My Handy Online Bookshelf:
(This list
only contains partial of the literature I collected in the past. I will keep posting
the rest of them)
Affymetrix
Technology:
·
·
Lu X.
The effect of GeneChip gene definitions on the microarray study of cancers. Bioessays 2006, 28(7): 739-46. [PDF]
·
Zhang
LM. Identical probes on different high-density oligonucleotide microarray can
produce different measurements of gene expression. BMC Genomics 2006 7:153. [PDF]
·
Okoniewski. Hybridization interaction between
probesets in short oligo microarray lead to spurious correlations. BMC
Bioinformatics 2006 7:276. [PDF]
·
Held GA. Relationship between gene expression
and observed intensities in DNA microarrays – a modeling study. NAR
2006 Vol. 34, No. 9 e70. [PDF]
·
Jones L.
Assessment of the relationship between pre-chip and post-chip quality measures
for Affymetrix GeneChip expression data. BMC
Bioinformatics 2006 7:211. [PDF]
·
Hochreiter S. A new summarization method for
Affymetrix probe level data. Bioinformatics 2006 22(8): 943-949.
[PDF]
·
McClintick JN. Effects of filtering on present calls
on analysis of microarray experiments. BMC Bioinformatics 2006 7:49. [PDF]
·
Gardina PJ. Alternative splicing and
differential gene expression in colon cancer detected by a whole genome exon
array. BMC Genomics 2006 7:325 [PDF]
·
Comparing Methods and Platforms:
·
Cheadle
C. A rapid method for microarray cross platform comparisons using gene
expression signatures. Molecular and Cellular Probes 2007, 21:35-46 [PDF]
·
Irizarry
RA. Comparison of Affymetrix GeneChip expression measures. Bioinformatics 2006 22(7):789-794. [PDF] (the most relevant, but with limitation
due to small probesets in spike-in)
·
Seo J. Probe set algorithms: is there a rational
best bet? BMC Bioinformatics 2006, 7: 395. [PDF]
·
Kuo WP.
A sequence-oriented comparison of gene expression measurements across different
hybridization-based technologies. Nat
Biotech 2006 24(7):832 [PDF]
·
Fujita
A. Evaluating different methods of microarray data normalization. Bioinformatics 2006 7:467. [PDF]
Analysis Related:
- Diboun I. Microarray analysis after RNA amplification can detect pronounced difference in gene expression using limma. BMC Genomics 2006 7:252. [PDF]
Classification and Prediction:
- Jeffery IB. Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. BMC Bioinformatics 2006, 7:359. [PDF]
Collaboration
Related:
- Bachtiary B. Gene expression profiling in cervical cancer: an exploration of intratumor heterogeneity. Clin Cancer Res.2006 12(19):5632. [PDF]
COBRA papers:
- Huber W. An introduction to low-level analysis methods of DNA microarray data. [PDF]
- von Heydebreck A. Differential expression with the Bioconductor project. [PDF]
BioC Documents:
- From CEL files to annotation of differentially expressed gene lists. [PDF]
- Wu Z, Irizarry RA, Gentleman R, Martinez-Murillo F, Spencer F. A model-based background adjustment for oligonucleotide expression arrays. Journal of the American Statistical Association. 2004;99:909–917. [PDF]
Gene Set Enrichment
Analysis
- Jiang Z. Extensions to gene set enrichment. Bioinformatics. 2007 23(3):306-13. [PDF]
- Subramanian A. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. PNAS 2005 102(43):15545-50. [PDF]
My Own Papers:
- GPM
- Splicing Variants
- Exon detection methods detection