Development of multiple interval mapping for mapping QTL in
... are moderately divided. When the QTL number is low and the heritability is high, applying QTL Cartographer/MIM to ordinal data directly may yield results similar to those from QTLC and bMIM. Though containing less information than continuous data, ordinal data can still yield similar estimations to ...
... are moderately divided. When the QTL number is low and the heritability is high, applying QTL Cartographer/MIM to ordinal data directly may yield results similar to those from QTLC and bMIM. Though containing less information than continuous data, ordinal data can still yield similar estimations to ...
Distribution and Concordance of N-Acetyltransferase Genotype and
... measured with a caffeine-based assay, as described by Butler et al. (22), with minor modifications. Subjects ingested two tablets, each containing 100 mg of caffeine, following an overnight fast. Subjects refrained from the consumption of caffeine- and methylxanthine-containing foods and beverages f ...
... measured with a caffeine-based assay, as described by Butler et al. (22), with minor modifications. Subjects ingested two tablets, each containing 100 mg of caffeine, following an overnight fast. Subjects refrained from the consumption of caffeine- and methylxanthine-containing foods and beverages f ...
Microarray Analysis
... Linz, by way of genomics data processing algorithms developed by the researchers and licensed by GNS.” ...
... Linz, by way of genomics data processing algorithms developed by the researchers and licensed by GNS.” ...
A survey on computational methods for enhancer and
... Difficulties in computational predictions of enhancer and enhancer-promoter associations Before going into the details of these computational methods, we first discuss the difficulties of the corresponding problems that explain the continuous need for better methods. These difficulties lie in severa ...
... Difficulties in computational predictions of enhancer and enhancer-promoter associations Before going into the details of these computational methods, we first discuss the difficulties of the corresponding problems that explain the continuous need for better methods. These difficulties lie in severa ...
Inference of homologous recombination in bacteria using whole
... Inference on an ARG with N=10 sequences, θ = 300, ρ = 50 and δ = 236 is considered on Figure 2. There are no instances of confidently inferred but incorrect recombination events in this example, with false-positive recombination intensity being limited to two types. Firstly, the edge of recombinatio ...
... Inference on an ARG with N=10 sequences, θ = 300, ρ = 50 and δ = 236 is considered on Figure 2. There are no instances of confidently inferred but incorrect recombination events in this example, with false-positive recombination intensity being limited to two types. Firstly, the edge of recombinatio ...
LINKAGE RELATIONS OF AUTOSOMAL FACTORS IN
... polydactylism. It appeared as a mutation in the four-toed White Leghorn. Like polydactylism it is dominant and variable in expression, but more commonly exhibits six toes than does the former. Duplication of digits in the wing are also common in the duplicate character. The character is easily ident ...
... polydactylism. It appeared as a mutation in the four-toed White Leghorn. Like polydactylism it is dominant and variable in expression, but more commonly exhibits six toes than does the former. Duplication of digits in the wing are also common in the duplicate character. The character is easily ident ...
Bayesian Learning of MicroRNA Targets from Sequence
... variables. Thus, the problem of finding functional miRNA targets consists of inferring which indicator variables are turned on and which are turned off, given the data. Consider two separate expression data sets profiling G messenger RNA transcripts and K microRNAs across T tissues. Let indices g = ...
... variables. Thus, the problem of finding functional miRNA targets consists of inferring which indicator variables are turned on and which are turned off, given the data. Consider two separate expression data sets profiling G messenger RNA transcripts and K microRNAs across T tissues. Let indices g = ...
Dissecting the Evolutionary Process of GENN
... • Single locus studies do not replicate • Identifying “the gene” associated with common disease has not been successful like it has for Mendelian disease • Mendelian single-gene disorders are now being considered complex traits with gene-gene interactions (modifier genes) ...
... • Single locus studies do not replicate • Identifying “the gene” associated with common disease has not been successful like it has for Mendelian disease • Mendelian single-gene disorders are now being considered complex traits with gene-gene interactions (modifier genes) ...
Seed plant phylogeny: Demise of the anthophyte
... angiosperms. Only a few analyses of ribosomal DNA linked angiosperms and Gnetales, and this with low statistical support. Analyses of the chloroplast gene rbcL placed Gnetales at the base of the seed plants, followed by angiosperms (an arrangement supported by more recent studies of photosystem gene ...
... angiosperms. Only a few analyses of ribosomal DNA linked angiosperms and Gnetales, and this with low statistical support. Analyses of the chloroplast gene rbcL placed Gnetales at the base of the seed plants, followed by angiosperms (an arrangement supported by more recent studies of photosystem gene ...
