Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease

The sequence of the human genome

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The Structure of Haplotype Blocks in the Human Genome

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The Future of Genetic Studies of Complex Human Diseases

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Identification of the Cystic Fibrosis Gene: Genetic Analysis

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A novel MHC class I-like gene is mutated in patients with hereditary haemochromatosis

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Identification of the breast cancer susceptibility gene BRCA2

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Tobacco smoking, estrogen receptor α gene variation and small low density lipoprotein level

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No Evidence for an Association Between Common Nonsynonymous Polymorphisms in Delta and Bristle Number Variation in Natural and Laboratory Populations of Drosophila melanogaster

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SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms

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Identification of mutations in Korean patients with amyotrophic lateral sclerosis using multigene panel testing

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Visual simultaneous detection of single nucleotide polymorphism of tumor susceptibility gene and marker alpha-fetoprotein based on double-labeled colloidal gold probe with lateral flow strip biosensor

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Speos: an ensemble graph representation learning framework to predict core gene candidates for complex diseases

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Deeper into the genome

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Polygenic Inherited Predisposition to Breast CancerPreprint

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A Genome-Wide Perspective of Human Diversity and Its Implications in Infectious DiseasePreprint

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Gene Variants Implicated in Steatotic Liver Disease: Opportunities for Diagnostics and Therapeutics

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Identity-by-descent filtering of exome sequence data for disease–gene identification in autosomal recessive disorders

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Whole exome sequencing of pediatric gastric adenocarcinoma reveals an atypical presentation of Li‐Fraumeni syndrome

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Measuring phenotype-phenotype similarity through the interactome

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The classification, genetic diagnosis and modelling of monogenic autoinflammatory disorders

Moghaddas, F., & Masters, S. L. (2018) · Clinical Science · doi:10.1042/cs20171498 · Cited by 30

Association between polymorphisms in RAPGEF1, TP53, NRF1 and type 2 diabetes in Chinese Han population

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Single-nucleotide variations in the genes encoding the mitochondrial Hsp60/Hsp10 chaperone system and their disease-causing potential

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Associating phenotypes with molecular events: recent statistical advances and challenges underpinning microarray experiments

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The role played by natural selection on Mendelian traits in humans

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The Epidemiologic Approach to Pharmacogenomics

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Neural Plasticity, Human Genetics, and Risk for Alcohol Dependence

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Personalized Cancer Medicine: From Molecular Diagnostics to Targeted Therapy with Natural Products

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Absence of Dystrophin Related Protein-2 disrupts Cajal bands in a patient with Charcot–Marie–Tooth disease

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In silico analysis of nonsynonymous single‐nucleotide polymorphisms (nsSNPs) of the SMPX gene

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Heterogeneous network embedding enabling accurate disease association predictions

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Aberrant promoter hypermethylation of p21 (WAF1/CIP1) gene and its impact on expression and role of polymorphism in the risk of breast cancer

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Cytogenetics and gene discovery in psychiatric disorders

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Pharmacogenomics, Nutrigenomics and Therapeutic Optimization in Alzheimer’s Disease

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Applying a new generation of genetic maps to understand human inflammatory disease

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The usefulness of different density SNP maps for disease association studies of common variants

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Success of Face Analysis Technology in Rare Genetic Diseases Diagnosed by Whole-Exome Sequencing: A Single-Center Experience

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Genetics of mitochondrial diseases: Current approaches for the molecular diagnosis

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Combined linkage analysis and exome sequencing identifies novel genes for familial goiter

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Exclusion of Class III Malocclusion Candidate Loci in Brazilian Families

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Quantifying the Intragenic Distribution of Human Disease Mutations

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Current and Emerging Technology Approaches in Genomics

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Regulatory variant in FZD 6gene contributes to nonsyndromic cleft lip and palate in an African‐American family

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Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey

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Genetic Analysis of Juvenile Rheumatoid Arthritis: Approaches to Complex Traits

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Analysis of Common Polymorphisms in Angiotensin-converting Enzyme and Apolipoprotein E Genes and Human Longevity in Colombia

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Quantitative Measures of Aggressive Periodontitis Show Substantial Heritability and Consistency With Traditional Diagnoses

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Genomics and complex liver disease: Challenges and opportunities

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Prediction of Candidate Primary Immunodeficiency Disease Genes Using a Support Vector Machine Learning Approach

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Haplotypes in the APOA1-C3-A4-A5 gene cluster affect plasma lipids in both humans and baboons

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Identifying Critical States of Complex Diseases by Single-Sample Jensen-Shannon Divergence

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SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS

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Association of ADRB1 and UCP3 Gene Polymorphisms with Insulin Sensitivity but Not Obesity

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LGI1 microdeletion in autosomal dominant lateral temporal epilepsy

