Maido Remm

Maido Remm

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Maido Remm

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AluMine: alignment-free method for the discovery of polymorphic Alu element insertions.

Mob DNA 2019 18;10:31. Epub 2019 Jul 18.

Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.

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http://dx.doi.org/10.1186/s13100-019-0174-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6639938PMC
July 2019

Multidrug resistant Pseudomonas aeruginosa in Estonian hospitals.

BMC Infect Dis 2018 Oct 11;18(1):513. Epub 2018 Oct 11.

Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, 50411, Tartu, Estonia.

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https://bmcinfectdis.biomedcentral.com/articles/10.1186/s128
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http://dx.doi.org/10.1186/s12879-018-3421-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182868PMC
October 2018

A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria.

PLoS Comput Biol 2018 10 22;14(10):e1006434. Epub 2018 Oct 22.

Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.

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http://dx.doi.org/10.1371/journal.pcbi.1006434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211763PMC
October 2018

Primer3_masker: integrating masking of template sequence with primer design software.

Bioinformatics 2018 06;34(11):1937-1938

Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.

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http://dx.doi.org/10.1093/bioinformatics/bty036DOI Listing
June 2018

PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads.

PeerJ 2018 2;6:e4588. Epub 2018 Apr 2.

Department of Bioinformatics, IMCB, University of Tartu, Tartu, Estonia.

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http://dx.doi.org/10.7717/peerj.4588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5885972PMC
April 2018

Method for the Identification of Taxon-Specific -mers from Chloroplast Genome: A Case Study on Tomato Plant ().

Front Plant Sci 2018 17;9. Epub 2018 Jan 17.

Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.

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http://dx.doi.org/10.3389/fpls.2018.00006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5776150PMC
January 2018

Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi.

Mycorrhiza 2017 Nov 20;27(8):761-773. Epub 2017 Jul 20.

Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai Str, 51005, Tartu, Estonia.

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http://dx.doi.org/10.1007/s00572-017-0791-yDOI Listing
November 2017

FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads.

Sci Rep 2017 05 31;7(1):2537. Epub 2017 May 31.

Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.

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http://dx.doi.org/10.1038/s41598-017-02487-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451431PMC
May 2017

GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists.

Gigascience 2015 3;4:58. Epub 2015 Dec 3.

Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010 Estonia ; Estonian Biocentre, Riia 23B, Tartu, 51010 Estonia.

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http://dx.doi.org/10.1186/s13742-015-0097-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4669650PMC
July 2016

Haplotype phasing and inheritance of copy number variants in nuclear families.

PLoS One 2015 8;10(4):e0122713. Epub 2015 Apr 8.

Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia; Estonian Biocentre, Tartu, Estonia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0122713PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390228PMC
March 2016

Fast masking of repeated primer binding sites in eukaryotic genomes.

Methods Mol Biol 2015 ;1275:1-16

Department of Bioinformatics, University of Tartu, Riia 23, Tartu, 51010, Estonia.

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http://dx.doi.org/10.1007/978-1-4939-2365-6_1DOI Listing
December 2015

MultiPLX: automatic grouping and evaluation of PCR primers.

Methods Mol Biol 2015 ;1275:127-42

Department of Bioinformatics, University of Tartu, Tartu, Estonia.

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http://dx.doi.org/10.1007/978-1-4939-2365-6_9DOI Listing
December 2015

Microbial population dynamics in response to Pectobacterium atrosepticum infection in potato tubers.

Sci Rep 2015 Jun 29;5:11606. Epub 2015 Jun 29.

Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, Tartu 51010, Estonia.

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http://dx.doi.org/10.1038/srep11606DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4484245PMC
June 2015

A recent bottleneck of Y chromosome diversity coincides with a global change in culture.

