2001
Metspalu, A.; Zernant, J.; Lohmussaar, E.; Magi, R.; Kepp, K.; Puurand, T.; Tonisson, N.; Valvas, L.; Pavel, H.; Slavin, G.; Andreson, R.; Kurg, A.; Remm, M. (2001). SNP analysis of the human chromosome 22 using APEX arrays. The American Journal of Human Genetics, 69 (4), 408−408.
1.1.
2000
Remm, M.; Sonnhammer, E. (2000). Classification of transmembrane protein families in the Caenorhabditis elegans genome and identification of human orthologs. Genome Research, 10 (11), 1679−1689.
1.1.
1999
Remm, M.; Remm, A.; Ustav, M. (1999). Human papillomavirus type 18 E1 protein is translated from polycistronic mRNA by a discontinuous scanning mechanism. Journal of Virology, 73 (4), 3062−3070.
1.1.
1995
Plumpton, M.; Sharp, NA.; Liddicoat, LH.; Remm, M.; Tucker, DO.; Hughes, FJ.; Russell, SM.; Romanos, MA. (1995). A high-capacity assay for inhibitors of human papillomavirus DNA-replication. Bio/Technology, 13 (11), 1210−1214.
1.1.
1992
Sturzbecher, HW.; Brain, R.; Addison, C.; Rudge, K.; Remm, M.; Grimaldi, M.; Keenan, E.; Jenkins, JR. (1992). A C-terminal alpha-helix plus basic region motif is the major structural determinant of p53 tetramerization. Oncogene, 7 (8), 1513−1523.
1.1.
1992
Remm, M.; Brain, R.; Jenkins, JR. (1992). The e2 binding-sites determine the efficiency of replication for the origin of human papillomavirus type-18. Nucleic Acids Research, 20 (22), 6015−6021.

Tööstusomand

10.03.2022

Maido Remm

https://www.etis.ee/CV/Maido_Remm/eng
11.07.1965
737 5001
524 7725
maido.remm@ut.ee
AAI-8161-2021
https://github.com/bioinfo-ut

Career

Institutions and positions
2003–...   
University of Tartu, Head of Chair of Bioinformatics, Institute of Molecular and Cell Biology (1,00)
2001–2015   
Estonian Biocentre, Senior Researcher (0,20)
1999–2000   
Karolinska Institute, Center for Genomics and Bioinformatics Research, Post-Doc (1,00)
1997–1998   
Uppsala University, Department of Molecular Biology, Post-Doc (1,00)
1990–1992   
Estonian Biocentre, Researcher (1,00)
 
 
Education
1992–1997   
Ph.D. Student, University of Tartu, ESTONIA
1983–1990   
University of Tartu, Faculty of Biology and Geography, graduated as biochemist.
 
 
R&D related managerial and administrative work
2008−...   
Member of International Society of Computational Biology (ISCB)
2007−...   
Member of University of Tartu programme committee for developing "Gene Technology" and "Biology" curricula for Master and Bachelor level.
2003−...   
Member of council, Institute of Molecular and Cellular Biology
2015−2017   
member of the expert panel of the Estonian Research Council
2008−2015   
Head of the Centre of Excellence in Genomics at Estonian Biocentre
2008−2009   
Member of Scientific Competence Council at Estonian Ministry of Education and Research
2005−2005   
Main organizer for the 7th annual Nordic Bioinformatics conference Bioinformatics2005 in Tartu (23 speakers, ca 200 participants, mostly from outside Estonia).
2004−2007   
Member of council, Faculty of Biology and Geography
2004−2005   
Installation of Linux based computer class and joining it with the Estonian GRID project
2004−2011   
Member of expert comission of Scientific Competence at Estonian Ministry of Education and Research.
2004−2012   
Representative of Estonia in board of Nordic Society of Bioinformatics.
2004−2007   
Member of council, Faculty of Biology and Geography, University of Tartu
 
 
Creative work
Textbook for graduate students "Principles of Bioinformatics" (2015).
http://www.tyk.ee/loodusteadused/00000011691.

Qualifications

Academic degrees
Maido Remm, Doctor's Degree, 1997, (sup) Mart Ustav, Human papillomavirus type 18: replication, transformation and gene expression, University of Tartu.
 
 
Honours & awards
2008, Maido Remm, National Science Award
2001, Maido Remm, EC project Genemill repatriation grant
 
 
Fields of research
ETIS CLASSIFICATION: 1. Biosciences and Environment; 1.12. Biotechnology, Molecular Biology, Cell Biology, Biophysics and Economic and Technological Research relating to Bio- and Environmental Sciences; CERCS CLASSIFICATION: B110 Bioinformatics, medical informatics, biomathematics, biometrics
ETIS CLASSIFICATION: 3. Health; 3.11. Biochemistry, Genetics, Microbiology, Biotechnology, Molecular Biology, Cell Biology, Biophysics and Bioinformatics relating to Health Studies; CERCS CLASSIFICATION: B110 Bioinformatics, medical informatics, biomathematics, biometrics
 
 

