Articles

Search Articles

Advanced search
Help

Catalogue

Articles

Databases

X
Search Filters
Format Format
Format Format
X
Sort by Item Count (A-Z)
Filter by Count
Journal Article (114) 114
Publication (20) 20
Book Review (11) 11
Book Chapter (3) 3
Dissertation (2) 2
Conference Proceeding (1) 1
Reference (1) 1
more...
Subjects Subjects
Subjects Subjects
X
Sort by Item Count (A-Z)
Filter by Count
genetics & heredity (41) 41
humans (36) 36
bayes theorem (34) 34
models, genetic (34) 34
phylogeny (34) 34
animals (31) 31
evolutionary biology (27) 27
bayesian analysis (24) 24
dna-sequences (24) 24
index medicus (24) 24
computer simulation (22) 22
research (22) 22
evolution (21) 21
alleles (20) 20
genetics (20) 20
phylogenetics (19) 19
monte carlo method (17) 17
algorithms (16) 16
inference (16) 16
population genetics (16) 16
evolution, molecular (15) 15
markov chains (15) 15
mutation (14) 14
biological taxonomies (13) 13
trees (13) 13
usage (13) 13
ecology (12) 12
genes (12) 12
biological sciences (11) 11
genetics, population (11) 11
likelihood functions (11) 11
markov chain monte carlo (11) 11
maximum-likelihood (11) 11
modeling (11) 11
models, statistical (11) 11
ancestral population sizes (10) 10
dna (10) 10
genetic aspects (10) 10
genetic variation (10) 10
models (10) 10
multidisciplinary sciences (10) 10
biochemistry & molecular biology (9) 9
classification - methods (9) 9
gene frequency (9) 9
genomics (9) 9
linkage disequilibrium (9) 9
model (9) 9
models, biological (9) 9
parametric models (9) 9
probability (9) 9
rates (9) 9
research article (9) 9
bayesian inference (8) 8
bayesian statistical decision theory (8) 8
biology (8) 8
datasets (8) 8
female (8) 8
genetic loci (8) 8
molecular evolution (8) 8
speciation (8) 8
time factors (8) 8
analysis (7) 7
deoxyribonucleic acid (7) 7
divergence (7) 7
evolutionary trees (7) 7
investigations (7) 7
parasites (7) 7
software (7) 7
species (7) 7
base sequence (6) 6
bayesian phylogenetic inference (6) 6
book reviews (6) 6
evolutionary genetics (6) 6
fossils (6) 6
genetic speciation (6) 6
genome, human (6) 6
genotype (6) 6
haplotypes (6) 6
male (6) 6
molecular biology (6) 6
nonfiction (6) 6
parasite hosts (6) 6
population (6) 6
population size (6) 6
recombination, genetic (6) 6
selection, genetic (6) 6
sequences (6) 6
topology (6) 6
biological evolution (5) 5
biology, miscellaneous (5) 5
books (5) 5
chromosome mapping (5) 5
coalescent (5) 5
divergence times (5) 5
estimation methods (5) 5
food and beverages (5) 5
gene trees (5) 5
genetic markers (5) 5
genetic research (5) 5
hot-spots (5) 5
more...
Library Location Library Location
Language Language
Publication Date Publication Date
Click on a bar to filter by decade
Slide to change publication date range


