Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Systems Biology: Comprehensive, methodical analysis of complex biological systems by monitoring responses to perturbations of biological processes. Large scale, computerized collection and analysis of the data are used to develop and test models of biological systems.Sociology: A social science dealing with group relationships, patterns of collective behavior, and social organization.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Physiological Phenomena: The functions and properties of living organisms, including both the physical and chemical factors and processes, supporting life in single- or multi-cell organisms from their origin through the progression of life.Sequence Analysis, Protein: A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Programming Languages: Specific languages used to prepare computer programs.Biology: One of the BIOLOGICAL SCIENCE DISCIPLINES concerned with the origin, structure, development, growth, function, genetics, and reproduction of animals, plants, and microorganisms.Artificial Intelligence: Theory and development of COMPUTER SYSTEMS which perform tasks that normally require human intelligence. Such tasks may include speech recognition, LEARNING; VISUAL PERCEPTION; MATHEMATICAL COMPUTING; reasoning, PROBLEM SOLVING, DECISION-MAKING, and translation of language.Databases, Factual: Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Systems Integration: The procedures involved in combining separately developed modules, components, or subsystems so that they work together as a complete system. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Pattern Recognition, Automated: In INFORMATION RETRIEVAL, machine-sensing or identification of visible patterns (shapes, forms, and configurations). (Harrod's Librarians' Glossary, 7th ed)Markov Chains: A stochastic process such that the conditional probability distribution for a state at any future instant, given the present state, is unaffected by any additional knowledge of the past history of the system.Databases, Protein: Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.Protein Interaction Mapping: Methods for determining interaction between PROTEINS.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Computer Graphics: The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.Models, Statistical: Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Information Storage and Retrieval: Organized activities related to the storage, location, search, and retrieval of information.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Gene Regulatory Networks: Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Proteome: The protein complement of an organism coded for by its genome.Bayes Theorem: A theorem in probability theory named for Thomas Bayes (1702-1761). In epidemiology, it is used to obtain the probability of disease in a group of people with some characteristic on the basis of the overall rate of that disease and of the likelihood of that characteristic in healthy and diseased individuals. The most familiar application is in clinical decision analysis where it is used for estimating the probability of a particular diagnosis given the appearance of some symptoms or test result.Molecular Biology: A discipline concerned with studying biological phenomena in terms of the chemical and physical interactions of molecules.Developmental Biology: The field of biology which deals with the process of the growth and differentiation of an organism.Models, Theoretical: Theoretical representations that simulate the behavior or activity of systems, processes, or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Synthetic Biology: A field of biological research combining engineering in the formulation, design, and building (synthesis) of novel biological structures, functions, and systems.Protein Conformation: The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Protein Folding: Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.Reproducibility of Results: The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.Signal Transduction: The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.

Ringo, Doty, Demeter and Simard, Cerebral Cortex 1994;4:331-343: a proof of the need for the spatial clustering of interneuronal connections to enhance cortical computation. (1/20328)

It has been argued that an important principle driving the organization of the cerebral cortex towards local processing has been the need to decrease time lost to interneuronal conduction delay. In this paper, I show for a simplified model of the cerebral cortex, using analytical means, that if interneuronal conduction time increases proportional to interneuronal distance, then the only way to increase the numbers of synaptic events occurring in a fixed finite time period is to spatially cluster interneuronal connections.  (+info)

The Genexpress IMAGE knowledge base of the human brain transcriptome: a prototype integrated resource for functional and computational genomics. (2/20328)

Expression profiles of 5058 human gene transcripts represented by an array of 7451 clones from the first IMAGE Consortium cDNA library from infant brain have been collected by semiquantitative hybridization of the array with complex probes derived by reverse transcription of mRNA from brain and five other human tissues. Twenty-one percent of the clones corresponded to transcripts that could be classified in general categories of low, moderate, or high abundance. These expression profiles were integrated with cDNA clone and sequence clustering and gene mapping information from an upgraded version of the Genexpress Index. For seven gene transcripts found to be transcribed preferentially or specifically in brain, the expression profiles were confirmed by Northern blot analyses of mRNA from eight adult and four fetal tissues, and 15 distinct regions of brain. In four instances, further documentation of the sites of expression was obtained by in situ hybridization of rat-brain tissue sections. A systematic effort was undertaken to further integrate available cytogenetic, genetic, physical, and genic map informations through radiation-hybrid mapping to provide a unique validated map location for each of these genes in relation to the disease map. The resulting Genexpress IMAGE Knowledge Base is illustrated by five examples presented in the printed article with additional data available on a dedicated Web site at the address http://idefix.upr420.vjf.cnrs.fr/EXPR++ +/ welcome.html.  (+info)

Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae. (3/20328)

Introns have typically been discovered in an ad hoc fashion: introns are found as a gene is characterized for other reasons. As complete eukaryotic genome sequences become available, better methods for predicting RNA processing signals in raw sequence will be necessary in order to discover genes and predict their expression. Here we present a catalog of 228 yeast introns, arrived at through a combination of bioinformatic and molecular analysis. Introns annotated in the Saccharomyces Genome Database (SGD) were evaluated, questionable introns were removed after failing a test for splicing in vivo, and known introns absent from the SGD annotation were added. A novel branchpoint sequence, AAUUAAC, was identified within an annotated intron that lacks a six-of-seven match to the highly conserved branchpoint consensus UACUAAC. Analysis of the database corroborates many conclusions about pre-mRNA substrate requirements for splicing derived from experimental studies, but indicates that splicing in yeast may not be as rigidly determined by splice-site conservation as had previously been thought. Using this database and a molecular technique that directly displays the lariat intron products of spliced transcripts (intron display), we suggest that the current set of 228 introns is still not complete, and that additional intron-containing genes remain to be discovered in yeast. The database can be accessed at http://www.cse.ucsc.edu/research/compbi o/yeast_introns.html.  (+info)

Bayesian inference on biopolymer models. (4/20328)

MOTIVATION: Most existing bioinformatics methods are limited to making point estimates of one variable, e.g. the optimal alignment, with fixed input values for all other variables, e.g. gap penalties and scoring matrices. While the requirement to specify parameters remains one of the more vexing issues in bioinformatics, it is a reflection of a larger issue: the need to broaden the view on statistical inference in bioinformatics. RESULTS: The assignment of probabilities for all possible values of all unknown variables in a problem in the form of a posterior distribution is the goal of Bayesian inference. Here we show how this goal can be achieved for most bioinformatics methods that use dynamic programming. Specifically, a tutorial style description of a Bayesian inference procedure for segmentation of a sequence based on the heterogeneity in its composition is given. In addition, full Bayesian inference algorithms for sequence alignment are described. AVAILABILITY: Software and a set of transparencies for a tutorial describing these ideas are available at http://www.wadsworth.org/res&res/bioinfo/  (+info)

DNA sequence chromatogram browsing using JAVA and CORBA. (5/20328)

DNA sequence chromatograms (traces) are the primary data source for all large-scale genomic and expressed sequence tags (ESTs) sequencing projects. Access to the sequencing trace assists many later analyses, for example contig assembly and polymorphism detection, but obtaining and using traces is problematic. Traces are not collected and published centrally, they are much larger than the base calls derived from them, and viewing them requires the interactivity of a local graphical client with local data. To provide efficient global access to DNA traces, we developed a client/server system based on flexible Java components integrated into other applications including an applet for use in a WWW browser and a stand-alone trace viewer. Client/server interaction is facilitated by CORBA middleware which provides a well-defined interface, a naming service, and location independence. [The software is packaged as a Jar file available from the following URL: http://www.ebi.ac.uk/jparsons. Links to working examples of the trace viewers can be found at http://corba.ebi.ac.uk/EST. All the Washington University mouse EST traces are available for browsing at the same URL.]  (+info)

Detecting selective expression of genes and proteins. (6/20328)

Selective expression of a gene product (mRNA or protein) is a pattern in which the expression is markedly high, or markedly low, in one particular tissue compared with its level in other tissues or sources. We present a computational method for the identification of such patterns. The method combines assessments of the reliability of expression quantitation with a statistical test of expression distribution patterns. The method is applicable to small studies or to data mining of abundance data from expression databases, whether mRNA or protein. Though the method was developed originally for gene-expression analyses, the computational method is, in fact, rather general. It is well suited for the identification of exceptional values in many sorts of intensity data, even noisy data, for which assessments of confidences in the sources of the intensities are available. Moreover, the method is indifferent as to whether the intensities are experimentally or computationally derived. We show details of the general method and examples of computational results on gene abundance data.  (+info)

Protein subcellular location prediction. (7/20328)

The function of a protein is closely correlated with its subcellular location. With the rapid increase in new protein sequences entering into data banks, we are confronted with a challenge: is it possible to utilize a bioinformatic approach to help expedite the determination of protein subcellular locations? To explore this problem, proteins were classified, according to their subcellular locations, into the following 12 groups: (1) chloroplast, (2) cytoplasm, (3) cytoskeleton, (4) endoplasmic reticulum, (5) extracell, (6) Golgi apparatus, (7) lysosome, (8) mitochondria, (9) nucleus, (10) peroxisome, (11) plasma membrane and (12) vacuole. Based on the classification scheme that has covered almost all the organelles and subcellular compartments in an animal or plant cell, a covariant discriminant algorithm was proposed to predict the subcellular location of a query protein according to its amino acid composition. Results obtained through self-consistency, jackknife and independent dataset tests indicated that the rates of correct prediction by the current algorithm are significantly higher than those by the existing methods. It is anticipated that the classification scheme and concept and also the prediction algorithm can expedite the functionality determination of new proteins, which can also be of use in the prioritization of genes and proteins identified by genomic efforts as potential molecular targets for drug design.  (+info)

A two-dimensional model of brightness perception based on spatial filtering consistent with retinal processing. (8/20328)

We have applied a multiple scale, 2-D model of brightness perception to a broad range of brightness phenomena. The filters encapsulate only processing that is well established to occur in retinal ganglion cells. Their outputs are then combined in the simplest way compatible with the earliest levels of cortical processing. Not only essential features of a number of the phenomena but also more subtle shading effects are reproduced. Because of the retinal nature of this model, these results would appear to support previous speculation that much of the ground work for brightness perception is performed at the retinal level.  (+info)

