Publikatsioonid

2023

      • Pajuste FD and Remm M . (2023). GeneToCN: an alignment-free method for gene copy number estimation directly from next-generation sequencing reads. Sci Rep 13(1):17765. [Full Text]
      • Kaplinski L, Möls M, Puurand T, Remm M . (2023). DOCEST-fast and accurate estimator of human NGS sequencing depth and error rate. Bioinform Adv 3(1):vbad084. [Full Text]

2022

      • Bonturi N, Pinheiro MJ, de Oliveira PM, Rusadze E, Eichinger T, Liudžiūtė G, De Biaggi JS, Brauer A, Remm M, Miranda EA, Ledesma-Amaro R, Lahtvee PJ. (2022). Development of a dedicated Golden Gate Assembly platform (RtGGA) for Rhodotorula toruloides. Metabolic Engineering Communications, 15:e00200. [Full Text]

2021

      • Aun E, Kisand V, Laht M, Telling K, Kalmus P, Väli Ü, Brauer A, Remm M, Tenson T. (2021). Molecular Characterization of Enterococcus Isolates From Different Sources in Estonia Reveals Potential Transmission of Resistance Genes Among Different Reservoirs. Front Microbiol, 12:601490, doi: 10.3389/fmicb.2021.601490. [Full Text]
      • Kaplinski L, Möls M, Puurand T, Pajuste FD, Remm M (2021). KATK: Fast genotyping of rare variants directly from unmapped sequencing reads. Human Mutation, 42(6):777-786. doi: 10.1002/humu.24197. [Full Text]
      • Bellabarba A, Bacci G, Decorosi F, Aun E, Azzarello E, Remm M, Giovannetti L, Viti C, Mengoni A and Pini F. (2021). Competitiveness for Nodule Colonization in Sinorhizobium meliloti: Combined In Vitro-Tagged Strain Competition and Genome-Wide Association Analysis. mSystems 6(4):e0055021. [Full Text]
      • Modica MV, Ahmad R, Ainsworth S, Anderluh G, Antunes A, Beis D, Caliskan F, Serra MD, Dutertre S, Moran Y, Nalbantsoy A, Oukkache N, Pekar S, Remm M, von Reumont BM, Sarigiannis Y, Tarallo A, Tytgat J, Undheim EAB, Utkin Y, Verdes A, Violette A, Zancolli G. (2021). The new COST Action European Venom Network (EUVEN) – synergy and future perspectives of modern venomics. GigaScience, 10(3) doi: 10.1093/gigascience/giab019. [Full Text]
      • 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, 148:111678. [Abstract]

2020

      • Raime K, Krjutškov K and Remm M. (2020). Method for the Identification of Plant DNA in Food Using Alignment-Free Analysis of Sequencing Reads: A Case Study on Lupin. Front. Plant Sci., 11:646. [Full text]
      • Rosendahl S, Tamman H, Brauer A, Remm M and Hõrak R. (2020). Chromosomal toxin-antitoxin systems in Pseudomonas putida are rather selfish than beneficial. Scientific Reports, 10:9230. [Full text]
      • Telling K, Brauer A, Laht M, Kalmus P, Toompere K, Kisand V, Maimets, M, Remm M, Tenson T and Lutsar I. (2020). Characteristics of Extended-Spectrum Beta-Lactamase-Producing Enterobacteriaceae and Contact to Animals in Estonia. Microorganisms, 8:1130. [Full text]
      • 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 Genet., 16(8):e1008981. [Full text]

