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A framework for oligonucleotide microarray preprocessing

https://doi.org/10.1093/bioinformatics/btq431
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1038/nature02168openalex-snapshot
The International HapMap Project
inferredcites →https://doi.org/10.1093/bioinformatics/19.2.185openalex-snapshot
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
inferredcites →https://doi.org/10.1093/bioinformatics/btg405openalex-snapshot
affy—analysis of Affymetrix GeneChip data at the probe level
inferredcites →https://doi.org/10.1093/bioinformatics/btk046openalex-snapshot
Comparison of Affymetrix GeneChip expression measures
inferredcites →https://doi.org/10.1093/bioinformatics/btp470openalex-snapshot
R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips
inferredcites →https://doi.org/10.1093/bioinformatics/btp624openalex-snapshot
Quantifying uncertainty in genotype calls
inferredcites →https://doi.org/10.1093/biostatistics/4.2.249openalex-snapshot
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
inferredcites →https://doi.org/10.1093/biostatistics/kxl042openalex-snapshot
Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data
inferredcites →https://doi.org/10.1101/gr.202801openalex-snapshot
Methylation-Specific Oligonucleotide Microarray: A New Potential for High-Throughput Methylation Analysis
inferredcites →https://doi.org/10.1101/gr.7301508openalex-snapshot
Comprehensive high-throughput arrays for relative methylation (CHARM)
inferredcites →https://doi.org/10.1186/gb-2004-5-10-r80openalex-snapshot
Bioconductor: open software development for computational biology and bioinformatics
inferredcites →https://doi.org/10.1186/gb-2006-7-8-404openalex-snapshot
Feature-level exploration of a published Affymetrix GeneChip control dataset.
inferredcites →https://doi.org/10.1186/gb-2007-8-4-r64openalex-snapshot
Discovery of tissue-specific exons using comprehensive human exon microarrays
inferredcites →https://doi.org/10.1214/07-aoas155openalex-snapshot
Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays
inferredcites →https://doi.org/10.2202/1544-6115.1002openalex-snapshot
Use of Mixture Models in a Microarray-Based Screening Procedure for Detecting Differentially Represented Yeast Mutants

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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inferred← citeshttps://doi.org/10.1002/pros.23809openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pul2.12319openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/sctm.18-0260openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/stem.2635openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/trc2.12373openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-4939-3578-9_7openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-4939-7528-0_4openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s11033-022-07976-zopenalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s11103-020-01001-2openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s12026-023-09398-wopenalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s13577-022-00744-yopenalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.ab.2024.115619openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.acthis.2017.07.007openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.ajog.2015.08.028openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.ajog.2018.01.009openalex-snapshot
Evidence of cardiac involvement in the fetal inflammatory response syndrome: disruption of gene networks programming cardiac development in nonhuman primates
inferred← citeshttps://doi.org/10.1016/j.ajog.2018.10.003openalex-snapshot
Placental transcriptional and histologic subtypes of normotensive fetal growth restriction are comparable to preeclampsia
inferred← citeshttps://doi.org/10.1016/j.ajpath.2017.06.003openalex-snapshot
UV Irradiation of Skin Enhances Glycolytic Flux and Reduces Migration Capabilities in Bone Marrow–Differentiated Dendritic Cells
inferred← citeshttps://doi.org/10.1016/j.ajpath.2018.06.013openalex-snapshot
Distinct Gene Expression Profiles Define Anaplastic Grade in Retinoblastoma
inferred← citeshttps://doi.org/10.1016/j.animal.2025.101721openalex-snapshot
Meta-analysis of the effects of bovine in vitro embryo production on gene expression
inferred← citeshttps://doi.org/10.1016/j.annemergmed.2019.09.020openalex-snapshot
