Weekly seminar in bioinformatics and computational biology
Established in November 2011
Head of the seminar: Dr. Sergey V. Malov Objectives:
Wednesday 10.07.2019 at 3pm. Alexander Tiskin (Department of Computer Science, University of Warwick, United Kingdom) "The surprising algebra of sequence alignment".
Wednesday, 26.06.2019 at 3pm. Dr Michael Stich (Aston University, Birmingham UK) "RNA replicators as computational model for evolution".
Wednesday, June 5th 2019 at 3pm. Elizaveta Shmakova (Nova Southeastern University's Halmos College of Natural Sciences and Oceanography) Annotating and Characterizing the Dominant Microbial Symbionts in the Common Caribbean Sponge Genus Cinachyrella with Metagenomic Data
Wednesday, 5.05.2019 at 3pm. Anna Gorbunova (Theodosius Dobzhansky Center for Genome Bioinformatics): Genome Russia Project and personalized medicine
Wednesday, 17.04.2019 at 3pm. Dasha Zhernakova : Reconstructing human past using ancient and modern genomics).
Wednesday 10.04.2019 at 3pm Valentin Shimansky: Optimisation of in-silico HLA typing methods for "bake-off" and "Russian genome" projects.
Wednesday, 03.04.2019 at 3pm. Anastasia Turenko. "HLA-typing and genome analysis"
Wednesday, 27.03.2019 at 3pm. Gaik Tamazian "Comparative analysis of Felidae genome organization".
Wednesday, March 06 2019 at 3pm. Daisuke Hirata: "Mitochondrial genome analysis of Genome Russia data set".
Wednesday 27 2019 at 5pm.
Nikita Artomov, (Harvard University, Massachusetts General Hospital, Broad Institute) "A platform for case-control matching enables association studies without genotype sharing".
Wednesday, December 26 2018 at 3pm. Igor Evsukov Everything you wanted to know about CRISPR/Cas but were afraid to ask.
Thursday, December 20th 2018 at 3pm. Anton Logachev ( Theodosius Dobzhansky Center for Genome Bioinformatics) "Y-chromosomal Haplogroup analysis in GenomeRussia project".
Wednesday, December 5 2018 at 3pm. Evgenii Bakin and Oksana Statcevich Statistical model for N1-zone formation in a sequence of IGH genes
Wednesday, November 21 2018 at 15-00.Ksenia Krasheninnikova "Idenitifcation of synteny blocks and evolutionary breakpoints regions in genomes of 11 Felidae species and their mammalian outgrips".
Wednesday, November 14 2018 at 15-00.
Dash Zhernakova "Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome"
Wednesday, October 31 2018 at 15-00.
Vladimir Brukhin "Assembly and comparative analysis of some apomictic Boechera species genomes"
Wednesday, October 24 2018 at 15-00. Sergey Hosid ("High Expression of CD146-Regulating MicroRNAs in Late EPCs Confirm Existence of “True” Pre-late EPCs").
Wednesday October 17 2018 at 15-00.
Sergey Malov "On an advanced framework for genes flow and genes flow barriers analysis".
Abstract:We discuss an advanced framework of genes flow analysis and genes flow barriers discovery. Populations for the analysis should be selected carefully to be original and located in its area sufficiently large time. The keynote of the framework is to evaluate whole genome allele frequencies at each point of Earth sphere from allele frequencies of available populations. We extend known framework based on the Nadaraja-Watson method by using Georgiev’s approach, which is more robust for different population sizes. At each point on a geographic grid we select one of four directions (N-S,NE-SW,E-W,SE-NW) of minimal local changes in allele frequencies over whole genome to obtain a direction of genes flow, and select one of eight directions (N,NE,E,SE,S,SW,W,NW) of maximal local changes in allele frequencies to discover genes flow barriers. The advanced framework is applied to combined whole genome dataset of samples located on the territory of Russian Federation.
Wednesday October 24.10.2018 at 15-00. Sergey Hosid ("High Expression of CD146-Regulating MicroRNAs in Late EPCs Confirm Existence of “True” Pre-late EPCs").
Wednesday October 17 2018 at 15-00. Sergey Malov "On an advanced framework for genes flow and genes flow barriers analysis".
Monday 22nd 2018 at 13:00, Klaus Koepfli will give a talk "How Genomics can Inform Management of Ex Situ Populations of Endangered Species." in the Dobzhansky Center
19th of July (Thursday) at 11:00 at the Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University 41 Sredniy Prospekt, Vasilievsky Island (metro Vasileostrovskaya) Prof. Nikolay Alexandrov from Inari (USA) will give a talk "3000 rice genomes" which was done within the International Rice Project involving the International Rice Research Institute in Philippines and also lab of Pavel Pevzner at UCSD.
