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.

*  PLOS Computational Biology: Explain Bioinformatics to Your Grandmother!

What are you working on? You have certainly been asked that question many times, whether it be at a Saturday night party, during a discussion with your neighbors, or at a family gathering. Communicating with a lay audience about scientific subjects and making them attractive is a difficult task. But difficult or not, you will have to do it for many years, not only with your family and friends, but also with your colleagues and collaborators. So, better learn now! Although not usually taught, the ability to explain your work to others is an essential skill in science, where communication plays a key role. Using some examples of the French Regional Student Group activities, we discuss here (i) why it is important to have such communication skills, (ii) how you can get involved in these activities by using existing resources or working with people who have previous experience, and (iii) what you get out of this amazing experience. We aim to motivate you and provide you with tips and ideas to get involved
journals.plos.org/ploscompbiol/article/comment?id=info:doi/10.1371/annotation/2032e267-bd91-442c-86b8-f4968437960e

*  Zika! Computational Biology to the Rescue | Biomedical Computation Review

Zika! Computational Biology to the Rescue. Advances in computational modeling of viral epidemics and viruses themselves produce ... Basic biology and drug discovery. All have a role to play in dealing with what is shaping up to be one of the greatest global ... To understand biology-and provide appropriate medical care-scientists need to understand interactions across multiple scales. ... And it does so on IBM's World Community Grid (WCG), which draws its computational horsepower from more than 700,000 volunteers ...
biomedicalcomputationreview.org/content/zika-computational-biology-rescue

*  WHY MAJOR IN COMPUTATIONAL BIOLOGY | Computer Science

WHY MAJOR IN COMPUTATIONAL BIOLOGY. About the Program. Scientific discovery is the result of creative interplay between ... Computational models play an increasingly important role in deducing the consequences of explanatory models, yet biologists are ... this degree program will be better positioned to develop productive careers in the burgeoning fields of computational biology ... In part this results from a lack of interdisciplinary training in both biological and computational sciences. This program ...
cs.fsu.edu/academics/why-major-in-computational-biology/

*  Bioinformatics: Bioinformatics and Sequence Analysis | Lund University

... the application of computational methods to biological and biomedical problems, is a rapidly growing field. Modern biochemists ... in Chemistry, Physics, Computational science, Mathematics or Mathematical statistics including at least 15 ECTS credits of ... 120 ECTS credits in Molecular Biology or Biomedicine or an undergraduate degree corresponding to a B.Sc. ... Bioinformatics, the application of computational methods to biological and biomedical problems, is a rapidly growing field. ...
lunduniversity.lu.se/lubas/i-uoh-lu-BINP11

*  Journal of Computational Biology

... cutting-edge methods in computational biology and bioinformatics. ... Journal of Computational Biology. Co-Editors-in-Chief: Sorin ... In general, JOURNAL OF COMPUTATIONAL BIOLOGY follows the conventions of the CBE Style Manual (Council of Biology Editors, ... JOURNAL OF COMPUTATIONAL BIOLOGYprovides a forum for communicating scientific and technical issues associated with the analysis ... If published in JOURNAL OF COMPUTATIONAL BIOLOGY, the paper cannot be published anywhere else in the same form, regardless of ...
liebertpub.com/openaccess/journal-of-computational-biology/31/

*  Publications - Computational Biology Lab

Computational Biology lab (Li lab) at Case Western Reserve University ...
https://sites.google.com/a/case.edu/jingli/research/publications

*  RECOMB and Journal of Computational Biology

RECOMB and Journal of Computational Biology/Mary Ann Liebert, Inc Publisher of authoritative peer-reviewed journals in the most ... of the Journal of Computational Biology 20th Anniversary: Highly Influential Papers in Computational Biology will be invited to ... Journal of Computational Biology is now. the Official Journal of In 1997, Co-Editors-in-Chief Sorin Istrail, PhD, and Michael S ... Although computational biology and bioinformatics papers have been published in a number of other journals and conferences, and ...
liebertpub.com/lpages/recomb-cmb/62/

*  Algorithms for Computational Biology - Third | María Botón-Fernández | Springer

