Genomes and Genes
Experts and Doctors on algorithms in Moscow, Russia
Locale: Moscow, Russia
- Lebedev D, Marshak D. Amacrine cell contributions to red-green color opponency in central primate retina: a model study. Vis Neurosci. 2007;24:535-47 pubmed..A key prediction is that GABA and glycine depolarize two of the four types of central midget ganglion cells; this may reflect lower levels of the potassium chloride co-transporter in their dendrites. ..
- Brazhe A, Mathiesen C, Lauritzen M. Multiscale vision model highlights spontaneous glial calcium waves recorded by 2-photon imaging in brain tissue. Neuroimage. 2013;68:192-202 pubmed publisher..Blood vessels uniquely reshaped GCWs and were associated with secondary GCW events. We conclude that the MVM provides unique possibilities to study spatiotemporally correlated Ca(2+) signaling in brain tissue. ..
- Sokolov V, Pohl P. Membrane transport of singlet oxygen monitored by dipole potential measurements. Biophys J. 2009;96:77-85 pubmed publisher..Consequently, the membrane cannot act as a barrier to (1)O(2) diffusion. Differences in the reaction rates at the cytoplasmic and extracellular membrane leaflets may be attributed only to (1)O(2) quenchers inside the membrane. ..
- Frenkel F, Korotkov E. Using triplet periodicity of nucleotide sequences for finding potential reading frame shifts in genes. DNA Res. 2009;16:105-14 pubmed publisher..We aimed to have revealed lower bound for the number of genes in which a shift between RF and TP is possible. Further ways to increase the number of revealed RF shifts are discussed. ..
- Borisov A, Vasil kov S. [Modeling of energy migration and trapping in purple bacteria. Analysis of extreme formulae]. Biofizika. 2002;47:283-94 pubmed
- Kondratovich A, Pokhilko A, Ataullakhanov F. Spatiotemporal dynamics of contact activation factors of blood coagulation. Biochim Biophys Acta. 2002;1569:86-104 pubmed..The maximum concentration of the active factors was estimated at 2 x 10(8) molecules per mm(2) at the glass surface (irrespective of stirring). At the plastic surface, this value was 15--30 times lower. ..
- Orlova N, Orlov A, Vorobiev I. A modular assembly cloning technique (aided by the BIOF software tool) for seamless and error-free assembly of long DNA fragments. BMC Res Notes. 2012;5:303 pubmed publisher..This approach may be used to generate long artificial DNA fragments such as in vitro spliced cDNAs. ..
- Polyansky A, Chugunov A, Volynsky P, Krylov N, Nolde D, Efremov R. PREDDIMER: a web server for prediction of transmembrane helical dimers. Bioinformatics. 2014;30:889-90 pubmed publisher..g. receptor tyrosine kinases. PREDDIMER can be accessed for free on the web at http://model.nmr.ru/preddimer/ firstname.lastname@example.org Supplementary data are available at Bioinformatics online. ..
- Oparina N, Kalinina O, Gelfand M, Kisselev L. Common and specific amino acid residues in the prokaryotic polypeptide release factors RF1 and RF2: possible functional implications. Nucleic Acids Res. 2005;33:5226-34 pubmed..Presumably, they also take part in stop codon binding and discrimination. Elucidation of potential functional role(s) of the newly identified SDP/IR zones requires further experiments. ..
- Nekrasov A, Zinchenko A. Structural features of the interfaces in enzyme-inhibitor complexes. J Biomol Struct Dyn. 2010;28:85-96 pubmed..ADD- sites possess an increased ability towards adaptive conformational changes thus enabling effective protein interaction. ..
- Yarygin K, Tyakht A, Larin A, Kostryukova E, Kolchenko S, Bitner V, et al. Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses. PLoS ONE. 2017;12:e0176154 pubmed publisher..Our approach offers a convenient method to add value to accumulated "shotgun" metagenomic data by helping researchers state and assess novel biological hypotheses. ..
- Korotkov E, Korotkova M, Frenkel F, Kudriashov N. [The informational concept of searching for periodicity in symbol sequences]. Mol Biol (Mosk). 2003;37:436-51 pubmed..Hidden periodicity has been detected in various genes, testifying to their quantum structure. The functional and structural role of hidden periodicity is discussed. ..
