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From patterns to pathways: gene expression data analysis comes of age

https://doi.org/10.1038/ng1033
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What this work says

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

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Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning
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Gene-Expression Profiles in Hereditary Breast Cancer
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Bootstrapping cluster analysis: Assessing the reliability of conclusions from microarray experiments
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Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications
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Cluster analysis and display of genome-wide expression patterns
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Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation
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Knowledge-based analysis of microarray gene expression data by using support vector machines
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Singular value decomposition for genome-wide expression data processing and modeling
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Testing for Differentially-Expressed Genes by Maximum-Likelihood Analysis of Microarray Data
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Tissue Classification with Gene Expression Profiles
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Using Bayesian Networks to Analyze Expression Data
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Analysis Techniques for Microarray Time-Series Data
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A Paradigm for Class Prediction Using Gene Expression Profiles
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Clustering Gene Expression Patterns
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Support vector machine classification and validation of cancer tissue samples using microarray expression data
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Model-based clustering and data transformations for gene expression data
inferredcites →https://doi.org/10.1093/bioinformatics/17.4.309openalex-snapshot
Validating clustering for gene expression data
inferredcites →https://doi.org/10.1093/bioinformatics/17.4.319openalex-snapshot
Use of keyword hierarchies to interpret gene expression patterns
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Aligning gene expression time series with time warping algorithms
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Feature selection for DNA methylation based cancer classification
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Inferring subnetworks from perturbed expression profiles
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Rich probabilistic models for gene expression
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Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles
inferredcites →https://doi.org/10.1093/bioinformatics/18.11.1462openalex-snapshot
Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data
inferredcites →https://doi.org/10.1093/bioinformatics/18.5.735openalex-snapshot
Adaptive quality-based clustering of gene expression profiles
inferredcites →https://doi.org/10.1093/bioinformatics/18.suppl_1.s233openalex-snapshot
Discovering regulatory and signalling circuits in molecular interaction networks
inferredcites →https://doi.org/10.1101/gr.9.11.1106openalex-snapshot
Exploring Expression Data: Identification and Analysis of Coexpressed Genes
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Estimating the Number of Clusters in a Data Set Via the Gap Statistic
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Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
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Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale
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The Transcriptional Program of Sporulation in Budding Yeast
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Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring
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Signaling and Circuitry of Multiple MAPK Pathways Revealed by a Matrix of Global Gene Expression Profiles
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Bioinformatics and Clinical Informatics: The Imperative to Collaborate
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A stability based method for discovering structure in clustered data
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COMBINING LOCATION AND EXPRESSION DATA FOR PRINCIPLED DISCOVERY OF GENETIC REGULATORY NETWORK MODELS
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DISCOVERY OF CAUSAL RELATIONSHIPS IN A GENE-REGULATION PATHWAY FROM A MIXTURE OF EXPERIMENTAL AND OBSERVATIONAL DNA MICROARRAY DATA
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DISCOVERY OF REGULATORY INTERACTIONS THROUGH PERTURBATION: INFERENCE AND EXPERIMENTAL DESIGN
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MUTUAL INFORMATION RELEVANCE NETWORKS: FUNCTIONAL GENOMIC CLUSTERING USING PAIRWISE ENTROPY MEASUREMENTS
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PRINCIPAL COMPONENTS ANALYSIS TO SUMMARIZE MICROARRAY EXPERIMENTS: APPLICATION TO SPORULATION TIME SERIES
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A NONPARAMETRIC SCORING ALGORITHM FOR IDENTIFYING INFORMATIVE GENES FROM MICROARRAY DATA
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USING GRAPHICAL MODELS AND GENOMIC EXPRESSION DATA TO STATISTICALLY VALIDATE MODELS OF GENETIC REGULATORY NETWORKS
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Global gene expression profiling of multiple myeloma, monoclonal gammopathy of undetermined significance, and normal bone marrow plasma cells
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In silico prediction of protein-protein interactions in human macrophages
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'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns
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New feature subset selection procedures for classification of expression profiles
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Permutation-validated principal components analysis of microarray data
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Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data
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Model-Based Clustering, Discriminant Analysis, and Density Estimation
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Classification
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The Analysis of Time Series
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The Analysis of Time Series: An Introduction
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Algorithms for Clustering Data
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Biostatistical Analysis
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Resampling-Based Multiple Testing.
