LOMR.00.058 Seminars in bioinformatics 8 EAP
On Thursday at 14:15 in room 118 (Riia str 23).

Current plan: BI seminars 2019-2020

BI Seminars (2019/2020)

Name Date Title
Age Brauer 24.10.2019 [J Club] Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes (1)
Fanny-Dhelia Pajuste 17.10.2019 [WS] Koopiaarvu määramine k-meeride abil
Aare Abroi 10.10.2019 [J Club] Optimizing de novo genome assembly from PCR-amplified metagenomes (1)
Mihkel Vaher 03.10.2019 [WS] StrainSeeker 2
Triinu Kõressaar 26.09.2019 [J Club] Engineered toxin–intein antimicrobials can selectively target and kill antibiotic-resistentbacteria in mixed populations (1)
Maido Remm 19.09.2019 [J Club] [BC]2 Basel Computational Biology Conference (1,2)

BI Seminars (2018/2019)

Name Date Title
Kairi Raime 12.06.2019 [J Club] Environmental DNA signatures in honey (1)
Erki Aun 05.06.2019 [J Club] Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data (1)
Carmen Oroperv 23.05.2019 [WS] Katvust mõjutavate parameetrite hindamine
Siimo Kangruoja 08.05.2019 [WS] GM taimede detekteerimine k-meeride abil
Lauris Kaplinski 24.04.2019 [J Club] What Every Computer Scientist Should Know About Floating-Point Arithmetic (1)
Carmen Oroperv 17.04.2019 [WS] Katvust mõjutavate parameetrite hindamine
Fanny-Dhelia Pajuste 10.04.2019 [J Club] AMYCNE: Confident copy number assessment using whole genome sequencing data (1)
Mikk Puustusmaa 05.04.2019 [WS] Phylocube, teaching and PhD thesis
Carmen Oroperv 13.03.2019 [J Club] Uus CNVde tuvastamise meetod, selle kasutamine CNVde tuvastamiseks epilepsia patsientide andmestikus ja madala katvusega regioonides (1,2)
Aneth Lvovs 06.03.2019 [WS] Horisontaalse geeniülekande tuvastamismeetodite võrdlemine endogeensete bornaviiruslike elementide näitel
Aneth Lvovs 27.02.2019 [J Club] Systematic estimation of insertion dates of endogenous bornavirus-like elements in vesper bats (1)
Age Brauer 20.02.2019 [WS] Antibiotic resistance genes, genomic mutations altering sensitivity to muropeptides, and teaching
Aare Abroi 13.02.2019 [J Club] A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences (1)
Triinu Kõressaar 06.02.2019 [J Club] Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis (1)
Fanny-Dhelia Pajuste 30.01.2019 [WS] Detecting Amylase Gene Copy Numbers from WGS Reads
Reidar Andreson 16.01.2019 [WS] Conco, Araucaria Sequencing and BCF
Märt Möls 09.01.2019 [J Club] The ASA’s Statement on p-Values: Context, Process, and Purpose (1,2)
Triinu Kõressaar 12.12.2018 [WS] Creating plasmid database
Age Brauer 05.12.2018 [J Club] Antimicrobial Resistance – Genomes, Big Data and Emerging Technologies (1)
Tarmo Puurand 28.11.2018 [WS] Alu & VNTR
Tarmo Puurand 21.11.2018 [J Club] Human Endogenous Retrovirus-K (1,2,3,4)
Mihkel Vaher 14.11.2018 [WS] StrainSeeker 2
Reidar Andreson 07.11.2018 [J Club] Targeted Sequencing of Venom Genes from Cone Snail Genomes Improves Understanding of Conotoxin Molecular Evolution (1)
Lauris Kaplinski 31.10.2018 [WS] GenomeTester4 latest developments
Mihkel Vaher 24.10.2018 [J Club] A novel fast vector method for genetic sequence comparison (1)
Kairi Raime 17.10.2018 [WS] K-meeridel põhineva meetodi arendus taimede tuvastamiseks sekveneerimise toorlugemitest
Heleri Kirsip 10.10.2018 [J Club] A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection (1)
Erki Aun 03.10.2018 [WS] PhenotypeSeeker
Maido Remm 26.09.2018 [J Club] Fast and sensitive protein alignment using DIAMOND (1)

BI Seminars (2017/2018)

