1,124 resources related to Phylogeny
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The conference program will consist of plenary lectures, symposia, workshops andinvitedsessions of the latest significant findings and developments in all the major fields ofbiomedical engineering.Submitted papers will be peer reviewed. Accepted high quality paperswill be presented in oral and postersessions, will appear in the Conference Proceedings and willbe indexed in PubMed/MEDLINE & IEEE Xplore
2019 IEEE International Symposium on Information Theory (ISIT)
Information theory and coding theory and their applications in communications and storage, data compression, wireless communications and networks, cryptography and security, information theory and statistics, detection and estimation, signal processing, big data analytics, pattern recognition and learning, compressive sensing and sparsity, complexity and computation theory, Shannon theory, quantum information and coding theory, emerging applications of information theory, information theory in biology.
Cluster Computing, Grid Computing, Edge Computing, Cloud Computing, Parallel Computing, Distributed Computing
This conference is a forum for researchers and designers to present and discuss various aspects of VLSI design, EDA, embedded systems, and enabling technologies. The program will consist of regular paper sessions, special sessions, embedded tutorials, panel discussions, design contest, industrial exhibits and tutorials. This is the premier conference/exhibition in this area in India, attracting designers, EDA professionals, and EDA tool users. The program committee for the conference has a significant representation from the EDA research community and a large fraction of the papers published in this conference are EDA-related
The scope includes theoretical advances, applications, and ideas in the fields of information sciences and systems including: Information Theory,Coding Theory, Image Processing, Communications, Signal Processing, Machine Learning, Statistical Inference,, Security and Privacy, Energy Systems, Networking, Systems and Control, Biological Systems
Specific topics of interest include, but are not limited to, sequence analysis, comparison and alignment methods; motif, gene and signal recognition; molecular evolution; phylogenetics and phylogenomics; determination or prediction of the structure of RNA and Protein in two and three dimensions; DNA twisting and folding; gene expression and gene regulatory networks; deduction of metabolic pathways; micro-array design and analysis; proteomics; ...
The IEEE Computational Intelligence Magazine (CIM) publishes peer-reviewed articles that present emerging novel discoveries, important insights, or tutorial surveys in all areas of computational intelligence design and applications.
Computer, the flagship publication of the IEEE Computer Society, publishes peer-reviewed technical content that covers all aspects of computer science, computer engineering, technology, and applications. Computer is a resource that practitioners, researchers, and managers can rely on to provide timely information about current research developments, trends, best practices, and changes in the profession.
Design and analysis of algorithms, computer systems, and digital networks; methods for specifying, measuring, and modeling the performance of computers and computer systems; design of computer components, such as arithmetic units, data storage devices, and interface devices; design of reliable and testable digital devices and systems; computer networks and distributed computer systems; new computer organizations and architectures; applications of VLSI ...
Physics, medicine, astronomy—these and other hard sciences share a common need for efficient algorithms, system software, and computer architecture to address large computational problems. And yet, useful advances in computational techniques that could benefit many researchers are rarely shared. To meet that need, Computing in Science & Engineering (CiSE) presents scientific and computational contributions in a clear and accessible format. ...
Seventh International Symposium on Signal Processing and Its Applications, 2003. Proceedings., 2003
Phenotyping cells and tracking their functional states are key tasks in cell biology and molecular medicine. Current cell classification methods are idiosyncratic to specific fields and based on ad hoc discovery of presumed univariate markers. We propose a general theory of phenotyping based on broadly distributed multivariate markers as the metrics of classification and standard pattern recognition algorithms as the ...
2018 1st International Conference on Bioinformatics, Biotechnology, and Biomedical Engineering - Bioinformatics and Biomedical Engineering, 2018
Melanocortin 4 receptor (MC4R) is a candidate gene for growth traits in the ruminant. The objective of this study to identify variation of the MC4R gene in cattle, buffalo, sheep, and goat. Genomic DNA of MC4R gene was obtained from Genbank in NCBI of 8 cattle, 2 buffaloes, 4 sheep, and 4 goats. We compare the partial genomic sequences from ...