Projects in progress

Completed projects

Dissertations under supervision

Supervised dissertations

Publications

Category
Year
Publication
 
3.2.
2022
Bonturi, Nemailla; Pinheiro, Marina Julio; Monteiro de Oliveira, Paola; Rusadze, Eka; Eichinger, Tobias; Liudziute, Gintare; Sabedotti De Biaggi, Juliano; Brauer, Age; Remm, Maido; Miranda, Everson Alves; Ledesma-Amaro, Rodrigo; Lahtvee, Petri-Jaan (2022). Development of a dedicated Golden Gate Assembly platform (RtGGA) for Rhodotorula toruloides. bioRxiv. DOI: 10.1101/2022.03.02.482697.
1.1.
2021
Erki Aun, Veljo Kisand, Mailis Laht, Kaidi Telling, Piret Kalmus, Ülo Väli, Age Brauer, Maido Remm and Tanel Tenson (2021). Molecular Characterization of Enterococcus Isolates From Different Sources in Estonia Reveals Potential Transmission of Resistance Genes Among Different Reservoirs. Frontiers in Microbiology, 12, 1−13. DOI: 10.3389/fmicb.2021.601490.
1.1.
2021
Kaplinski, Lauris; Möls, Märt; Puurand, Tarmo; Pajuste, Fanny‐Dhelia; Remm, Maido (2021). KATK: fast genotyping of rare variants directly from unmapped sequencing reads. Human Mutation, 42 (6). DOI: 10.1002/humu.24197.
1.1.
2021
Modica, Maria Vittoria; Ahmad, Rafi; Ainsworth, Stuart; Anderluh, Gregor; Antunes, Agostinho; Beis, Dimitris; Caliskan, Figen; Serra, Mauro Dalla; Dutertre, Sebastien; Moran, Yehu; Nalbantsoy, Ayse; Oukkache, Naoual; Pekar, Stano; Remm, Maido; von Reumont, Bjoern Marcus; Sarigiannis, Yiannis; Tarallo, Andrea; Tytgat, Jan; Undheim, Eivind Andreas Baste; Utkin, Yuri ... Zancolli, Giulia (2021). The new COST Action European Venom Network (EUVEN)-synergy and future perspectives of modern venomics. GigaScience, 10 (3), ARTN giab019. DOI: 10.1093/gigascience/giab019.
1.1.
2021
Bellabarba, Agnese; Bacci, Giovanni; Decorosi, Francesca; Aun, Erki; Azzarello, Elisa; Remm, Maido; Giovannetti, Luciana; Viti, Carlo; Mengoni, Alessio; Pini, Francesco; Medema, Marnix (2021). Competitiveness for Nodule Colonization in Sinorhizobium meliloti: Combined In Vitro - Tagged Strain Competition and Genome-Wide Association Analysis. mSystems, 6 (4). DOI: 10.1128/mSystems.00550-21.
1.1.
2021
Mildenberger, J.; Remm, M.; Atanassova, M. (2021). Self-assembly potential of bioactive peptides from Norwegian sea cucumber Parastichopus tremulus for development of functional hydrogels. LWT - Food Science and Technology, 148, ARTN 111678. DOI: 10.1016/j.lwt.2021.111678.
1.1.
2020
Raime, Kairi; Krjutškov, Kaarel; Remm, Maido (2020). Method for the Identification of Plant DNA in Food Using Alignment-Free Analysis of Sequencing Reads: A Case Study on Lupin. Frontiers in Plant Science, 11, 646−646. DOI: 10.3389/fpls.2020.00646.
1.1.
2020
Örd, Tiit; Puurand, Tarmo; Örd, Daima; Annilo, Tarmo; Möls, Märt; Remm, Maido; Örd, Tõnis (2020). A human-specific VNTR in the TRIB3 promoter causes gene expression variation between individuals. PLoS Genetics, 16(8) e1008981. DOI: 10.1371/journal.pgen.1008981.
1.1.
2020
Telling, Kaidi; Brauer, Age; Laht, Mailis; Kalmus, Piret; Toompere, Karolin; Kisand, Veljo; Maimets, Matti; Remm, Maido; Tenson, Tanel; Lutsar, Irja (2020). Characteristics of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae and Contact to Animals in Estonia. Microorganisms, 8 (8), ARTN 1130. DOI: 10.3390/microorganisms8081130.
1.1.
2020
Rosendahl, Sirli; Tamman, Hedvig; Brauer, Age; Remm, Maido; Hõrak, Rita (2020). Chromosomal toxin-antitoxin systems in Pseudomonas putida are rather selfish than beneficial. Scientific Reports, 10 (1), 9230. DOI: 10.1038/s41598-020-65504-0.
1.1.
2019
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.
1.1.
2019
Saag, Lehti; Laneman, Margot; Varul, Liivi; Malve, Martin; Valk, Heiki; Razzak, Maria A.; Shirobokov, Ivan G.; Khartanovich, Valeri I.; Mikhaylova, Elena R.; Kushniarevich, Alena; Scheib, Christiana Lyn; Solnik, Anu; Reisberg, Tuuli; Parik, Juri; Saag, Lauri; Metspalu, Ene; Rootsi, Siiri; Montinaro, Francesco; Remm, Maido; Magi, Reedik ... Tambets, Kristiina (2019). The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East. Current Biology, 29 (10), 1701−1728. DOI: 10.1016/j.cub.2019.04.026.
1.1.
2019
Jõers, Arvi; Vind, Kristiina; Hernández, Sara B; Maruste, Regina; Pereira, Marta D; Brauer, Age; Remm, Maido; Cava, Felipe; Tenson, Tanel (2019). Muropeptides Stimulate Growth Resumption from Stationary Phase in Escherichia coli. Scientific Reports, 9, 18043. DOI: 10.1038/s41598-019-54646-5.
1.1.
2019