Tuesday, May 8th at 2pm. Alex Zelikovsky (Atlanta) : “Scalable Reconstruction of Intra-Host Viral Population from NGS Reads”
Wednesday, August 23. at 2:00om. Anna Kukekova (University of Illinois) Genome analyses of tame and aggressive SILver Foxes; The Baleyev experiment revisited
Journal club meeting will be on Thursday, July 13 at 3:00pm. Anna Gorbunova will present the article “A global reference for human genetic variation” Nature 526, 68-74, 2015
Journal club will held on Thursday, June 22, at 3:00pm. Sergey Kliver talk about an article: “An integrated map of structural variation in 2,504 human genomes” Nature 526, 75-81 (2015).
Journal club will held on Friday, Jube 9-th at 2:00pm. Sergey Malov will present article A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe 2013
Journal club meeting will on June 1 at 2:00pm. Igor Evsukov discuss an article Reconstructing genetic history of Siberian and Northeastern European populations. Genome Research CSHL 2016 http://www.genome.org/cgi/doi/10.1101/gr.202945.115
Wednesday, April 19 at 2:00pm. Dasha Zherakova discuss the article Genomic analyses inform on migration events during the peopling of Eurasia. 238 NATURE VOL 538, 13 OcTObER 2016 doi:10.1038/nature19792
Thursday, April 6 at 2:00pm Lab’s journal club Gaik Tamazian Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals. 2015, Nature Communications DOI: 10.1038/ncomms9018 www.nature.com/naturecommunications
Thursday, March 23 at 2:00pm Lab’s journal club, Vladimir Brukhin by article “Swedish Population Substructure Revealed by GenomeWide Single Nucleotide Polymorphism Data”, PLoS One, 2011, 6(2).
Wednesday Dec. 14 2016 at 2:00pm. Alexandros Triantafyllidis (Aristotle University of Thessaloniki, Macedonia, Greece) “Phylogenetic investigations of animals in Greece”.
Monday, October 31 at 1:00 Jose Horacio Grau Museum für Naturkunde Berlin Current genomic projects at the Museum für Naturkunde Berlin Wednesday Sept. 28 2016 at 2:00pm. Chupov Vladimir (Komarov Botanical Institute RAS): New elements of macro evolutionary process in angiosperms
Wednesday Sept. 7 2016 at 2:00pm. Gaik Tamazian Benchmarking R implementations of multiple Pearson’s chi-square test Monday, 29.08.2016 at 2:00pm. Prof. Baskar Rammamurthy (Indian Institute of Technology Madras (IITM)) “Hybridization and parental age affects somatic mutation rates in Arabidopsis”.
Wednesday, 27.07.2016 в 3:00pm Irina Karpova (LLC Roche Diagnostics Rus). Expectation turned into Reality: single molecular sequencing from Roche
Friday, July 7 at 2:00pm Andrey Yurchenko The search for pathogenic mutations in the genomes of patients with autoimmune hepatitis.
Friday, July 1 at 2:00pm Ryuichi MASUDA (Professor, Hokkaido University, Japan) : Phylogeography and population genetics of Blakiston’s fish owls on Hokkaido Island, Japan and Daisuke HIRATA (PhD student, Hokkaido University, Japan): Molecular phylogeography of the brown bear (Ursus arctos) in Hokkaido and Eurasian Continent,revealed by complete mitochondrial DNA sequences
Thursday, June 16 at 2pm we are having a guest seminar by Dr. Sasha Kagansky from the University of Edinburg. Topic: “Metabolo-Epigenetics and Cancer”
April 26 at 4:30pm Lev V. Utkin (Telematics Department, Peter the Great Saint-Petersburg Polytechnic University). A simple and fast GWAS algorithm by means of analysis of pairs of individuals
April 22 at 2:00pm Florence Haseltine (President of Haseltine Systems; Founder – Society for Women’s Health Research (SWHR); Emerita Scientist NIH) Global Virus Network – Planning for the Future
April 20 at 2:00pm Oleg Glotov Molecular-genetic analysis of mutations in children with rare endocrine diseases in North -West Russia by NGS technology
April 13 at 2:00pm Anton Logachev Interconnection of cytoskeletal components and detergent-resistance membranes during hyphal growth in basidiomycete Schizophyllum commune
06.04.2016 at 2pm Alexey Meshkov (Head of the Laboratory of Molicular Genetics in Federal State Institution National Research Center for Preventive Medicine of the Ministry of Healthcare of the Russian Federation) ATHEROGEN-IVANOVO study «The study of the development and progression ofATHEROsclerosis, including taking into account the GENetic and epigenetic factors of cardiovascular risk – a substudy of the ESSE-RF» – design, main results so far and plans.
