Systematic differences in discovery of genetic effects on gene expression and complex traits

Regularization Paths for Generalized Linear Models via Coordinate Descent

Friedman, J., Hastie, T., & Tibshirani, R. (2010) · Journal of Statistical Software · doi:10.18637/jss.v033.i01 · Cited by 19,927 · see citing works

Analysis of protein-coding genetic variation in 60,706 humans

Exome Aggregation Consortium, Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., O’Donnell-Luria, A. H., Ware, J. S., Hill, A. J., et al. (2016) · Nature · doi:10.1038/nature19057 · Cited by 9,587 · see citing works

The mutational constraint spectrum quantified from variation in 141,456 humans

Karczewski, K. J., Francioli, L. C., Tiao, G., Cummings, B. B., Alföldi, J., Wang, Q., Collins, R. L., Laricchia, K. M., Ganna, A., Birnbaum, D. P., et al. (2020) · Nature · doi:10.1038/s41586-020-2308-7 · Cited by 9,434 · see citing works

Integrative analysis of 111 reference human epigenomes

Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368 · cited 1× · see citing works

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

Schizophrenia Working Group of the Psychiatric Genomics Consortium, Bulik-Sullivan, B. K., Loh, P.-R., Finucane, H. K., Ripke, S., Yang, J., Patterson, N., Daly, M. J., Price, A. L., & Neale, B. M. (2015) · Nature Genetics · doi:10.1038/ng.3211 · Cited by 5,559 · see citing works

The GTEx Consortium atlas of genetic regulatory effects across human tissues

The GTEx Consortium, Aguet, F., Anand, S., Ardlie, K. G., Gabriel, S., Getz, G. A., Graubert, A., Hadley, K., Handsaker, R. E., Huang, K. H., et al. (2020) · Science · doi:10.1126/science.aaz1776 · Cited by 5,547 · see citing works

Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics

Giambartolomei, C., Vukcevic, D., Schadt, E. E., Franke, L., Hingorani, A. D., Wallace, C., & Plagnol, V. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004383 · Cited by 4,261 · see citing works

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

Durinck, S., Spellman, P. T., Birney, E., & Huber, W. K. (2009) · Nature Protocols · doi:10.1038/nprot.2009.97 · Cited by 4,081 · see citing works

Genetic effects on gene expression across human tissues

GTEx Consortium (2017) · Nature · doi:10.1038/nature24277 · Cited by 4,036 · see citing works

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716 · see citing works

The Human Transcription Factors

Lambert, S. A., Jolma, A., Campitelli, L. F., Das, P. K., Yin, Y., Albu, M., Chen, X., Taipale, J., Hughes, T. R., & Weirauch, M. T. (2018) · Cell · doi:10.1016/j.cell.2018.01.029 · Cited by 3,399 · see citing works

Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets

Zhu, Z., Zhang, F., Hu, H., Bakshi, A., Robinson, M. R., Powell, J. E., Montgomery, G. W., Goddard, M. E., Wray, N. R., Visscher, P. M., et al. (2016) · Nature Genetics · doi:10.1038/ng.3538 · Cited by 3,352 · see citing works

An Expanded View of Complex Traits: From Polygenic to Omnigenic

Boyle, E. A., Li, Y. I., & Pritchard, J. K. (2017) · Cell · doi:10.1016/j.cell.2017.05.038 · Cited by 2,851 · see citing works

Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression

Võsa, U., Claringbould, A., Westra, H.-J., Bonder, M. J., Deelen, P., Zeng, B., Kirsten, H., Saha, A., Kreuzhuber, R., Yazar, S., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00913-z · Cited by 2,607 · see citing works

Partitioning heritability by functional annotation using genome-wide association summary statistics

ReproGen Consortium, Finucane, H. K., Schizophrenia Working Group of the Psychiatric Genomics Consortium, The RACI Consortium, Bulik-Sullivan, B., Gusev, A., Trynka, G., Reshef, Y., Loh, P.-R., Anttila, V., et al. (2015) · Nature Genetics · doi:10.1038/ng.3404 · Cited by 2,604 · see citing works

Integrative approaches for large-scale transcriptome-wide association studies

Gusev, A., Ko, A., Shi, H., Bhatia, G., Chung, W., Penninx, B. W. J. H., Jansen, R., de Geus, E. J. C., Boomsma, D. I., Wright, F. A., et al. (2016) · Nature Genetics · doi:10.1038/ng.3506 · Cited by 2,479 · see citing works

A promoter-level mammalian expression atlas

The FANTOM Consortium and the RIKEN PMI and CLST (DGT) (2014) · Nature · doi:10.1038/nature13182 · Cited by 1,982 · see citing works

A gene-based association method for mapping traits using reference transcriptome data

Gamazon, E. R., Wheeler, H. E., Shah, K. P., Mozaffari, S. V., Aquino-Michaels, K., Carroll, R. J., Eyler, A. E., Denny, J. C., Nicolae, D. L., Cox, N. J., et al. (2015) · Nature Genetics · doi:10.1038/ng.3367 · Cited by 1,762 · see citing works

The UCSC Genome Browser Database: update 2006

Hinrichs, A. S. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj144 · Cited by 1,646 · see citing works

Effective gene expression prediction from sequence by integrating long-range interactions

Avsec, Ž., Agarwal, V., Visentin, D., Ledsam, J. R., Grabska-Barwinska, A., Taylor, K. R., Assael, Y., Jumper, J., Kohli, P., & Kelley, D. R. (2021) · Nature Methods · doi:10.1038/s41592-021-01252-x · Cited by 1,326 · see citing works

Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS

Nicolae, D. L., Gamazon, E., Zhang, W., Duan, S., Dolan, M. E., & Cox, N. J. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000888 · Cited by 1,292 · see citing works

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

Fulco, C. P., Nasser, J., Jones, T. R., Munson, G., Bergman, D. T., Subramanian, V., Grossman, S. R., Anyoha, R., Doughty, B. R., Patwardhan, T. A., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0538-0 · Cited by 1,111 · see citing works

The selection and function of cell type-specific enhancers

Heinz, S., Romanoski, C. E., Benner, C., & Glass, C. K. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3949 · Cited by 1,010 · see citing works

Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

Fairfax, B. P., Humburg, P., Makino, S., Naranbhai, V., Wong, D., Lau, E., Jostins, L., Plant, K., Andrews, R., McGee, C., et al. (2014) · Science · doi:10.1126/science.1246949 · Cited by 764 · see citing works

Common Regulatory Variation Impacts Gene Expression in a Cell Type–Dependent Manner

Dimas, A. S., Deutsch, S., Stranger, B. E., Montgomery, S. B., Borel, C., Attar, H., Ingle, C., Beazley, C., Arcelus, M. G., Sekowska, M., et al. (2009) · Science · doi:10.1126/science.1174148 · Cited by 729 · see citing works