Name Date Title
Triinu Kõressaar 30.05.2018 Tööseminar
Sylvia Krupp 23.05.2018 Tööseminar
Marlen Timm 16.05.2018 Tööseminar
Carmen Oroperv 09.05.2018 Tööseminar
Brigitta-Robin Raudne 02.05.2018 Tööseminar
Kristina Kasvandik 25.04.2018 Tööseminar
Janika Slepnjov 18.04.2018 Tööseminar
Aneth Lvovs 11.04.2018 Tööseminar
Lauris Kaplinski 28.03.2018 [J Club] The evolutionary anthropology of war (1
Tarmo Puurand 21.03.2018 Tööseminar
Kairi Raime 14.03.2018 [J Club] Quinolizidine Alkaloid Biosynthesis in Lupins and Prospects for Grain Quality Improvement (1,2)
Reidar Andreson 07.03.2018 Õppetöö korraldamine
Heleri Kirsip 28.02.2018 [J Club] Systematic survey of non-retroviral virus-like elements in eukaryotic genomes (1)
Mikk Puustusmaa 21.02.2018 Tööseminar
Erki Aun 14.02.2018 [J Club] AmPEP: Sequence-based prediction of antimicrobial peptides using distribution patterns of amino acid properties and random forest (1)
Märt Möls 07.02.2018 [J Club] The nature of nurture: Effects of parental genotypes (1)
Mihkel Vaher 01.02.2018 The Fragments of VirSeeker
Aneth Lvovs 25.01.2018 [J Club] Variable RNA expression from recently acquired, endogenous viral elements (EVE) of white spot syndrome virus (WSSV) in shrimp (1)
Age Brauer 11.01.2018 [J Club] The microbiomes of blowflies and houseflies as bacterial transmission reservoirs (1)
Märt Roosaare 04.01.2018 PlasmidSeeker
Lauris Kaplinski 13.12.2017 Tööseminar
Aare Abroi 07.12.2017 [J Club] Yrgide nakatised (1,2)
Kairi Raime 30.11.2017 K-meeridel põhineva meetodi väljatöötamine taimede tuvastamiseks sekveneerimise toorandmetest
Triinu Kõressaar 23.11.2017 [J Club] Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle (1)
Heleri Kirsip 16.11.2017 Endogeensete viiruslike elementide uurimine
Tarmo Puurand 09.11.2017 [J Club] Birth of a W sex chromosome by horizontal transfer of Wolbachia bacterial symbiont genome (1)
Fanny-Dhelia Pajuste 02.11.2017 Geenide koopia arvu määramine k-meeride abil (amülaasi geeni näitel) ja muud k-meeridega seotud uuringud
Reidar Andreson 26.10.2017 [J Club] Graphene nanodevices for DNA sequencing (1)
Erki Aun 19.10.2017 ResistomeSeeker: a novel k-mer-based tool for alignment-free identification of phenotype-associated genomic biomarkers
Mikk Puustusmaa 12.10.2017 [J Club] A breakthrough that could change the face of combating multidrug-resistant bacteria – SNAPP (1)
Age Brauer 05.10.2017 Antibiootikumide resistentsusega seotud geenid bakterigenoomides
Mihkel Vaher 28.09.2017 [J Club] VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data (1)
Maido Remm 21.09.2017 Konverentsil BC2 (Basel Computational Biology Conference) kuuldud huvitavamad ettekanded (1)

BI Seminars (2016/2017)

Name Date Title
Heleri Kirsip 10.11.2016 Endogenous bornavirus elements in eukaryotes and the usage of them in antiviral immunity. (1)
Mihkel Vaher 27.10.2016 Eukaryotic association module in phage WO genomes from Wolbachia. (1)
Märt Roosaare 29.09.2016 Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. (1)
Maido Remm 15.09.2016 Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. (1)

BI Seminars (2015/2016)

Name Date Title
Fanny-Dhelia Pajuste 11.05.2016 Integration of string and de Bruijn graphs for genome assembly (1)
Tarmo Puurand 30.03.2016 Mucins (1, 2, 3, 4, 5)
Triinu Kõressaar 16.03.2016 Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes (1)
Kaarel Koitne 20.01.2016 MicroRNA-s as potential biomarkers for noninvasive detection of fetal trisomy 21 (1)
Mihkel Vaher 02.12.2015 Assembly and alignment-free method of phylogeny reconstruction from NGS data (1)
Ulvi Gerst Talas 04.11.2015 Could Secondary DNA Transfer Falsely Place Someone at the Scene of a Crime? (1)
Reidar Andreson 22.10.2015 Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome (1)
Märt Roosaare 08.10.2015 Uudiseid k-meride abil bakterite leidmisest (1, 2)
Maido Remm 24.09.2015 BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs(1)

BI Seminars (2014/2015)

