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101. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/55.pdf
Why are genome regulatory regions AT-enriched? Alexander A. Osypov Laboratory of Cell Genome Functioning, Institute of Cell Biophysics of RAS, 142290, Pushchino MR, Russia, aosypov@gmail.com Genome DNA physical properties define its shape in the functional space and influence its interactions with proteins, esp. for transcription regulation. ... Binding frequency of RNA polymerase to DNA along the genome, measured in direct experiment, correlates to the calculated electrostatic potential. ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/55.pdf -- 101.0 Кб -- 15.06.2015
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102. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/58.pdf
A model of protein evolution within local fitness landscape changing with time D.R. Usmanova, F.A. Kondrashov Centre for Genomic Regulation, Barcelona, Spain, dinara.usmanova@crg.eu Each amino acid in protein interacts with others. Thus fitness contribution of specific amino acid in particular site depends on the whole genetic background. ... In more details we allow fitness contribution of specific amino acid in particular site switch from being acceptable to being deleterious and vice versa. ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/58.pdf -- 127.4 Кб -- 15.06.2015
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103. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/59.pdf
Prediction of cation binding sites using structural water L. A. Uroshlev, V. J. Makeev Vavilov Institute of General Genetics RAS, Engelhardt Institute of Molecular Biology RAS; leoniduroshlev@gmail.com Introduction Bivalent cations are well-known protein cofactors. ... The ion binding pockets are local, have specific structures, and thus can be recognized as structural motifs. ... Contribution of protein atoms of different types and structural water into pseudoenergy of binding for differ ion types. ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/59.pdf -- 93.6 Кб -- 15.06.2015
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104. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/53.pdf
Antisense interactions of long noncoding RNAs in human cells Ivan Antonov Research Centre for Medical Genetics, Moscow, Russia ivan.antonov@gatech.edu Mikhail Skoblov Research Centre for Medical Genetics, Moscow, Russia Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia mskoblov@generesearch.ru Long noncoding RNAs (lncRNAs) are a large and diverse class of transcribed RNA molecules with a length of more than 200 nucleotides that do not encode proteins. ... Mol Cell. ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/53.pdf -- 130.7 Кб -- 15.06.2015
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105. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/52.pdf
... Michael Y. Galperin , Eugene V. Koonin National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA, galperin @ncbi.nlm.nih.gov, koonin@ncbi.nlm.nih.gov Armen Y. Mulkidjanian School of Physics, University of OsnabrЭck, D-49069 OsnabrЭck, Germany; Faculty of Bioengineering and Bioinformatics, and A.N. Belozersky ... Life Evol. ... Deamer, D.W. (2008) Origins of life: how leaky were primitive cells, Nature, 454: 3738. ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/52.pdf -- 123.0 Кб -- 15.06.2015
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106. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/49.pdf
... The typical data processing workflow for protein identification and/or quantification in MSbased shotgun proteomics consists of a number of nontrivial procedures, including denoising and deisotoping of MS data, peptide identification using a protein database search, postsearch processing and validation, protein inference and quantification. ... Pyteomics includes parsers for common data formats used in MSbased proteomics, which can help bridging a gap between different formats. ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/49.pdf -- 212.3 Кб -- 15.06.2015
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107. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/51.pdf
Method to predict the percentage of cell types in human blood Anna Igolkina, Maria Samsonova St.Petersburg Polytechnical University, Polytechnicheskaya 29, igolkinaanna11@gmail.com Motivat ion and Aim: Blood is the most invest igated heterogeneous tissue. ... Gene expressio n data from blood genomics studies is widely used in medical diagnosis. ... Here we develop a method to predict the percentage of cell types in a blood sample fro m who le geno me gene expressio n data. ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/51.pdf -- 172.1 Кб -- 15.06.2015
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108. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/45.pdf
Modeling the role of positivel y charged moieties in hydrolysis of nucleoside triphosphates Daria N. Shalaeva School of Physics, University of OsnabrЭck, D-49069 OsnabrЭck, Germany; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University , 119991 Moscow , Russia; shalaevad@gmail.com Dmitry A. Cherepanov A.N. Frumkin Institute of Physical Chemistry and Electrochemistry of the RAS, ... D.V. Dibrova, E.V. Koonin, and M.Y. Galperin. ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/45.pdf -- 70.6 Кб -- 15.06.2015
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109. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/40.pdf
Selection pressure on breast cancer somatic mutations revealed by bioinformatics sequence analysis I.E. Vorontsov1, I.V. Kulakovskiy2,1, G.N. Khimulya1, D.D. Nikolaeva3, V.J. Makeev 1 2 3 4 1,2,4 Vavilov Institute of General Genetics, Gubkina str. 3, Moscow, Russia, ilya.vorontsov@vigg.ru Engelhardt Institute of Molecular Biology, Vavilova str. ... In particular, SNVs in promoters and enhancers may alter transcription factor (TF) DNA binding and thus affect efficiency of transcription initiation. ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/40.pdf -- 173.4 Кб -- 15.06.2015
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110. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/47.pdf
... Syktyvkar, 167001, Russia In typical biological assay performed in a high-throughput mode, either expression levels for individual genes or other quantifiable variables are assessed in parallel. ... In high dimensional space, the data become sparse. ... As a proof-of-principle, we showed that this approach produces surprisingly good results in separation of normal and affected samples both for analysis of human malignancies and for chronic progressive conditions like psoriasis [4]. ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/47.pdf -- 41.1 Кб -- 15.06.2015
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111. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/43.pdf