Colocalization of GWAS and eQTL Signals Detects Target Genes

Hormozdiari, F., van de Bunt, M., Segrè, A. V., Li, X., Joo, J. W. J., Bilow, M., Sul, J. H., Sankararaman, S., Pasaniuc, B., & Eskin, E. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.10.003 · Cited by 697 · see citing works

A brief history of human disease genetics

Claussnitzer, M., Cho, J. H., Collins, R., Cox, N. J., Dermitzakis, E. T., Hurles, M. E., Kathiresan, S., Kenny, E. E., Lindgren, C. M., MacArthur, D. G., et al. (2020) · Nature · doi:10.1038/s41586-019-1879-7 · Cited by 697 · see citing works

Single-cell eQTL mapping identifies cell type–specific genetic control of autoimmune disease

Yazar, S., Alquicira-Hernandez, J., Wing, K., Senabouth, A., Gordon, M. G., Andersen, S., Lu, Q., Rowson, A., Taylor, T. R. P., Clarke, L., et al. (2022) · Science · doi:10.1126/science.abf3041 · Cited by 682 · see citing works

Genome-wide enhancer maps link risk variants to disease genes

Nasser, J., Bergman, D. T., Fulco, C. P., Guckelberger, P., Doughty, B. R., Patwardhan, T. A., Jones, T. R., Nguyen, T. H., Ulirsch, J. C., Lekschas, F., et al. (2021) · Nature · doi:10.1038/s41586-021-03446-x · Cited by 669 · see citing works

RNA splicing is a primary link between genetic variation and disease

Li, Y. I., van de Geijn, B., Raj, A., Knowles, D. A., Petti, A. A., Golan, D., Gilad, Y., & Pritchard, J. K. (2016) · Science · doi:10.1126/science.aad9417 · Cited by 660 · see citing works

A scored human protein–protein interaction network to catalyze genomic interpretation

Li, T., Wernersson, R., Hansen, R. B., Horn, H., Mercer, J., Slodkowicz, G., Workman, C. T., Rigina, O., Rapacki, K., Stærfeldt, H., et al. (2016) · Nature Methods · doi:10.1038/nmeth.4083 · Cited by 613 · see citing works

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

Gasperini, M., Hill, A. J., McFaline-Figueroa, J. L., Martin, B., Kim, S., Zhang, M. D., Jackson, D., Leith, A., Schreiber, J., Noble, W. S., et al. (2019) · Cell · doi:10.1016/j.cell.2018.11.029 · Cited by 613 · see citing works

An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci

Mountjoy, E., Schmidt, E. M., Carmona, M., Schwartzentruber, J., Peat, G., Miranda, A., Fumis, L., Hayhurst, J., Buniello, A., Karim, M. A., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00945-5 · Cited by 581 · see citing works

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

Battle, A., Mostafavi, S., Zhu, X., Potash, J. B., Weissman, M. M., McCormick, C., Haudenschild, C. D., Beckman, K. B., Shi, J., Mei, R., et al. (2014) · Genome Research · doi:10.1101/gr.155192.113 · Cited by 547 · see citing works

Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases

Gusev, A., Lee, S. H., Trynka, G., Finucane, H., Vilhjálmsson, B. J., Xu, H., Zang, C., Ripke, S., Bulik-Sullivan, B., Stahl, E., et al. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.10.004 · Cited by 544 · see citing works

High-Resolution Mapping of Expression-QTLs Yields Insight into Human Gene Regulation

Veyrieras, J.-B., Kudaravalli, S., Kim, S. Y., Dermitzakis, E. T., Gilad, Y., Stephens, M., & Pritchard, J. K. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000214 · Cited by 536 · see citing works

Cell type–specific genetic regulation of gene expression across human tissues

Kim-Hellmuth, S., Aguet, F., Oliva, M., Muñoz-Aguirre, M., Kasela, S., Wucher, V., Castel, S. E., Hamel, A. R., Viñuela, A., Roberts, A. L., et al. (2020) · Science · doi:10.1126/science.aaz8528 · Cited by 530 · see citing works

Linkage disequilibrium–dependent architecture of human complex traits shows action of negative selection

Gazal, S., Finucane, H. K., Furlotte, N. A., Loh, P.-R., Palamara, P. F., Liu, X., Schoech, A., Bulik-Sullivan, B., Neale, B. M., Gusev, A., et al. (2017) · Nature Genetics · doi:10.1038/ng.3954 · Cited by 525 · see citing works

Trans effects on gene expression can drive omnigenic inheritance

Liu, X., Li, Y. I., & Pritchard, J. K. (2019) · Cell · doi:10.1016/j.cell.2019.04.014 · Cited by 523 · see citing works

Approximately independent linkage disequilibrium blocks in human populations

Berisa, T., & Pickrell, J. K. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv546 · Cited by 491 · see citing works

Identification of context-dependent expression quantitative trait loci in whole blood

Zhernakova, D. V., Deelen, P., Vermaat, M., van Iterson, M., van Galen, M., Arindrarto, W., van 't Hof, P., Mei, H., van Dijk, F., Westra, H.-J., et al. (2017) · Nature Genetics · doi:10.1038/ng.3737 · Cited by 441 · see citing works

Nonlinear control of transcription through enhancer–promoter interactions

Zuin, J., Roth, G., Zhan, Y., Cramard, J., Redolfi, J., Piskadlo, E., Mach, P., Kryzhanovska, M., Tihanyi, G., Kohler, H., et al. (2022) · Nature · doi:10.1038/s41586-022-04570-y · Cited by 415 · see citing works

Signatures of negative selection in the genetic architecture of human complex traits

Zeng, J., de Vlaming, R., Wu, Y., Robinson, M. R., Lloyd-Jones, L. R., Yengo, L., Yap, C. X., Xue, A., Sidorenko, J., McRae, A. F., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0101-4 · Cited by 391 · see citing works

A population genetic interpretation of GWAS findings for human quantitative traits

Simons, Y. B., Bullaughey, K., Hudson, R. R., & Sella, G. (2018) · PLoS Biology · doi:10.1371/journal.pbio.2002985 · Cited by 363 · see citing works

Index and biological spectrum of human DNase I hypersensitive sites

Meuleman, W., Muratov, A., Rynes, E., Halow, J., Lee, K., Bates, D., Diegel, M., Dunn, D., Neri, F., Teodosiadis, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2559-3 · Cited by 331 · see citing works

Dynamic landscape of immune cell-specific gene regulation in immune-mediated diseases

Ota, M., Nagafuchi, Y., Hatano, H., Ishigaki, K., Terao, C., Takeshima, Y., Yanaoka, H., Kobayashi, S., Okubo, M., Shirai, H., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.056 · Cited by 322 · see citing works

Where Are the Disease-Associated eQTLs?

