Chronicle:
School FutureBiotech. Klyazma, Russia, 6-10.08.2012
• M.S.Gelfand. Bioinformatics: A one-hour overview (invited lecture)
Shool Genomic Data Analysis. Novogorsk, Russia, 02-11.07.2012
• M.S.Gelfand. Bioinformatics: A one-hour overview (invited lecture)
The 8th Int. Conf. on Bioinformatics of Genome Regulation and Structure / Systems Biology. Novosiborsk, Russia, 25-29.06.2012
• A.D.Kaznadzey, P.V.Shelyakin. Diversion of genome loci and co-localization patterns study of the protein families from different functional classes of the bacterial carbohydrate mechanism
• M.D.Logacheva, R.A.Sutormin, S.A.Naumenko, N.V.Demidenko, D.V.Vinogradov, M.S.Gelfand, A.A.Penin. A draft genome sequence of tartary buckwheat Fagopyrum tataricum
• M.Pyatnitsky, I.Mazo, N.Daraselia, M.Shkrob, E.Kotelnikova. Cluster analysis of significant regulators as new approach to patients subtyping
• M.Pyatnitsky, E.Kotelnikova, M.Shkrob, A.Ferlini, N.Daraselia, I.Mazo, E.Schwartz. Novel approach to meta-analysis of microarray datasets for identification of new biomarkers and potential drug targets
Russian-Germany Seminar«Regulation and Evolution of Cellular Systems” Moscow, Russia, 20-23.06.2012
• Y.Kurmangaliev. Functional implications of splicing polymorphisms in the human genome (short talk)
• S.Denisov. Positive and negative selection in splice sites (poster)
• R.Soldatov. Statistical methods of comparative genomic analysis based on diffusion approximation (poster)
• I.Suvorova. Comparative analysis of the GntR-family transcription factors and their binding sites (poster)
• S.Vinogradova. GA-rich binding sites of lncRNA HOTAIR (poster)
Int. Conf. “Instabilities and Control of Excitable Networks”. Dolgoprudny, Russia, 25-30.05.2012
• M.S.Gelfand. Networks in molecular biology (invited lecture)
IEEE Int. Symp. on Biomedical Imaging ISBI’2012. Barcelona, Spain, 02-05.05.2012
• G.V. Ponomarev, M.S. Gelfand, M.D. Kazanov. A multilevel thresholding combined with edge detection and shape-based recognition for segmentation of fetal ultrasound images. IEEE International Symposium on Biomedical Imaging, Barcelona, Spain, 2012. (1st Prize at Fetal Femur Challenge: Biometric Measurements from Fetal Ultrasound Images)
The 8th Winter Symposium on Chemometrcs “Modern Methods on Data Analysis”. Drakino, Russia, 27.02-02.03.2012
• E.E.Khrameeva, G.G.Fedonin, M.S.Gelfand. The impact of interchromosomal associations on the functional state of the human genome (talk)
• P.Mazin, M.Gelfand, P.Khaitovich. Age changes and tissue differences of alternative splicing in the human brain (talk)
Seminar at University of Texas, Brownsville, 14.02.2012
• M.S.Gelfand
ISBA16. Mexico, Dec. 2011
• E. Ian, O.N. Sekurova, D. Malko, E. Fjaervik, H. Bredholt, M. Gelfand, S.B. Zotchev. Actinomycetes from two marine sponges collected in the Norwegian fjord: diversity and clues on marine adaptation from the draft genome sequence analyses
The 17th Nitrogen Fixation Congress. Fremantle, Australia, 27.11-01.12.2011
• J. Jalovaja.Comparative-genomic reconstruction of the nifa regulon evolution in alphaproteobacteria (short talk)
ASBMB Special Symposium “Chemical, Synthetic and Systems Biology: New Directions of Biochemistry”. Snowbird, UT, USA, 12-16.10.2011
• O. Tsoy. Evolution of transcriptional regulation in Enterobacteriales (poster)
The 5th International Moscow Conference on Computational Molecular Biology, MCCMB-2011. Moscow. Russia, 21-14.07.2011
• N.Bykova, R.Soldatov, A.Mironov. A probabilistic approach to an evolution study of sequence properties (talk)
• E.Khrameeva, M.Gelfand. Interlaboratory and interplatform comparisons of 117 mRNA and genome sequencing experiments (short talk)
• D.Pervouchine, E.Khrameeva, O.Nikolaenko, M.Gelfand, A.Mironov. Use of hash tables for RNA structure prediction (short talk)
• A.Artemov, D.Pervouchine, A.Favorov, A.Mironov. Kinetic model explains correlation between DNA methylation and tissue-specific alternative splicing (poster)
• N.Bykova, A.Mironov. Inference of ancestral states for character evolution: the case of uncertain data at terminal nodes (poster)
• E.Ermakova, M.Gelfand, D.Rodionov. CodY regulon in Bacillaceae (poster)
• S.Garushyants, M.Kazanov. Horizontal gene transfer and genome evolution in Methanosarcina (poster)
• E.Gordienko, M.Kazanov, M.Gelfand. Evolution of bacterial pan-genomes (poster)
• M.Kazanov, S.Leyn, P.Novichkov, D.Rodionov. Functional annotation of regulons controlled by RNA regulatory elements in complete bacterial genomes (poster)
• P.Shelyakin, A.Kaznadzey. Evolution study and classification of carbohydrate metabolism genome loci in bacteria (poster)
• S.Leyn, M.Kazanov, P.Novichkov, D.Rodionov Reference collection of transcriptional regulons in Bacillales family of bacteria (poster)
• P.Mazin, M.Gelfand, P.Khaitovich. Splicing differences in primate brain development (poster)
• A.Nikulova, A.Favorov, A.Mironov. An approach to predict cis-regulatory modules and identify conserved regualtory grammar in eukaryptic genomes (poster)
• V.Stepanova, D.Rodionov. Genomic analysis of transcriptional regulation of aromatic amino acids metabolism in gamma-proteobacteria (poster)
• S.Vinogradova, A.Mironov. Genome-wide analysis of possible ncRNA structures (poster)
