Genomes and Genes
Summary: One of the biological sciences concerned with the origin, structure, development, growth, function, genetics, and reproduction of animals, plants, and microorganisms.
Publications186 found, 100 shown here
- Identification of biological relationships from text documents using efficient computational methodsMathew Palakal
Department of Computer and Information Science, Indiana University Purdue University Indianapolis, 723 West Michigan St SL 280, Indianapolis, IN 46202 USA
J Bioinform Comput Biol 1:307-42. 2003..For the thousand abstracts, 53 relationships were extracted of which 43 were correct, giving a specificity of 81 percent. These results are promising for multi-object identification and relationship finding from biological documents...
- Next-generation sequencing transforms today's biologyStephan C Schuster
Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Building, University Park, Pennsylvania 16802, USA
Nat Methods 5:16-8. 2008..However, before stepping into the limelight, next-generation sequencing had to overcome the inertia of a field that relied on Sanger-sequencing for 30 years...
- The second wave of synthetic biology: from modules to systemsPriscilla E M Purnick
Department of Electrical Engineering, Princeton University, Princeton, New Jersey 08544, USA
Nat Rev Mol Cell Biol 10:410-22. 2009Synthetic biology is a research field that combines the investigative nature of biology with the constructive nature of engineering...
- Feature point tracking and trajectory analysis for video imaging in cell biologyI F Sbalzarini
Institute of Computational Science, ETH Zurich, 8092 Zurich, Switzerland
J Struct Biol 151:182-95. 2005..the automated detection and quantitative analysis of particle trajectories as recorded by video imaging in cell biology. The tracking process requires no a priori mathematical modeling of the motion, it is self-initializing, it ..
- Web API for biology with a workflow navigation systemYeondae Kwon
Laboratory for Research and Development of Biological Databases, Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411 8540, Japan
Nucleic Acids Res 37:W11-6. 2009DNA Data Bank of Japan (DDBJ) provides Web-based systems for biological analysis, called Web APIs for biology (WABI). So far, we have developed over 20 SOAP services and several workflows that consist of a series of method invocations...
- Graph theory and networks in BiologyO Mason
Hamilton Institute, National University of Ireland, Maynooth, Co Kildare, Ireland
IET Syst Biol 1:89-119. 2007A survey of the use of graph theoretical techniques in Biology is presented...
- Directing experimental biology: a case study in mitochondrial biogenesisMatthew A Hibbs
Lewis Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Princeton, New Jersey, United States of America
PLoS Comput Biol 5:e1000322. 2009..experimentally validated on a large scale, leaving many bioinformatic methods unproven and underutilized in the biology community...
- Self-organization in cell biology: a brief historyEric Karsenti
Eric Karsenti is at the Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Nat Rev Mol Cell Biol 9:255-62. 2008..Self-organization concepts that were first developed in chemistry and physics and then applied to various morphogenetic problems in biology over the past century are now beginning to be applied to the organization of the living cell.
- Modular cell biology: retroactivity and insulationDomitilla Del Vecchio
Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
Mol Syst Biol 4:161. 2008..We introduce, in particular, a mechanism based on a phosphorylation-dephosphorylation cycle. This mechanism enjoys a remarkable insulation property, due to the fast timescales of the phosphorylation and dephosphorylation reactions...
- Biology, one molecule at a timeAchillefs N Kapanidis
Department of Physics and Interdisciplinary Research Collaboration in Bionanotechnology, Clarendon Laboratory, University of Oxford, Oxford, UK
Trends Biochem Sci 34:234-43. 2009..The single-molecule approach to biology offers distinct advantages over the conventional approach of taking bulk measurements; this additional ..
- Structural biology and chemistry of the terpenoid cyclasesDavid W Christianson
Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA
Chem Rev 106:3412-42. 2006
- The evolving biology and treatment of prostate cancerRussel S Taichman
University of Michigan Comprehensive Cancer Center, Ann Arbor, Michigan, USA
J Clin Invest 117:2351-61. 2007..As the population ages and prostate cancer prevalence increases, challenges remain in the diagnosis of clinically relevant prostate cancer as well as the management of the metastatic and androgen-independent metastatic disease states...
- Curious parallels and curious connections--phylogenetic thinking in biology and historical linguisticsQuentin D Atkinson
Department of Psychology, University of Auckland, Private Bag 92019, Auckland 1020, New Zealand
Syst Biol 54:513-26. 2005..of process, there are a number of equally curious parallels and connections between the development of methods in biology and historical linguistics...
- George Emil Palade: charismatic virtuoso of cell biologyAlan M Tartakoff
Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
Nat Rev Mol Cell Biol 3:871-6. 2002..This focus on the logic of organelles defined a crucial turning point in biomedical science. The following article sketches Palade's research, as part of a larger community that flourished after the Second World War...
