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La fouille de textes (text mining) comme outil de création automatique de réseaux génétiques. Avec l’amélioration constante de la vitesse et de l’accessibilité des techniques de génomique, transcriptomique et protéomique, la quantité de données disponible pour ces secteurs de recherche ne cesse d’augmenter. Malheureusement, la majorité de ces informations est encore stockée sous forme de documents textes non structurés et ce malgré la présence de certaines bases de données spécialisées. Toutefois, une technique existe pour interpréter automatiquement ces documents textes et en retirer les informations utiles : la “fouille de textes” (text mining). Bien que généralement utilisée dans d’autres secteurs que la biologie, par exemple pour extraire les mots revenant le plus souvent sur twitter, elle est toutefois capable d’isoler des informations bien plus ciblées telle que la relation entre deux gènes. Cette technique consiste à appliquer des analyses statistiques sur l’ensemble des mots issus d’un groupe de textes qui aura préalablement subi différents traitements tels que la séparation en phrases, la suppression de la ponctuation, etc … Le but était ici de développer un package R capable de rechercher automatiquement, sur base d’un ou plusieurs mot clé spécifiés par l’utilisateur (Chlamydomonas reinhardtii, …), les documents disponibles sur une base de données (“PubMed”, …), de les analyser et d’en extraire un réseau génétique d’interactions entre les différents gènes issus de ces documents. Au final, malgré l’identification de relations entre gènes d’espèces différentes à cause de sa capacité à isoler les gènes de plusieurs espèces, les prédictions générées par notre modèle peuvent être considérées comme satisfaisantes (score F1 de 68% pour l’identification des gènes dans le corpus CRAFT) compte tenu du fait qu’il n’utilise aucune ressource externe spécifique au type d’organisme analysé. La version finale de la librairie R “GeneMining” construite tout au long de ce mémoire est disponible sur le site http://www.biosys.ulg.ac.be/students/Lete/GeneMining_0.4.0.tar.gz. Enfin, les résultats intermédiaires obtenus au cours de ce mémoire ont fait l’objet de l’écriture d’un article pour la sixième conférence internationale de bioinformatique et sciences biomédicales à Singapour. L’article en question peut être consulté à l’adresse suivante : http://www.biosys.ulg.ac.be/students/Lete/ICBBS2017.pdf.
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The management of wildlife populations and their habitats are interdisciplinary fields that encompass many scientific disciplines that also impact the lives of people. Therefore, these are truly applied sciences where human dimensions play an important role.This book highlights the importance of conducting rigorous studies to design and implement the effective management and restoration of wild populations and their habitats. A new paradigm in conservation is developing that goes beyond the boundaries of protected areas to achieve the goal of sustainable development. The 16 papers in this book, including reviews and a project report, cover a broad range of topics, exploring a diversity of subjects that are representative of current practices and novel applications.We would like to thank both the MDPI publishers and editorial staff for their support and help during the process of editing this book, in addition to the authors for their contributions.
Research & information: general --- Geography --- road safety --- roadkill --- clustering --- growth rate --- traffic intensity --- mitigation measures --- roadkill analysis --- movement patterns --- habitat characterisation --- multiple criteria --- multi-objective ranking --- environmental awareness --- machine learning --- random forest model --- structural equation modelling --- latent class analysis --- visitor mapping --- social-ecological systems --- cultural rural landscape --- protected areas --- rewilding --- rural socioeconomics --- forest expansion --- rural to urban land conversion --- biocultural heritage --- biodiversity --- naturalness --- land-cover change --- habitat quality --- InVEST --- ecosystem-based approach and assessment --- nature-based solution --- decision-making support --- national park management --- wildlife protection --- biodiversity conservation --- policy framework --- policy formulation --- China --- agricultural management --- amphibians --- beta diversity --- community ecology --- metacommunities --- constructed wetlands --- bats --- urban ecology --- long-term monitoring --- acoustics --- city parks --- community dynamics --- conservation evaluation --- at-risk species --- golden-winged warbler --- landowner incentives --- New England cottontail --- Natural Resources Conservation Service --- U.S. Department of Agriculture --- Working Lands for Wildlife --- camera-trapping --- conservation puma --- relative integrated anthropization index --- INRA --- South American grey fox --- habitat adaptability --- habitat model --- habitat selection --- habitat suitability --- use versus availability --- Maxent --- presence points --- GPS radio-collars --- anthropogenic variables --- species distribution models --- Spermophilus citellus --- maximum entropy modeling --- species distribution modeling --- climate change refugia --- urodela --- salamandridae --- caudata --- biosphere reserve --- habitat restoration --- species management --- life project --- activity patterns --- Lepus granatensis --- population decline --- niche --- Oryctolagus cuniculus --- roadside census --- predator-prey relationships --- spatio-temporal behavior --- abundance --- distance sampling --- population density --- R package --- wildlife survey --- uncertainty --- occupancy modeling --- road ecology --- road safety --- roadkill --- clustering --- growth rate --- traffic intensity --- mitigation measures --- roadkill analysis --- movement patterns --- habitat characterisation --- multiple criteria --- multi-objective ranking --- environmental awareness --- machine learning --- random forest model --- structural equation modelling --- latent class analysis --- visitor mapping --- social-ecological systems --- cultural rural landscape --- protected areas --- rewilding --- rural socioeconomics --- forest expansion --- rural to urban land conversion --- biocultural heritage --- biodiversity --- naturalness --- land-cover change --- habitat quality --- InVEST --- ecosystem-based approach and assessment --- nature-based solution --- decision-making support --- national park management --- wildlife protection --- biodiversity conservation --- policy framework --- policy formulation --- China --- agricultural management --- amphibians --- beta diversity --- community ecology --- metacommunities --- constructed wetlands --- bats --- urban ecology --- long-term monitoring --- acoustics --- city parks --- community dynamics --- conservation evaluation --- at-risk species --- golden-winged warbler --- landowner incentives --- New England cottontail --- Natural Resources Conservation Service --- U.S. Department of Agriculture --- Working Lands for Wildlife --- camera-trapping --- conservation puma --- relative integrated anthropization index --- INRA --- South American grey fox --- habitat adaptability --- habitat model --- habitat selection --- habitat suitability --- use versus availability --- Maxent --- presence points --- GPS radio-collars --- anthropogenic variables --- species distribution models --- Spermophilus citellus --- maximum entropy modeling --- species distribution modeling --- climate change refugia --- urodela --- salamandridae --- caudata --- biosphere reserve --- habitat restoration --- species management --- life project --- activity patterns --- Lepus granatensis --- population decline --- niche --- Oryctolagus cuniculus --- roadside census --- predator-prey relationships --- spatio-temporal behavior --- abundance --- distance sampling --- population density --- R package --- wildlife survey --- uncertainty --- occupancy modeling --- road ecology
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The management of wildlife populations and their habitats are interdisciplinary fields that encompass many scientific disciplines that also impact the lives of people. Therefore, these are truly applied sciences where human dimensions play an important role.This book highlights the importance of conducting rigorous studies to design and implement the effective management and restoration of wild populations and their habitats. A new paradigm in conservation is developing that goes beyond the boundaries of protected areas to achieve the goal of sustainable development. The 16 papers in this book, including reviews and a project report, cover a broad range of topics, exploring a diversity of subjects that are representative of current practices and novel applications.We would like to thank both the MDPI publishers and editorial staff for their support and help during the process of editing this book, in addition to the authors for their contributions.
