Mapping complex disease traits with global gene expression

Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls

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Genetics of Food Intake Self-Regulation in Childhood: Literature Review and Research Opportunities

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A General Framework for Weighted Gene Co-Expression Network Analysis

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Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease

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The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease

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The human disease network

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Common loss-of-function variants of the epidermal barrier protein filaggrin are a major predisposing factor for atopic dermatitis

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Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease

the NIDDK IBD Genetics Consortium, Barrett, J. C., the Belgian-French IBD Consortium, the Wellcome Trust Case Control Consortium, Hansoul, S., Nicolae, D. L., Cho, J. H., Duerr, R. H., Rioux, J. D., Brant, S. R., et al. (2008) · Nature Genetics · doi:10.1038/ng.175 · Cited by 2,593

Heritability in the genomics era — concepts and misconceptions

Visscher, P. M., Hill, W. G., & Wray, N. R. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2322 · Cited by 1,921

An Oncogene-Induced DNA Damage Model for Cancer Development

Halazonetis, T. D., Gorgoulis, V. G., & Bartek, J. (2008) · Science · doi:10.1126/science.1140735 · Cited by 1,851

MCC-SP: a powerful integration method for identification of causal pathways from genetic variants to complex disease

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Association study between asthma and single nucleotide polymorphisms of ORMDL3, GSDMB, and IL1RL1 genes in an Algerian population

Ziani, M., Henry, A. P., & Hall, I. P. (2021) · Egyptian Journal of Medical Human Genetics · doi:10.1186/s43042-021-00163-y · Cited by 3

Recombination Fraction

Xu, S. (2012) · Springer eBooks · doi:10.1007/978-0-387-70807-2_2 · Cited by 3

Cryptic genetic variation of expression quantitative trait locus architecture revealed by genetic perturbation in Caenorhabditis elegans

van Wijk, M. H., Riksen, J. A. G., Elvin, M., Poulin, G. B., Maulana, M. I., Kammenga, J. E., Snoek, B. L., & Sterken, M. G. (2023) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkad050 · Cited by 3

The Role of Gene Expression Regulation on Genetic Risk of Age-Related Macular Degeneration

Ratnapriya, R. (2023) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-27681-1_10 · Cited by 3

Intelligent phenotype-detection and gene expression profile generation with generative adversarial networks

Ravaee, H., Manshaei, M. H., Safayani, M., & Sartakhti, J. S. (2023) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2023.111636 · Cited by 3

QTL Mapping of Molecular Traits for Studies of Human Complex Diseases

Liu, C. (2012) · Translational bioinformatics · doi:10.1007/978-94-007-5558-1_5 · Cited by 3

SNPs and TFBS Associated with High Altitude Sickness*

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Identifying progression related disease risk modules based on the human subcellular signaling networks

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One Decade Later: What has Gene Expression Profiling Told us About Neuronal Cell Types, Brain Function and Disease?

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An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Paracchini, S., Monaco, A. P., & Knight, J. C. (2010) · Journal of Visualized Experiments · doi:10.3791/2279 · Cited by 3

Genome-wide association studies in kidney diseases: Quo Vadis?

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A new approach to dissecting complex traits by combining quantitative trait transcript (QTT) mapping and diallel cross analysis

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Expression quantitative trait analysis reveals fine germline transcript regulation in mouse lung tumors

Cotroneo, C. E., Dassano, A., Colombo, F., Pettinicchio, A., Lecis, D., Dugo, M., Cecco, L. D., Dragani, T. A., & Manenti, G. (2016) · Cancer Letters · doi:10.1016/j.canlet.2016.02.054 · Cited by 3

Characterization of RNA

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Deciphering mechanisms underlying the genetic variation of general production and liver quality traits in the overfed mule duck by pQTL analyses

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Characterization of normal facial features and their association with genes

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Quantifying the impact of genetically regulated expression on complex traits and diseasesPreprint

Cai, M., Chen, L., Liu, J., & Yang, C. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/546580 · Cited by 3

Risks associated with clinical databases.