- Adding a little reality to building ontologies for biologyPhillip Lord
School of Computing Science, Newcastle University, Newcastle upon Tyne, United Kingdom
PLoS ONE 5:e12258. 2010Many areas of biology are open to mathematical and computational modelling. The application of discrete, logical formalisms defines the field of biomedical ontologies. Ontologies have been put to many uses in bioinformatics...
- Textpresso: an ontology-based information retrieval and extraction system for biological literatureHans Michael Muller
Division of Biology and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, USA
PLoS Biol 2:e309. 2004..Textpresso can be accessed at http://www.textpresso.org or via WormBase at http://www.wormbase.org...
- Biotechnology of flavonoids and other phenylpropanoid-derived natural products. Part I: Chemical diversity, impacts on plant biology and human healthFilippos Ververidis
Laboratory of Plant Biochemistry and Biotechnology, Department of Plant Sciences, Technological Educational Institute of Crete, Heraklion, Crete, Greece
Biotechnol J 2:1214-34. 2007....
- Mechanisms, biology and inhibitors of deubiquitinating enzymesKerry Routenberg Love
Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nat Chem Biol 3:697-705. 2007....
- Clinical and therapeutical implications of EPC biology in atherosclerosisN Werner
Medizinische Klinik und Poliklinik II, Universitatsklinikum Bonn, Germany
J Cell Mol Med 10:318-32. 2006..In this review we focus on the role of circulating endothelial progenitor cells in endothelial cell repair mechanisms at the vascular wall and their potentially protective and therapeutic role in atherosclerotic disease...
- Transforming growth factor-beta : biology and clinical relevanceIsaac Yi Kim
Department of Urology, University of California at Irvine, Orange, CA 92868, USA
J Biochem Mol Biol 38:1-8. 2005..In this report, we will review these clinical implications of transforming growth factor-beta ...
- Designing and encoding models for synthetic biologyLukas Endler
EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
J R Soc Interface 6:S405-17. 2009A key component of any synthetic biology effort is the use of quantitative models. These models and their corresponding simulations allow optimization of a system design, as well as guiding their subsequent analysis...
- Evolution in health and medicine Sackler colloquium: Making evolutionary biology a basic science for medicineRandolph M Nesse
Department of Psychiatry and Psychology, University of Michigan, Room 3018, East Hall, 530 Church Street, Ann Arbor, MI 48104, USA
Proc Natl Acad Sci U S A 107:1800-7. 2010New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully...
- A treasure trove for lipoprotein biologyAldons J Lusis
Nat Genet 40:129-30. 2008
- Biology and health inequalityEric Brunner
Departmentof Epidemiology and Public Health, University College London, London, United Kingdom
PLoS Biol 5:e267. 2007
- Returning to our roots: making plant biology research relevant to future challenges in agricultureSteven J Rothstein
Department of Molecularand Cellular Biology, University of Guelph, Guelph, ON, Canada
Plant Cell 19:2695-9. 2007
- Structure, biochemistry and biology of hepoxilins: an updateSantosh Nigam
Eicosanoid and Lipid Research Division and Centre for Experimental Gynecology and Breast Research, Charité University Medical Centre Benjamin Franklin, Berlin, Germany
FEBS J 274:3503-12. 2007..The present review gives an update on the biochemistry, biology and clinical aspects of hepoxilin-based drug development...
- Pulp biology: progress during the past 25 yearsHenry O Trowbridge
University of Pennsylvania, USA
Aust Endod J 29:5-12. 2003....
- The semantic web and biologyTor-Kristian Jenssen
Dept of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, 0310 Oslo, Norway
Drug Discov Today 7:992. 2002
- Scientific illiteracy and the partisan takeover of biologyLiza Gross
PLoS Biol 4:e167. 2006
- The biology and diagnostic applications of plasma RNAY M Dennis Lo
Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region, China
Ann N Y Acad Sci 1022:135-9. 2004..development of robust extraction and quantification protocols for circulating RNA, new information regarding its biology and characteristics has been obtained...
- Free radicals in biology and medicine: from inflammation to biotechnologyOkezie I Aruoma
Faculty of Health and Social Care, London South Bank University, 103 Borough Road, London, UK
Biofactors 27:1-3. 2006
- [Advances in plant proteomics. II. Application of proteome techniques to plant biology research]Song Lin Ruan
Plant Molecular Biology and Proteomics Lab, Institute of BiotechnologyHangzhou Academy of Agriculture Science, Hangzhou 310024, China
Yi Chuan 28:1633-48. 2006..The prospects of plant proteomics are discussed...