This book constitutes the proceedings of the Third InternationalConference on Algorithms for Computational Biology, AlCoB 2016 ... Algorithms for Computational Biology. Book Subtitle. Third International Conference, AlCoB 2016, Trujillo, Spain, June 21-22, ... Algorithms for Computational Biology. Third International Conference, AlCoB 2016, Trujillo, Spain, June 21-22, 2016, ... This book constitutes the proceedings of the Third InternationalConference on Algorithms for Computational Biology, AlCoB 2016 ...
springer.com/us/book/9783319388267

*  SCS Directory - Computational Biology Department | Carnegie Mellon School of Computer Science

Assistant Department Head for Education; Assistant Teaching Professor ...
cs.cmu.edu/directory/cbd?order=field_last_name&page=1&sort=desc

*  Transactions on Computational Systems Biology VI - Google Books

The 9 papers selected for this special issue discuss various aspects of computational methods, algorithm and techniques in ... The 5th Transactions on Computational Systems Biology volume, edited by Gordon Plotkin, features carefully selected and ... Computational_Systems_Bi.html?hl=de&id=w5W8CdomtZYC&utm_source=gb-gplus-shareTransactions on Computational Systems Biology VI. ... Transactions on Computational Systems Biology VI. Band 4220 von Lecture Notes in Computer Science. Transactions on ...
https://books.google.de/books?id=w5W8CdomtZYC&hl=de

*  Publications | Computational Biology and Informatics Laboratory

... of the Computational Biology and Informatics Laboratory, School of Medicine, University of Pennsylvania, 1997 ... Yan B, Chen G, Saigal K, Yang X, Jensen ST, Van Waes C, Stoeckert CJ, Chen Z. (2008) Systems biology-defined NF-kappaB regulons ... 2008) Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium ... 2006) Computational modeling of the Plasmodium falciparum interactome reveals protein functionon a genome-wide scale Genome Res ...
cbil.upenn.edu/publications

*  Downloads | Computational Biology and Informatics Laboratory

at the University of ...
cbil.upenn.edu/downloads/

*  DSpace@MIT: Browsing Computational and Systems Biology by Title

Browsing Computational and Systems Biology by Title Research and Teaching Output of the MIT Community. ... Computational insights into the ecology of the human microbiota  Smillie, Christopher Scott (Massachusetts Institute of ... Computational design of orthogonal antiparallel homodimeric coiled coils  Negron, Christopher (Massachusetts Institute of ... Experimental and computational analysis of epidermal growth factor receptor pathway phosphorylation dynamics  ...
https://dspace.mit.edu/handle/1721.1/54826/browse?type=title

*  Our Mission | Computational Biology and Informatics Laboratory

Welcome to the Computational Biology and Informatics Laboratory (CBIL) in the Institute for Biomedical Informatics. The goal of ... CBIL is directed by Chris Stoeckert who is faculty in the Department of Genetics and the Genomics and Computational BIology ...
cbil.upenn.edu

*  ISCB Kicks off Contest to Improve Computational Biology Articles on Wikipedia | GenomeWeb

The International Society for Computational Biology has launched a competition that aims to improve existing Wikipedia articles ... Computational Biology has launched a competition that aims to improve existing Wikipedia articles about computational biology. ... ISCB Kicks off Contest to Improve Computational Biology Articles on Wikipedia. Jul 20, 2012 ... Home » ISCB Kicks off Contest to Improve Computational Biology Articles on Wikipedia ...
https://genomeweb.com/informatics/iscb-kicks-contest-improve-computational-biology-articles-wikipedia

*  BIOL 5496/CSE 7800: Computational Molecular Biology Journal Club

Computational Molecular Biology Journal Club. Welcome to the home page for BIOL 5496/CSE 7800, the Computational Molecular ... RFECS: a random-forest based algorithm for enhancer identification from chromatin state. PLOS Computational Biology 9:e1002698 ... Participants in the Journal Club present recent published research in the areas of computational molecular biology, systems ... Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25, 2009. ...
cse.wustl.edu/~jbuhler/cmb-journal-club/cmb-journal-club-fall-2015.html

*  PLOS ONE: Computational biology

Create a weekly email alert for: Computational biology You can change these options by clicking profile then "Alerts and ... Get an email alert for Computational biology * Get the RSS feed for Computational biology ...
journals.plos.org/plosone/browse/Computational_Biology

*  Opportunity: Scientist -- Computational Biology/Bioinformatics -- Human Genetics @ Top pharmaceutical company in Germany -...