Name Date Title
Triinu Kõressaar 29.04.2015 A new antibiotic kills pathogens without detectable resistance
Ulvi Gerst Talas 22.04.2015 Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads
Reidar Andreson 01.04.2015 RIEMS: a software pipeline for sensitive and comprehensive
taxonomic classification of reads from metagenomics datasets

Age Brauer 18.03.2015 Antibiootikumide reisistentsusgeenide annotatsioon ja erinevate resistoomide võrdlemine
Mikk Puustusmaa 04.03.2015 Digital information preservation in DNA
(1, 2, 3)
Mihkel Vaher 18.02.2015 A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
Kairi Raime 21.01.2015 Biparental inheritance through uniparental transmission: the doubly uniparental inheritance of mitochondrial DNA
(1, 2, 3)
Aare Abroi 07.01.2015 Kuidas keskkonnast tekivad geenid
(1, 2)
Fanny-Dhelia Pajuste 03.12.2014 Omega: an Overlap-graph de novo Assembler for Metagenomics
Heleri Kirsip 19.11.2014 The Amborella Genome and the Evolution of Flowering Plants
Tarmo Puurand 05.11.2014 VNTRseek‐a computational tool to detect tandem
repeat variants in high‐throughput sequencing data
Silja Laht 21.10.2014 Comparing genomes(1)
Märt Roosaare 08.10.2014 Kraken: ultrafast metagenomic sequence classification using exact alignments(1)

BI Seminars (2013/2014)

Name Date Title
Maido Remm 30.05.2014 Pealkiri
Tarmo Puurand 10.06.2014 Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements
Kairi Raime 23.05.2014 Exploiting extension bias in polymerase chain reaction to improve primer specificity in ensembles of nearly identical DNA templates
Reidar Andreson 16.05.2014 Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies
Märt Möls 09.05.2014 Lugemisest tingitud nihe artikli tulemustes
Triinu Kõressaar 25.04.2014 Strain/species identification in metagenomes using genome-specific markers
Lauris Kaplinski 11.04.2014 Trolls just want to have fun
Ulvi Gerst Talas 28.03.2014 Deep sequencing of large library selec3ons allows computational discovery of diverse sets of zinc fingers that bind common targets
Fanny-Dhelia Pajuste 21.03.2014 Exploring high dimensional data with Butterfly: a novel classification algorithm based on discrete dynamical systems
Silja Laht 18.03.2014 Publication bias
Mikk Puustusmaa 14.03.2014 Landscape and variation of RNA secondary structure across the human transcriptome
Maarja Lepamets 28.02.2014 Determination of sRNA Expressions by RNA-seq in Yersinia pestis Grown In Vitro and during Infection
Mikk Eelmets 21.02.2014 Causes and Effects of N-Terminal Codon Bias in Bacterial Genes
Reidar Andreson 14.02.2014 RNA-seq studies – which is more important: increase sequencing depth or the number of biological replicas?
Märt Roosaare 7.02.2014 High-molecular-mass hyaluronan mediates the cancer resistance of the naked mole rat
Aare Abroi 31.01.2014 Vana asja uurimisest kaasaegsete meetoditega
Kairi Raime  17.01.2014 Single-nucleotide polymorphisms and other mismatches reduce performance of quantitative PCR assays (1)
 Ulvi Gerst-Talasi  10.01.2014 Specificity control for read alignments using an artificial reference genome-guided false discovery rate (1)
 Reedik Mägi  13.12.2013 Common and low-frequency variants associated with genome-wide recombination rate (1)
 Triinu Kõressaari  06.12.2013 Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis (1)
 Lauri Saag  29.11.2013  Sekveneerimisplatformide tulemuste erinevus ja ühilduvus (1, 2)
 Lauris Kaplinski  22.11.2013 Topoisomerase II minimizes DNA entanglements by proofreading DNA topology after DNA strand passage (1)
 Tarmo Puurands  8.11.2013 Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans (1, 2, 3)
 Tõnu Margus  8.11.2013 Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans (1, 2, 3)
 Silja Laht  4.11.2013 Quality of computationally inferred gene ontology annotations (1)
 Mikk Puustusmaa 25.10.2013 DNA sequencing using electrical conductance measurements of a DNA polymerase (1)
 Aare Abroi 11.10.2013  Kuidas teise põlvkonna sekveneerimisega saadakse “huvitavaid” tulemusi ja kuidas nendest tulemustest mõnikord lahti saab (1)
Maido Remm 4.10.2013  Absolute quantification by droplet digital PCR versus analog real-time PCR (1)

BI Seminars (2012/2013)