- A multisolute osmotic virial equation for solutions of interest in biologyJ A W Elliott
Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada T6G 2G6
J Phys Chem B 111:1775-85. 2007The osmotic virial equation was used to predict osmolalities of solutions of interest in biology. The second osmotic virial coefficients, Bi, account for the interactions between identical solute molecules...
- Large-scale optimization-based classification models in medicine and biologyEva K Lee
Center for Operations Research in Medicine and HealthCare, School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, GA 30332 0205, USA
Ann Biomed Eng 35:1095-109. 2007..In all these applications, the predictive model yields correct classification rates ranging from 80 to 100%. This provides motivation for pursuing its use as a medical diagnostic, monitoring and decision-making tool...
- Popper, laws, and the exclusion of biology from genuine scienceDavid N Stamos
Department of Philosophy, York University, 4700 Keele St, North York, ON, Canada M3J 1P3
Acta Biotheor 55:357-75. 2007..It is then argued that biology arguably has no genuine laws of its own...
- Recent insights into the biology and biomedical applications of Flock House virusP A Venter
Department of Molecular Biology, CB262, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA 92037, USA
Cell Mol Life Sci 65:2675-87. 2008..Finally, applications for FHV as an epitopepresenting system are described with particular reference to its recent use for the development of a novel anthrax antitoxin and vaccine...
- From Darwinism to evolutionary biologyU Kutschera
Science 321:1157-8. 2008
- Structural biology in fragment-based drug designChristopher W Murray
Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
Curr Opin Struct Biol 20:497-507. 2010..Here we examine the recent literature looking at how structural biology has been used in a variety of successful fragment-screening applications...
- On the growth of scientific knowledge: yeast biology as a case studyXionglei He
State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat Sen University, Guangzhou, China
PLoS Comput Biol 5:e1000320. 2009..These findings reveal collective human behaviors in scientific research and help design better strategies in future knowledge exploration...
- Innovations in teaching undergraduate biology and why we need themWilliam B Wood
Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309 0347, USA
Annu Rev Cell Dev Biol 25:93-112. 2009..Their widespread adoption could have a major impact on the introductory training of biology students.
- Toward a conceptual framework for biologySamuel M Scheiner
Division of Environmental Biology, National Science Foundation, Arlington, Virginia 22230, USA
Q Rev Biol 85:293-318. 2010..progresses faster when researchers operate within an explicit framework of concepts and theories, but currently biology has no explicit, overarching conceptual framework and few general theories...
- Responsive magnetic resonance imaging contrast agents as chemical sensors for metals in biology and medicineEmily L Que
Department of Chemistry, University of California, Berkeley, CA 94720, USA
Chem Soc Rev 39:51-60. 2010..and the life sciences offers a broad palette of opportunities for researchers with interests ranging from coordination chemistry and spectroscopy to supramolecular chemistry and molecular recognition to metals in biology and medicine.
- Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systemsCaleb J Bashor
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158 2517, USA
Annu Rev Biophys 39:515-37. 2010..and the goal of predictively and quantitatively understanding its function is one of the next great challenges in biology. Much of what we know about the cell concerns its constituent parts, but to a great extent we have yet to decode ..
- Categorical data analysis in experimental biologyBo Xu
Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
Dev Biol 348:3-11. 2010The categorical data set is an important data class in experimental biology and contains data separable into several mutually exclusive categories...
- A versatile and efficient high-throughput cloning tool for structural biologyEric R Geertsma
Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
Biochemistry 50:3272-8. 2011..numbers of open reading frames into expression vectors are of critical importance for challenging structural biology projects...
- Symmetry breaking in biologyRong Li
Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA
Cold Spring Harb Perspect Biol 2:a003475. 2010..Symmetry breaking is essential for cell movement, polarity, and developmental patterning. Amplification of initial asymmetry is key to the conserved mechanisms involved...
- The application of low shear modeled microgravity to 3-D cell biology and tissue engineeringStephen Navran
Synthecon, Inc, 8042 El Rio, Houston, Texas 77054, USA
Biotechnol Annu Rev 14:275-96. 2008..become widely recognized that in vitro culture systems must become three dimensional to correctly model in vivo biology. Attempts to modify conventional 2-D culture technology to accommodate 3-D cell growth such as embedding cells in ..
- Claude Bernard and Judah Folkman: nothing makes sense in medicine except in the light of biologyGerald Weissmann
FASEB J 22:943-6. 2008
- The challenges and scope of theoretical biologyDavid C Krakauer
Santa Fe Institute, Santa Fe, NM, USA
J Theor Biol 276:269-76. 2011..In this respect biology resembles alternative model-rich frameworks, such as economics and engineering...