Acting as the key interface to the NGS lab within the Computational Biology group and play a driving role in the definition of ... Excellent knowledge and a broad spectrum in bioinformatics and computational biology with a focus on topics related to RNA-Seq ... PhD degree or equivalent qualification in Computational Biology or related fields several years of post-PhD experience with a ... Opportunity: Scientist -- Computational Biology/Bioinformatics -- Human Genetics @ Top pharmaceutical company in Germany. ...
https://bioinformatics.org/forums/forum.php?forum_id=12794

*  Opportunity: Director of Computational Biology and Genomics @ Pharma company based in South Germany - Bioinformatics.org

Opportunity: Director of Computational Biology and Genomics @ Pharma company based in South Germany. Submitted by Eugene Mc ... At least 5 years of experience within the field of Computational Biology in a pharmaceutical industry or biotech background ... As a Director you are overall responsible for leading and managing the research group Computational Biology & Genomics (~20 ... As a Director you are accountable for budget and headcount of the Group Computational Biology & Genomics. ...
https://bioinformatics.org/forums/forum.php?forum_id=12795

*  New Computational Tool for Cancer Treatment - Biology Online

Home » Biology Articles » Bioinformatics » New Computational Tool for Cancer Treatment. New Computational Tool for Cancer ... Biology-Online.org. All Rights Reserved. Register , Login , About Us , Contact Us , Link to Us , Privacy Policy ... Welcome to biology-online.org! Please login to access all site features. Create an account. ... This is a satisfactory proof of principle showing that computational techniques can produce very effective inhibitors for ...
biology-online.org/articles/computational-tool-cancer-treatment.html

*  PLOS Computational Biology: Information Flow Analysis of Interactome Networks

To this end, we present a novel computational approach to identify central proteins while considering the confidence of data ...
journals.plos.org/ploscompbiol/article/comments?id=10.1371/journal.pcbi.1000350&imageURI=info:doi/10.1371/journal.pcbi.1000350.g008

*  PLOS Computational Biology: Intrinsic Disorder in the Human Spliceosomal Proteome

Author Summary In eukaryotic cells, introns are spliced out of proteincoding mRNAs by a highly dynamic and extraordinarily plastic molecular machine called the spliceosome. In recent years, multiple regions of intrinsic structural disorder were found in spliceosomal proteins. Intrinsically disordered regions lack stable native three-dimensional structure in solutions, which makes them structurally flexible and/or able to switch between different conformations. Hence, intrinsically disordered regions are the ideal candidate responsible for the spliceosome's plasticity. Intrinsically disordered regions are also frequently the sites of post-translational modifications, which were also proven to be important in spliceosome dynamics. In this article, we describe the results of a structural bioinformatics analysis focused on intrinsic disorder in the spliceosomal proteome. We systematically analyzed all known human spliceosomal proteins with regards to the presence and type of intrinsic disorder. Almost a
journals.plos.org/ploscompbiol/article/comments?id=10.1371/journal.pcbi.1002641&imageURI=info:doi/10.1371/journal.pcbi.1002641.t002

*  PLOS Computational Biology: Microbial Co-occurrence Relationships in the Human Microbiome

Author Summary The human body is a complex ecosystem where microbes compete, and cooperate. These interactions can support health or promote disease, e.g. in dental plaque formation. The Human Microbiome Project collected and sequenced ca. 5,000 samples from 18 different body sites, including the airways, gut, skin, oral cavity and vagina. These data allowed the first assessment of significant patterns of co-presence and exclusion among human-associated bacteria. We combined sparse regression with an ensemble of similarity measures to predict microbial relationships within and between body sites. This captured known relationships in the dental plaque, vagina, and gut, and also predicted novel interactions involving members of under-characterized phyla such as TM7. We detected relationships necessary for plaque formation and differences in community composition among dominant members of the gut and vaginal microbiomes. Most relationships were strongly niche-specific, with only a few hub microorganisms
journals.plos.org/ploscompbiol/article/figure?id=10.1371/journal.pcbi.1002606.g005