- Bezsonov E, Groenning M, Galzitskaya O, Gorkovskii A, Semisotnov G, Selyakh I, et al. Amyloidogenic peptides of yeast cell wall glucantransferase Bgl2p as a model for the investigation of its pH-dependent fibril formation. Prion. 2013;7:175-84 pubmed publisher..6. The results obtained allowed us to suggest a new simple approach for the isolation of Bgl2p from Saccharomyces cerevisiae cell wall. ..
- Bolotin D, Mamedov I, Britanova O, Zvyagin I, Shagin D, Ustyugova S, et al. Next generation sequencing for TCR repertoire profiling: platform-specific features and correction algorithms. Eur J Immunol. 2012;42:3073-83 pubmed publisher..Thus, this correction enhances the accuracy of clonotype identification and quantification as well as overall TCR diversity measurements. ..
- Lorenz M, Abdi N, Scheckenbach F, Pflug A, BÃ¼lbÃ¼l A, Catapano A, et al. Automatic identification of variables in epidemiological datasets using logic regression. BMC Med Inform Decis Mak. 2017;17:40 pubmed publisher..However, the performance of the algorithm is poor, which may require backup strategies. ..
- Novoseltsev V, Michalski A, Novoseltseva J, YASHIN A, Carey J, Ellis A. An age-structured extension to the vectorial capacity model. PLoS ONE. 2012;7:e39479 pubmed publisher..A limiting factor in the construction and evaluation of new age-dependent mortality models is the paucity of data characterizing vector mortality patterns, particularly for free ranging vectors in the field. ..
- Lapshina E, Volodin I, Volodina E, Frey R, Efremova K, Soldatova N. The ontogeny of acoustic individuality in the nasal calls of captive goitred gazelles, Gazella subgutturosa. Behav Processes. 2012;90:323-30 pubmed publisher..Our results suggest updating acoustic individuality in nasal calls of adolescent goitred gazelles accordingly to the newly emerged acoustic variation...
- Sutormin R, Rakhmaninova A, Gelfand M. BATMAS30: amino acid substitution matrix for alignment of bacterial transporters. Proteins. 2003;51:85-95 pubmed..g., the BLOSUM series) and one for TM-segments (the BATMAS series), and the choice of the TM-matrix should be different for eukaryotic and bacterial proteins...
- Kalinina O, Makeev V, Sutormin R, Gelfand M, Rakhmaninova A. The channel in transporters is formed by residues that are rare in transmembrane helices. In Silico Biol. 2003;3:197-204 pubmed..We applied this method to a variety of transmembrane proteins with resolved 3D structure. The predictions are in sufficiently good agreement with the real protein structure...
- Makeev V, Lifanov A, Nazina A, Papatsenko D. Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information. Nucleic Acids Res. 2003;31:6016-26 pubmed..We discuss the role of the hierarchy in understanding transcriptional regulation and in detection of transcription regulatory regions in genomes. ..
- Kulakovskiy I, Favorov A, Makeev V. Motif discovery and motif finding from genome-mapped DNase footprint data. Bioinformatics. 2009;25:2318-25 pubmed publisher..Also we discuss possible overfitting of constructed motifs. Software and the collection of regulatory motifs are freely available at http://line.imb.ac.ru/DMMPMM. ..
- Korotaevskiy A, Hanin L, Khanin M. Non-linear dynamics of the complement system activation. Math Biosci. 2009;222:127-43 pubmed publisher..Results obtained in this work serve as an important stepping stone for the study of functioning of the CS as a whole as well as for developing methods for control of pathogenic processes. ..
- Ogneva I, Lebedev D, Shenkman B. Transversal stiffness and Young's modulus of single fibers from rat soleus muscle probed by atomic force microscopy. Biophys J. 2010;98:418-24 pubmed publisher..The data may be useful for understanding mechanics of muscle fibers when it is subjected to both axial and transversal strain and stress. ..
- Krivandin A, Murugova T, Kuklin A, Muranov K, Poliansky N, Aksenov V, et al. Study of ?-crystallin structure by small angle neutron scattering with contrast variation. Biochemistry (Mosc). 2010;75:1324-30 pubmed
- Sinauridze E, Romanov A, Gribkova I, Kondakova O, Surov S, Gorbatenko A, et al. New synthetic thrombin inhibitors: molecular design and experimental verification. PLoS ONE. 2011;6:e19969 pubmed publisher..5 years at room temperature and at 4°C. The high efficacy, stability and low acute toxicity reveal that the inhibitors that were developed may be promising for potential medical applications. ..