• I.Zharov, M.Gelfand, A.Kazakov. Regulation of multiddrug resistance genes by transcriptional factors from the MerR family (poster)
Berlin Summer Meeting. Berlin, Germany, 23-25.06.2011
• E.Ermakova. CodY regulon in Bacillaceae (poster)
The 17th Albany conversation. Albany, USA, 14-18.06.2011
• A.Y.Panchin, E.N.Shustrova, I.I.Artamonova. Recently duplicated human genes: basics of evolution (poster)
• E.E.Khrameeva, A.A.Mironov, M.S.Gelfand. The impact of interchromosomal associations on the functional state of the human genome (short talk)
The 111th meeting of the American Society of Microbiology. New Orlean, USA, 20-24.05.2011
• E. N. Gordienko, M. D. Kazanov, M. S. Gelfand. Evolution of Bacterial Pan-genomes (poster)
ISBRA 2011. Changsha, China, 27-29.05.2011
• E.Ermakova. CodY regulon in Bacillaceae (poster)
Russian-German seminar «Regulation and Evolution of Cellular Systems” Munich, Germany, 10-13.05.2011
• A.Mironov. RNA and epigenomics (plenary lecture)
• I.Suvorova. Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gamma-proteobacteria (short talk)
• A.Nikulova. An approach to identify conserved regualtory grammar and predict cis-regulatory modules in eukaryptic genomes (poster)
• O.Tsoy. Evolution of transcriptional regulation in bacteria (poster)
• S.Garushyants. Horizontal gene transfer and genome evolution in Methanosarcina (poster)
• S.Vinogradova. Genome-wide analysis of possible RNA structures (poster)
Meeting on Nonparametric Statistics. Marseille, France, 13-17.12.2010
• F. Enikeeva
EMBO Conference series “From Functional Genomics to Systems Biology”. Heidelberg, Germany, 13-16.11. 2010
• E. Ermakova, M. Gelfand, S. Nuzhdin, D. Malko. Chqnges in inclusion rate of alternatively spliced gene regions in Drosophila are accompanied by higher nucleotide substitution rate (poster)
CRISPR Meeting 2010. Wageningen, The Netherlands, 21-22.10.2010
• I. Artamonova
The 24th International Mammalian Genome Conference. Heraklion, Greece, 17-23.10.2010
• E. Khraneeva, A. Mironov and M. Gelfand. Association between spatial proximity and functional similarity in human genome (talk. Student satellite symposium)
CSH-Asia Ñonference “Computational Biology”. Suzhou, China, 27.09-1.10.2010
• M.S. Gelfand. Evolution of bacterial regulatory systems (invited talk)
• A.Y. Panchin, E.N. Shustrova, M.S. Gelfand, I.I. Artamonova. Evolution of recently duplicated human genes (poster)
• P. Mazin, J. Xiong, X/Liu, Z. Yan, W. Chan, M. Gelfand, P. Khaitovich. Splicing changes in human brain over the course of lifespan (talk)
The 28th European Meeting of Statisticians EMS2010. Piraeus, Greece, 17-22.08.2010
• F. Enikeeva. On two estimates related to the change-point problem (talk)
The 5th IAPR Int. Conf. “Pattern Recognition in Bioinformatics” PRIB2010. Lecture Notes in Bioinformatics LNBI-6282. Nijmegen, Netherland, 22-24.09.2010
• G.G. Fedonin, M.S.Gelfand. Machine Learning Study of DNA Binding by Transcription Factors from the LacI family (talk)
The 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2010). Boston, USA, 11-13.07.2010
• E. Khrameeva. Spatial proximity and similarity of functional states of genome domains (talk/SIG)
• I. Artamonova, V.Sorokin, M.Gelfand. Evolutionary dynamics of CRISPR systems in the Ocean metagenome (poster)
Viruses of Microbes. Paris, France, 21-25.06.2010
• I. Artamonova, V.Sorokin, M.Gelfand. Evolution of CRISPR-cassettes in the Ocean metagenome (poster)
Royal Holloway University of London, 8.11.2010
• F. Enikeeva. On two estimates related to the change-point problem
Kolloquium der International Research Training Group GRK 1384 und der Giessener Biochemischen Institute Justus-Liebig-Universitat Giessen, 11.03.2010
• M.S. Gelfand. Alternative splicing: A playground of evolution
RECESS Retreat 2010 Schloss Hohenkammer, 20-23.06.2010
• N. Bykova. Evolution of signal peptides
• M. Borisova. Evolution of the LexA/DinR family of transcription factors and the motifs they recognize in DNA
• O. Tsoy. Bacterial ethanolamine metabolism: comparative genomics of spoiled food
• A. Nikulova. Predictin and structural analysis of the evolutionary conserved enhancers in Drosohila genomes
• M. Gelfand. Alternative splicing as a playground of evolution
French-Russian Seminar on Next Generation Sequencing Zvenigorod, 14-17.06.2010
• A.E. Khrameeva, A.A.Mironov. Long range correlations in the genome and chromatin (talk)
• M. Gelfand. Age- and tissue-specific alternative splicing in the human brain (talk)
International Humboldt Conference “Fundamental science and innovations in modernization of Russia and world development” Moscow 22-24.04.2010
• M.Gelfand Reform of Research Institutions in Russia
2nd International Congress-Partnering & Exhibition on Biotechnology and Bioenergy Moscow, 13-15.04.2010
• M.S. Gelfand. Evolution of bacterial regulatory systems, or Why not all bacteria are like E.coli
Swiss-Russian seminar "Comparative genomics and transcriptome diversity", Leysin, 3-6.2.2010
• M. Gelfand. Alternative splicing as a playground of evolution
• S. Denisov. How selection acts on mammalian splice sites
• A. Panchin. Evolution of alternative splicing patterns in human paralogous genes
• D. Pervushin. Evidence for widespread conservation of RNA structures that are associated with splicing
• E. Khrameeva. Comparative genomics of long-range DNA interactions in eukaryotes