Kõiv, Viia; Arbo, Krõõt; Maiväli, Ülo; Kisand, Veljo; Roosaare, Mart; Remm, Maido; Tenson, Tanel (2019). Endophytic bacterial communities in peels and pulp of five root vegetables. PLoS ONE, 14 (1), ARTN e0210542. DOI: 10.1371/journal.pone.0210542.
1.1.
2019
Bilozor, Anastasia; Balode, Arta; Chakhunashvili, Giorgi; Chumachenko, Tetyana; Egorova, Svetlana; Ivanova, Marina; Kaftyreva, Liidia; Kõljalg, Siiri; Kõressaar, Triinu; Lysenko, Olga; Miciuleviciene, Jolanta; Mändar, Reet; Lis, Danuta O.; Wesolowska, Monika Pomorska; Ratnik, Kaspar; Remm, Maido; Rudzko, Jelena; Rööp, Tiiu; Saule, Mara; Sepp, Epp ... Naaber, Paul (2019). Application of Molecular Methods for Carbapenemase Detection. Frontiers in Microbiology, 10, ARTN 1755. DOI: 10.3389/fmicb.2019.01755.
1.1.
2019
Sepp, Epp; Andreson, Reidar; Balode, Arta; Bilozor, Anastasia; Brauer, Age; Egorova, Svetlana; Huik, Kristi; Ivanova, Marina; Kaftyreva, Lidia; Kõljalg, Siiri; Koressaar, Triinu; Makarova, Maria; Miciuleviciene, Jolanta; Pai, Kristiine; Remm, Maido; Rööp, Tiiu; Naaber, Paul (2019). Phenotypic and Molecular Epidemiology of ESBL-, AmpC-, and Carbapenemase-Producing Escherichia coli in Northern and Eastern Europe. Frontiers in Microbiology, 10, ARTN 2465. DOI: 10.3389/fmicb.2019.02465.
1.1.
2019
Puurand, Tarmo; Kukuškina, Viktoria; Pajuste, Fanny-Dhelia; Remm, Maido (2019). AluMine: alignment-free method for the discovery of polymorphic Alu element insertions. Mobile DNA, 10, 31−31. DOI: 10.1186/s13100-019-0174-3.
1.1.
2018
Raime, Kairi; Remm, Maido (2018). Method for the Identification of Taxon-Specific k-mers from Chloroplast Genome: A Case Study on Tomato Plant (Solanum lycopersicum). Frontiers in Plant Science, 9, 6. DOI: 10.3389/fpls.2018.00006.
1.1.
2018
Roosaare, Märt; Puustusmaa, Mikk; Möls, Märt; Vaher, Mihkel; Remm, Maido (2018). PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads. PeerJ. DOI: 10.7717/peerj.4588.
1.1.
2018
Kõressaar, Triinu; Lepamets, Maarja; Kaplinski, Lauris; Raime, Kairi; Andreson, Reidar; Remm, Maido (2018). Primer3_masker: integrating masking of template sequence with primer design software. Bioinformatics, 34 (11), 1937−1938. DOI: 10.1093/bioinformatics/bty036.
1.1.
2018
Aun, Erki; Brauer, Age; Kisand, Veljo; Tenson, Tanel; Remm, Maido (2018). A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria. PLoS Computational Biology, 14 (10), ARTN e1006434. DOI: 10.1371/journal.pcbi.1006434.
1.1.
2018
Telling, Kaidi; Laht, Mailis; Brauer, Age; Remm, Maido; Kisand, Veljo; Maimets, Matti; Tenson, Tanel; Lutsar, Irja (2018). Multidrug resistant Pseudomonas aeruginosa in Estonian hospitals. BMC Infectious Diseases, 18 (1), ARTN 513. DOI: 10.1186/s12879-018-3421-1.
1.1.
2017
Vasar, Martti; Andreson, Reidar; Davison, John; Jairus, Teele; Moora, Mari; Remm, Maido; Young, J. Peter W.; Zobel, Martin; Öpik, Maarja (2017). Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi. Mycorrhiza, 27 (8), 761−773. DOI: 10.1007/s00572-017-0791-y.
1.1.
2017
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 (1), 2537−2537. DOI: 10.1038/s41598-017-02487-5.
1.1.
2017
Roosaare, Märt; Vaher, Mihkel; Kaplinski, Lauris; Möls, Märt; Andreson, Reidar; Lepamets, Maarja; Kõressaar, Triinu; Naaber, Paul; Kõljalg, Siiri; Remm, Maido (2017). StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees. PeerJ, 5, ARTN e3353−e3353. DOI: 10.7717/peerj.3353.
1.1.
2016
Jakobson, Liina1; Vaahtera, Lauri; Tõldsepp, Kadri; Nuhkat, Maris; Wang, Cun; Wang, Yuh-Shuh; Hõrak, Hanna; Valk, Ervin; Pechter, Priit; Sindarovska, Yana; Tang, Jing; Xiao, Chuanlei; Xu, Yang; Gerst Talas, Ulvi; Garcia-Sosa, Alfonso T.; Kangasjärvi, Saijaliisa; Maran, Uko; Remm, Maido; Roelfsema, M. Rob G.; Hu, Honghong ... Brosche, Mikael (2016). Natural Variation in Arabidopsis Cvi-0 Accession Reveals an Important Role of MPK12 in Guard Cell CO2 Signaling. PLoS Biology, 1/25−25/25. DOI: 10.1371/journal.pbio.2000322.
1.1.
2016
Brauer, Age; Telling, Kaidi; Laht, Mailis; Kalmus, Piret; Lutsar, Irja; Remm, Maido; Kisand, Veljo; Tenson, Tanel (2016). Plasmid with colistin resistance gene mcr-1 in ESBL-producing Escherichia coli strains isolated from pig slurry in Estonia. Antimicrobial Agents and Chemotherapy, 60 (11), 6933−36. DOI: 10.1128/AAC.00443-16.
1.1.
2016