1. Full Text Unguided species delimitation using DNA sequence data from multiple loci
by Yang, Ziheng and Rannala, Bruce
Molecular Biology and Evolution, ISSN 0737-4038, 12/2014, Volume 31, Issue 12, pp. 3125 - 3135
A method was developed for simultaneous Bayesian inference of species delimitation and species phylogeny using the multispecies coalescent model. The method... 
Bayesian species delimitation | multispecies coalescent | species tree | nearest-neighbor interchange | guide tree | reversible-jump MCMC | EVOLUTIONARY BIOLOGY | BIOCHEMISTRY & MOLECULAR BIOLOGY | GENETICS & HEREDITY | ACCURACY | Fishes - genetics | Markov Chains | Algorithms | Animals | Computer Simulation | Bayes Theorem | Lizards - genetics | Models, Genetic | Phylogeny | Multilocus Sequence Typing | Monte Carlo Method | Uncertainty | Simulation | Genes | Phylogenetics | Topology | Bayesian analysis | Deoxyribonucleic acid--DNA | Fast Track
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
2. Full Text Molecular phylogenetics: Principles and practice
by Yang, Ziheng and Rannala, Bruce
Nature Reviews Genetics, ISSN 1471-0056, 05/2012, Volume 13, Issue 5, pp. 303 - 314
Phylogenies are important for addressing various biological questions such as relationships among species or genes, the origin and spread of viral infection... 
MAXIMUM-LIKELIHOOD-ESTIMATION | EVOLUTIONARY TREES | DNA-SEQUENCES | ANCESTRAL POPULATION SIZES | GENETICS & HEREDITY | SPECIES DIVERGENCE TIMES | SUBSTITUTION MODELS | BAYESIAN-ESTIMATION | MULTIPLE SEQUENCE ALIGNMENT | AMINO-ACID REPLACEMENT | CHAIN MONTE-CARLO | Models, Biological | Base Sequence | Humans | Molecular Sequence Data | Female | Male | Software | Models, Statistical | Phylogeny | Usage | Cladistic analysis | Molecular genetics | Research | Nucleotide sequencing | Methods | DNA sequencing
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
3. Full Text Inferring speciation tunes under an episodic molecular clock
by Rannala, Bruce and Yang, Ziheng
Systematic Biology, ISSN 1063-5157, 05/2007, Volume 56, Issue 3, pp. 453 - 466
MCMC | Divergence times | Bayesian method | Molecular clock
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
4. Full Text The art and science of species delimitation
by Bruce RANNALA
动物学报：英文版, ISSN 1674-5507, 2015, Volume 61, Issue 5, pp. 846 - 853
DNA-based approaches to systematics have changed dramatically during the last two decades with the rise of DNA barcoding methods and newer multi-locus methods... 
划界 | 物种鉴定 | 种类划分 | 序列数据 | 艺术与科学 | 基于模型 | 贝叶斯方法 | 测序技术 | Bayesian species delimitation | Multi-species coalescent | Species concepts | GENE TREES | COALESCENT | ZOOLOGY | MULTIPLE LOCI | IDENTIFICATION | MULTILOCUS SEQUENCE DATA | FAIL | TREE INFERENCE
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
5. Full Text Bayesian species delimitation using multilocus sequence data
by Ziheng Yang and Bruce Rannala and Scott V. Edwards
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 5/2010, Volume 107, Issue 20, pp. 9264 - 9269
In the absence of recent admixture between species, bipartitions of individuals in gene trees that are shared across loci can potentially be used to infer the... 
Datasets | Biological taxonomies | Lizards | Plant roots | Genetic loci | Evolutionary genetics | Inference | Phylogeny | Species | Modeling | Bayesian phylogenetic inference | Coalescent | Biological species concept | Reversible jump | Markov chain Monte Carlo | DNA-SEQUENCES | reversible jump | MULTIDISCIPLINARY SCIENCES | ANCESTRAL POPULATION SIZES | MODEL | biological species concept | INFERENCE | coalescent | GENOTYPES | EVOLUTIONARY TREES | MULTIPLE LOCI | LIKELIHOOD | Base Sequence - genetics | Markov Chains | Species Specificity | Humans | Algorithms | Animals | Computer Simulation | Bayes Theorem | Models, Genetic | Monte Carlo Method | Rotifera | Bayesian statistical decision theory | Monte Carlo method | Phylogenetic trees | Usage | Research | Population genetics | Phylogenetics | Bayesian analysis | Genes | Biological Sciences
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
6. Full Text Improved reversible jump algorithms for Bayesian species delimitation
by Rannala, Bruce and Yang, Ziheng
Genetics, ISSN 0016-6731, 2013, Volume 194, Issue 1, pp. 245 - 253
Several computational methods have recently been proposed for delimiting species using multilocus sequence data. Among them, the Bayesian method of Yang and... 
DNA-SEQUENCES | TREES | INFERENCE | MULTILOCUS DATA | ANCESTRAL POPULATION SIZES | GENETICS & HEREDITY | Fishes - genetics | Markov Chains | Algorithms | Animals | Species Specificity | Computer Simulation | Bayes Theorem | Databases, Genetic | Lizards - genetics | Models, Genetic | Monte Carlo Method | Bayesian statistical decision theory | Markov processes | Usage | Research | Biological diversity | Bayesian analysis | species delimitation | reversible jump | Bayesian inference | Markov chain Monte Carlo | Investigations