Gene Expression Profiles in Children With Suspected Sepsis
inferred← citeshttps://doi.org/10.1016/j.aquatox.2022.106310openalex-snapshot
Symptomatic and asymptomatic domoic acid exposure in zebrafish (Danio rerio) revealed distinct non-overlapping gene expression patterns in the brain
inferred← citeshttps://doi.org/10.1016/j.arbres.2024.11.011openalex-snapshot
Synergic Integration of the miRNome, Machine Learning and Bioinformatics for the Identification of Potential Disease-Modifying Agents in Obstructive Sleep Apnea
inferred← citeshttps://doi.org/10.1016/j.arbres.2026.08.018openalex-snapshot
Endothelial Cell Transcriptomics Reveal Activation of Ribosomal-related Pathways in Chronic Thromboembolic Pulmonary Hypertension
inferred← citeshttps://doi.org/10.1016/j.archoralbio.2015.06.008openalex-snapshot
Transcriptional analysis of human cranial compartments with different embryonic origins
inferred← citeshttps://doi.org/10.1016/j.bbalip.2021.158908openalex-snapshot
Immunomodulating effects of 13- and 16-hydroxylated docosahexaenoyl ethanolamide in LPS stimulated RAW264.7 macrophages
inferred← citeshttps://doi.org/10.1016/j.bbalip.2022.159160openalex-snapshot
Inhibition of Δ-6 desaturase reduces fatty acid re-esterification in 3T3-L1 adipocytes independent of changes in n3-PUFA cellular content
inferred← citeshttps://doi.org/10.1016/j.bbamcr.2020.118845openalex-snapshot
Acute depletion of telomerase components DKC1 and NOP10 induces oxidative stress and disrupts ribosomal biogenesis via NPM1 and activation of the P53 pathway
inferred← citeshttps://doi.org/10.1016/j.bbi.2023.07.025openalex-snapshot
Circulating short chain fatty acids and fatigue in patients with head and neck cancer: A longitudinal prospective study
inferred← citeshttps://doi.org/10.1016/j.bbr.2013.08.032openalex-snapshot
Sleep–wake dynamics under extended light and extended dark conditions in adult zebrafish
inferred← citeshttps://doi.org/10.1016/j.bbrc.2018.10.117openalex-snapshot
Expression profile analysis of differentially expressed genes in ruptured intracranial aneurysms: In search of biomarkers
inferred← citeshttps://doi.org/10.1016/j.bbrc.2023.03.001openalex-snapshot
An extracellular matrix stiffness-induced breast cancer cell transcriptome resembles the transition from ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC)
inferred← citeshttps://doi.org/10.1016/j.bbrep.2026.102562openalex-snapshot
Deciphering the molecular crosstalk between type 2 diabetes and pancreatic cancer through cross-disease co-expression network analysis
inferred← citeshttps://doi.org/10.1016/j.bcp.2021.114692openalex-snapshot
MicroRNA-495/TGF-β/FOXC1 axis regulates multidrug resistance in metaplastic breast cancer cells
inferred← citeshttps://doi.org/10.1016/j.biocel.2021.106055openalex-snapshot
Tissue-specific smooth muscle cell subtypes identified by transcriptional profiling
inferred← citeshttps://doi.org/10.1016/j.biopsych.2018.07.010openalex-snapshot
Transcriptomic Evidence for Alterations in Astrocytes and Parvalbumin Interneurons in Subjects With Bipolar Disorder and Schizophrenia
inferred← citeshttps://doi.org/10.1016/j.bpsgos.2024.100430openalex-snapshot
Intrinsic Gene Expression Correlates of the Biophysically Modeled Diffusion Magnetic Resonance Imaging Signal
inferred← citeshttps://doi.org/10.1016/j.cancergen.2016.10.003openalex-snapshot
Differences in global DNA methylation of testicular seminoma are not associated with changes in histone modifications, clinical prognosis, BRAF mutations or gene expression
inferred← citeshttps://doi.org/10.1016/j.canlet.2015.07.017openalex-snapshot
mTOR inhibitors counteract tamoxifen-induced activation of breast cancer stem cells
inferred← citeshttps://doi.org/10.1016/j.canlet.2024.216739openalex-snapshot
Identification of a 9-gene signature to enhance biochemical recurrence prediction in primary prostate cancer: A benchmarking study using ten machine learning methods and twelve patient cohorts
inferred← citeshttps://doi.org/10.1016/j.ccell.2019.02.005openalex-snapshot
The Proteogenomic Landscape of Curable Prostate Cancer
inferred← citeshttps://doi.org/10.1016/j.ccell.2020.10.004openalex-snapshot
YTHDF3 Induces the Translation of m6A-Enriched Gene Transcripts to Promote Breast Cancer Brain Metastasis
inferred← citeshttps://doi.org/10.1016/j.ceca.2020.102309openalex-snapshot
Budgeting at the Ca2+ store: a PIP(2)eline to starve LSCs?