Title: A Research on Bioinformatics Prediction of Protein Subcellular Localization. VOLUME: 4 ISSUE: 3. Author(s):Gang Fang, Guirong Tao and Shemin Zhang. Affiliation:Department of Life Science, Xian University of Arts and Science, Xian 710065, China.. Keywords:Bioinformatics, prediction, protein subcellular localization, localizome, proteomics, database. Abstract: Protein subcellular localization is one of the key characteristic to understand its biological function. Proteins are transported to specific organelles and suborganelles after they are synthesized. They take part in cell activity and function efficiently when correctly localized. Inaccurate subcellular localization will have great impact on cellular function. Prediction of protein subcellular localization is one of the important areas in protein function research. Now it becomes the hot issue in bioinformatics. In this review paper, the recent progress on bioinformatics research of protein subcellular localization and its prospect ...
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... (JIB) is an international open access journal publishing original peer-reviewed research articles in all aspects of integrative bioinformatics. Molecular biology produces huge amounts of data in the post-genomic era. This includes data describing metabolic mechanisms and pathways, structural genomic organization, patterns of regulatory regions; proteomics, transcriptomics, and metabolomics. On the one hand, analysis of this data uses essentially the methods and concepts of computer science; on the other hand, the range of biological tasks solved by researchers determines the range and scope of the data. Currently, there are about 1,000 database systems and various analytical tools available via the Internet which are directed at solving various biological tasks. The challenge we have is to integrate these list-parts and relationships from genomics and proteomics at novel levels of understanding. Integrative Bioinformatics is a new area of research using the ...
The 7th International Conference on Bioinformatics and Computational Biology (BICoB) provides an excellent venue for researchers and practitioners in the fields of bioinformatics to present and publish their research results and techniques. Bioinformatics and computational biology continue to be a vibrant research area with broadening applications and new emerging challenges. In recent years, bioinformatics and computational biology have experience significant advances driven by computational techniques in bioinformatics. The BICoB conference seeks original and high quality papers in the fields of bioinformatics, computational biology, systems biology, medical informatics and the related areas. Work in the computational methods related to, or with application in, bioinformatics is also encouraged including: bio-data mining, text mining, machine learning, biomathematics, modeling and simulation, pattern recognition, data visualization, biostatistics, .etc. The topics of interest include (and are ...
Biological network alignment aims to find regions of topological and functional (dis)similarities between molecular networks of different species. Then, network alignment can guide the transfer of biological knowledge from well-studied model species to less well-studied species between conserved (aligned) network regions, thus complementing valuable insights that have already been provided by genomic sequence alignment. Here, we review computational challenges behind the network alignment problem, existing approaches for solving the problem, ways of evaluating their alignment quality, and the approaches biomedical applications. We discuss recent innovative efforts of improving the existing view of network alignment. We conclude with open research questions in comparative biological network research that could further our understanding of principles of life, evolution, disease, and therapeutics.
Learn the data skills necessary for turning large sequencing datasets into reproducible and robust biological findings. With this practical guide, youll learn how to use freely available open source tools to extract meaning from large complex biological data sets. At no other point in human history has our ability to understand lifes complexities been so dependent on our skills to work with and analyze data. This intermediate-level book teaches the general computational and data skills you need to analyze biological data. If you have experience with a scripting language like Python, youre ready to get started. Go from handling small problems with messy scripts to tackling large problems with clever methods and tools Process bioinformatics data with powerful Unix pipelines and data tools Learn how to use exploratory data analysis techniques in the R language Use efficient methods to work with genomic range data and range operations Work with common genomics data file formats like FASTA, FASTQ, ...
We may wonder that as a biologist why should we learn algorithms, which are intended for computer science. The answer is straightforward. The convergence of Biology and computer science is called as BIOINFORMATICS. To be a real Biologist we have to acquire skills in Biology as well as in computer science. Biological skills include Cell life cycle, double helix structure of DNA, Transcription, and Translation and down the line. In Computer Science, we should learn about how to write efficient computer program for solving BioInformatics problems. In this point I like to remember that one of the man (Crick) who finds the DNA double Helix structure is not a Biologist but he is a physicist. ...
Citation Machine™ helps students and professionals properly credit the information that they use. Cite your letter in EURASIP Journal on Bioinformatics and Systems Biology format for free.
Citation Machine™ helps students and professionals properly credit the information that they use. Cite your photograph in EURASIP Journal on Bioinformatics and Systems Biology format for free.
Andreas Beyer, Michael Schroeder (Eds.): Proceedings of the German Conference on Bioinformatics, GCB 2008, September 9-12, 2008, Dresden, Germany. LNI 136 GI 2008 ...
We supply infrastructure and expertise for the bioinformatics and scientific IT needs of researchers, providing hardware and software for research-oriented tasks. We have various web-based interactive tools at our disposal, e.g. a local copy of the UCSC (University of California, Santa Cruz) Genome Browser, Shiny Server for interactive analysis, and an internal Galaxy server. We also have access to bioinformatics software solutions such as methylKit, genomation, RCAS, netSmooth, and a GNU Guix bioinformatics software repository.. We provide additional specialized IT services geared towards bioinformatics end users as well as a mobile teaching system for scientists. In addition, we offer courses and consultation sessions on bioinformatics, IT skills, and programming.. We provide additional specialized IT services geared towards bioinformatics end- users as well as a mobile teaching system for scientists. In addition, we offer courses and consultation sessions on bioinformatics, IT skills, and ...
DISCRETE APPLIED MATHEMATICS CALL FOR PAPERS FOR THE COMPUTATIONAL MOLECULAR BIOLOGY SERIES We are happy to announce that our collection of Special Issues on Computational Molecular Biology has become the ,,Computational Molecular Biology Series,,, an ongoing regular feature of Discrete Applied Mathemtaics. Series Editors: Sorin Istrail, Pavel Pevzner, Ron Shamir Submission Deadline for the next volume: August 1, 1998 Dont ask [only] what mathematics can do for biology, ask what biology can do for mathematics. Stanislaw Ulam Manuscripts are solicited for a volume of Discrete Applied Mathematics on topics concerning the development of new combinatorial and algorithmic techniques in computational molecular biology. This volume will be the third in the Computational Molecular Biology Series of Discrete Applied Mathematics, which publishes papers on the mathematical and algorithmic foundations of the inherently discrete aspects of computational biology. The refereeing of the papers in this ...
Genomics-based drug discovery utilizing sequencing data for elucidation of candidate targets has led to the development of a number of successful treatments in the last decades. However, the molecular driver signals for many complex diseases cannot be easily derived from genome sequencing. Functional profiling studies, such as those involving the detection of protein interaction networks or the effects of perturbations with small molecules or siRNAs on cellular phenotypes, offer a complementary approach for the identification of molecular vulnerabilities that can be exploited in the development of new treatment strategies. The goal of this thesis was to develop computational systems biology methods for supporting such functional endeavors, and through their application use cases, to elucidate novel disease driver signals in cancer and Alzheimers disease networks. The availability of functional profiling data (such as biochemical target selectivity information or efficacy readouts) for numerous ...
A brief Biography: Dr Andrey Kajava holds a position of Director of Research at the Centre National de la Recherche Scientifique (CNRS) in France. He is a head of Structural Bioinformatics and Molecular Modeling group at the Centre de Recherche de Biochimie Macromoléculaire (Montpellier, France). In the past, he conducted research in several prestigious laboratories in Russia, Germany, Belgium, Switzerland and United States. His group is using methods of theoretical structural biology and bioinformatics to understand principles of protein structures and biomolecular interactions. The obtained knowledge is applied for prediction of protein structures and functions, drug design, as well as for de novo design of proteins. Topics of our particular interest are: proteins with tandem repeats, amyloids and prions. The results of his work can be applied in materials science, biotechnology, nanotechnology and medicine.. ...
Only a small fraction of known proteins have been functionally characterized, making protein function prediction essential to propose annotations for uncharacterized proteins. In recent years many function prediction methods have been developed using various sources of biological data from protein sequence and structure to gene expression data. Here we present the CombFunc web server, which makes Gene Ontology (GO)-based protein function predictions. CombFunc incorporates ConFunc, our existing function prediction method, with other approaches for function prediction that use protein sequence, gene expression and protein-protein interaction data. In benchmarking on a set of 1686 proteins CombFunc obtains precision and recall of 0.71 and 0.64 respectively for gene ontology molecular function terms. For biological process GO terms precision of 0.74 and recall of 0.41 is obtained. ...
With your expertise in computational biology, you contribute input to experimental design, quality control, basic and downstream analysis of single cell RNA-Seq data. You generate results from computational biology analysis such as single cell RNA-Seq related algorithms, pathway analysis, biomarker analyses, gene prioritization, etc. Moreover, you keep track of relevant literature and integrate publicly available relevant datasets that can enhance the interpretation of the results. Participating in the publication of results in peer-reviewed journals and at scientific congresses is also your task. You are also responsible for interfacing with collaborators in the ICL and BI experimental groups as well as the ICL and BI computational biology groups.
Genomics, Bioinformatics and Computational Biology: we do genomics and bioinformatics data analysis on genome sequences. And we developped a novel computational algorithms, Codon and Amino acid Unified Sequence Alignment (CAUSA), and a set of user-friendly computer programs for molecular evolutionary analysis, which revealled some novel mechanisms for molecular evolution, such as codon splitting, codon fusion and InDel-induced partial frameshifting ...
Bioinformatics community open to all people. Strong emphasis on open access to biological information as well as Free and Open Source software.