Authors:
Monika Karmin Lauri Saag Mário Vicente Melissa A Wilson Sayres Mari Järve Ulvi Gerst Talas Siiri Rootsi Anne-Mai Ilumäe Reedik Mägi Mario Mitt Luca Pagani Tarmo Puurand Zuzana Faltyskova Florian Clemente Alexia Cardona Ene Metspalu Hovhannes Sahakyan Bayazit Yunusbayev Georgi Hudjashov Michael DeGiorgio Eva-Liis Loogväli Christina Eichstaedt Mikk Eelmets Gyaneshwer Chaubey Kristiina Tambets Sergei Litvinov Maru Mormina Yali Xue Qasim Ayub Grigor Zoraqi Thorfinn Sand Korneliussen Farida Akhatova Joseph Lachance Sarah Tishkoff Kuvat Momynaliev François-Xavier Ricaut Pradiptajati Kusuma Harilanto Razafindrazaka Denis Pierron Murray P Cox Gazi Nurun Nahar Sultana Rane Willerslev Craig Muller Michael Westaway David Lambert Vedrana Skaro Lejla Kovačevic Shahlo Turdikulova Dilbar Dalimova Rita Khusainova Natalya Trofimova Vita Akhmetova Irina Khidiyatova Daria V Lichman Jainagul Isakova Elvira Pocheshkhova Zhaxylyk Sabitov Nikolay A Barashkov Pagbajabyn Nymadawa Evelin Mihailov Joseph Wee Tien Seng Irina Evseeva Andrea Bamberg Migliano Syafiq Abdullah George Andriadze Dragan Primorac Lubov Atramentova Olga Utevska Levon Yepiskoposyan Damir Marjanovic Alena Kushniarevich Doron M Behar Christian Gilissen Lisenka Vissers Joris A Veltman Elena Balanovska Miroslava Derenko Boris Malyarchuk Andres Metspalu Sardana Fedorova Anders Eriksson Andrea Manica Fernando L Mendez Tatiana M Karafet Krishna R Veeramah Neil Bradman Michael F Hammer Ludmila P Osipova Oleg Balanovsky Elza K Khusnutdinova Knut Johnsen Maido Remm Mark G Thomas Chris Tyler-Smith Peter A Underhill Eske Willerslev Rasmus Nielsen Mait Metspalu Richard Villems Toomas Kivisild

Genome Res 2015 Apr 13;25(4):459-66. Epub 2015 Mar 13.

Estonian Biocentre, Tartu, 51010, Estonia; Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom;

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https://bib.irb.hr/datoteka/715300.2015_Genome_Res._Karmin-A
Web Search
http://genome.cshlp.org/lookup/doi/10.1101/gr.186684.114
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http://dx.doi.org/10.1101/gr.186684.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381518PMC
April 2015

Structural genomic variation as risk factor for idiopathic recurrent miscarriage.

Hum Mutat 2014 Aug 24;35(8):972-82. Epub 2014 Jun 24.

Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.

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http://dx.doi.org/10.1002/humu.22589DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285182PMC
August 2014

Limnobacter spp. as newly detected phenol-degraders among Baltic Sea surface water bacteria characterised by comparative analysis of catabolic genes.

Syst Appl Microbiol 2013 Dec 4;36(8):525-32. Epub 2013 Sep 4.

Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, Tartu 51010, Estonia. Electronic address:

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http://dx.doi.org/10.1016/j.syapm.2013.07.004DOI Listing
December 2013

Position-specific scoring matrix and hidden Markov model complement each other for the prediction of conopeptide superfamilies.

Biochim Biophys Acta 2013 Apr 22;1834(4):717-24. Epub 2013 Jan 22.

Atheris Laboratories, Case Postale 314, CH-1233 Bernex-Geneva, Switzerland.

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http://dx.doi.org/10.1016/j.bbapap.2012.12.015DOI Listing
April 2013

Primer3--new capabilities and interfaces.

Nucleic Acids Res 2012 Aug 22;40(15):e115. Epub 2012 Jun 22.

Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg 69120, Germany.

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http://dx.doi.org/10.1093/nar/gks596DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424584PMC
August 2012

ConoDictor: a tool for prediction of conopeptide superfamilies.

Nucleic Acids Res 2012 Jul 31;40(Web Server issue):W238-41. Epub 2012 May 31.

Atheris Laboratories, Case postale 314, CH-1233 Bernex-Geneva, Switzerland.

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http://dx.doi.org/10.1093/nar/gks337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394318PMC
July 2012

Characterization of species-specific repeats in 613 prokaryotic species.

DNA Res 2012 Jun 24;19(3):219-30. Epub 2012 Feb 24.

Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.

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http://dx.doi.org/10.1093/dnares/dss006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372372PMC
June 2012

Identification and classification of conopeptides using profile Hidden Markov Models.