Kolloquium der International Research Training Group GRK 1384 und der Giessener Biochemischen Institute, Justus-Liebig-Universitat Giessen, 11.03.2010
• M.S. Gelfand. Alternative splicing: A playground of evolution
2nd Spanish-Russian forum on information and communication technologies, Madrid, Spain, September 2009
• M.S. Gelfand. Bioinformatics: data-driven molecular biology
Evolutionary Biology Retreat, WSBS MSU, September, 2009
• M.S. Gelfand. Evolution of regulatory systems (report)
• I.I. Artamonova
• O.V. Kalinina
4th Int. Moscow Conf. on Computational Molecular Biology, Moscow, July 2009
• Bykova N., Mironov A. Evolution of signal peptide appearance/disappearance in bacterial genomes (poster)
• Denisov S., Gaydukova A., Mironov A., Favorov A., Nurtdinov R., Gelfand M. Evolution of sequences under strong selection: splice sites and Shine-Dalgarno boxes (poster)
• Malko D., Ermakova E., Gelfand M. Evolution of structure and sequence in alternatively spliced Drosphila genes (poster)
• Khrameeva E., Mironov A., Gelfand M., Pervouchine D. Regulation of splicing by small non-coding RNAs (poster)
• Korostelev Y., Laikova O., Rakhmaninova A., Gelfand M. An online tool for search of correlations between sequences of DNA-binding proteins and their binding sites (short talk)
• Mazin P., Khaitovich P., Mironov A., Gelfand M. Investigation of age-related alternative splicing changes in human brain using Solexa sequencing (poster)
• Nikulova A., Mironov A. Prediction of regulatory elements in Drosphila genomes using Hidden Markov model based on the arrangement of transcription factor binding sites (poster)
• Pertsovskaya I., Artemov A., Oparina N., Favorov A., Mironov A., Vinogradov D. CpG islands: evolution of ‘non-objects’ in the genome (poster)
• Petrova S.A., Vitreschak A.H. Regulation of ribosomal genes in bacteria: comparative genomics analysis (poster)
• Vinogradova S., Vinogradov D., Mironov A. Codon usage bias: biological function or neutral marker? (poster)
• Sorokin V., Artamonova I. Evolutionary dynamics of CRISPR-cassettes (poster)
• Kalinina O., Russell R. Predicting novel protein-small molecule interactions using molecular modeling techniques (poster)
• Kurmangaliev E. Patterns of evolution in protein phosphorylation sites (poster)
• Miteva D.S., Stepanova V.V., Rakhmaninova A.B. Correlations between DNA-binding domains and their DNA binding sites (poster)
• Neverov A., Favorov A.V., Mironov A.A., Chulanov V.P. The base-calling algorithmg with vocabulary (poster)
• Osterman A., Rodionov D. Some like it sweet: towards genomic ancyclopaedia of sugar catabolism in bacteria (talk)
• Panchin A., Gelfand M., Ramensky V., Artamonova I. Major trends in the evolution of young human paralogs (short talk)
• Ramensky V., Nurtdinov R., Neverov A., Mironov A., Gelfand M. Positive selection and laternative splicing of human genes (short talk)
• Stavrovskaya E., Rodionov D.A., Mironov A.A., Dubchak I., Novichkov P.S. Statistical approach for discovering evolutionary conserved members of regulon (poster)
• Tsoy O., Ravcheyev D., Mushegian A. Ethanolamine utilization: study of evolution and regulation using comparative genomics (poster)
• Vakhrusheva A., Kazanov M., Mironov A., Bazykin G Capture and release of coding DNA: evolution of bacterial genes by shift of stop codons (poster)
16th Conversaton Albany’2009 (Albany, USA, June 2009)
• M.S.Gelfand. Comparative genomics of alternative splicing (invited talk)
• I.Artamonova. Evolutionary dynamics of CRUSPR-cassettes in the metagenome Sorcerer II (talk)
RECOMB (Tucson, USA, May 2009)
• M.S.Gelfand. Alternative splicing as a playground of evolution (keynote talk)
109th General Meeting of the American Society for Microbiology (Philadelphia, USA, May 2009)
• M.S.Gelfand. Riboswitches and transcription factors: Rapid evolutionary changes of regulatory systems (invited session talk)
5th International Symposium "Bioinformatics Research and Applications" ISBRA 2009 (Ft. Lauderdale, USA, May 2009)
• M.S.Gelfand. Evolution of regulatory systems in bacteria (keynote talk)
RECESS Meeting (Munich, Germany, April 2009)
• M.S.Gelfand. (talk)
• A.A. Mironov
• A. Nikulova
First RECOMB Satellite Conference on Bioinformatics Education (San Diego, USA, March 2009)
• M.S.Gelfand. From computer to a lab bench and back: How comparative genomics leads to the discovery of bacterial transporters with a new mode of action (invited talk)
• Y.Korostelev, O.N.Laikova, A.B.Rakhmaninova, M.S.Gelfand. Correlations between amino acid sequences of transcription factors and their DNA binding sites (poster)
CASB-20 Meeting (San Diego, USA, March 2009)
• M.S. Gelfand. Evolution of bacterial regulatory systems (invited talk)
MS. Gelfand. Comparative genomic analysis of T-box regulation: identification of new structural classes and reconstruction of evolution (seminar). Burnham Institute, La Jolla, October 2008
MS. Gelfand. Alternative splicing: A playground of evolution(seminar). University of California, San Diego, October 2008
MS. Gelfand. Alternative splicing: A playground of evolution (seminar). University of Soutnern California, October 2008
3rd Workshop on Algorithms in Bioinformatics (Moscow, October 2008)
• MS. Gelfand. M.Gelfand. Alternative splicing as a playground of evolution (invited talk).