Cophylogeny and disparate rates of evolution in sympatric lineages
... (speciation of the associate independent of the host), and failure of the associate to diverge when the host diverges (‘‘missing the boat’’; Paterson and Gray, 1997) may disrupt perfect correspondence among taxa. By comparing the phylogenies (or the data upon which those phylogenies are based) of ho ...
... (speciation of the associate independent of the host), and failure of the associate to diverge when the host diverges (‘‘missing the boat’’; Paterson and Gray, 1997) may disrupt perfect correspondence among taxa. By comparing the phylogenies (or the data upon which those phylogenies are based) of ho ...
Complementary hierarchical clustering
... and Gordon (1999). Cluster analysis is an unsupervised learning procedure with the goal of grouping data into clusters, with members within a cluster being closer to each other than to members outside that cluster. In order to quantify how close one data point is to another, a distance measure is re ...
... and Gordon (1999). Cluster analysis is an unsupervised learning procedure with the goal of grouping data into clusters, with members within a cluster being closer to each other than to members outside that cluster. In order to quantify how close one data point is to another, a distance measure is re ...
clValid: An R Package for Cluster Validation
... algorithms currently exist, many of which have shown some promise in the analysis of genomic data (Herrero et al. 2001; McLachlan et al. 2002; Dembele and Kastner 2003; Fu and Medico 2007). Deciding which clustering method to use can therefore be a daunting task for the researcher conducting the exp ...
... algorithms currently exist, many of which have shown some promise in the analysis of genomic data (Herrero et al. 2001; McLachlan et al. 2002; Dembele and Kastner 2003; Fu and Medico 2007). Deciding which clustering method to use can therefore be a daunting task for the researcher conducting the exp ...
Bioinformatics - [email protected]
... taxa (approximately 1022 trees) - Algorithm - Establish minimally acceptable criteria - Evaluate all n taxa trees, discard ones not meeting criteria - Evaluate n+1 taxa trees using remaining 4 taxa trees as bases - Repeat until all taxa have been evaluated - Select optimal remaining tree ...
... taxa (approximately 1022 trees) - Algorithm - Establish minimally acceptable criteria - Evaluate all n taxa trees, discard ones not meeting criteria - Evaluate n+1 taxa trees using remaining 4 taxa trees as bases - Repeat until all taxa have been evaluated - Select optimal remaining tree ...
View Tutorial
... compared across multiple species will not be identical, but will display insertions, deletions, or substitutions of nucleotides. Since DNA codes for protein, similar changes occur in protein sequences. Over long periods of time, substantial changes can accumulate, such that two modern proteins with ...
... compared across multiple species will not be identical, but will display insertions, deletions, or substitutions of nucleotides. Since DNA codes for protein, similar changes occur in protein sequences. Over long periods of time, substantial changes can accumulate, such that two modern proteins with ...
TCGA-Assembler User Manual - University of Chicago
... downloaded from Firehose website, which will be used by the examples in this user manual. There are four subfolders in the UserManualExampleData folder. The RawData.TCGA-Assembler subfolder is used to hold data downloaded from TCGA DCC by TCGA-Assembler. The ProcessedData.TCGAAssembler subfolder is ...
... downloaded from Firehose website, which will be used by the examples in this user manual. There are four subfolders in the UserManualExampleData folder. The RawData.TCGA-Assembler subfolder is used to hold data downloaded from TCGA DCC by TCGA-Assembler. The ProcessedData.TCGAAssembler subfolder is ...
0 1 0 1 1 1 0 0 1 0
... – The entropy of a data set is given by - p log2(p) - (1 - p) log2(1 - p) where p is the fraction of examples that belong to class predisposed. – The information gain of the split is given by the entropy of the original data set minus the weighted sum of entropies of the two data sets resulting from ...
... – The entropy of a data set is given by - p log2(p) - (1 - p) log2(1 - p) where p is the fraction of examples that belong to class predisposed. – The information gain of the split is given by the entropy of the original data set minus the weighted sum of entropies of the two data sets resulting from ...
Package ‘siggenes’ October 14, 2014
... summarizes how many observations in this group show which level at which variable. These matrices can be generated using the function rowTables from the package scrime. For details on how to specify this list, see the examples section on this man page, and the help for rowChisqMultiClass in the pack ...
... summarizes how many observations in this group show which level at which variable. These matrices can be generated using the function rowTables from the package scrime. For details on how to specify this list, see the examples section on this man page, and the help for rowChisqMultiClass in the pack ...