2019

      • 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. [Full text]
      • Jõers A, Vind K, Hernández SB, Maruste R, Pereira M, Brauer A, Remm M, Cava F and Tenson T. (2019). Muropeptides Stimulate Growth Resumption from Stationary Phase in Escherichia coli. Scientific Reports, 9: 18043. [Full text]
      • Sepp E, Andreson R, Balode A, Bilozor A, Brauer A, Egorova S, Huik K, Ivanova M, Kaftyreva L, Kõljalg S, Kõressaar T, Makarova M, Miciuleviciene J, Pai K, Remm M, Rööp T, Naaber P. (2019). Phenotypic and Molecular Epidemiology of ESBL-, AmpC-, and Carbapenemase-Producing Escherichia coli in Northern and Eastern Europe. Front Microbiol., 10:2465.[Full text]
      • Org T, Hensen K, Kreevan R, Mark E, Sarv O, Andreson R, Jaakma Ü, Salumets A, Kurg A. (2019). Genome-wide histone modification profiling of inner cell mass and trophectoderm of bovine blastocysts by RAT-ChIP. PLoS ONE, 14(11):e0225801.  [Full text]
      • Žilina O, Rekker K, Kaplinski L, Sauk M, Paluoja P, Teder H, Ustav EL, Tõnisson N, Reimand T, Ridnõi K, Palta P, Vermeesch JR, Krjutškov K, Kurg A, Salumets A. (2019). Creating basis for introducing non-invasive prenatal testing in the Estonian public health setting. Prenat Diagn., 39:13. [Full text]
      • Bilozor A, Balode A, Chakhunashvili G, Chumachenko T, Egorova S, Ivanova M, Kaftyreva L, Kõljalg S, Kõressaar T, Lysenko O, Miciuleviciene J, Mändar R, Lis DO, Wesolowska MP, Ratnik K, Remm M, Rudzko J, Rööp T, Saule M, Sepp E, Shyshporonok J, Titov L, Tsereteli D, Naaber P. (2019). Application of Molecular Methods for Carbapenemase Detection. Front Microbiol., 10:1755. [Full text]
      • 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. Curr Biol., 29(10):1701-1711. [Full text]
      • Kõiv V, Arbo K, Maiväli Ü, Kisand V, Roosaare M, Remm M, Tenson T. (2019). Endophytic bacterial communities in peels and pulp of five root vegetables. PLoS One, 14:e0210542. [Full text]
      • Tasa T, Krebs K, Kals M, Mägi R, Lauschke VM, Haller T, Puurand T, Remm M, Esko T, Metspalu A, Vilo J, Milani L. (2018). Genetic variation in the Estonian population: pharmacogenomics study of adverse drug effects using electronic health records. Eur J Hum Genet.,  27:442-454. [Full text]
      • Kirsip H, Abroi A. (2019). Protein Structure-Guided Hidden Markov Models (HMMs) as A Powerful Method in the Detection of Ancestral Endogenous Viral Elements. Viruses, 11:E320. [Full Text]
      • Puustusmaa M, Abroi A. (2019). cRegions-a tool for detecting conserved cis-elements in multiple sequence alignment of diverged coding sequences. PeerJ., 6:e6176. [Full Text]

2018

      • Aun E, Brauer A, Kisand V, Tenson T and Remm M. (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):e1006434. [Full text]
      • Telling K, Laht M, Brauer A, Remm M, Kisand V, Maimets M, Tenson T and Lutsar I. (2018). Multidrug resistant Pseudomonas aeruginosa in Estonian hospitals. BMC Infect Dis., 18(1): 513. [Full text]
      • Roosaare M, Puustusmaa M, Möls M, Vaher M, and Remm M. (2018). PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads. PeerJ, 6: e4588. [Full Text]
      • Sauk M, Žilina O, Kurg A, Ustav EL, Peters M, Paluoja P, Roost AM, Teder H, Palta P, Brison N, Vermeesch JR, Krjutškov K, Salumets A and Kaplinski L. (2018). NIPTmer: rapid k-mer-based software package for detection of fetal aneuploidies. Scientific Reports, 8(1):5616. [Full Text]
      • Raime K and Remm M. (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. [Full Text]
      • Kõressaar T, Lepamets M, Kaplinski L, Raime K, Andreson R and Remm M. (2018). Primer3_masker: integrating masking of template sequence with primer design software. Bioinformatics, 34:1937–1938. [Full text]

2017

      • Vasar M, Andreson R, Davison J, Jairus T, Moora M, Remm M, Young JPW, Zobel M, Öpik M. (2017). Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi. Mycorrhiza, 27: 761-773. [Full Text]
      • Pajuste FD, Kalpinski L, Möls M, Puurand T, Lepamets M, Remm M. (2017). FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads. Scientific Reports, 7:2537 [Full Text]
      • Roosaare M, Vaher M, Kaplinski L, Möls M, Andreson R, Lepamets M, Kõressaar T, Naaber P, Kõljalg S, Remm M. (2017). StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees. PeerJ, 5: e3353. [Full Text]
      • Puustusmaa M, Kirsip H, Gaston K, Abroi A. (2017). The Enigmatic Origin of Papillomavirus Protein Domains. Viruses, 9:E240. [Full Text]
      • Sillaste G, Kaplinski L, Meier R, Jaakma Ü, Eriste E, Salumets A. (2017). A novel hypothesis for histone-to-protamine transition in Bos taurus spermatozoa. Reproduction (Cambridge, England), 153(3): 241-251 [Full Text]