4th EMBO Conference “"From Functional Genomics to Systems Biology" (Heldelberg, November 2008)
• EO. Ermakova, D.B. Malko, M.S. Gelfand. Evolution of alternatively spliced conding regions in 11 Drosophila genomes (poster)
European Conference on Computational Biology ECCB-08 (Cagliary, Italy, September 2008) http://www.eccb08.org/index.php?pageId=1
• OV. Kalinina , R.B. Russell Predicting drug-target promiscuity via ligand/protein superimpositions: phosphodiesterases as an illustrative example (poster)
• VA. Sorokin, M.S. Gelfand, I.I. Artamonova. Prokaryotic immunity systems of the CRISPR type in metagenomes.(poster)
MS. Gelfand. Evolution of bacterial regulatory systems (seminar). Cologne University, July 2008.
Berlin Summer Meeting: Systems Biology (Berlin, June 2008)
• MS. Gelfand. Evolution of bacterial regulatory systems (invited talk).
HHMI International Research Scholars conference (Lisbon, June 2008)
• MS. Gelfand. Comparative genomic analysis of T-box regulation: identification of new structural classes and reconstruction of evolution (invited talk).
6th Int. Conf. on Bioinformatics of Genome Regulation and Structure BGRS'2008 (Novosibirsk, June 2008)
• AA. Belostotsky, V.A. Boeva, E.O. Ermakova, A.V. Favorov, M.V. Fridman, A. Heinzel, I.V. Kulakovsky, V.J. Makeev, D.B. Malko, Y.A. Medvedeva, N.J. Oparina. Integration of genome, transcriptome and regulatory information for functional genomics of eukaryotes (talk)
• DD. Pervouchine, V.A. Raker, M.S. Gelfand, A.A. Mironov. Association of RNA structures and splicing (talk)
• KYu. Popadin . TRNA’s free energy and evolution of mitochondrial genome (talk)
• I. Pertsovskaya, N. Oparina, D. Vinogradov, A. Favorov, A. Mironov. CPG islands evolution: CPG dinucleotides death and birth probabilities in different genome regions (talk)
• S. Denisov, R. Nurtdinov, P. Mazin, A. Kazakov, G. Kovaleva, M. Gelfand. RASDB – regulation of alternative splicing database (poster)
• Ju. Medvedeva, M.V. Fridman, N.Ju. Oparina, D.B. Malko, E.O. Ermakova, V.Ju. Makeev. Reduced level of synonymous substitution in CPG containing codons suggests functional role of intragenic and 3’ CPG islands in human genes (poster)
• DV. Vinogradov, A.A. Mironov. Genome-wide assessment of the codon usage conservation (poster)
• PV. Mazin, A.A. Mironov, A.B. Rakhmaninova, M.S. Gelfand, O.V.Kalinina. SDPFOX: a tool to predict protein specificity and specificity determinants from multiple sequence alignment (poster)
• AD. Neverov, S.G. Orlov, A.A. Mironov, V.P. Chulanov. The new tool for oligonucleotide design for virus genotyping using multiple alignment (poster)
Joint BSC - IRB Barcelona Conference Grand Challenges in Computational Biology (Barcelona, June 2008)
• D. Vinogradov
• I. Pertsovskaya
Bioinformatics-2008 (Warsaw, Poland, April 2008)
• M. Gelfand
Helmholtz Russian-German Workshop on Systems Biology. (Moscow, 27-29 Feb 2008)
• I.I. Artamonova. A recently discovered type of the bacterial immunity, the CRISPR system, in metagenomes (poster)
• M.S. Gelfand. Regulatory systems in bacteria: from comparative genomics to reconstruction of evolutionary history (invited talk)
• A.E. Kazakov. Identification of microcin C-like antibiotic systems (poster)
• A.G. Vitreschak. Comparative genomic analysis of T-box regulatory systems in bacteria (poster)
GA. Bazykin. University of Michigan (Ann-Arbor, Feb-March 2008)
OV. Kalinina. EMBL (Heidenlberg, Germany, Jan-May 2008)
DA. Rodionov. Burnham Institute (La Jolla, USA., November 2007 - July 2008)
MS. Gelfand. Evolution of bacterial regulatory systems. Wageningen University, Jan, 2008. (ïðåçåíòàöèÿ)
M. Yurieva. Stowers Institute (Kanzas City, USA, November 2007 - April 2008)
O. Tsoy. Stowers Institute (Kanzas City, USA, September 2007 - February 2008)
M. Tsyganova. Leuden University (Netherlands, August-October 2007)
3rd Int. Moscow Conference on Computational Molecular Biology MCCMB’07 (Moscow, Russia, July 2007)
• G.A. Bazykin, F.A.Kondrashov, M.Brudno, A.Poliakov, I.Dubhak, A.S.Kondrashov. Extensive parallelism in protein evolution (talk)
• M.J. Cipriano, A.E.Kazakov, D.Ravcheev, A.Arkin, M.S.Gelfand, I.Dubchak. RegTransBase (RTB) – a database of regulatory sequences and interactions in prokaryotic genomes (poster)
• S. Denisov, R.Nurtdinov, D.Vinogradov, A.Kazakov, G.Kovaleva, M.Gelfand. RASDB – regulation of alternative splicing database (poster)
• F.N. Enikeeva, M.S.Gelfand, K.V.Severinov. Restriction-modification systems and bacteriohage: who wins? (poster)
• F.N. Enikeeva, E.A.Kotelnikova, M.S.Gelfand, V.J.Makeev. A model of evolution with constant selective pressure for regulatory DNA sites (poster)
• K. Gorbunov, D.Rodionov, O.Laikova, M.Gelfand, V.Lyubetsky. Reconstrcutin of ancestral regulatory signal along a phylogeny (poster)