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The association of serum level and polymorphisms of IFN-γ (rs2069705) with the susceptibility to cutaneous leishmaniasis

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Copy Number Variation in Asthma: An Integrative Review

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Analysis of chromatin structure reveals the connection between sQTLs and the splicing of distant genes

Eralp, B., & Sefer, E. (2025) · Scientific Reports · doi:10.1038/s41598-025-28138-8 · Cited by 2

A network based covariance test for detecting multivariate eQTL in saccharomyces cerevisiae

Yuan, H., Li, Z., Tang, N. L. S., & Deng, M. (2016) · BMC Systems Biology · doi:10.1186/s12918-015-0245-0 · Cited by 2

A Coprecipitation-Based Validation Methodology for Interactions Identified Using Protein Microarrays

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A multi-modal framework improves prediction of tissue-specific gene expression from a surrogate tissue

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Network analysis of aging acceleration reveals systematic properties of 11 types of cancers

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Analysis of subcellular RNA fractions demonstrates significant genetic regulation of gene expression in human brain post-transcriptionally

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Recent Advances in Genetically Engineered Microorganisms and their Risks: A Review

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Analysis of Posttraumatic Stress Disorder Gene Expression Profiles in a Prospective, Community-Based Cohort

Dahrendorff, J., Wani, A. H., Keller, T. E., Armstrong, D. L., Qu, A., Wildman, D. E., Valero, M. C., Koenen, K. C., Aiello, A. E., & Uddin, M. (2024) · Human Biology · doi:10.1353/hub.2017.a935047 · Cited by 2

Identification and Functional Assessment of Candidate Causal Cis -Regulatory Variants Underlying Electrocardiographic QT Interval GWAS Loci

Kadagandla, S., Gunamalai, L., Lee, D., & Kapoor, A. (2025) · Circulation Genomic and Precision Medicine · doi:10.1161/circgen.124.005032 · Cited by 3

Genomics of cardiac electrical function

Lodder, E. M., & Bezzina, C. R. (2013) · Briefings in Functional Genomics · doi:10.1093/bfgp/elt029 · Cited by 2

Pluralistic and stochastic gene regulation: examples, models and consistent theory

Salas, E. N., Shu, J., Cserhati, M. F., Weeks, D. P., & Ladunga, I. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw042 · Cited by 2

A block mixture model to map eQTLs for gene clustering and networking

Wang, N., Gosik, K., Li, R., Lindsay, B. G., & Wu, R. (2016) · Scientific Reports · doi:10.1038/srep21193 · Cited by 2

Epigenetic Approaches to Define the Molecular and Genetic Risk Architectures of Schizophrenia

Kundaković, M., Peter, C. J., Roussos, P., & Akbarian, S. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-801829-3.00013-6 · Cited by 2

Statistical Methods and Software for Substance Use and Dependence Genetic Research

Lan, T., Yang, B., Zhang, X., Wang, T., & Lu, Q. L. (2019) · Current Genomics · doi:10.2174/1389202920666190617094930 · Cited by 2

eQTL Mapping Using Transcription Factor Affinity

Mariella, E., Grassi, E., & Provero, P. (2019) · Methods in molecular biology · doi:10.1007/978-1-0716-0026-9_3 · Cited by 2

Genome Scanning for Quantitative Trait Loci

Xu, S. (2012) · Springer eBooks · doi:10.1007/978-0-387-70807-2_8 · Cited by 2

Mapping of Expression Quantitative Trait Loci Using RNA-seq Data

Sun, W., & Hu, Y. (2014) · Springer eBooks · doi:10.1007/978-3-319-07212-8_8 · Cited by 2

GEPdb: a database for investigating the ternary association of genotype, gene expression and phenotype

Ryu, D., Cho, S., Kim, H., Lee, S., & Kim, W. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu240 · Cited by 2

Use of Single Molecule Fluorescent In Situ Hybridization (SM-FISH) to Quantify and Localize mRNAs in Murine Oocytes