30.03.2016 at 2pm Vladimir Brukhin Sequencing, Assembly, and Annotation of the Highly Heterozygous Genome of the Apomictic Plant Boechera divaricarpa
16.03.2016 at 2pm Tatiana V. Tatarinova “Bioinformatic analysis of the DNA of indigenous peoples of Siberia by the example of the study of Kets’ genomes.”
09.12.2015 at 2pm Sergey Malov: On non precisely observed right censored survival data analysis
02.12.2015 at 2:00 Alexey Antonik On programming of high-performance statistical computational algorithms
18.11.2015 at 2:00pm Anastasia Shubina (“Science for life extension” foundation”): “Meta-analysis of the impact of food on health and longevity”
11.11.2015 at 2:00pm Alexander Predeus (Bioinformatics Institute, St.-Petersburg): GeneQuery: A phenotype search tool based on gene co-expression clustering
28.10.2015 at 2:00pm Ksenia Krasheninnikova Whole genome alignment in comparative analysis of mammalian genomes
21.10.2015 at 14-00 Zhicheng Carl Lin (Fulbright Scholar, Associate Neurobiologist McLean Hospital, Assistant Professor Harvard Medical School): “A stressor sensitive genetic pathway in alcohol abuse”.
16.10.2015 at 3:00pm Yosuki Tanigawa Development of mtDNA assembler and its application of caracal cat
14.10.15 at 2:00pm Sidorov Svyatoslav: A comparison of several scaffolders on vertebrate whole genome assemblies: work in progress
10.09.2015 at 3:30pm Tomas Marques Bonet (Universitat Pompeu Fabra, Barcelona, Spain): “Human comparative genomics: great ape genome variation and epigenetic evolution”
27.05.2015 2:00pm Jose Lopez (Nova Southeastern University) Lessons from the Deepwater Horizon Oil Spill in the Gulf of Mexico
13.05.2015 2:00PM Rubtsova Elizabeth. Comparative analysis of Sym-gene organization in Rhizobium leguminosarum bv. viciae strains, isolated from different host plants and demonstrating clear differences in symbiotic specificity.
13.05.2015 2:00PM Kopat’ Vladimir. Detection and comparative genetic characterization of expected transitive forms between free-living bacteria and nodule-forming legumes symbionts.
29.04.2015 2:00PM Alexej Novogilov “Ethnographic and physical-anthropological characteristic of Russian population in Eastern Europe”
22.04.2015 2:00PM Gaik Tamazian Investigating heterozygosity in the cheetah genome
15.04.2015 2:00PM Andrey Afanasyev (CEO, iBinom (service for genomic data analysis and interpretation for physicians and geneticists)): Next Generation Sequencing as a Diagnostic Platform in USA (inspired by The Molecular Medicine Tri Conference 2015)
08.04.2015 2:00PM Michael Rayko: Modern approaches to transcriptome assembly and analysis
25.03.2015 2:00PM Irina Shchukina: Statistical methods for GWAS and their software implementations.
18.03.2015 2:00PM Gaik Tamazian and Vladimir Brukhin: Botswana genome variation study: current results.
11.03.2015 2:00PM Sergey Malov: “Survival analysis: an improved the actuatrial estimator”
04.03.2015 2:00PM Anna Gorbunova: “Bioinformatics and translational medicine”
25.02.2015 2:00PM Anton Logachev. “New repeats in genomes: filtration and classification”.
18.02.2015 2:00PM Gaik Tamazian: Meta-analysis: theory and application to genome-wide association studies
11.02.2015 2:00PM Serguei Simonov T. Dobzhansky center web-representation extension.
26.11.2014 2:00PM Dennis V. Lavrov (Department of Ecology, Evolution, and Organismal Biology, Iowa State University, USA): Unusual mitochondrial genomes and genes in non-bilaterian animals.
12.11 2:30 PM Gaik Tamazian Simulation of the protein conformational motion based on its coarse-grained representation
05.11 2:00 PM Sergey Malov On signal localization problem and Genome Wide Association Track Chromosome Highway (GWATCH)
29.09 2:30 PM Yury O. Chernoff (School of Biology, Georgia Institute of Technology, Atlanta, USA and Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia) Proteins as information carriers in biology and pathology
24.09 в 2-00 PM Evgeny Andronov (All-Russia Research Institute for Agricultural Microbiology, St.-Petersburg, Pushkin) Study of evolutionary processes in soil microbiome on the gene-, genome- and metagenome level in the laboratory of microbiological monitoring ARRIAM
17.09 2:30 PM Peter Kharchenko (Center for Biomedical Informatics, Harvard Medical School, Boston, MA,USA): “Analysis of heterogeneity in single-cell measurements of mammalian tissues with pathway over dispersion”.