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A Simple Sequentially Rejective Multiple Test Procedure

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

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Analysis of E.coli Promoter Regions Using Classification, Association and Clustering Algorithms
inferred← citeshttps://doi.org/10.1007/978-3-662-54135-7_6openalex-snapshot
Die funktionelle Analyse von Genomen
inferred← citeshttps://doi.org/10.1007/b95439openalex-snapshot
Support Vector Machines: Theory and Applications
inferred← citeshttps://doi.org/10.1007/s00109-003-0461-8openalex-snapshot
Not just for housekeeping: protein initiation and elongation factors in cell growth and tumorigenesis
inferred← citeshttps://doi.org/10.1007/s00216-003-2088-6openalex-snapshot
Protein microarrays: new tools for pharmaceutical development
inferred← citeshttps://doi.org/10.1007/s00299-009-0709-zopenalex-snapshot
Molecular analyses of the rice glutamate dehydrogenase gene family and their response to nitrogen and phosphorous deprivation
inferred← citeshttps://doi.org/10.1007/s00335-013-9484-9openalex-snapshot
Genetic factors involved in risk for methamphetamine intake and sensitization
inferred← citeshttps://doi.org/10.1007/s00359-025-01771-4openalex-snapshot
Divergent sensory transcriptomic profiles in positive and negative learning in Bicyclus Anynana butterflies
inferred← citeshttps://doi.org/10.1007/s00438-006-0182-0openalex-snapshot
The transcription factor Gcr1 stimulates cell growth by participating in nutrient-responsive gene expression on a global level
inferred← citeshttps://doi.org/10.1007/s10044-014-0369-7openalex-snapshot
Meta-classifiers for high-dimensional, small sample classification for gene expression analysis
inferred← citeshttps://doi.org/10.1007/s10142-005-0006-zopenalex-snapshot
Associating phenotypes with molecular events: recent statistical advances and challenges underpinning microarray experiments
inferred← citeshttps://doi.org/10.1007/s10994-014-5475-7openalex-snapshot
Expectation propagation in linear regression models with spike-and-slab priors
inferred← citeshttps://doi.org/10.1007/s11033-012-1561-8openalex-snapshot
Reconstruction of metabolic network in the bovine mammary gland tissue
inferred← citeshttps://doi.org/10.1007/s11033-014-3129-2openalex-snapshot
Effect of dietary n-3 polyunsaturated fatty acids on transcription factor regulation in the bovine endometrium
inferred← citeshttps://doi.org/10.1007/s11042-019-7181-8openalex-snapshot
Pattern analysis of genetics and genomics: a survey of the state-of-art
inferred← citeshttps://doi.org/10.1007/s11103-006-0034-7openalex-snapshot
Distinct developmental defense activations in barley embryos identified by transcriptome profiling
inferred← citeshttps://doi.org/10.1007/s11357-003-0002-yopenalex-snapshot
AgingDB: A database for oxidative stress and calorie restriction in the study of aging
inferred← citeshttps://doi.org/10.1007/s11434-012-5196-xopenalex-snapshot
A new approach to dissecting complex traits by combining quantitative trait transcript (QTT) mapping and diallel cross analysis
inferred← citeshttps://doi.org/10.1007/s11517-018-1785-4openalex-snapshot
Vibroarthrography for early detection of knee osteoarthritis using normalized frequency features
inferred← citeshttps://doi.org/10.1007/s13204-021-01932-2openalex-snapshot
Development of a new methodology to determine size differences of nanoparticles with nanoparticle tracking analysis