• O.V. Kalinina, R.B.Russell, M.S.Gelfand. Identification of functionally important sites in poorly characterized protein families (poster)
• A. Kazakov, M.Gelfand, K.Severinov. Distribution of microcin J-like and mocrocin C-like antibiotic systems (poster)
• Y.D. Korostelev, O.N.Laikova, AB.Rakhmaninova. Position-specific correlations between sequences of LacI family DNA-binding domains and their operators (poster)
• G.Yu. Kovaleva. Regulation of methionine and cysteine biosynthesis in streptococci (poster)
• Y.Z. Kurmangaliev. Exon skipping and activation of cryptic sites as consequences of splicing mutations (poster)
• E. Litvinova, A.B.Rakhmaninova. Statistics of closely related strain proteomes revealed striking differences in their composition (poster)
• A.V. Lyubetskaya. Biobliometrics of bioinformatics (poster)
• D.B. Malko, E.O. Ermakova. Evolution of splicing in insects (poster)
• P.V. Mazin, A.B. Rakhmaninova, O.V. Kalinina. SDPClust: a new tool for prediction of protein specificity in MPA (poster)
• I.V. Merkeev, A.A. Mironov. The database of phylogenetic orthologous groups (PHOG): the algorithm of its construction and its applicationsin comparative genomics (talk)
• A.A. Nikulova, A.A. Mironov. Computational prediction and analysis of transcriptional regulatory modules in mammals (poster)
• I.M. Pertsovskaya, A.A. Mironov. Evolution of CpG islands in mammalian genomes (poster)
• D. Pervouchine, A.A. Mironov. An evidence for regulation of splicing by RNA secondary structures: conserved complementary motifs in Drosophila introns (talk)
• V. Ramensky, R. Nurtdinov, A. Neverov, A. Mironov, M. Gelfand. Positive selection and alternative splicing in human genes (poster)
• D.A. Rodionov. Comparative genomic analysis of transcriptional regulatory networks in Shewanella species and other gamma-proteobacteria (talk)
• E. Stavrovskaya, M. Cipriano, I.L. Dubchak, A.A. Mironov, M.S. Gelfand. Automated search for regulatory motifs in upstream regions of genes from the functional subsystems (poster)
• O. Tsoy, W. Zakirzianova, D.A. Ravcheev. Stories about the evolution of regulators: huw FruR became CRA and RbsR became PurR (talk)
• A.G. Vitreschak, A.A. Mironov, V.A. Lyubetsky, M.S. Gelfand. Function and evolution of the T-box regulation in bacteria (poster)
15th Annu. Int. Conf. On Intelligent Systems for Molecular Biology and 6th European Conf. On Computational Biology ISMB/ECCB’07 (Vienna, Austria, June 2007)
• M.S. Gelfand. Evolution of bacterial regulatory systems (Special Interest Group)
• D.A. Rodionov, Mikhail Gelfand, Margaret Romine, and Andrei Osterman. Comparative Genomics of Transcriptional Regulation of Metabolic Pathways in Shewanella Species (poster)
• M.S. Gelfand. Evolution of alternative splicing (Highlights Track)
• G.Yu. Kovaleva, M.Gelfand. Regulation of methionine and cysteine biosynthesis in Streptococci (Poster)
• A.E. Kazakov, K. Severinov and M.S. Gelfand. Identification of microcin J-like and microcin C-like antibiotic systems (Poster)
• E.O. Ermakova, R.N. Nurtdinov, and M.S. Gelfand. Ovelapping alternative donor splicing sites in the human genome (Poster)
Conference "Genome dynamics: From replication to post-translation and turnover". Howard Hughes Medical Institute (Chevy Chase, USA, March 2007)
• M.S.Gelfand. Transcriptional regulation of iron homeostasis in alpha-proteobacteria: Reconstruction of evolution of a complex regulatory system (oral)
Joint Genomics: GTL Awardee Workshop V and Metabolic Engineering 2007 and USDA-DOE Plant Feedstock Genomics for Bioenergy Awardee Workshop 2007 (Bethesda, USA, Feb 2007)
• D.A.Rodionov, M.S.Gelfand, M.F.Romine, A.L.Osterman. Comparative genomics of transcriptional regulation of metabolic pathways in Shewanella species (poster)
Pacific Symposium on Biocomputing 2007 (USA, January 2007)
• Cipriano M, Kazakov A, Arkin A, Gelfand MS, Dubchak I. Protein-DNA Interactions and Gene Regulation: Integrating Structure, Sequence and Function (poster)
5th European Conference on Computational Biology ECCB’2006 (Eilat, Israel January 2007)
• G. Kovaleva, M.Gelfand. Evolution of the Methionine Biosynthesis Regulation in Streptococci (poster)
• A.V. Gerasimova, D.A.Ravcheev, M.S.Gelfand. Multiple Regulation of Respiration in Gamma-Proteobacteria: FNR, ArcA, NarP and ModE Regulons (poster)
• I.I. Artamonova, G.Frishman, M.S.Gelfand, D.Frishman. Association Rule Mining and Protein Databases: Exceptions Point to Annotation Errors (poster), "Top 5 Posters" prize
• E.D. Stavrovskaya, V.J.Makeev, I.V.Merkeev, A.A.Mironov. Tool for Automatic Detection of Co-regulated Genes (poster)
Joint Genomics: GTL Awardee Workshop V and Metabolic Engineering 2007 and USDA-DOE Plant Feedstock Genomics for Bioenergy Awardee Workshop (Bethesda, USA, Feb. 2007).