Evolutionary History of Free-Swimming and
... as for locomotion. The points at issue are which of these lifestyles represents the primitive condition for urochordates, and which lifestyle was possessed by the ancestor of all chordates. Haeckel (1868) extended his recapitulation theory to this case and proposed that the first chordates were free ...
... as for locomotion. The points at issue are which of these lifestyles represents the primitive condition for urochordates, and which lifestyle was possessed by the ancestor of all chordates. Haeckel (1868) extended his recapitulation theory to this case and proposed that the first chordates were free ...
Whole-transcriptome RNAseq analysis from minute amount of total
... system, TruSeqTM RNA sample preparation, which employs polyA selection for mRNA enrichment and Invitrogen’s RiboMinusTM kit which depletes rRNA. We considered the following criteria in evaluating the RNA-seq methods, some of which are described in literature (10): library complexity, the number of u ...
... system, TruSeqTM RNA sample preparation, which employs polyA selection for mRNA enrichment and Invitrogen’s RiboMinusTM kit which depletes rRNA. We considered the following criteria in evaluating the RNA-seq methods, some of which are described in literature (10): library complexity, the number of u ...
Title: Statistical Evidence for Common Ancestry
... An underlying assumption of the Penny et al. SA model, which also affects many other statistical tests of common ancestry (Baum et al. 2015), is that there are no functional constraints that might result in proteins derived from SA nonetheless showing a common hierarchical structure. This need not b ...
... An underlying assumption of the Penny et al. SA model, which also affects many other statistical tests of common ancestry (Baum et al. 2015), is that there are no functional constraints that might result in proteins derived from SA nonetheless showing a common hierarchical structure. This need not b ...
Chapter 3 Clustering Microarray Data
... to uncover by giving equal weight to all the genes. Their procedure, Clustering Objects on Subsets of Attributes (COSA) computes distances between samples, giving the expression levels gene- and sample-specific weights. These distances are then passed to a distance-based clustering algorithm, such a ...
... to uncover by giving equal weight to all the genes. Their procedure, Clustering Objects on Subsets of Attributes (COSA) computes distances between samples, giving the expression levels gene- and sample-specific weights. These distances are then passed to a distance-based clustering algorithm, such a ...
Do-it-yourself poster template - College of Education and Human
... and MSP2, all from the blood stage, Pfs48_45 from the sexual stage, and SSP2 from the liver stage. Wow this is complicated is anyone actually reading this. The main focus of this research, though, is to isolate MSP1_19 and insert it into the pGEM-T easy vector as well as a plant expression referred ...
... and MSP2, all from the blood stage, Pfs48_45 from the sexual stage, and SSP2 from the liver stage. Wow this is complicated is anyone actually reading this. The main focus of this research, though, is to isolate MSP1_19 and insert it into the pGEM-T easy vector as well as a plant expression referred ...
Package `DESeq`
... you may pass a value for nn different from the default (0.7) if the fit seems too smooth or too rough by setting lp_extra_agrs=list(nn=0.9). As another example, you can set locfit_extra_args=list(maxk=200) if you get the error that locfit ran out of nodes. See the documentation of the locfit package ...
... you may pass a value for nn different from the default (0.7) if the fit seems too smooth or too rough by setting lp_extra_agrs=list(nn=0.9). As another example, you can set locfit_extra_args=list(maxk=200) if you get the error that locfit ran out of nodes. See the documentation of the locfit package ...
Slide 1
... • The original papers on the Gaussian process (Mackay 1998; Neal 1997) did not view this method as an approach for variable selection and imposed a Gamma prior on the parameters. However, does provide information about the relevance of any QTL with value near zero indicating an irrelevant QTL. • ...
... • The original papers on the Gaussian process (Mackay 1998; Neal 1997) did not view this method as an approach for variable selection and imposed a Gamma prior on the parameters. However, does provide information about the relevance of any QTL with value near zero indicating an irrelevant QTL. • ...
View - OhioLINK Electronic Theses and Dissertations Center
... knowledge inherent within the data. An example of this would be karyotype data that are kept in a text string format called the International System for Human Cytogenetic Nomenclature (ISCN; Shaffer et al., 2013). These text strings are not machine-readable. For knowledge to be extracted for resear ...
... knowledge inherent within the data. An example of this would be karyotype data that are kept in a text string format called the International System for Human Cytogenetic Nomenclature (ISCN; Shaffer et al., 2013). These text strings are not machine-readable. For knowledge to be extracted for resear ...