Adenovirus vector induced innate immune responses: impact upon efficacy and toxicity in gene therapy and vaccine applications
ZC Hartman, DM Appledorn, A Amalfitano - Virus research, 2008 - Elsevier
Extensively characterized, modified, and employed for a variety of purposes, adenovirus
(Ad) vectors are generally regarded as having great potential by many applied virologists …
(Ad) vectors are generally regarded as having great potential by many applied virologists …
Stable feature selection for biomarker discovery
Feature selection techniques have been used as the workhorse in biomarker discovery
applications for a long time. Surprisingly, the stability of feature selection with respect to …
applications for a long time. Surprisingly, the stability of feature selection with respect to …
Integrating structured biological data by kernel maximum mean discrepancy
Motivation: Many problems in data integration in bioinformatics can be posed as one
common question: Are two sets of observations generated by the same distribution? We …
common question: Are two sets of observations generated by the same distribution? We …
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.
L Shi, G Campbell, WD Jones… - Nature …, 2010 - search.ebscohost.com
Gene expression data from microarrays are being applied to predict preclinical and clinical
endpoints, but the reliability of these predictions has not been established. In the MAQC-II …
endpoints, but the reliability of these predictions has not been established. In the MAQC-II …
Testing significance relative to a fold-change threshold is a TREAT
DJ McCarthy, GK Smyth - Bioinformatics, 2009 - academic.oup.com
Motivation: Statistical methods are used to test for the differential expression of genes in
microarray experiments. The most widely used methods successfully test whether the true …
microarray experiments. The most widely used methods successfully test whether the true …
The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements.
L Shi, LH Reid, WD Jones, R Shippy… - Nature …, 2006 - europepmc.org
Over the last decade, the introduction of microarray technology has had a profound impact
on gene expression research. The publication of studies with dissimilar or altogether …
on gene expression research. The publication of studies with dissimilar or altogether …
[HTML][HTML] Ontology-based meta-analysis of global collections of high-throughput public data
I Kupershmidt, QJ Su, A Grewal, S Sundaresh… - PloS one, 2010 - journals.plos.org
Background The investigation of the interconnections between the molecular and genetic
events that govern biological systems is essential if we are to understand the development …
events that govern biological systems is essential if we are to understand the development …
Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project
TA Patterson, EK Lobenhofer… - Nature …, 2006 - nature.com
Microarray-based expression profiling experiments typically use either a one-color or a two-
color design to measure mRNA abundance. The validity of each approach has been amply …
color design to measure mRNA abundance. The validity of each approach has been amply …
The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements
Nature biotechnology, 2006 - nature.com
Over the last decade, the introduction of microarray technology has had a profound impact
on gene expression research. The publication of studies with dissimilar or altogether …
on gene expression research. The publication of studies with dissimilar or altogether …
Volcano plots in analyzing differential expressions with mRNA microarrays
W Li - Journal of bioinformatics and computational biology, 2012 - World Scientific
A volcano plot displays unstandardized signal (eg log-fold-change) against noise-
adjusted/standardized signal (eg t-statistic or-log10 (p-value) from the t-test). We review the …
adjusted/standardized signal (eg t-statistic or-log10 (p-value) from the t-test). We review the …