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Genetic Architecture of Untargeted Lipidomics in Cardiometabolic-Disease Patients Combines Strong Polygenic Control and Pleiotropy

Brial, F., Hedjazi, L., Sonomura, K., Hageh, C. A., Zalloua, P., Matsuda, F., & Gauguier, D. (2022) · Metabolites · doi:10.3390/metabo12070596 · Cited by 2

Animal Models: Allelic Determinants for BMD

Blank, R. D. (2013) · Wiley eBooks · doi:10.1002/9781118453926.ch9 · Cited by 2

Reaction network analysis in biochemical signaling pathways

Martínez‐Forero, I., Peláez, A. I., & Villoslada, P. (2011) · Tesis Doctorals en Xarxa (Consorci de Serveis Universitaris de Catalunya) · Cited by 2

Principles for the post-GWAS functional characterisation of risk lociPreprint

Monteiro, Á. N. A., Coetzee, G. A., Freedman, M. L., Biasi, M. D., Casey, G., Duggan, D., Risch, A., Plass, C., Liu, P., James, M. A., et al. (2010) · Nature Precedings · doi:10.1038/npre.2010.5162.1 · Cited by 2

eQTL Mapping via Effective SNP Ranking and ScreeningPreprint

Rhyne, J., Tzeng, J., Zhang, T., & Jeng, X. J. (2018) · arXiv (Cornell University) · doi:10.48550/arxiv.1804.02737 · Cited by 2

Functional variants in hematopoietic transcription factor footprints and their roles in the risk of immune system diseasesPreprint

Kubota, N., & Suyama, M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.22.436360 · Cited by 2

Principles for the post-GWAS functional characterisation of risk lociPreprint

Casey, G., Liu, P., Biasi, M. D., Tichelaar, J. W., Carlson, C., Vikis, H. G., Duggan, D., You, M., Mills, I. G., Freedman, M. L., et al. (2011) · Nature Precedings · doi:10.1038/npre.2011.5162.2 · Cited by 2

Linking histology and molecular state across human tissuesPreprint

Jones, A., Gundersen, G. W., & Engelhardt, B. E. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.10.495669 · Cited by 2

Mammalian Cortical Regional Specification

Ypsilanti, A. R., & Rubenstein, J. L. R. (2023) · Wiley eBooks · doi:10.1002/9781119860914.ch21 · Cited by 2

Cell type-specific network analysis in Diversity Outbred mice identifies genes potentially responsible for human bone mineral density GWAS associationsPreprint

Dillard, L. J., Calabrese, G. M., Mesner, L. D., & Farber, C. R. (2024) · eLife · doi:10.7554/elife.100832 · Cited by 2

An Integrated Approach to Plant Biology via Multi-Analogous Methods

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Informatics and computational methods in natural product drug discovery

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Identification of CTHRC1 as a novel candidate for neurodevelopmental disorders

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A Graphical Method for Identifying Gene Clusters From RNA Sequencing Data

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Mismapping of sequencing reads from polymorphic duplications generates spurious trans-eQTLs

Aqil, A., Huang, B. Y. H., Pavlidis, P., McCoy, R. C., & Gökçümen, Ö. (2026) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2026.07.004 · Cited by 2

Time-Course Microarray Data Analysis

Xu, S. (2012) · Springer eBooks · doi:10.1007/978-0-387-70807-2_23 · Cited by 1

The emergence of genomics in mouse asthma models

Stupka, E. (2009) · Drug Discovery Today Disease Models · doi:10.1016/j.ddmod.2010.06.002 · Cited by 1

Exploring Trans-acting regulators of gene expression associated with metabolic syndrome: a coupled application of factor analysis and linkage analysis

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MOSCATO: a supervised approach for analyzing multi-Omic single-Cell data

Towle-Miller, L. M., & Miecznikowski, J. C. (2022) · BMC Genomics · doi:10.1186/s12864-022-08759-3 · Cited by 1