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
7. Full Text Conceptual issues in bayesian divergence time estimation
by Rannala, Bruce
Philosophical Transactions of the Royal Society B: Biological Sciences, ISSN 0962-8436, 07/2016, Volume 371, Issue 1699, pp. 20150134 - 20150134
Bayesian inference of species divergence times is an unusual statistical problem, because the divergence time parameters are not identifiable unless both... 
Fossil calibrations | Bayesian inference | Divergence time estimation | divergence time estimation | BIOLOGY | fossil calibrations | TREE | INFERENCE | FOSSILS | Phylogeny | Time Factors | Bayes Theorem | Evolution, Molecular | Fossils | 1001
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
8. Full Text Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci
by Rannala, Bruce and Yang, Ziheng
Genetics, ISSN 0016-6731, 08/2003, Volume 164, Issue 4, pp. 1645 - 1656
Monte Carlo method | Apes | Usage | Human beings | Nucleotide sequence | DNA | Evolution | Genetics | Genetic aspects | Man | Research | Population genetics
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
9. Full Text Efficient Bayesian Species Tree Inference under the Multispecies Coalescent
by Rannala, Bruce and Yang, Ziheng
Systematic Biology, ISSN 1063-5157, 09/2017, Volume 66, Issue 5, pp. 823 - 842
Abstract We develop a Bayesian method for inferring the species phylogeny under the multispecies coalescent (MSC) model. To improve the mixing properties of... 
multispecies coalescent | species tree | SPR | nodeslider | MCMC | Bayes factor | Bayesian inference | MAXIMUM-LIKELIHOOD | DNA-SEQUENCES | SEQUENCE DATA | ANCESTRAL POPULATION SIZES | MODEL | DIVERGENCE TIMES | PHYLOGENETIC INFERENCE | GENE TREES | EVOLUTIONARY BIOLOGY | MULTIPLE LOCI | MULTILOCUS DATA | Algorithms | Animals | Crotalus - classification | Models, Biological | Computer Simulation | Bayes Theorem | Crotalus - genetics | Shrews - classification | Classification - methods | Phylogeny | Shrews - genetics | Markov process | Nearest-neighbor | Genes | Topology | Statistics | Mitochondria | Simulation | Efficiency | Pruning | Bayesian analysis | Species | Heuristic
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
10. Full Text Bayesian Inference of Recent Migration Rates Using Multilocus Genotypes
by Wilson, Gregory A and Rannala, Bruce
Genetics, ISSN 0016-6731, 03/2003, Volume 163, Issue 3, pp. 1177 - 1191
A new Bayesian method that uses individual multilocus genotypes to estimate rates of recent immigration (over the last several generations) among populations... 
INDIVIDUALS | MAXIMUM-LIKELIHOOD-ESTIMATION | GENETICS & HEREDITY | POPULATION-STRUCTURE | PATTERNS | GENE FLOW | COALESCENT APPROACH | Gene Frequency | Humans | Wolves - genetics | Probability | Genotype | Chromosome Mapping | Models, Statistical | Linkage Disequilibrium | Likelihood Functions | Animals | Computer Simulation | Bayes Theorem | Centaurea - genetics | Animal Migration | Models, Genetic | Bayesian statistical decision theory | Emigration and immigration | Migrations of nations | Genetic aspects | Models | Bayesian analysis | Gene loci
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
11. Full Text The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods
by Adam D. Leaché and Bruce Rannala
Systematic Biology, ISSN 1063-5157, 3/2011, Volume 60, Issue 2, pp. 126 - 137
Numerous simulation studies have investigated the accuracy of phylogenetic inference of gene trees under maximum parsimony, maximum likelihood, and Bayesian... 
Biological taxonomies | Estimate reliability | Demography | Genetic concordance | Phylogenetics | Inference | Genetic loci | Population size | Species | Estimation methods | tree shape | incomplete lineage sorting | multilocus data | phylogeny reconstruction | simulation | Coalescence | gene trees | COALESCENT | MAXIMUM-LIKELIHOOD | DNA-SEQUENCES | ANCESTRAL POPULATION SIZES | BAYESIAN PHYLOGENETIC INFERENCE | EVOLUTIONARY BIOLOGY | MODELS | EXPLORATION | DIVERGENCE | DISCORDANCE | Plants - genetics | Computer Simulation | Genetic Speciation | Bayes Theorem | Classification - methods | Phylogeny | Plants - classification | Trees | Accuracy | Computer simulation | Genes | Probability | Estimating techniques | Comparative analysis | Bayesian analysis
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
12. Full Text Bayesian species identification under the multispecies coalescent provides significant improvements to DNA barcoding analyses
by Yang, Ziheng and Rannala, Bruce
Molecular Ecology, ISSN 0962-1083, 06/2017, Volume 26, Issue 11, pp. 3028 - 3036