- Liposomes in biology and medicineReto A Schwendener
Institute of Molecular Cancer Research, University of Zurich, Switzerland
Adv Exp Med Biol 620:117-28. 2007..Due to their versatility and vast body of known properties liposome-based formulations will continue to occupy a leading role among the large selection of emerging DDS...
- Bright ideas for chemical biologyLuke D Lavis
Department of Chemistry, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
ACS Chem Biol 3:142-55. 2008Small-molecule fluorescent probes embody an essential facet of chemical biology. Although numerous compounds are known, the ensemble of fluorescent probes is based on a modest collection of modular "core" dyes...
- Protein structure databases with new web services for structural biology and biomedical researchDaron M Standley
Institute for Protein Research, Osaka University, Suita, Osaka 565 0871, Japan
Brief Bioinform 9:276-85. 2008..Several applications have been developed at PDBj for structural biology and biomedical studies: (i) a Java-based molecular graphics viewer, jV; (ii) display of electron density maps for ..
- Synthetic biology: engineering Escherichia coli to see lightAnselm Levskaya
Biophysics Program, University of California, San Francisco, California 94143, USA
Nature 438:441-2. 2005..This spatial control of bacterial gene expression could be used to 'print' complex biological materials, for example, and to investigate signalling pathways through precise spatial and temporal control of their phosphorylation steps...
- Error bars in experimental biologyGeoff Cumming
School of Psychological Science and 2Department of Biochemistry, La Trobe University, Melbourne, Victoria, Australia 3086
J Cell Biol 177:7-11. 2007..Different types of error bars give quite different information, and so figure legends must make clear what error bars represent. We suggest eight simple rules to assist with effective use and interpretation of error bars...
- MicroRNAs from the Planarian Schmidtea mediterranea: a model system for stem cell biologyDasaradhi Palakodeti
Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, Connecticut 06030-3301, USA
RNA 12:1640-9. 2006..Planarians are therefore an excellent model system for studying many aspects of stem cell biology. Here we report the cloning and initial characterization of 71 miRNAs from the planarian Schmidtea mediterranea...
- The concept of allostasis in biology and biomedicineBruce S McEwen
Laboratory of Neuroendocrinology, The Rockefeller University, Box 165, 1230 York Avenue, New York, NY 10021, USA
Horm Behav 43:2-15. 2003..If allostatic load is chronically high, then pathologies develop. Type 2 allostatic overload does not trigger an escape response, and can only be counteracted through learning and changes in the social structure...
- Mathematics is biology's next microscope, only better; biology is mathematics' next physics, only betterJoel E Cohen
Laboratory of Populations, Rockefeller and Columbia Universities, New York, New York, USA
PLoS Biol 2:e439. 2004
- Cell biology should be taught as science is practisedStephen E DiCarlo
Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
Nat Rev Mol Cell Biol 7:290-6. 2006..This transformation requires a significant shift in the approach and attitude of the instructors and students, as well as in the procedures and techniques that are required to teach cell biology.
- The dystroglycan complex: from biology to cancerAlessandro Sgambato
Centro di Ricerche Oncologiche Giovanni XXIII, Istituto di Patologia Generale, Catholic University, Rome, Italy
J Cell Physiol 205:163-9. 2005..This paper reviews the available information on the biology of DG, the abnormalities found in human cancers, and the implications of these findings with respect to our ..
- Targeted development of registries of biological partsJean Peccoud
Virginia Bioinformatics Institute, Blacksburg, Virginia, United States of America
PLoS ONE 3:e2671. 2008..of novel biological systems by combining basic building blocks represents a dominant paradigm in synthetic biology. Creating and maintaining a database of these building blocks is a way to streamline the fabrication of complex ..
- Literature Lab: a method of automated literature interrogation to infer biology from microarray analysisPhillip G Febbo
Institute for Genome Science and Policy, Duke University, Durham, North Carolina, USA
BMC Genomics 8:461. 2007..e. pathway names, medical subject heading (MeSH) terms, etc)...
- Metabolite profiling in plant biology: platforms and destinationsJoachim Kopka
Max Planck Institute of Molecular Plant Physiology, Am Muhlenberg 1, 14476 Golm, Germany
Genome Biol 5:109. 2004..These techniques will be useful for answering important biological questions in the future...
- Are the current ontologies in biology good ontologies?Larisa N Soldatova
Computer Science Department, The University of Wales, Penglais, Aberystwyth, Ceredigion, SY23 3DB, UK
Nat Biotechnol 23:1095-8. 2005..The failure of many bio-ontologies to follow international standards for ontology design and description is hampering their application and threatens to restrict their future use...