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Next Generation Sequencing in the Clinical Domain: Clinical Advantages, Practical, and Ethical Challenges

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Clinical prediction of antidepressant response in mood disorders: Linear multivariate vs. neural network models

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Genetics of age-related macular degeneration

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IGENT: efficient entropy based algorithm for genome-wide gene-gene interaction analysis

Kwon, M., Park, M., & Park, T. (2014) · BMC Medical Genomics · doi:10.1186/1755-8794-7-s1-s6 · Cited by 27

The Genetics of Cancer Susceptibility: From Mouse to Man

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Single-nucleotide polymorphism discovery by targeted DNA photocleavage

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TERMINOLOGICAL MAPPING FOR HIGH THROUGHPUT COMPARATIVE BIOLOGY OF PHENOTYPES

Lussier, Y. A., & LI, J. (2003) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789812704856_0020 · Cited by 27

Integration of association statistics over genomic regions using Bayesian adaptive regression splines

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The mathematical limits of genetic prediction for complex chronic disease

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Allelic Association: Linkage Disequilibrium Structure and Gene Mapping

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Monogenic Models: What Have the Single Gene Disorders Taught Us?

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Haplotype inference for present–absent genotype data using previously identified haplotypes and haplotype patterns

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PAX9 polymorphisms and susceptibility to sporadic tooth agenesis: a case–control study in southeast China

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Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing

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Understanding the molecular genetics of congenital cataract may have wider implications for age related cataract

Moore, A. T. (2003) · British Journal of Ophthalmology · doi:10.1136/bjo.88.1.2 · Cited by 26

Different sets of QTLs influence fitness variation in yeast

Romano, G. H., Gurvich, Y., Lavi, O., Ulitsky, I., Ron Shamir, A., & Kupiec, M. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.1 · Cited by 29

Discordant MZ Twins With Cleft Lip and Palate: A Model for Identifying Genes in Complex Traits

Mansilla, M. A., Kimani, J. W., Mitchell, L. E., Christensen, K., Boomsma, D. I., Daack‐Hirsch, S., Nepomucena, B., Wyszynski, D. F., Félix, T. M., Martin, N. G., et al. (2005) · Twin Research and Human Genetics · doi:10.1375/1832427053435373 · Cited by 26

Linkage analysis and the study of Mendelian disease in the era of whole exome and genome sequencing

Teare, M. D., & Santibanez‐Koref, M. (2014) · Briefings in Functional Genomics · doi:10.1093/bfgp/elu024 · Cited by 25

Prioritization of orphan disease-causing genes using topological feature and GO similarity between proteins in interaction networks

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A Novel Candidate Disease Genes Prioritization Method Based on Module Partition and Rank Fusion

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DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases

Zhang, W., Chen, Y., Sun, F., & Jiang, R. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-55 · Cited by 25

An Overview of Association Mapping

Oraguzie, N. C., & Wilcox, P. L. (2007) · Springer eBooks · doi:10.1007/978-0-387-36011-9_1 · Cited by 28

Design and Analysis of Genetic Association Studies to Finely Map a Locus Identified by Linkage Analysis: Sample Size and Power Calculations

Hanson, R. L., Looker, H. C., Ma, L., Muller, Y. L., Baier, L. J., & Knowler, W. C. (2005) · Annals of Human Genetics · doi:10.1111/j.1529-8817.2005.00230.x · Cited by 24

One step closer to fixing association studies: evidence for age- and gender-specific allele frequency variations and deviations from Hardy-Weinberg expectations in controls

Payami, H., Zhu, M., Montimurro, J. S., Keefe, R. G., McCulloch, C. C., & Moses, L. (2005) · Human Genetics · doi:10.1007/s00439-005-0057-1 · Cited by 25

A systems biology approach to the global analysis of transcription factors in colorectal cancer

Pradhan, M. P., Prasad, N. K., & Palakal, M. J. (2012) · BMC Cancer · doi:10.1186/1471-2407-12-331 · Cited by 26

Genomics meets proteomics: identifying the culprits in disease

Stunnenberg, H. G., & Hubner, N. C. (2013) · Human Genetics · doi:10.1007/s00439-013-1376-2 · Cited by 26

Post genome-wide association studies functional characterization of prostate cancer risk loci

Jiang, J., Cui, W., Vongsangnak, W., Hu, G., & Shen, B. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-s8-s9 · Cited by 25

Transcriptome-Based Differentiation of Closely-Related Miscanthus Lines

Chouvarine, P., Cooksey, A. M., McCarthy, F., Ray, D. A., Baldwin, B. S., Burgess, S. C., & Peterson, D. G. (2012) · PLoS ONE · doi:10.1371/journal.pone.0029850 · Cited by 25

