| 9.00-9.30 | Registration, morning cofee |
| 9.30-10.00 BBA | Opening remarks |
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10.00-11.30 BBA | Bioinformatics meets cytology |
| 30 min. | Peter Kharchenko | Interpreting chromatin states in model organisms |
| 15 min. | Maksim Imakaev | Chromatin folding in eucaryotes: matching 3D genome structure to polymer models using molecular dynamics simulations |
| 30 min. | Sergei Strelkov | Towards the molecular archtecture of intermediate filaments |
| 15 min. | Armen Mulkidjanian | Evolution of membrane bioenergetics |
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11.30-12.00 room 227 | Cofee break |
12.00-13.30 BBA | RNA |
| 15 min. | Loredana Martignetti | Identification of shortened 3'-untranslated regions and impact on microRNA regulation |
| 15 min. | Vladimir Kuznetsov | Ovarian cancer patient's risk stratification based on miRNA-mRNA interactome |
| 15 min. | Dmitri Pervouchine | Use of hash tables for RNA structure prediction |
| 15 min. | Slavica Dimitrieva | Practicality and time complexity of a sparsified RNA folding algorithm |
| 15 min. | Konstantin Gunbin | Human and neanderthal miRNA genes are not so similar |
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13.15-14.30 | Lunch |
14.30-16.00 BBA | Gene expression and transcriptomics |
| 30 min. | Shekhar Mande | Prediction of genome-wide interactions reveals communication signals during mycobacterial latency |
| 30 min. | Ivan Gorlov | Variance based identification of candidate genes using gene expression data |
| 15 min. | Alexander Ivliev | Prediction of human cilia-related genes by analysis of open-access transcriptomic and proteomic resources |
| 15 min. | Leonid Peshkin | Mapping gene expression in two Xenopus species: evolutionary constraints and developmental flexibility |
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16.00-18.00 Lobby | Cofee break and poster session
(see list of posters) |
16.00-18.00 BBA | Computer demonstrations etc. |
| ca. 18.00 | Departure for conference dinner (buses) |
| ca. 19.00-22.30 | Conference dinner (restaurant Kremlevsky, Staraya ploschad') |
| 10.00-10.30 | Hangover coffee |
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10.30-12.30 | Statistical genetics and genomics (S.Sunyaev) |
| 30 min. | Michael Lässig | Mutational load generates genomic modularity |
| 30 min. | Suzanne Leal | The power of complex trait rare variant association methods |
| 30 min. | Paul de Bakker | An amino acid polymorphism centric view of classical HLA associations in complex traits |
| 30 min. | Luda Diatchenko | Translational studies in the genomic era |
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12.30-14.00 | Lunch |
14.00-16.15 | 50th anniversary of IITP (Jubilee session) |
| 15 min. | | Introductory remarks |
| 30 min. | Pavel Pevzner | De novo sequencing of peptide antibiotics |
| 30 min. | Vadim Gladyshev | Understanding aging through genome analysis |
| 30 min. | Philipp Khaitovich | A molecular survey across lifespan: human brain evolution and aging |
| 30 min. | Evgeny Zdobnov | Comparative genomics of Arthropods |
16.15-16.45 | Cofee break |
16.45-18.00 BBA | Molecular evolution |
| 30 min. | Georgii Bazykin | Detecting past positive selection through ongoing negative selection |
| 15 min. | Sergey Naumenko | The fitness conferred by recently replaced amino acids rapidly declines with time |
| 15 min. | Evgeniy Leushkin | Adaptive amino acid replacements triggered by indels in Drosophila proteins |
| 15 min. | Dilrini De Silva | Characterising selection in human conserved non-coding elements (CNEs) from the HapMap and 1000 Genomes projects |
16.45-18.00 M1 | Algorithms |
| 20 min. | Manju Bansal | Structural features based identification and prediction of promoter regions in whole genome sequences |
| 20 min. | Mireille Régnier | Computing the p-values of selections in huge sets |