Name Date Title
Maido Remm 17.06.2013 (1)
Aare Abroi 10.06.2013 (1)
Tõnu Margus 27.05.2013 The African coelacanth genome provides insights into tetrapod evolution (1)
Märt Möls 20.05.2013 Deconvolution Estimation in Measurement Error Models: The R Package decon (1)
Maarja Lepamets 06.05.2013 REvolver: Modeling Sequence Evolution under Domain Constraints (1)
Lauris Kaplinski 29.04.2013 The social and scientific temporal correlates of genotypic intelligence and the Flynn effect (1)
Reidar Anderson 22.04.2013 AGORA: Assembly Guided by Optical Restriction Alignment (1)
Silja Laht 15.04.2013 Varajase toitumise mõju hilisemale tervisele (1), (2)
Reedik Mägi 8.04.2013 Finding the sources of missing heritability in a yeast cross (1)
Tarmo Puurand 1.04.2013 Viinamarja värvi määravad geenid (1, 2)
Mikk Eelmets 25.03.2013 The genomic signature of dog domestication reveals adaptation to a starch-rich diet (1)
Triinu Kõressaar 18.03.2013 Two methods for full-length RNA sequencing for low quantities of cells and single cells (1)
Aleksander Sudakov 11.03.2013 A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor (1)
Kairi Raime 04.02.2013 Identifying personal genomes by surname inference (1)
Ulvi Gerst-Talas 28.02.2013 From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software (1)
Märt Roosaare 21.01.2013 HMM-FRAME: accurate protein domain classification for metagenomic sequences containing frameshift errors (1)
Mikk Puustusmaa 14.01.2013 Proto-genes and de novo gene birth (1)
Viktorija Kukuškina 07.01.2013 Homosexuality as a Consequence of Epigenetically Canalized Sexual Development (1)
Tõnu Möls 10.12.2012 Search for causality in ecological studies
Märt Möls 3.12.2012 A Linear Non-Gaussian Acyclic Model for Causal Discovery - LINGAM algoritm (1)
Tõnu Margus 24.11.2012 Finished bacterial genomes from shotgun sequence data (1)
Tarmo Puurand 19.11.2012 An integrated map of genetic variation from 1092 human genomes (1)
Silja Laht 12.11.2012 The oyster genome reveals stress adaptation and complexity of shell formation (1)
Reidar Andreson 5.11.2012 Long non-coding RNAs in  C. elegans
Reedik Mägi 29.10.2012 FTO genotype is associated with phenotypic variability of body mass index ()
Mikk Eelmets 22.10.2012 Rate of de novo mutations and the importance of father’s age to disease riskv (1)
Triinu Kõressaar 15.10.2012 SOAPindel: Efficient identification of indels from short paired reads (1)
Lauris Kaplinski 8.10.2012 The genetic roots of inter-population IQ differences (1, 2)
Aleksander Sudakov  1.10.2012 Paleovirology and virally derived immunity(1)
Maido Remm  24.09.2012 Genome sequencing reveals insights into physiology and longevity of the naked mole rat (1)

BI Seminars (2011/2012)

Name Date Title
Maido Remm 28.05.2012 Assessing Individual Differences in Genome-Wide Gene Expression in Human Whole Blood: Reliability Over Four Hours and Stability Over 10 Months (1)
Tõnu Möls 21.05.2012 Statistical puzzles in ecological studies
Märt Möls 14.05.2012 Identifying Key Statistical Papers From 1985 to 2002 Using Citation Data for Applied Biostatisticians (1)
Tõnu Margus 07.05.2012 A Role for Neuronal piRNAs in the Epigenetic Control of Memory-Related Synaptic Plasticity (1)
Mikk Eelmets 23.04.2012 A systematic survey of loss-of-function variants in human protein-coding genes (1)
Lauris Kaplinski 16.04.2012 The mechanics behind DNA sequence-dependent properties of the nucleosome (1)
Ulvi Gerst-Talas 09.04.2012 Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA (1)
Reedik Mägi 02.04.2012 Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis (1)
Silja Laht 26.03.2012 Phylo ja Kodanukiteadus (1)
Aare Abroi 19.03.2012 Kuidas eristada konvergentset ja divergentset evolutsiooni? Küsimused ja taustinformatsioon ettekandjalt, vastused kuulajatelt ja kaasamõtlejatelt (1, 2)
Triinu Kõressar 12.03.2012 Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor (1)
Aleksander Sudakov 5.03.2012 Sequences from Ancestral Single-Stranded DNA Viruses in Vertebrate Genomes (1)
Age Tats 27.02.2012 Korduselemendid inimese genoomis (1)
Radko Avi 20.02.2012 Human Microbiome
Reidar Anderson 13.02.2012 A Critical evaluation of genome assemblies and assembly algorithms (1)
Tarmo Puurand 06.02.2012 Detection of mtDNA heteroplasmy from second generetion sequencing data (1, 2, 3)
Aleksander Sudakov 12.12.2011 SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data (1)
Tarmo Puurand 05.12.2011 Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes (1)
Tõnu Möls 28.11.2011  Arutelu kolme artikli statistiliste meetodite üle
Märt Möls 21.11.2011 On the Adjustment for Covariates in Genetic Association Analysis: A Novel, Simple Principle to Infer Direct Causal Effects (1)
Lauris Kaplinski 14.11.2011  A draft genome of Yersinia pestis from victims of the Black Death (1)
Tõnu Margus 07.11.2011 Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures (Nature  PROTOCOL)  2011 (1)
Triinu Kõressaar 24.10.2011 A matter of life or death: How microsatellites emerge in and vanish from the human genome (1)
Ulvi Gerst-Talas 17.10.2011 Widespread RNA and DNA Sequence Differences in the Human Transcriptome (1)
Mikk Eelmets 10.10.2011 CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing (1)
Age Brauer 03.10.2011 Antibiotic resistance is ancient (1)
Reidar Andreson 26.09.2011 Assemblathon 1: A competitive assessment of de novo short read assembly methods (1)
Maido Remm 19.09.2011 Mapping copy number variation by population-scale genome sequencing (1)