1999 IEEE Pacific Rim Conference on Communications, Computers and Signal Processing (PACRIM 1999). Conference Proceedings (Cat. No.99CH36368), 1999
A molecular phylogenetic tree is a tree-structured graph that represents the evolutionary process of genes, and is constructed from sequence data (such as DNA sequences) obtained from several organisms. Although molecular phylogenetic trees are fundamental data structures in evolutionary analysis, no database system is available that can match trees in the database against a user-supplied tree by comparing tree structures. ...
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011
The haplotype inference problem (HIP) asks to find a set of haplotypes which resolve a given set of genotypes. This problem is important in practical fields such as the investigation of diseases or other types of genetic mutations. In order to find the haplotypes which are as close as possible to the real set of haplotypes that comprise the genotypes, ...
International Conference on Computational Intelligence and Multimedia Applications (ICCIMA 2007), 2007
For the construction of a phylogenetic network, it is essential to know if the new sequence that is being inserted is the result of mutations or due to events like recombinations. Recombination is a process of formation of new genetic sequences by piecing together segments of previously existing sequences . Once it is determined that it is a recombination process, ...
Phenotyping cells and tracking their functional states are key tasks in cell biology and molecular medicine. Current cell classification methods are idiosyncratic to specific fields and based on ad hoc discovery of presumed univariate markers. We propose a general theory of phenotyping based on broadly distributed multivariate markers as the metrics of classification and standard pattern recognition algorithms as the method of class discovery. We present a real-world test case based on the vertebrate retina and demonstrate that pattern recognition methods can extract singular populations of neurons from complex heterocellular arrays: populations visualized solely as elements in a micromolecular N-space. The applications of this computational approach to cell phenotyping range from phylogenetics to drug discovery to environmental monitoring.
Melanocortin 4 receptor (MC4R) is a candidate gene for growth traits in the ruminant. The objective of this study to identify variation of the MC4R gene in cattle, buffalo, sheep, and goat. Genomic DNA of MC4R gene was obtained from Genbank in NCBI of 8 cattle, 2 buffaloes, 4 sheep, and 4 goats. We compare the partial genomic sequences from Genbank in NCBI of cattle, buffalo, sheep, and goat MC4R genes using BioEdit and MUSCLE program to identify variation of MC4R in 4 species. To perform phylogenetic tree, all sequence were aligned firstly and the phylogenetic tree was performed using MEGA ver, 5.0 software. According to the results of data analysis, we found 110 variations of MC4R in 4 species. The variation includes 12 at 5'UTR, 72 located in exon and 26 found at 3'UTR. There were 19 SNPs in the exon region that change amino acids. The main result of phylogenetic tree indicated cattle have a close relationship to Buffalo. The results of this study are further evidence for the role of MC4R as a candidate gene in the ruminant.
A molecular phylogenetic tree is a tree-structured graph that represents the evolutionary process of genes, and is constructed from sequence data (such as DNA sequences) obtained from several organisms. Although molecular phylogenetic trees are fundamental data structures in evolutionary analysis, no database system is available that can match trees in the database against a user-supplied tree by comparing tree structures. In this paper, we propose a phylogenetic tree database system with a retrieval function that matches trees having similar structure. The tree data stored in the database are transformed from document images published in biological journals using a pattern- recognition program developed by us. To retrieve phylogenetic trees from the database according to their structures, we propose a method of determining the structural similarity between trees that is based on the split distance method. Our structural similarity measure shows high correlation with the log- likelihood difference that is widely used for comparing phylogenetic trees, and the computation time of our measure is much shorter than that of the log- likelihood difference, which relies on sequence comparison.
The haplotype inference problem (HIP) asks to find a set of haplotypes which resolve a given set of genotypes. This problem is important in practical fields such as the investigation of diseases or other types of genetic mutations. In order to find the haplotypes which are as close as possible to the real set of haplotypes that comprise the genotypes, two models have been suggested which are by now well-studied: The perfect phylogeny model and the pure parsimony model. All known algorithms up till now for haplotype inference may find haplotypes that are not necessarily plausible, i.e., very rare haplotypes or haplotypes that were never observed in the population. In order to overcome this disadvantage, we study in this paper, a new constrained version of HIP under the above-mentioned models. In this new version, a pool of plausible haplotypes H̃ is given together with the set of genotypes G, and the goal is to find a subset H ⊆ H̃ that resolves G. For constrained perfect phylogeny haplotyping (CPPH), we provide initial insights and polynomial-time algorithms for some restricted cases of the problem. For constrained parsimony haplotyping (CPH), we show that the problem is fixed parameter tractable when parameterized by the size of the solution set of haplotypes.