• D.A.Rodionov. Poster "Comparative genomics of transcriptional regulation of metabolic pathways in Shewanella species" by D.A. Rodionov, M.S. Gelfand, M.F. Romine, A.L. Osterman
German-Russian Symposium Tatisee, Germany Oct. 2006
• M.Gelfand Alternative spicing: a playground of evolution (invited talk)
D. Ravcheev. Lawrence Berkeley National Laboratory (Berkeley, USA, Sept.-Nov. 2006)
M.S. Gelfand. Comparative genomics of RNA regulatory elements (seminar). Dharmacon, Inc. Boulder, USA. Oct. 4, 2006.
M.S. Gelfand. Comparative genomics and evolution of regulatory interactions in bacteria (seminar). Stowers Institute Kanzas City, USA. Oct 2, 2006.
International Summer School and Workshop 2006 on Evolutionary Genomics, Berlin, Germany, Sep. 2006
• E.A. Permina. The genomics sigma-B regulon in different Gram-positive bacteria (contributed talk)
Meeting of HHMI International Research Scholars. Janelia Farm, USA, Sep. 2006.
• M.S. Gelfand. Evolution of alternative splicing (talk).
M.S. Gelfand. Comparative genomics and evolution of regulatory interactions in bacteria (seminar). Lawrence Berkeley National Lab. Berkeley, USA. Sep 22, 2006.
M.S. Gelfand. Several levels of evolution of regulatory interactions in bacteria (seminar). Burnham Institute. La Jolla, USA. Sep. 20, 2006
CASB Distinguished Lecture Series, University of California at San Diego. La Jolla, USA. Sep. 19, 2006
• M.S. Gelfand. Comparative genomics and evolution of regulatory interactions in bacteria (presentation).
Keystone Symposium "Multi-Protein Complexes Involved in Cell Regulation". Cambridge, UK. September 2006.
• O.V. Kalinina. Applying specificity determinants to identification of protein active sites and other functional features (poster).
Biometals 2006. Welches, USA. August 2006.
• D.A. Rodionov. Comparative Genomics of Metal Uptake Transporters and Regulatory Systems in Bacteria (poster and short talk).
Nels Thorstensen from University of British Columbia, Vancouver, Canada, May-August 2006, 3-month training course
Project: Conservation of co-expression graph in bacteria
8th Int. Engelhardt Conf. On Molecular Biology "RNA-protein interactions" Sergiev Posad, Russia August 2006
MS. Gelfand. Riboswitches (invited talk)
5th Int. Conf. on Bioinformatics of Genome Regulation and Structure BGRS'2006 (Novosibirsk, July 2006)
• Ramensky VE. with Nurtdinov R., Neverov A., Mironov AA., Gelfand MS. Human genome polymorphism and alternative splicing (talk)
• Vitreschak AG. with Lyubetsky VA., Mironov AA., Gelfand MS. Evolutional and functional analysis of T-box regulon in bacteria (talk)
• Kovaleva GYu. and Gelfand MS. Transcriptional regulation of the methionine biosynthesis in actinobacteria and streptococci (poster)
• Mironov AA. Threshold selection using the rank statistics (talk)
• Stavrovskaya ED. with Makeev VYu, Merkeev IV., Mironov AA. Tool for automatics detection of co-regulated genes (poster)
3rd Annual RECOMB Satellite Workshop on Regulatory Genomics (Singapore, July 2006)
• Gelfand MS. Evolution of Bacterial Regulatory Systems (invited talk) presentation
Math-CS Camp for High School Students
History of the Genetic Code
• lecture: gelfand-genetic-code
• problem: gelfand-singapore-problem
• solution: gelfand-singapore-solution
Workshop "Algorithms in Bioinformatics" AlBio06 (Moscow, July 11-13, 2006)
• MS. Gelfand. Comparative genomics for functional annotation of bacterial genomes (invited talk) (presentation)
• AA. Mironov. Using of rang statistics for threshold selection (invited talk)
4th Bertinoro Computational Biology Meeting "Evolution of and Comparative Approaches to Gene Regulation" (Bertinoro, Italy, June 2006)
• MS. Gelfand. Evolution of regulatory interactions in bacteria (presentation)
• DA. Ravcheev. Regulation of respiration in gamma-proteobacteria: Evolution of multiple regulatory systems
OV. Kalinina EMBL (Heidelberg, Germany, March-June 2006)
Human Genome Meeting HGM2006 (Helsinki, Finland, May 31- June 3 2006)
• EO.Ermakova. Evolutionary patterns of alternatively spliced coding regions of mammalian and Drosophila genes (poster)
AE. Kazakov Lawrence Berkeley National Laboratory (USA, February-March 2006)
AV. Gerasimova, EA. Permina. Lawrence Berkeley National Laboratory (USA, November-December 2005)
OV. Kalinina EMBL (Heidelberg, Germany, October-November 2005)
DA. Rodionov. Burnham Institute (La Jolla CA, USA, September 2005 – September 2006)
1st Russian-Bavarian Conference on Bio-Medical Computing (Munich, October 13-14, 2005)
• MS. Gelfand. Comparative genomics of bacteria: functional annotation, metabolic reconstruction, regulatory systems (invited talk)
Seminar at Institute of Bioinformatic, GSF (Munich, October 13, 2005)
• MS. Gelfand. Evolution of alternative splicing (presentation)
4th European Conference on Computational Biology ECCB’05 (Madrid, Spain, September 28 - October 2, 2005)
• MS. Gelfand. Specificity-determining positions in protein alignments (invited talk at workshop “Current approaches for function prediction during genome annotation”)
