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Phenotype Prediction and Genome-Wide Association Study Using Deep Convolutional Neural Network of Soybean

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Spring Is Coming: Genetic Analyses of the Bud Break Date Locus Reveal Candidate Genes From the Cold Perception Pathway to Dormancy Release in Apple (Malus × domestica Borkh.)

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Bioinformatic tools and internet resources for functional annotation of polymorphic loci detected by genome wide association studies of multifactorial diseases (review)

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Dissecting closely linked association signals in combination with the mammalian phenotype database can identify candidate genes in dairy cattle

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Development and Characterization of Near-Isogenic Lines Revealing Candidate Genes for a Major 7AL QTL Responsible for Heat Tolerance in Wheat

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Transcription Factor-7-Like-2 (TCF7L2) in Atherosclerosis: A Potential Biomarker and Therapeutic Target

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Alzheimer’s Disease Genetics: Review of Novel Loci Associated with Disease

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Mapping genetic variants for nonsense-mediated mRNA decay regulation across human tissues

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Genome-Wide Association Study to Identify QTL for Carcass Traits in Korean Hanwoo Cattle

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Historical museum samples enable the examination of divergent and parallel evolution during invasion

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Large-Scale Multi-Omics Studies Provide New Insights into Blood Pressure Regulation

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Pesticide contamination drives adaptive genetic variation in the endemic mayfly Andesiops torrens within a semi-arid agricultural watershed of Chile

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Genetic variation in GC and CYP2R1 affects 25-hydroxyvitamin D concentration and skeletal parameters: A genome-wide association study in 24-month-old Finnish children

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Functional SNPs in the Human Autoimmunity-Associated Locus 17q12-21

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Genome-Wide Association Study (GWAS) for Resistance to Sclerotinia sclerotiorum in Common Bean

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Integration of genome-wide association studies and gene coexpression networks unveils promising soybean resistance genes against five common fungal pathogens

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Identifying high-confidence capture Hi-C interactions using CHiCANE

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Primary Biliary Cholangitis in British Columbia First Nations: Clinical features and discovery of novel genetic susceptibility loci

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Chromatin landscapes and genetic risk for juvenile idiopathic arthritis

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Implicating candidate genes at GWAS signals by leveraging topologically associating domains

Way, G. P., Youngstrom, D. W., Hankenson, K. D., Greene, C. S., & Grant, S. F. A. (2017) · European Journal of Human Genetics · doi:10.1038/ejhg.2017.108 · Cited by 21 · see citing works

Two transects reveal remarkable variation in gene flow on opposite ends of a European toad hybrid zone

van Riemsdijk, I., Arntzen, J. W., Bucciarelli, G. M., McCartney‐Melstad, E., Rafajlović, M., Scott, P. A., Toffelmier, E. M., Shaffer, H. B., & Wielstra, B. (2023) · Heredity · doi:10.1038/s41437-023-00617-6 · Cited by 25 · see citing works

Germline BRCA mutation in male carriers—ripe for precision oncology?

Leão, R., Price, A. J., & Hamilton, R. J. (2017) · Prostate Cancer and Prostatic Diseases · doi:10.1038/s41391-017-0018-5 · Cited by 18 · see citing works

Characterization of near-isogenic lines confirmed QTL and revealed candidate genes for plant height and yield-related traits in common wheat

Zhang, Y., Liu, H., & Yan, G. (2021) · Molecular Breeding · doi:10.1007/s11032-020-01196-8 · Cited by 19 · see citing works

PhenomeXcan: Mapping the genome to the phenome through the transcriptomePreprint

Pividori, M., Rajagopal, P. S., Barbeira, A., Liang, Y., Melia, O., Bastarache, L. A., Park, Y., Wen, X., & Im, H. K. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/833210 · Cited by 18 · see citing works

Trans-ancestral dissection of urate- and gout-associated major loci SLC2A9 and ABCG2 reveals primate-specific regulatory effects

Takei, R., Cadzow, M. J., Markie, D., Bixley, M., Phipps‐Green, A. J., Major, T. J., Li, C., Choi, H. K., Li, Z., Hu, H., et al. (2020) · Journal of Human Genetics · doi:10.1038/s10038-020-0821-z · Cited by 18 · see citing works

Identification and Validation of a Chromosome 4D Quantitative Trait Locus Hotspot Conferring Heat Tolerance in Common Wheat (Triticum aestivum L.)

