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All fields Title Creator / Publisher Keyword Year AND OR AND NOT All fields Title Creator / Publisher Keyword Year AND OR AND NOT All fields Title Creator / Publisher Keyword Year AND OR AND NOT All fields Title Creator / Publisher Keyword Year AND OR AND NOT All fields Title Creator / Publisher Keyword Year Sort by creator [A → Z]' creator [Z → A]' publishing year ↑ (asc)' publishing year ↓ (desc)' title [A → Z]' title [Z → A]' Simple Search Hits 1 – 17 of 17 1 Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets. Aubry, Marc; Monnier, Annabelle; Chicault, Céline; De Tayrac, Marie; Galibert, Marie-Dominique; Burgun, Anita; Mosser, Jean In: ISSN: 1471-2105 ; BMC Bioinformatics ; https://hal.archives-ouvertes.fr/hal-00094484 ; BMC Bioinformatics, BioMed Central, 2006, 7, pp.241. ⟨10.1186/1471-2105-7-241⟩ (2006) Abstract: 18 p. ; International audience ; BACKGROUND: Large-scale genomic studies based on transcriptome technologies provide clusters of genes that need to be functionally annotated. The Gene Ontology (GO) implements a controlled vocabulary organised into three hierarchies: cellular components, molecular functions and biological processes. This terminology allows a coherent and consistent description of the knowledge about gene functions. The GO terms related to genes come primarily from semi-automatic annotations made by trained biologists (annotation based on evidence) or text-mining of the published scientific literature (literature profiling). RESULTS: We report an original functional annotation method based on a combination of evidence and literature that overcomes the weaknesses and the limitations of each approach. It relies on the Gene Ontology Annotation database (GOA Human) and the PubGene biomedical literature index. We support these annotations with statistically associated GO terms and retrieve associative relations across the three GO hierarchies to emphasise the major pathways involved by a gene cluster. Both annotation methods and associative relations were quantitatively evaluated with a reference set of 7397 genes and a multi-cluster study of 14 clusters. We also validated the biological appropriateness of our hybrid method with the annotation of a single gene (cdc2) and that of a down-regulated cluster of 37 genes identified by a transcriptome study of an in vitro enterocyte differentiation model (CaCo-2 cells). CONCLUSION: The combination of both approaches is more informative than either separate approach: literature mining can enrich an annotation based only on evidence. Text-mining of the literature can also find valuable associated MEDLINE references that confirm the relevance of the annotation. Eventually, GO terms networks can be built with associative relations in order to highlight cooperative and competitive pathways and their connected molecular functions. Keyword: [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]; [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]; [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics; Controlled; Genetic; MESH: Algorithms; MESH: Artificial Intelligence; MESH: Documentation; MESH: Evidence-Based Medicine; MESH: Humans; MESH: MEDLINE; MESH: Models; MESH: Multigene Family; MESH: Natural Language Processing; MESH: Proteins; MESH: Terminology as Topic; MESH: Vocabulary; Statistical URL: https://hal.archives-ouvertes.fr/hal-00094484/file/1471-2105-7-241.pdf https://hal.archives-ouvertes.fr/hal-00094484/document https://doi.org/10.1186/1471-2105-7-241 https://hal.archives-ouvertes.fr/hal-00094484 BASE Hide details 2 Behind the Scenes Joseph Grimes. - 2006 BASE Show details 3 Dynamic evidence models in a DBN phone recognizer William Schuler; Tim Miller; Stephen Wu... In: http://www.cs.umn.edu/~schuler/paper_is2006.pdf (2006) BASE Show details 4 Misperception in sentences but not in words: Speech perception and the phonological buffer Jacquemot, Charlotte; Dupoux, Emmanuel; Decouche, Odile... In: ISSN: 0264-3294 ; EISSN: 1464-0627 ; Cognitive Neuropsychology ; https://hal.archives-ouvertes.fr/hal-02326841 ; Cognitive Neuropsychology, Taylor & Francis (Routledge), 2006, 23 (6), pp.949-971. ⟨10.1080/02643290600625749⟩ (2006) BASE Show details 5 abstract knowledge of the English dative alternation via a production study. The studies Erin Conwell; Katherine Demuth In: http://titan.cog.brown.edu/research/infant_lab/Early verb prod Conwell.pdf (2006) BASE Show details 6 Evidence, Justification, and Interlocutor Gender McGarry, Theresa In: ETSU Faculty Works (2006) BASE Show details 7 What works? Evidence-based practice in the treatment of word retrieval disorders Nickels, Lyndsey. - : The Speech Pathology Association of Australia Ltd, 2006 BASE Show details 8 Cross-cultural adaptation of a tobacco questionnaire for Punjabi, Cantonese, Urdu and Sylheti speakers: qualitative research for better clinical practice, cessation services and research Hanna, Lisa; Hunt, Sonja; Bhopal, Raj S. - : BMJ Publishing Group Ltd, 2006 BASE Show details 9 Combining Evidence from Homologous Datasets Feng, Ao; Allan, James In: DTIC (2006) BASE Show details 10 The neural correlates of phonological short-term memory: A repetitive transcranial magnetic stimulation study Romero, L; Walsh, V; Papagno, C In: J COGNITIVE NEUROSCI , 18 (7) 1147 - 1155. (2006) (2006) BASE Show details 11 Evidence : the knowledge of most worth Waters, Donna. - : The University of Sydney, 2006. : Faculty of Medicine, 2006 BASE Show details 12 The Composition Of Normative Groups And Diagnostic Decision Making: Shooting Ourselves In The Foot Pena, Elizabeth D.; Spaulding, Tammie J.; Plante, Elena. - 2006 BASE Show details 13 The Bench to Practice to Bench Cycle of Evidence-based Practice Orange, JB; Johnson, Andrew M. In: Andrew M. Johnson (2006) BASE Show details 14 Where do all the undergraduate and new graduate nurses go and why? A search for empirical research evidence Gaynor, L.; Gallasch, T.; Yorkston, E. K.. - : Australian Nursing Federation, 2006 BASE Show details 15 Cognitive modelling and the behaviour genetics of reading Castles, Anne; Bates, Timothy; Coltheart, Max. - : Blackwell Publishing, 2006 BASE Show details 16 What is orthographic processing skill and how does it relate to word identification in reading? Burt, JS. - : Blackwell Publishing, 2006 BASE Show details 17 Making Evidence-Based Decisions about Child Language Intervention in Schools. Gillam, Sandra Laing; Gillam, Ronald B. In: Communicative Disorders and Deaf Education Faculty Publications (2006) BASE Show details

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