2016

      • Jakobson L, Vaahtera L, Tõldsepp K, Nuhkat M, Wang C, Wang YS, Hõrak H, Valk E, Pechter P, Sindarovska Y, Tang J, Xiao C, Xu Y, Gerst Talas U, García-Sosa AT, Kangasjärvi S, Maran U, Remm M, Roelfsema MR, Hu H, Kangasjärvi J, Loog M, Schroeder JI, Kollist H, Brosché M. (2016). Natural Variation in Arabidopsis Cvi-0 Accession Reveals an Important Role of MPK12 in Guard Cell CO2 Signaling. PLoS Biology, 14(12): e2000322 [Full Text]
      • Brauer A, Telling K, Laht M, Kalmus P, Lutsar I, Remm M, Kisand V, Tenson T. (2016). Plasmid with Colistin Resistance Gene mcr-1 in Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strains Isolated from Pig Slurry in Estonia. Antimicrobial Agents and Chemotherapy, 60 (11): 6933-6936 [Full Text]
      • Puustusmaa M, Abroi A. (2016). Conservation of the E8 CDS of the E8^E2 protein among mammalian papillomaviruses. Journal of General Virology, 97(9): 2333-45 [Abstract]
      • Toubiana J, Okada S, Hiller J, Oleastro M, Lagos Gomez M, Aldave Becerra JC, Ouachée-Chardin M, Fouyssac F, Girisha KM, Etzioni A, Van Montfrans J, Camcioglu Y, Kerns LA, Belohradsky B, Blanche S, Bousfiha A, Rodriguez-Gallego C, Meyts I, Kisand K, Reichenbach J, Renner ED, Rosenzweig S, Grimbacher B, van de Veerdonk FL, Traidl-Hoffmann C, Picard C, Marodi L, Morio T, Kobayashi M, Lilic D, Milner JD, Holland S, Casanova J-L, Puel A, Cypowyj S, Thumerelle C, Toulon A, Bustamante J, Tahuil N, Salhi A, Boiu S, Chopra C, Di Giovanni D, Bezrodnik L, Boutros J, Thomas C, Lacuesta G, Jannier S, Korganow A-S, Paillard C, Boutboul D, Bué M, Marie-Cardine A, Bayart S, Migaud M, Weiss L, Karmochkine M, Garcia-Martinez J-M, Stephan J-L, Bensaid P, Jeannoel G-P, Witte T, Baumann U, Harrer T, Navarrete C, Benjamin AT, Firinu D, Pignata C, Picco P, Mendoza D, Lugo Reyes SO, Lozano CT, Ortega-Cisneros M, Cortina M, Mesdaghi M, Nabavi M, Español T, Martínez-Saavedra MT, Rezaei N, Zoghi S, Pac M, Barlogis V, Revon-Rivière G, Haimi-Cohen Y, Spiegel R, Miron D, Bouchaib J, Blancas-Galicia L, Toth B, Drexel B, Rohrlich PS, Lesens O, Hoernes M, Drewe E, Abinum M, Sawalle-Belohradsky J, Kindle G, Depner M, Milani L, Nikopensius T , Remm M, Gerst Talas U, Tucker M, Willis M, Leonard S, Meuwissen H, Ferdman RM, Wallace M, Desai MM, Taur P, Badolato R, Soltesz B, Schnopp C, Jansson AF, Ayvaz D, Shabashova N, Chernyshova L, Bondarenko A, Moshous D, Neven B, Boubidi C, Ailal F, Giardino G, Del Giacco S, Bougnoux M-E, Imai K, Okawa T, Mizoguchi Y, Ozaki Y, Takeuchi M, Hayakawa A, Lögering B, Reich K, Buhl T, Eyerich K, Schaller M, Arkwright PD, Gennery AR, Cant AJ, Warris A, Henriet S, Mekki N, Barbouche R, Mustapha IB, Bodemer C, Polak M, Grimprel E, Burgel P-R, Fischer A, Hermine O, Debré M, Kocacyk D, Dhalla F, Patel SY, Moens L, Haerynck F, Dullaers M, Hoste L, Sanal O, Sebnem Kilic S, Roesler J, Lanternier F, Lortholary O, Fieschi C, Church JA, Roifman C, Netea AG and on behalf of the International STAT1 Gain-of-Function Study Group. (2016). Heterozygous STAT1 gain-of-function mutations underlie an unexpectedly broad clinical phenotype. Blood, 127 (25): 3154-3164 [Full Text]