*  PLOS Computational Biology: Internal Representations of Temporal Statistics and Feedback Calibrate Motor-Sensory Interval Timing

Author Summary Human performance in a timing task depends on the context of recently experienced time intervals. In fact, people may use prior experience to improve their timing performance. Given the relevance of time for both sensing and acting in the world, how humans learn and represent temporal information is a fundamental question in neuroscience. Here, we ask subjects to reproduce the duration of time intervals drawn from different distributions (different temporal contexts). We build a set of models of how people might behave in such a timing task, depending on how they are representing the temporal context. Comparison between models and data allows us to establish that in general subjects are integrating task-relevant temporal information with the provided error feedback to enhance their timing performance. Analysis of the subjects' responses allows us to reconstruct their internal representation of the temporal context, and we compare it with the true distribution. We find that with the help
journals.plos.org/ploscompbiol/article/figure?id=10.1371/journal.pcbi.1002771.g002

*  Meeting Summaries and Scientific Reports - NHLBI, NIH

Systems Biology. Mitochondrial Dysfunction Working Group, Executive Summary (2007): see Computational Biology and Informatics, ... Computational Biology and Informatics. NHLBI Working Group on Electronic Health Records: Research Priorities to Improve ... Vascular Biology. Blood Vessel Maturation: Arteriogenesis, Working Group Executive Summary (2005). Computational Modeling ... Computational Models for Analyzing Genotype-Phenotype Associations in Rare Diseases, Working Group Executive Summary (2008) ...
https://nhlbi.nih.gov/research/meetingsandreports

*  Computational Biology | Open Access Articles | Digital Commons Network™

Open access academic research from top universities on the subject of Computational Biology ... All Articles in Computational Biology Follow Faceted Search 742 full-text articles. Page 1 of 26. ... Computational Biology Institute. Drosophila melanogaster is an outstanding model to study the molecular and functional basis of ... Computational Biology Institute. Salinity gradients are critical habitat determinants for freshwater organisms. Silverside ...
network.bepress.com/life-sciences/genetics-and-genomics/computational-biology/