| 20 min. | Ivo Grosse | De novo discovery of differentially abundant DNA binding sites including their positional preference |
| 20 min. | Julie Bernauer | Evaluating mixture models for building RNA knowledge-based potentials |
| ca. 18.00 | Departure for excursion |
| 9.30-10.00 | Morning coffee |
10.00-11.30 BBA | Regulatory networks |
| 30 min. | Esko Ukkonen | Modeling regulatory complexes using both TF-DNA and TF-TF interactions |
| 30 min. | Igor Zhulin | Molecular evolution of a complex signal transduction system |
| 30 min. | Dmitry Rodionov | Comparative genomics approaches for reconstruction of transcriptional regulatory networks in Bacteria |
11.30-12.00 | Coffee break |
12.00-13.30 BBA | Protein-DNA binding motifs and their evolution |
| 30 min. | Yuriy Orlov | Integrative analysis of transcription factors binding profiles regulating embryonic stem cell identity based on ChIP-seq and expression arrays technologies |
| 15 min. | Armita Nourmohammad | Formation and functional conservation of regulatory binding site complexes in eukaryotes |
| 15 min. | Dmitry Ravcheev | Comparative genomics based reconstruction of transcription regulation network in Staphylococcaceae |
| 30 min. | Andrey Mironov | A probabilistic approach to an evolution study of sequence properties |
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10.00-13.30 M1 | Indian-Russian seminar |
| 20 min. | R.G.Efremov | Protein-membrane binding as a self-adaptive process: a computational view |
| 20 min. | Akash Ranjan | From protein-protein interaction prediction to elucidation of missing metabolic pathway enzymes |
| 20 min. | Pinak Chakrabarti | Protein-protein interfaces – structural features, and changes brought about by complex formation |
| 20 min. | Oxana Galzitskaya | Influence of organization of native structure on its folding: Modeling of protein folding |
11.30-12.00 | Cofee break |
| 20 min. | Payel Ghosh | Study of DNA binding proteins in E. coli and their role in organization of nucleoid structure |
| 20 min. | Sharmila Mande | Towards understanding the gut microbiota of a malnourished child |
| 20 min. | Debasisa Mohanty | Computational studies for understanding mechanistic details of newly discovered post-translational modifications |
13.30-15.00 | Lunch |
15.00-16.15 BBA | Protein structure and protein-protein interactions |
| 30 min. | Alexey Nesvizhskii | Computational methods for modeling AP/MS protein-protein interaction data |
| 15 min. | Alexey Stukalov | Bayesian inference of protein complexes from mass spectrometry data |
| 15 min. | Anatoly Ruvinsky | Structure fluctuations and configuration instabilities in proteins |
| 15 min. | Sergiy Garbuzynskiy | Golden triangle for protein folding rates |
16.15-16.45 | Cofee break |
16.45-18.45 BBA | RECESS session |
| 15 min. | Dmitry Ivankov | Analysis of cleaved N-terminal sequences coming from MS/MS proteomics for E.coli and S.cerevisiae |
| 30 min. | Stefan Kramer | Data mining methods for cheminformatics |
| 30 min. | Dmitry Korkin | Computational biology of host-pathogen interactions |
| 30 min. | Dmitry Frishman | Exploring the fold space of membrane proteins |
| 15 min. | Evgenia Kriventseva | Correlating evolutionary and functional traits in vertebrates, arthropods, and fungi |
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16.45-19.00 M1 | BioUML/Skolkovo session |
| 15 min. | I.I.Goryanin | Bioinformatics in Skolkovo. Opportunities and challenges |
| 40 min. | F.A.Kolpakov | BioUML — open source plug-in based platform for bioinformatics: invitation to collaboration |
| 10 min. | V.V.Poroikov | BioUML: the PASS plug-in for prediction of biological activity of substances on the basis of their structural formulae |
| 10 min. | V.Yu.Makeev | BioUML: the ChIPMunk plugin for motif discovery in ChIP-Seq data |
| 10 min. | A.Zinoviev | BioUML: a plug-in for model reduction |
| 20 min. | A.Kel | GeneXplain platform for systems medicine |
| 15 min. | | Closing remarks |
| ca. 19.00 | Departure for excursion |
| 9.30-10.00 | Morning coffee |