Umans, B. D., Battle, A., & Gilad, Y. (2021) · Trends in Genetics · doi:10.1016/j.tig.2020.08.009 · Cited by 296 · see citing works

Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation

Jerber, J., Seaton, D. D., Cuomo, A. S. E., Kumasaka, N., Haldane, J., Steer, J., Patel, M. J., Pearce, D., Andersson, M. H. L., Bonder, M. J., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00801-6 · Cited by 288 · see citing works

Landscape of stimulation-responsive chromatin across diverse human immune cells

Calderon, D., Nguyen, M. L. T., Mezger, A., Kathiria, A. S., Müller, F., Nguyen, V. Q., Lescano, N., Wu, B., Trombetta, J. J., Ribado, J. V., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0505-9 · Cited by 282 · see citing works

Quantifying genetic effects on disease mediated by assayed gene expression levels

Yao, D. W., O’Connor, L. J., Price, A. L., & Gusev, A. (2020) · Nature Genetics · doi:10.1038/s41588-020-0625-2 · Cited by 274 · see citing works

Extreme Polygenicity of Complex Traits Is Explained by Negative Selection

O'Connor, L. J., Schoech, A. P., Hormozdiari, F., Gazal, S., Patterson, N., & Price, A. L. (2019) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2019.07.003 · Cited by 268 · see citing works

Genetic Control of Expression and Splicing in Developing Human Brain Informs Disease Mechanisms

Walker, R. L., Ramaswami, G., Hartl, C., Mancuso, N., Gandal, M. J., de la Torre-Ubieta, L., Paşaniuc, B., Stein, J. L., & Geschwind, D. H. (2019) · Cell · doi:10.1016/j.cell.2019.09.021 · Cited by 259 · see citing works

Limited statistical evidence for shared genetic effects of eQTLs and autoimmune-disease-associated loci in three major immune-cell types

Chun, S., Casparino, A., Patsopoulos, N. A., Croteau-Chonka, D. C., Raby, B. A., De Jager, P. L., Sunyaev, S. R., & Cotsapas, C. (2017) · Nature Genetics · doi:10.1038/ng.3795 · Cited by 259 · see citing works

Dynamic genetic regulation of gene expression during cellular differentiation

Strober, B. J., Elorbany, R., Rhodes, K., Krishnan, N., Tayeb, K., Battle, A., & Gilad, Y. (2019) · Science · doi:10.1126/science.aaw0040 · Cited by 219 · see citing works

A Map of Transcriptional Heterogeneity and Regulatory Variation in Human Microglia

Young, A. M. H., Kumasaka, N., Calvert, F., Hammond, T. R., Knights, A., Panousis, N., Park, J. S., Schwartzentruber, J., Liu, J., Kundu, K., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00875-2 · Cited by 213 · see citing works

Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens

Morris, J. A., Caragine, C., Daniloski, Z., Domingo, J., Barry, T., Lu, L., Davis, K., Ziosi, M., Glinos, D. A., Hao, S., et al. (2023) · Science · doi:10.1126/science.adh7699 · Cited by 208 · see citing works

Multiple causal variants underlie genetic associations in humans

Abell, N. S., DeGorter, M. K., Gloudemans, M. J., Greenwald, E., Smith, K. S., He, Z., & Montgomery, S. B. (2022) · Science · doi:10.1126/science.abj5117 · Cited by 186 · see citing works

Integrative Modeling of eQTLs and Cis-Regulatory Elements Suggests Mechanisms Underlying Cell Type Specificity of eQTLs

Brown, C. D., Mangravite, L. M., & Engelhardt, B. E. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003649 · Cited by 173 · see citing works

An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability

Li, L., Huang, K.-L., Gao, Y., Cui, Y., Wang, G. T., Elrod, N. D., Li, Y., Chen, Y. E., Ji, P., Peng, F., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00864-5 · Cited by 172 · see citing works

Co-expression networks reveal the tissue-specific regulation of transcription and splicingPreprint

Saha, A., Kim, Y., Gewirtz, A. D., Jo, B., Gao, C., McDowell, I. C., Engelhardt, B. E., & Battle, A. J. (2017) · Genome Research · doi:10.1101/gr.216721.116 · Cited by 171 · see citing works

Quantification of frequency-dependent genetic architectures in 25 UK Biobank traits reveals action of negative selection

Schoech, A. P., Jordan, D. M., Loh, P.-R., Gazal, S., O’Connor, L. J., Balick, D. J., Palamara, P. F., Finucane, H. K., Sunyaev, S. R., & Price, A. L. (2019) · Nature Communications · doi:10.1038/s41467-019-08424-6 · Cited by 157 · see citing works

The missing link between genetic association and regulatory function

Connally, N. J., Nazeen, S., Lee, D., Shi, H., Stamatoyannopoulos, J. A., Chun, S., Cotsapas, C. J., Cassa, C. A., & Sunyaev, S. R. (2022) · eLife · doi:10.7554/elife.74970 · Cited by 144 · see citing works

Measuring intolerance to mutation in human genetics

Fuller, Z. L., Berg, J. J., Mostafavi, H., Sella, G., & Przeworski, M. (2019) · Nature Genetics · doi:10.1038/s41588-019-0383-1 · Cited by 139 · see citing works

Probabilistic colocalization of genetic variants from complex and molecular traits: promise and limitations

Hukku, A., Pividori, M., Luca, F., Piqué-Regi, R., Im, H. K., & Wen, X. (2020) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2020.11.012 · Cited by 128 · see citing works

Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci

Gutiérrez‐Arcelus, M., Baglaenko, Y., Arora, J., Hannes, S. K., Luo, Y., Amariuta, T., Teslovich, N. C., Rao, D. A., Ermann, J., Jonsson, A. H., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0579-4 · Cited by 115 · see citing works

Enhancer Domains Predict Gene Pathogenicity and Inform Gene Discovery in Complex Disease

Wang, X., & Goldstein, D. B. (2020) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2020.01.012 · Cited by 99 · see citing works

Mediation Analysis Demonstrates That Trans-eQTLs Are Often Explained by Cis-Mediation: A Genome-Wide Analysis among 1,800 South Asians

Pierce, B. L., Lin, T., Chen, L., Rahaman, R. O., Argos, M., Jasmine, F., Roy, S., Paul-Brutus, R., Westra, H.-J., Franke, L., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004818 · Cited by 92 · see citing works

Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts

Nair, S., Kim, D. S., Perricone, J., & Kundaje, A. B. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz352 · Cited by 69 · see citing works

The impact of cell type and context-dependent regulatory variants on human immune traits