Toubiana, Julie; Okada, Satoshi; Hiller, Julia; Oleastro, Matias; Lagos Gomez, Macarena; Aldave Becerra, Juan Carlos; Ouachée-Chardin, Marie; Fouyssac, Fanny; Girisha, Katta Mohan; Etzioni, Amos; Van Montfrans, Joris; Camcioglu, Yildiz; Kerns, Leigh Ann; Belohradsky, Bernd; Blanche, Stéphane; Bousfiha, Aziz; Rodriguez-Gallego, Carlos; Meyts, Isabelle; Kisand, Kai; Reichenbach, Janine ... , (2016). Heterozygous STAT1 gain-of-function mutations underlie an unexpectedly broad clinical phenotype. Blood, 127 (25), 3154−3164. DOI: 10.1182/blood-2015-11-679902.
1.1.
2015
Kõiv, V.; Roosaare, M.; Vedler, E; Kivistik., P A; Toppi, K.; Schryer, DW.; Remm, M.; Tenson, T; Mäe, A. (2015). Microbial population dynamics in response to Pectobacterium atrosepticum infection in potato tubers. Scientific Reports, 5 (11606), 1−18. DOI: 10.1038/srep11606.
1.1.
2015
Palta, Priit; Kaplinski, Lauris; Nagirnaja, Liina; Veidenberg, Andres; Möls, Märt; Nelis, Mari; Esko, Tõnu; Metspalu, Andres; Laan, Maris; Remm, Maido (2015). Haplotype phasing and inheritance of copy number variants in nuclear families. PLoS ONE, 10 (4), UNSP e0122713. DOI: 10.1371/journal.pone.0122713.
1.1.
2015
Kaplinski, Lauris; Lepamets, Maarja; Remm, Maido (2015). GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists. GigaScience, 4 (58), 1−8. DOI: 10.1186/s13742-015-0097-y.
1.1.
2015
Karmin, Monika; Saag, Lauri; Vicente, Mário; Wilson Sayres, Melissa A; Järve, Mari; Talas, Ulvi Gerst; Rootsi, Siiri; Ilumäe, Anne-Mai; Mägi, Reedik; Mitt, Mario; Pagani, Luca; Puurand, Tarmo; Faltyskova, Zuzana; Clemente, Florian; Cardona, Alexia; Metspalu, Ene; Sahakyan, Hovhannes; Yunusbayev, Bayazit; Hudjashov, Georgi; DeGiorgio, Michael ... Kivisild, Toomas (2015). A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Research, 25 (4), 459−466. DOI: 10.1101/gr.186684.114.
3.1.
2015
Andreson, Reidar; Kaplinski, Lauris; Remm Maido (2015). Fast masking of repeated primer binding sites in eukaryotic genomes. In: Basu, Chhandak (Ed.). PCR Primer Design (1−16). New York: Springer. (Methods in Molecular Biology). DOI: 10.1007/978-1-59745-528-2_10.
3.1.
2015
Kaplinski, Lauris; Remm, Maido (2015). MultiPLX: automatic grouping and evaluation of PCR primers. In: Basu, Chhadank (Ed.). PCR Primer Design (127−142). New York: Springer. (Methods in Molecular Biology). DOI: 10.1007/978-1-59745-528-2_14.
5.2.
2015
Naaber, Paul; Balode, Arta; Egorova, Svetlana; Huik, Kristi; Ivanova, Marina; Kaftyreva, Lidia; Kõljalg, Siiri; Kõressaar, Triinu; Lillo, Jana; Löhr, Iren; Miciuleviciene, Jolanta; Pai, Kristiine; Pavelkovich, Anastassia; Remm, Maido; Sepp, Epp (2015). The epidemiology of CTX-M group genes among clinical Escherichia coli strains in Estonia, Latvia, Lithuania, Norway and Russia.
1.1.
2014
van den Brand, Marre; Peters, Remco P. H.; Catsburg, Arnold; Rubenjan, Anna; Broeke, Ferdi J.; van den Dungen, Frank A. M.; van Weissenbruch, Mirjam M.; van Furth, A. Marceline; Kõressaar, Triinu; Remm, Maido; Savelkoul, Paul H. M.; Bos, Martine P. (2014). Development of a multiplex real-time PCR assay for the rapid diagnosis of neonatal late onset sepsis. Journal of Microbiological Methods, 106, 8−15. DOI: 10.1016/j.mimet.2014.07.034.
1.1.
2014
Sothiselvam, S; Liu, B; Han, W; Ramu, H; Klepacki, D; Atkinson, GC; Brauer, A; Remm, M; Tenson, T; Schulten, K; Vázquez-Laslop, N; Mankin, AS. (2014). Macrolide antibiotics allosterically predispose the ribosome for translation arrest. Proceedings of the National Academy of Sciences, 111 (27), 9804−9809. DOI: 10.1073/pnas.1403586111.
1.1.
2014
Nagirnaja, Liina; Palta, Priit; Kasak, Laura; Rull, Kristiina; Christiansen, Ole B.; Nielsen, Henriette S.; Steffensen, Rudi; Esko, Tõnu; Remm, Maido; Laan, Maris (2014). Structural genomic variation as risk factor for idiopathic recurrent miscarriage. Human Mutation, 35 (8), 972−982. DOI: 10.1002/humu.22589.
1.1.
2013
Vedler, Eve; Heinaru, Eeva; Jutkina, Jekaterina; Viggor, Signe; Kõressaar, Triinu; Remm, Maido; Heinaru, Ain (2013). Limnobacter spp. as newly detected phenol-degraders among Baltic Sea surface water bacteria characterized by comparative analysis of catabolic genes. Systematic and Applied Microbiology, 36 (8), 525−532. DOI: 10.1016/j.syapm.2013.07.004.
1.1.
2013
Koua, D; Laht, S; Kaplinski, L; Stöcklin, R; Remm, M; Favreau, P; Lisacek, F (2013). Position-specific scoring matrix and hidden Markov model complement each other for the prediction of conopeptide superfamilies. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1834 (4), 717−724. DOI: 10.1016/j.bbapap.2012.12.015.
1.1.
2013
