Tools
Sorted by:
Try your query at:
 |
 |
 |
 |
 |
 |
Results 1 - 10
of
50,052
Comparison of discrimination methods for the classification of tumors using gene expression data
- JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
, 2002
"... A reliable and precise classification of tumors is essential for successful diagnosis and treatment of cancer. cDNA microarrays and high-density oligonucleotide chips are novel biotechnologies increasingly used in cancer research. By allowing the monitoring of expression levels in cells for thousand ..."
Abstract
-
Cited by 770 (6 self)
- Add to MetaCart
gene expression data is an important aspect of this novel approach to cancer classification. This article compares the performance of different discrimination methods for the classification of tumors based on gene expression data. The methods include nearest-neighbor classifiers, linear discriminant
PAML: a program package for phylogenetic analysis by maximum likelihood
- COMPUT APPL BIOSCI 13:555–556
, 1997
"... PAML, currently in version 1.2, is a package of programs for phylogenetic analyses of DNA and protein sequences using the method of maximum likelihood (ML). The programs can be used for (i) maximum likelihood estimation of evolutionary parameters such as branch lengths in a phylogenetic tree, the tr ..."
Abstract
-
Cited by 1459 (17 self)
- Add to MetaCart
, the transition/transversion rate ratio, the shape parameter of the gamma distribution for variable evolutionary rates at sites, and rate parameters for different genes; (ii) likelihood ratio test of hypotheses concerning sequence evolution, such as rate con-stancy and independence among sites and rate constancy
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes
- Nucleic Acids Res
, 2006
"... The TRANSFAC database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel on composite elements have been further enhanced on various levels. A new web interface with different search options and inte ..."
Abstract
-
Cited by 482 (5 self)
- Add to MetaCart
The TRANSFAC database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel on composite elements have been further enhanced on various levels. A new web interface with different search options
A Bayesian Framework for the Analysis of Microarray Expression Data: Regularized t-Test and Statistical Inferences of Gene Changes
- Bioinformatics
, 2001
"... Motivation: DNA microarrays are now capable of providing genome-wide patterns of gene expression across many different conditions. The first level of analysis of these patterns requires determining whether observed differences in expression are significant or not. Current methods are unsatisfactory ..."
Abstract
-
Cited by 491 (6 self)
- Add to MetaCart
Motivation: DNA microarrays are now capable of providing genome-wide patterns of gene expression across many different conditions. The first level of analysis of these patterns requires determining whether observed differences in expression are significant or not. Current methods are unsatisfactory
Metabolic stability and epigenesis in randomly connected nets
- Journal of Theoretical Biology
, 1969
"... “The world is either the effect of cause or chance. If the latter, it is a world for all that, that is to say, it is a regular and beautiful structure.” Marcus Aurelius Proto-organisms probably were randomly aggregated nets of chemical reactions. The hypothesis that contemporary organisms are also r ..."
Abstract
-
Cited by 657 (5 self)
- Add to MetaCart
: behave with great order and stability; undergo behavior cycles whose length predicts cell replication time as a function of the number of genes per cell; possess different modes of behavior whose number per net predicts roughly the number of cell types in an organism as a function of its number of genes
Exploration, normalization, and summaries of high density oligonucleotide array probe level data.
- Biostatistics,
, 2003
"... SUMMARY In this paper we report exploratory analyses of high-density oligonucleotide array data from the Affymetrix GeneChip R system with the objective of improving upon currently used measures of gene expression. Our analyses make use of three data sets: a small experimental study consisting of f ..."
Abstract
-
Cited by 854 (33 self)
- Add to MetaCart
SUMMARY In this paper we report exploratory analyses of high-density oligonucleotide array data from the Affymetrix GeneChip R system with the objective of improving upon currently used measures of gene expression. Our analyses make use of three data sets: a small experimental study consisting
Alternative isoform regulation in human tissue transcriptomes
- Nature
, 2008
"... Through alternative processing of pre-mRNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes based on deep sequencing of ..."
Abstract
-
Cited by 545 (6 self)
- Add to MetaCart
of cDNA fragments, yielding a digital inventory of gene and mRNA isoform expression. Analysis of mappings of sequence reads to exon-exon junctions indicated that 92-94% of human genes undergo alternative splicing (AS), ∼86 % with a minor isoform frequency of 15% or more. Differences in isoform
A greedy algorithm for aligning DNA sequences
- J. COMPUT. BIOL
, 2000
"... For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic programming approaches and yet produce an alignment that is guaranteed to be theoretically optimal. We introduce a new greedy a ..."
Abstract
-
Cited by 585 (16 self)
- Add to MetaCart
For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic programming approaches and yet produce an alignment that is guaranteed to be theoretically optimal. We introduce a new greedy
Model-Based Analysis of Oligonucleotide Arrays: Model Validation, Design Issues and Standard Error Application
, 2001
"... Background: A model-based analysis of oligonucleotide expression arrays we developed previously uses a probe-sensitivity index to capture the response characteristic of a specific probe pair and calculates model-based expression indexes (MBEI). MBEI has standard error attached to it as a measure of ..."
Abstract
-
Cited by 775 (28 self)
- Add to MetaCart
of accuracy. Here we investigate the stability of the probe-sensitivity index across different tissue types, the reproducibility of results in replicate experiments, and the use of MBEI in perfect match (PM)-only arrays. Results: Probe-sensitivity indexes are stable across tissue types. The target gene
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation
, 2002
"... There are many sources of systematic variation in cDNA microarray experiments which affect the measured gene expression levels (e.g. differences in labeling efficiency between the two fluorescent dyes). The term normalization refers to the process of removing such variation. A constant adjustment is ..."
Abstract
-
Cited by 718 (9 self)
- Add to MetaCart
There are many sources of systematic variation in cDNA microarray experiments which affect the measured gene expression levels (e.g. differences in labeling efficiency between the two fluorescent dyes). The term normalization refers to the process of removing such variation. A constant adjustment
Results 1 - 10
of
50,052