Chemoresistance is a major limitation for breast cancer therapy. In the present study, bioinformatics analyses were performed to investigate microRNA (miRNA)-mediated mechanism of breast cancer chemoresistance and to identify molecular targets. In the present study, we identified 22 DE-miRNAs in chemoresistant breast cancer and chemosensitive tissues based on the GEO database GSE71142. Then, by the target gene software of miRWalk2.0, we identified the potential target genes of these chemoresistance-related miRNAs. The enrichment and function analyses showed that these target genes may participate in many important cancer-related biological processes, molecular functions and signaling pathways.. Among the dysregulated miRNAs, miR-196a-5p (upregulation) and miR-4472 (downregulation) were found to have the greatest expression fold change between chemoresistant and chemosensitive tissues. miR-196a-5p has been previously reported to be overexpressed in triple-negative breast cancer compared with ...
Computational Biology & Bioinformatics Team: Currently 2 senior research scientists (Joohyun Kim and Nayong Kim) focused on assisting bioinformatics and broader computational biology efforts, especially in connection with LBRN = Louisiana Biomedical Research Network. CCT search underway to hire a "Senior Bioinformatics Computational Scientist" Software tools. ...
The Fulbright Program in Ukraine is pleased to invite you to a seminar "Total Synthesis of Natural Products as a Driving Force for Chemical and Biological Discovery" by Fulbright Ph.D. student 2011-2016 Nataliia Shymanska, to be held on Tuesday, December 1, 2015, 6:00 p.m., at the Fulbright Office (20 Esplanadna Street, Suite 904, M "Palats Sportu", Kyiv).. Total Synthesis of Natural Products as a Driving Force for Chemical and Biological Discovery. Untreatable infections, a result of multi-drug resistance of pathogenic bacteria (Enterococcus spp., Staphylococcus aureus, Pseudomonas aeruginosa etc.) to antibiotics, continue to be a major threat to public health and modern medicine.. The numbers are alarming: out of 400,000 instances of infections caused by resistant pathogens 25,000 were lethal (Europe, 2007); 54% of isolated bacterial strains of Staphylococcus Aureus from Ukrainian hospitals in 2010 were resistant to antimicrobial treatments.. Despite the world-wide pressing clinical need, the ...
The target audience is upper-year undergraduate students in the biological sciences, or biology graduate students who are just beginning their studies and need a refresher on some of the topics mentioned above. Computer scientists who are interested in biology might also find this course useful - the biology isnt too complex.. After finishing Bioinformatic Methods II, students will be familiar with databases and tools for exploring patterns in proteins and promoters, analyzing protein-protein interaction networks as well as protein tertiary structures, and using gene expression databases to make hypotheses. Bioinformatic Methods I provides further practical approaches for sequence analysis.. Do you teach the same course to students on campus? If so, in what ways does the MOOC version differ from on-campus version ...
Immunoinformatics involves the application of computational methods to immunological problems. Prediction of B- and T-cell epitopes has long been the focus of immunoinformatics, given the potential translational implications, and many tools have been developed. With the advent of next-generation sequencing (NGS) methods, an unprecedented wealth of information has become available that requires more-advanced immunoinformatics tools. Based on information from whole-genome sequencing, exome sequencing and RNA sequencing, it is possible to characterize with high accuracy an individual’s human leukocyte antigen (HLA) allotype (i.e., the individual set of HLA alleles of the patient), as well as changes arising in the HLA ligandome (the collection of peptides presented by the HLA) owing to genomic variation. This has allowed new opportunities for translational applications of epitope prediction, such as epitope-based design of prophylactic and therapeutic vaccines, and personalized cancer immunotherapies
Graduate Group in Bioinformatics seeks a second renewal of its training program in Bioinformatics and Computational Biology. The program focuses on training you...
Focuses on bioinformatics and its importance in the sciences. Seeks to apply and understand bioinformatics tools as they pertain to analyses of genomes, protein structure/function, gene families, and molecular evolution. Uses bioinformatics tools to mine databases for information relevant to answering questions relating to molecular structure, function, and evolution. Analyzes relationships between known protein structure and model protein structures. Illustrates how multiple alignments and database searching are used to gather data about gene sequences. Describes how to identify genes and infer gene structure. Differentiates between the types of phylogenetic analyses available and appropriate programs for specific questions. Applies students’ existing content knowledge toward practical bioinformatic applications Offers students an opportunity to develop skills in analysis, problem solving, and communication as applied to bioinformatics ...
BMC Bioinformatics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all ...
Bioinformatics community open to all people. Strong emphasis on open access to biological information as well as Free and Open Source software.
ZENBU, a new, freely available bioinformatics tool developed at the RIKEN Center for Life Science Technology in Japan, enables researchers to quickly and easily integrate, visualize and compare large amounts of genomic information resulting from large-scale, next-generation sequencing experiments. Next-generation sequencing has revolutionized functional genomics, with protocols such as RNA-seq, ChIP-seq and CAGE being used widely around the world. The power of these techniques lies in the fact that they enable the genome-wide discovery of transcripts and transcription factor binding sites, which is key to understanding the molecular mechanisms underlying cell function in healthy and diseased individuals and the development of diseases like cancer. The integration of data from multiple experiments is an important aspect of the interpretation of results, however the growing number of datasets generated makes a thorough comparison and analysis of results cumbersome. In a report published today in the
The availability of immunome-mining tools has fueled the design and development of vaccines by a process that was at first called "vaccinomics" by Brusic and Petrovsky in 2002, "reverse vaccinology" by Rappuoli in 2003 and, more recently, "immunome-derived or genome-derived vaccine design" by Pederson; De Groot and Martin; and Doytchinova, Taylor, and Flower.. The theory behind these descriptors is that a minimal set of antigens that induce a competent immune response to a pathogen or neoplasm can be discovered using immunoinformatics, and that administration of these epitopes, in the right delivery vehicle and with the correct adjuvant, will result in a degree of protection against infection by the pathogen. In its most minimalist form, an IDV would contain only adjuvanted B-cell and T-cell epitopes in delivery vehicles such as liposomes. When these minimal components are packaged in an appropriate delivery vehicle, the complete package comprises an immunome-derived vaccine.. Compared to ...
Bioinformatics is the application of information technology (informatics) to biological data. Informatics is the representation, organization, manipulation, distribution, maintenance, and use of digital information. When applied to biological data, informatics provides databases and analytical tools for answering biological questions. Bioinformatics is inherently interdisciplinary, involving aspects of biology, computer science, mathematics, physics, and chemistry. While computers have been used to analyze biological data since their invention, the need for computational methods has recently exploded due to the huge amounts of data produced by genome sequencing projects and other high-throughput technologies. Bioinformatics techniques are being used to move the field of biology from a "one gene at a time" approach, to the analysis of whole systems. In this course, students will learn current bioinformatics techniques to address systems-level biological questions. Topics include sequence ...
Bioinformatics is the application of information technology (informatics) to biological data. Informatics is the representation, organization, manipulation, distribution, maintenance, and use of digital information. When applied to biological data, informatics provides databases and analytical tools for answering biological questions. Bioinformatics is inherently interdisciplinary, involving aspects of biology, computer science, mathematics, physics, and chemistry. While computers have been used to analyze biological data since their invention, the need for computational methods has recently exploded due to the huge amounts of data produced by genome sequencing projects and other high-throughput technologies. Bioinformatics techniques are being used to move the field of biology from a "one gene at a time" approach, to the analysis of whole systems. In this course, students will learn current bioinformatics techniques to address systems-level biological questions. Topics include sequence ...
Information on vertebrate proteins (mainly those from mouse and human) that are thought to, or known to, be localised to the cell nucleus. Where known, the sub-nuclear compartment where the proteins have been found are reported. Also stored is information on the amino acid sequence, predicted protein size and isoelectric point, as well as any repeats, motifs or domains within the protein sequence. Biological and molecular functions of the proteins are described using GO terms.. ...
Overview. Bioinformatics has become an essential component of computationally intensive functional genomics, comparative genomics, gene discovery, transcriptional regulatory networks, biochemical pathway analysis, molecular modeling, proteomics and rational drug design. It helps to analyze genes on a massive scale to dissect the precise understanding of the biological processes at the molecular level. Bioinformatics is widely regarded as the key to decipher the staggering functional genomics and genotyping data in the 21st century.. Envisaging the potential of bioinformatics in modern biological research, KBIRVO, SankaraNethralaya established Center for Bioinformatics by 2010, to provide a platform for education and research in bioinformatics and its application to Vision Science. The ultimate goal of this multidisciplinary center is to focus on research and education in the rapidly emerging fields of bioinformatics and computational biology which deal with the analysis, integration and ...
Bioinformatics Algorithms (Part 1) with Pavel Pevzner, Phillip E. C. Compeau,. The course Bioinformatics Algorithms (Part 1) by Pavel Pevzner, Phillip E. C. Compeau, and Nikolay Vyahhi from University of California, San Diego will be offered free of charge to everyone on the Coursera platform. Sign up at http://www.coursera.org/course/bioinformatics. ...
Database of compound genetic marker called SNPSTR which combines a STR marker with one or more tightly linked SNPs. Here, the SNP(s) and the microsatellite are less than 250 base pairs apart so each SNPSTR can be considered a small haplotype with no recombination occurring between the two individual markers.. ...
The International Symposium on Bioinformatics Research and Applications (ISBRA) provides a forum for the exchange of ideas and results among researchers, developers, and practitioners working on all aspects of bioinformatics and computational biology and their applications. Submissions presenting original research are solicited in all areas of bioinformatics and computational biology, including the development of experimental or commercial systems. Topics of interest include but are not limited to. ...
The International Symposium on Bioinformatics Research and Applications (ISBRA) provides a forum for the exchange of ideas and results among researchers, developers, and practitioners working on all aspects of bioinformatics and computational biology and their applications. Submissions presenting original research are solicited in all areas of bioinformatics and computational biology, including the development of experimental or commercial systems. Topics of interest include but are not limited to. ...