Nikopensius, T; Annilo, T; Jagomägi, T; Gilissen, C; Kals, M; Krjutškov, K; Mägi, R; Eelmets, M; Gerst-Talas, U; Remm, M; Saag, M; Hoischen, A; Metspalu, A (2013). Non-syndromic Tooth Agenesis Associated with a Nonsense Mutation in Ectodysplasin-A (EDA). Journal of Dental Research, 92 (6), 507−511. DOI: 10.1177/0022034513487210.
3.1.
2013
Remm, Maido; Krjutškov, Kaarel; Metspalu, Andres (2013). Primer Design for Large-Scale Multiplex PCR and Arrayed Primer Extension (APEX). In: Tania Nolan; Stephen A. Bustin (Ed.). PCR Technology: Current Innovation - 3rd Edition (199−207). CRC PRESS.
1.1.
2012
Võsa, L; Sudakov, A; Remm, M; Ustav, M; Kurg, R. (2012). Identification and analysis of papillomavirus E2 protein binding sites in the human genome. Journal of Virology, 86 (1), 348−357. DOI: 10.1128/JVI.05606-11.
1.1.
2012
Brauer, A.; Kurz, A.; Stockwell, T.; Baden-Tillson, H.; Heidler, J.; Wittig, I.; Kauferstein, S.; Mebs, D.; Stöcklin, R.; Remm, M. (2012). The Mitochondrial Genome of the Venomous Cone Snail Conus consors. PLoS ONE, 7 (12), e51528 .
1.1.
2012
Untergasser, Andreas; Cutcutache, Ioana; Koressaar, Triinu; Ye, Jian; Faircloth, Brant C; Remm, Maido; Rozen, Steve. (2012). Primer3 - new capabilities and interfaces. Nucleic Acids Research, 40 (15), e115. DOI: 10.1093/nar/gks596.
1.1.
2012
Laht S, Koua D, Kaplinski L, Lisacek F, Stöcklin R, Remm M (2012). Identification and classification of conopeptides using profile Hidden Markov Models. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1824, 488−492. DOI: 10.1016/j.bbapap.2011.12.004.
1.1.
2012
Terrat Y, Biass D, Dutertre S, Favreau P, Remm M, Stöcklin R, Piquemal D, Ducancel F. (2012). High-resolution picture of a venom gland transcriptome: Case study with the marine snail Conus consors. Toxicon, 59, 34−46.
1.1.
2012
Koressaar, Triinu; Remm, Maido (2012). Characterization of Species-Specific Repeats in 613 Prokaryotic Species. DNA Research, 19 (3), 219−230. DOI: 10.1093/dnares/dss006.
1.1.
2012
Koua, D.; Brauer, A.; Laht, S.; Kaplinksi, L.; Favreau, P.; Remm, M.; Lisacek, F.; Stöcklin, R. (2012). ConoDictor: a tool for prediction of conopeptide superfamilies. Nucleic Acids Research, 40, W238−W241. DOI: 10.1093/nar/gks337.
1.1.
2012
Saare, Merli; Sõritsa, Deniss; Vaidla, Kadri; Palta, Priit; Remm, Maido; Laan, Martti; Karro, Helle; Sõritsa, Andrei; Salumets, Andres; D'Hooghe, Thomas; Peters, Maire (2012). No evidence of somatic DNA copy number alterations in eutopic and ectopic endometrial tissue in endometriosis. Human Reproduction, 27 (6), 1857−1864. DOI: 10.1093/humrep/des125.
1.1.
2011
Scheler, O.; Kaplinski, L.; Glynn, B.; Palta, P.; Parkel, S.; Toome, K.; Maher, M.; Barry, T.; Remm, M.; Kurg, A. (2011). Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes. BMC Biotechnology, 11, 11−17. DOI: 10.1186/1472-6750-11-17.
1.1.
2011
Knapp, D.C.; Serva, S.; D'Onofrio, J.; Keller, A.; Lubys, A.; Kurg, A.; Remm, M.; Engels, JW. (2011). Fluoride-Cleavable, Fluorescently Labelled Reversible Terminators: Synthesis and Use in Primer Extension. Chemistry - A European Journal, 17 (10), 2903−2915. DOI: 10.1002/chem.201001952.
1.1.
2011
Siibak, Triinu; Peil, Lauri; Doenhoefer, Alexandra; Tats, Age; Remm, Maido; Wilson, Daniel N.; Tenson, Tanel; Remme, Jaanus (2011). Antibiotic-induced ribosomal assembly defects result from changes in the synthesis of ribosomal proteins. Molecular Microbiology, 80 (1), 54−67. DOI: 10.1111/j.1365-2958.2011.07555.x.
1.1.
2011
Männik, K; Parkel, S; Palta, P; Zilina, O; Puusepp, H; Esko, T; Mägi, R; Nõukas, M; Veidenberg, A; Nelis, M; Metspalu, A; Remm, M; Ounap, K; Kurg, A. (2011). A parallel SNP array study of genomic aberrations associated with mental retardation in patients and general population in Estonia. European Journal of Medical Genetics, 54 (2), 136−143.
1.1.
2011
Metspalu, M.; Romero, IG.; Yunusbayev, B.; Chaubey, G.; Mallick, CB.; Hudjashov, G.; Nelis, M.; Mägi, R.; Metspalu, E.; Remm, M.; Pitchappan, R.; Singh, L.; Thangaraj, K.; Villems, R.; Kivisild, T. (2011). Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia. The American Journal of Human Genetics, 89 (6), 731−44. DOI: 10.1016/j.ajhg.2011.11.010.
1.1.
2011
Chaubey, Gyaneshwer; Metspalu, Mait; Choi, Ying; Mägi, Reedik; Gallego Romero, Irene; Soares, Pedro; van Oven, Mannis; Behar, Doron M; Rootsi, Siiri; Hudjashov, Georgi; Basu Mallick, Chandana; Karmin, Monika; Nelis, Mari; Parik, Jüri; Goverdhana Reddy, Alla; Metspalu, Ene; vanDriem, George; Xue, Yali; Tyler-Smith, Chris; Thangaraj, Kumarasamy ... Kivisild, Toomas. (2011). Population Genetic Structure in Indian Austroasiatic speakers: The Role of Landscape Barriers and Sex-specific Admixture. Molecular Biology and Evolution, 28(2), 1013−24.