- GeneNotes--a novel information management software for biologistsPengyu Hong
BioX program, Department of Statistics and HRP, Stanford University, Stanford, CA 94305 4065, USA
BMC Bioinformatics 6:20. 2005..Biologists often feel overwhelmed by the huge amount of and the great diversity of distributed heterogeneous biological information...
- Using the biological taxonomy to access biological literature with PathBinderHJ Ding
Department of Electrical and Computer Engineering, Iowa State University, Ames, IA 50011, USA
Bioinformatics 21:2560-2. 2005..Although the current project requires this function only for plant taxa, the principle is extensible to the entire taxonomy. AVAILABILITY: www.plantgenomics.iastate.edu/PathBinderH. Source code and databases on request...
- Computer simulations improve university instructional laboratoriesNicola J Gibbons
Cell and Chromosome Biology Group, Department of Biological Sciences, School of Business and Management, Brunel University, Uxbridge, Middlesex UB8 3PH, United Kingdom
Cell Biol Educ 3:263-9. 2004Laboratory classes are commonplace and essential in biology departments but can sometimes be cumbersome, unreliable, and a drain on time and resources...
- Enhancing HMM-based biomedical named entity recognition by studying special phenomenaJie Zhang
Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
J Biomed Inform 37:411-22. 2004..To our best knowledge, our system is the first one that copes with the cascaded phenomena...
- Comparison of character-level and part of speech features for name recognition in biomedical textsNigel Collier
National Institute of Informatics, 2 1 2 Hitotsubashi, Chiyoda ku, Tokyo 101 8430, Japan
J Biomed Inform 37:423-35. 2004The immense volume of data which is now available from experiments in molecular biology has led to an explosion in reported results most of which are available only in unstructured text format...
- Gene name identification and normalization using a model organism databaseAlexander A Morgan
MITRE Corporation, 202 Burlington Road, Mail Stop K325, Bedford, MA 01730 1420, USA
J Biomed Inform 37:396-410. 2004b>Biology has now become an information science, and researchers are increasingly dependent on expert-curated biological databases to organize the findings from the published literature...
- MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH termsAmira Djebbari
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Bioinformatics 21:3324-6. 2005..AVAILABILITY: The software is available at http://www.tm4.org. SUPPLEMENTARY INFORMATION: Results from the analysis of significant genes from the published Ang II study...
- Searching the Mouse Genome Informatics (MGI) resources for information on mouse biology from genotype to phenotypeDavid Shaw
MGI User Support, The Jackson Laboratory, Bar Harbor, Maine, USA
Curr Protoc Bioinformatics . 2004..jax.org/) resource provides the research community with access to information on the genetics, genomics, and biology of the laboratory mouse...
- PubSearch and PubFetch: a simple management system for semiautomated retrieval and annotation of biological information from the literatureDanny Yoo
Carnegie Institution, Stanford, California, USA
Curr Protoc Bioinformatics . 2006For most systems in biology, a large body of literature exists that describes the complexity of the system based on experimental results...
- iHOP web servicesJose M Fernandez
Structural Biology and Biocomputing Program, CNIO and Computer Science and Artificial Intelligence Laboratory, MIT
Nucleic Acids Res 35:W21-6. 2007..ihop-net.org/UniPub/iHOP/info/logs/). Here we describe a public programmatic API that enables the integration of main iHOP functionalities in bioinformatic programs and workflows...
- CARGO: a web portal to integrate customized biological informationIldefonso Cases
SCOMPBio Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, Madrid, Spain
Nucleic Acids Res 35:W16-20. 2007..The tool is designed to be used by experimental biologists with no training in bioinformatics. In the current state, the system presents a list of human cancer genes. Available at http://cargo.bioinfo.cnio.es...
- The BioPrompt-box: an ontology-based clustering tool for searching in biological databasesClaudio Corsi
Dipartimento di Informatica, University of Pisa, Italy
BMC Bioinformatics 8:S8. 2007High-throughput molecular biology provides new data at an incredible rate, so that the increase in the size of biological databanks is enormous and very rapid...
- Science teaching must evolveAndrew Moore
Science and Society Programme at the European Molecular Biology Organization (EMBO, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
Nature 453:31-2. 2008
- JColorGrid: software for the visualization of biological measurementsMarcin P Joachimiak
Department of Plant and Microbial Biology, 461 Koshland Hall, University of California Berkeley, CA 94720 3102, USA
BMC Bioinformatics 7:225. 2006..g. micro-array analysis tools), often associated with steep learning curves and requiring expert knowledge...
- BIOZON: a system for unification, management and analysis of heterogeneous biological dataAaron Birkland
Department of Computer Science, Cornell University, Ithaca, NY, USA
BMC Bioinformatics 7:70. 2006Integration of heterogeneous data types is a challenging problem, especially in biology, where the number of databases and data types increase rapidly...