This three day course is intended to open doors to applying statistics - whether directly increasing skills and personally undertaking analyses, or by expanding knowledge towards identifying collaborators. The end goal is to drive confident engagement with data analysis and further training - increasing the quality and reliability of interpretation, and putting that interpretation and subsequent presentation into the hands of the researcher. Each day of the course will deliver a mixture of lectures, workshops and hands-on practicals - and will focus on the following specific elements. Day 1 focuses on basic approaches and the computer skills required to do downstream analysis. Covering: Basic skills for data manipulation in R. How to prepare your data effectively. Principles of experimental design and how this influences analysis. On day 2, participants will explore the core concepts of statistics - so that they can begin to see how they can be applied to their own work, and to also help with ...
This three day course is intended to open doors to applying statistics - whether directly increasing skills and personally undertaking analyses, or by expanding knowledge towards identifying collaborators. The end goal is to drive confident engagement with data analysis and further training - increasing the quality and reliability of interpretation, and putting that interpretation and subsequent presentation into the hands of the researcher. Each day of the course will deliver a mixture of lectures, workshops and hands-on practicals - and will focus on the following specific elements. Day 1 focuses on basic approaches and the computer skills required to do downstream analysis. Covering: Basic skills for data manipulation in R. How to prepare your data effectively. Principles of experimental design and how this influences analysis. On day 2, participants will explore the core concepts of statistics - so that they can begin to see how they can be applied to their own work, and to also help with ...
The data available for biological systems are diverse in nature and include various types such as sequences, structures, expression data, interactions, pathways, systems data, phenotype(s) and population data [1]. The rate at which the data are generated has increased exponentially due to technological advances in the fields of genomics, transcriptomics, proteomics, structural genomics, metabolomics, systems biology etc. [2]. The changing nature of studies in areas such as personalized genomics and translational medicine has further accelerated the pace of data generation resulting in greater volumes of data [3, 4]. As the biological data constitutes an important component of Big Data, it demands novel solutions to curate, compile, organize, archive, query and analyse in order to deal with three Vs, namely, volume, velocity and variety [2, 5-7]. Various types of primary data along with annotations continue to be useful for processing, analysis and interpretation of inherently complex high ...
The Bioinformatics and Computational Biology program, which supports the National Centers for Biomedical Computing, aims to develop novel, cutting-edge software and data management tools to effectively mine the vast wealth of biomedical data generated from sophisticated modern laboratory techniques and facilitate data sharing between researchers.
Biology has transformed into a quantitative science with the advent of technologies that produce large amounts of data, whose analyses demand advanced computation. The bioinformatics research group in CSE develops computational tools to enable biological discoveries.. In Proteomics (the study of active proteins in a cell), the group is engaged in the analysis of mass spectrometry data to identify and quantify proteins, discover post-translational modifications and processing, sub-cellular localization, the genes that encode these proteins, and study of proteins from non-cultured organisms (meta-proteomics). In Genomics/Genetics, the group studies problems relating to genome rearrangements, structural variation, deep-sequencing, and population genetics. In each case, our focus is on novel analyses of data from high throughput technologies including sequencing, genotyping, mass-spectrometry. CSE Bioinformatics is an integral part of a vibrant Bioinformatics PhD program on campus with faculty from ...
The Plant domain has been the subject of several attempts to structure and formally define terms and corresponding relations, such as their anatomical features, developmental stages, and the application of particular experimental procedures to a biological problem. However, a focus on experimental assays in order to describe the whole experimental procedure, to the best of our knowledge, has only been attempted in the context of a very general description based on classical views of the scientific method. In this study, we focus on the development and proposal of an ontology dedicated to the description of these experimental procedures, regardless of the scientific questions that prompted the assays. This ontology includes entities from three distinct realms (biological, physical and data), which include both experimental products, their relations and the protocols describing their manipulation. The final outcome is a useful and comprehensive ontology in the plant domain, to be used as a log ...
Analysis of a microarray experiment often results in a list of hundreds of disease-associated genes. In order to suggest common biological processes and functions for these genes, Gene Ontology annotations with statistical testing are widely used. However, these analyses can produce a very large number of significantly altered biological processes. Thus, it is often challenging to interpret GO results and identify novel testable biological hypotheses. We present fast software for advanced gene annotation using semantic similarity for Gene Ontology terms combined with clustering and heat map visualisation. The methodology allows rapid identification of genes sharing the same Gene Ontology cluster. Our R based semantic similarity open-source package has a speed advantage of over 2000-fold compared to existing implementations. From the resulting hierarchical clustering dendrogram genes sharing a GO term can be identified, and their differences in the gene expression patterns can be seen from the heat map.
ZENBU, a new, freely available bioinformatics tool developed at the RIKEN Center for Life Science Technology in Japan, enables researchers to quickly and easily integrate, visualize and compare large amounts of genomic information ...
Bioinformatics, also known as computational biology, is the study of biological systems through computational and statistical models. Molecular Biology is the study of the molecular components of living things. This major requires knowledge of biology, computer science, and information technology.. Rensselaer is one of the few universities to offer an undergraduate program in this emerging field. Most of the instructors maintain active research programs in different aspects of computational biology, from database analysis to molecular simulations.. Graduates are encouraged to continue their studies in one of the growing number of worldwide computational biology graduate programs. While those who enter the workplace often are hired into the pharmaceutical industry, medical informatics, agricultural bioinformatics, database management, or the biotech industry.. ...
High-throughput proteomics experiments involving tandem mass spectrometry produce large volumes of complex data that require sophisticated computational analyses. As such, the field offers many challenges for computational biologists. In this article, we briefly introduce some of the core computational and statistical problems in the field and then describe a variety of outstanding problems that readers of PLoS Computational Biology might be able to help solve.
Oxford has particular strengths in bioinformatics and statistical genetics in the Department of Statistics and the Wellcome Trust Centre for Human Genetics, which is part of the Nuffield Department of Clinical Medicine. Groups in these departments have developed many of the methods now used worldwide in genetic association studies in humans and rodent models and in high-throughput DNA sequence analysis. DNA and protein sequence analysis and functional annotation is concentrated in the Department of Statistics and the MRC Functional Genomics Unit. There is a strong tradition of protein structure analysis in several groups in Oxford, notably in the Structural Biology Division of the Nuffield Department of Clinical Medicine and the Structural Bioinformatics and Computational Biochemistry Unit in the Department of Biochemistry. An exciting new development is the Big Data Institute, a centre of excellence for the analysis of large and complex data sets for health research aiming to develop, evaluate ...
Jitendra Narayan. BioinformaticsOnline(BOL) founder. http://bioinformaticsonline.com/about Within the broad domain of bioinformatics and computational biology, I mainly focus on chromosomal breakpoint and amniotes evolution. I (We) develop certain computational pipeline, and algorithms to harness the huge amount .... Tags: Bioinformatics, Computational Biology, Chromosomal Breakpoints, Avian Genomics, Evolutionary Biology, Adaptation, Selection, Mammalian Genomics, Molecular Evolution, GWAS, Rotifers. Skills: Bioinformatics, R, Bioconductor, Perl, BioPerl, Java, BioJava. ...
Our goal is to consolidate campus-wide expertise on computational molecular science to facilitate interdisciplinary research in several strategic areas at the Beckman Institute and Illinois, and eventually establish a world-leading thrust in the frontier of theory-driven computational molecular science," Zhang said.. CMS is profoundly interdisciplinary. It embodies physics, which underpins the underlying fundamental principles; chemistry, which both explores higher-level emergent principles and creates novel synthetic routes of remarkable organic, inorganic, bio-molecular building blocks that can self-assemble to structures with unique properties; and molecular biology and medical science, which are imperative to improve our health and quality of life.. "This group is an intellectual powerhouse with ambitious aspirations to advance important problems in molecular design thinking. Their activities cut across a number of experimental projects in the institute and so, wisely, the new CMS group ...
Bioinformatics and computational biology are two related disciplines that have developed from the need to analyze and interpret large, complex datasets which ha...
The International Max Planck Research School for Computational Biology and Scientific Computing (IMPRS-CBSC) is embedded in a variety of scientific groups working at the interface of life sciences (molecular bio-logy, genome research) and formal sciences (mathematics, computer science). Its research focus is on the mathematical and computational side of research in sequence analysis, theoretical structural biology, computational chemistry and drug design, molecular evo-lution, genome analysis, and data analysis methods in functional genomics.. ...
Instruction Dr. Lamont instructs courses in genetic regulation of livestock immunology and applied poultry and swine breeding and genetics. She also serves as a graduate faculty member in the graduate major programs of animal breeding and genetics, bioinformatics and computational biology, genetics, and immunobiology. Research Dr. Lamonts area of research is molecular genetics and immunogenetics of poultry, including the identification of molecular markers and genes controlling bacterial resistance, antibody kinetics, growth, body composition, skeletal integrity and other biological traits; physiological genetics; gene expression; and the major histocompatibility complex genes.
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The Computational Biology Facility offers a range of services across protein sequence and structure bioinformatics to help you predict, understand and redesign protein activities.
The leading peer-reviewed journal in the analysis, management, and visualization of cellular information at the molecular level, offering articles on novel, cutting-edge methods in computational biology and bioinformatics.
The leading peer-reviewed journal in the analysis, management, and visualization of cellular information at the molecular level, offering articles on novel, cutting-edge methods in computational biology and bioinformatics.
