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Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection.
A statistical model is proposed for the probe-level data, and model-based estimates for gene expression indexes are developed, which help to identify and handle cross-hybridizing probes and contaminating array regions.
Genome-wide expression analysis reveals dysregulation of myelination-related genes in chronic schizophrenia
- Y. Hakak, J.R. Walker, A. Fienberg
- Psychology, MedicineProceedings of the National Academy of Sciences…
- 10 April 2001
DNA microarray analysis was used to assay gene expression levels in postmortem dorsolateral prefrontal cortex of schizophrenic and control patients, and differential expression of myelination-related genes suggesting a disruption in oligodendrocyte function in schizophrenia were identified.
An integrated encyclopedia of DNA elements in the human genome
- I. Dunham, A. Kundaje, L. Lochovsky
- Biology
- 1 September 2012
Panel C shows several SNPs associated with Crohn’s disease and other inflammatory diseases that reside in a large gene desert on chromosome 5, along with some epigenetic features suggestive of function.
A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb.
- S. Vokes, Hongkai Ji, W. Wong, A. McMahon
- BiologyGenes & Development
- 1 October 2008
These studies provide the first comprehensive characterization of the transcriptional output of a Shh-patterning process in the mammalian embryo and a framework for elaborating regulatory networks in the developing limb.
Statistical inferences for isoform expression in RNA-Seq
The results show that isoform expression inference in RNA-Seq is possible by employing appropriate statistical methods and statistical inferences are obtained from the posterior distribution by importance sampling.
An integrated system CisGenome for analyzing ChIP-chip and ChIP-seq data
- Hongkai Ji, Hui Jiang, Wenxiu Ma, David S. Johnson, R. Myers, W. Wong
- Biology, Computer ScienceNature Biotechnology
- 6 October 2008
We present CisGenome, a software system for analyzing genome-wide chromatin immunoprecipitation (ChIP) data. CisGenome is designed to meet all basic needs of ChIP data analyses, including…
TileMap: create chromosomal map of tiling array hybridizations
- Hongkai Ji, W. Wong
- BiologyBioinform.
- 15 September 2005
The goal of this paper is to develop effective statistical tools to identify genomic loci that show transcriptional or protein binding patterns of interest and a two-step approach is proposed and is implemented in TileMap.
SeqMap: mapping massive amount of oligonucleotides to the genome
SeqMap is a tool for mapping large amount of short sequences to the genome and supports FASTA input format and various output formats, and provides command line options for tuning almost every aspect of the mapping process.
SMAD4-dependent barrier constrains prostate cancer growth and metastatic progression
- Z. Ding, Chang-Jiun Wu, R. DePinho
- BiologyNature
- 10 February 2011
This model-informed progression analysis, together with genetic, functional and translational studies, establishes SMAD4 as a key regulator of PCA progression in mice and humans.
Detection of splice junctions from paired-end RNA-seq data by SpliceMap
A computational method, SpliceMap, to detect splice junctions from RNA-seq data is presented, which does not depend on any existing annotation of gene structures and is capable of finding novel splicing junctions with high sensitivity and specificity.
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