PSI Protein Classifier: PSI Protein Classifier is a program generalizing the results of both successive and independent iterations of the PSI-BLAST program. PSI Protein Classifier determines belonging of the found by PSI-BLAST proteins to the known families.Clonal Selection Algorithm: In artificial immune systems, Clonal selection algorithms are a class of algorithms inspired by the clonal selection theory of acquired immunity that explains how B and T lymphocytes improve their response to antigens over time called affinity maturation. These algorithms focus on the Darwinian attributes of the theory where selection is inspired by the affinity of antigen-antibody interactions, reproduction is inspired by cell division, and variation is inspired by somatic hypermutation.List of systems biology conferences: Systems biology is a biological study field that focuses on the systematic study of complex interactions in biological systems, thus using a new perspective (integration instead of reduction) to study them. Particularly from year 2000 onwards, the term is used widely in the biosciences.David Glass (sociologist): 1970sMac OS X Server 1.0Protein subcellular localization prediction: Protein subcellular localization prediction (or just protein localization prediction) involves the computational prediction of where a protein resides in a cell.Interval boundary element method: Interval boundary element method is classical boundary element method with the interval parameters.
Lattice protein: Lattice proteins are highly simplified computer models of proteins which are used to investigate protein folding.Ontario Genomics Institute: The Ontario Genomics Institute (OGI) is a not-for-profit organization that manages cutting-edge genomics research projects and platforms.The Ontario Genomics Institute OGI also helps scientists find paths to the marketplace for their discoveries and the products to which they lead, and it works through diverse outreach and educational activities to raise awareness and facilitate informed public dialogue about genomics and its social impacts.RDF query language: An RDF query language is a computer language, specifically a query language for databases, able to retrieve and manipulate data stored in Resource Description Framework format.Nencki Institute of Experimental Biology: The Nencki Institute of Experimental Biology is a Polish scientific research organization and a part of Polish Academy of Sciences headquartered in Warsaw, Poland. Founded in 1918, it is a leading institution in the country in the field of neurobiology, molecular biology and biochemistry.Mexican International Conference on Artificial Intelligence: MICAI (short for Mexican International Conference on Artificial Intelligence) is the name of an annual conference covering all areas of Artificial Intelligence (AI), held in Mexico. The first MICAI conference was held in 2000.CS-BLASTMatrix model: == Mathematics and physics ==Vladimir Andreevich Markov: Vladimir Andreevich Markov (; May 8, 1871 – January 18, 1897) was a Russian mathematician, known for proving the Markov brothers' inequality with his older brother Andrey Markov. He died of tuberculosis at the age of 25.Human Proteinpedia: Human Proteinpedia is a portal for sharing and integration of human proteomic data,.Kandasamy et al.Internet organizations: This is a list of Internet organizations, or organizations that play or played a key role in the evolution of the Internet by developing recommendations, standards, and technology; deploying infrastructure and services; and addressing other major issues.Immersive technologyProtein–protein interactionDNA sequencer: A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine).List of molecular graphics systems: This is a list of software systems that are used for visualizing macromolecules.Inverse probability weighting: Inverse probability weighting is a statistical technique for calculating statistics standardized to a population different from that in which the data was collected. Study designs with a disparate sampling population and population of target inference (target population) are common in application.Conference and Labs of the Evaluation Forum: The Conference and Labs of the Evaluation Forum (formerly Cross-Language Evaluation Forum), or CLEF, is an organization promoting research in multilingual information access (currently focusing on European languages). Its specific functions are to maintain an underlying framework for testing information retrieval systems and to create repositories of data for researchers to use in developing comparable standards.Extracellular: In cell biology, molecular biology and related fields, the word extracellular (or sometimes extracellular space) means "outside the cell". This space is usually taken to be outside the plasma membranes, and occupied by fluid.Biological network: A biological network is any network that applies to biological systems. A network is any system with sub-units that are linked into a whole, such as species units linked into a whole food web.Gene signature: A gene signature is a group of genes in a cell whose combined expression patternItadani H, Mizuarai S, Kotani H. Can systems biology understand pathway activation?Reaction coordinatePlant Proteome Database: The Plant Proteome Database is a National Science Foundation-funded project to determine the biological function of each protein in plants.Sun Q, Zybailov B, Majeran W, Friso G, Olinares PD, van Wijk KJ.Hyperparameter: In Bayesian statistics, a hyperparameter is a parameter of a prior distribution; the term is used to distinguish them from parameters of the model for the underlying system under analysis.Dda (DNA-dependent ATPase): Dda (short for DNA-dependent ATPase; also known as Dda helicase and Dda DNA helicase) is the 439-amino acid 49,897-atomic mass unit protein coded by the Dda gene of the bacteriophage T4 phage, a virus that infects enterobacteria.Michael K. Denk: Michael K. Denk (or Karl Michael Denk) is a Professor of chemistry at the University of Guelph, Ontario.Von Neumann regular ring: In mathematics, a von Neumann regular ring is a ring R such that for every a in R there exists an x in R such that . To avoid the possible confusion with the regular rings and regular local rings of commutative algebra (which are unrelated notions), von Neumann regular rings are also called absolutely flat rings, because these rings are characterized by the fact that every left module is flat.Cellular microarray: A cellular microarray is a laboratory tool that allows for the multiplex interrogation of living cells on the surface of a solid support. The support, sometimes called a "chip", is spotted with varying materials, such as antibodies, proteins, or lipids, which can interact with the cells, leading to their capture on specific spots.Branching order of bacterial phyla (Gupta, 2001): There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla.Coles PhillipsProtein primary structure: The primary structure of a peptide or protein is the linear sequence of its amino acid structural units, and partly comprises its overall biomolecular structure. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end.Synthetic genomics: Synthetic genomics is a nascent field of synthetic biology that uses aspects of genetic modification on pre-existing life forms with the intent of producing some product or desired behavior on the part of the life form so created.Database of protein conformational diversity: The Database of protein conformational diversity (PCDB) is a database of diversity of protein tertiary structures within protein domains as determined by X-ray crystallography. Proteins are inherently flexible and this database collects information on this subject for use in molecular research.Molecular evolution: Molecular evolution is a change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes.Knotted protein: Knotted proteins are proteins whose backbones entangle themselves in a knot. One can imagine pulling a protein chain from both termini, as though pulling a string from both ends.Generalizability theory: Generalizability theory, or G Theory, is a statistical framework for conceptualizing, investigating, and designing reliable observations. It is used to determine the reliability (i.FERM domain: In molecular biology, the FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane.Pituitary-specific positive transcription factor 1: POU domain, class 1, transcription factor 1 (Pit1, growth hormone factor 1), also known as POU1F1, is a transcription factor for growth hormone.DNA binding site: DNA binding sites are a type of binding site found in DNA where other molecules may bind. DNA binding sites are distinct from other binding sites in that (1) they are part of a DNA sequence (e.