Web pages for Laboratory for Bioinformatics and Computational biology at the Faculty of Electrical Engineering and Computing, University of Zagreb
on computational discovery is about to appear, although fewer papers were received than the editors wished (Simon, Valdes-Perez & Sleeman, forthcoming). Data-mining in scientific databases is an active area of research, as are other computational approaches applied to individual sciences, e.g., intelligent systems in molecular biology. It is becoming more difficult to locate computational discovery work because much of it is published in scientific journals--a good sign that the methods of producing results of interest to practicing scientists. Buchanan (e.g., Lee et al., 1996) continues work on rule induction applied to various scientific databases. Simon is studying the difficult problems of constructing diagrammatic representations (Larkin & Simon, 1987; Qin & Simon, 1995) and of modeling relations between diagrammatic and verbal reasoning (Tabachneck-Schijf, Leonardo, & Simon, 1996). Zytkow continues to work on various aspects of discovery, including analyzing the components needed for an ...
Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2005, Embassy Suites Hotel La Jolla, La Jolla, CA, USA, November 14 & 15, 2005. IEEE 2005, ISBN 0-7803-9388-0 ...
... , Computational Chemistry List, Resource for Computational Chemists, molecular modeling, and associated archives
... , Computational Chemistry List, Resource for Computational Chemists, molecular modeling, and associated archives
OpenHelix provides on-line and onsite training on bioinformatics and genomics resources. OpenHelix encourages faster and more effective research by enabling the efficient use of publicly available tools to access biological data. OpenHelix tutorial suites on publicly available biomedical resources include an online narrated tutorial as well as PowerPoint slides, handouts and exercises. Customers can effectively and efficiently learn to use a resource and save time and money when teaching others by using the downloadable materials.
Prices in US$ apply to orders placed in the Americas only. Prices in GBP apply to orders placed in Great Britain only. Prices in € represent the retail prices valid in Germany (unless otherwise indicated). Prices are subject to change without notice. Prices do not include postage and handling if applicable. RRP: Recommended Retail Price ...
InProceedings{boden_et_al:OASIcs:2013:4233, author = {Marcus Boden and Martin Sch{o}neich and Sebastian Horwege and Sebastian Lindner and Chris Leimeister and Burkhard Morgenstern}, title = {{Alignment-free sequence comparison with spaced k-mers}}, booktitle = {German Conference on Bioinformatics 2013}, pages = {24--34}, series = {OpenAccess Series in Informatics (OASIcs)}, ISBN = {978-3-939897-59-0}, ISSN = {2190-6807}, year = {2013}, volume = {34}, editor = {Tim Bei{\ss}barth and Martin Kollmar and Andreas Leha and Burkhard Morgenstern and Anne-Kathrin Schultz and Stephan Waack and Edgar Wingender}, publisher = {Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik}, address = {Dagstuhl, Germany}, URL = {http://drops.dagstuhl.de/opus/volltexte/2013/4233}, URN = {urn:nbn:de:0030-drops-42334}, doi = {10.4230/OASIcs.GCB.2013.24}, annote = {Keywords: Alignment-free sequence comparison, phylogeny reconstruction ...
Get this from a library! Complex systems and computational biology approaches to acute inflammation. [Yoram Vodovotz; Gary An;] -- The Translational Dilemma, the difficulty in achieving effective translation of basic mechanistic biomedical knowledge into effective therapeutics, is the greatest challenge in biomedical research. ...
Genautica was formed by a group of investors, senior scientists, technologists and business professionals dedicated to identifying, funding and capturing value in the rapidly expanding field of Next Generation Sequencing (NGS), genomics and biotechnology in general. Genautica has a strong vision for the potentials of next generation sequencing-based genomics in medicine and other related industries: better diagnostics; next-generation cancer therapies; novel bioinformatics platforms that support research and cutting-edge therapies in the health sciences; genetic expression systems for building proprietary organisms and "platform hosts"- essentially rationally designed nano-machines for the manufacturing of drugs, fuels, foods, intermediate raw materials and industrial feedstocks. It is our expectation that the increasing speed and decreasing costs of full genomic sequencing, along with the rapidly escalating computational capabilities to handle the vast amount of genomic data, will generate many ...
Using H. sapiens?M. tuberculosis H37Rv as a model, we have conducted a systematic computational study on host?pathogen PPIs. We have identified important reliable pathogen PPI datasets that can be used for the analysis of host?pathogen PPIs studies in Chapter 2, which also enables the topological and sequence properties analysis for the first time on the pathogen side. We have developed one of currently most compre- hensive pathway databases?IntPath?in Chapter 3, which for the first time enables functional analysis on both host and pathogen. We have proposed two prediction ap- proaches: the accurate DDI-based prediction approach in Chapter 4 and the accurate homology-based prediction approach in Chapter 5. Both of these prediction approaches have better performance than their conventional counterparts. We have provided high- quality predicted H. sapiens?M. tuberculosis H37Rv PPIs datasets that can be used for a variety of purposes. Based on the predicted H. sapiens?M. tuberculosis H37Rv PPIs, we ...
Researchers from the University of California, San Diego, recently developed a new computational strategy to search for molecules that could be developed into treatments for glioblastoma. The mouse-model study, published in the journal Oncotarget, found that one molecule shrank the average tumor size by half. The newly discovered molecule works against glioblastoma tumors by wedging itself in the temporary interface between two proteins whose binding is essential for the tumors survival and growth. This study is the first to demonstrate successful inhibition of this type of protein, known as a transcription factor. "Most drugs target stable pockets within proteins, so when we started out, people thought it would be impossible to inhibit the transient interface between two transcription factors," said first author of the study. "But we addressed this challenge and created a new strategy for drug design - one that we expect many other researchers will immediately begin implementing in the ...
Bioinformatics & Computational Biology at Princeton University includes bioinformatics, functional genomics, and immune system modeling.. ...
BME 132 Introduction to Computational Biology (Credit Units: 4) The use of theories and methods based on computer science, mathematics, and physics in molecular biology and biochemistry. Basics in biomolecular modeling. Analysis of sequence and structural data of biomolecules. Analysis of biomolecular functions. Prerequisite: MATH 2D or MATH 3A or STATS 7 or STATS 8. Same as COMPSCI 183 and BIO SCI M123. Concurrent with BME 232, MOLBIO 223. (Design units: 0) ...
View Notes - MIT6_047f08_lec21_slide21 from EECS 6.047 / 6. at MIT. MIT OpenCourseWare http:/ocw.mit.edu 6.047 / 6.878 Computational Biology: Genomes, Networks, Evolution Fall 2008 For information
3D protein structure similarity searching is one of the important processes performed in structural bioinformatics, since it allows for protein function identification and reconstruction of phylogeny for weakly related organisms. Due to the complexity of 3D protein structures and exponential growth of protein structures in public repositories, like the Protein Data Bank, the process is time-consuming and requires increased computational resources.
OpenHelix provides on-line and onsite training on bioinformatics and genomics resources. OpenHelix encourages faster and more effective research by enabling the efficient use of publicly available tools to access biological data. OpenHelix tutorial suites on publicly available biomedical resources include an online narrated tutorial as well as PowerPoint slides, handouts and exercises. Customers can effectively and efficiently learn to use a resource and save time and money when teaching others by using the downloadable materials.
In this section of bioafrica we provide you with publications, manuscripts, papers, on bioinformatics, genomics and drug resistance. HIV, TB and other pathogens publications
View Notes - ps12002 from HST. 508 at MIT. Harvard-MIT Division of Health Sciences and Technology HST.508: Genomics and Computational Biology I. Biology (35 points total) The following questions
Your program may require taking courses in more than 1 department, so you will have a thorough comprehension of the area. Pursuing a biology internship may be huge aid in making an educated choice about your interest in biology. research paper for sale Computational biology is just one of the most exciting regions of contemporary science.. Its very rewarding to be part of this undertaking and to learn of all of the scientific discoveries enabled by KBase. It introduces the notion of near-decomposability. The objective of the program is to construct a diverse cohort of new researchers in the area.. Opportunities exist for students to take part in training http://www.northeastern.edu/executive-orders/ whilst studying at partner institutions also. Business leaders have started to deal with the problem of creating more science and technology work in the United States to keep them from being exported. Research positions typically take a doctorate degree.. You dont necessarily have to be a ...
... : CENTER OF EXCELLENCE IN BIOMARKER RESEARCH & INDIVIDUALIZED MEDICINE (SCHOOL OF BRIM) : The University of Toledo
Constraints and Molecular Biology: Constraint Programming techniques can be efficiently used for predicting structure of a protein which is considered one of the most important problem in Computational Biology. The protein structure prediction problem has effectively been transformed to a constraint minimization problem with finite domain and Boolean variables. The Oz language was then used to implement the constraint problem. Certain variables have been defined for the entire constraint problem of predicting the protein structure. Later constraint optimization has been used to minimize the variable surface. A perfect conformation was found on all possible sequences in finding the sequence length and also the optimal surface. Hence constraint techniques can be effectively applied to solving problems in computational biology.. This entry was posted on Wednesday, April 14th, 2010 at 9:39 pm and is filed under Scientific Applications. You can follow any responses to this entry through the RSS 2.0 ...
<p>The course will teach advanced methods and applications of computational biology for highthroughput data analysis in molecular biology.</p>
Note that presentation at computer science and most bioinformatics conferences is subject to peer review. Further, top-ranked bioinformatics and computer science conferences have reviewing standards as rigorous as journals in the area. ...
Cancer arises when genes in a cell are changed in such a way that they cause the cell to divide uncontrolled. For this to happen, however, a multitude of specific changes have to coincide. It is the task of this Research Program to analyze the genome, i.e., the complete set of genes, in order to lay the foundation for developing new diagnostic and treatment methods. This involves mapping the genome, localizing genes within the genetic material, and investigating the functions of cancer-relevant genomic areas. The vast amounts of data accumulated in the process are being captured and evaluated using bioinformatic methods. By combining approaches from mathematics, statistics, physics, and computer sciences with computer-assisted simulation techniques, the theoretical groups of the Research Program are bridging the gap to experimental research. The methods developed within the Research Program are being directly utilized in many areas within collaborations with numerous divisions of the Center: in ...
Pharmaceutical Bioinformatics. (7.5 credits, Autumn18/19, weeks 36-44, 50%. 7.5 credits, Spring18/19, weeks 04-13, 50%.). The course aims to provide basic knowledge of how bioinformatics tools can be used to solve problems within pharmacology, pharmacy, and pharmaceutical chemistry.