Lu, L., Liu, H., Wu, Y., & Yan, G. (2022) · Plants · doi:10.3390/plants11060729 · Cited by 18 · see citing works

A genome-wide association study of corneal astigmatism: The CREAM Consortium.

Shah, R. L., Li, Q., Zhao, W., Tedja, M. S., Tideman, J. W. L., Khawaja, A. P., Fan, Q., Yazar, S., Williams, K. M., Verhoeven, V. J. M., et al. (2018) · PubMed Central · doi:10.7892/boris.114871 · Cited by 18 · see citing works

Using Whole Genome Sequencing in an African Subphenotype of Myasthenia Gravis to Generate a Pathogenetic Hypothesis

Nel, M., Mulder, N., Europa, T. A., & Heckmann, J. M. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00136 · Cited by 17 · see citing works

Identification of Candidate Genes for Root Traits Using Genotype–Phenotype Association Analysis of Near-Isogenic Lines in Hexaploid Wheat (Triticum aestivum L.)

Halder, T., Liu, H., Chen, Y., Yan, G., & Siddique, K. H. M. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22073579 · Cited by 17 · see citing works

Mapping gene and gene pathways associated with coronary artery disease: a CARDIoGRAM exome and multi-ancestry UK biobank analysis

Hariharan, P., & Dupuis, J. (2021) · Scientific Reports · doi:10.1038/s41598-021-95637-9 · Cited by 17 · see citing works

Genetics of Base Coat Colour Variations and Coat Colour-Patterns of the South African Nguni Cattle Investigated Using High-Density SNP Genotypes

Kunene, L. M., Muchadeyi, F. C., Hadebe, K., Mészáros, G., Sölkner, J., Dugmore, T., & Dzomba, E. F. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.832702 · Cited by 16 · see citing works

Mining the cucumber core collection: phenotypic and genetic characterization of morphological diversity for fruit quality characteristics

Lin, Y., Weng, Y., Fei, Z., & Grumet, R. (2024) · Horticulture Research · doi:10.1093/hr/uhae340 · Cited by 15 · see citing works

Gene-based association analysis identifies 190 genes affecting neuroticism

Belonogova, N. M., Zorkoltseva, I. V., Tsepilov, Y. A., & Axenovich, T. I. (2021) · Scientific Reports · doi:10.1038/s41598-021-82123-5 · Cited by 15 · see citing works

The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos)

Farleigh, K., Vladimirova, S. A., Blair, C. N., Bracken, J. T., Koochekian, N., Schield, D. R., Card, D. C., Finger, N., Henault, J. A., Leaché, A. D., et al. (2021) · Molecular Ecology · doi:10.1111/mec.16070 · Cited by 15 · see citing works

Host genetic factors associated with the range limit of a European hantavirus

Saxenhofer, M., Labutin, A., White, T. A., & Heckel, G. (2021) · Molecular Ecology · doi:10.1111/mec.16211 · Cited by 15 · see citing works

Genome-Wide Association Study to Map Genomic Regions Related to the Initiation Time of Four Growth Stage Traits in Soybean

Yan, W., Karikari, B., Chang, F., Zhao, F., Zhang, Y., Li, D., Zhao, T., & Jiang, H. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.715529 · Cited by 14 · see citing works

Long non-coding RNA repertoire and open chromatin regions constitute midbrain dopaminergic neuron - specific molecular signatures

Gendron, J., Sauty-Colace, C., Beaume, N., Cartonnet, H., Guégan, J., Ulveling, D., Pardanaud-Glavieux, C., Moszer, I., Cheval, H., & Ravassard, P. (2019) · Scientific Reports · doi:10.1038/s41598-018-37872-1 · Cited by 14 · see citing works