inferred← citeshttps://doi.org/10.1016/b0-12-475570-4/00055-xopenalex-snapshot
Functional Genomics of Aging
inferred← citeshttps://doi.org/10.1016/b978-0-08-046884-6.00237-2openalex-snapshot
Interpretation of Toxicogenomics Data
inferred← citeshttps://doi.org/10.1016/b978-0-12-374729-7.00051-2openalex-snapshot
Microarray Analysis of Stem Cells and Differentiation
inferred← citeshttps://doi.org/10.1016/b978-0-12-385942-6.00034-2openalex-snapshot
Microarray Analysis of Stem Cells and Differentiation
inferred← citeshttps://doi.org/10.1016/b978-0-12-394423-8.00001-9openalex-snapshot
Signal Correlations in Ecological Niches Can Shape the Organization and Evolution of Bacterial Gene Regulatory Networks
inferred← citeshttps://doi.org/10.1016/b978-0-12-819443-0.00014-3openalex-snapshot
Statistical characterization and classification of colon microarray gene expression data using multiple machine learning paradigms
inferred← citeshttps://doi.org/10.1016/b978-0-323-98352-5.00006-9openalex-snapshot
Effective dimensionality reduction model with machine learning classification for microarray gene expression data
inferred← citeshttps://doi.org/10.1016/b978-0-443-21980-1.00006-1openalex-snapshot
Gene expression analysis
inferred← citeshttps://doi.org/10.1016/b978-012088387-5/50014-5openalex-snapshot
Microarray Analysis of Gene Expression Changes in Aging
inferred← citeshttps://doi.org/10.1016/b978-012436643-5/50093-6openalex-snapshot
(Post) Genomic Stem Cell
inferred← citeshttps://doi.org/10.1016/b978-012436643-5/50147-4openalex-snapshot
Microarray Analysis of Stem Cells and Differentiation
inferred← citeshttps://doi.org/10.1016/j.aei.2018.07.002openalex-snapshot
Automatic code compliance with multi-dimensional data fitting in a BIM context
inferred← citeshttps://doi.org/10.1016/j.arr.2009.10.006openalex-snapshot
Next-generation sequencing in aging research: Emerging applications, problems, pitfalls and possible solutions
inferred← citeshttps://doi.org/10.1016/j.artmed.2007.07.008openalex-snapshot
A multiple kernel support vector machine scheme for feature selection and rule extraction from gene expression data of cancer tissue
inferred← citeshttps://doi.org/10.1016/j.artmed.2011.06.003openalex-snapshot
Integration of gene signatures using biological knowledge
inferred← citeshttps://doi.org/10.1016/j.autrev.2005.05.004openalex-snapshot
Genes and goals: An approach to microarray analysis in autoimmunity
inferred← citeshttps://doi.org/10.1016/j.beha.2009.04.002openalex-snapshot
The impact of gene profiling in chronic myeloid leukaemia
inferred← citeshttps://doi.org/10.1016/j.biopsych.2005.03.031openalex-snapshot
Deficient Hippocampal Neuron Expression of Proteasome, Ubiquitin, and Mitochondrial Genes in Multiple Schizophrenia Cohorts
inferred← citeshttps://doi.org/10.1016/j.biosystems.2010.10.017openalex-snapshot
Rhodobase, a meta-analytical tool for reconstructing gene regulatory networks in a model photosynthetic bacterium
inferred← citeshttps://doi.org/10.1016/j.cbpa.2004.10.009openalex-snapshot
Using genome-wide transcriptional profiling to elucidate small-molecule mechanism
inferred← citeshttps://doi.org/10.1016/j.chemolab.2006.05.008openalex-snapshot
Cross model validated feature selection based on gene clusters
inferred← citeshttps://doi.org/10.1016/j.cmpb.2019.01.004openalex-snapshot
Speeding up the discovery of combinations of differentially expressed genes for disease prediction and classification
inferred← citeshttps://doi.org/10.1016/j.cmpb.2019.04.008openalex-snapshot
