Reading assessment for Unit 2
... d. next-generation sequencing methods 4. In addition to gene expression studies, microarrays can be used for a. investigating DNA copy number b. looking at sites of in vivo protein-DNA binding c. identifying transcription factor binding sites d. looking at single nucleotide polymorphisms (SNPs) e. a ...
... d. next-generation sequencing methods 4. In addition to gene expression studies, microarrays can be used for a. investigating DNA copy number b. looking at sites of in vivo protein-DNA binding c. identifying transcription factor binding sites d. looking at single nucleotide polymorphisms (SNPs) e. a ...
Bioinformatics needs to adopt statistical thinking
... in bioinformatics. Molecular evolution has made heavy use of maximum likelihood estimation for phylogeny construction. But the large-scale data sets we are confronted with now pose many new problems, mostly statistical in nature. In gene expression analysis, technological problems and biological var ...
... in bioinformatics. Molecular evolution has made heavy use of maximum likelihood estimation for phylogeny construction. But the large-scale data sets we are confronted with now pose many new problems, mostly statistical in nature. In gene expression analysis, technological problems and biological var ...
Evolutionary Representations of Biological History
... The use of models that dismiss processes known to have played an important role in shaping the current biological variation among species is a real thorn in the side of phylogenetics. 3. The epistemological framework: Many trees are better than one In phylogenetics there is a large debate on the fac ...
... The use of models that dismiss processes known to have played an important role in shaping the current biological variation among species is a real thorn in the side of phylogenetics. 3. The epistemological framework: Many trees are better than one In phylogenetics there is a large debate on the fac ...
BIOLOGY - Learner
... By selecting a particular class of morphological characters, researchers may also bias the analysis in such a way that groups with certain characteristics cluster with others for reasons other than homology. For instance, if the set of characters were weighted toward those involved in carnivory, car ...
... By selecting a particular class of morphological characters, researchers may also bias the analysis in such a way that groups with certain characteristics cluster with others for reasons other than homology. For instance, if the set of characters were weighted toward those involved in carnivory, car ...
Diapositiva 1 - Universidad Autonoma de Madrid
... Homoplasy - misleading evidence of phylogeny • If misinterpreted as homology, the absence of tails would be evidence for a wrong tree grouping humans with frogs and lizards with dogs ...
... Homoplasy - misleading evidence of phylogeny • If misinterpreted as homology, the absence of tails would be evidence for a wrong tree grouping humans with frogs and lizards with dogs ...
Hierarchical clustering
... Another approach to hierarchical clustering is model-based clustering, which is based on the assumption that the data are generated by a mixture of underlying probability distributions. The mclust function fits model-based clustering models. It also fits models based on heuristic criteria similar to ...
... Another approach to hierarchical clustering is model-based clustering, which is based on the assumption that the data are generated by a mixture of underlying probability distributions. The mclust function fits model-based clustering models. It also fits models based on heuristic criteria similar to ...
Two Steps Genetic Programming for Big Data
... variety make traditional data mining algorithms invalid. In this paper, we deal with big data by solving distributed and high-dimensional problems. We propose a novel algorithm to effectively extract knowledge from big data. According to the empirical study, the propose method can handle big data so ...
... variety make traditional data mining algorithms invalid. In this paper, we deal with big data by solving distributed and high-dimensional problems. We propose a novel algorithm to effectively extract knowledge from big data. According to the empirical study, the propose method can handle big data so ...
Matlab Bioinfo Toolbox QuickGuide
... reroot(…) Change the root of a phylogenetic tree seqinsertgaps(…)Insert gaps into nucleotide or amino acid sequence ...
... reroot(…) Change the root of a phylogenetic tree seqinsertgaps(…)Insert gaps into nucleotide or amino acid sequence ...
Introductory to database handling
... It contains basic objects, called records or entries The records contain fields, which contain defined types of data, somehow related to that record A nuclotid sequence database would contain for example all kinds of nucleotides as records, and nucleotide properties (length, name, origin, etc) as fi ...
... It contains basic objects, called records or entries The records contain fields, which contain defined types of data, somehow related to that record A nuclotid sequence database would contain for example all kinds of nucleotides as records, and nucleotide properties (length, name, origin, etc) as fi ...
ppt - College of Computer and Information Science
... Using data for another purpose is common. It is important to anticipate that data will be used for many purposes. Data is reused by transforming it. ...
... Using data for another purpose is common. It is important to anticipate that data will be used for many purposes. Data is reused by transforming it. ...
EP:NG Tutorial
... – Eigenvalues are characteristic values of the principal components – the higher the eigenvalue, the more variability in the dataset it describes – The first few components can thus describe a large proportion of the data ...
... – Eigenvalues are characteristic values of the principal components – the higher the eigenvalue, the more variability in the dataset it describes – The first few components can thus describe a large proportion of the data ...
file - BioMed Central
... Figure S1. Scatter plots of evolutionary rate of annuals against that of perennials for both nuclear and chloroplast genes estimated by the outgroup-dependent method. Cases in all 4 annual-perennial cross-comparison are shown. The dash line is the diagonal line with a slope equals to 1, and the red ...
