Author: Guanqun Shi
Publisher:
ISBN: 9781124940571
Category : Bioinformatics
Languages : en
Pages : 75
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Book Description
The accurate identification of orthologous genes across different species is a critical and challenging problem in comparative genomics and has a wide spectrum of biological applications including gene function inference, evolutionary studies and systems biology. During the past several years, many methods have been proposed for ortholog assignment based on sequence similarity, phylogenetic approaches, synteny information, and genome rearrangement. Although these methods share many commonly assigned orthologs, each method tends to produce an ortholog assignment significantly different from the others.
Author: Zheng Fu
Publisher:
ISBN:
Category : Gene mapping
Languages : en
Pages : 282
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Book Description
Author: Peter Markstein
Publisher: World Scientific
ISBN: 1860948731
Category : Computers
Languages : en
Pages : 472
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Book Description
This volume contains about 40 papers covering many of the latest developments in the fast-growing field of bioinformatics. The contributions span a wide range of topics, including computational genomics and genetics, protein function and computational proteomics, the transcriptome, structural bioinformatics, microarray data analysis, motif identification, biological pathways and systems, and biomedical applications. Abstracts from the keynote addresses and invited talks are also included. The papers not only cover theoretical aspects of bioinformatics but also delve into the application of new methods, with input from computation, engineering and biology disciplines. This multidisciplinary approach to bioinformatics gives these proceedings a unique viewpoint of the field. Sample Chapter(s). Chapter 1: Whole-Genome Analysis of Dorsal Gradient Thresholds in the Drosophila Embryo (102 KB). Contents: Learning Predictive Models of Gene Regulation (C Leslie); Algorithms for Selecting Breakpoint Locations to Optimize Diversity in Protein Engineering by Site-Directed Protein Recombination (W Zheng et al.); Cancer Molecular Pattern Discovery by Subspace Consensus Kernel Classification (X Han); Transcriptional Profiling of Definitive Endoderm Derived from Human Embryonic Stem Cells (H Liu et al.); A Markov Model Based Analysis of Stochastic Biochemical Systems (P Ghosh et al.); Clustering of Main Orthologs for Multiple Genomes (Z Fu & T Jiang); Extraction, Quantification and Visualization of Protein Pockets (X Zhang & C Bajaj); Consensus Contact Prediction by Linear Programming (X Gao et al.); An Active Visual Search Interface for Medline (W Xuan et al.); Exact and Heuristic Algorithms for Weighted Cluster Editing (S Rahmann et al.); Reconcilation with Non-binary Species Trees (B Vernot et al.); and other papers. Readership: Research and application community in bioinformatics, systems biology, medicine, pharmacology and biotechnology. Graduate researchers in bioinformatics and computational biology.
Author: Peter Markstein
Publisher: World Scientific
ISBN: 1908979097
Category : Science
Languages : en
Pages : 472
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Book Description
This volume contains about 40 papers covering many of the latest developments in the fast-growing field of bioinformatics. The contributions span a wide range of topics, including computational genomics and genetics, protein function and computational proteomics, the transcriptome, structural bioinformatics, microarray data analysis, motif identification, biological pathways and systems, and biomedical applications. Abstracts from the keynote addresses and invited talks are also included.The papers not only cover theoretical aspects of bioinformatics but also delve into the application of new methods, with input from computation, engineering and biology disciplines. This multidisciplinary approach to bioinformatics gives these proceedings a unique viewpoint of the field./a
Author: Matthew Daratha Whiteside
Publisher:
ISBN:
Category : Bioinformatics
Languages : en
Pages : 372
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Book Description
Orthologs are genes that diverged from an ancestral gene when the species diverged. High-throughput computational methods for ortholog prediction are a key component of many computational biology analyses. A fundamental premise in these analyses is that orthologs (when predicted correctly) are functionally equivalent and can be used to transfer gene annotations across species. Currently, many existing ortholog prediction methods generate a sizeable number of incorrect ortholog predictions, especially in cases of complex gene evolution. My thesis examines the functional equivalence hypothesis further and presents one solution that increases the precision of ortholog prediction. To examine the use of orthologs in computational analysis, I conducted and evaluated three projects that employ ortholog prediction in distinct ways. In these projects, orthologs were used to (1) identify conserved, unique genes in metazoan species, (2) validate predicted gene regulatory modules in Pseudomonas aeruginosa, and (3) construct a transcriptional regulatory network in Aspergillus fumigatus. I identified factors affecting ortholog prediction in these specific use cases, demonstrating how successive gene duplications, incomplete genomes and rapid evolution of gene regulation can impact the results for such analyses. To improve ortholog prediction, I evaluated and augmented an existing method called Ortholuge. Ortholuge is a computational method that increases the precision of ortholog prediction in a high-throughput setting. I evaluated the performance of Ortholuge, showing that its approach of classifying orthologs based on their relative phylogenetic divergence does identify orthologs that are more functionally equivalent. I compared Ortholuge to contemporary methods QuartetS and OMA, and showed that Ortholuge consistently identifies functionally-equivalent orthologs across a range of taxonomic distances. I also further developed Ortholuge's functionality by reducing run-time, increasing accuracy and improving usability through a number of modifications. Lastly, to make Ortholuge results available to the research community, I developed a database of Ortholuge ortholog predictions for bacteria and archaea species. This online database provides high-level visualization of orthologs and the ability to easily run complex queries to retrieve genes that are shared or unique between specified taxa. Overall, this work contributes an enhanced method for precise high-throughput ortholog identification and increases our understanding of the functional equivalences between orthologs.