(1/20328) 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.

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)

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

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)

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

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)

(4/20328) Bayesian inference on biopolymer models.

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)

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

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)

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

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)

(7/20328) Protein subcellular location prediction.

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)

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

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)



PLOS Computa


  • PLOS Computational Biology 9:e1002698, 2013. (wustl.edu)
  • PLOS Computational Biology: Explain Bioinformatics to Your Grandmother! (plos.org)

Bioinformatics


  • Over the years, RECOMB became the top, most-competitive conference devoted to analytical rigorous methods in computational biology and bioinformatics. (liebertpub.com)
  • Although computational biology and bioinformatics papers have been published in a number of other journals and conferences, and there has been an explosion of new journals since 2004, no other venue comes close to these 17 volumes in analytical rigor and innovation inspired by genomics and cell biology. (liebertpub.com)
  • The senior author(s) of the Journal of Computational Biology 20th Anniversary: Highly Influential Papers in Computational Biology will be invited to write an accompanying paper, a new type of journal paper, "critical synthesis of current methods in computational biology and bioinformatics," about the technical developments since the "classic" paper. (liebertpub.com)
  • A Mary Ann Liebert, Inc., publishers book, "Computational Biology and Bioinformatics: The State of the Analytical Method," will contain all of these highly influential papers and their associated critical syntheses of the first 20 years of Journal of Computational Biology . (liebertpub.com)
  • Students participating in this degree program will be better positioned to develop productive careers in the burgeoning fields of computational biology and bioinformatics. (fsu.edu)
  • The 9 papers selected for this special issue discuss various aspects of computational methods, algorithm and techniques in bioinformatics such as gene expression analysis, biomedical literature mining and natural language processing, protein structure prediction, biological database management and biomedical information retrieval. (google.de)
  • Participants in the Journal Club present recent published research in the areas of computational molecular biology, systems biology, and bioinformatics. (wustl.edu)
  • Excellent knowledge and a broad spectrum in bioinformatics and computational biology with a focus on topics related to RNA-Seq, single cell RNA-Seq and other NGS applications. (bioinformatics.org)
  • According to Olivier Michielin, Assistant Member at the Lausanne Branch of LICR and leader of the SIB Swiss Institute of Bioinformatics Molecular Modeling group, 'This is a satisfactory proof of principle showing that computational techniques can produce very effective inhibitors for specific cancer targets with high yield. (biology-online.org)

genomics


  • CBIL is directed by Chris Stoeckert who is faculty in the Department of Genetics and the Genomics and Computational BIology Graduate Group in the Perelman School of Medicine and a member of the Penn Genome Frontiers Institute at the University of Pennsylvania. (upenn.edu)
  • A great opportunity is available with a world-leading Pharma company based in South Germany for a Director of Genomics and Computational Biology within the research department. (bioinformatics.org)
  • As a Director you are overall responsible for leading and managing the research group Computational Biology & Genomics (~20 reports) within the department Target Discovery Research. (bioinformatics.org)
  • As a Director you are accountable for budget and headcount of the Group Computational Biology & Genomics. (bioinformatics.org)

molecular biology


  • It will accept papers on the computational, mathematical, and statistical aspects of molecular biology. (liebertpub.com)
  • In 1997, Co-Editors-in-Chief Sorin Istrail, PhD, and Michael S. Waterman, PhD, along with Pavel Pevzner, founded the Annual International Conference on Research in Computational Molecular Biology (RECOMB). (liebertpub.com)
  • ISCB made the announcement at the 20th annual international conference on Intelligent Systems for Molecular Biology, held here this week. (genomeweb.com)
  • Welcome to the home page for BIOL 5496/CSE 7800, the Computational Molecular Biology Journal Club. (wustl.edu)