10.00-13.30 BBA | Medical Bioinformatics |
| 30 min. | Alexander Kel | Modeling of pathway plasticity in cancer |
| 20 min. | Ekaterina Kotelnikova | Meta-analysis for discovery of disease biomarkers with implicated mechanistic models |
| 20 min. | Olga Gorlova | Derived SNP allele are more frequently used as a risk-associated variants in common human diseases |
| 20 min. | Olga Kalinina | Discovering novel drug-target interactions via superimposition of 3D structures |
11.30-12.00 | Cofee break |
| 30 min. | Alexander Grishin | Using structure-based drug design to promote the development of persistent chlamydial infection treatment |
| 20 min. | Vladimir Poroikov | In silico screening and rational design of multitargeted drugs |
| 20 min. | Kasia Bozek | Physicochemical and structural properties determining HIV-1 coreceptor usage |
| 20 min. | Ivan Anishchenko | Development of novel anti-HIV-1 agents based on glycosphingolipids by computer modeling and chemical synthesis: beta-galactosylceramide and the envelope GP120 V3 loop |
10.00-13.30 M1 | French-German-Russian seminar |
| 20 min. | Dmitrij Afonnikov | Analysis of the transcriptome of the human parasitic trematode Opisthorchis felineus |
| 20 min. | Rolf Backofen | Non-coding RNAs: The cell's dark matter |
| Julie Bernauer | Evaluating Mixture Models for building RNA knowledge-based potentials |
| 20 min. | Valentina Boeva | Predicting copy number alterations and structural variants using-paired end sequencing data |
| 20 min. | Jeremie Bourdon | Average-case analysis methods dedicated to the study of Biological Networks |
16.00-16.30 | Cofee break |
| 30 min. | David James Sherman | Addressing scaling-out challenges for comparative genomics |
| 20 min. | Maria Samsonova | Modeling of gap gene expression in Drosophila Kruppel mutants |
| 20 min. | Andrei Zinovyev | Deciphering mechanisms of miRNA action on translation by mathematical modeling |
| 20 min. | Laurence Calzone | Mathematical approach to account for mutations in bladder tumours |
13.30-15.00 | Lunch |
15.00-16.30 BBA | Sequencing (and) errors |
| 30 min. | Limsoon Wong | Co-regulating miRNA clusters are functionally conserved but widely dispersed in protein-protein interaction networks |
| 15 min. | Sergey Nikolenko | Hammer 2.0: Bayesian error correction for non-uniform coverage |
| 15 min. | Ekaterina Khrameeva | Interlaboratory and interplatform comparisons of 117 mRNA and genome sequencing experiments |
| 15 min. | Rene te Boekhorst | Identification of sources of error affecting base calling in next generation Illumina/Solexa sequencing |
| 15 min. | Irina Abnizova | Statistical analysis of errors' context for Illumina sequencing |
| | | |
15.00-16.30 M1 | Modeling and systems biology |
| 30 min. | Alexander Beliaev | Systems biology and sybthetic bioengineering for bioenergy applications |
| 15 min. | Maksim Zakhartsev | Dynamic model of anaerobic energy metabolism of yeast Saccharomyces cerevisiae |
| 15 min. | Sergey Vakulenko | Flexible and robust patterning by centralized gene networks |
| 30 min. | Lilia M. Iakoucheva | A systems biology approach to unravel the underlying functional modules involved in autism |
16.30-17.00 | Cofee break |
17.00-18.45 BBA | Evolution of genomes |
| 15 min. | Milana Frenkel-Morgenstern | Potential function of proteins encoded by chimeric transcripts |
| 15 min. | Ivan Antonov | Finding and sorting out frameshifts in 1100+ prokaryotic genomes: programmed frameshifts, pseudogenes and sequencing errors |
| 30 min. | Roderic Guigo | Measuring alternative splicing variability |
| 30 min. | Sergei Maslov | Homologous recombination and horizontal gene transfer play a dominant role in evolution of bacterial genomes |
| 30 min. | Max Alekseyev | Challenges in comparative genomics: from biological problems to combinatorial algorithms (and back) |
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18.54-19.0 | Closing ceremony |
ca 19.00 | Farewell party |