SDPR expression in human trabecular meshwork and its potential role in racial disparities of glaucoma

Shui, Y., Liu, Y., Huang, A., & Siegfried, C. J. (2024) · Scientific Reports · doi:10.1038/s41598-024-61071-w · Cited by 1

Microarray Differential Expression Analysis

Xu, S. (2012) · Springer eBooks · doi:10.1007/978-0-387-70807-2_17 · Cited by 1

Hard Work Ahead: Fine Mapping and Functional Follow-up of Susceptibility Alleles in Cancer GWAS

Koster, R., & Chanock, S. J. (2015) · Current Epidemiology Reports · doi:10.1007/s40471-015-0049-1 · Cited by 1

Hierarchical Clustering of Microarray Data

Xu, S. (2012) · Springer eBooks · doi:10.1007/978-0-387-70807-2_18 · Cited by 1

Major Gene Detection

Xu, S. (2012) · Springer eBooks · doi:10.1007/978-0-387-70807-2_6 · Cited by 1

Non-coding RNA in Neurodegeneration

Ciccodicola, A., Ambrosio, M. R., Scarpato, M., & Costa, V. (2012) · Current Geriatrics Reports · doi:10.1007/s13670-012-0023-4 · Cited by 1

Bayesian Multiple QTL Mapping

Xu, S. (2012) · Springer eBooks · doi:10.1007/978-0-387-70807-2_15 · Cited by 1

From Biological Warfare to the Brighter Side of Rice Research

Costa, L. M. (2012) · Plant and Cell Physiology · doi:10.1093/pcp/pcs039 · Cited by 1

Low latencies as conditione sine qua non for interactive data exploration and timely collaboration

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Clinical Impact of Current Genetics Findings

Weidinger, S., & Kabesch, M. (2011) · Pediatric and adolescent medicine · doi:10.1159/000328159 · Cited by 1

Integrated approaches to functionally characterize novel factors in lipoprotein metabolism

Runz, H. (2012) · Current Opinion in Lipidology · doi:10.1097/mol.0b013e328350fc3d · Cited by 1

Applying In Silico Integrative Genomics to Genetic Studies of Human Disease

Saccone, S. F. (2012) · International review of neurobiology · doi:10.1016/b978-0-12-388408-4.00007-1 · Cited by 1

Gene Expression and Profiling

Zhou, Y. G., Xu, C., Zhang, J., & Deng, H. (2016) · Translational bioinformatics · doi:10.1007/978-94-017-7543-4_3 · Cited by 1

Development of a tissue augmented Bayesian model for expression quantitative trait loci analysis

Zhuang, Y., Wade, K. J., Saba, L. M., & Kechris, K. J. (2019) · Mathematical Biosciences & Engineering · doi:10.3934/mbe.2020007 · Cited by 1

The polygenic nature of rheumatoid arthritis

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FastLORS: Joint modelling for expression quantitative trait loci mapping in R

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Using Collaborative Mixed Models to Account for Imputation Uncertainty in Transcriptome-Wide Association Studies

Shi, X., Yang, C., & Liu, J. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-0947-7_7 · Cited by 1

Handling High-Throughput Omics Data for Systems Genetics Analysis

Pesce, F., & Protopapa, P. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1507-2_12 · Cited by 1

QTL Mapping in Other Populations

Xu, S. (2012) · Springer eBooks · doi:10.1007/978-0-387-70807-2_12 · Cited by 1

QTL Mapping of Molecular Traits for Studies of Human Complex Diseases

Liu, C. (2018) · Translational bioinformatics · doi:10.1007/978-981-13-1071-3_6 · Cited by 1

Transcriptomics insights into interpreting AMD-GWAS discoveries for biological and clinical applications

Ratnapriya, R. (2022) · Journal of Translational Genetics and Genomics · doi:10.20517/jtgg.2021.54 · Cited by 1

Genome‐wide Association Studies: The Success, Failure and Future

Ku, C., Yun, L. E., Yudi Pawitan, Y., & Kee‐Seng, C. (2009) · Wiley eBooks · doi:10.1002/9780470015902.a0021995 · Cited by 1