Mu, Z., Wei, W., Fair, B. J., Miao, J., Zhu, P., & Li, Y. (2021) · Genome biology · doi:10.1186/s13059-021-02334-x · Cited by 67 · see citing works

Nonlinear control of transcription through enhancer-promoter interactions

Zuin, J., Roth, G., Zhan, Y., Cramard, J., Redolfi, J., Piskadlo, E., Mach, P., Kryzhanovska, M., Tihanyi, G., Kohler, H., et al. (2021) · doi:10.1101/2021.04.22.440891 · Cited by 67 · see citing works

Genes with High Network Connectivity Are Enriched for Disease Heritability

Kim, S. S., Dai, C. L., Hormozdiari, F., van de Geijn, B., Gazal, S., Park, Y., O’Connor, L. J., Amariuta, T., Loh, P., Finucane, H. K., et al. (2019) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2019.03.020 · Cited by 54 · see citing works

Brain-trait-associated variants impact cell-type-specific gene regulation during neurogenesis

Aygün, N., Elwell, A. L., Liang, D., Lafferty, M. J., Cheek, K. E., Courtney, K. P., Mory, J. T., Hadden-Ford, E., Krupa, O., de la Torre-Ubieta, L., et al. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.07.011 · Cited by 54 · see citing works

Evidence of reduced recombination rate in human regulatory domains

Liu, Y., Sarkar, A., Kheradpour, P., Ernst, J., & Kellis, M. (2017) · Genome biology · doi:10.1186/s13059-017-1308-x · Cited by 45 · see citing works

Relating pathogenic loss-of-function mutations in humans to their evolutionary fitness costs

Agarwal, I., Fuller, Z. L., Myers, S. R., & Przeworski, M. (2023) · eLife · doi:10.7554/elife.83172 · Cited by 40 · see citing works

SNP-to-gene linking strategies reveal contributions of enhancer-related and candidate master-regulator genes to autoimmune disease

Dey, K. K., Gazal, S., van de Geijn, B., Kim, S. S., Nasser, J., Engreitz, J., & Price, A. L. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100145 · Cited by 29 · see citing works

Genoppi is an open-source software for robust and standardized integration of proteomic and genetic data

Pintacuda, G., Lassen, F. H., Hsu, Y.-H. H., Kim, A., Martín, J. M., Małolepsza, E., Lim, J., Fornelos, N., Eggan, K. C., & Lage, K. (2021) · Nature Communications · doi:10.1038/s41467-021-22648-5 · Cited by 27 · see citing works

Leveraging gene co-regulation to identify gene sets enriched for disease heritability

Siewert, K. M., Kim, S. S., Yao, D. W., Shi, H., & Price, A. L. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2022.01.005 · Cited by 19 · see citing works

Partitioning gene-mediated disease heritability without eQTLs

Weiner, D. J., Gazal, S., Robinson, E., & O’Connor, L. J. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2022.01.010 · Cited by 17 · see citing works

Maintenance of Complex Trait Variation: Classic Theory and Modern Data

Koch, E. M., & Sunyaev, S. R. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.763363 · Cited by 17 · see citing works

eQTL mapping in fetal-like pancreatic progenitor cells reveals early developmental insights into diabetes risk

Nguyen, J., Arthur, T. D., Fujita, K., Salgado, B. M., Donovan, M. K. R., Aguiar, L. R., Arias, A. D., Benaglio, P., Berggren, W. T., Belmonte, J. C. I., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42560-4 · Cited by 16 · see citing works

eQTL mapping in fetal-like pancreatic progenitor cells reveals early developmental insights into diabetes riskPreprint

Nguyen, J., Arthur, T. D., Fujita, K., Salgado, B. M., Donovan, M. K. R., Matsui, H., Kim, J. H., D'Antonio-Chronowska, A., D'Antonio, M., & Frazer, K. (2023) · bioRxiv · doi:10.1101/2021.03.17.435846 · Cited by 5 · see citing works

Supplementary Data for 'Systematic differences in discovery of genetic effects on gene expression and complex traits'

Mostafavi, H. (2023) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.6618072 · Cited by 2 · see citing works

Code Repository for 'Systematic Differences in Discovery of Genetic Effects on Gene Expression and Complex Traits'

Hakha-Most (2023) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.8248812 · Cited by 1 · see citing works

Spatially resolved mapping of cells associated with human complex traits

Song, L., Chen, W., Hou, J., Guo, M., & Yang, J. (2025) · Nature · doi:10.1038/s41586-025-08757-x · Cited by 141 · see citing works

Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data

Yuan, Q., & Duren, Z. (2025) · Nature Biotechnology · doi:10.1038/s41587-024-02182-7 · Cited by 118 · see citing works

Cell-type-specific and disease-associated expression quantitative trait loci in the human lung

Natri, H. M., Azodi, C. B. D., Peter, L. M., Taylor, C. J., Chugh, S., Kendle, R., Chung, M.-I., Flaherty, D. K., Matlock, B. K., Calvi, C. L., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01702-0 · Cited by 117 · see citing works

Genetic regulation of gene expression across multiple tissues in chickens

Guan, D., Bai, Z., Zhu, X., Zhong, C., Hou, Y., Zhu, D., Li, H., Lan, F., Diao, S., Yao, Y., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02155-9 · Cited by 93 · see citing works

Bayesian estimation of gene constraint from an evolutionary model with gene features

Zeng, T., Spence, J. P., Mostafavi, H., & Pritchard, J. K. (2024) · Nature Genetics · doi:10.1038/s41588-024-01820-9 · Cited by 77 · see citing works

Sources of gene expression variation in a globally diverse human cohort

Taylor, D. J., Chhetri, S. B., Tassia, M. G., Biddanda, A., Yan, S. M., Wojcik, G. L., Battle, A. J., & McCoy, R. C. (2024) · Nature · doi:10.1038/s41586-024-07708-2 · Cited by 80 · see citing works

Massively parallel characterization of regulatory elements in the developing human cortex

Deng, C., Whalen, S., Steyert, M., Ziffra, R., Przytycki, P. F., Inoue, F., Pereira, D. A., Capauto, D., Norton, S., Vaccarino, F. M., et al. (2024) · Science · doi:10.1126/science.adh0559 · Cited by 72 · see citing works

Systemic lupus erythematosus genetics: insights into pathogenesis and implications for therapy

Ghodke‐Puranik, Y., Olferiev, M., & Crow, M. K. (2024) · Nature Reviews Rheumatology · doi:10.1038/s41584-024-01152-2 · Cited by 53 · see citing works

Multiomic QTL mapping reveals phenotypic complexity of GWAS loci and prioritizes putative causal variants

Arthur, T. D., Nguyen, J., Henson, B. A., D’Antonio‐Chronowska, A., Jaureguy, J., Silva, N., Arias, A. D., Benaglio, P., Berggren, W. T., Borja, V., et al. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.100775 · Cited by 39 · see citing works