Biochim Biophys Acta 2012 Mar 30;1824(3):488-92. Epub 2011 Dec 30.

Estonian Biocentre, Tartu, Estonia.

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http://dx.doi.org/10.1016/j.bbapap.2011.12.004DOI Listing
March 2012

High-resolution picture of a venom gland transcriptome: case study with the marine snail Conus consors.

Toxicon 2012 Jan 6;59(1):34-46. Epub 2011 Nov 6.

Laboratoire d'Ingénierie des Anticorps pour la Santé (LIAS), CEA/DSV/iBiTec-s/SPI, CEA Saclay, Bt. 152, 91191 Gif-sur-Yvette Cedex, France.

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http://dx.doi.org/10.1016/j.toxicon.2011.10.001DOI Listing
January 2012

A computational study of elongation factor G (EFG) duplicated genes: diverged nature underlying the innovation on the same structural template.

PLoS One 2011 4;6(8):e22789. Epub 2011 Aug 4.

Department of Bioinformatics, Institute of Molecular and Cell Biology at University of Tartu, Tartu, Estonia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022789PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3150367PMC
December 2011

Antibiotic-induced ribosomal assembly defects result from changes in the synthesis of ribosomal proteins.

Mol Microbiol 2011 Apr 1;80(1):54-67. Epub 2011 Mar 1.

Institutes of Molecular and Cell Biology Technology, University of Tartu, Tartu, Estonia.

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http://dx.doi.org/10.1111/j.1365-2958.2011.07555.xDOI Listing
April 2011

Fluoride-cleavable, fluorescently labelled reversible terminators: synthesis and use in primer extension.

Chemistry 2011 Mar 3;17(10):2903-15. Epub 2011 Feb 3.

Institut für Organische Chemie und Chemische Biologie, J.W. Goethe Universität Frankfurt am Main, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany.

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http://dx.doi.org/10.1002/chem.201001952DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3110862PMC
March 2011

Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes.

BMC Biotechnol 2011 Feb 28;11:17. Epub 2011 Feb 28.

Dept, of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.

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http://dx.doi.org/10.1186/1472-6750-11-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051898PMC
February 2011

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 Symp Ser (Oxf) 2008 (52):345-6

Institut für Organische Chemie und Chemische Biologie, J. W. Goethe Universität Frankfurt am Main, Max-von-Laue Str. 7, D-60438 Frankfurt am Main, Germany.

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http://dx.doi.org/10.1093/nass/nrn174DOI Listing
November 2010

Detection of tmRNA molecules on microarrays at low temperatures using helper oligonucleotides.

BMC Biotechnol 2010 Apr 28;10:34. Epub 2010 Apr 28.

Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu, 51010, Estonia.

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http://dx.doi.org/10.1186/1472-6750-10-34DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873282PMC
April 2010

Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms.

Bioinformatics 2009 Jun 8;25(11):1349-55. Epub 2009 Apr 8.

Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.

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http://dx.doi.org/10.1093/bioinformatics/btp241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682524PMC
June 2009

Fluorescent labeling of NASBA amplified tmRNA molecules for microarray applications.

BMC Biotechnol 2009 May 15;9:45. Epub 2009 May 15.

Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.

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http://dx.doi.org/10.1186/1472-6750-9-45DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2685129PMC
May 2009

Preferred and avoided codon pairs in three domains of life.

BMC Genomics 2008 Oct 8;9:463. Epub 2008 Oct 8.

Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Riia str. 23, Tartu 51010, Estonia.

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http://dx.doi.org/10.1186/1471-2164-9-463DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2585594PMC
October 2008

Array-MAPH: a methodology for the detection of locus copy-number changes in complex genomes.

Nat Protoc 2008 ;3(5):849-65

Department of Cytogenetics, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus.

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http://dx.doi.org/10.1038/nprot.2008.49DOI Listing
August 2008

Predicting failure rate of PCR in large genomes.

Nucleic Acids Res 2008 Jun 20;36(11):e66. Epub 2008 May 20.

Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia.

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http://dx.doi.org/10.1093/nar/gkn290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2441781PMC
June 2008

Fast masking of repeated primer binding sites in eukaryotic genomes.