2015

      • Kaplinski L, Lepamets M, Remm M. (2015). GenomeTester4: a toolkit for performing basic set operations – union, intersection and complement on k-mer lists. GigaScience, 4:58 [Full Text]
      • Kõiv V, Roosaare M, Vedler E, Kivistik PA, 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 [Full Text]
      • Palta P, Kaplinski L, Nagirnaja L, Veidenberg A, Möls M, Nelis M, Esko T, Metspalu A, Laan M, Remm M. (2015). Haplotype Phasing and Inheritance of Copy Number Variants in Nuclear Families. PLOS ONE, 10 (4): e0122713 [Full Text]
      • Andreson R, Kaplinski L, Remm M. (2015). Fast masking of repeated primer binding sites in eukaryotic genomes. Methods in Molecular Biology, 1275:1-16 [Abstract]
      • Kaplinski L, Remm M. (2015). MultiPLX: automatic grouping and evaluation of PCR primers. Methods in Molecular Biology, 1275:127-42 [Abstract]
      • Karmin M, Saag L, Vicente M, Wilson Sayres MA, Järve M, Talas UG, Rootsi S, Ilumäe AM, Mägi R, Mitt M, Pagani L, Puurand T, Faltyskova Z, Clemente F, Cardona A, Metspalu E, Sahakyan H, Yunusbayev B, Hudjashov G, DeGiorgio M, Loogväli EL, Eichstaedt C, Eelmets M, Chaubey G, Tambets K, Litvinov S, Mormina M, Xue Y, Ayub Q, Zoraqi G, Korneliussen TS, Akhatova F, Lachance J, Tishkoff S, Momynaliev K, Ricaut FX, Kusuma P, Razafindrazaka H, Pierron D, Cox MP, Sultana GN, Willerslev R, Muller C, Westaway M, Lambert D, Skaro V, Kovačevic L, Turdikulova S, Dalimova D, Khusainova R, Trofimova N, Akhmetova V, Khidiyatova I, Lichman DV, Isakova J, Pocheshkhova E, Sabitov Z, Barashkov NA, Nymadawa P, Mihailov E, Seng JW, Evseeva I, Migliano AB, Abdullah S, Andriadze G, Primorac D, Atramentova L, Utevska O, Yepiskoposyan L, Marjanovic D, Kushniarevich A, Behar DM, Gilissen C, Vissers L, Veltman JA, Balanovska E, Derenko M, Malyarchuk B, Metspalu A, Fedorova S, Eriksson A, Manica A, Mendez FL, Karafet TM, Veeramah KR, Bradman N, Hammer MF, Osipova LP, Balanovsky O, Khusnutdinova EK, Johnsen K, Remm M, Thomas MG, Tyler-Smith C, Underhill PA, Willerslev E, Nielsen R, Metspalu M, Villems R, Kivisild T. (2015). A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Research, 25: 459-466 [Full Text]

2014

      • Huik K, Avi R, Uibopuu H, Pauskar M, Margus T, Karki T, Krispin T, Kool P, Rüütel K, Talu A, Abel-Ollo K, Uusküla A, Carrillo A, He W, Ahuja SK, Lutsar I. (2014). Association between HIV-1 tropism and CCR5 human haplotype E in a Caucasian population.Journal of acquired immune deficiency syndromes, 66(3):239-44 [Abstract]
      • Meitern R, Andreson R, Hõrak P. (2014). Profile of whole blood gene expression following immune stimulation in a wild passerine. BMC Genomics, 15:533 [Full Text]
      • van den Brand M, Peters RP, Catsburg A, Rubenjan A, Broeke FJ, van den Dungen FA, van Weissenbruch MM, van Furth AM, Kõressaar T, Remm M, Savelkoul PH, Bos MP. (2014). Development of a multiplex real-time PCR assay for the rapid diagnosis of neonatal late onset sepsis. Journal of Microbiological Methods, 106C:8-15 [Full Text]
      • 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 of the United States of America, 111(27):9804-9 [Full Text]
      • Nagirnaja L, Palta P, Kasak L, Rull K, Christiansen OB, Nielsen HS, Steffensen R, Esko T, Remm M, Laan M. (2014). Structural genomic variation as risk factor for idiopathic recurrent miscarriage. Human Mutation, 35(8):972-82 [Full Text]
      • Fromer M, Pocklington AJ, Kavanagh DH, Williams HJ, Dwyer S, Gormley P, Georgieva L, Rees E, Palta P, Ruderfer DM, Carrera N, Humphreys I, Johnson JS, Roussos P, Barker DD, Banks E, Milanova V, Grant SG, Hannon E, Rose SA, Chambert K, Mahajan M, Scolnick EM, Moran JL, Kirov G, Palotie A, McCarroll SA, Holmans P, Sklar P, Owen MJ, Purcell SM, O’Donovan MC. (2014). De novo mutations in schizophrenia implicate synaptic networks. Nature, 506(7487):179-84 [Full Text]