- Extraction of biological interaction networks from scientific literatureAndre Skusa
NRW International Graduate School in Bioinformatics and Genome Research, Bielefeld University, Postfach 10 01 31, D 33501 Bielefeld, Germany
Brief Bioinform 6:263-76. 2005b>Biology can be regarded as a science of networks: interactions between various biological entities (eg genes, proteins, metabolites) on different levels (eg gene regulation, cell signalling) can be represented as graphs and, thus, ..
- Distributed modules for text annotation and IE applied to the biomedical domainHarald Kirsch
EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Int J Med Inform 75:496-500. 2006..The server and the underlying software are available to the public...
- Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data StructuresJacob Koehler
Rothamsted Research, BAB division, Harpenden, UK
In Silico Biol 5:33-44. 2005..The system is developed under the GPL license and can be downloaded from http://sourceforge.net/projects/ondex/..
- YeastHub: a semantic web use case for integrating data in the life sciences domainKei Hoi Cheung
Center for Medical Informatics, Yale University New Haven, CT 06520, USA
Bioinformatics 21:i85-96. 2005....
- Biological data integration using Semantic Web technologiesC Pasquier
Institute of Developmental Biology and Cancer, University of Nice Sophia Antipolis, Parc Valrose, 06108 Nice Cedex 2, France
Biochimie 90:584-94. 2008Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined...
- The emerging in-silico scientist: how text-based bioinformatics is bridging biology and artificial intelligenceJonathan D Wren
Advanced Center for Genome Technology, Department of Botany and Microbiology, The University of Oklahoma, Norman 73019, USA
IEEE Eng Med Biol Mag 23:87-93. 2004
- Rutabaga by any other name: extracting biological namesLynette Hirschman
The MITRE Corporation, MS K312, 202 Burlington Rd, Bedford, MA 01730, USA
J Biomed Inform 35:247-59. 2002..We conclude by outlining a research agenda to raise performance of named entity tagging to a level where it can be used to perform tasks of biological importance...
- Accomplishments and challenges in literature data mining for biologyLynette Hirschman
The MITRE Corporation, USA
Bioinformatics 18:1553-61. 2002We review recent results in literature data mining for biology and discuss the need and the steps for a challenge evaluation for this field...
- Information extraction from biomedical textJerry R Hobbs
USC Information Sciences Institute, Marina del Rey, CA 90292, USA
J Biomed Inform 35:260-4. 2002..In other domains, the technology plateaued at about 60% recall and precision. Even if applications to biomedical text do no better than this, they could still prove to be of immense help to curatorial activities...
- GENIA corpus--semantically annotated corpus for bio-textminingJ-D Kim
CREST, Japan Science and Technology Corporation, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
Bioinformatics 19:i180-2. 2003..RESULTS: GENIA corpus version 3.0 consisting of 2000 MEDLINE abstracts has been released with more than 400,000 words and almost 100,000 annotations for biological terms...
- Evaluation of text data mining for database curation: lessons learned from the KDD Challenge CupAlexander S Yeh
The MITRE Corporation, 202 Burlington Road, Bedford, MA 01730, USA
Bioinformatics 19:i331-9. 2003..We report on the evaluation results and describe the techniques used by the top performing groups...
- Extracting synonymous gene and protein terms from biological literatureHong Yu
Department of Computer Science, Columbia University, New York, NY, USA
Bioinformatics 19:i340-9. 2003..Our evaluation shows that our extraction techniques could be a valuable supplement to resources such as SWISSPROT, as our systems were able to capture gene and protein synonyms not listed in the SWISSPROT database...
- Evolving strategies for the incorporation of bioinformatics within the undergraduate cell biology curriculumJerry E Honts
Department of Biology, Drake University, 2507 University Avenue, Des Moines, Iowa 50325, USA
Cell Biol Educ 2:233-47. 2003Recent advances in genomics and structural biology have resulted in an unprecedented increase in biological data available from Internet-accessible databases...
- BioRAT: extracting biological information from full-length papersDavid P A Corney
Bioinformatics Unit, Department of Computer Science, University College London, Gower Street, London, WC1E 6BT, UK
Bioinformatics 20:3206-13. 2004..Overall, BioRAT recalled 20.31% of the target facts from the abstracts with 55.07% precision, and achieved 43.6% recall with 51.25% precision on full-length papers...
- How effective are simulated molecular-level experiments for teaching diffusion and osmosis?Eli Meir
Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Cell Biol Educ 4:235-48. 2005Diffusion and osmosis are central concepts in biology, both at the cellular and organ levels. They are presented several times throughout most introductory biology textbooks (e.g...