Methods Mol Biol 2007 ;402:201-18

Department of Bioinformatics at University of Tartu, Estonia.

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http://dx.doi.org/10.1007/978-1-59745-528-2_10DOI Listing
November 2007

MultiPLX: automatic grouping and evaluation of PCR primers.

Methods Mol Biol 2007 ;402:287-304

Department of Bioinformatics at University of Tartu, Estonia.

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http://dx.doi.org/10.1007/978-1-59745-528-2_14DOI Listing
November 2007

Translation initiation region sequence preferences in Escherichia coli.

BMC Mol Biol 2007 Oct 31;8:100. Epub 2007 Oct 31.

Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia.

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http://dx.doi.org/10.1186/1471-2199-8-100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2176067PMC
October 2007

Enhancements and modifications of primer design program Primer3.

Bioinformatics 2007 May 22;23(10):1289-91. Epub 2007 Mar 22.

Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Riia str. 23, Tartu 51010, Estonia.

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http://dx.doi.org/10.1093/bioinformatics/btm091DOI Listing
May 2007

Haplotypes in the human Foxo1a and Foxo3a genes; impact on disease and mortality at old age.

Eur J Hum Genet 2007 Mar 24;15(3):294-301. Epub 2007 Jan 24.

Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands.

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http://dx.doi.org/10.1038/sj.ejhg.5201766DOI Listing
March 2007

Detection of small genomic imbalances using microarray-based multiplex amplifiable probe hybridization.

Eur J Hum Genet 2007 Feb 22;15(2):162-72. Epub 2006 Nov 22.

Department of Cytogenetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.

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http://dx.doi.org/10.1038/sj.ejhg.5201738DOI Listing
February 2007

The whole genome tagSNP selection and transferability among HapMap populations.

Pac Symp Biocomput 2006 :535-43

Department of Bioinformatics, University of Tartu, Riia str. 23 Tartu, 51010, Estonia.

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January 2007

Phylogenetic distribution of translational GTPases in bacteria.

BMC Genomics 2007 Jan 10;8:15. Epub 2007 Jan 10.

Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.

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http://dx.doi.org/10.1186/1471-2164-8-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1780047PMC
January 2007

SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W651-5

Department of Bioinformatics, University of Tartu, Estonia.

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http://dx.doi.org/10.1093/nar/gkl125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538889PMC
July 2006

GENOMEMASKER package for designing unique genomic PCR primers.

BMC Bioinformatics 2006 Mar 27;7:172. Epub 2006 Mar 27.

Department of Bioinformatics, University of Tartu, Tartu, Estonia.

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http://dx.doi.org/10.1186/1471-2105-7-172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1450303PMC
March 2006

Highly expressed proteins have an increased frequency of alanine in the second amino acid position.

BMC Genomics 2006 Feb 16;7:28. Epub 2006 Feb 16.

Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, Estonia.

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http://dx.doi.org/10.1186/1471-2164-7-28DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1397820PMC
February 2006

MultiPLX: automatic grouping and evaluation of PCR primers.

Bioinformatics 2005 Apr 14;21(8):1701-2. Epub 2004 Dec 14.

Department of Bioinformatics, University of Tartu, Tartu, Estonia.

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http://dx.doi.org/10.1093/bioinformatics/bti219DOI Listing
April 2005

X-chromosome as a marker for population history: linkage disequilibrium and haplotype study in Eurasian populations.

Eur J Hum Genet 2005 Apr;13(4):452-62

Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Estonia.

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http://dx.doi.org/10.1038/sj.ejhg.5201340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1450114PMC
April 2005

Inparanoid: a comprehensive database of eukaryotic orthologs.

Nucleic Acids Res 2005 Jan;33(Database issue):D476-80

Center for Genomics and Bioinformatics, Karolinska Institutet, S-171 77 Stockholm, Sweden.

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http://dx.doi.org/10.1093/nar/gki107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540061PMC
January 2005

High-density genotyping and linkage disequilibrium in the human genome using chromosome 22 as a model.

Curr Opin Chem Biol 2002 Feb;6(1):24-30

Estonian Biocentre, University of Tartu, Riia str. 23, Tartu 51010, Estonia.

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http://dx.doi.org/10.1016/s1367-5931(01)00285-xDOI Listing
February 2002