Genomes and Genes
Summary: Collections of facts, assumptions, beliefs, and heuristics that are used in combination with databases to achieve desired results, such as a diagnosis, an interpretation, or a solution to a problem (From McGraw Hill Dictionary of Scientific and Technical Terms, 6th ed).
- Rother K, Rother M, Boniecki M, Puton T, Bujnicki J. RNA and protein 3D structure modeling: similarities and differences. J Mol Model. 2011;17:2325-36 pubmed publisher..We also highlight the areas where the differences between RNA and proteins require the development of RNA-specific solutions. ..
- Rodríguez González A, Labra Gayo J, Colomo Palacios R, Mayer M, Gómez Berbís J, García Crespo A. SeDeLo: using semantics and description logics to support aided clinical diagnosis. J Med Syst. 2012;36:2471-81 pubmed publisher..In this paper, we provide a well-structured ontology for automated diagnosis in the medical field and a three-fold formalization based on Description Logics with the use of Semantic Web technologies. ..
- Magrane M. UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011;2011:bar009 pubmed publisher..Database URL: http://www.uniprot.org/ ..
- Chopra G, Kalisman N, Levitt M. Consistent refinement of submitted models at CASP using a knowledge-based potential. Proteins. 2010;78:2668-78 pubmed publisher..These improvements in structure and stereochemistry prove the usefulness of our computationally inexpensive, powerful and automatic refinement protocol. ..
- Mobilio D, Walker G, Brooijmans N, Nilakantan R, Denny R, Dejoannis J, et al. A protein relational database and protein family knowledge bases to facilitate structure-based design analyses. Chem Biol Drug Des. 2010;76:142-53 pubmed publisher..Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue. ..
- Wu M, Lin X. Prior biological knowledge-based approaches for the analysis of genome-wide expression profiles using gene sets and pathways. Stat Methods Med Res. 2009;18:577-93 pubmed publisher..We discuss the assumptions of these methods and their pros and cons. We illustrate these methods by application to a type II diabetes data set. ..
- Jimeno Yepes A, McInnes B, Aronson A. Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation. BMC Bioinformatics. 2011;12:223 pubmed publisher..Furthermore, the MSH WSD data set has been generated automatically reusing already existing annotations and, therefore, can be regenerated from subsequent UMLS versions. ..
- Tuszynska I, Bujnicki J. DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking. BMC Bioinformatics. 2011;12:348 pubmed publisher..In both bound and unbound docking tests, DARS-RNP showed the highest ability to identify native-like structures. Python implementations of DARS-RNP and QUASI-RNP are freely available for download at http://iimcb.genesilico.pl/RNP/ ..
- . Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012;40:D71-5 pubmed publisher..A key development at UniProt is the provision of complete, reference and representative proteomes. UniProt is updated and distributed every 4 weeks and can be accessed online for searches or download at http://www.uniprot.org. ..
- McDonagh E, Whirl Carrillo M, Garten Y, Altman R, Klein T. From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource. Biomark Med. 2011;5:795-806 pubmed publisher..This review summarizes the methods we use to drive this expanded scope of 'Knowledge Acquisition to Clinical Applications', the new features available on our website and our future goals. ..
- Schramm C, Hannigan B, Donald J, Keasar C, Saven J, Degrado W, et al. Knowledge-based potential for positioning membrane-associated structures and assessing residue-specific energetic contributions. Structure. 2012;20:924-35 pubmed publisher..Hence, focusing on the uniqueness of membrane-associated proteins and peptides, we quantitatively parameterize their cross-membrane propensity, thus facilitating structural refinement, characterization, prediction, and design. ..
- Liang M. Integrative pathway knowledge bases as a tool for systems molecular medicine. Physiol Genomics. 2007;30:209-12 pubmed..A potentially powerful approach is to build integrative pathway knowledge bases that link organ systems function with molecules.
- Tosatto S. The victor/FRST function for model quality estimation. J Comput Biol. 2005;12:1316-27 pubmed..An executable version of the Victor/FRST function for Linux PCs is available for download from the URL http://protein.cribi.unipd.it/frst/. ..
- Kuperman G, Reichley R, Bailey T. Using commercial knowledge bases for clinical decision support: opportunities, hurdles, and recommendations. J Am Med Inform Assoc. 2006;13:369-71 pubmed
- Sabb F, Bearden C, Glahn D, Parker D, Freimer N, Bilder R. A collaborative knowledge base for cognitive phenomics. Mol Psychiatry. 2008;13:350-60 pubmed publisher..has stimulated development of impressive repositories of biological knowledge at the genomic level and new knowledge bases are rapidly being developed in a 'bottom-up' fashion...
- Gao M, Skolnick J. DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucleic Acids Res. 2008;36:3978-92 pubmed publisher..DBD-Hunter is freely available at http://cssb.biology.gatech.edu/skolnick/webservice/DBD-Hunter/. ..
- Ciccarese P, Wu E, Wong G, Ocana M, Kinoshita J, Ruttenberg A, et al. The SWAN biomedical discourse ontology. J Biomed Inform. 2008;41:739-51 pubmed publisher..We ground its development theoretically, present its design approach, explain its main classes and their application, and show its relationship to other ongoing activities in biomedicine and bio-ontologies. ..