Statistical characterization and classification of colon microarray gene expression data using multiple machine learning paradigms
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2006.08.004openalex-snapshot
Identification of critical genes in microarray experiments by a Neuro-Fuzzy approach
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2018.11.011openalex-snapshot
Genetic algorithm for assigning weights to gene expressions using functional annotations
inferred← citeshttps://doi.org/10.1016/j.copbio.2004.01.003openalex-snapshot
Bioinformatics and cellular signaling
inferred← citeshttps://doi.org/10.1016/j.critrevonc.2007.04.001openalex-snapshot
Gene expression profiling in sarcomas
inferred← citeshttps://doi.org/10.1016/j.drudis.2009.05.005openalex-snapshot
New tools for functional genomic analysis
inferred← citeshttps://doi.org/10.1016/j.ejor.2010.03.020openalex-snapshot
Detecting relevant variables and interactions in supervised classification
inferred← citeshttps://doi.org/10.1016/j.fbr.2007.09.002openalex-snapshot
Of patterns and pathways: microarray technologies for the analysis of filamentous fungi
inferred← citeshttps://doi.org/10.1016/j.gene.2016.09.033openalex-snapshot
A supervised weighted similarity measure for gene expressions using biological knowledge
inferred← citeshttps://doi.org/10.1016/j.ins.2005.11.015openalex-snapshot
MDSM: Microarray database schema matching using the Hungarian method
inferred← citeshttps://doi.org/10.1016/j.jacc.2007.09.008openalex-snapshot
The Role of Endomyocardial Biopsy in the Management of Cardiovascular Disease
inferred← citeshttps://doi.org/10.1016/j.jad.2009.04.007openalex-snapshot
Altered expression of lipid metabolism and immune response genes in the frontal cortex of suicide completers
inferred← citeshttps://doi.org/10.1016/j.jbi.2004.06.001openalex-snapshot
Correspondence analysis of microarray time-course data in case–control design
inferred← citeshttps://doi.org/10.1016/j.jbi.2008.12.010openalex-snapshot
A neural network-based biomarker association information extraction approach for cancer classification
inferred← citeshttps://doi.org/10.1016/j.jneumeth.2003.09.026openalex-snapshot
Development of rapid staining protocols for laser-capture microdissection of brain vessels from human and rat coupled to gene expression analyses
inferred← citeshttps://doi.org/10.1016/j.knosys.2025.113978openalex-snapshot
Projection-Iterative-Methods-based Optimizer: A novel metaheuristic algorithm for continuous optimization problems and feature selection
inferred← citeshttps://doi.org/10.1016/j.mib.2005.12.010openalex-snapshot
Salmonella transcriptomics: relating regulons, stimulons and regulatory networks to the process of infection
inferred← citeshttps://doi.org/10.1016/j.mod.2004.09.004openalex-snapshot
A Xenopus tropicalis oligonucleotide microarray works across species using RNA from Xenopus laevis
inferred← citeshttps://doi.org/10.1016/j.molbrainres.2003.10.023openalex-snapshot
Profiling of genes associated with transcriptional responses in mouse hippocampus after transient forebrain ischemia using high-density oligonucleotide DNA array
inferred← citeshttps://doi.org/10.1016/j.mrfmmm.2004.01.012openalex-snapshot
Frontiers in nutrigenomics, proteomics, metabolomics and cancer prevention
inferred← citeshttps://doi.org/10.1016/j.mrfmmm.2005.02.006openalex-snapshot
Comparison of supervised clustering methods to discriminate genotoxic from non-genotoxic carcinogens by gene expression profiling
