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 ...
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 ...
... 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 ...
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 ...
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
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
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 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 ...
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 ...
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 ...
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 ...
Bioinformatics - [email protected]
... taxa (approximately 1022 trees)
- Establish minimally acceptable criteria
- Evaluate all n taxa trees, discard ones not
- Evaluate n+1 taxa trees using remaining 4 taxa
trees as bases
- Repeat until all taxa have been evaluated
- Select optimal remaining tree
... 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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
... 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 ...
... • 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 ...
Quantitative comparative linguistics
Statistical methods have been used in comparative linguistics since at least the 1950s (see Swadesh list). Since about the year 2000, there has been a renewed interest in the topic, based on the application of methods of computational phylogenetics and cladistics to define an optimal tree (or network) to represent a hypothesis about the evolutionary ancestry and perhaps its language contacts. The probability of relatedness of languages can be quantified and sometimes the proto-languages can be approximately dated.The topic came the attention of the popular press in 2003 after the publication of a short study on Indo-European in Nature (Gray and Atkinson 2003). A volume of articles on Phylogenetic Methods and the Prehistory of Languages was published in 2006 as the result of a conference held in Cambridge in 2004.A goal of comparative historical linguistics is to identify instances of genetic relatedness amongst languages. The steps in quantitative analysis are (i) to devise a procedure based on theoretical grounds, on a particular model or on past experience, etc. (ii) to verify the procedure by applying it to some data where there exists a large body of linguistic opinion for comparison (this may lead to a revision of the procedure of stage (i) or at the extreme of its total abandonment) (iii) to apply the procedure to data where linguistic opinions have not yet been produced, have not yet been firmly established or perhaps are even in conflict.Applying phylogenetic methods to languages is a multi-stage process (a) the encoding stage - getting from real languages to some expression of the relationships between them in the form of numerical or state data, so that those data can then be used as input to phylogenetic methods (b) the representation stage - applying phylogenetic methods to extract from those numerical and/or state data a signal that is converted into some useful form of representation, usually two dimensional graphical ones such as trees or networks, which synthesise and ""collapse"" what are often highly complex multi dimensional relationships in the signal (c) the interpretation stage - assessing those tree and network representations to extract from them what they actually mean for real languages and their relationships through time.