Microarray experiments and factors which affect their reliability

Sources of High Variance between Probe Signals in Affymetrix Short Oligonucleotide Microarrays

(2014) Roman Jaksik et al.   SENSORS

Development of a simple microarray for genotyping HIV-1 drug resistance mutations in the reverse transcriptase gene in rural Tanzania

(2014) Pax Masimba et al.   TROPICAL MEDICINE & INTERNATIONAL HEALTH

IVT-seq reveals extreme bias in RNA sequencing

(2014) Nicholas F Lahens et al.   GENOME BIOLOGY

Detection and correction of probe-level artefacts on microarrays

(2013) Tobias Petri et al.   BMC BIOINFORMATICS

Physicochemical factors affecting the stability of two pigments: R-phycoerythrin of Grateloupia turuturu and B-phycoerythrin of Porphyridium cruentum

(2013) Mathilde Munier et al.   FOOD CHEMISTRY

Optimizing SNP microarray probe design for high accuracy microbial genotyping

(2013) Shea N. Gardner et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Targeted resequencing of HIV variants by microarray thermodynamics

(2013) Wahyu W. Hadiwikarta et al.   NUCLEIC ACIDS RESEARCH

Application of High-Density DNA Resequencing Microarray for Detection and Characterization of Botulinum Neurotoxin-Producing Clostridia

(2013) Jessica Vanhomwegen et al.   PLoS One

Genomic DNA Enrichment Using Sequence Capture Microarrays: a Novel Approach to Discover Sequence Nucleotide Polymorphisms (SNP) in Brassica napus L

(2013) Wayne E. Clarke et al.   PLoS One

AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data

(2012) Mario Fasold et al.   BIOINFORMATICS

Estimating RNA-quality using GeneChip microarrays

(2012) Mario Fasold et al.   BMC GENOMICS

Cheek swabs, SNP chips, and CNVs: Assessing the quality of copy number variant calls generated with subject-collected mail-in buccal brush DNA samples on a high-density genotyping microarray

(2012) Stephen W Erickson et al.   BMC Medical Genetics

ChIP-Chip Identifies SEC23A, CFDP1, and NSD1 as TFII-I Target Genes in Human Neural Crest Progenitor Cells

(2012) Aleksandr V. Makeyev et al.   CLEFT PALATE-CRANIOFACIAL JOURNAL

High-density oligonucleotide-based resequencing assay for mutations causing syndromic and non-syndromic forms of thoracic aortic aneurysms and dissections

(2012) Ushanthine Kathiravel et al.   MOLECULAR AND CELLULAR PROBES

SCOREM: statistical consolidation of redundant expression measures

(2012) Stephanie Schneider et al.   NUCLEIC ACIDS RESEARCH

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Use of Non-Amplified RNA Samples for Microarray Analysis of Gene Expression

(2012) Hiroko Sudo et al.   PLoS One

caCORRECT2: Improving the accuracy and reliability of microarray data in the presence of artifacts

(2011) Richard A Moffitt et al.   BMC BIOINFORMATICS

The impact of quantitative optimization of hybridization conditions on gene expression analysis

(2011) Peter Sykacek et al.   BMC BIOINFORMATICS

Bias detection and correction in RNA-Sequencing data

(2011) Wei Zheng et al.   BMC BIOINFORMATICS

Genomewide characterization of non-polyadenylated RNAs

(2011) Li Yang et al.   GENOME BIOLOGY

Washing scaling of GeneChip microarray expression

(2010) Hans Binder et al.   BMC BIOINFORMATICS

Delineation of amplification, hybridization and location effects in microarray data yields better-quality normalization

(2010) Marc Hulsman et al.   BMC BIOINFORMATICS

Chromatin-dependent binding of the S. cerevisiae HMGB protein Nhp6A affects nucleosome dynamics and transcription

(2010) N. L. Dowell et al.   GENES & DEVELOPMENT

Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)

(2010) Kerstin Kaufmann et al.   Nature Protocols

Reconstructed Ancestral Sequences Improve Pathogen Identification Using Resequencing DNA Microarrays

(2010) Nicolas Berthet et al.   PLoS One

Validation and implementation of array comparative genomic hybridisation as a first line test in place of postnatal karyotyping for genome imbalance

(2010) Joo Wook Ahn et al.   Molecular Cytogenetics

Comparability of Microarray Data between Amplified and Non Amplified RNA in Colorectal Carcinoma

(2009) Roland S. Croner et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs

(2009) Giorgio Grillo et al.   NUCLEIC ACIDS RESEARCH

Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances

(2009) T. LaFramboise   NUCLEIC ACIDS RESEARCH

Interlaboratory and Interplatform Comparison of Microarray Gene Expression Analysis of HepG2 Cells Exposed to Benzo(a)pyrene

(2009) Sarah L. Hockley et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Design and analysis of mismatch probes for long oligonucleotide microarrays

(2008) Ye Deng et al.   BMC GENOMICS

Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays

(2008) Amandine Bemmo et al.   BMC GENOMICS

Amplification biases: possible differences among deviating gene expressions

(2008) Séverine A Degrelle et al.   BMC GENOMICS

Microarray-based mutation detection in thedystrophingene

(2008) Madhuri R. Hegde et al.   HUMAN MUTATION

Validation of microarray-based resequencing of 93 worldwide mitochondrial genomes

(2008) Anne Hartmann et al.   HUMAN MUTATION

The beginning of the end for microarrays?

(2008) Jay Shendure   NATURE METHODS

Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction

(2008) H. Koltai et al.   NUCLEIC ACIDS RESEARCH

Modeling background intensity in DNA microarrays

(2008) K. M. Kroll et al.   PHYSICAL REVIEW E

The T7-Primer Is a Source of Experimental Bias and Introduces Variability between Microarray Platforms

(2008) Ron M. Kerkhoven et al.   PLoS One

Genotyping of Bacillus cereus Strains by Microarray-Based Resequencing

(2008) Michael E. Zwick et al.   PLoS One

Efficacy of RNA amplification is dependent on sequence characteristics: Implications for gene expression profiling using a cDNA microarray

(2007) Nina Duftner et al.   GENOMICS