Signatures of selection in Charolais beef cattle identified by genome‐wide analysis

Jahuey‐Martínez, F. J., Parra‐Bracamonte, G. M., Sifuentes‐Rincón, A. M., & Moreno-Medina, V. R. (2019) · Journal of Animal Breeding and Genetics · doi:10.1111/jbg.12399 · Cited by 14 · see citing works

The broken Alzheimer’s disease genome

Roque, C. G., Phatnani, H. P., & Hengst, U. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100555 · Cited by 13 · see citing works

Broadening our understanding of the genetics of Juvenile Idiopathic Arthritis (JIA): Interrogation of three dimensional chromatin structures and genetic regulatory elements within JIA-associated risk loci

Jiang, K., Kessler, H. A., Park, Y., Sudman, M., Thompson, S. D., & Jarvis, J. N. (2020) · PLoS ONE · doi:10.1371/journal.pone.0235857 · Cited by 13 · see citing works

A Candidate-Gene Approach Identifies Novel Associations Between Common Variants in/Near Syndromic Obesity Genes and BMI in Pediatric and Adult European Populations

Wang, D. X., Kaur, Y., Alyass, A., & Meyre, D. (2019) · Diabetes · doi:10.2337/db18-0986 · Cited by 13 · see citing works

Core and accessory genomic traits of Vibrio cholerae O1 drive lineage transmission and disease severity

Maciel-Guerra, A., Babaarslan, K., Baker, M., Rahman, A. S. M. Z., Hossain, M., Sadique, A., Alam, J., Uzzaman, S., Sarker, M. F. R., Sultana, N., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-52238-0 · Cited by 12 · see citing works

Investigating Genetic Diversity and Genomic Signatures of Hatchery-Induced Evolution in Gilthead Seabream (Sparus aurata) Populations

Gkagkavouzis, K., Papakostas, S., Maroso, F., Karaiskou, N., Carr, A. R., Nielsen, E. E., Bargelloni, L., & Triantafyllidis, A. (2021) · Diversity · doi:10.3390/d13110563 · Cited by 12 · see citing works

Effects of Maternal Nutrition on Female Offspring Weight Gain and Sexual Development

Cracco, R. C., Bussiman, F. D. O., Polizel, G. H. G., Furlan, É., Garcia, N. P., Poit, D. A. S., Pugliesi, G., & Santana, M. H. D. A. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.737382 · Cited by 12 · see citing works

Prospecting genomic regions associated with milk production traits in Egyptian buffalo

Abdel-Shafy, H., Awad, M. A. A., El-Regalaty, H., El‐Assal, S. E., & Abou-Bakr, S. (2020) · Journal of Dairy Research · doi:10.1017/s0022029920000953 · Cited by 12 · see citing works

Expression quantitative trait locus studies in the era of single-cell omics

Luo, J., Wu, X., Cheng, Y., Chen, G., Wang, J., & Song, X. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1182579 · Cited by 11 · see citing works

Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data

Baazaoui, I., Bedhiaf‐Romdhani, S., Mastrangelo, S., Lenstra, J. A., Silva, A. D., Benjelloun, B., & Ciani, E. (2024) · Frontiers in Veterinary Science · doi:10.3389/fvets.2024.1339321 · Cited by 11 · see citing works

Genome‐phenotype‐environment associations identify signatures of selection in a panmictic population of threespine stickleback

Strickland, K., Räsänen, K., Kristjánsson, B., Phillips, J. S., Einarsson, Á., Snorradóttir, R. G., Bartrons, M., & Jónsson, Z. (2023) · Molecular Ecology · doi:10.1111/mec.16845 · Cited by 10 · see citing works

Genetic variants for head size share genes and pathways with cancer

Knol, M. J., Poot, R. A., Evans, T. E., Satizábal, C. L., Mishra, A., Sargurupremraj, M., der Auwera, S. V., Duperron, M., Jian, X., Hostettler, I. C., et al. (2024) · Cell Reports Medicine · doi:10.1016/j.xcrm.2024.101529 · Cited by 14 · see citing works