Unlocking gene regulation with sequence-to-function models

Sasse, A., Chikina, M. D., & Mostafavi, S. (2024) · Nature Methods · doi:10.1038/s41592-024-02331-5 · Cited by 34 · see citing works

The contribution of genetic determinants of blood gene expression and splicing to molecular phenotypes and health outcomes

Tokolyi, A., Persyn, E., Nath, A. P., Burnham, K. L., Marten, J., Vanderstichele, T., Tardáguila, M., Stacey, D., Farr, B. W., Iyer, V., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02096-3 · Cited by 36 · see citing works

Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function

Loeb, G. B., Kathail, P., Shuai, R. W., Chung, R., Grona, R. J., Peddada, S., Sevi̇m, V., Federman, S., Mader, K., Chu, A. Y., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01904-6 · Cited by 32 · see citing works

Epigenomic insights into common human disease pathology

Bell, C. G. (2024) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-024-05206-2 · Cited by 32 · see citing works

Single-cell eQTL analysis identifies genetic variation underlying metabolic dysfunction-associated steatohepatitis

Hong, S. E., Mun, S. J., Lee, Y. J., Yoo, T., Suh, K., Kang, K. W., Son, M. J., Kim, W. K., & Choi, M. (2025) · Nature Genetics · doi:10.1038/s41588-025-02237-8 · Cited by 30 · see citing works

Mapping enhancer–gene regulatory interactions from single-cell data

Sheth, M. U., Qiu, W., Ma, X. R., Gschwind, A. R., Jagoda, E., Tan, A. S., Galante, J., Ray, J., Amgalan, D., Einarsson, H., et al. (2026) · Nature Genetics · doi:10.1038/s41588-026-02695-8 · Cited by 29 · see citing works

Deep-learning prediction of gene expression from personal genomes

Drusinsky, S., Whalen, S., & Pollard, K. S. (2026) · Genome biology · doi:10.1186/s13059-025-03926-7 · Cited by 29 · see citing works

A Novel Macrophage Subpopulation Conveys Increased Genetic Risk of Coronary Artery Disease

Jiang, J., Hiron, T. K., Agbaedeng, T. A., Malhotra, Y., Drydale, E., Bancroft, J. M., Ng, E., Reschen, M. E., Davison, L. J., & O’Callaghan, C. A. (2024) · Circulation Research · doi:10.1161/circresaha.123.324172 · Cited by 31 · see citing works

Specificity, length and luck drive gene rankings in association studies

Spence, J. P., Mostafavi, H., Ota, M., Milind, N., Gjorgjieva, T., Smith, C. J., Simons, Y. B., Sella, G., & Pritchard, J. K. (2025) · Nature · doi:10.1038/s41586-025-09703-7 · Cited by 43 · see citing works

Update on the genetics of allergic diseases

Lawson, L. P., Parameswaran, S., Panganiban, R. A. M., Constantine, G. M., Weirauch, M. T., & Kottyan, L. C. (2025) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2025.03.012 · Cited by 27 · see citing works

Decoding sequence determinants of gene expression in diverse cellular and disease states

Lal, A., Karollus, A., Gunsalus, L. M., Garfield, D., Nair, S., Tseng, A. M., Gordon, M. G., Blischak, J., Geijn, B. V. D., Bhangale, T., et al. (2026) · Nature Methods · doi:10.1038/s41592-026-03102-0 · Cited by 24 · see citing works

Fine-mapping causal tissues and genes at disease-associated loci

Strober, B. J., Zhang, M. J., Amariuta, T., Rossen, J., & Price, A. L. (2025) · Nature Genetics · doi:10.1038/s41588-024-01994-2 · Cited by 22 · see citing works

Adipose tissue eQTL meta-analysis highlights the contribution of allelic heterogeneity to gene expression regulation and cardiometabolic traits

Brotman, S. M., Moustafa, J. S. E.-S., Guan, L., Broadaway, K. A., Wang, D., Jackson, A., Welch, R., Currin, K. W., Tomlinson, M., Vadlamudi, S., et al. (2025) · Nature Genetics · doi:10.1038/s41588-024-01982-6 · Cited by 32 · see citing works

Estimating the impact of single-cell RNA sequencing of human tissues on drug target validationPreprint

Dann, E., Teeple, E. A., Elmentaite, R., Meyer, K. B., Gaglia, G., Nestle, F. O., Savova, V., de Rinaldis, E., & Teichmann, S. A. (2024) · medRxiv · doi:10.1101/2024.04.04.24305313 · Cited by 22 · see citing works

Macroevolutionary divergence of gene expression driven by selection on protein abundance

Cope, A. L., Schraiber, J. G., & Pennell, M. W. (2025) · Science · doi:10.1126/science.ads2658 · Cited by 20 · see citing works

Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq

Liu, W., Saelens, W., Rainer, P., Biočanin, M., Gardeux, V., Gralak, A. J., van Mierlo, G., Gebhart, A., Russeil, J., Liu, T., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02343-7 · Cited by 11 · see citing works

Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage

Naqvi, S., Kim, S., Tabatabaee, S., Pampari, A., Kundaje, A., Pritchard, J. K., & Wysocka, J. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.100780 · Cited by 18 · see citing works

eQTLs identify regulatory networks and drivers of variation in the individual response to sepsis

Burnham, K. L., Milind, N., Lee, W., Kwok, A. J., Cano-Gamez, K., Mi, Y., Geoghegan, C. G., Zhang, P., Addison, J., Galley, H. F., et al. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100587 · Cited by 21 · see citing works

Identifying genetic variants that influence the abundance of cell states in single-cell data

Rumker, L., Sakaue, S., Reshef, Y., Kang, J. B., Yazar, S., Alquicira-Hernández, J., Valencia, C., Lagattuta, K. A., Mah-Som, A. Y., Nathan, A., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01909-1 · Cited by 19 · see citing works

Genome-wide large-scale multi-trait analysis characterizes global patterns of pleiotropy and unique trait-specific variants

Qi, G., Chhetri, S. B., Ray, D., Dutta, D., Battle, A. J., Bhattacharjee, S., & Chatterjee, N. (2024) · Nature Communications · doi:10.1038/s41467-024-51075-5 · Cited by 20 · see citing works

Social-Science Genomics: Progress, Challenges, and Future Directions

Benjamin, D., Cesarini, D., Turley, P., & Young, A. S. (2024) · doi:10.3386/w32404 · Cited by 20 · see citing works

Genetic architecture of oral glucose-stimulated insulin release provides biological insights into type 2 diabetes aetiology