inferred← citeshttps://doi.org/10.1016/j.neucom.2008.09.025openalex-snapshot
Multi-objective clustering ensemble for gene expression data analysis
inferred← citeshttps://doi.org/10.1016/j.neucom.2011.03.054openalex-snapshot
Analysis of complexity indices for classification problems: Cancer gene expression data
inferred← citeshttps://doi.org/10.1016/j.nut.2003.09.020openalex-snapshot
Gene expression profiling of adipose tissue:
inferred← citeshttps://doi.org/10.1016/j.partic.2014.10.004openalex-snapshot
A method for assessing nanomaterial dispersion quality based on principal component analysis of particle size distribution data
inferred← citeshttps://doi.org/10.1016/j.phrs.2005.09.001openalex-snapshot
In vivo drug-response in patients with leukemic non-Hodgkin's lymphomas is associated with in vitro chemosensitivity and gene expression profiling
inferred← citeshttps://doi.org/10.1016/j.phytochem.2006.09.026openalex-snapshot
Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses
inferred← citeshttps://doi.org/10.1016/j.pt.2004.02.008openalex-snapshot
DNA microarray analysis of protozoan parasite gene expression: outcomes correlate with mechanisms of regulation
inferred← citeshttps://doi.org/10.1016/j.reprotox.2004.09.008openalex-snapshot
Ontogeny of transcription profiles during mouse early craniofacial development
inferred← citeshttps://doi.org/10.1016/j.taap.2006.03.009openalex-snapshot
Gene interaction network analysis suggests differences between high and low doses of acetaminophen
inferred← citeshttps://doi.org/10.1016/j.talanta.2008.03.045openalex-snapshot
Classification of genomic data: Some aspects of feature selection
inferred← citeshttps://doi.org/10.1016/j.tig.2004.04.007openalex-snapshot
Transcripts of aging
inferred← citeshttps://doi.org/10.1016/j.tig.2004.09.007openalex-snapshot
Genetics, statistics and human disease: analytical retooling for complexity
inferred← citeshttps://doi.org/10.1016/j.tim.2009.04.004openalex-snapshot
What we can learn about Escherichia coli through application of Gene Ontology
inferred← citeshttps://doi.org/10.1016/j.tox.2005.05.020openalex-snapshot
Molecular responses to xenoestrogens: Mechanistic insights from toxicogenomics
inferred← citeshttps://doi.org/10.1016/j.tox.2006.05.017openalex-snapshot
Identification of early molecular pathways affected by paraquat in rat lung
inferred← citeshttps://doi.org/10.1016/j.visres.2010.03.021openalex-snapshot
Gene profiling in experimental models of eye growth: Clues to myopia pathogenesis
inferred← citeshttps://doi.org/10.1016/s0014-5793(03)00522-2openalex-snapshot
Integration and cross‐validation of high‐throughput gene expression data: comparing heterogeneous data sets
inferred← citeshttps://doi.org/10.1016/s0037-1963(03)00193-8openalex-snapshot
Gene expression profiling as a tool for the diagnosis of acute leukemias
inferred← citeshttps://doi.org/10.1016/s0074-7696(07)61006-7openalex-snapshot
New Technologies Used in the Study of Human Melanoma
inferred← citeshttps://doi.org/10.1016/s0076-6879(03)70023-8openalex-snapshot
DNA Microarrays and Bacterial Gene Expression
inferred← citeshttps://doi.org/10.1016/s0076-6879(06)10016-6openalex-snapshot
[16] DamID: Mapping of In Vivo Protein–Genome Interactions Using Tethered DNA Adenine Methyltransferase
inferred← citeshttps://doi.org/10.1016/s0076-6879(06)20010-7openalex-snapshot
Microarray Analysis of Stem Cells and Differentiation
inferred← citeshttps://doi.org/10.1016/s0165-6147(03)00197-4openalex-snapshot
What is the relevance of bioinformatics to pharmacology?