25.06.2014 2:00 PM Nikita N. Khromov-Borisov (First Pavlov State Medical University of St. Petersburg): Reproducibility of results in the genetics of predispositions and their predictive values
30.05.2014 11-00 AM Alexey Vikharev (ITMO) Rigid protein docking using graph theory and a computational geometry methods
28.05.2014 2-00 PM Lev V. Utkin (Forest Technical University) Some models of genomic selection
21.05.2014 2:00 PM Ivan Smetannikov (ITMO) The effective method for protein chain self-intersection search
7.05.2014 2:00 PM Sergei Lebedev (St. Petersburg University of RAS, JetBrains) Probabilistic models for bisulfites-sequencing data
14.05.2014 Sergey Postovalov (Novosibirsk State Technical University) A power comparison of the association tests for genome-wide association studies
30.04.2014 2:00 PM Владимир Брюхин & Гайк Тамазян: Полногеномное метилирование цитозинов у домашней кошки
23.04.2014 Lena Gerwick (Center for Marine Biotechnology and Biomedicine, SIO, UCSD) What are we learning about the genomes of marine filamentous cyanobacteria?
16.04.2014 Alexey Makunin 3rd B chromosome conference. NGS applications for chromosome research
12.03.2014 2-00PM Petr Strelkov (Dept. Ichthyology & Hydrobiology) Hybridization in North European Seas
5.03.2014 2-00PM Properties of decision-making methods based on pairwise comparisons
26.02.2014 2-00PM Shmileva Elena (Chebishev laboratory, SPSU) Geostatistical methods for heavy-tailed data
19.02.2014 Sergey Malov Signal localization in genome association discovery
25.12.2013 2pm: Kolubaeva Svetlana Nikolaevna (Chief, laboratory medical genetic, Military medical academy): Genetic in Military medical academy
18.12.2013 Sergey Knyazev (The laboratory of bioinformatics, ITMO): Modelling of Conformational Changes of Proteins by CMA-ES
04.12.2013 Gaik Tamazian: Cat genome project: research reproducibility issue
27.11.2013 Maria G. Samsonova (Head of Dept. Computational Biology SPbSTU): Variability and robustness of developmental processes
13.11.2013 Elizaveta Bonch-Osmolovskaya New thermophilic prokaryotes: from phenotype to the genome and back
06.11.2013 Ekaterina Chernyaeva Genetic Diversity of the Russian Mycobacterium tuberculosis Strains. Genome variation Database GMTV
30.10.2013 Vladimir Brukhin Epigenetics – Second Genome Code and Phenotypic Plasticity
22.10.2013 Mike Rayko Gluconacetobacter genome assembly: a story full of pain, disappointment and cellulose
16.10.2013 Anna Tsapieva (Institute of Experimental Medicine of the NW branch of RAMS) Genomic analysis of probiotic Enterococcus faecium strains 09.10.2013 Gaik Tamazian Mathematical aspects of one decision-making support method
11.09.2013 Boris Zhorov (Mc Master University) Computational Structural Pharmacology and Toxicology of Ion Channels
03.07.2013 Ilya Minkin (Academic University) C-Sibelia: a tool for bacterial genomes comparison
22.05.2013 Sergey Knyazev, Dr. Yuri Porozov (National University of ITMO, Russia) Simulation of protein conformational motions
08.05.2013 Ekaterina Chernyaeva Whole Genome Sequencing of Russian Mycobacterium tuberculosis strains
24.04.2013 Serguei Simonov Browser for a genome
17.04.2013. Irina Lyadova Immunological Biomarkers of TB activity and progression
10.04.2013. Alexey Makunin De novo genetic linkage map construction from sperm single-cell sequencing with CRI-MAP
3.04.2013 Sergey Malov Goodness of fit survival testing in AIDS research
27.03.2013 Gaik Tamazian LASTZ sequence alignment program
20.03.2013 Alexey Makunin Construction of genetic linkage map in domestic cat based on 70,000 SNP array
6.03.2013 Serguei Simonov Approaces to genetic sequences analysis
27.02.2013 Mikhail Rotkevich. On Multivariate Normal Probabilities in Multiple Testing
20.02.2013 Gaik Tamazian Higher Criticism for Multiple Comparisons
13.02.2013 Pavel Dobrynin Study of genotype variations in Cheetah using NGS data
06.02.2013 Anton Svitin GWAS Highway: road full of promise
30.01.2013 Alexey Antonik Coverage problem revisited