Common and ethnic-specific genetic determinants of hemoglobin concentration between Taiwanese Han Chinese and European Whites: findings from comparative two-stage genome-wide association studies

Timoteo, V. J., Chiang, K.-M., Yang, H., & Pan, W. (2022) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2022.109126 · Cited by 10 · see citing works

Dissecting Meta-Analysis in GWAS Era: Bayesian Framework for Gene/Subnetwork-Specific Meta-Analysis

Chimusa, E. R., & Defo, J. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.838518 · Cited by 10 · see citing works

Genomic Regions, Molecular Markers, and Flanking Genes of Metribuzin Tolerance in Wheat (Triticum aestivum L.)

Kurya, B., Mia, M. S., Liu, H., & Yan, G. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.842191 · Cited by 9 · see citing works

Combined ATAC-seq, RNA-seq, and GWAS analysis reveals glycogen metabolism regulatory network in Jinjiang oyster (Crassostrea ariakensis)

Wu, B., 中国水产科学院黄海水产研究所海水养殖生物育种与可持续产出全国重点实验室, 山. 青. 2., Chen, X., Hu, J., Wang, Z., Wang, Y., Xu, D.-Y., Guo, H., Shao, C., Zhou, L., et al. (2023) · 动物学研究 · doi:10.24272/j.issn.2095-8137.2023.021 · Cited by 9 · see citing works

A Genome-Wide Association Study Identifies Novel Risk Loci for Sarcopenia in a Taiwanese Population

Wu, S., & Chen, W. (2021) · Journal of Inflammation Research · doi:10.2147/jir.s338724 · Cited by 9 · see citing works

cageminer : an R/Bioconductor package to prioritize candidate genes by integrating genome-wide association studies and gene coexpression networks

Almeida‐Silva, F., & Venâncio, T. M. (2022) · in silico Plants · doi:10.1093/insilicoplants/diac018 · Cited by 9 · see citing works

Validation of genotype imputation in Southeast Asian populations and the effect of single nucleotide polymorphism annotation on imputation outcome

Lert-itthiporn, W., Suktitipat, B., Grove, H., Sakuntabhai, A., Malasit, P., Tangthawornchaikul, N., Matsuda, F., & Suriyaphol, P. (2018) · BMC Medical Genetics · doi:10.1186/s12881-018-0534-8 · Cited by 8 · see citing works

Comprehensive identification of pleiotropic loci for body fat distribution using the NHGRI‐EBI Catalog of published genome‐wide association studies

Kaur, Y., Wang, D. X., Liu, H., & Meyre, D. (2018) · Obesity Reviews · doi:10.1111/obr.12806 · Cited by 9 · see citing works

11β-Hydroxylase (CYP11B1) gene variants and new-onset depression in later life

Ancelin, M., Norton, J. L., Ritchie, K. A., Chaudieu, I., & Ryan, J. L. (2021) · Journal of Psychiatry and Neuroscience · doi:10.1503/jpn.190177 · Cited by 9 · see citing works

New Technologies to Study Functional Genomics of Age-Related Macular Degeneration

Nguyen, T., Urrutia-Cabrera, D., Liou, R. H.-C., Luu, C. D., Guymer, R. H., & Wong, R. C. B. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.604220 · Cited by 9 · see citing works

Identification of healthspan-promoting genes in Caenorhabditis elegans based on a human GWAS study

Saul, N., Dhondt, I., Kuokkanen, M., Perola, M., Verschuuren, C., Wouters, B., von Chrzanowski, H., Vos, W. H. D., Temmerman, L., Luyten, W. H. M. L., et al. (2022) · Biogerontology · doi:10.1007/s10522-022-09969-8 · Cited by 10 · see citing works

Analysis of chromatin data supports a role for CD14+ monocytes/macrophages in mediating genetic risk for juvenile idiopathic arthritis

Crinzi, E. A., Haley, E. K., Poppenberg, K. E., Jiang, K., Tutino, V. M., & Jarvis, J. N. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.913555 · Cited by 9 · see citing works

CRISPR/Cas9 genome editing demonstrates functionality of the autoimmunity-associated SNP rs12946510

