A5058866764- Advanced Numerical Methods in Computational Mathematics
- Differential Equations and Numerical Methods
- Advanced Mathematical Modeling in Engineering
- RNA and protein synthesis mechanisms
- Computational Fluid Dynamics and Aerodynamics
- RNA Research and Splicing
- Heat and Mass Transfer in Porous Media
- Genomics and Phylogenetic Studies
- Fluid Dynamics and Turbulent Flows
- Nanofluid Flow and Heat Transfer
- Lattice Boltzmann Simulation Studies
- RNA modifications and cancer
- Aquatic and Environmental Studies
- Machine Learning in Bioinformatics
- Gas Dynamics and Kinetic Theory
- Material Science and Thermodynamics
- Algorithms and Data Compression
- Freezing and Crystallization Processes
- Assisted Reproductive Technology and Twin Pregnancy
- Electrostatics and Colloid Interactions
- Differential Equations and Boundary Problems
- Evolution and Genetic Dynamics
- Reproductive Biology and Fertility
- Genetic diversity and population structure
- Nanopore and Nanochannel Transport Studies
Keldysh Institute of Applied Mathematics
1993-2023
Russian Academy of Sciences
1999-2019
Nuclear Safety Institute
2012-2019
University of Arizona
2013-2018
University of Nebraska–Lincoln
2014
New Mexico State University
2009-2013
Baylor College of Medicine
2012
Beijing Institute of Genomics
2012
Chinese Academy of Sciences
2012
University of Southampton
2011
Genetic nonself recognition systems such as vegetative incompatibility operate in many filamentous fungi to regulate hyphal fusion between genetically dissimilar individuals and restrict the spread of virulence-attenuating mycoviruses that have potential for biological control pathogenic fungi. We report here use a comparative genomics approach identify seven candidate polymorphic genes associated with four (vic) loci chestnut blight fungus Cryphonectria parasitica. Disruption alleles one...
Background The fat body is the main organ of intermediary metabolism in insects and principal source hemolymph proteins. As part our ongoing efforts to understand mosquito physiology identify novel targets for insect control, we have conducted a transcriptome analysis Aedes aegypti before response blood feeding. Results We created two non-normalized EST libraries, one from bodies non-blood fed (NBF) another mosquitoes 24 hrs post-blood meal (PBM). 454 pyrosequencing libraries resulted...
Convection-diffusion equations provide the basis for describing heat and mass transfer phenomena as well processes of continuum mechanics. To handle flows in porous media, fundamental issue is to model correctly convective transport individual phases. Moreover, compressible pressure equation itself just a time-dependent convection-diffusion equation. For different problems, may be written various forms. The most popular formulation employs divergent (conservative) form. In some cases,...
By comparing sequences of human, mouse and rat orthologous genes, we show that in 5′-untranslated regions (5′-UTRs) mammalian cDNAs but not 3′-UTRs or coding sequences, AUG is conserved to a significantly greater extent than any the other 63 nt triplets. This effect likely reflect, primarily, bona fide evolutionary conservation, rather cDNA annotation artifacts, because excess upstream AUGs (uAUGs) seen 5′-UTRs containing stop codons in-frame with start many are found different frames,...
Background Angiotensin-converting enzyme (ACE) (EC 4.15.1) metabolizes many biologically active peptides and plays a key role in blood pressure regulation vascular remodeling. Elevated ACE levels are associated with different cardiovascular respiratory diseases. Methods Results Two Belgian families 8-16-fold increase level were incidentally identified. A novel heterozygous splice site mutation of intron 25 - IVS25+1G>A (c.3691+1G>A) cosegregating elevated plasma was identified both...
The Baum-Welch learning procedure for Hidden Markov Models (HMMs) provides a powerful tool tailoring HMM topologies to data use in knowledge discovery and clustering. A linear memory recently proposed by Miklós, I. Meyer, I.M. describes sparse version of the algorithm with modifications original probabilistic table make independent sequence length (and linearly dependent on state number). description technique has some errors that we amend. We then compare corrected implementation variety...
GC 5' splice sites (5'ss) are present in ∼1% of human introns, but factors promoting their efficient selection poorly understood. Here, we describe a case X-linked agammaglobulinemia resulting from 5'ss activated by mutation BTK intron 3. This was intrinsically weak, yet it selected >90% primary transcripts the presence strong and intact natural GT counterpart. We show that this required high density GAA/CAA-containing splicing enhancers exonized segment promoted SR proteins 9G8, Tra2β SC35....
Abstract The GT dinucleotide in the first two intron positions is most conserved element of U2 donor splice signals. However, a small fraction sites, replaced by GC. A substantial enrichment GC sites alternatively spliced genes has been observed previously human, nematode and Arabidopsis, suggesting that signals are important for regulation alternative splicing. We used parsimony analysis to reconstruct evolution inferred 298 > conversion events compared 40 primate rodent genomes. Thus,...
Predicting and proper ranking of canonical splice sites (SSs) is a challenging problem in bioinformatics machine learning communities. Any progress SSs recognition will lead to better understanding splicing mechanism. We introduce several new approaches combining priori knowledge for improved SS detection. First, we design our Bayesian sensor based on oligonucleotide counting. To further enhance prediction quality, applied de novo motif detection tool MHMMotif intronic ends exons. combine...
Abstract Motivation: Microsatellites are among the most useful genetic markers in population biology. High-throughput sequencing of microsatellite-enriched libraries dramatically expedites traditional process screening recombinant for microsatellite markers. However, sorting through millions reads to distill high-quality polymorphic requires special algorithms tailored tolerate errors locus reconstruction, distinguish paralogous loci, rarify raw originating from same amplicon and sort out...
Background Bovine tuberculosis (bTB) is an enduring contagious disease of cattle that has caused substantial losses to the global livestock industry. Despite large-scale eradication efforts, bTB continues persist. Current tests rely on measurement immune responses in vivo (skin tests), and vitro (bovine interferon-γ release assay). Recent developments are characterized by interrogating expression increasing number genes participate response. Currently used assays have disadvantages limited...
Polymorphic variants and mutations disrupting canonical splicing isoforms are among the leading causes of human hereditary disorders. While there is a substantial evidence aberrant causing Mendelian diseases, implication such events in multi-genic disorders yet to be well understood. We have developed new tool (SpliceScan II) for predicting effects genetic on cis-regulatory elements. The novel Bayesian non-canonical 5'GC splice site (SS) sensor used our allows inference exons. Our performed...
Ionic current blockade signal processing, for use in nanopore detection, offers a promising new way to analyze single molecule properties, with potential implications DNA sequencing. The alpha-Hemolysin transmembrane channel interacts translocating nontrivial way, frequently evidenced by complex ionic flow pattern. Typically, recorded signals have several levels of blockade, various durations, all obeying fixed statistical profile given molecule. Hidden Markov Model (HMM) based duration...
Abstract New implicit finite difference schemes for solving the time‐dependent incompressible Navier‐Stokes equations using primitive variables and non‐staggered grids are presented in this paper. A priori estimates discrete solution of methods obtained. Employing operator approach, some requirements on operators scheme formulated order to derive a which is essentially consistent with initial differential equations. The inherit fundamental properties corresponding allows be estimate similar...
Ionic current blockade signal processing, for use in nanopore detection, offers a promising new way to analyze single molecule properties with potential implications DNA sequencing. The α-Hemolysin transmembrane channel interacts translocating nontrivial way, frequently evidenced by complex ionic flow pattern readily distinguishable modes of toggling. Effective processing such signals requires developing machine learning methods capable the various classification and knowledge discovery...