BI Seminars (2010/2011)

Name Date Title
Andres Veidenberg 07.02.2011 Nascent transcript sequencing visualizes transcription at nucleotide resolution (1)
Age Tats 31.01.2011 Quake: quality-aware detection and correction of sequencing errors (1)
Silja Laht 24.01.2011 Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-seq reads (1)
Aleksander Sudakov 17.01.2011 Differential effects of chromatin regulators and transcription factors on gene regulation: a nucleosomal perspective (1)
Priit Palta 10.01.2011 De novo rates and selection of large copy number variatio (1)
Tõnu Möls 13.12.2010 Kullback-Leibleri Divergentsi kasutamine makrozoobentosel põhineva
ökoloogilise indeksi tegemiseks
Märt Möls 06.12.2010 Populatsiooni struktuuri arvessevõtmisest ülegenoomsetes uuringutes
Tõnu Margus 29.11.2010 Structural and Biochemical Characterization of the Human Cyclophilin Family of Peptidyl‐Prolyl Isomerases
Tarmo Puurand 22.11.2010 Project of 1000 genomes
Triinu Kõressaar 15.11.2010 Mobile Interspersed Repeats Are Major Structural Variants in the Human Genome
Lauris Kaplinski 08.11.2010 RAPID Detection of Gene–Gene Interactions in Genome-Wide Association Studies
Ulvi Gerst-Talas 25.10.2010 A window into third-generation sequencing ( 1)
Mikk Eelmets 18.10.2010 Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing
Maido Remm 11.10.2010 Personal Genome Sequencing with Complete Genomics Technology

BI Seminars (2009/2010)

Name Date Title
Maido Remm 29.09.2009 Signals of recent positive selection in a worldwide sample of human populations (1, 2, 3, 4)
Andres Veidenberg 20.10.2009 Personalized copy number and segmental duplication map using next-generation sequencing
Mikk Eelmets 27.10.2009
Lauris Kaplinski 03.11.2009
Tõnu Margus 17.11.2009 Arvutibioloogid uurivad saba; kuidas embrüonaalse arengu käigus muutub mRNA poly(A) pikkus
Silja Laht 24.11.2009 Anitkeha signatuurid eesnäärme vähi korral (1)
Tarmo Puurand 01.12.2009 Genetic variation and recent positive selection in worldwide human populations(1)
Triinu Kõressaar 12.01.2010 Multiplex primer prediction software for divergent targets ( 1)
Tõnu Möls 02.02.2010 Mutations 35delG and M34T of GJB2 gene among children with early onset hearing loss in Estonia
Märt Möls 09.02.2010 On Multiple-Testing Correction in Genome-Wide Association Studies
Aleksander Sudakov 16.02.2010 Statistically motivated multiple sequence alignment (1)
Age Tats 02.03.2010 Recent de novo origin of human protein-coding genes (1)
Andres Veidenberg 09.03.2010 Exome sequencing identifies the cause of a mendelian disorder (1)
Maido Remm 16.03.2010 A core gut microbiome in obese and lean twins (1)
Berit Peeters 23.03.2010 Variability in gene expression underlies incomplete penetrance
Lauris Kaplinski 30.03.2010 Protein secondary structure appears to be robust under in silico evolution
Mikk Eelmets 06.04.2010 De novo assembly of human genomes with massively parallel short read sequencing
Märt Heinsoo 13.04.2010
Ksenja 20.04.2010 Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content (1)
Silja Laht 04.05.2010 A Fast Method for Large-Scale De Novo Peptide and Miniprotein Structure Prediction
Tarmo Puurand 11.05.2010 Chromosome instability is common in human cleavage-­stage embryos
Tõnu Margus 18.05.2010 Recent Trends in Ribosomology (Orvieto Conference)
Triinu Kõressaar 25.05.2010 An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation (1)
Tõnu Möls 01.06.2010 Infovõit kui vahend bioloogiliste andmete analüüsimiseks
Märt Möls 08.06.2010 Erinevused kaksikute ja ülegenoomsete uuringute vahel