Madsen, A. L., Bonàs‐Guarch, S., Gheibi, S., Prasad, R. B., Vangipurapu, J., Ahuja, V., Cataldo, L. R., Dwivedi, O. P., Hatem, G., Atla, G., et al. (2024) · Nature Metabolism · doi:10.1038/s42255-024-01140-6 · Cited by 20 · see citing works

Cell type and dynamic state govern genetic regulation of gene expression in heterogeneous differentiating cultures

Popp, J. M., Rhodes, K., Jangi, R., Li, M., Barr, K., Tayeb, K., Battle, A. J., & Gilad, Y. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100701 · Cited by 19 · see citing works

Nonlinear transcriptional responses to gradual modulation of transcription factor dosage

Domingo, J., Minaeva, M., Morris, J. A., Ghatan, S., Ziosi, M., Sanjana, N. E., & Lappalainen, T. (2024) · doi:10.1101/2024.03.01.582837 · Cited by 18 · see citing works

Rhinovirus infection of airway epithelial cells uncovers the non-ciliated subset as a likely driver of genetic risk to childhood-onset asthma

Djeddi, S., Fernandez‐Salinas, D., Huang, G. X., Aguiar, V. R. C., Mohanty, C., Kendziorski, C. M., Gazal, S., Boyce, J. A., Ober, C., Gern, J. E., et al. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100636 · Cited by 19 · see citing works

Transcriptome‐Wide Association Studies (TWAS): Methodologies, Applications, and Challenges

Evans, P. D., Nagai, T. H., Konkashbaev, A. I., Zhou, D., Knapik, E. W., & Gamazon, E. R. (2024) · Current Protocols · doi:10.1002/cpz1.981 · Cited by 18 · see citing works

Osteoarthritis as an Enhanceropathy: Gene Regulation in Complex Musculoskeletal Disease

Roberts, J. B., & Rice, S. J. (2024) · Current Rheumatology Reports · doi:10.1007/s11926-024-01142-z · Cited by 17 · see citing works

Improved multiancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk

Lu, Z., Wang, X., Carr, M., Kim, A., Gazal, S., Mohammadi, P., Wu, L., Pirruccello, J. P., Kachuri, L., Gusev, A., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02262-7 · Cited by 24 · see citing works

Genome-Wide Methylation Analysis Reveals a KCNK3-Prominent Causal Cascade on Hypertension

Huang, D., Shang, W., Xu, M., Wan, Q., Zhang, J., Tang, X.-F., Shen, Y.-J., Wang, Y., & Yu, Y. (2024) · Circulation Research · doi:10.1161/circresaha.124.324455 · Cited by 12 · see citing works

Cross-cohort analysis of expression and splicing quantitative trait loci in TOPMed

Orchard, P., Blackwell, T. W., Kachuri, L., Castaldi, P. J., Cho, M. H., Christenson, S. A., Durda, P., Gabriel, S., Hersh, C. P., Huntsman, S., et al. (2026) · Science · doi:10.1126/science.adx2989 · Cited by 16 · see citing works

Extensive co-regulation of neighboring genes complicates the use of eQTLs in target gene prioritization

Tambets, R., Kolde, A., Kolberg, P., Love, M. I., & Alasoo, K. (2024) · Human Genetics and Genomics Advances · doi:10.1016/j.xhgg.2024.100348 · Cited by 16 · see citing works

Integration of functional genomics and statistical fine-mapping systematically characterizes adult-onset and childhood-onset asthma genetic associations

Zhong, X., Mitchell, R., Billstrand, C., Thompson, E. E., Sakabe, N. J., Aneas, I., Salamone, I. M., Gu, J., Sperling, A. I., Schoettler, N., et al. (2025) · Genome Medicine · doi:10.1186/s13073-025-01459-z · Cited by 16 · see citing works

Gene expression QTL mapping in stimulated iPSC-derived macrophages provides insights into common complex diseases

Panousis, N. I., Garwany, O. E., Knights, A. J., Rop, J., Kumasaka, N., Imaz, M., Vilarino, L. B., Tsingene, A., Tokolyi, A., Barnett, A., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-61670-9 · Cited by 16 · see citing works

Buffering and non-monotonic behavior of gene dosage response curves for human complex traitsPreprint

Milind, N., Smith, C. J., Zhu, H., Gjorgjieva, T., Spence, J. P., & Pritchard, J. K. (2024) · medRxiv · doi:10.1101/2024.11.11.24317065 · Cited by 15 · see citing works

Characterizing selection on complex traits through conditional frequency spectra

Patel, R. A., Weiß, C. L., Zhu, H., Mostafavi, H., Simons, Y. B., Spence, J. P., & Pritchard, J. K. (2024) · Genetics · doi:10.1093/genetics/iyae210 · Cited by 15 · see citing works

Variant-specific priors clarify colocalisation analysis

Pullin, J. M., & Wallace, C. (2025) · PLoS Genetics · doi:10.1371/journal.pgen.1011697 · Cited by 17 · see citing works

Systematic prioritization of functional variants and effector genes underlying colorectal cancer risk

Law, P., Studd, J. B., Smith, J. S., Vijayakrishnan, J., Harris, B. T., Mandelia, M., Mills, C., Dunlop, M. G., & Houlston, R. S. (2024) · Nature Genetics · doi:10.1038/s41588-024-01900-w · Cited by 16 · see citing works

An atlas of single-cell eQTLs dissects autoimmune disease genes and identifies novel drug classes for treatment

Wang, L., Markus, H., Chen, D., Chen, S., Zhang, F., Gao, S., Khunsriraksakul, C., Chen, F., Olsen, N. J., Foulke, G., et al. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.100820 · Cited by 13 · see citing works

Impact of disease-associated chromatin accessibility QTLs across immune cell types and contexts

Mu, Z., Randolph, H. E., Aguirre‐Gamboa, R., Ketter, E., Dumaine, A., Locher, V., Brandolino, C., Liu, X., Kaufmann, D., Barreiro, L. B., et al. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.101061 · Cited by 14 · see citing works

Biological insights into schizophrenia from ancestrally diverse populations

Bigdeli, T. B., Chatzinakos, C., Bendl, J. M., Barr, P. B., Venkatesh, S., Gorman, B. R., Clarence, T., Genovese, G., Iyegbe, C. O., Peterson, R. E., et al. (2026) · Nature · doi:10.1038/s41586-025-10000-6 · Cited by 21 · see citing works

Integrating leiomyoma genetics, epigenomics, and single-cell transcriptomics reveals causal genetic variants, genes, and cell types

Buyukcelebi, K., Duval, A. J., Abdula, F., Elkafas, H., Seker-Polat, F., & Adli, M. (2024) · Nature Communications · doi:10.1038/s41467-024-45382-0 · Cited by 17 · see citing works

Perspective on recent developments and challenges in regulatory and systems genomics