Ustiugova, A. S., Dvorianinova, E. M., Melnikova, N. V., Dmitriev, A. A., Kuprash, D. V., & Afanasyeva, M. A. (2022) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2022.166599 · Cited by 8 · see citing works

GWAS and Beyond: Using Omics Approaches to Interpret SNP Associations

Chen, H., Petty, L. E., Bush, W. S., Naj, A. C., & Below, J. E. (2019) · Current Genetic Medicine Reports · doi:10.1007/s40142-019-0159-z · Cited by 8 · see citing works

Association of PTPN22 SNP1858 (rs2476601) and Gene SNP1123 (rs2488457) Polymorphism With Primary Immune Thrombocytopenia Susceptibility: A Meta-Analysis of Case-Control Studies and Trial Sequential Analysis

Tian, H., Xu, W., Wen, L., Tang, L., Zhang, X., Song, T., Yang, C., & Huang, P. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.893669 · Cited by 8 · see citing works

Investigating the role of genetic variation in vgll3 and six6 in the domestication of gilthead seabream (Sparus aurata Linnaeus) and European seabass (Dicentrarchus labrax Linnaeus)

Moulistanos, A., Nikolaou, T., Sismanoglou, S., Gkagkavouzis, K., Karaiskou, N., Antonopoulou, E., Triantafyllidis, A., & Papakostas, S. (2023) · Ecology and Evolution · doi:10.1002/ece3.10727 · Cited by 6 · see citing works

Identification of Immune complement function as a determinant of adverse SARS-CoV-2 infection outcomePreprint

Ramlall, V., Thangara, P. M., Tatonetti, N. P., & Shapira, S. D. (2020) · doi:10.21203/rs.3.rs-26451/v1 · Cited by 8 · see citing works

Computational analysis of five neurodegenerative diseases reveals shared and specific genetic loci

Maselli, F., D’Antona, S., Utichi, M., Arnaudi, M., Castiglioni, I., Porro, D., Papaleo, E., Gandellini, P., & Cava, C. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.10.031 · Cited by 7 · see citing works

Examination of a novel expression-based gene-SNP annotation strategy to identify tissue-specific contributions to heritability in multiple traits

Mize, T. J., & Evans, L. M. (2022) · European Journal of Human Genetics · doi:10.1038/s41431-022-01244-1 · Cited by 6 · see citing works

A Panel of rSNPs Demonstrating Allelic Asymmetry in Both ChIP-seq and RNA-seq Data and the Search for Their Phenotypic Outcomes through Analysis of DEGs

Korbolina, E., Bryzgalov, L., Ustrokhanova, D. Z., Postovalov, S., Poverin, D. V., Damarov, I. S., & Merkulova, T. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22147240 · Cited by 6 · see citing works

Major Breakthrough in Mapping Disease-Related Genes: The HapMap

Komaroff, A. L. (2005) · Journal watch · doi:10.1056/jw200511040000004

SNP-based pathway enrichment analysis for genome-wide association studies

Weng, L., Macciardi, F. M., Subramanian, A., Guffanti, G., Potkin, S. G., Yu, Z., & Xie, X. S. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-99 · Cited by 121 · see citing works

Genetically indistinguishable SNPs and their influence on inferring the location of disease-associated variantsPreprint

Lawrence, R., Evans, D. M., Morris, A. P., Ke, X., Hunt, S. E., Paolucci, M., Ragoussis, J., Deloukas, P., Bentley, D., & Cardon, L. R. (2005) · Genome Research · doi:10.1101/gr.4217605 · Cited by 33 · see citing works

Identifying genes targeted by disease-associated non-coding SNPs with a protein knowledge graph

Vlietstra, W. J., Vos, R., van Mulligen, E. M., Jenster, G. W., & Kors, J. A. (2022) · PLoS ONE · doi:10.1371/journal.pone.0271395 · Cited by 5 · see citing works

ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework

Zhang, K., Chang, S., Cui, S., Guo, L., Zhang, L., & Wang, J. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr391 · Cited by 70 · see citing works