An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent. Keywords: Protein function prediction, Disease gene prioritizationpublishedVersio

An Expanded Evaluation of Protein Function Prediction Methods Shows an Improvement In Accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent

La France centrale aux IV^e-III^e s. av. n. ère (Auvergne, Berry et Orléanais)

27 fig., 2 annexes, bibliogr. p. 172-176.International audienc

Geophysical investigation of a large landslide in glaciolacustrine clays in the Trièves area (French Alps)

International audienceSlope movements in clay deposits are spread all over the world and result from complex deformation processes, including internal strains in the landslide body and slipping along rupture surfaces. Such mass movements are likely to generate changes in the geophysical parameters characterizing the ground, which can be used to map the landslide body. In the last decade, geophysical techniques have been increasingly used for landslide investigation purposes. However, the success of any geophysical technique is overall controlled by the existence of a geophysical contrast differentiating the body to be mapped. For landslides affecting thick clay materials (from soft clay to shale or marl), electrical and seismic techniques have been mainly applied in the past. In this study, we attempt to physically characterize the deformation within a large slide (Avignonet) affecting laminated clays which were deposited in a glacially dammed lake during the Würm period. Clay deposits, which cover an area of 300 km2 south of Grenoble (French Alps) and have a maximum thickness of 200 m, overlay compact alluvial layers and marly limestone of Mesozoic age. Piezometric data at Avignonet show that the water table is very shallow, implying that the slide developed in saturated clay. Several seismic and electrical profiles were performed in order to tentatively correlate the variations of P-wave (Vp) velocity, S-wave velocity (Vs) and electrical resistivity with geotechnical data and morphological observations. In such saturated and fine material, it turned out that only the S-wave velocity exhibits significant variations with the displacement rates and the morphological features. Vs values at shallow depth were found to be inversely correlated with displacement rates measured by GPS, with a division by at least a factor of 2 between the zones unaffected and strongly deformed by the landslide. These results suggest that Vs mapping could provide valuable information on the deformation state of the clay material and that the evolution of Vs with time could be used as an indicator for characterizing the landslide activity in the subsurface, including the evolution into a flow

Le Pâtural Clermont-Ferrand Puy-de-Dôme

Ce volume rend compte de dix années de fouilles sur une installation du second âge du Fer de la Grande Limagne d'Auvergne. Les prospections et les opérations d'archéologie préventive montrent que cette plaine, très fertile, située entre l'Allier et la chaîne des Puys a connu une occupation très importante et une exploitation intensive durant l'époque gauloise. Engagée en 1986 dans le cadre d'un programme de recherche de l'université de Sheffield, qui s'était préalablement intéressée à l'agglomération contemporaine « d'Aulnat », et conclue en 1995 par une campagne de sauvetage confiée à l'AFAN, l'étude du site du Pâtural se solde par la première étude monographique publiée d'un site laténien auvergnat. Ce DARA n° 30 est donc un livre très attendu qui doit beaucoup à l'investissement de quelques-uns et de Yann Deberge en particulier. L'approche méthodique des vestiges immobiliers, confrontée à l'examen de la dispersion des restes, permet une analyse exemplaire du développement du site. Faisant suite à plusieurs occupations plus anciennes - funéraire au vie siècle, domestique au ve siècle -, une installation nouvelle est implantée au tournant du iiie siècle et du iie siècle av. J.-C. Constituée d'une plateforme fossoyée abritant divers bâtiments, elle suscite la comparaison avec les « fermes indigènes », bien connues dans les plaines du Bassin parisien. L'occupation prend une autre tournure dans le courant du iie siècle, puisque l'abondance des vestiges suggère le regroupement d'une population plus importante au sein d'un « hameau » dont les recherches récentes ont encore livré peu d'exemples. Ce hameau ne survivra pas au-delà de la fin du IIe siècle av. J.-C. Le peuplement des Limagnes subit en effet, à ce moment-là, une forte réorganisation liée à un autre événement capital : l'apparition d'un oppidum central au cœur du territoire arverne. L'ouvrage comporte, en outre, une présentation systématique des abondants mobiliers découverts, datés dans leur grande majorité des iiie et iie siècles av. J.-C., ainsi que plusieurs contributions spécialisées sur l'artisanat, les résidus animaux et végétaux… Une documentation inédite livrée exhaustivement, des interprétations étayées d'analyses rigoureuses, des analyses fondées sur des observations méticuleuses, le tout dans le cadre d'une coordination éditoriale exigeante, font de la monographie du Pâtural un modèle du genre qui intéressera, bien au-delà du cercle des antiquisants, tous ceux que la question de la publication archéologique intéresse

La conquête de la montagne : des premières occupations humaines à l’anthropisation du milieu

International audienc

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

BACKGROUND: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. RESULTS: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. CONCLUSIONS: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.Submitted to Genome Biologystatus: publishe