Author: Rita Casadio
Publisher: Springer
ISBN: 3540318127
Category : Science
Languages : en
Pages : 446
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Book Description
We are pleased to present the proceedings of the 5th Workshop on Algorithms in Bioinformatics (WABI 2005) which took place in Mallorca, Spain, October 3–6, 2005.
Author: Alberto Apostolico
Publisher: Springer Science & Business Media
ISBN: 3540332952
Category : Computers
Languages : en
Pages : 631
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Book Description
This book constitutes the refereed proceedings of the 10th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2006, held in Venice, Italy in April 2006. The 40 revised full papers presented together with abstracts of 7 keynote talks were carefully reviewed and selected from 212 submissions. As the top conference in computational molecular biology, RECOMB addresses all current issues in algorithmic, theoretical, and experimental bioinformatics.
Author: Dillon Burgess
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
Identification of genes that show similarity between different organisms, a.k.a orthologous genes, is an open problem in computational biology. The purpose of this thesis is to create an algorithm to group orthologous genes using machine learning. Following an optimization step to find the best characterization based on training data, we represented sequences of genes or proteins with kmer vectors. These kmer vectors were then clustered into orthologous groups using hierarchical clustering. We optimized the clustering phase with the same training data for the method and parameter selection. Our results indicated that use of protein sequences with k=2 and scaling the data for each kmer provided the best results. We employed Pearson’s correlation as the distance metric and used complete linkage in the agglomeration step. The number of clusters are calculated based on four different approaches that evaluates optimum number of clusters. This algorithm was pitted against OrthoDB which is an orthologous gene grouping algorithm that has been proven to work well. The results show that when small datasets were used, our algorithm performed better than OrthoDB. When larger genome-level datasets were used, OrthoDB outperformed our algorithm as long as the input data to OrthoDB was divided based on organism count. Our algorithm has an advantage over OrthoDB in that the data doesn’t have to be divided by organism; it can be given as one file. The proposed algorithm runs much faster than OrthoDB and is the first approach, to the best of our knowledge, that uses unsupervised machine learning techniques that does not rely on sequence alignment or phylogeny to identify orthologues genes. Overall, our algorithm provides a novel solution that is fast, practical, and unlike existing approaches can be applied to data sets such as metagenomics where the underlying number of organisms is unknown.
Author: Russ Altman
Publisher: World Scientific
ISBN: 981277243X
Category : Biology
Languages : en
Pages : 526
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Book Description
The Pacific Symposium on Biocomputing (PSB) 2007 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2007 will be held January 3OCo7, 2007 at the Grand Wailea, Maui. Tutorials will be offered prior to the start of the conference. PSB 2007 will bring together top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology. The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputing''s OC hot topics.OCO In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field. Sample Chapter(s). Chapter 1: Protein Interactions and Disease (106 KB). Contents: Protein Interactions and Disease; Computational Approaches to Metabolomics; New Frontiers in Biomedical Text Mining; Biodiversity Informatics: Managing Knowledge Beyond Humans and Model Organisms; Computational Proteomics: High-Throughput Analysis for Systems Biology; DNA-Protein Interactions: Integrating Structure, Sequence, and Function. Readership: Academia and industry in the fields of biocomputing, bioinformatics and computational biology."
Author: Sing-Hoi Sze
Publisher:
ISBN:
Category :
Languages : en
Pages : 152
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Book Description