- Intelligent design: who has designs on your students' minds?Geoff Brumfiel
Nature 434:1062-5. 2005
- A new paradigm for mentored undergraduate research in molecular microbiologySusan Carson
Biotechnology Program and Department of Plant Biology, North Carolina State University, Raleigh, NC 27695, USA
CBE Life Sci Educ 6:343-9. 2007....
- Understanding randomness and its impact on student learning: lessons learned from building the Biology Concept Inventory (BCI)Kathy Garvin-Doxas
Center for Integrated Plasma Studies, and Developmental Biology Department, University of Colorado, Boulder, CO 80309, USA
CBE Life Sci Educ 7:227-33. 2008While researching student assumptions for the development of the Biology Concept Inventory (BCI; http://bioliteracy...
- Lysenko's contributions to biology and his tragediesYongsheng Liu
Department of Horticulture, Henan Institute of Science and Technology, Xinxiang, China
Riv Biol 97:483-98. 2004..Less well known is that he once made greater contributions to Biology and has been misunderstood in some aspects...
- The modern theory of biological evolution: an expanded synthesisUlrich Kutschera
Institut fur Biologie, Universitat Kassel, Heinrich Plett Strasse 40, 34109 Kassel, Germany
Naturwissenschaften 91:255-76. 2004..sexual selection and altruism, endosymbiosis and eukaryotic cell evolution, evolutionary developmental biology, phenotypic plasticity, epigenetic inheritance and molecular evolution, experimental bacterial evolution, and ..
- The triumph of Stephen Jay GouldRichard Lewontin
New York Rev Books 55:39-41. 2008..Reviews of Steven Rose's The richness of life: the essential Stephen Jay Gould and Stephen Jay Gould's Punctuated equilibrium...
- Biomedical ontologies: what part-of is and isn'tStefan Schulz
Department of Medical Informatics, University Hospital, Freiburg, Germany
J Biomed Inform 39:350-61. 2006..We analyze these ambiguities and make suggestions for a standardization of mereological relations in biomedical ontologies...
- Seeking a new biology through text miningAndrey Rzhetsky
University of Chicago, Chicago, IL 60637, USA
Cell 134:9-13. 2008..Hence, there is much interest in text mining, the use of computational tools to enhance the human ability to parse and understand complex text...
Research Grants154 found, 100 shown here
- STRUCTURE AND FUNCTION OF SIGNAL TRANSDUCING COMPONENTSSRINIVAS RAVI IYENGAR; Fiscal Year: 2007..abstract_text> ..
- Genetics of Wing and Cell-Size Evolution in NasoniaJohn Werren; Fiscal Year: 2007How new morphologies evolve is a fundamental question in biology. Most morphological evolution involves changes in the size of organs, which is basically achieved in two ways, by changes in cell size and cell number...
- Spectrum: Building Pathways to Biomedical Research Careers for Girls and Women oKimberly Tanner; Fiscal Year: 2007The Science Education Partnership and Assessment Laboratory (SEPAL) in the Department of Biology at San Francisco State University (SFSU) - in strong collaboration with the San Francisco Unified School District (SFUSD), the ..
- MECHANISMS OF INTERACTION BETWEEN SIGNALING PATHWAYSSRINIVAS RAVI IYENGAR; Fiscal Year: 2007..From these studies we anticipate that we will develop a predictive understanding of how the cannabinoid and Galphao regulated signaling network triggers neurite extension. ..
- Dynamics Underlying Tissue IntegritySusana R Neves; Fiscal Year: 2010..We will use the filtration barrier of the kidney cortex as our model system. We will use a combination of mathematical models and engineering approaches to develop a 3D tissue assembly. ..
- MECHANISMS OF INTERACTION BETWEEN SIGNALING PATHWAYSSRINIVAS RAVI IYENGAR; Fiscal Year: 2002..We anticipate that the proposed studies should provide new insights into how G protein coupling to other signal pathways can be used to evoke biological effects. ..
- STRUCTURE/FUNCTION OF SIGNAL TRANSDUCING COMPONENTSSRINIVAS RAVI IYENGAR; Fiscal Year: 2003..It is anticipated that these studies will lead to the identification of key intracellular sites that are potential targets for therapeutic agents that have their effects by modulation of G protein signaling pathways. ..
- SIGNALING PATHWAYS INTERACTIONS AND MAMMARY TUMORSRINIVAS RAVI IYENGAR; Fiscal Year: 2004..abstract_text> ..
- Functions of Regulatory Motifs in Signaling NetworksSRINIVAS RAVI V IYENGAR; Fiscal Year: 2010..We plan to use a systems biology approach to study how subunits of heterotrimeric Gi/o trigger neurite outgrowth in the Neuro-2A cell line and ..