BI Seminars (2008/2009)

Name Date Title
Reidar Andreson 14.10.2008 SeqMap & Solexa sequencing biases (1, 2)
Triinu, Lauris ja Priit 21.10.2008 HGM 2008
Aleksander Sudakov 28.10.2008 Vector sequence removal from sequencing reads (1)
Mikk Eelmets 04.11.2008 Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs (1)
Tarmo Puurand 25.11.2008 Copy number variation and evolution in humans and chimpanzees (1)
Andres Veidenberg 9.12.2008 Predicting Unobserved Phenotypes for complex Traits from Whole-Genome SNP Data (1)
Age Tats 20.01.2009 Real-Time DNA Sequencing from Single Polymerase Molecules(1)
Lauris Kaplinski 27.01.2009 Phylogenetic distances are encoded in networks of interacting pathways (1)
Maido Remm 03.02.2009 Positiivne selektsioon genoomides ehk mis teeb inimesest inimese (1)
Märt Möls 17.02.2009 Põhjuslikusest (1)
Priit Palta 03.03.2009
Triinu Kõressaar 10.03.2009 The impact of genomic neighbourhood on the evolution of human and chimpanzee transcriptome
Tõnu Margus 17.03.2009 Controlled Chaos:Tight regulation of unstructured proteins
Tõnu Möls 24.03.2009 Introduction to the SAS/Genetics software (Release 9.1.3)
Tarmo Puurand 31.03.2009 A burst of segmental duplications in the genome of the African great ape ancestor
Märt Heinsoo 21.04.2009 Stringent response
Mikk Eelmets 28.04.2009 Systems genetics of complex traits in Drosophila melanogaster
Lauris Kaplinski 05.05.2009 Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences
Triinu Kõressaar 12.05.2009 Title
Tõnu Margus 19.05.2009 Biological systems and system biolgy
Tõnu Möls 26.05.2009 Multivariate Statistical Methods
Märt Möls 02.06.2009 Title
Andres Veidenberg 09.06.2009 Segmental copy number variation shapes tissue transcriptomes

BI Seminars (2007/2008)

Name Date Title
Maarika Traat 09.10.2007 About regulatory motif finding (1)
Hélène Boeuf 16.10.2007 LIF (Leukaemia Inhibitory Factor) for LIFE, in mouse Embryonic Stem (ES) cells (room 217)
Ott Scheler 23.10.2007 SLIC project – tmRNA meets biosensing
Marion Reuter 30.10.2007 Evolution and multilevel optimization of the genetic code (1)
Siim Sõber 06.11.2007 Genome-wide strategies for detecting multiple loci that influence complex diseases (1)
Mari Nelis 13.11.2007 Fine mapping versus replication in whole-genome association studies (1)
Tarmo Puurand 20.11.2007 The medaka draft genome and insights into vertebrate genome evolution (1)
Tanel Tenson 27.11.2007 Structure-based activity prediction for an enzyme of unknown function (1)
Ilja Livenson 04.12.2007 BalticGrid – Baltimaade arvutusvõrk
Katrin Männik 11.12.2007 Relationships between diseases and copy number variations
Kaarel Krjutškov 08.01.2008 Computational epigenetics (1)
Eneli Oitmaa 15.01.2008 Digital PCR for the molecular detection of fetal chromosomal aneuploidy (1)
Tõnu Margus 22.01.2008 Déjà vu—A study of duplicate citations in Medline (1)
Aleksander Sudakov 29.01.2008 Fast model-based protein homology detection without alignment (1)
Maido Remm 12.02.2008 The Diploid Genome Sequence of an Individual Human (1)
Mikk Eelmets 19.02.2008 Analysis of European Genetic Substructure (1, 2)
Age Tats 26.02.2008 How does eukaryotic gene prediction work? (1, 2)
Reidar Andreson 04.03.2008 Conserved elements forming G-quadruplex structures in the first intron of human genes (1)
Triinu Kõressaar 11.03.2008 The genome-wide determinants of human
and chimpanzee microsatellite evolution