• II. Artamonova, G. Frishman, M.S. Gelfand, D. Frishman. Correcting annotation errors by association rules mining (poster)
• OV. Kalinina, M.S.Gelfand, A.A.Mironov, A.B.Rakhmaninova. Specificity-determining positions in multimeric proteins are often located on the subunit interaface (poster)
• GYu. Kovaleva, M.Gelfand. Identification of a candidate alpha-isopropylmalate carrier (poster)
• MS. Gelfand. Riboswitches: the oldest regulatory system? Seminar in Centre de Regulacio Genomica (Barcelona, Spain, 22 September 2005)
BioSapiens Workshop (Madrid, Spain, September 2005)
• AV. Gerasimova
1st Conf. on New Frontiers in Microbiology and Infection (Villars-sur-Ollon, Switherland, September 2005)
• Gerasimova AV, Gelfand MS. Comparative analysis of transcriptional regulation in E.coli and related genomes: FNR, ArcA, NarP, NadR, and ModE regulons (poster + short talk)
2nd Moscow Conference on Computational Molecular Biology MCCMB’2005 (Moscow, Russia; July 2005)
• O. Kalinina, A. Rakhmaninova. Intersubunit contacts are often facilitated by specificity-determining positions (talk)
• A. Neverov, L. Milanesi. A pipeline for computational gene recognition in the Saccharopolyspora erythraea genome (poster)
• D. Rodionov. A universal regulatory system of ribonucleotide reductase genes in bacterial genomes (talk)
• A. Gerasimova, D. Ravcheev. How gamma-proteobacteria switch the mode of respiration: A comparative genomic analysis (talk)
• M.S. Gelfand. Evolution of alternative splicing (talk)
• M.S. Gelfand. Evolution of bacterial regulatory systems (report)
• A. Mironov. An efficient algorithm for identification of clusters of transcription factor binding sites (talk)
• Z. Wunderlich, G. Kolesov, M. Slutsky, M. Gelfand, O. Laikova, and L. Mirny. Biological implications of protein-DNA sliding (talk)
• E. Ermakova. Alternatively spliced regions evolve faster (poster)
• A. Gerasimova. Evolution of transcriptional regulation in closely related genomes: the NadR regulon of Enterobacteriaceae (poster)
• A. Gerasimova. ModE-regulation in Enterobacteriaceae (poster)
• D. Malko. Comparative analysis of the alternative splicing of orthologous fruit flies and mosquito genes (poster)
• G. Kovaleva. Comparative analysis of regulation of methionine-cysteine biosynthesis in ascomycetes (poster)
• V. Zakirzianova, D. Ravcheev. A comparative genomic analysis of an evolving of regulatory system: how FruR became Cra (poster)
• M. Tsiganova, D. Ravcheev. Regulation of respiration in Escherichia coli: the comparison of microarray and genomics data (poster)
• E. Stavrovskaya, V. Makeev, A. Mironov. ClusterTree-RS: the binary tree algorithm for identification of co-regulated genes by clustering regulatory signals (poster)
• D. Reshetov, O. Kalinina, A. Rakhmaninova. Computational analysis of functional specificity of the dicarboxylate/amino acid:cation (Na+ or H+) symporter (DAACS) family (poster)
• V. Ramensky, A. Neverov, R. Nurtdinov, A.Mironov M. Gelfand. Human SNPs and alternative splicing (talk)
• E. Permina. The regulation of general stress response in Bacilli group (poster)
• A. E. Kazakov, E. A. Permina, O. V. Kalinina and M. S. Gelfand. Regulation of heavy metal resistance in Eubacteria (poster)
• R. Nurtdinov, A. Neverov, D. Malko, I. Kosmodemiansky, A. Mironov. EDAS: EST-derived alternative splicing database (poster)
• O. Koborova, O. Kalinina, A. Rakhmaninova. Analysis of functional specificity of LacY proton/sugar symport family permeases (poster)
• S. Denisov, D. Klimov, M. Skoblov, S. Borinskaya, N. Yankovsky, A. Mironov. Is there correlation between the level of transcription and SNP density in the human genome? (poster)
• D. Rodionov, P. Hebbeln, M. Gelfand, and T. Eitinger. Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters (poster)
• N.S. Sadovskaya. Identification of transmembrane segments in Fad L and its orthologs using HMM-B2TMR (poster)
• I. Artamonova, G. Frishman, M.S. Gelfand and D. Frishman. Application of the association rules mining to the correction of annotation errors (talk)
• L. Danilova, D. Pervouchine, A. Favorov, A. Mironov. RNAKinetics: a web server that models secondary structure kinetics of an elongating RNA (poster)
M.Gelfand. Evolution of alternative splicing. Seminars at Berlex, Inc. (Richmond, CA, USA) and Fox Chase Cancer Center (Philadelphia, USA), June 2005
E.A.Kotelnikova. Evolution of DNA binding sites of bacterial transcription factors
(Ph.D. Thesis - mathematics/biophysics, Moscow State Univesity, Department of Physics), June 23, 2005
Meeting of HHMI International Research Scholars (Merida, Mexica June 2005)
• A.V.Gerasimova, A.E.Kazakov, E.A.Kotelnikova, G.Yu.Kovaleva, O.N.Laikova, A.A.Mironov, D.A.Ravcheev, D.A.Rodionov, M.S.Gelfand Functional annotation and metabolic reconstruction of bacterial genomes, and evolution of regulatory systems (poster)
D.Rodionov. Comparative genomic analysis of nickel and cobalt transport in bacteria. Seminar at Institute of Biology, Humboldt University (Berlin, Germany) May 2005.