On completion of the course you should be able to:
  • understand and describe how bioinformatics tools can be used within pharmaceutical research
  • use bio- and chemoinformatics programs for e.g. sequence alignment, 3D visualisation, and structure-activity relationship based methods such as proteochemometrics
  • seek relevant information in biological and chemical databases
  • calculate the properties (descriptors) of potential drugs, and correlate these to target protein interactions through bioinformatic modelling
  • interpret and validate results of above-mentioned methods
The aim of Symposium on Bioinformatics and Bioforensics (SBB18) is to provide a platform for researchers, engineers, academicians as well as industrial professionals to present their research results and development activities in bioinformatics and bioforensics. SBB18 invites original and unpublished work from individuals active in the broad theme of the symposium. Authors should submit their papers online using EDAS. Unregistered authors should first create an account in EDAS to log on. Further guidelines for submission are posted at: http://icacci-conference.org/2018/content/paper-submission-guidelines . The program committee solicits previously unpublished papers offering novel research contributions in any aspect of bioinformatics and bioforensics.. ...
Constraints and Molecular Biology: Constraint Programming techniques can be efficiently used for predicting structure of a protein which is considered one of the most important problem in Computational Biology. The protein structure prediction problem has effectively been transformed to a constraint minimization problem with finite domain and Boolean variables. The Oz language was then used to implement the constraint problem. Certain variables have been defined for the entire constraint problem of predicting the protein structure. Later constraint optimization has been used to minimize the variable surface. A perfect conformation was found on all possible sequences in finding the sequence length and also the optimal surface. Hence constraint techniques can be effectively applied to solving problems in computational biology.. Read More ...
For projects requiring NGS, we provide access to an experienced scientific team who will work with you from early study design through to delivery of bioinformatics data (with your chosen provider) to ensure end-to-end delivery for your project. ...
While combinatorial models of transcriptional regulation can be inferred for metazoan systems from a priori biological knowledge, validation requires extensive and time-consuming experimental work. Thus, there is a need for computational methods that can evaluate hypothesized cis regulatory codes before the difficult task of experimental verification is undertaken. We have developed a novel computational framework (termed
The Robinson Lab at the Jackson Laboratory for Genomic Medicine develops algorithms and computational resources for understanding human disease based on phenotyopes, model organisms, and genomics.
The bioinformatics analysis minor immerses students in the core challenges and strengths of the field of bioinformatics, as well as the ethical issues involved. Students gain hands-on experience implementing some of the core algorithms utilized by professionals in the field. This minor is closed to students majoring in bioinformatics.. ...
Science Of Cycles is the vehicle which brings the latest cutting-edge discoveries confirming long and short-term cyclical events between our Galaxy-Sun-Earth with charged particles as the conduit. Website:http://scienceofcycles.com Email: [email protected] Scientific Endorsements: http://scienceofcycles.com/about-mitch-battros/ | Science of Cycles
Which industries are seeing strong enterprise adoption of cloud computing? The pharmaceutical industry, for one. Chemical and Engineering News highlights how several drug makers are test-driving the cloud. Among them is Eli Lilly & Co., which has used Amazons EC2 platform to rapidly deploy compute capacity. "We were recently able to launch a 64-machine cluster computer working on bioinformatics sequence information, complete the work, and shut it down in 20 minutes," Lillys Dave Powers told the magazine. "It cost $6.40. To do that internally-to go from nothing to getting a 64-machine cluster installed and qualified-is a 12-week process.". ...
One of the first reports showing stable, energy efficient model towards improved protein function prediction screening in-silico structure based
Journal-ref: S. Qatawneh, A. Alneaimi, Th. Rawashdeh, M. Muhairat, R. Qahwaji and S. Ipson,"Efficient Prediction of DNA-Binding Proteins using Machine Learning", International Journal on Bioinformatics & Biosciences (IJBB) Vol.2, No.2, June 2012 ...
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Technology Networks is an internationally recognised publisher that provides access to the latest scientific news, products, research, videos and posters.
The jobs currently available in bioinformatics involve the design and implementation of programs and systems for the storage, management and analysis of vast amounts of DNA sequence data. Such positions require in-depth programming and relational database skills, which very few biologists possess, and so it is largely the computational specialists who are filling these roles.As the bioinformatics field matures there will be a huge demand for outreach to the biological community to sift through gigabases of genomic sequence in search of novel targets. It will be in these areas that biologists with the necessary computational skills will find their niche ...
Yet, this potential cannot be unlocked without addressing issues related to integration and analysis of data from different sources. Big Data management and analysis call for development of new tools, software and methodologies. As a result, translational bioinformatics has emerged to provide a platform for the integration of different biological techniques, statistical analysis methods and information technologies to translate basic molecular, genetic, cellular, and clinical data into clinical applications in order to improve human health and cure diseases. Efficient analysis of big medical data is required for a better understanding of diseases especially complex diseases and development of predictive, preventive and better personalized diagnostics and therapeutics. In short, the knowledge gained can provide an insight into factors that influence individual and public health and disease. In an endeavor to enable newer biological discoveries, the aim here is to translate the basic information ...
AIDS Healthcare Foundation (AHF) provides cutting-edge medicine and advocacy in 39 countries. We are the largest HIV/AIDS medical care provider in the U.S.
Welcome to the official website of the 2012 International Conference on Bioinformatics and Computational Biology, BIOCOMP BG 2012, which will be held in Varna, Bulgaria, during the period of September 20-21, 2012. There will be a strong focus on the bioinformatics challenges, arising from the extraordinary developments in high throughput technologies. BIOCOMP BG 2012 aims to bring researchers, scientists, engineers, and scholar students together so they can exchange and share their experiences, new ideas and research results about all aspects of Bioinformatics and Computational Biology, as well as to discuss the practical challenges they have encountered and the solutions adopted to solve them ...
Looking for online definition of Ab Initio Gene Prediction in the Medical Dictionary? Ab Initio Gene Prediction explanation free. What is Ab Initio Gene Prediction? Meaning of Ab Initio Gene Prediction medical term. What does Ab Initio Gene Prediction mean?
The Bioinformatics Links Directory features curated links to molecular resources, tools and databases. The links listed in this directory are selected on the basis of recommendations from bioinformatics experts in the field. We also rely on input from our community of bioinformatics users for suggestions. Starting in 2003, we have also started listing all links contained in the NAR Webserver issue.
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The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software - to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundations software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too.. When we speak of "free" software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things.. To protect your rights, we need to ...
Protein structure prediction is an important problem in the post-genome era, which is one possible way to fill the gap between the rapid-growth sequences and the relative small number of proteins with experimentally determined structures. Despite the structural genomics initiatives and biochemical efforts, the cheapest and fastest way to obtain structural information is through prediction algorithms. Structure prediction, even in the absence of homology, is the first step of the sequence-structure-function paradigm. Great progress has been achieved in protein structure prediction during the last decades. The development of high-quality prediction methods has also been boosted by objective community-wide assessment experiments. However, the ultimate goal of protein structure prediction remains far away to reach. New algorithms, theory and advanced prediction techniques are necessary to facilitate the progress ...
The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is web ready: written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components.. AVAILABILITY AND IMPLEMENTATION: The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/Supplementary information: Supplementary data are available at Bioinformatics online.. CONTACT: [email protected] ...
TY - JOUR. T1 - Linkers of Cell Polarity and Cell Cycle Regulation in the Fission Yeast Protein Interaction Network. AU - Vaggi, Federico. AU - Dodgson, James. AU - Bajpai, Archana. AU - Chessel, Anatole. AU - Jordán, Ferenc. AU - Sato, Masamitsu. AU - Carazo-Salas, Rafael Edgardo. AU - Csikász-Nagy, Attila. PY - 2012/10. Y1 - 2012/10. N2 - The study of gene and protein interaction networks has improved our understanding of the multiple, systemic levels of regulation found in eukaryotic and prokaryotic organisms. Here we carry out a large-scale analysis of the protein-protein interaction (PPI) network of fission yeast (Schizosaccharomyces pombe) and establish a method to identify linker proteins that bridge diverse cellular processes - integrating Gene Ontology and PPI data with network theory measures. We test the method on a highly characterized subset of the genome consisting of proteins controlling the cell cycle, cell polarity and cytokinesis and identify proteins likely to play a key ...
Peptides are routinely identified from mass spectrometry-based proteomics experiments by matching observed spectra to peptides derived from protein databases. The error rates of these identifications can be estimated by target-decoy analysis, which involves matching spectra to shuffled or reversed peptides. Besides estimating error rates, decoy searches can be used by semi-supervised machine learning algorithms to increase the number of confidently identified peptides. As for all machine learning algorithms, however, the results must be validated to avoid issues such as overfitting or biased learning, which would produce unreliable peptide identifications. Here, we discuss how the target-decoy method is employed in machine learning for shotgun proteomics, focusing on how the results can be validated by cross-validation, a frequently used validation scheme in machine learning. We also use simulated data to demonstrate the proposed cross-validation schemes ability to detect overfitting.. ...
Ziemer, Tim (2020). "Biology of the Auditory System". Psychoacoustic Music Sound Field Synthesis. Current Research in ... it seems to suggest possible computational pathways of the MON. The MON is likely involved in the integration of sophisticated ...
... allowing practitioners to focus on their specific problems and leaving PPLs to handle the computational details for them.[24][ ... "Comparison of Parameter Estimation Methods in Stochastic Chemical Kinetic Models: Examples in Systems Biology". AIChE Journal ... which removed many of the computational problems, and an increasing interest in nonstandard, complex applications.[50] Despite ...
The phylogenetic tree and computational phylogenetic methods such as maximum likelihood analysis are introduced. The tale ends ... biology). ...
The Nutritious Rice for the World project is carried out by Ram Samudrala's Computational Biology Research Group at the ... "PLoS Biology. 5 (4): e76. doi:10.1371/journal.pbio.0050076. PMC 1828141. PMID 17373854.. ... The Clean Energy project is sponsored by the scientists of Harvard University's Department of Chemistry and Chemical Biology.[ ... sponsored by the scientists of Harvard University's Department of Chemistry and Chemical Biology.[92] Further calculations ...
"dCLIP: a computational approach for comparative CLIP-seq analyses". Genome Biology. 15 (1): R11. doi:10.1186/gb-2014-15-1-r11 ...