Lauris Kaplinski 18.03.2008 Possible quantum computations in human brain – implications and criticism (1, 2, 3)
Reedik Mägi 25.03.2008 Singleton SNPs in the human genome and implications for genome-wide association studies (1)
Hedi Peterson 01.04.2008 Dynamic remodeling of individual nucleosomes across a eucaryotic genome in response to transcriptional perturbation (1)
Priit Adler 08.04.2008 Comparing whole genomes using DNA microarrays (1)
Andres Veidenberg 15.04.2008 Deletion-mutant mtDNA increases in somatic tissues but decreases in female germ cells with age (1)
Priit Palta 29.04.2008 Genotype, haplotype and copy-number variation in worldwide human populations (1)
Tõnu Möls 06.05.2008 Combinatorial partitioning methods for detecting genetic interactions that have phenotypic effect
Märt Möls 13.05.2008 PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data (1)

BI Seminars (2006/2007)

Name Date Title
Reidar Andreson 29.09.2006 The studies about “motorproteins” (1, 2)
Tõnu Margus 09.10.2006 Being positive about selection (1, 2, 3, 4)
Triinu Kõressaar 13.10.2006 Evidence of Influence of Genomic DNA Sequence
on Human X Chromosome Inactivation
Tarmo Puurand 20.10.2006 A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC (1)
Siim Sõber 27.10.2006 A genomic code for nucleosome positioning (1)
Maido Remm 03.11.2006 WindowMasker: window-based masker for
sequenced genomes
Age Tats 10.11.2006 Genome-wide survey for biologically functional pseudogenes (1)
Hedi Peterson 17.11.2006 Mammalian transcription start sites – new knowledge from 2006 (1, 2)
Priit Palta 08.12.2006
Bio-inspired Programmable Self-assembly on DNA Templates

Lauris Kaplinski 05.01.2007 SNiPer-HD: improved genotype calling accuracy by an
expectation-maximization algorithm for high-density SNP arrays
Aleksander Sudakov 12.01.2007 Short blocks from the noncoding parts of the human genome have
instances within nearly all known genes and relate to biological
Mikk Eelmets 19.01.2007 Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays (1)
Tõnu Möls 26.01.2007 Genetic relatedness analysis: classical and new approaches (1)
Taavi Võsumaa 29.01.2007 GENECODIS: A web-based tool for finding significant concurrent annotations in gene lists (1)
Hedi Peterson 12.02.2007 Global
reconstruction of the human metabolic network based on genomic and
bibliomic data
Triinu Kõressaar 19.02.2007 Segmentation and
intensity estimation of microarray images using a gamma-t mixture model
Age Tats 26.02.2007 Prediction of highly expressed genes in microbes based on chromatin accessibility (1)
Priit Adler 05.03.2007 A scalable method for integration and functional analysis of multiple microarray datasets (1)
Tarmo Puurand 12.03.2007 Global variation in copy number in the
human genome
Reedik Mägi 19.03.2007 Scientific indices and research evaluation (1, 2)
Maido Remm 26.03.2007 A highly effective de novo repeat masker for newly sequenced genomes
Tõnu Margus 02.04.2007
Towards fully automated structure-based function prediction in structural genomics
Siim Sõber 09.04.2007 A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2
explains most human eye-color variation
Taavi Võsumaa 16.04.2007
Nanopore sequencing technology: nanopore preparations
Reedik Mägi 23.04.2007 A worldwide survey of haplotype variation and linkage disequilibrium in the human genome (1)
Mikk Eelmets 07.05.2007 A 3D pattern matching algorithm for DNA sequences (1)
Aleksander Sudakov 14.05.2007
Discovering Motifs in Ranked Lists of DNA Sequences
Lauris Kaplinski 28.05.2007 Decoding Randomly Ordered DNA Arrays (1)
Elin Org 31.05.2007 Genomewide association studies (1)
Priit Adler 04.06.2007 Coexpression Analysis of Human
Genes Across Many Microarray
Data Sets

BI Seminars (2005/2006)