Zeitlinger, J., Roy, S., Ay, F., Mathelier, A., Medina-Rivera, A., Mahony, S., Sinha, S. K., & Ernst, J. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbaf106 · Cited by 14 · see citing works

Three open questions in polygenic score portability

Wang, J. Y., Lin, N., Zietz, M., Mares, J. A., Smith, O. S., Rathouz, P. J., & Harpak, A. (2026) · Nature Communications · doi:10.1038/s41467-026-68565-3 · Cited by 13 · see citing works

Specificity, length, and luck: How genes are prioritized by rare and common variant association studiesPreprint

Spence, J. P., Mostafavi, H., Ota, M., Milind, N., Gjorgjieva, T., Smith, C. J., Simons, Y. B., Sella, G., & Pritchard, J. K. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.12.628073 · Cited by 13 · see citing works

Integrating genetic data with biological insight: A practical guide to cis-Mendelian randomization

Karhunen, V., Woolf, B. A. R., Bhatnagar, P., Gill, D., & Burgess, S. (2026) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2026.03.011 · Cited by 13 · see citing works

Exponential family measurement error models for single-cell CRISPR screens

Barry, T., Roeder, K., & Katsevich, E. (2024) · Biostatistics · doi:10.1093/biostatistics/kxae010 · Cited by 12 · see citing works

Trans-eQTL hotspots shape complex traits by modulating cellular states

Renganaath, K., & Albert, F. W. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.100873 · Cited by 11 · see citing works

Realizing the promise of genome-wide association studies for effector gene prediction

Costanzo, M. C., Harris, L. W., Ji, Y., McMahon, A., Burtt, N. P., & Flannick, J. A. (2025) · Nature Genetics · doi:10.1038/s41588-025-02210-5 · Cited by 12 · see citing works

Allele frequency impacts the cross-ancestry portability of gene expression prediction in lymphoblastoid cell lines

Saitou, M., Dahl, A. W., Wang, Q., & Liu, X. (2024) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2024.10.009 · Cited by 12 · see citing works

An encyclopedia of human enhancer–gene regulatory interactions

Gschwind, A. R., Mualim, K. S., Karbalayghareh, A., Sheth, M. U., Dey, K. K., Jagoda, E., Nurtdinov, R., Xi, W., Tan, A. S., Galante, J., et al. (2026) · Nature · doi:10.1038/s41586-026-10781-4 · Cited by 148 · see citing works

Adipose tissue eQTL meta-analysis reveals the contribution of allelic heterogeneity to gene expression regulation and cardiometabolic traitsPreprint

Brotman, S. M., Moustafa, J. S. E.-S., Guan, L., Broadaway, K. A., Wang, D., Jackson, A., Welch, R., Currin, K. W., Tomlinson, M., Vadlamudi, S., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.26.563798 · Cited by 11 · see citing works

Efficient count-based models improve power and robustness for large-scale single-cell eQTL mappingPreprint

Zhang, Z., Kim, A., Suboc, N., Mancuso, N., & Gazal, S. (2025) · medRxiv · doi:10.1101/2025.01.18.25320755 · Cited by 12 · see citing works

Instrumental variable and colocalization analyses identify endotrophin and HTRA1 as potential therapeutic targets for coronary artery disease

Lee, P. C., Jung, I., Thussu, S., Patel, V., Wagoner, R., Burks, K. H., Amrute, J., Elenbaas, J. S., Kang, C. J., Young, E. P., et al. (2024) · iScience · doi:10.1016/j.isci.2024.110104 · Cited by 10 · see citing works

Predicting gene expression from histone marks using chromatin deep learning models depends on histone mark function, regulatory distance and cellular states

Murphy, A. E., Askarova, A., Lenhard, B., Skene, N. G., & Marzi, S. J. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkae1212 · Cited by 10 · see citing works

Eleven Grand Challenges for Inflammatory Bowel Disease Genetics and Genomics

Gibson, G. C., Rioux, J. D., Cho, J. H., Haritunians, T., Thoutam, A., Abreu, M. T., Brant, S. R., Kugathasan, S., McCauley, J. L., Silverberg, M. S., et al. (2024) · Inflammatory Bowel Diseases · doi:10.1093/ibd/izae269 · Cited by 9 · see citing works

Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms

Wenz, B. M., He, Y., Chen, N.-C., Pickrell, J. K., Li, J. H., Dudek, M. F., Li, T., Keener, R., Voight, B. F., Brown, C. D., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03538-1 · Cited by 10 · see citing works

Transcripts with high distal heritability mediate genetic effects on complex metabolic traits

Tyler, A. L., Mahoney, J. M., Keller, M. P., Baker, C. N., Gaca, M., Srivastava, A., Gyuricza, I. G., Braun, M., Rosenthal, N. A., Attie, A., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-61228-9 · Cited by 10 · see citing works

Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks

Ho, C., Dippel, M. A., McQuade, M. S., Nguyen, L. P., Mishra, A., Pribitzer, S., Hardy, S. R., Chandok, H., Chardon, F. M., McDiarmid, T. A., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02301-3 · Cited by 11 · see citing works

Higher eQTL power reveals signals that boost GWAS colocalization

Rosen, J. D., Broadaway, K. A., Brotman, S. M., Mohlke, K., & Love, M. I. (2025) · bioRxiv · doi:10.1016/j.ajhg.2026.02.009 · Cited by 15 · see citing works

FastGxC: Fast and Powerful Context-Specific eQTL Mapping in Bulk and Single-Cell DataPreprint

Krockenberger, L., Lu, A. C., Thompson, M., Liu, C., Gordon, M. G., Ramste, A., Carcamo‐Orive, I., Knowles, J. W., Dahl, A. W., Ye, C., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.06.17.448889 · Cited by 10 · see citing works

Genome‐Wide Aggregated Trans Effects Analysis Identifies Genes Encoding Immune Checkpoints as Core Genes for Rheumatoid Arthritis

Spiliopoulou, A., Iakovliev, A., Plant, D., Sutcliffe, M. A., Sharma, S., Çubuk, C., Lewis, M., Pitzalis, C., Barton, A. C., & McKeigue, P. (2025) · Arthritis & Rheumatology · doi:10.1002/art.43125 · Cited by 9 · see citing works

scMultiMap: Cell-type-specific mapping of enhancers and target genes from single-cell multimodal data

Su, C., Lee, D., Jin, P., & Zhang, J. (2025) · Nature Communications · doi:10.1038/s41467-025-59306-z · Cited by 8 · see citing works

Early establishment and life course stability of sex biases in the human brain transcriptome

Benoit‐Pilven, C., Asteljoki, J. V., Leinonen, J. T., Karjalainen, J. M., Daly, M. J., & Tukiainen, T. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.100890 · Cited by 9 · see citing works