2013

      • Vedler E, Heinaru E, Jutkina J, Viggor S, Koressaar T, Remm M, Heinaru A. (2013). Limnobacter spp. as newly detected phenol-degraders among Baltic Sea surface water bacteria characterised by comparative analysis of catabolic genes. Systematic and Applied Microbiology, 36(8):525-32 [Full Text]
      • Nikopensius T, Annilo T, Jagomägi T, Gilissen C, Kals M, Krjutskov 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 [Full Text]
      • 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  [Full Text]
      • Keis M, Remm J, Ho SYW, Davison J, Tammeleht E, Tumanov IL, Saveljev AP, Männil P, Kojola I, Abramov AV, Margus T, Saarma U. (2013). Complete mitochondrial genomes and a novel spatial genetic method reveal cryptic phylogeographic structure and migration patterns among brown bears in north-western Eurasia. Journal of Biogeography, 40(5):915–927 [Full Text]
      • b14930Remm M, Krjutškov K, Metspalu A. (2013). Primer Design for Large-Scale Multiplex PCR and Arrayed Primer Extension. In Nolan, T., Bustin, Stephen A. (eds.) PCR Technology: Current Innovations, 3rd Edition. pp. 199-208. CRC Press [Full Text]

2012

      • Scheler O, Kindt JT, Qavi AJ, Kaplinski L, Glynn B, Barry T, Kurg A, Bailey RC. (2012). Label-free, multiplexed detection of bacterial tmRNA using silicon photonic microring resonators.Biosensors and Bioelectronics, 36 (1): 56-61
        [Full Text]
      • Clark C, Palta P, Joyce CJ, Scott C, Grundberg E, Deloukas P, Palotie A, Coffey AJ. (2012). A Comparison of the Whole Genome Approach of MeDIP-Seq to the Targeted Approach of the Infinium HumanMethylation450 BeadChip® for Methylome Profiling. PLoS ONE, 7 (11): e50233 [Full Text]
      • Lommer M, Specht M, Roy A-S, Kraemer L, Andreson R, Gutowska MA,Wolf J, Bergner SV, Schilhabel MB, Klostermeier UC, Beiko RG, Rosenstiel P, Hippler M, LaRoche J. (2012). Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation. Genome Biology, 13(7): R66 [Full Text]
      • 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. doi:10.1371/journal.pone.0051528 [Full Text]
      • Untergrasser A, Cutcutache I, Kõressaar T, Ye J, Faircloth BC, Remm M, Rozen SG. (2012). Primer3—new capabilities and interfaces. Nucleic Acids Research, 40(15): e115 [Full Text]
      • Koua D, Brauer A, Laht S, Kaplinski L, Favreau P, Remm M, Lisacek F, Stöcklin R. (2012). ConoDictor: a tool for prediction of conopeptide superfamilies. Nucleic Acids Research, 40/W1: W238-W241 [Full Text]
      • Henn T, Möls T. (2012). Littoral macroinvertebrates in Estonian lowland lakes: the effects of habitat, season, eutrophication and land use on some metrics of biological quality. Fundamental and  Applied Limnology,180(2): 145-156 [Abstract]
      • Kõressaar T, Remm M. (2012). Characterization of Species-Specific Repeats in 613 Prokaryotic Species. DNA Research, 19(3):219-230 [Full Text]

      • 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, 1824/3: 488–492 [Full Text]
      • Saare M, Sõritsa D, Vaidla K, Palta P, Remm M, Laan M, Karrol H, Sõritsa A, Salumets A, D’Hooghe T, Peters M. (2012). No evidence of somatic DNA copy number alterations in eutopic and ectopic endometrial tissue in endometriosis. Human Reproduction, 27(6): 1857-64 [Full Text]
      • 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(1): 34-46 [Full Text]
      • 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 [Full Text]

2011

      • Coffey AJ , Kokocinski F, Calafato MS, Scott CE, Palta P, Drury E, Joyce CJ, LeProust EM, Harrow J, Hunt S, Lehesjoki A-E, Turner TJ, Hubbard TJ, Palotie A. (2011). The GENCODE exome: sequencing the complete human exome. European Journal of Human Genetics, 19(7): 827–831 [Full Text]
      • Margus T, Remm M, TensonT. (2011). A Computational Study of Elongation Factor G (EFG) Duplicated Genes: Diverged Nature Underlying the Innovation on the Same Structural Template. PLoS ONE, 6(8): e22789 [Full Text]