road safety --- roadkill --- clustering --- growth rate --- traffic intensity --- mitigation measures --- roadkill analysis --- movement patterns --- habitat characterisation --- multiple criteria --- multi-objective ranking --- environmental awareness --- machine learning --- random forest model --- structural equation modelling --- latent class analysis --- visitor mapping --- social–ecological systems --- cultural rural landscape --- protected areas --- rewilding --- rural socioeconomics --- forest expansion --- rural to urban land conversion --- biocultural heritage --- biodiversity --- naturalness --- land-cover change --- habitat quality --- InVEST --- ecosystem-based approach and assessment --- nature-based solution --- decision-making support --- national park management --- wildlife protection --- biodiversity conservation --- policy framework --- policy formulation --- China --- agricultural management --- amphibians --- beta diversity --- community ecology --- metacommunities --- constructed wetlands --- bats --- urban ecology --- long-term monitoring --- acoustics --- city parks --- community dynamics --- conservation evaluation --- at-risk species --- golden-winged warbler --- landowner incentives --- New England cottontail --- Natural Resources Conservation Service --- U.S. Department of Agriculture --- Working Lands for Wildlife --- camera-trapping --- conservation puma --- relative integrated anthropization index --- INRA --- South American grey fox --- habitat adaptability --- habitat model --- habitat selection --- habitat suitability --- use versus availability --- Maxent --- presence points --- GPS radio-collars --- anthropogenic variables --- species distribution models --- Spermophilus citellus --- maximum entropy modeling --- species distribution modeling --- climate change refugia --- urodela --- salamandridae --- caudata --- biosphere reserve --- habitat restoration --- species management --- life project --- activity patterns --- Lepus granatensis --- population decline --- niche --- Oryctolagus cuniculus --- roadside census --- predator–prey relationships --- spatio-temporal behavior --- abundance --- distance sampling --- population density --- R package --- wildlife survey --- uncertainty --- occupancy modeling --- road ecology --- n/a --- social-ecological systems --- predator-prey relationships
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This collection of 25 research papers comprised of 22 original articles and 3 reviews is brought together from international leaders in bioinformatics and biostatistics. The collection highlights recent computational advances that improve the ability to analyze highly complex data sets to identify factors critical to cancer biology. Novel deep learning algorithms represent an emerging and highly valuable approach for collecting, characterizing and predicting clinical outcomes data. The collection highlights several of these approaches that are likely to become the foundation of research and clinical practice in the future. In fact, many of these technologies reveal new insights about basic cancer mechanisms by integrating data sets and structures that were previously immiscible.
cancer treatment --- extreme learning --- independent prognostic power --- AID/APOBEC --- HP --- gene inactivation biomarkers --- biomarker discovery --- chemotherapy --- artificial intelligence --- epigenetics --- comorbidity score --- denoising autoencoders --- protein --- single-biomarkers --- gene signature extraction --- high-throughput analysis --- concatenated deep feature --- feature selection --- differential gene expression analysis --- colorectal cancer --- ovarian cancer --- multiple-biomarkers --- gefitinib --- cancer biomarkers --- classification --- cancer biomarker --- mutation --- hierarchical clustering analysis --- HNSCC --- cell-free DNA --- network analysis --- drug resistance --- hTERT --- variable selection --- KRAS mutation --- single-cell sequencing --- network target --- skin cutaneous melanoma --- telomeres --- Neoantigen Prediction --- datasets --- clinical/environmental factors --- StAR --- PD-L1 --- miRNA --- circulating tumor DNA (ctDNA) --- false discovery rate --- predictive model --- Computational Immunology --- brain metastases --- observed survival interval --- next generation sequencing --- brain --- machine learning --- cancer prognosis --- copy number aberration --- mutable motif --- steroidogenic enzymes --- tumor --- mortality --- tumor microenvironment --- somatic mutation --- transcriptional signatures --- omics profiles --- mitochondrial metabolism --- Bufadienolide-like chemicals --- cancer-related pathways --- intratumor heterogeneity --- estrogen --- locoregionally advanced --- RNA --- feature extraction and interpretation --- treatment de-escalation --- activation induced deaminase --- knockoffs --- R package --- copy number variation --- gene loss biomarkers --- cancer CRISPR --- overall survival --- histopathological imaging --- self-organizing map --- Network Analysis --- oral cancer --- biostatistics --- firehose --- Bioinformatics tool --- alternative splicing --- biomarkers --- diseases genes --- histopathological imaging features --- imaging --- TCGA --- decision support systems --- The Cancer Genome Atlas --- molecular subtypes --- molecular mechanism --- omics --- curative surgery --- network pharmacology --- methylation --- bioinformatics --- neurological disorders --- precision medicine --- cancer modeling --- miRNAs --- breast cancer detection --- functional analysis --- biomarker signature --- anti-cancer --- hormone sensitive cancers --- deep learning --- DNA sequence profile --- pancreatic cancer --- telomerase --- Monte Carlo --- mixture of normal distributions --- survival analysis --- tumor infiltrating lymphocytes --- curation --- pathophysiology --- GEO DataSets --- head and neck cancer --- gene expression analysis --- erlotinib --- meta-analysis --- traditional Chinese medicine --- breast cancer --- TCGA mining --- breast cancer prognosis --- microarray --- DNA --- interaction --- health strengthening herb --- cancer --- genomic instability
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