Quantitative studies of DNA methylation and gene expression in neuropsychiatric traits

van Eijk, K. R. (2014) · Utrecht University Repository (Utrecht University) · Cited by 1

Molecular studies of dyslexia : regulation and function of DYX1C1

Tammimies, K. (2011) · Figshare · Cited by 1

Molecular Basis of Complex Traits

Polychronakos, C. (2011) · Wiley eBooks · doi:10.1002/9780470015902.a0021448 · Cited by 1

Estudo comparativo de redes gênicas de expressão de genes associados à diabetes mellitus tipo 2 (DM2) e genótipos de risco da doença

Vaquero, A. R. (2013) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/d.5.2013.tde-28052013-102800 · Cited by 1

RNA‐Seq and Human Complex Disease

Ciccodicola, A., Aversa, R., Esposito, R., & Costa, V. (2013) · Wiley eBooks · doi:10.1002/9780470015902.a0024990 · Cited by 1

Etude de l'interaction Theobroma cacao-Moniliophtora perniciosa

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Nonparametric Reduced-Rank Regression for Multi-SNP, Multi-Trait Association MappingPreprint

Valente, A. M., Ginsburg, G. S., & Engelhardt, B. E. (2015) · arXiv (Cornell University) · doi:10.48550/arxiv.1512.02306 · Cited by 1

The regulator-executor-phenotype architecture shaped by natural selectionPreprint

Chen, H., Wu, C.-I., & He, X. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/026443 · Cited by 1

Uma abordagem de integração de dados de redes PPI e expressão gênica para priorizar genes relacionados a doenças complexas

Simões, S. N. (2015) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.95.2015.tde-17112015-172846 · Cited by 1

The Evolutionary Implication of Gene Expression Variation in Eukaryotes: From Yeast to Human

Li, J. (2012) · Library and Archives Canada (Government of Canada) · Cited by 1

Genetic and epigenetic mechanisms in the aetiology of orofacial clefts

Alvizi, L. (2018) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.41.2018.tde-12122017-172943 · Cited by 1

Haplotype-based eQTL mapping finds evidence for complex gene regulatory regions poorly tagged by marginal SNPsPreprint

Brown, R., Sankararaman, S., & Paşaniuc, B. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/314229 · Cited by 1

Animal Models

Bassett, J. H. D., Williams, G. R., & Blank, R. D. (2018) · Wiley eBooks · doi:10.1002/9781119266594.ch44 · Cited by 1

Identification of expression quantitative trait loci (eQTL) and candidate genes associated with water holding capacity in porcine meat

Çınar, M. U. (2011) · bonndoc (University of Bonn) · Cited by 1

Model-based analysis of polymorphisms in an enhancer reveals cis-regulatory mechanismsPreprint

Khajouei, F., Samper, N., Djabrayan, N., Lunt, B., Jiménez, G., & Sinha, S. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.07.939264 · Cited by 1

Not by systems alone: replicability assessment of disease expression signalsPreprint

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Quantitative Genetic Scoring, or how to put a number on an arbitrary genetic regionPreprint

Schoenmacker, G., Vlaming, P., Pallesen, J., Pikulina, M., Ghamarian, A., Demontis, D., Børglum, A. D., Galesloot, T. E., Poelmans, G., Franke, B., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.15.422886 · Cited by 1

STATISTICAL METHODS IN GENETIC STUDIES

Gao, C. (2021) · Digital Commons - Michigan Tech (Michigan Technological University) · doi:10.37099/mtu.dc.etdr/1284 · Cited by 1

Cell type-specific network analysis in Diversity Outbred mice identifies genes potentially responsible for human bone mineral density GWAS associationsPreprint

Dillard, L. J., Calabrese, G. M., Mesner, L. D., & Farber, C. R. (2024) · eLife · doi:10.7554/elife.100832.1 · Cited by 1

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