1.1.
2011
Margus, T.; Remm, M.; Tenson, T. (2011). A Computational Study of Elongation Factor G (EFG) Duplicated Genes: Diverged Nature Underlying the Innovation on the Same Structural Template. PLoS ONE, 6, e22789.
5.1.
2011
Nagirnaja, L.; Kasak, L.; Palta, P.; Rull, K.; Christiansen, O.B.; Esko, T.; Remm, M.; Metspalu, A.; Laan, M. (2011). Role of DNA copy number variations in genetic predisposition to recurrent pregnancy loss. Journal of Reproductive Immunology, 90: 9th Congress of the European Society for Reproductive Immunology and European Society for Human Reproduction and Embryology Early Pregnancy Special Interest Group; Copenhagen, Denmark; August 23-26, 2011. UK: Elsevier Ireland Ltd, 145. (2). DOI: 10.1016/j.jri.2011.06.028.
5.1.
2011
Nagirnaja, L.; Kasak, L.; Palta, P.; Rull, K.; Christiansen, OB.; Esko, T.; Remm, M.; Metspalu, A.; Laan, M. (2011). DNA copy number variations in recurrent miscarriage. Placenta: International Federation of Placenta Associations - 14th European Placenta Group Meeting 2011 14.-17. 09.2011 Geilo, Norra. Elsevier Ireland Ltd, A140−A140. (32; 9).
1.1.
2010
Kaplinski, L.; Scheler, O.; Parkel, S.; Palta, P.; Toome, K.; Kurg, A.; Remm, M. (2010). Detection of tmRNA molecules on microarrays at low temperatures using helper oligonucleotides. BMC Biotechnology, 10 (34), 1−10. DOI: 10.1186/1472-6750-10-34.
1.1.
2010
Oitmaa, E.; Peters, M.; Vaidla, K.; Andreson, R.; Mägi, R.; Slavin, G.; Velthut, .; Tõnisson, N.; Reimand, T.; Remm, M.; Schneider, M.; Õunap, K.; Salumets, A.; Metspalu, A. (2010). Molecular diagnosis of Down Syndrome using Quantitative APEX-2 microarrays. Prenatal Diagnosis, 30, 1170−1177. DOI: 10.1002/pd.2639.
1.1.
2009
Scheler, O.; Glynn, B.; Parkel, S.; Palta, P.; Toome, K.; Kaplinski, L.; Remm, M.; Maher, M.; Kurg, A. (2009). Fluorescent labeling of NASBA amplified tmRNA molecules for microarray applications. BMC Biotechnology, 15 (9), 45−50. DOI: 10.1186/1472-6750-9-45.
1.1.
2009
Koressaar, T.; Jõers, K.; Remm, M. (2009). Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms. Bioinformatics, 25 (11), 1349−1355.
1.1.
2009
Nelis, M.; Esko, T.; Mägi, R.; Zimprich, F.; Zimprich, A.; Toncheva, D.; Karachanak, S.; Piskácková, T.; Balascák, I.; Peltonen, L.; Jakkula, E.; Rehnström, K.; Lathrop, M.; Heath, S.; Galan, P.; Schreiber, S.; Meitinger, T.; Pfeufer, A.; Wichmann, HE.; Melegh, B. ... Metspalu, A. (2009). Genetic structure of Europeans: a view from the North-East. PLoS ONE, 4(5), e5472.
1.1.
2008
Tats, A.; Tenson, T.; Remm, M. (2008). Preferred and avoided codon pairs in three domains of life. BMC Genomics, 9, 463.
1.1.
2008
Krjutskov, K.; Andreson, R.; Mägi, R.; Nikopensius, T.; Khrunin, A.; Mihailov, E.; Tammekivi, V.; Sork, H.; Remm, M.; Metspalu, A. (2008). Development of a single tube 640-plex genotyping method for detection of nucleic acid variations on microarrays. Nucleic Acids Research, 36 (12), e75.
1.1.
2008
Kousoulidou, L.; Männik, K.; Zilina, O.; Parkel, S.; Palta, P.; Remm, M.; Kurg, A.; Patsalis, P.C. (2008). Application of two different microarray-based copy-number detection methodologies - array-comparative genomic hybridization and array-multiplex amplifiable probe hybridization - with identical amplifiable target sequences. Clinical Chemistry and Laboratory Medicine (CCLM), 46 (5), 722−724.
1.1.
2008
Tamm, R.; Oselin, K.; Kallassalu, K.; Magi, R.; Anier, K.; Remm, M.; Metspalu, A. (2008). Thiopurine S-methyltransferase (TPMT) pharmacogenetics: three new mutations and haplotype analysis in the Estonian population. Clinical Chemistry and Laboratory Medicine (CCLM), 46 (7), 974−979.
1.1.
2008
Andreson, R.; Möls, T.; Remm, M. (2008). Predicting failure rate of PCR in large genomes. Nucleic Acids Research, 36 (11), e66. DOI: 10.1093/nar/gkn290.
1.1.
2008
Kousoulidou, L.; Männik, K.; Sismani, C.; Zilina, O.; Parkel, S.; Puusepp, H.; Tõnisson, N.; Palta, P.; Remm, M.; Kurg, A.; Patsalis, P. C. (2008). Array-MAPH: a methodology for the detection of locus copy-number changes in complex genomes. Nature Protocols, 3 (5), 849−865. DOI: 10.1038/nprot.2008.49.
5.1.
2008
Knapp, D.C.; Keller, A.; D'Onofrio, J.; Lubys, A.; Serva, S.; Kurg, A.; Remm, M.; Kwiatkowski, M.; Engels, J.W. (2008). Synthesis of four colors fluorescently labelled 3'-O-blocked nucleotides with fluoride cleavable blocking group and linker for array based Sequencing-by-Synthesis applications. Nucleic Acids Symposium Series, 52, 345−346.