inferred← citeshttps://doi.org/10.1016/s0166-526x(05)46001-8openalex-snapshot
Chapter 1 Emerging technologies—the way forward on improving protein analysis
inferred← citeshttps://doi.org/10.1016/s0531-5565(03)00168-2openalex-snapshot
New trends in bioinformatics: from genome sequence to personalized medicine
inferred← citeshttps://doi.org/10.1016/s0580-9517(06)36024-2openalex-snapshot
24 Bioinformatic Prediction of Yeast Gene Function
inferred← citeshttps://doi.org/10.1016/s0889-8588(03)00063-7openalex-snapshot
Ovarian cancer screening
inferred← citeshttps://doi.org/10.1016/s0893-6080(03)00103-5openalex-snapshot
An accelerated procedure for recursive feature ranking on microarray data
inferred← citeshttps://doi.org/10.1016/s0959-440x(03)00078-2openalex-snapshot
Gene selection in microarray data: the elephant, the blind men and our algorithms
inferred← citeshttps://doi.org/10.1016/s1016-8478(23)17582-0openalex-snapshot
Clustering Approaches to Identifying Gene Expression Patterns from DNA Microarray Data
inferred← citeshttps://doi.org/10.1016/s1359-6446(05)03451-3openalex-snapshot
The transcriptome's drugable frequenters
inferred← citeshttps://doi.org/10.1016/s1741-8364(04)02383-2openalex-snapshot
Hardware and software systems for accelerating common bioinformatics sequence analysis algorithms
inferred← citeshttps://doi.org/10.1016/s1741-8364(04)02386-8openalex-snapshot
Practical computational approaches to inferring protein function
inferred← citeshttps://doi.org/10.1017/cbo9780511607493openalex-snapshot
Cluster and Classification Techniques for the Biosciences
inferred← citeshttps://doi.org/10.1017/cbo9780511806087.019openalex-snapshot
Functional Genomics
inferred← citeshttps://doi.org/10.1017/cbo9781139680349.005openalex-snapshot
Transcriptional Mechanisms Regulating Pulmonary Epithelial Maturation:
inferred← citeshttps://doi.org/10.1021/ac1008578openalex-snapshot
Temperature and Time-Resolved Total Internal Reflectance Fluorescence Analysis of Reusable DNA Hydrogel Chips
inferred← citeshttps://doi.org/10.1023/a:1026088615145openalex-snapshot
Large-Scale Computational Modeling of Genetic Regulatory Networks
inferred← citeshttps://doi.org/10.1038/msb.2008.8openalex-snapshot
Formulating genome‐scale kinetic models in the post‐genome era
inferred← citeshttps://doi.org/10.1038/ng1030openalex-snapshot
Options available—from start to finish—for obtaining data from DNA microarrays II
inferred← citeshttps://doi.org/10.1038/ng1031openalex-snapshot
Fundamentals of experimental design for cDNA microarrays
inferred← citeshttps://doi.org/10.1038/ng1034openalex-snapshot
Post-analysis follow-up and validation of microarray experiments
inferred← citeshttps://doi.org/10.1038/ng1038openalex-snapshot
Molecular portraits and the family tree of cancer
inferred← citeshttps://doi.org/10.1038/nrc2294openalex-snapshot
The properties of high-dimensional data spaces: implications for exploring gene and protein expression data
inferred← citeshttps://doi.org/10.1038/nrd1202openalex-snapshot
Target discovery
inferred← citeshttps://doi.org/10.1038/nrg1047openalex-snapshot
Nutrigenomics: goals and strategies
inferred← citeshttps://doi.org/10.1038/nrg1128openalex-snapshot
Evolutionary and ecological functional genomics
inferred← citeshttps://doi.org/10.1038/nrm1941openalex-snapshot
Proteome chips for whole-organism assays
inferred← citeshttps://doi.org/10.1038/nrn1219openalex-snapshot
Neural crest specification: migrating into genomics
inferred← citeshttps://doi.org/10.1038/nrn1518openalex-snapshot
DNA-microarray analysis of brain cancer: molecular classification for therapy
inferred← citeshttps://doi.org/10.1038/s41540-017-0009-0openalex-snapshot
Integrating personalized gene expression profiles into predictive disease-associated gene pools
inferred← citeshttps://doi.org/10.1038/s41540-025-00586-yopenalex-snapshot
Constraint based modeling of drug induced metabolic changes in a cancer cell line
inferred← citeshttps://doi.org/10.1038/s41559-018-0682-4openalex-snapshot
Early neurogenomic response associated with variation in guppy female mate preference
inferred← citeshttps://doi.org/10.1038/sj.gene.6363976openalex-snapshot
Fine mapping the phenotype in autoimmune disease: the promise and pitfalls of DNA microarray technologies
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