- Nogales J, Palsson B, Thiele I. A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol. 2008;2:79 pubmed publisher..Taken together, this work illustrates the utility of iJN746 as i) a knowledge-base, ii) a discovery tool, and iii) an engineering platform to explore P. putida's potential in bioremediation and bioplastic production. ..
- Vastrik I, D EUSTACHIO P, Schmidt E, Joshi Tope G, Gopinath G, Croft D, et al. Reactome: a knowledge base of biologic pathways and processes. Genome Biol. 2007;8:R39 pubmed..Finally, we describe the use of Reactome both as a learning resource and as a computational tool to aid in the interpretation of microarrays and similar large-scale datasets. ..
- Reeves A, Biancardi A, Apanasovich T, Meyer C, Macmahon H, van Beek E, et al. The Lung Image Database Consortium (LIDC): a comparison of different size metrics for pulmonary nodule measurements. Acad Radiol. 2007;14:1475-85 pubmed..This metric is not intended as a gold standard for nodule size; rather, it is intended to facilitate the selection of unique repeatable size limited nodule subsets. ..
- Yip Y, Famiglietti M, Gos A, Duek P, David F, Gateau A, et al. Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase. Hum Mutat. 2008;29:361-6 pubmed publisher..In this regard, SAP information in UniProtKB/Swiss-Prot complements nicely those existing in genomic and phenotypic databases, and is valuable for the understanding of SAPs and diseases. ..
- Sahoo S, Bodenreider O, Rutter J, Skinner K, Sheth A. An ontology-driven semantic mashup of gene and biological pathway information: application to the domain of nicotine dependence. J Biomed Inform. 2008;41:752-65 pubmed publisher..RESOURCE PAGE: http://knoesis.wright.edu/research/lifesci/integration/structured_data/JBI-2008/ ..
- Makino Y, Itoh N. A knowledge-based structure-discriminating function that requires only main-chain atom coordinates. BMC Struct Biol. 2008;8:46 pubmed publisher..Despite the reduced representation of input structures, DFMAC showed considerable structure discrimination ability. The function can be applied to the identification of near-native structures in structure prediction experiments. ..
- Hoffmann R. A wiki for the life sciences where authorship matters. Nat Genet. 2008;40:1047-51 pubmed publisher..Here I discuss a dynamic collaborative knowledge base for the life sciences that provides authors with due credit and that can evolve via continual revision and traditional peer review into a rigorous scientific tool. ..
- Regenbogen S, Wilkins A, Lichtarge O. COMPUTING THERAPY FOR PRECISION MEDICINE: COLLABORATIVE FILTERING INTEGRATES AND PREDICTS MULTI-ENTITY INTERACTIONS. Pac Symp Biocomput. 2016;21:21-32 pubmed..We conclude that collaborative filtering can integrate information across multiple types of biological entities, and that as a first step towards precision medicine it can compute drug repurposing hypotheses. ..
- Svedholm A, Lindeman M. The separate roles of the reflective mind and involuntary inhibitory control in gatekeeping paranormal beliefs and the underlying intuitive confusions. Br J Psychol. 2013;104:303-19 pubmed publisher..The results support a model in which both intuitive and non-reflective thinking styles and involuntary inhibitory processes give way to embracing culturally acquired paranormal beliefs. ..
- Wicht A, Wetter T, Klein U. A web-based system for clinical decision support and knowledge maintenance for deterioration monitoring of hemato-oncological patients. Comput Methods Programs Biomed. 2013;111:26-32 pubmed publisher..However, the real time behavior of our approach which data becoming available as time passes still has to be evaluated and observational studies need to be conducted. ..
- Garla V, Brandt C. Semantic similarity in the biomedical domain: an evaluation across knowledge sources. BMC Bioinformatics. 2012;13:261 pubmed publisher..Future evaluations of semantic similarity measures should utilize benchmarks powered to detect significant differences in measure accuracy. ..
- Pakhomov S, McInnes B, Lamba J, Liu Y, Melton G, Ghodke Y, et al. Using PharmGKB to train text mining approaches for identifying potential gene targets for pharmacogenomic studies. J Biomed Inform. 2012;45:862-9 pubmed publisher..Our results show that this approach is not only feasible but may also find new gene targets not identifiable by other methods thus making it a valuable tool for pathway-driven pharmacogenomics research. ..
- KAUFMANN K, Lemmon G, Deluca S, Sheehan J, Meiler J. Practically useful: what the Rosetta protein modeling suite can do for you. Biochemistry. 2010;49:2987-98 pubmed publisher..Most recently, Rosetta has been used to solve the X-ray crystallographic phase problem. ..
- Hinz U. From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. Cell Mol Life Sci. 2010;67:1049-64 pubmed publisher..uniprot.org/ ). It also evokes precautions that are necessary for successful predictions and extrapolations. ..