Name Date Title
Tarmo Puurand 19.09.2005 HLA
03.10.2005 Ülevaade konverentsidest
Triinu Kõressaar 10.10.2005 MikroRNA tuvastamine in silico
Siim Sõber 17.10.2005 Prediction of miRNA targets
Reidar Andreson 24.10.2005 A critical examination of predictions for oligo properties
Age Tats 31.10.2005 Evolutionarily conserved elements
Maido Remm 07.11.2005 Initial sequence of the chimpanzee genome and comparison with the human
Tõnu Margus 14.11.2005 Minimaalne genoom
Reedik Mägi 28.11.2005 How many tagging SNPs does it take to cover the whole human genome?
Priit Adler 12.12.2005 Discovering statistically significant pathways in expression profiling studies
Priit Palta 19.12.2005 Microarray normalization
Name Date Title
Taavi Võsumaa 09.01.2006 Emission Characteristics of Fluorescent Labels with Respect toTemperatureChanges and Subsequent Effects onDNA Microchip Studies
Pavlos Pavlidis 16.01.2006
Tõnu Möls 23.01.2006
Lauris Kaplinski 30.01.2006
Tarmo Puurand 13.02.2006 Structural variation in the human genome
Lauris Kaplinski 27.02.2006
Tõnu Margus 06.03.2006
Priit Adler 13.03.2006 Pathway recognition and augmentation by computational analysis of microarray expression data
Pavlos Pavlidis 20.03.2006
Triinu Kõressaar 27.03.2006 OrthologID: automation of genomescale ortholog identification within a parsimony framework
Reedik Mägi 03.04.2006 Intellectual ability and cortical development in children and adolescents
Age Tats 10.04.2006 Inference and analysis of the relative stability of bacterial chromosomes
Taavi Võsumaa 17.04.2006 Phylogenetic fate mapping
Priit Palta 24.04.2006 Widening the spectrum of human genetic variation
Tõnu Möls 08.05.2006
Siim Sõber 15.05.2006
Reidar Andreson 22.05.2006 Highly conserved non-coding sequences in vertebrates
Maido Remm 29.05.2006
Radko Avi 05.06.2006

BI Seminars (2004/2005)

Name Date Title
Priit Palta 15.09.2004 Detection of large-scale variation in the human genome
Leopold Parts 22.09.2004 Computational Prediction of Enzyme Active Sites
Tarmo Puurand 29.09.2004 Complex SNP-related sequence variation in segmental genome duplications
Hedi Peterson 06.10.2004 Inimese mittekodeeriva DNA suuremahuline klasterdamine
Reidar Andreson 13.10.2004 Unikaalsete ja populaarsete oligote selekteerimine
Tõnu Margus 20.10.2004 Kuidas genoomis ära tunda teistest liikidest pärit (valkude)geene
Radko Avi 27.10.2004 Ultraconserved Elements in the Human Genome
Kessy Abarenkov 03.11.2004 Intraspecific gene genealogies: trees grafting into networks
Triinu Kõressaar 10.11.2004 Tandeemsete korduste leidmise programme…
Eero Raudsepp 17.11.2004 Filling gaps in a metabolic network using expression information
Maido Remm 24.11.2004
Advanced sequencing technologies: methods and goals
Age Tats 08.12.2004 Kõrge efektiivsusega siRNA järjestuste leidmine
Lauris Kaplinski 15.12.2004 Rational design of DNA sequences for nanotechnology, microarrays and
molecular computers using Eulerian graphs
Reedik Mägi 12.01.2005 Peakomponentide analüüsil põhinev tagSNP valik
Aleksander Sudakov 09.02.2005 Horisontaalse geeniülekande detekteerimise meetodite ülevaade
Tarmo Puurand 16.02.2005 A comman inversion under selection in Europeans
Matti Kankainen 23.02.2005 Geeni regulatsioonist
Priit Palta 02.03.2005 Genoomsete amplifikatsioonide ja deletsioonide mõju geeniekspressioonile (inimese kõhunäärme kartsinoomi näitel)
Reidar Andreson 09.03.2005 Kordusjärjestuste identifitseerimisest uue meetodiga
Tõnu Margus 16.03.2005 Oligonukleotiidide esinemissagedus genoomides ja mida see võimaldab teada saada
Radko Avi 23.03.2005 Characterization of Evolutionary Rates and Constraints in Three Mammalian Genomes
Triinu Kõressaar 06.04.2005 A Fractional Programming Approach to efficient DNA Melting Temperature Calculation
Maido Remm 20.04.2005 Rapid analysis of the DNA-binding specificities of transcription factors
with DNA microarrays
Age Tats 27.04.2005 Variation in the strength of selected codon usage bias among bacteria
Aleksander Sudakov 04.05.2005 A new computational method for the detection of horizontal gene transfer events
Reedik Mägi 11.05.2005 Populatsioonide võrdlusest
Meelis Olev 18.05.2005 Dual-genome primer design for construction of DNA microarrays
Hedi Peterson 01.06.2005 Begin at the beginning: Predicting genes with 5′ UTRs (geeniennustaja N-SCAN)
Eero Raudsepp 15.06.2005