Methods in Molecular Biology. 1757. pp. 141-161. doi:10.1007/978-1-4939-7737-6_7. ISBN 978-1-4939-7736-9. . PMID 29761459.. ... Computational Systems Bioinformatics Conference, 2005. Workshops and Poster Abstracts. IEEE. pp. 37-8. doi:10.1109/CSBW.2005.48 ... genomics and biology of the laboratory mouse to facilitate the study of human health and disease.[2][3] The database integrates ... "Searching the Mouse Genome Informatics (MGI) resources for information on mouse biology from genotype to phenotype". Curr ...
Bio Booster Armor Guyver. *Blade Runner - movie based on the novel Do Androids Dream of Electric Sheep in which blade runners ... Note that they use the term "computational intelligence" as a synonym for artificial intelligence. ... Kurzweil, Raymond (2005). The Singularity Is Near: When Humans Transcend Biology. Viking Adult. ISBN 0-670-03384-7. . OCLC ... Biotechnology - field of applied biology that uses living organisms and bioprocesses in engineering, technology, medicine, and ...
"Positioning of proteins in membranes: A computational approach" (PDF). Protein Science 15 (6): 1318-1333. PMC 2242528. PMID ... BMC Structural Biology 7 (44): 44. PMC 1934363. PMID 17603894. doi:10.1186/1472-6807-7-44.. ...
There is a bidirectional relationship between biology and culture; by embodying societally determined gender roles we reinforce ...
Chemical biology. *Chronobiology. *Cognitive biology. *Computational biology. *Conservation biology. *Developmental biology. * ... molecular biology, biochemistry, proteomics and genetics. It is often applied in a context that is as much scientific as ...
Obeležen sa fluorom-18 on je korišten kao radioligand za pozitronsku emisionu tomografiju.[3] On je između ostalog bio korišten ... Annual Reports in Computational Chemistry 4: 217-241. doi:10.1016/S1574-1400(08)00012-1. ... Nuclear Medicine and Biology 25 (4): 343-350. doi:10.1016/S0969-8051(97)00229-1. Cite uses deprecated parameter ,month=. (help) ...
Computational Biology Department (CBD). *Microsoft Research - University of Trento Centre for Computational and Systems Biology ... "International Journal of Computational Biology and Drug Design. 1 (4): 347-367. doi:10.1504/IJCBDD.2008.022207. PMID 20063463. ... "IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8 (1): 194-205. doi:10.1109/TCBB.2009.69. PMID 21071807.. ... Methods in Molecular Biology™. 452. pp. 179-97. doi:10.1007/978-1-60327-159-2_9. ISBN 978-1-58829-707-5. . PMID 18566765.. ...
Houk and Wheeler also provide compelling computational evidence for the importance of direct interaction in pi stacking.[14] In ... This finding is of particular relevance to biology, and suggests that the contribution of pi systems to phenomena such as ... The Hunter-Sanders model has been criticized by numerous research groups offering contradictory experimental and computational ... Houk and Wheeler's [14] computational model of substituent direct interactions in pi stacking. ...
Biolohiya ng ebolusyonaryong pag-unlad (Evolutionary developmental biology). *Biohiya pang-tabang na tubig (Freshwater Biology) ... Pisika pangkomputasyonal (Computational physics). *Pisika ng kondensadong materya (Condensed matter physics). *Kriyonika ( ...
Jordan, D.; Steiner, M. (1999). "Configuration Spaces of Mechanical Linkages". Discrete and Computational Geometry. 22: 297-315 ... An important difference between biological and engineering linkages is that revolving bars are rare in biology and that usually ... R. Connelly and E. D. Demaine, "Geometry and Topology of Polygonal Linkages," Chapter 9, Handbook of discrete and computational ...
1978). Psychology and biology of language and thought : essays in honor of Eric Lenneberg. Academic Press. ISBN 978-0124977501 ... Together with Noam Chomsky he published papers on the mathematical and computational aspects of language and its syntax, two ... Miller and his co-authors tried to explain through an artificial-intelligence computational perspective how animals plan and ...
In the scope of its subject, chemistry occupies an intermediate position between physics and biology. It is sometimes called ...
Kimball, John W. (2003-08-07). "Hydrogen". Kimball's Biology Pages. பார்த்த நாள் 2008-03-04. ... Computational Chemistry Wiki. *Basic Hydrogen Calculations of Quantum Mechanics. *Hydrogen (University of Nottingham) ...
In the scope of its subject, chemistry occupies an intermediate position between physics and biology.[3] It is sometimes called ... Since the end of the Second World War, the development of computers has allowed a systematic development of computational ... Biochemistry is also associated with molecular biology and genetics.. *Inorganic chemistry is the study of the properties and ... chemical biology, chemo-informatics, electrochemistry, environmental chemistry, femtochemistry, flavor chemistry, flow ...
Chemical biology. *Clinical chemistry. *Fullerene chemistry. *Medicinal chemistry. *Molecular biology. *Neurochemistry. * ...
"PLoS Computational Biology. 4 (4): e1000055. arXiv:0705.0902. Bibcode:2008PLSCB...4E0055L. doi:10.1371/journal.pcbi.1000055. ... "School of Biology, Georgia Institute of Technology. Retrieved 12 March 2017.. *. Geneve, Robert. "Leaf" (PDF). PLS 220: ... "Basic Biology. Adam Purcell. Retrieved 17 February 2017.. *. Simpson, Michael G. "Plants of San Diego County, California". ... Journal of Theoretical Biology. 259 (3): 440-448. doi:10.1016/j.jtbi.2009.05.002. PMID 19446571.. ...
The field may also be referred to as computational biology, and can be defined as, "conceptualizing biology in terms of ... 2).[1] Depending on the tools and applications, it often overlaps with the (related) fields of molecular biology, bio- ... molecular biology, biochemistry, cell biology, embryology, genetics, microbiology) and conversely provides methods to support ... "Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 2 (1): 3-22. doi:10.1002/wsbm.42. PMC 3894835. PMID 20836007.. ...
Annual Reports in Computational Chemistry 4: 217-241. doi:10.1016/S1574-1400(08)00012-1. ... ipak visoke doze ne pokazuju da bi klinički tok bio smrtonosan.[29] Gotovo je nemoguće precizno odrediti smrtonosnu dozu ...
Computational Imaging VIII. 7533: 75330R. Bibcode:2010SPIE.7533E..0RH. CiteSeerX 10.1.1.175.3054. doi:10.1117/12.850771.. ... "Magnetic Resonance Materials in Physics, Biology and Medicine. 26 (1): 99-113. doi:10.1007/s10334-012-0353-4. ISSN 0968-5243. ... Qi, J.; R. Leahy (2006). "Iterative reconstruction techniques in emission computed tomography". Physics in Medicine and Biology ... PET and SPECT are capable of detecting areas of molecular biology detail (even prior to anatomic change). PET scanning does ...
Human biology (Page 201/464) Archived 2 January 2017 at the Wayback Machine Daniel D. Chiras. Jones & Bartlett Learning, 2005. ... Computer vision researchers have been able to build computational models for perception that exhibit a similar behavior and are ...
Gusfield, Dan (15 January 1997). Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. ... Makalowska I, Lin CF, Makalowski W (February 2005). "Overlapping genes in vertebrate genomes". Computational Biology and ... Regis E (2009). What Is Life?: investigating the nature of life in the age of synthetic biology. Oxford: Oxford University ... "Molecular biology of the cell (4th ed.). New York: Garland Science. ISBN 0-8153-4072-9. . Archived from the original on 2 ...
Revisiting natural products with modern chemistry and target-finding tools from biology (reversed genomics) is one option for ... Increasingly accurate computational platforms for modelling interactions are being developed. There is also a paradigm shift in ... Durrant JD, McCammon JA (Oct 2011). "Molecular dynamics simulations and drug discovery". BMC Biology. 9: 71. doi:10.1186/1741- ...
Chemical biology. *Chronobiology. *Cognitive biology. *Computational biology. *Conservation biology. *Developmental biology. * ... "Anatomy and Cell Biology. 43 (3): 280-283. doi:10.5115/acb.2010.43.4.280. PMC 3026179. PMID 21267401.. ... "Anatomy & Cell Biology. 43 (3): 280-283. doi:10.5115/acb.2010.43.4.280. PMC 3026179. PMID 21267401.. ... "Anatomy & Cell Biology. 43 (3): 280-283. doi:10.5115/acb.2010.43.4.280. PMC 3026179. PMID 21267401.. ...
... Hofestädt R, Kolchanov N (Eds) (2010) ... 2010). Computational Systems Biology: German/Russian Network of Computational Systems Biology. Medizinische Informatik und ... Computational Systems Biology: German/Russian Network of Computational Systems Biology. Medizinische Informatik und ... Computational Systems Biology: German/Russian Network of Computational Systems Biology. Medizinische Informatik und ...
Some notable examples include Journal of Computational Biology and PLOS Computational Biology. The PLOS computational biology ... Computational evolutionary biology[edit]. Computational biology has assisted the field of evolutionary biology in many ... Cancer computational biology[edit]. Cancer computational biology is a field that aims to determine the future mutations in ... Computational pharmacology[edit]. Computational pharmacology (from a computational biology perspective) is "the study of the ...
Sponsored by the International Society for Computational Biology, the Computational Biology series publishes the very latest, ... Sponsored by the International Society for Computational Biology, the Computational Biology series publishes the very latest, ... Systems Biology. - Imaging and Visualization. - Computational Proteomics. - Molecular Structural Biology. - Evolution and ... The series offers publications that present the state-of-the-art regarding the problems in question; show computational biology ...
Dr Philip Lewis is an Honorary Reader in the Cell and Developmental Biology department at UCL. His work focuses on mathematical ... Understand the uses of modelling in biology with reference to examples drawn across the spectrum of bioscience research. ... Research in the field of Systems Biology is highly interdisciplinary. It often involves biologists working with colleagues from ... and computational approaches to biological research. He delivers the Dynamic Biological Systems module to UCL undergraduates ...
... Research. We construct computational models to improve our knowledge of biomedical processes and ... Contact Computational Biology. Postbus 513 5600 MB Eindhoven T:. +31 (0)40 247 5537. F:. +31 (0)40 243 4970. E:. r.a.v.dijck. ... The research group Computational Biology contributes to the education of the Department of Biomedical Engineering ...
... Bioinformatics & Computational Biology at Princeton University includes bioinformatics, functional ...
Computational biology is an interdisciplinary field that applies mathematical, statistical, and computer science methods to ... In Computational Biology, expert practitioners present a broad survey of computational biology methods by focusing on their ... Computational Biology. Editors. * David Fenyö Series Title. Methods in Molecular Biology. Series Volume. 673. Copyright. 2010. ... Authoritative and easy to use, Computational Biology is an ideal guide for all scientists interested in quantitative biology. ...
Allen School faculty and students collaborate with researchers in biology and medicine on a wide range of computational ... Biology is fast becoming an information science, with large databases and sophisticated algorithms now essential tools in the ... A team led by professor Rajesh Rao published the results of a study that employs computational methods to explain human choices ... Seelig Lab for Synthetic Biology. Members of the Seelig Lab aim to advance our understanding of how biological organisms ...
Computational biology. [David Fenyo;] -- Computational biology is an interdisciplinary field that applies mathematical, ... biology_methods> # Computational Biology--methods a schema:Intangible ;. schema:name "Computational Biology--methods"@en ;. . ... In Computational Biology, expert practitioners present a broad survey of computational biology methods by focusing on their ... In Computational Biology, expert practitioners present a broad survey of computational biology methods by focusing on their ...
This book constitutes the refereed proceedings of the 6th International Conference on Computational Methods in Systems Biology ... Computational Methods in Systems Biology. 6th International Conference CMSB 2008, Rostock, Germany, October 12-15, 2008. ... This book constitutes the refereed proceedings of the 6th International Conference on Computational Methods in Systems Biology ... On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology ...
This book explains the algorithmic foundations and computational approaches underlying areas of structural biology including ... and computational biology. They can carry out such tasks as predicting a natural language sentence, or segmenting an image into ... Over the past decade, novel algorithms have been developed both for analyzing biological data and for synthetic biology ... Becoming conversant with the intricacies of molecular biology and its extensive technical vocabulary can be a challenge, though ...
Computational molecular biology is a new discipline, bringing together computational, statistical, experimental, and ... Learning and Inference in Computational Systems Biology. Edited by Neil D. Lawrence, Mark Girolami, Magnus Rattray and Guido ... The MIT Press Series on Computational Molecular Biology is intended to provide a unique and effective venue for the rapid ... An overview of algorithms important to computational structural biology that addresses such topics as NMR and design and ...