inferred← citeshttps://doi.org/10.1016/j.cell.2014.08.029openalex-snapshot
Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human
inferred← citeshttps://doi.org/10.1016/j.cell.2014.12.032openalex-snapshot
Hematopoietic Stem Cell Arrival Triggers Dynamic Remodeling of the Perivascular Niche
inferred← citeshttps://doi.org/10.1016/j.cell.2018.05.027openalex-snapshot
A Milieu Molecule for TGF-β Required for Microglia Function in the Nervous System
inferred← citeshttps://doi.org/10.1016/j.cell.2018.09.040openalex-snapshot
Nervous System Regionalization Entails Axial Allocation before Neural Differentiation
inferred← citeshttps://doi.org/10.1016/j.cellsig.2019.109410openalex-snapshot
Butyrate mediated regulation of RNA binding proteins in the post-transcriptional regulation of inflammatory gene expression
inferred← citeshttps://doi.org/10.1016/j.celrep.2016.06.061openalex-snapshot
Gene Expression Architecture of Mouse Dorsal and Tail Skin Reveals Functional Differences in Inflammation and Cancer
inferred← citeshttps://doi.org/10.1016/j.celrep.2016.12.015openalex-snapshot
Amplification of Adipogenic Commitment by VSTM2A
inferred← citeshttps://doi.org/10.1016/j.celrep.2017.05.018openalex-snapshot
Effect of Human Genetic Variability on Gene Expression in Dorsal Root Ganglia and Association with Pain Phenotypes
inferred← citeshttps://doi.org/10.1016/j.celrep.2018.05.021openalex-snapshot
Prediction of Adipose Browning Capacity by Systematic Integration of Transcriptional Profiles
inferred← citeshttps://doi.org/10.1016/j.celrep.2019.03.066openalex-snapshot
Pulsatile MEK Inhibition Improves Anti-Tumor Immunity and T Cell Function in Murine Kras Mutant Lung Cancer
inferred← citeshttps://doi.org/10.1016/j.celrep.2019.08.093openalex-snapshot
Hippocampal Subregions Express Distinct Dendritic Transcriptomes that Reveal Differences in Mitochondrial Function in CA2
inferred← citeshttps://doi.org/10.1016/j.celrep.2019.12.053openalex-snapshot
LIN28B Underlies the Pathogenesis of a Subclass of Ewing Sarcoma
inferred← citeshttps://doi.org/10.1016/j.celrep.2020.107539openalex-snapshot
LIN28B Underlies the Pathogenesis of a Subclass of Ewing Sarcoma
inferred← citeshttps://doi.org/10.1016/j.celrep.2020.108203openalex-snapshot
The Gene-Regulatory Footprint of Aging Highlights Conserved Central Regulators
inferred← citeshttps://doi.org/10.1016/j.celrep.2021.109308openalex-snapshot
Cell-intrinsic glial pathology is conserved across human and murine models of Huntington’s disease
inferred← citeshttps://doi.org/10.1016/j.celrep.2021.110244openalex-snapshot
Vitamin D receptor, STAT3, and TET2 cooperate to establish tolerogenesis
inferred← citeshttps://doi.org/10.1016/j.celrep.2022.111346openalex-snapshot
Mast cell regranulation requires a metabolic switch involving mTORC1 and a glucose-6-phosphate transporter
inferred← citeshttps://doi.org/10.1016/j.celrep.2022.111434openalex-snapshot
Molecular mechanism of RIPK1 and caspase-8 in homeostatic type I interferon production and regulation
inferred← citeshttps://doi.org/10.1016/j.celrep.2023.112106openalex-snapshot
DRAK2 contributes to type 1 diabetes by negatively regulating IL-2 sensitivity to alter regulatory T cell development
inferred← citeshttps://doi.org/10.1016/j.celrep.2024.113687openalex-snapshot
Circulating tumor cells reveal early predictors of disease progression in patients with stage III NSCLC undergoing chemoradiation and immunotherapy
inferred← citeshttps://doi.org/10.1016/j.celrep.2024.113794openalex-snapshot
ZEB1 shapes AML immunological niches, suppressing CD8 T cell activity while fostering Th17 cell expansion
inferred← citeshttps://doi.org/10.1016/j.celrep.2025.115722openalex-snapshot
MYC plus class IIa HDAC inhibition drives mitochondrial dysfunction in non-small cell lung cancer
inferred← citeshttps://doi.org/10.1016/j.celrep.2025.116795openalex-snapshot
Age-independent and targetable transcription factor networks regulating CD8+ T cell senescence in aging humans
inferred← citeshttps://doi.org/10.1016/j.celrep.2026.117447openalex-snapshot
HIF-1α and HIF-2α differentially regulate alveolar macrophage maturation and function
inferred← citeshttps://doi.org/10.1016/j.cjca.2020.08.013openalex-snapshot
The Long Noncoding RNA Landscape of Cardiac Regeneration in Zebrafish
inferred← citeshttps://doi.org/10.1016/j.clim.2026.110715openalex-snapshot
Monocytes from patients with chronic non-bacterial osteomyelitis (CNO) exhibit increased ‘classically activated’ phenotypes and altered DNA methylation patterns
inferred← citeshttps://doi.org/10.1016/j.cmet.2014.03.032openalex-snapshot