5.1.
2008
Glynn, B.; Lacey, K.; Palta, P.; Kaplinski, L.; Remm, M.; Barry, T.; Smith, T.; Maher, M. (2008). Demonstration of the application of the tmRNA transcript of the bacterial ssrA gene as a molecular diagnostic target using a combination of NASBA and BiaCore technologies. International Journal of Antimicrobial Agents, 29, S392.
5.1.
2008
Palta, P.; Parkel, S.; Veidenberg, A.; Mannik, K.; Puusepp, H.; Zilina, O.; Kurg, A.; Remm, M. (2008). Web-based database platform for large-scale copy number variation studies. Cellular Oncology, 30 (3), 270.
5.2.
2008
Oitmaa, Eneli; Krjutskov, Kaarel; Mägi, Reedik ; Andreson, Reidar ; Raukas, Elve; Remm, Maido; Tõnisson, Neeme; Schneider, Marion; Metspalu, Andres (2008). Molecular diagnostics of Down syndrome using quantitative APEX microarrays. RBM online, vol.16-suppl. 3: Eighth International Symposium of Preimplantation Genetic Diagnosis, Barcelona, April 23-26, 2008. , S17.
1.1.
2007
Magi, R.; Pfeufer, A.; Nelis, M.; Montpetit, A.; Metspalu, A.; Remm, M. (2007). Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation. BMC Genomics, 8 (159), x.
1.1.
2007
Kousoulidou, L.; Parkel, S.; Zilina, O.; Palta, P.; Puusepp, H.; Remm, M.; Turner, G.; Boyle, J.; van Bokhoven, H.; de Brouwer, A.; Van Esch, H.; Froyen, G.; Ropers, H.-H.; Chelly, J.; Moraine, C.; Gecz, J.; Kurg, A.; Patsalis, P. (2007). Screening of 20 patients with X-linked mental retardation using chromosome X–specific array-MAPH. European Journal of Medical Genetics, 50 (6), 399−410.
1.1.
2007
Koressaar, T.; Remm, M. (2007). Enhancements and modifications of primer design program Primer3. Bioinformatics, 23 (10), 1289−1291.
1.1.
2007
Kuningas, M.; Mägi, R.; Westendorp, R.G.; Slagboom, P.E.; Remm, M.; van Heemst, D. (2007). Haplotypes in the human Foxo1a and Foxo3a genes; impact on disease and mortality at old age. European Journal of Human Genetics, 15 (3), 294−301. DOI: 10.1038/sj.ejhg.5201766.
1.1.
2007
Margus, T.; Remm, M.; Tenson, T. (2007). Phylogenetic distribution of translational GTPases in bacteria. BMC Genomics, 8, 15. DOI: 10.1186/1471-2164-8-15.
1.1.
2007
Patsalis, P.C.; Kousoulidou, L.; Männik, K.; Sismani, C.; Žilina, O.; Parkel, S.; Puusepp, H.; Tõnisson, N.; Palta, P.; Remm, M.; Kurg, A. (2007). Detection of small genomic imbalances using microarray-based multiplex amplifiable probe hybridization. European Journal of Human Genetics, 15 (2), 162−172. DOI: 10.1038/sj.ejhg.5201738.
3.1.
2007
Kaplinski, L.; Remm, M. (2007). MultiPLX: Automatic Grouping and Evaluation of PCR Primers. In: A.Yuryev (Ed.). PCR Primer Design (367). . Humana Press.
3.1.
2007
Andreson, R.; Kaplinski, L.; Remm, M. (2007). Fast Masking of Repeated Primer Binding Sites in Eukaryotic Genomes. In: Yuryev, A. (Ed.). PCR Primer Design (367). . Humana Press. (July 2007 ).
1.1.
2006
Andreson, R.; Puurand, T.; Remm, M. (2006). SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes. Nucleic Acids Research, 34, W651−W656.
1.1.
2006
Montpetit, A.; Nelis, M.; Laflamme, P.; Magi, R.; Ke, X.Y.; Remm, M.; Cardon, L.; Hudson, T.J.; Metspalu, A. (2006). An evaluation of the performance of tag SNPs derived from HapMap in a Caucasian population. PLoS Genetics, 2 (3), 282−290.
1.1.
2006
Andreson, R; Reppo, E; Kaplinski, L; Remm, M (2006). GENOMEMASKER package for designing unique genomic PCR primers. BMC Bioinformatics, 7, 172.
1.1.
2006
Tats, A.; Remm, M.; Tenson, T. (2006). Highly expressed proteins have an increased frequency of alanine in the second amino acid position. BMC Genomics, 7, 28.
3.2.
2006
Mägi, R.; Kaplinski, L.; Remm, M. (2006). The Whole Genome TagSNP Selection and Transferability Among HapMap Populations. Pacific Symposium on Biocomputing 2006: 2006. World Scientific Publ Co Pte Ltd, 535−543.
1.1.
2005
Mueller, J. C.; Lõhmussaar, E.; Mägi, R.; Remm, M.; Bettecken, T.; Lichtner, P.; Huber, S.; Illig, T; Luedemann, J.; Schreiber, S.; Wichmann, H. E.; Pramstaller, P.; Romeo, G.; Testa, A.; Metspalu, A.; Meitinger, T. (2005). Linkage Disequilibrium Patterns and tagSNP Transferability among European Populations. The American Journal of Human Genetics, 76 (3), 387−398.
1.1.
2005
Laan, M.; Wiebe, V.; Khusnutdinova, E.; Remm, M.; Paabo, S. (2005). X-chromosome as a marker for population history: linkage disequilibrium and haplotype study in Eurasian populations. European Journal of Human Genetics, 13 (4), 452−462.