- Modeling Cell Regulatory NetworksSRINIVAS RAVI IYENGAR; Fiscal Year: 2009..From such analysis we hope to define the key criteria involved in determining the characteristics of microdomains of signaling molecules within the cell. ..
- STRUCTURE/FUNCTION OF SIGNAL TRANSDUCING COMPONENTSSRINIVAS RAVI IYENGAR; Fiscal Year: 1999..Such understanding could lead to new long acting therapeutic agents for many diseases. ..
- Re-engineering the MEGA software packageSudhir Kumar; Fiscal Year: 2009..These core software enhancements will contribute to the longevity of MEGA for use in molecular evolution, bioinformatics, functional genomics, computational biology, and basic biomedicine applications.
- Capillary Electrophoresis and Protein BiophysicsGeorge Whitesides; Fiscal Year: 2007..used to separate, characterize, and manipulate proteins is broadly important in biochemistry and molecular biology: areas of application include proteomics and systems biology, purification of protein therapeutics, use in lab-on-..
- Inequality, social capital and health in BolivaWilliam Leonard; Fiscal Year: 2007....
- Molecular Imaging of G-Protein-Coupled Receptors for Drug DevelopmentSTANLEY OPELLA; Fiscal Year: 2007..This research will be multidisciplinary, involving synthetic organic chemistry, molecular biology, structural biology, NMR spectroscopy, and computer calculations...
- Cognitive Functions Linked to Frontal LobeAdele Diamond; Fiscal Year: 2007..Insights into the conditions under which children can succeed may yield procedures that might prove helpful to those afflicted with disorders affecting these critical functions. ..
- Old Westbury Neuroscience Research Institute MIDARPGeorge Stefano; Fiscal Year: 2007..The proposed research program plans to develop greater program expertise in molecular biology. Additionally, it proposes to add a new faculty with NIDA interests...
- USE OF ADIPOSE-DERIVED PREADIPOCYTES IN BONE DISOREDERSJeffrey Gimble; Fiscal Year: 2002..This has commercial application to orthopedic and periodontal surgical treatments of joint replacement, fracture repair, and bone resorption secondary to tooth decay...
- NMR STUDIES OF BIOLOGICAL SUPRAMOLECULAR STRUCTURESSTANLEY OPELLA; Fiscal Year: 2007..The peptide sequences under investigation extend the biological of the research to AIDS, malaria, influenza, and neurochemistry. ..
- ACTIN ASSEMBLY DURING YEAST POLARIZED CELL GROWTHRong Li; Fiscal Year: 2003..In addition, how cells break symmetry and establish a polarity is a profound problem in cell biology. Understanding cell's intrinsic ability to polarize may lead to fundamental insights into the physical principles ..
- Human Breast Cancer Stem Cell SurrogatesWENDY A contact WOODWARD; Fiscal Year: 2010..This approach could be used to select patients for individualized therapy using targeted sensitizing agents based on the proposed preclinical studies. ..
- Structure and mechanism of the AMP-activated protein kinaseLawrence Shapiro; Fiscal Year: 2010..Our preliminary results and the further work proposed will provide high-resolution structural information on AMPK, and should directly enable the rational design of AMPK-directed therapeutics. ..
- MOLECULAR BASIS OF CADHERIN MEDIATED CELL ADHESIONLawrence Shapiro; Fiscal Year: 2010....
- Computational Analysis of Gene Expression Pattern ImagesSudhir Kumar; Fiscal Year: 2009..will fulfill the day-to-day needs of basic and applied researchers as well as students in many areas of molecular biology crucial in human health research, including computational genomics, molecular genetics, developmental biology, ..
- Single-Molecule Studies of Synaptic VesiclesDaniel Chiu; Fiscal Year: 2009....
- NFkB Targets and Neural Crest DevelopmentMichael Klymkowsky; Fiscal Year: 2009..Together these observation should have important implications for understanding the behavior of molecular and inductive networks in general and the prevention and/or amelioration of neural crest defects in particular. ..
- Nanoparticles with Tailored Monolayers for DNA TransfectionVINCENT ROTELLO; Fiscal Year: 2006Nucleic acid transfection is one of the most important tools in modern biology, and an emerging tool for biomedical applications. In our proposed research, we will use gold nanoparticles as transfection vectors...
- Computatonal Analysis of Gene Expression Pattern ImagesSudhir Kumar; Fiscal Year: 2005..FlyExpress informatics system will directly facilitate basic and applied research in many areas of molecular biology crucial in human health research, including computational genomics, molecular genetics, developmental biology, ..