      • Timm H, Käiro K, Möls T, Virro T. (2011). An index to assess hydromorphological quality of Estonian surface waters based on macroinvertebrate taxonomic composition. Limnologica – Ecology and Management of Inland Waters, 41(4): 398-410 [Full Text]
      • Männik K, Parkel S, Palta P, Žilina O, Puusepp H, Esko T, Mägi R, Nõukas M, Veidenberg A, Nelis M, Metspalu A, Remm M, Õunap 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 [Full Text]
      • Coffey AJ, Kokocinski F, Calafato MS, Scott CE, Palta P, Drury E, Joyce CJ, LeProust EM, Harrow J, Hunt S, Lehesjoki AE, Turner DJ, Hubbard TJ, Aarno Palotie A. (2011). The GENCODE exome: sequencing the complete human exome. European Journal of Human Genetics, 19(7): 827-831 [Full text]
      • 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,11/17 [Full text]
      • Knapp DC, 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 [Full Text]
      • Chaubey G, Metspalu M, Choi Y, Mägi R, Irene Gallego Romero I, Soares P, van Oven M , Behar DM, Rootsi S, Hudjashov G, Mallick CB, Karmin M, Nelis M, Parik J, Goverdhana Reddy A, Metspalu E, van Driem G, Yali Xue Y, Tyler-Smith C, Thangaraj K, Singh L, Remm M, Richards MB, Lahr MM, Kayser M, Villems R, Kivisild T. (2011). Population Genetic Structure in Indian Austroasiatic speakers: The Role of Landscape Barriers and Sex-specific Admixture. Molecular Biology and Evolution, 28(2): 1013-1024 [Full Text] [Abstract]

      • Siibak T, Peil L, Dönhöfer A, Tats A, Remm M, Wilson DN, Tenson T, Remme J. (2011). Antibiotic-induced ribosomal assembly defects result from changes in the synthesis of ribosomal proteins. Molecular Microbiology , 80(1): 54-67 [Abstract]

2010

        • Oitmaa E, Peters M, Vaidla K, Andreson R, Mägi R, Slavin G, Velthut A, Tõnisson N, Reimand T, Remm M, Schneider M, Ounap K, Salumets A, Metspalu A. (2010). Molecular diagnosis of Down syndrome using quantitative APEX-2 microarrays. Prenatal Diagnosis, 30(12-13):1170-77 [Abstract]
        • Kasari V, Kurg K, Margus T, Tenson T, Kaldalu N. (2010). The Escherichia coli mqsR and ygiT genes encode a new toxin-antitoxin pair. Journal of Bacteriology,192(11): 2908-19 [Abstract]
        • Teek R, Kruustük K, Zordania R, Joost K, Reimand T, Möls T, Oitmaa E, Kahre T, Tõnisson N, Ounap K. (2010). Prevalence of c.35delG and p.M34T mutations in the GJB2 gene in Estonia. International Journal of Pediatric Otorhinolaryngology, 74(9): 1007-12 [Abstract]
        • 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 [Full Text]
        • Viltrop T, Krjutškov K, Palta P, Metspalu A. (2010). Comparison of DNA extraction methods for multiplex polymerase chain reaction. Analytical Biochemistry, 398(2): 260–262 [Full Text]

      • Walters RG, Jacquemont S, Valsesia A, de Smith AJ, Martinet D, Andersson J, Falchi M, Chen F, Andrieux J, Lobbens S, Delobel B, Stutzmann F, El-Sayed Moustafa JS, Che`vre J-C, Lecoeur C, Vatin V, Bouquillon S, Buxton JL, Boute O, Holder-Espinasse M, Cuisset J-M, Lemaitre M-P, Ambresin A-E, Brioschi A, Gaillard M, Giusti V, Fellmann F, Ferrarini A, Hadjikhani N, Campion D, Uilmatre A, Goldenberg A, Calmels N, Mande J-L, Le Caignec C, David A, Isidor B, Cordier M-P, Dupuis-Girod S, Labalme A, Sanlaville D, Be´ri-Dexheimer M, Jonveaux P,Leheup B, Õunap K, Bochukova EG, Henning E, Keogh J, Ellis R J, MacDermot KD, van Haelst MM, Vincent-Delorme C, Plessis G, Touraine R, Philippe A, Malan V, Mathieu-Dramard M, Chiesa J, Blaumeiser B, Kooy RF, Caiazzo R, Pigeyre M, Balkau B, Sladek R, Bergmann S, Mooser V, Waterworth D, Reymond A, Vollenweider P, Waeber G, Kurg A, Palta P, Esko T, Metspalu A, Nelis M, Elliott P,Hartikainen A-L, McCarthy MI, Peltonen L, Carlsson L, Jacobson P,Sjöström L, Huang N, Hurles ME, O’Rahilly S, Farooqi IS, Männik K,Jarvelin M-R, Pattou F, Meyre D, Walley AJ, Coin LJM, Blakemore AIF, Froguel P, Beckmann JS. (2010). A new highly penetrant form of obesity due to deletions on chromosome 16p11.2. Nature, 463(4):671-675 [Full Text]

