Cargando…

Simulation-Based Evaluation of Methods, Data Types, and Temporal Sampling Schemes for Detecting Recent Population Declines

Understanding recent population trends is critical to quantifying species vulnerability and implementing effective management strategies. To evaluate the accuracy of genomic methods for quantifying recent declines (beginning <120 generations ago), we simulated genomic data using forward-time meth...

Descripción completa

Detalles Bibliográficos
Autores principales:	Reid, Brendan N, Pinsky, Malin L
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2022
Materias:	Genomics Paper
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9801984/ https://www.ncbi.nlm.nih.gov/pubmed/36104155 http://dx.doi.org/10.1093/icb/icac144

Ejemplares similares

Detecting parallel polygenic adaptation to novel evolutionary pressure in wild populations: a case study in Atlantic cod (Gadus morhua)
por: Reid, Brendan N., et al.
Publicado: (2023)

Temporal changes in nasopharyngeal carriage of Streptococcus pneumoniae serotype 1 genotypes in healthy Gambians before and after the 7-valent pneumococcal conjugate vaccine
por: Ebruke, Chinelo, et al.
Publicado: (2015)

Detecting laterally transferred genes: use of entropic clustering methods and genome position
por: Azad, Rajeev K., et al.
Publicado: (2007)

Compensating for population sampling in simulations of epidemic spread on temporal contact networks
por: Génois, Mathieu, et al.
Publicado: (2015)

Genome of the endangered Guatemalan Beaded Lizard, Heloderma charlesbogerti, reveals evolutionary relationships of squamates and declines in effective population sizes
por: Dyson, Carl J, et al.
Publicado: (2022)

XSim: Simulation of Descendants from Ancestors with Sequence Data
por: Cheng, Hao, et al.
Publicado: (2015)

Comprehensive and realistic simulation of tumour genomic sequencing data
por: O’Sullivan, Brian, et al.
Publicado: (2023)

Genetic decline and recovery of a demographically rebuilt fishery species
por: Hoey, Jennifer A., et al.
Publicado: (2022)

Recent Progress in Plasmonic Biosensing Schemes for Virus Detection
por: Mauriz, Elba
Publicado: (2020)

Detection of KRAS mutations in plasma cell-free DNA of colorectal cancer patients and comparison with cancer panel data for tissue samples of the same cancers
por: Min, Suji, et al.
Publicado: (2019)

A Genomic Selection Index Applied to Simulated and Real Data
por: Ceron-Rojas, J. Jesus, et al.
Publicado: (2015)

Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes
por: Pathak, Ankit K, et al.
Publicado: (2022)

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project
por: Mu, Xinmeng Jasmine, et al.
Publicado: (2011)

Copy number analysis of whole-genome data using BIC-seq2 and its application to detection of cancer susceptibility variants
por: Xi, Ruibin, et al.
Publicado: (2016)

A reference genome assembly of the declining tricolored blackbird, Agelaius tricolor
por: Ballare, Kimberly M, et al.
Publicado: (2022)

Purebred and Crossbred Genomic Evaluation and Mate Allocation Strategies To Exploit Dominance in Pig Crossbreeding Schemes
por: González-Diéguez, David, et al.
Publicado: (2020)

High neural activity accelerates the decline of cognitive plasticity with age in Caenorhabditis elegans
por: Li, Qiaochu, et al.
Publicado: (2020)

Extensions of BLUP Models for Genomic Prediction in Heterogeneous Populations: Application in a Diverse Switchgrass Sample
por: Ramstein, Guillaume P., et al.
Publicado: (2019)

Data scheme and data format for transferable force fields for molecular simulation
por: Kanagalingam, Gajanan, et al.
Publicado: (2023)

Disentangling the spatial and temporal causes of decline in a bird population
por: Plard, Floriane, et al.
Publicado: (2020)

The association between copy number aberration, DNA methylation and gene expression in tumor samples
por: Sun, Wei, et al.
Publicado: (2018)

Integrated genome-wide analysis of genomic changes and gene regulation in human adrenocortical tissue samples
por: Gara, Sudheer Kumar, et al.
Publicado: (2015)

Application of OU processes to modelling temporal dynamics of the human microbiome, and calculating optimal sampling schemes
por: Kenney, Toby, et al.
Publicado: (2020)

Monte Carlo simulation of OLS and linear mixed model inference of phenotypic effects on gene expression
por: Walker, Jeffrey A.
Publicado: (2016)

Simulation and Experimentation of a Grounding Network Detection Scheme Based on a Low-Frequency Electromagnetic Method
por: Duan, Qingming, et al.
Publicado: (2023)

OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes
por: Swenson, David W. H., et al.
Publicado: (2018)

Complete genome sequence of Bacillus thuringiensis strain RC340, isolated from a temperate forest soil sample in New England
por: Sullivan, Brendan, et al.
Publicado: (2023)

Identification of non-coding genetic variants in samples from hypoxemic respiratory disease patients that affect the transcriptional response to hypoxia
por: Roche, Olga, et al.
Publicado: (2016)

Novel Circo-Like Virus Detected in a Croatian Bat Population
por: Šimić, Ivana, et al.
Publicado: (2019)

Re-Examining Mortality Sources and Population Trends in a Declining Seabird: Using Bayesian Methods to Incorporate Existing Information and New Data
por: Reid, Tim, et al.
Publicado: (2013)

Recently published Streptomyces genome sequences
por: Harrison, James, et al.
Publicado: (2014)

Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods
por: Kaynak, Burak T., et al.
Publicado: (2022)

Comparing Aberration Detection Methods with Simulated Data
por: Hutwagner, Lori, et al.
Publicado: (2005)

Evaluating Methods of Updating Training Data in Long-Term Genomewide Selection
por: Neyhart, Jeffrey L., et al.
Publicado: (2017)

dbPSHP: a database of recent positive selection across human populations
por: Li, Mulin Jun, et al.
Publicado: (2014)

A Chromosome-Level Reference Genome for the Black-Legged Kittiwake (Rissa tridactyla), a Declining Circumpolar Seabird
por: Sozzoni, Marcella, et al.
Publicado: (2023)

Mitochondrial diversity within modern human populations
por: Carter, Robert W.
Publicado: (2007)

Detection of Ki-ras mutations in tissue and plasma samples of patients with pancreatic cancer using PNA-mediated PCR clamping and hybridisation probes
por: Däbritz, J, et al.
Publicado: (2005)

Nearly Complete Genome Sequence of a Novel Phlebovirus-Like Virus Detected in a Human Plasma Sample by High-Throughput Sequencing
por: Laubscher, Florian, et al.
Publicado: (2019)

Genome-Enhanced Detection and Identification (GEDI) of plant pathogens
por: Feau, Nicolas, et al.
Publicado: (2018)

Cannot write session to /tmp/vufind_sessions/sess_p7nklvvbue64k9b0a6dqfbotuk