Annual Meeting of the Italian Bioinformatics Society BITS-2005 (Milan, Italy, 2005, March)
• M.S. Gelfand. Comparative genomics (tutorial)
• M.S. Gelfand. Riboswitches: possibly the oldest regulatory system (invited talk)
• G. Kovaleva, G.Bazykin, M.Brudno, M.Gelfand. Conservation rate of transcription factor binding sites in Saccharomyces genomes (poster)
• E. Stavrovskaya, A.Mironov. Binary tree for clustering of regulatory signals (poster)
A. Gerasimova. Comparative genomics analysis of respiration switches in gamma-proteobacteria.
Seminar in NRC (National Institute for Medical Research) (Great Britain, London, 2005, January)
M.S. Gelfand. Riboswitches: the oldest regulatory system? Seminar in INRA (France, Paris, 2004, December)
International BCB Workshop on Gene Annotation Analysis & Alternative Splicing (Germany, Berlin, 2004, December)
• M.S. Gelfand. Evolution of alternative splicing
M.S. Gelfand. Evolution of bacterial regulatory systems.
Seminar in Institute of Bioinformatics GSF (Munich, 2004, October)
12th Int. Conf. on Intelligent Systems for Molecular Biology ISMB’2004 (Glasgow, Great Britain, 2004, August)
• O. Kalinina, P.S. Novichkov, A.A. Mironov, M.S. Gelfand, A.B. Rakhmaninova. SDPpred: a method for prediction of amino acid residues that determine differences in functional specificity of homologous proteins (poster)
• A. Gerasimova, D.A. Ravcheev, A.B. Rakhmaninova, M.S. Gelfand.
Computer analysis of aerobic-anaerobic regulation in gamma-proteobacteria (poster)
International Conference "Bioinformatics of Genome Structure and Regulation" BGRS’2004 (Novosibirsk, July, 2004)
• O. Kalinina., Novichkov P.S., Mironov A.A., Gelfand M.S., Rakhmaninova A.B. SDPPRED: A method for prediction of amino acid residues that determine differences in functional specificity of homologous proteins (talk)
• Gerasimova A.V., Ravcheyev D.A., Gelfand M.S., Rakhmaninova A.B. Complex analysis of respiration switch in gamma-proteobacteria (talk)
• M.S. Gelfand. Evolution of bacterial regulatory systems (report)
• Denisov S.V., Gelfand M.S. Conservation of alternative splicing regulatory signal UGCAUG in mouse and human genomes (poster)
• Favorov A.V., Gelfand,M.S., Gerasimova,A. V., Mironov,A.A., Makeev,V.J. Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length and its validation on the ArcA binding sites (talk)
• Kazakov A.E., Kalinina O.V., Permina E.A., Gelfand M.G Bacterial metal resistance systems regulated by transcription regulators of the MerR family (poster)
• E.D.Stavrovskaya, A.A.Mironov. Binary tree for clustering of regulatory signals (poster)
• I.A. Kosmodemiansky, M.S. Gelfand, A.A. Mironov. Classification of EST libraries by tissue specificity and cell origin (poster)
• Kovaleva G.Y., Mironov A.A., Gelfand M.S. The conservation of transcription factor-binding sites in Saccharomyces genomes (poster)
• M.S. Gelfand. EU-NIS Partnering in Bio-Informatics (invited talk at a special session)
8th Meeting of the European Calcium Society (Great Britain, Cambridge, 2004, July)
• A.B. Rakhmaninova, O.V. Kalinina, A.A. Minin. Discriminative sites in conserved core of diferent annexin subfamilies of vertebrates (poster)
Second International Conference "Genomics, Proteomics and Bioinformatics for Medicine" (Moscow, July, 2004)
• M.S. Gelfand. Comparative genomics of bacterial regulatory systems and its medical applications (invited talk)
Meeting of HHMI International Research Scholars (Estonia, Tallin, 2004, July)
• M.S. Gelfand, A.V. Gerasimova, A.E. Kazakov, E.A. Kotelnikova, O.N. Laikova, A.A. Mironov, E.A. Permina, D.A. Ravcheev, D.A. Rodionov, A.G. Vitreschak. Comparative genomics, metabolic reconstruction, and analysis of regulation in bacterial genomes (talk)