For the construction of a phylogenetic network, it is essential to know if the new sequence that is being inserted is the result of mutations or due to events like recombinations. Recombination is a process of formation of new genetic sequences by piecing together segments of previously existing sequences . Once it is determined that it is a recombination process, it is then necessary to determine the number of recombinations required for the generation of this sequence. This is because, in certain cases more than one recombination event are necessary. Here we propose an algorithm which determines the sequences already existing in the network that are likely to be responsible for the creation of the given sequence.
Nipah virus glycoprotein and nucleoprotein sequences were studied using fractal dimension and Shannon entropy. The nucleotide atomic number fluctuation forms the basis of the phylogeny study. The classification reproduces the main results of traditional phylogeny analysis, but with better ability to distinguish closely related strains. The fractal dimension correlation with the GC pair content in the glycoprotein sequence and di- nucleotide entropy in the nucleoprotein suggests different evolutionary mechanisms or strategies. Extension to other flu virus suggests that low fractal dimensionality in the nucleoprotein sequence could be a marker for the Nipah and Spanish-flu-like viruses.
A new distance measure called quadratic divergence distance is used to analyze characteristics between two genome sequences, based on the frequency matrices extracted from Chaos Game Representation (CGR). We generate phylogenetic trees with this distance through Hierarchical Clustering for several complete mitochondrial sequences. And compared with tree generated by CLUSTALW, our program expresses some particular features, which is of significant value of bioinformatics.
Azospirillum brasilense(A. brasilense) is considered to be important plant- growth promoting bacterium. In order to study its unknown genes, phylogenetic footprinting was performed on it and its five orthologous strains. Because of serial implementation by single computer, the efficiency is low. Research shows that the whole process consists of lots of repeated, data-independent operations, e.g. the extraction of textual information, the comparison of DNA sequences etc. Under LAN environment, a parallel way for implementing phylogenetic footprinting by multiple computers based on client/server mode was proposed. While making full use of resources, the efficiency is increased remarkably.
To elucidate the function of S-allele and the possible molecular mechanism of gametophytic self-incompatibility (GSI) in Chinese white pear (Pyrus bretschneideri Rehd.), full length cDNA encoding S<sub>20</sub>-RNase was cloned by rapid amplification of cDNA ends (RACE) approach from the cultivar 'Donghuang' (S<sub>8</sub>S<sub>20</sub>), and analyzed by bioinformatics method. S<sub>20</sub>-RNase displayed typical sequence features of pear S<sub>20</sub>-RNases, i.e. five conserved regions and a hypervariable (HV) region. The predicted three-dimension (3D) structure of the S<sub>20</sub>-RNase was similar to that of 53-RNase of Japanese pear (P. pyrifolia), indicating that the S<sub>20</sub>-RNase gene behaves as RNase rejecting pollen tube growth with the same S-haplotype as S<sub>3</sub>-RNase does in GSI response. At the amino acid level, S<sub>20</sub>-RNase showed 31.5% to 90.8% similarities with other rosaceous S-RNases. Phylogenetic analysis revealed that rosaceous S-RNases occurred before divergence of species, but after divergence of subfamilies Maloideae and Amygdaloideae.
Clustering algorithms are widely used in bioinformatics to classify data, as in the analysis of gene expression and in the building of phylogenetic trees. Biological data often describe parallel and spontaneous processes. To capture these features, we propose a new clustering algorithm that employs the concept of message passing. Message passing clustering (MPC) allows data objects to communicate with each other and produces clusters in parallel, thereby making the clustering process intrinsic. We have proved that MPC shares similarity with hierarchical clustering (HC) but offers significantly improved performance because it takes into account both local and global structure. We analyzed 35 sets of simulated dynamic gene expression data, achieving a 95% hit rate in which 639 genes out of total 674 genes were correctly clustered. We have also applied MPC to a real data set to build a phylogenetic tree from aligned mycobacterium sequences. The results show higher classification accuracies as compared to traditional clustering methods such as HC.
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