Anderson's disease/chylomicron retention disease in a Japanese patient with uniparental disomy 7 and a normal SAR1B gene protein coding sequence

Okada, T., Miyashita, M., Fukuhara, J., Sugitani, M., Ueno, T., Bouma, M. E., & Aggerbeck, L. P. (2011) · Orphanet Journal of Rare Diseases · doi:10.1186/1750-1172-6-78 · Cited by 25

Neuropeptide gene polymorphisms and human behavioural disorders

Inui, A. (2003) · Nature Reviews Drug Discovery · doi:10.1038/nrd1252 · Cited by 25

Aging syndrome genes and premature coronary artery disease

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A model-based approach to selection of tag SNPs

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Effects of Natural Selection on Interpopulation Divergence at Polymorphic Sites in Human Protein-Coding Loci

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Systems Biology: Applications in Drug Discovery

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Familial Colorectal Cancer Type X

Zetner, D. B., & Bisgaard, M. L. (2017) · Current Genomics · doi:10.2174/1389202918666170307161643 · Cited by 24

Predicting Physical Appearance from DNA Data—Towards Genomic Solutions

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Case-only exome sequencing and complex disease susceptibility gene discovery: study design considerations

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Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks

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Gene–disease relationship discovery based on model-driven data integration and database view definition

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REVIEWS IN BASIC AND CLINICAL GASTROENTEROLOGY

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GENOMICS, PROTEOMICS AND BIOINFORMATICS

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The Genetics and Development of Scoliosis

Kusumi, K., & Dunwoodie, S. L. (2009) · Springer eBooks · doi:10.1007/978-1-4419-1406-4 · Cited by 25

Predicting disease-related genes by path structure and community structure in protein–protein networks

Hu, K., Hu, J.-B., Tang, L., Xiang, J., Ma, J.-L., Gao, Y.-Y., Li, H.-J., & Zhang, Y. (2018) · Journal of Statistical Mechanics Theory and Experiment · doi:10.1088/1742-5468/aae02b · Cited by 24

Predicting disease-genes based on network information loss and protein complexes in heterogeneous network

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Predicting Genetic Variation Severity Using Machine Learning to Interpret Molecular Simulations

McCoy, M., Hamre, J. R., Klimov, D. K., & Jafri, M. S. (2020) · Biophysical Journal · doi:10.1016/j.bpj.2020.12.002 · Cited by 24

Utilization of a zebra finch BAC library to determine the structure of an avian androgen receptor genomic region

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Genetic Analysis of Multiple Sclerosis in Europeans

Barcellos, L. F., & Thomson, G. (2003) · Journal of Neuroimmunology · doi:10.1016/j.jneuroim.2003.08.004 · Cited by 25

How well do HapMap SNPs capture the untyped SNPs?

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Association of the HLA region with multiple sclerosis as confirmed by a genome screen using >10,000 SNPs on DNA chips

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Predicting Type 1 Diabetes Candidate Genes using Human Protein-Protein Interaction Networks

Gao, S. (2009) · Journal of Computer Science & Systems Biology · doi:10.4172/jcsb.1000025 · Cited by 23

A Comprehensive In Silico Analysis of the Functional and Structural Impact of Nonsynonymous SNPs in the ABCA1 Transporter Gene

Marín, F. R., Soler‐Rivas, C., Martín‐Hernández, R., & Rodríguez‐Casado, A. (2014) · Cholesterol · doi:10.1155/2014/639751 · Cited by 25

Genome Editing in Neurosciences

Jaenisch, R., Gage, F. H., & Zhang, F. (2017) · Research and perspectives in neurosciences · doi:10.1007/978-3-319-60192-2 · Cited by 23

A genome-wide case-only test for the detection of digenic inheritance in human exomes

Kerner, G., Bouaziz, M., Cobat, A., Bigio, B., Timberlake, A. T., Bustamante, J. C., Lifton, R. P., Casanova, J., & Abel, L. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1920650117 · Cited by 23

Approaches to identify genes for complex human diseases: Lessons from Mendelian disorders

Dean, M. C. (2003) · Human Mutation · doi:10.1002/humu.10259 · Cited by 91

Approaching Inherited Disease on a Genomic Scale

Freudenberg, J., Fu, Y., & Ptáček, L. J. (2005) · Current Genomics · doi:10.2174/138920205775067693

Searching for genetic determinants in the new millennium

Risch, N. J. (2000) · Nature · doi:10.1038/35015718 · Cited by 1,839

Positional cloning moves from perditional to traditional

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Genetics of complex diseases: from mouse to man and back

Warden, C. H., Rotter, J. I., & Lusis, A. J. (1994) · Springer eBooks · doi:10.1007/978-94-009-0371-5_4