2009

      • Eva-Liis Loogväli E-L, Kivisild T , Margus T, Villems R. (2009). Explaining the Imperfection of the Molecular Clock of Hominid Mitochondria. PLoS ONE, 4(12): e8260 [Full Text]
      • Org T, Rebane A, Kisand K, Laan M, Haljasorg U, Andreson R, Peterson P. (2009). AIRE activated tissue specific genes have histone modifications associated with inactive chromatin. Hum Mol Genet, 18(24): 4699-710 [Abstract]
      • Krjutškov K, Viltrop T, Palta P, Metspalu E, Tamm E, Suvi S, Sak K, Merilo A, Sork H, Teek R, Nikopensius T, Kivisild T, Metspalu A. (2009). Evaluation of the 124-plex SNP typing microarray for forensic testing. Forensic Sci. Int. Genet., 4(1):43-8 [Full Text]
      • 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, 9:45 [Full Text]
      • 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, Polgár N, Toniolo D, Gasparini P, D’Adamo P, Klovins J, Nikitina-Zake L, Kucinskas V, Kasnauskiene J, Lubinski J, Debniak T, Limborska S, Khrunin A, Estivill X, Rabionet R, Marsal S, Julià A, Antonarakis SE, Deutsch S, Borel C, Attar H, Gagnebin M, Macek M, Krawczak M, Remm M, Metspalu A. (2009). Genetic Structure of Europeans: A View from the North–East. PLoS ONE, 4(5): e5472 [Full Text]
      • Kõressaar 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. [Full Text]

2008

      • Rull K, Nagirnaja L, Ulander VM, Kelgo P, Margus T, Kaare M, Aittomäki K, Laan M. (2008). Chorionic Gonadotropin Beta gene variants are associated with recurrent miscarriage in two European populations. The Journal of Clinical Endocrinology and Metabolism, 93(12):4697-4706 [Full Text]
      • Tats A, Tenson T, Remm M. (2008). Preferred and avoided codon pairs in three domains of life. BMC Genomics, 9(1):463. [Abstract]
      • Krjutškov K, Andreson R, Mägi R , Nikopensius T, Khrunin A, Mihailov A, 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. [Full Text]
      • Andreson R, Möls T, Remm M. (2008). Predicting failure rate of PCR in large genomes. Nucleic Acids Research, 36(11):e66. [Full Text]
      • Kousoulidou L, Männik K, Zilina O, Parkel S, Palta P, Remm M, Kurg A and Patsalis PC. (2008). Application of two different microarray-based copy-number detection methodologies – array-CGH and array-MAPH – with identical amplifiable target sequences. Clinical Chemistry and Laboratory Medicine, 46(5):722-724 [Abstract]
      • Nature Protocols vol 3, issue 9Kousoulidou L, Männik K, Sismani C, Žilina O, Parkel S, Puusepp H, Tõnisson N, Palta P, Remm M, Kurg A and Patsalis PC. (2008). Array-MAPH: a methodology for the detection of locus copy-number changes in complex genomes. Nature Protocols, 3(5):849-865 [Abstract]
      • Tamm R, Oselin K, Kallassalu K, Magi R, Anier K, Remm M and Metspalu A. (2008). Thiopurine S-methyltransferase (TPMT) pharmacogenetics: three new mutations and haplotype analysis in the Estonian population. Clinical Chemistry and Laboratory Medicine, 46(7):974-979 [Abstract]