23.01.2013 Olga Bajenova Genetic mechanisms of carcinogenesis and metastasis in human: search for new diagnostic markers to prevent metastasis
26.12.2012 Sergey Nikolenko BayesHammer: Bayesian clustering for error correction in single-cell sequencing
12.12.2012 Alla Lapidus Microbial genome assembly and finishing
5.12.2012. Антон Логачев Генетические расстояния и их оценка. Модели нуклеотидных замен
28.11.2012. Сергей Симонов Об одном подходе к распознаванию посттрансляционных модификаций протеинов
15.10.2012 Dr. Stephen O’Brien A Magic Gene-CCR5-∆32-From discovery to Clinical Benefit in a Generation
08.10.2012 Алексей Макунин Привязка нуклеотидной последовательности генома к физическому положению на хромосомах
24.09.2012 Гайк Тамазян Вариант адаптивного случайного поиска для глобальной оптимизации
17.09.2012 Павел Добрынин Encode project writes eulogy for junk DNA
10.09.2012 Сергей Малов Задачи множественного тестирования при анализе полного генома на наличие ассоциаций
20.08.2012 Алексей Антоник О задаче покрытия ДНК
13.08.2012 А.П. Козлов выступит с докладом Феномен активации эволюционно-новых генов в опухолях
6.08.2012 Николай Черкасов Обзор баз данных MySQL, FIlemaker
30.07.2012 Компьютерные инструменты в генетических исследованиях. Алексей Макунин: Программы для сборки геномов de-novo; Павел Добрынин Программы для выравнивания последовательностей
23.07.2012 Сергей Малов выступит с докладом Компьютерные инструменты в генетических исследованиях. Статистические пакеты R-project и SAS
16.07.2012.Michael V. Okun’ (Bioinformatical Center at Vienna University & PhD student in Botanical institute RAS): Next Generation Sequencing Technologies
02.07.2012. Chernyaeva Ekaterina Mycobacterium tuberculosis complex genetic diversity . Global phylogeny and biological features.
25.06.2012. Shevchenko Andrei HIV prevalence and subtypes, stage of HIV infection, transmission and life cycle, HIV genome and the genetic diversity of HIV population inside the body.
18.06.2012. Logachev Anton. Modern phylogenetic reconstruction in Eukaryota: assembling tree of life
04.06.2012. Galaktionov Nikolai. Gorilla genome, technique and results.
27.05.2012. Kozlov A. P. On research perspectives of the Theodosius Dobzhansky Center for Genome Informatics.
21.05.2012. Dobrynin Pavel. Homology searches by protein Blast and the chacterization of the new age of genes.
14.05.2012. Andronov Eugeniy. The evolutionary space for 16S rRNA gene.
16.04.2012. Antonik Alexei. Topological methods in biology.
09.04.2012. Malov Sergey. Multiple hypothesis testing.
26.03.2012. Galaktionov Nikolai. Domestication of mobile elements a source of novel genes formation.
19.03.2012. Matveev Ivan. Изогнутость ДНК, центромеры и перицентромеры.
12.03.2012. Dobrynin Pavel & Malov Sergey. On the motif finding problem (discussion).
20.02.2012. Galaktionov Nickolai. Samples preparation for genome sequencing.
13.02.2012. Dobrynin Pavel. DNA microarrays.
06.02.2012. Discussion: 1) classification and the support vector machine method (Malov S.V., part 3 of the talk at 16.01.12); 2) study of broad set of genes with the specific phenotype (Dobrinin P.); 3) on a simple problem of covering whole genome length by short random reads and genome assembling (Malov S.V.).
30.01.2012. Tsarev Fedor. “Combining de Bruijn graph and overlaps graph approaches for de novo genome assembly“.
23.01.2012. Malov Sergey. Methods of comparative genetics (part 2, probabilistic tools in clustering).
16.01.2012. Malov Sergey. Methods of comparative genetics (part 1, clustering).
26.12.2011. Chernyaeva Ekaterina. Genomic information in the Internet and data mining.
19.12.2011. Malov Sergey. Hidden Markov processes with applications in bioinformatics.
12.12.2011. Chernyaeva Ekaterina. Discussion of main directions in the research project.
05.12.2011. Iurasov Dmitry. Alignment algorithms.
28.11.2011. Dobrynin Pavel. On genome structure and gene annotation.
21.11.2011. Matunina Ekaterina. On cells and proteins.