Computational Molecular Biology in the School of Computer Science Computational molecular biology is an active area of research ... Degree in Biological Sciences/Computational Biology, the Professional Masters Program in Computational Biology, and the Merck ... Graduate student applicants wishing to participate in the Merck Computational Biology and Chemistry graduate program at ... is interested in the application of artificial intelligence to problems in computational molecular biology.. ...
... cutting-edge methods in computational biology and bioinformatics. ... Journal of Computational Biology. Co-Editors-in-Chief: Sorin ... Journal of Computational Biology is the leading peer-reviewed journal in computational biology and bioinformatics, publishing ... Special Issue: RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2014. Journal of Computational Biology is now the ... Journal of Computational Biology is under the editorial leadership of Co-Editors-in-Chief Sorin Istrail, PhD, Brown University ...
Description: This course is an introduction to the study of Algorithmic and Computational problems in molecular biology. ... COT 4461: Computational Biology. Course Description for Computational Biology. COT4461: Computational Biology ...
Computational biology Is the Subject Area "Computational biology" applicable to this article? Yes. No. ...
1. Introduction to Biology: Genome; Central Dogma; RNA, DNA, Proteins; and Cell Challenges for computational biology: * ... Molecular Biology Notes on the web * Introduction to Computational Molecular Biology, by Setubal & Meidanis, PWS Publishing ... Computational Biology:. G22.3033.004. Lecturers: Professor B. Mishra. with. Dr. L. Parida and Dr. R. Daruwala Office Hours: By ...
... cutting-edge methods in computational biology and bioinformatics. ... Journal of Computational Biology. Co-Editors-in-Chief: Sorin ... Journal of Computational Biology is the leading peer-reviewed journal in computational biology and bioinformatics, publishing ... Journal of Computational Biology is under the editorial leadership of Co-Editors-in-Chief Sorin Istrail, PhD, Brown University ... DNA and Cell Biology DNA and Cell Biology. Combining mechanistic and clinical studies from multiple systems in a single ...
... at The University of Western Australia studies biological questions using mathematics, statistics and ... Understanding biology using computational simulation and analysis. Our research groups address fundamental and applied ... Evolutionary biology. The evolutionary biology research group studies species evolutionary processes such as sexual selection ... We use a range of computational methods and modelling to explore:. *the evolution of resistance to biocides in weeds, pathogens ...
Computational biology and bioinformatics. Computational biology and bioinformatics. .addthis_counter.addthis_bubble_style { ... Analyzing Network Data in Biology and Medicine An Interdisciplinary Textbook for Biological, Medical and Computational ... Receive email alerts on new books, offers and news in Computational biology and bioinformatics. ... Python Programming for Biology Bioinformatics and Beyond. Stevens, Tim J. Boucher, Wayne Published: February 2015Published: ...
Below is a list of all articles, highlights, profiles, projects, and organizations related specifically to computational ... Below is a list of all articles, highlights, profiles, projects, and organizations related specifically to computational ...
algorithms bioinformatics combinatorics computational biology computational complexity discrete mathematics genome alignments ... Algorithms for Computational Biology. First International Conference, AlCoB 2014, Tarragona, Spain, July 1-3, 2014, Proceedigns ... networks phylogeny proteomics sequence alignment sequence analysis sequence assembly structure prediction systems biology ...
Computational Biology program uses cutting-edge quantitative techniques to increase our understanding of biology. ... Director, Bioinformatics & Computational Biology. We designed WPIs BCB Program to educate students to feel comfortable in the ... Bioinformatics involves the collection, management, and analysis of biological data; Computational Biology is the development ... We also have a Bioinformatics & Computational Biology Summer Research Program for High School Students. ...
Junior Research Group Computational Genome Biology. Dr. Bernd Fischer. Cells are automatically segmented in images from a high- ... We will develop computational methods that aim to predict the phenotypic outcome of drug treatments and combinations of drugs ... The computational methods will be instrumental for cancer proteomics in basic and biomarker research and for the construction ... We will develop computational and statistical methods required for the analysis of emerging, cutting-edge data, especially from ...
bioSyntax: syntax highlighting for computational biology.. Babaian A1,2, Ebou A3, Fegen A4, Kam HY5, Novakovsky GE6, Wong J7, ... Computational biology requires the reading and comprehension of biological data files. Plain-text formats such as SAM, VCF, GTF ... bioSyntax supports computational scientists in parsing and comprehending their data efficiently and thus can accelerate ...
  • PLoS Computational Biology. (birmingham.ac.uk)
  • Modeling latently infected cell activation: viral and latent reservoir persistence, and viral blips in HIV-infected patients on potent therapy, Rong L, Perelson A, 2009, PLoS Computational Biology , 5, (issue 10): e1000533. (physiomeproject.org)
  • Bipartite graphs in systems biology and medicine: a survey of methods and applications. (ibg.edu.tr)
  • From the 26th of July to the 2nd of August 2014 our resident physicists and chemists spent each morning listening to talks on quantum Monte Carlo and related computational electronic structure methods, followed by afternoons that were often full of mountain walking, caving, canyoning and other activities but - for pretty much the first time ever in history of events at TTI - were equally often cancelled because of the appalling weather. (psi-k.net)
  • In Meshfree Methods for Partial Differential Equations VI , volume 89 of Lecture Notes in Computational Science and Engineering , pages 1-23. (uni-stuttgart.de)
  • Computational Methods: numerical methods for non-linear heat equations, reaction-diffusion equations, coupled hyperbolic-parabolic system of equations. (psu.edu)
  • Big datasets generated on the newest "omics" platforms significantly help in establishing a comprehensive view and understanding of tumor biology. (ugent.be)
  • Gene families specific to, or with significantly changed membership in, particular lineages compared to outgroups may reflect important lineage-specific changes in biology. (researchsquare.com)
  • Here we describe a computational protocol to identify gene families that vary greatly in gene count across a species tree. (researchsquare.com)
  • We combined computational protein design, next-generation gene synthesis, and a high-throughput protease susceptibility assay to measure folding and stability for more than 15,000 de novo designed miniproteins, 1000 natural proteins, 10,000 point mutants, and 30,000 negative control sequences," wrote the article's authors. (genengnews.com)
  • Our computational method uses an old idea that cancer genes often require 'two hits' before they cause cancer. (eurekalert.org)
  • We combined data from many different projects and by applying a new computational method were able to identify important cancer genes that were not identified by the original studies. (eurekalert.org)
  • Research in our School of Life Sciences covers a wide spectrum of biology from genes to ecosystems, and this broad-based structure provides opportunities for developing novel ideas and inter-disciplinary projects. (essex.ac.uk)
  • K.P. Wilkie, C.S. Drapaca, S. Sivaloganathan, Aging Impact on the Brain Biomechanics with Application to Hydrocephalus, Mathematical Medicine and Biology, vol.29, issue 2 (2012): 145-161. (psu.edu)
  • She was first introduced to computational biology in Tuncay Baubec's lab at University of Zurich where she was studying DNA methylation in cancer. (vaquerizaslab.org)
  • During her PhD, she plans to combine her new-found interest in high-dimensional data with her longstanding interest in cancer biology. (vaquerizaslab.org)
  • Its applicability to complex motor systems, however, has been largely impossible so far due to the computational difficulties that reinforcement learning encounters in high dimensional continuous state-action spaces. (mpg.de)
  • However, these effects remain poorly understood due to the computational difficulties in solving hydrodynamic interactions (HIs) between arbitrarily shaped particles in confined space. (aps.org)
  • These findings suggest that not only Aβ but that also altered APP processing during the course of AD may have effects on stem cell biology. (pnas.org)
  • Dr Stephen Pickett is a Scientific Director within the Computational Sciences department, based in Stevenage. (smi-online.co.uk)
  • Students wishing to continue their education in biology-related graduate or professional school programs will need to supplement the basic biology curriculum with additional course work in the natural sciences. (cmc.edu)
  • Stochastic reaction-diffusion processes are widely used to model such behaviour in disciplines ranging from systems biology to the social sciences, yet they are notoriously difficult to simulate and calibrate to observational data. (newton.ac.uk)
  • Theories of eye movement control during active vision tasks such as reading and scene viewing have primarily been developed and tested using data from eye tracking and computational modeling, and little is currently known about the neurocognition of active vision. (storysteel.gq)
  • As a result of next-generation genome sequencing, biology and biotechnology have become data-rich. (oecd-ilibrary.org)
  • L'équipe ADVANSE (ADVanced Analytics for data SciencE) a été créée en 2014 et est rattachée au LIRMM dans le pôle Données. (lirmm.fr)
  • New NGS instruments that allow ever-increasing speeds of sequencing-data collection with incredible efficiency, along with sharp reductions in cost, are revolutionizing modern biology in unimaginable ways as genome sequencing projects are rapidly becoming commonplace. (jove.com)
  • The rapid advances in sequencing technologies and exponential data accumulation have created a great need for computational platforms that will allow researchers to access, analyze and understand this information. (jove.com)
  • He is an expert in medical data analysis and the application of computational techniques on the medical data. (metcentre.ie)
  • Dr Fahy also provided bench marking data for an international study involving over 25 research groups worldwide to assess the variability of computational fluid dynamic modelling in cerebral aneurysm (ASME 2012). (metcentre.ie)
  • The program emphasizes aspects of Big Data and High-Performance Computing convergence, convergent research for algorithm development and efficient use of novel architectures, and community-building activities for computational and data-enabled science. (nsf.gov)
  • We show on several examples from systems biology and epidemiology that the method yields consistently accurate parameter estimates, and can be used effectively for model selection. (newton.ac.uk)
  • Re-define the workflows and possibilities of cell biology by joining our virtual event!This event offers an overview of how live-cell analysis enables real-time analysis for the full work. (labroots.com)
  • On the other hand, spatio-temporal point processes offer several computational advantages from the statistical perspective. (newton.ac.uk)
  • First, the sensory cues used for odor-guided searches (odor plumes) are notoriously complex and unable to be completely predicted by computational models. (uw.edu)
  • Jahnavi completed her Bachelor's in Biotechnology in India and her Master's in Biology at ETH Zurich . (vaquerizaslab.org)
  • Casey Holliday and his team developed three-dimensional models of the skull of the American alligator using cutting-edge imaging and computational tools. (eurekalert.org)
  • Now, researchers at the University of Missouri and the University of Southern Indiana have developed three-dimensional models of the skull of the American alligator using cutting-edge imaging and computational tools. (eurekalert.org)
  • In 2015, he won 1st prize in the posters competition of the International Society for Vascular Surgery (Athens, Greece), presenting a computational study on aortic arch aneurysms endovascular latest treatments. (metcentre.ie)
  • We believe that our results offer a pathway to understanding fundamental questions in biology, e.g., anomalous macromolecular diffusion in cells, and serve as a route to design and optimize drug-delivering platforms. (aps.org)
  • To achieve a large scale network akin to biology, a power and area efficient electronic neuron is essential. (iitgn.ac.in)