2007

      • Vimberg V, Tats A, Remm M and Tenson T. (2007). Translation initiation region sequence preferences in Escherichia coli. BMC Molecular Biology, 2007, 8:100 [Abstract] [Full Text]
      • 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, Chelly J, Moraine C, Gecz J, Kurg A and Patsalis PC. (2007). Screening of 20 patients with X-linked mental retardation using chromosome X-specific array-MAPHEuropean Journal of Medical Genetics, 50(6):399-410 [Full Text]
      • Kaplinski L and Remm M. (2007). MultiPLX: Automatic Grouping and Evaluation of PCR. In Yuryev, A (ed.) PCR Primer Design (367). Humana Press [Abstract]
      • Andreson R, Kaplinski L and Remm M. (2007) Fast Masking of Repeated Primer Binding Sites in Eukaryotic Genomes. In Yuryev, A. (ed.) PCR Primer Design (367). Humana Press [Abstract]
      • Mägi R, Pfeufer A, Nelis M, Montpetit A, Metspalu A and Remm M. (2007). Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation. BMC Genomics, 8(1):159 [Full Text
      • Kõressaar T, Remm M. (2007). Enhancements and modifications of primer design program Primer3. Bioinformatics, 23(10):1289-91[Full Text]
      • Patsalis PC, Kousoulidou L, Männik K, Sismani C, Zilina O, Parkel S, Puusepp H, Tõnisson T, Palta P, Remm M and Kurg A. (2007). Detection of small genomic imbalances using microarray-based multiplex amplifiable probe hybridization.
        Eur. J Hum Gen., 15(2):162 – 172 [Full Text]
      • Kuningas M, Mägi, R, Westendorp RGJ, Slagboom PE, Remm M and van Heemst D. (2007). Haplotypes in the human Foxo1a and Foxo3a genes; impact on disease and mortality at old age. Eur. J Hum Gen., 15(3):294 – 301 [Abstract]
      • Margus T, Remm M and Tenson T. (2007). Phylogenetic distribution of translational GTPases in bacteria. BMC Genomics, 8:15 [Full Text]

2006

      • Andreson R, Puurand T and Remm M. (2006). SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes. Nucleic Acids Res. 34:W651-5. [Full Text]

      • Andreson R, Reppo E, Kaplinski L and Remm M. (2006). GENOMEMASKER package for designing unique genomic PCR primers. BMC Bioinformatics, 7:172. [Full Text]
      • Montpetit A, Nelis M, Laflamme P, Magi R, Ke X, Remm M, Cardon L, Hudson TJ and Metspalu A. (2006). An Evaluation of the Performance of Tag SNPs Derived from HapMap in a Caucasian Population. PLos Genetics, 2(3):e27. [Full Text]
      • Kaminski S, Brym P, Rusc A, Wojcik E, Ahman A and Mägi R. (2006). Associations between milk performance traits in Holstein cows and 16 candidate SNPs identified by arrayed primer extension (APEX) microarray. Anim Biotechnol. 17(1):1-11. [Abstract]
      • Mägi R, Kaplinski L and Remm M. (2006). The Whole Genome TagSNP Selection and Transferability Among HapMap Populations. Pacific Symposium of Biocomputing, 535-543 [Full Text]
      • Tats A, Remm M and Tenson T. (2006). Highly expressed proteins have an increased frequency of alanine in the second amino acid position. BMC Genomics,7:28. [Full Text]

2005

      • Kaplinski L, Andreson R, Puurand T and Remm M. (2005). MultiPLX: automatic grouping and evaluation of PCR primers. Bioinformatics, 21(8):1701-2.[PDF]
      • Mueller JC, Lõhmussaar E, Mägi R, Remm M, Bettecken T, Lichtner P, Huber S, Illig T, Luedemann J, Schreiber S, Wichmann HE, Pramstaller P, Romeo G, Testa A, Metspalu A and Meitinger T. (2005). Comparative analysis of linkage disequilibrium patterns and tagSNP transferability among European populations and HapMap CEPH trios. Am. J. Hum. Genet., 76(3):387-398. [Full Text]
      • O’Brien K, Remm M and Sonnhammer E. (2005). Inparanoid: The eukaryotic ortholog database. Nucl. Acids Res., 33:D476-D480. [Full Text][PDF]

      • Laan M, Wiebe V, Khusnutdinova E, Remm M and Pääbo S. (2005). X-chromosome as a marker for population history: linkage disequilibrium and haplotype study in Eurasian populations. Eur. J Hum Gen., 13(4):452-62. [Full Text]

2003

      • Remm M, Kurg A and Metspalu A. (2003). PCR and arrayed primer extension (APEX) for genome-wide linkage disequilibrium (LD) and haplotype mapping. PCR Technology: Current Innovations, 2nd Edition, 131-140.

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, Lohmussaar E, Zernant J, Tonisson N, Remm M, Magi R, Puurand T, Vilo J, Kurg A, Rice K, Deloukas P, Mott R, Metspalu A, Bentley DR, Cardon LR and Dunham I. (2002). A first-generation linkage disequilibrium map of human chromosome 22. Nature, 418(6897):544-548. [Abstract]

      • Remm M and 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. [Full Text]

2001

      • Remm M, Storm C and Sonnhammer EL. (2001). Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol., 314(5):1041-1052. [Full Text]

2000

    • Remm M and Sonnhammer EL. (2000). Classification of transmembrane protein families in the Caenorhabditis elegans genome and identification of human orthologs. Genome Res., 10(11):1679-1689. [Full Text]