... ACSN has been initiated as a project focused on intracellular molecular interactions and signaling pathways involved in carcinogenesis. However, many important aspects of tumor behavior such as metastasis, immune response escape, stimulation of angiogenesis cannot be understood without considering the intercellular interactions of cancer cells with their microenviroment. ... We have represented both antiand pro-tumor aspects of immune response signaling of these cell types. ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/43.pdf -- 83.8 Кб -- 15.06.2015
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112. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/48.pdf
... Correlation graph showing connections between independent components computed for 22 datasets collecting tumor sample transcriptomes in various types of cancer (6671 tumor samp les are considered altogether in all datasets). ... We've made particular effort to understand the meaning of the components for one particular dataset for bladder cancer, produced at Institut Curie (CIT bladder cancer dataset, where CIT stands for Identitity Card of a Tumor in French) [3]. ... Cell Reports 9(4), 12351245. ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/48.pdf -- 623.7 Кб -- 15.06.2015
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113. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/46.pdf
l gene expression by RNA-seq data in brain structures of laboratory animals w ith aggressive and tolerant behavior Anato ly O. Bra gin, Nata ly N. K udr ya vt se va, Arcad y L. Mark e l, Yur iy L. Or lo v, In stitu te o f Cyto lo g y a nd Gen etics, La vren tyeva ... No vo sibirsk Sta te Un iversity, No vo sib irsk , Ru ssia , kylakovaekaterina@gmail.com , anastasia.spitsina@gmail.com Aggress ive be ha vio r is a co mp le x be ha ... There a re no ma jor ge ne s repor ted. ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/46.pdf -- 101.9 Кб -- 15.06.2015
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114. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/44.pdf
Sequence and structural analysis of related proteins in distant viral species Saskia Metzler, Silvia Caprari, Olga V. Kalinina Max Planck Institute for Informatics, Campus E1 4, 66123, SaarbrЭcken, Germany, kalinina@mpiinf.mpg.de Unlike cellular organisms, viruses do not constitute a monophyletic group, in which the phylogenetic history can be traced back to a common ancestor. The origin and relatedness of different virus families is currently a subject of active discussion. ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/44.pdf -- 93.1 Кб -- 15.06.2015
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115. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/42.pdf
Context analysis of SNP containing sites in mammalian genomes Nataly S. Safronova Novosibirsk State University, Novosibirsk, Russia, taschasafronova@mail.ru Irina Abnizova Welcome Trust Sanger ... Cytology and Genetics, Novosibirsk, Russia {bob,brukaro,orlov}@bionet.nsc.ru Due to technological breakthrough in the next-generation sequencing (NGS) technologies volume of available genomic ... Association of SNP position in human genome with mononucleotide repeats was shown earlier. ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/42.pdf -- 259.5 Кб -- 15.06.2015
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116. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/37.pdf
MetaFast : fast reference-free graph-based comparison of shotgun metagenomic data Sergey V. Kazakov1, Vladimir I. Ulyantsev1, Veronika B. Dubinkina2,3, Alexander V. Tyakht2, Dmitry G. Alexeev 1 2 3 2 ,3 ITMO University ... (State Un iversity), Dolgoprudny, Russia Since the emergence of high-throughput genomic sequencing technologies, a huge volume of data has been accumulated describing complex microbial communities ( microbiota ) ... Example of MetaFast output on a set of real data. ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/37.pdf -- 361.7 Кб -- 15.06.2015
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117. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/35.pdf
Computer tool for gene expression data processing and correlation analysis Anastasia M. Spitsina, Novosibirsk State University, 630090, Novosibirks, 2 Pirogova Str. , anastasia.spitsina@gmail.com Natalya ... databases (BioGPS (http://biogps.org/), GEO NCBI (http://www.ncbi.nlm.nih.gov/geo/)) has accumulated a large body of experimental data obtained using DNA microarrays ... So the aim of this work was to develop and improve own program for data processing and analysis of gene expression. ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/35.pdf -- 162.0 Кб -- 15.06.2015
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118. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/33.pdf
Detection of short size mutations and copy number alterations in ultra-deep targeted sequencing data Valentina Boeva, Emmanuel Barillot, Institut Curie, valentina.boeva@curie.fr Jean-Francois Laes OncoDNA, jf.laes@oncodna.com The emergence of the amplicon sequencing technique, which followed whole exome sequencing, promises a revolution in cancer diagnostics and treatment. ... Visualization of the typical configuration of read mappings (with Integrative Genomics Viewer). ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/33.pdf -- 200.9 Кб -- 15.06.2015
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119. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/34.pdf
Determination of the size of folding nuclei of protofibrils from the concentration dependence of the rate and lag-time of their formation Oxana V. Galzitskaya, Nikita V. Dovidchenko, Olga M. Selivanova, Maria Yu. ... For insulin and LysPro insulin we have Lrel 2-3, which means that it is definitely an exponential growth scenario. One can roughly define three types of possible mechanisms of exponential growth: growth from the surface, bifurcation, and fragmentation. ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/34.pdf -- 166.4 Кб -- 15.06.2015
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120. http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/39.pdf
Search for simple and composite auxin responsive elements in Arabidopsis thaliana genome. ... AR Fs bind in target promoters to the specific sites called AuxRE s (Auxin Response Elements) with the TGTCN N (most frequently TGTCTC) consensus core sequence. ... To test which model predicts AuxREs associated with auxin response better , we performed meta-analysis of publicly available 23 microarray experiments with auxin treatments (Mironova et al., ...
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Ссылки http://mccmb.belozersky.msu.ru/2015/proceedings/abstracts/39.pdf -- 110.9 Кб -- 15.06.2015
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