... Figure S1. Scatter plots of evolutionary rate of annuals against that of perennials for both nuclear and chloroplast genes estimated by the outgroup-dependent method. Cases in all 4 annual-perennial cross-comparison are shown. The dash line is the diagonal line with a slope equals to 1, and the red ...
Language Diversity - University College Dublin
... he Greek historian Herodotus reports that Psamtik, a seventh-century pharaoh of Egypt, arranged that two newborn babies should be reared in isolation until their first words together could be heard. Their first recorded utterance was bekos. This the pharaoh’s scribes discovered to be the word for brea ...
... he Greek historian Herodotus reports that Psamtik, a seventh-century pharaoh of Egypt, arranged that two newborn babies should be reared in isolation until their first words together could be heard. Their first recorded utterance was bekos. This the pharaoh’s scribes discovered to be the word for brea ...
Many of the slides that I`ll use have been borrowed from Dr. Paul
... The gene trees that we draw depict genealogical relationships – regardless of whether or not nucleotide differences distinguish the “gene copies” at the tips of the tree. ...
... The gene trees that we draw depict genealogical relationships – regardless of whether or not nucleotide differences distinguish the “gene copies” at the tips of the tree. ...
Species Tree and Most Likely Gene Tree
... The work in the paper assumes a perfect method for inferring the gene tree. But gene trees are usually estimated from mutational data. The anomaly zones for different topologies usually include short internal branches. But if these branches ...
... The work in the paper assumes a perfect method for inferring the gene tree. But gene trees are usually estimated from mutational data. The anomaly zones for different topologies usually include short internal branches. But if these branches ...
The Graph of Life
... and then add the remaining species using as few edges as possible. Weights indicate number of species. ...
... and then add the remaining species using as few edges as possible. Weights indicate number of species. ...
Analysis of Time-Series Gene Expression Data : Methods
... • The transformation of the raw expression data to a sequence of symbols and the subsequent analysis of the symbolic representation of the time series. • This type of approach, motivated by recent advances in the symbolic representation of streaming data, effectively reduces the dimensionality of th ...
... • The transformation of the raw expression data to a sequence of symbols and the subsequent analysis of the symbolic representation of the time series. • This type of approach, motivated by recent advances in the symbolic representation of streaming data, effectively reduces the dimensionality of th ...
Comparison of Microarray Pre-Processing Methods
... number of false positives, generated after pre-processing, is used as a second criterion for comparison and measures the specificity of the pre-processing technique. Procedures of testing for similar levels of expression between any two genes may be either parametric or non-parametric with use typic ...
... number of false positives, generated after pre-processing, is used as a second criterion for comparison and measures the specificity of the pre-processing technique. Procedures of testing for similar levels of expression between any two genes may be either parametric or non-parametric with use typic ...
Presentazione di PowerPoint
... To reconstruct the history of genes families, under the hypothesis that every family member derives from a duplication process of another member, means to put the set of members into a tree, that we call paralogy tree, in which the root represents the most ancient gene of the family, and each direct ...
... To reconstruct the history of genes families, under the hypothesis that every family member derives from a duplication process of another member, means to put the set of members into a tree, that we call paralogy tree, in which the root represents the most ancient gene of the family, and each direct ...
Evolution, 2e
... An example of phylogenetic analysis Molecular clocks and timing of branching events Difficulties in Phylogenetic Analysis ...
... An example of phylogenetic analysis Molecular clocks and timing of branching events Difficulties in Phylogenetic Analysis ...
Introduction to microarry
... If the probability to make a false positive when doing t test for a single gene is p=0.05, for 5000 genes you can expect 5000x0.05=250 false positives. To ensure the probability to make one mistake over the entire 5000 genes is still 0.05 (Family-wised error rate) p-value for each gene need to be ad ...
... If the probability to make a false positive when doing t test for a single gene is p=0.05, for 5000 genes you can expect 5000x0.05=250 false positives. To ensure the probability to make one mistake over the entire 5000 genes is still 0.05 (Family-wised error rate) p-value for each gene need to be ad ...
RNA-seq
... of differential allelic expression, SNPs, splice variants, new genes or isoforms. • It is not limited to a set number of probes. • It is NOT impacted by background signal or saturation that causes problems in studying highand low-expression transcripts. ...
... of differential allelic expression, SNPs, splice variants, new genes or isoforms. • It is not limited to a set number of probes. • It is NOT impacted by background signal or saturation that causes problems in studying highand low-expression transcripts. ...
LOVELY AS A TREE
... Trees are a source of beauty and resources. This exhibit celebrates the beauty, utility, diversity, and abundance of trees. The author first became fascinated with depictions of trees on stamps with the United States issue of American Trees in 1978. This exhibit presents stamps showing trees from ar ...
... Trees are a source of beauty and resources. This exhibit celebrates the beauty, utility, diversity, and abundance of trees. The author first became fascinated with depictions of trees on stamps with the United States issue of American Trees in 1978. This exhibit presents stamps showing trees from ar ...