Informatics Laboratory


  • Welcome to the Computational Biology and Informatics Laboratory (CBIL) in the Institute for Biomedical Informatics. (upenn.edu)

Systems Biology


  • books.google.de - The 5th Transactions on Computational Systems Biology volume, edited by Gordon Plotkin, features carefully selected and enhanced contributions initially presented at the 2005 IEEE International Conference on Granular Computing. (google.de)

2016


  • This book constitutes the proceedings of the Third InternationalConference on Algorithms for Computational Biology, AlCoB 2016, held inTrujillo, Spain, in June 2016. (springer.com)

interdisciplinary


  • In part this results from a lack of interdisciplinary training in both biological and computational sciences. (fsu.edu)

biological


  • JOURNAL OF COMPUTATIONAL BIOLOGY provides a forum for communicating scientific and technical issues associated with the analysis and management of biological information at the molecular level. (liebertpub.com)
  • analytical chemistry techniques or molecular biological experimental work, guided by computational structural analysis. (fsu.edu)

papers


  • The 17 annual RECOMB special issues featured the most competitively selected papers presenting innovation in computational methods. (liebertpub.com)
  • The 9 papers selected for this special issue discuss various aspects of computational. (google.de)
  • A growing willingness to share results as quickly as possible through channels like bioRxiv (biorxiv.org), a website where scientists post papers before they have been published in peer-reviewed journals, also meant that modelers and researchers could more speedily adapt their computational tools as new information became available. (biomedicalcomputationreview.org)

experimental


  • Acting as the key interface to the NGS lab within the Computational Biology group and play a driving role in the definition of experimental design strategies and coordinate the implementation and development of the LIMS. (bioinformatics.org)

Drug Discovery


  • Carrying out data analyses to generate and test hypotheses in the context of new therapeutic concepts in collaboration with other members of the Computational Biology group or scientists from BI's Therapeutic Areas for Drug Discovery (Cardiometabolic Research, Central Nervous System Research, Inflammation & Respiratory Research, Immune Modulation & Research Beyond Borders). (bioinformatics.org)

Journal


  • Your submission to the Journal of Computational Biology provides you with robust tools and support to ensure maximum impact and readership for your work. (liebertpub.com)
  • If published in JOURNAL OF COMPUTATIONAL BIOLOGY , the paper cannot be published anywhere else in the same form, regardless of language, without the consent of the Publisher. (liebertpub.com)
  • To recognize exceptional achievement in analytical rigorous methods in computational biology, starting this anniversary year, Mary Ann Liebert, Inc., publishers will be offering an annual Journal of Computational Biology - RECOMB Mary Ann Liebert Rosalind Franklyn Analytical Rigor Computational Biology Prize of $1,000 for the top - breakthrough paper in the annual RECOMB special issue distinguishing itself with analytical rigor. (liebertpub.com)

research


  • This research-driven company is looking for talented Bioinformaticians/Computational Biologists/Scientists with NGS experience and a particular focus on Human Genetics (GWAS) to join their Research Department in South-West Germany. (bioinformatics.org)

years


  • To a large extent, says Alessandro Vespignani, PhD , a computational modeler at Northeastern University, that lightning-fast reaction reflects years of hard work and investment in computational modeling (including such initiatives as MIDAS-Models of Infectious Disease Agents, an NIH-funded network of computational modelers), as well as grim experience with the H1N1 pandemic and the West African Ebola epidemic. (biomedicalcomputationreview.org)

play


  • Computational models play an increasingly important role in deducing the consequences of explanatory models, yet biologists are routinely hindered by the limitations of models currently available as software. (fsu.edu)

issues


  • This program seeks to achieve two goals: 1) to develop an understanding of the issues associated with developing biologically meaningful computational models, and 2) to give students the broad-based education that is needed to create a set of models directed towards solving a practical biomedical problem. (fsu.edu)

experience


  • Experience with other type of omics data, network biology or machine learning is an additional asset. (bioinformatics.org)

proof


  • As was said in the preface of the first RECOMB special issue, "this volume is proof positive of the emergence of a new discipline, computational biology. (liebertpub.com)