- Hachad H, Overby C, Argon S, Yeung C, Ragueneau Majlessi I, Levy R. e-PKGene: a knowledge-based research tool for analysing the impact of genetics on drug exposure. Hum Genomics. 2011;5:506-15 pubmed..This review gives a brief description of the database organisation, its search functionalities and examples of use. ..
- Anderson P, Beeley J, Monteiro P, de Soet H, Andrian S, Amaechi B, et al. A European Core Curriculum in Cariology: the knowledge base. Eur J Dent Educ. 2011;15 Suppl 1:18-22 pubmed publisher..The different supporting competences are elaborated and explained. The problems of implementing a curriculum that truly integrates this foundation knowledge into the clinical teaching are discussed. ..
- Bernonille S, Nies J, Pedersen H, Guillot B, Maazi M, Berg A, et al. Three different cases of exploiting decision support services for adverse drug event prevention. Stud Health Technol Inform. 2011;166:180-8 pubmed..This paper presents recent progress as regards the exploitation of the PSIP KB and the results obtained in the three different medical applications. ..
- Xu R, Li L, Wang Q. dRiskKB: a large-scale disease-disease risk relationship knowledge base constructed from biomedical text. BMC Bioinformatics. 2014;15:105 pubmed publisher..scale is limited due to the lack of large-scale machine understandable disease phenotype relationship knowledge bases. Our study innovates a semi-supervised iterative pattern learning approach that is used to build an precise, ..
- Sheikheldin G, Krantzberg G, Schaefer K. Science-seeking behaviour of Conservation Authorities in Ontario. Environ Manage. 2010;45:912-21 pubmed publisher..Our findings will be of interest to both policy/program communities and science providers. ..
- Takeda T, Corona R, Guo J. A knowledge-based orientation potential for transcription factor-DNA docking. Bioinformatics. 2013;29:322-30 pubmed publisher..The new potential is available at http://bioinfozen.uncc.edu/Protein_DNA_orientation_potential.tar. ..
- Carenini M. ReMINE: an ontology-based risk management platform. Stud Health Technol Inform. 2009;148:32-42 pubmed..The underlying ontological system will support the semantic correlation of data with the hospital processes. ..
- Kahl K, Alte C, Sipos V, Kordon A, Hohagen F, Schweiger U. A randomized study of iterative hypothesis testing in undergraduate psychiatric education. Acta Psychiatr Scand. 2010;122:334-8 pubmed publisher..We conclude that teaching IHT to medical students may enhance their clinical ability to recognize complex disease patterns. Further studies are required concerning the enhancement of clinical skills in the psychiatric specialty. ..
- Kim J, Kim J, Han X, Rebholz Schuhmann D. Extending the evaluation of Genia Event task toward knowledge base construction and comparison to Gene Regulation Ontology task. BMC Bioinformatics. 2015;16 Suppl 10:S3 pubmed publisher..However, the converted GE data did not help GRO task participants, due to overfitting and the ontology gap. ..
- Phan J, Moffitt R, Stokes T, Liu J, Young A, Nie S, et al. Convergence of biomarkers, bioinformatics and nanotechnology for individualized cancer treatment. Trends Biotechnol. 2009;27:350-8 pubmed publisher..This bio-nano-info convergence holds great promise for molecular diagnosis and individualized therapy of cancer and other human diseases. ..
- Bader J. Stumbling into the age of evidence. Dent Clin North Am. 2009;53:15-22, vii pubmed publisher..The emergence of the concept of evidence-based dentistry--and its fundamental construct, the systematic review--marks what can be considered a fundamental shift in how the dental knowledge base has grown and developed over time. ..
- Bush W, Dudek S, Ritchie M. Biofilter: a knowledge-integration system for the multi-locus analysis of genome-wide association studies. Pac Symp Biocomput. 2009;:368-79 pubmed
- Huang J, Townsend C, DOU D, Liu H, Tan M. OMIT: a domain-specific knowledge base for microRNA target prediction. Pharm Res. 2011;28:3101-4 pubmed publisher..Thus, it will help clinicians make sound decisions when treating cancer patients. ..
- Nirenburg S, McShane M, Beale S, Catizone R. A cognitive architecture for simulating bodies and minds. AMIA Annu Symp Proc. 2011;2011:905-14 pubmed..We organize the discussion around four aspects of agent modeling and how they are utilized in the two applications: physiological simulation, modeling an agent's knowledge and learning, decision-making and language processing. ..
- Bouaud J, Seroussi B, Falcoff H, Julien J, Simon C, Denké D. Consequences of the verification of completeness in clinical practice guideline modeling: a theoretical and empirical study with hypertension. AMIA Annu Symp Proc. 2009;2009:60-4 pubmed..The same analysis on a sample of 435 actual patients medical records showed that 55% were covered by CPGs. The characterization of guideline-based CDSSs should be based on empirical data estimated from the target population of CPGs. ..
- Lange P, Huesgen P, Overall C. TopFIND 2.0--linking protein termini with proteolytic processing and modifications altering protein function. Nucleic Acids Res. 2012;40:D351-61 pubmed publisher..Hence, TopFIND supports in depth investigation of protein termini information to spark new hypotheses on protein function by correlating cleavage events and termini with protein domains and mutations. ..