DNA barcoding methods use a single locus (usually the mitochondrial COI gene) to assign unidentified specimens to known species in a library based on a genetic... 
barcoding | species delimitation | bpp | species identification | DNA | coalescent | DNA barcoding | DELIMITATION | SEQUENCE DATA | BIOCHEMISTRY & MOLECULAR BIOLOGY | ANCESTRAL POPULATION SIZES | MODEL | RARITY | TAXONOMY | EVOLUTIONARY BIOLOGY | ECOLOGY | MULTIPLE LOCI | TREE ESTIMATION | Models, Genetic | Gene Library | DNA Barcoding, Taxonomic | Genes, Mitochondrial | Computer Simulation | Bayes Theorem | Genetic research | Analysis | Bar codes | COI protein | Divergence | Thresholds | Computer simulation | Genetic distance | Biodiversity | Gene sequencing | Species diversity | Mitochondria | Computer applications | Species | Bayesian analysis | Deoxyribonucleic acid--DNA
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
13. Full Text Inferring Speciation Times under an Episodic Molecular Clock
by Bruce Rannala and Ziheng Yang
Systematic Biology, ISSN 1063-5157, 6/2007, Volume 56, Issue 3, pp. 453 - 466
We extend our recently developed Markov chain Monte Carlo algorithm for Bayesian estimation of species divergence times to allow variable evolutionary rates... 
Datasets | Cats | Divergent evolution | Branches | Genetic loci | Calibration | Phylogeny | Modeling | We they distinction | Fossils | MAXIMUM-LIKELIHOOD | DNA-SEQUENCES | Bayesian method | divergence times | MCMC | RADIATION | EVOLUTIONARY BIOLOGY | molecular clock | EVOLUTION | TREES | MODELS | ESTIMATING DIVERGENCE TIMES | GENES | DATES | FOSSIL | Algorithms | Animals | Time Factors | Computer Simulation | Genetic Speciation | Humans | Bayes Theorem | Classification - methods | Models, Genetic | Evolution, Molecular | Felidae - classification | Medical research | Computer simulation | Ratings & rankings | Evolution | Stochastic models | Estimates | Methods
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
14. Full Text Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci
by Rannala, Bruce and Yang, Ziheng
Genetics, ISSN 0016-6731, 08/2003, Volume 164, Issue 4, pp. 1645 - 1656
The effective population sizes of ancestral as well as modern species are important parameters ill models of population genetics and human evolution. The... 
MIGRATION | MAXIMUM-LIKELIHOOD-ESTIMATION | PHYLOGENY | TREES | MODERN HUMANS | GENETICS | GENETICS & HEREDITY | HOMINOIDS | INFERENCE | COALESCENT APPROACH | REGION | Genetics, Population | Markov Chains | Reproducibility of Results | Species Specificity | Humans | Pan troglodytes - genetics | Models, Statistical | Hominidae - genetics | Algorithms | Animals | Time Factors | Base Sequence | Population Density | Alleles | Bayes Theorem | Monte Carlo Method | Evolution, Molecular | Evolution | Population genetics | Deoxyribonucleic acid | DNA
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
15. Full Text The Bayesian revolution in genetics
by Beaumont, Mark A and Rannala, Bruce
Nature Reviews Genetics, ISSN 1471-0056, 04/2004, Volume 5, Issue 4, pp. 251 - 261
Bayesian statistics allow scientists to easily incorporate prior knowledge into their data analysis. Nonetheless, the sheer amount of computational power that... 
MAXIMUM-LIKELIHOOD-ESTIMATION | DNA-SEQUENCES | HUMAN GENOME | GENETICS & HEREDITY | LINKAGE-DISEQUILIBRIUM | POPULATION-GROWTH | MARKOV-CHAIN | MICROSATELLITE ANALYSIS | LOCAL SEQUENCE ALIGNMENT | SINGLE-NUCLEOTIDE POLYMORPHISMS | CHAIN MONTE-CARLO | Quantitative Trait, Heritable | Humans | Bayes Theorem | Genetics - statistics & numerical data | Probability | Models, Genetic | Genome, Human | Biometry | Genetic Linkage
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights
16. Full Text The Influence of Gene Flow on Species Tree Estimation: A Simulation Study
by Adam D. Leaché and Rebecca B. Harris and Bruce Rannala and Ziheng Yang
Systematic Biology, ISSN 1063-5157, 1/2014, Volume 63, Issue 1, pp. 17 - 30
Gene flow among populations or species and incomplete lineage sorting (ILS) are two evolutionary processes responsible for generating gene tree discordance and... 
Biological taxonomies | Gene flow | Phylogenetics | Population estimates | Genetic loci | Population size | Inference | Topology | Species | Animal migration behavior | MPEST | coalescence | dilation | simulation | migration | BEST | compression | BEAST | introgression | COALESCENT | DNA-SEQUENCES | POPULATION SIZES | MODEL | INFERENCE | ACCURACY | EVOLUTIONARY BIOLOGY | SPECIATION | TESTING HYBRIDIZATION | DIVERGENCE | HISTORY | Gene Flow | Computer Simulation | Genetic Speciation | Alleles | Bayes Theorem | Classification - methods | Models, Genetic | Phylogeny | Estimating techniques | Simulation | Bayesian analysis | Genomics | Genes
Journal Article
Details down arrow
Digital rights down arrow
loading Loading Rights