LOMR.00.058 Bioinformaatika töögrupi seminarid 8 EAP
Neljapäeviti, Riia 23 ruumis 118, kell 14:15

Viimane seminaride plaan: BI seminarid 2021-2022

BI Seminarid (2021/2022)

Nimi

Kuupäev

Pealkiri

BI Seminarid (2020/2021)

Nimi	Kuupäev	Pealkiri
Erki Aun	05.11.2020	[J Club] Interpretable genotype-to-phenotype classifiers with perfromance quarantees (1)
Tarmo Puurand	29.10.2020	[TS] Tööseminar
Andrea Jõesaar	23.10.2020	[J Club] Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes (1)
Reidar Andreson	15.10.2020	[TS] Listeria projekt ja teised
Märt Möls	08.10.2020	[TS] K-meeride teooria
Mihkel Vaher	01.10.2020	[TS] Strainseeker2
Maido Remm	24.09.2020	[J Club] Kraken 2

BI Seminarid (2019/2020)

Nimi	Kuupäev	Pealkiri
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	[TS] 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	[TS] 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 Seminarid (2018/2019)

Nimi	Kuupäev	Pealkiri
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	[TS] Katvust mõjutavate parameetrite hindamine
Siimo Kangruoja	08.05.2019	[TS] 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	[TS] 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	[TS] 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	[TS] 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	[TS] 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	[TS] Amülaasi geenide koopia arvu määramine personaalsete genoomide toor-andmetest
Reidar Andreson	16.01.2019	[TS] 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	[TS] Creating plasmid database
Age Brauer	05.12.2018	[J Club] Antimicrobial Resistance – Genomes, Big Data and Emerging Technologies (1)
Tarmo Puurand	28.11.2018	[TS] Alu & VNTR
Tarmo Puurand	21.11.2018	[J Club] Human Endogenous Retrovirus-K (1,2,3,4)
Mihkel Vaher	14.11.2018	[TS] 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	[TS] 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	[TS] 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	[TS] PhenotypeSeeker
Maido Remm	26.09.2018	[J Club] Fast and sensitive protein alignment using DIAMOND (1)

BI Seminarid (2017/2018)

Nimi	Kuupäev	Pealkiri
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 Seminarid (2016/2017)

Nimi	Kuupäev	Pealkiri
Tarmo Puurand	12.01.2017	Inimese 4-nda kromosoomi q-õla kaugeima geeni koopiaarvu varieeruvus. (1, 2)
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 Seminarid (2015/2016)

Nimi	Kuupäev	Pealkiri
Fanny-Dhelia Pajuste	11.05.2016	Integration of string and de Bruijn graphs for genome assembly (1)
Tarmo Puurand	30.03.2016	Mutsiinid (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-d kui potentsiaalsed biomarkerid 21. kromosoomi trisoomia mitteinvasiivseks detekteerimiseks (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 Seminarid (2014/2015)

Nimi	Kuupäev	Pealkiri
Triinu Kõressaar	29.04.2015	A new antibiotic kills pathogens without detectable resistance (1)
Ulvi Gerst Talas	22.04.2015	Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads (1)
Reidar Andreson	01.04.2015	RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets (1)
Age Brauer	18.03.2015	Antibiootikumide reisistentsusgeenide annotatsioon ja erinevate resistoomide võrdlemine (1)
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 (1)
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 (1)
Heleri Kirsip	19.11.2014	The Amborella Genome and the Evolution of Flowering Plants (1)
Tarmo Puurand	05.11.2014	VNTRseek‐a computational tool to detect tandem repeat variants in high‐throughput sequencing data(1)
Silja Laht	21.10.2014	Comparing genomes(1)
Märt Roosaare	08.10.2014	Kraken: ultrafast metagenomic sequence classification using exact alignments(1)

BI Seminarid (2013/2014)

Nimi	Kuupäev	Pealkiri
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 Puurand	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 Seminarid (2012/2013)

Nimi	Kuupäev	Pealkiri
Maido Remm	17.06.2013	The latent human herpesvirus-6A genome specifically integrates in telomeres of human chromosomes in vivo and in vitro (1)
Aare Abroi	10.06.2013	Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote (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 Seminarid (2011/2012)

Nimi	Kuupäev	Pealkiri
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)
Reedik Mägi	31.10.2011	RARE VARIANT ASSOCIATION ANALYSIS METHODS (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 Seminarid (2010/2011)

Nimi	Kuupäev	Pealkiri
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 (1)

BI Seminarid (2009/2010)

Nimi	Kuupäev	Pealkiri
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 Seminarid (2008/2009)

Nimi	Kuupäev	Pealkiri
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 (1)
Tõnu Margus	17.03.2009	Controlled Chaos:Tight regulation of unstructured proteins (1), (2)
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 Seminarid (2007/2008)

Nimi	Kuupäev	Pealkiri
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 (1)
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 Seminarid (2006/2007)

Nimi	Kuupäev	Pealkiri
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 (1)
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 (1, 2)
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 (1)
Lauris Kaplinski	05.01.2007	SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays (1)
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 processes (1)
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 (1)
Triinu Kõressaar	19.02.2007	Segmentation and intensity estimation of microarray images using a gamma-t mixture model (1)
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 (1)
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 (1)
Siim Sõber	09.04.2007	A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variation (1)
Taavi Võsumaa	16.04.2007	Nanopore sequencing technology: nanopore preparations (1)
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 (1)
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 Seminarid (2005/2006)

Nimi	Kuupäev	Pealkiri
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 genome
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
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 Seminarid (2004/2005)

Nimi	Kuupäev	Pealkiri
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