- Ivliev A, t Hoen P, van Roon Mom W, Peters D, Sergeeva M. Exploring the transcriptome of ciliated cells using in silico dissection of human tissues. PLoS ONE. 2012;7:e35618 pubmed publisher..Taken together, our large-scale analysis of gene coexpression networks identifies novel genes related to human cell cilia...
- Ikryannikova L, Filimonova A, Malakhova M, Savinova T, Filimonova O, Ilina E, et al. Discrimination between Streptococcus pneumoniae and Streptococcus mitis based on sorting of their MALDI mass spectra. Clin Microbiol Infect. 2013;19:1066-71 pubmed publisher..Three peaks (6949, 9876 and 9975 m/z) were determined conferring the maximal statistical weight onto each model built. We find this approach to be promising for viridans streptococci discrimination. ..
- Kulakovskiy I, Levitsky V, Oshchepkov D, Bryzgalov L, Vorontsov I, Makeev V. From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites. J Bioinform Comput Biol. 2013;11:1340004 pubmed publisher..We demonstrate that diPWMs constructed by diChIPMunk outperform traditional PWMs constructed by ChIPMunk from the same ChIP-Seq data. Software website: http://autosome.ru/dichipmunk/ ..
- Zakharov A, Varlamova E, Lagunin A, Dmitriev A, Muratov E, Fourches D, et al. QSAR Modeling and Prediction of Drug-Drug Interactions. Mol Pharm. 2016;13:545-56 pubmed publisher..More than 4500 of these predicted DDIs that were not found in our training sets were confirmed by data from the DrugBank database. ..
- Nikulova A, Favorov A, Sutormin R, Makeev V, Mironov A. CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation. Nucleic Acids Res. 2012;40:e93 pubmed publisher..Compared with related methods, CORECLUST shows better performance at identification of CRMs conferring muscle-specific gene expression in vertebrates and early-developmental CRMs in Drosophila. ..
- Smirnov I, Thurner S. Formation of homophily in academic performance: Students change their friends rather than performance. PLoS ONE. 2017;12:e0183473 pubmed publisher..The lack of a social pull effect in classical educational settings could have important implications for the understanding of the observed persistence of segregation, inequality and social immobility in societies...
- Ivliev A, t Hoen P, Sergeeva M. Coexpression network analysis identifies transcriptional modules related to proastrocytic differentiation and sprouty signaling in glioma. Cancer Res. 2010;70:10060-70 pubmed publisher..In summary, this integrated analysis of the glioma transcriptome provided several novel insights into molecular heterogeneity and pathogenesis of glial tumors. ..
- Leontovich A, Tokmachev K, van Houwelingen H. The comparative analysis of statistics, based on the likelihood ratio criterion, in the automated annotation problem. BMC Bioinformatics. 2008;9:31 pubmed publisher..All these statistics are based on the likelihood ratio criterion. Some of the statistics yield a prediction quality that is significantly higher (up to 1.5 times higher) in comparison with the results obtained with the A4-procedure. ..
- Smirnov I, Carletti E, Kurkova I, Nachon F, Nicolet Y, Mitkevich V, et al. Reactibodies generated by kinetic selection couple chemical reactivity with favorable protein dynamics. Proc Natl Acad Sci U S A. 2011;108:15954-9 pubmed publisher..The organophosphate pesticide paraoxon is hydrolyzed by covalent catalysis with rate-limiting dephosphorylation. This reactibody is, therefore, a kinetically selected protein template that has enzyme-like catalytic attributes. ..
- Grishin D, Pokrovskaya M, Podobed O, Gladilina J, Pokrovsky V, Aleksandrova S, et al. [Prediction of protein thermostability from their primary structure: the current state and development factors]. Biomed Khim. 2017;63:124-131 pubmed publisher..Osoboe vnimanie udeleno prognosticheskomu potentsialu statisticheskikh metodov izucheniia termodinamicheskikh pokazatele? pervichno? struktury belka i otseneny ikh perspektivy. ..
- Shaytan A, Xiao H, Armeev G, Wu C, Landsman D, Panchenko A. Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning. Nucleic Acids Res. 2017;45:9229-9243 pubmed publisher..Our model provides the basis for further understanding the cooperative engagement and interplay between Cse4p protein and the A-tracts important for centromere function...