1.1.
2005
Kaplinski, L.; Andreson, R.; Puurand, T.; Remm, M. (2005). MultiPLX: automatic grouping and evaluation of PCR primers. Bioinformatics, 21 (8), 1701−1702.
1.1.
2005
O'Brien, KP.; Remm, M.; Sonnhammer, ELL. (2005). Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Research, 33, D476−D480.
5.2.
2005
Andreson, R.; Reppo, E.; Kaplinski, L.; Möls, T.; Remm, M. (2005). GENOMEMASKER package: tools for design of high quality genomic PCR primers. ECCB 2005, Spain, Madrid (28 sep. - 01 oct., 2005): European conference on computational biology, Madrid, 2005.
3.1.
2004
Remm, M.; Kurg, A.; Metspalu, A. (2004). Primer Design for Large-Scale Multiplex PCR and Arrayed Primer Extension (APEX). In: Weissensteiner, T.; Griffin, H.G.; Griffin, A. (Ed.). PCR Technology, Current Innovations, 2nd Edition (131−139). . Boca Raton: CRC PRESS.
5.2.
2003
Reppo, E.; Andreson, R.; Remm, M. (2003). GenomeMasker and GenomeTester: tools for design of high quality genomic PCR primers. Bioinformatics 2003, Helsinki, Finland, May 22-24, 2003: Bioinformatics 2003, Helsinki.
1.1.
2002
Remm, M.; Metspalu, A. (2002). High-density genotyping and linkage disequilibrium in the human genome using chromosome 22 as a model. Current Opinion in Chemical Biology, 6 (1), 24−30.
1.1.
2002
Dawson, E.; Abecasis, GR.; Bumpstead, S.; Chen, Y.; Hunt, S.; Beare, DM.; Pabial, J.; Dibling, T.; Tinsley, E.; Kirby, S.; Carter, D.; Papaspyridonos, M.; Livingstone, S.; Ganske, R.; Lohmmussaar, E.; Zernant, J.; Tonisson, N.; Remm, M.; Magi, R.; Puurand, T. ... Dunham, I. (2002). A first-generation linkage disequilibrium map of human chromosome 22. Nature, 418 (6897), 544−548.
5.1.
2002
Kepp, K.; Remm, M.; Lohmussaar, E.; Gerst-Talas, U. (2002). APEX scaling up. Optimisation of the high throughput Arrayed Primer Extension based DNA variation analysis for accurate and affordable large-scale projects. 10. , 297.
5.1.
2002
Lohmussaar, E.; Zernant, J.; Magi, R.; Kepp, K.; Puurand, T.; Tonisson, N.; Valvas, I.; Slavin, G.; Andreson, R.; Kurg, A.; Remm, M.; Metspalu, A. (2002). SNP analysis and linkage disequilibrium map of the human chromosome 22 using APEX arrays. European Journal of Human Genetics, 10, 299−299.
5.1.
2002
Lohmussaar, E.; Zernant, J.; Magi, R.; Puurano, T.; Tonisson, N.; Valvas, I.; Slavin, G.; Kurg, A.; Remm, M.; Metspalu, A. (2002). SNP analysis and linkage disequilibrium map of the human chromosome 22 using Arrayed Primer EXtension (APEX) technology. The American Journal of Human Genetics, 71 (4), 449−449.
5.2.
2002
Andreson, R.; Lukk, M.; Remm, M.; Vilo, J.; Metspalu, A. (2002). A comparison of different methods to find PCR primer binding sites in the human genome. Bioinformatics 2002, Bergen, Norway (aprill 4-7, 2002): Bioinformatics 2002, Bergen, 2002.
1.1.
2001
Remm, M.; Storm, CEV.; Sonnhammer, ELL. (2001). Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. Journal of Molecular Biology, 314 (5), 1041−1052.
5.1.
2001
Metspalu, A.; Zernant, J.; Lohmussaar, E.; Magi, R.; Kepp, K.; Puurand, T.; Tonisson, N.; Valvas, L.; Pavel, H.; Slavin, G.; Andreson, R.; Kurg, A.; Remm, M. (2001). SNP analysis of the human chromosome 22 using APEX arrays. The American Journal of Human Genetics, 69 (4), 408−408.
1.1.
2000
Remm, M.; Sonnhammer, E. (2000). Classification of transmembrane protein families in the Caenorhabditis elegans genome and identification of human orthologs. Genome Research, 10 (11), 1679−1689.
1.1.
1999
Remm, M.; Remm, A.; Ustav, M. (1999). Human papillomavirus type 18 E1 protein is translated from polycistronic mRNA by a discontinuous scanning mechanism. Journal of Virology, 73 (4), 3062−3070.
1.1.
1995
Plumpton, M.; Sharp, NA.; Liddicoat, LH.; Remm, M.; Tucker, DO.; Hughes, FJ.; Russell, SM.; Romanos, MA. (1995). A high-capacity assay for inhibitors of human papillomavirus DNA-replication. Bio/Technology, 13 (11), 1210−1214.
1.1.
1992
Sturzbecher, HW.; Brain, R.; Addison, C.; Rudge, K.; Remm, M.; Grimaldi, M.; Keenan, E.; Jenkins, JR. (1992). A C-terminal alpha-helix plus basic region motif is the major structural determinant of p53 tetramerization. Oncogene, 7 (8), 1513−1523.
1.1.
1992
Remm, M.; Brain, R.; Jenkins, JR. (1992). The e2 binding-sites determine the efficiency of replication for the origin of human papillomavirus type-18. Nucleic Acids Research, 20 (22), 6015−6021.

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10.03.2022