Early B Cell Factor 1 Regulates Adipocyte Morphology and Lipolysis in White Adipose Tissue
inferred← citeshttps://doi.org/10.1016/j.cmet.2017.09.006openalex-snapshot
PGC-1α Promotes Breast Cancer Metastasis and Confers Bioenergetic Flexibility against Metabolic Drugs
inferred← citeshttps://doi.org/10.1016/j.cmet.2020.04.011openalex-snapshot
Low-Dose Sorafenib Acts as a Mitochondrial Uncoupler and Ameliorates Nonalcoholic Steatohepatitis
inferred← citeshttps://doi.org/10.1016/j.cmet.2020.06.007openalex-snapshot
Age-Induced Reduction in Human Lipolysis: A Potential Role for Adipocyte Noradrenaline Degradation
inferred← citeshttps://doi.org/10.1016/j.cmet.2024.07.007openalex-snapshot
Hierarchical tricarboxylic acid cycle regulation by hepatocyte arginase 2 links the urea cycle to oxidative metabolism
inferred← citeshttps://doi.org/10.1016/j.cmet.2026.03.012openalex-snapshot
Mitochondrial metabolism regulates the immunogenic responsiveness of dendritic cells
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2019.107125openalex-snapshot
VWF, CXCL8 and IL6 might be potential druggable genes for acute coronary syndrome (ACS)
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2021.104470openalex-snapshot
New drug candidates for osteosarcoma: Drug repurposing based on gene expression signature
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2021.105177openalex-snapshot
Reconstruction of tissue-specific genome-scale metabolic models for human cancer stem cells
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2023.106867openalex-snapshot
Methodology to identify a gene expression signature by merging microarray datasets
inferred← citeshttps://doi.org/10.1016/j.crmicr.2026.100578openalex-snapshot
Early-life rotavirus infection susceptibility and later gastrointestinal cancer protection: Reverse antagonistic pleiotropy and potential vaccine benefits
inferred← citeshttps://doi.org/10.1016/j.csbj.2020.06.023openalex-snapshot
Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities
inferred← citeshttps://doi.org/10.1016/j.csbj.2022.12.054openalex-snapshot
Network-based identification and prioritization of key transcriptional factors of diabetic kidney disease
inferred← citeshttps://doi.org/10.1016/j.cyto.2019.154870openalex-snapshot
Regulation of interferon stimulated gene expression levels at homeostasis
inferred← citeshttps://doi.org/10.1016/j.cytox.2021.100056openalex-snapshot
Interferon stimulated binding of ISRE is cell type specific and is predicted by homeostatic chromatin state
inferred← citeshttps://doi.org/10.1016/j.devcel.2019.06.001openalex-snapshot
In Vivo Developmental Trajectories of Human Podocyte Inform In Vitro Differentiation of Pluripotent Stem Cell-Derived Podocytes
inferred← citeshttps://doi.org/10.1016/j.devcel.2024.06.011openalex-snapshot
Shifts in keratin isoform expression activate motility signals during wound healing
inferred← citeshttps://doi.org/10.1016/j.devcel.2024.08.009openalex-snapshot
Dual function of PHF16 in reinstating homeostasis of murine intestinal epithelium after crypt regeneration
inferred← citeshttps://doi.org/10.1016/j.dib.2019.104624openalex-snapshot
Dataset for dose and time-dependent transcriptional response to ionizing radiation exposure
inferred← citeshttps://doi.org/10.1016/j.dib.2021.106863openalex-snapshot
Differential gene expression data from the human central nervous system across Alzheimer's disease, Lewy body diseases, and the amyotrophic lateral sclerosis and frontotemporal dementia spectrum
inferred← citeshttps://doi.org/10.1016/j.ebiom.2017.07.016openalex-snapshot
Type I IFN and not TNF, is Essential for Cyclic Di-nucleotide-elicited CTL by a Cytosolic Cross-presentation Pathway
inferred← citeshttps://doi.org/10.1016/j.ebiom.2018.03.010openalex-snapshot
Long Non-Coding RNAs Associated with Metabolic Traits in Human White Adipose Tissue
inferred← citeshttps://doi.org/10.1016/j.ebiom.2018.06.012openalex-snapshot
A Systems-Level Analysis Reveals Circadian Regulation of Splicing in Colorectal Cancer
inferred← citeshttps://doi.org/10.1016/j.ebiom.2021.103352openalex-snapshot
VB10, a new blood biomarker for differential diagnosis and recovery monitoring of acute viral and bacterial infections
inferred← citeshttps://doi.org/10.1016/j.envpol.2022.120791openalex-snapshot
Foetal exposure to the bisphenols BADGE and BPAF impairs meiosis through DNA oxidation in mouse ovaries
inferred← citeshttps://doi.org/10.1016/j.envpol.2023.121715openalex-snapshot
Mild exposure to fine particulate matter promotes angiogenesis in non-small cell lung carcinoma
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