A map of blood regulatory variation in South Africans enables GWAS interpretation

Castel, S. E., Tluway, F. D., Emde, A., Smyth, N., Karim, M. A., Sengupta, D., Gray, O. A., Hendershott, M. C., von Baeyer, S. L., Burke, E. E., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02223-0 · Cited by 9 · see citing works

Multi-domain rule-based phenotyping algorithms enable improved GWAS signal

Newbury, A., Elhussein, A., & Gürsoy, G. (2025) · npj Digital Medicine · doi:10.1038/s41746-025-01815-8 · Cited by 9 · see citing works

Beyond Mendel: a call to revisit the genotype–phenotype map through new experimental paradigms

Tautz, D., Pallares, L. F., Andersson, L., Barghi, N., Barton, N., Bay, R. A., Chan, Y. F., Hancock, A. M., Kaiser, T. S., Koenig, D., et al. (2026) · Genetics · doi:10.1093/genetics/iyag024 · Cited by 9 · see citing works

Cis -regulatory Landscape Size, Constraint, and Tissue Specificity Associate with Gene Function and Expression

Benton, M. L., Ruderfer, D. M., & Capra, J. A. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad126 · Cited by 9 · see citing works

Untangling the genetics of beta cell dysfunction and death in type 1 diabetes

Robertson, C. C., Elgamal, R. M., Henry-Kanarek, B. A., Arvan, P., Chen, S., Dhawan, S., Eizirik, D. L., Kaddis, J. S., Vahedi, G., Parker, S. C. J., et al. (2024) · Molecular Metabolism · doi:10.1016/j.molmet.2024.101973 · Cited by 9 · see citing works

Impact of disease-associated chromatin accessibility QTLs across immune cell types and contextsPreprint

Mu, Z., Randolph, H. E., Aguirre‐Gamboa, R., Ketter, E., Dumaine, A., Locher, V., Brandolino, C., Liu, X., Kaufmann, D., Barreiro, L. B., et al. (2024) · medRxiv · doi:10.1101/2024.12.05.24318552 · Cited by 9 · see citing works

Comparative Genomics and Epigenomics of Transcriptional Regulation

Zhou, H., Clark, E. L., Guan, D., Lagarrigue, S., Fang, L., Cheng, H., Tuggle, C. K., Kapoor, M., Wang, Y., Giuffra, E., et al. (2024) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-111523-102217 · Cited by 8 · see citing works

Using omics data and genome editing methods to decipher GWAS loci associated with coronary artery disease

Chignon, A., & Lettre, G. (2025) · Atherosclerosis · doi:10.1016/j.atherosclerosis.2024.118621 · Cited by 9 · see citing works

Characterization of non-coding variants associated with transcription-factor binding through ATAC-seq-defined footprint QTLs in liver

Dudek, M. F., Wenz, B. M., Brown, C. D., Voight, B. F., Almasy, L. A., & Grant, S. F. A. (2025) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2025.03.019 · Cited by 8 · see citing works

Mutation–selection–drift balance models of complex diseases

Berg, J. J., Li, X., Riall, K., Hayward, L. K., & Sella, G. (2025) · Genetics · doi:10.1093/genetics/iyaf220 · Cited by 9 · see citing works

Single-cell eQTL mapping reveals cell-type-specific genetic regulation in lung cancer

Fu, Y., Wang, Y., Jin, C., Zhang, C., Cai, J., Gong, L., Jin, C., Chen, G., Mou, Y., Zhang, C., et al. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.101100 · Cited by 8 · see citing works

Protein–protein interactions shape trans-regulatory impact of genetic variation on protein expression and complex traits

Li, J., Li, Y., & Liu, X. (2026) · Nature Genetics · doi:10.1038/s41588-025-02449-y · Cited by 9 · see citing works

Multi-INTACT: integrative analysis of the genome, transcriptome, and proteome identifies causal mechanisms of complex traits

Okamoto, J., Yin, X., Ryan, B., Chiou, J., Luca, F., Piqué-Regi, R., Im, H. K., Morrison, J., Burant, C., Fauman, E. B., et al. (2025) · Genome biology · doi:10.1186/s13059-025-03480-2 · Cited by 9 · see citing works

Exploring genetic and epigenetic markers for predicting or monitoring response to cognitive-behavioral therapy in obsessive-compulsive disorder: A systematic review

Chen, Y., Wang, P., & Li, Z. (2025) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2025.106192 · Cited by 8 · see citing works

Discovery of genomic and transcriptomic pleiotropy between kidney function and soluble receptor for advanced glycation end products using correlated meta‐analyses: The Long Life Family Study

Feitosa, M. F., Lin, S. J., Acharya, S., Thyagarajan, B., Wojczynski, M. K., Kuipers, A. L., Kulminski, A. M., Christensen, K., Zmuda, J. M., Brent, M. R., et al. (2024) · Aging Cell · doi:10.1111/acel.14261 · Cited by 8 · see citing works

Conditional frequency spectra as a tool for studying selection on complex traits in biobanksPreprint

Patel, R. A., Weiß, C. L., Zhu, H., Mostafavi, H., Simons, Y. B., Spence, J. P., & Pritchard, J. K. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.15.599126 · Cited by 8 · see citing works

Nonlinear transcriptional responses to gradual modulation of transcription factor dosagePreprint

Domingo, J., Minaeva, M., Morris, J. A., Ghatan, S., Ziosi, M., Sanjana, N. E., & Lappalainen, T. (2024) · eLife · doi:10.7554/elife.100555 · Cited by 8 · see citing works

Population-scale multiome immune cell atlas reveals complex disease driversPreprint

Kanai, M., Delorey, T. M., Honkanen, J. K., Rodosthenous, R. S., Juvila, J., Murphy, S. M., Teixeira-Soldano, I., Hwang, H. S., Karjalainen, J. M., Halonen, J., et al. (2025) · medRxiv · doi:10.1101/2025.11.25.25340489 · Cited by 8 · see citing works

Noncoding rare variant associations with blood traits in 166,740 UK Biobank genomes

Ribeiro, D. M., Hofmeister, R. J., Rubinacci, S., & Delaneau, O. (2025) · Nature Genetics · doi:10.1038/s41588-025-02288-x · Cited by 12 · see citing works

Cell-type-resolved genetic variation shapes inflammatory bowel disease risk

Alegbe, T., Harris, B. T., Fachal, L., Ramirez-Navarro, L., Tutert, M., Krzak, M., Ghouraba, M., Strickland, M., Ozols, M., Cohen, C. E., et al. (2026) · Nature · doi:10.1038/s41586-026-10627-z · Cited by 8 · see citing works

Expression quantitative trait loci (eQTL): from population genetics to precision medicine

Wong, Z. Q., Deng, L., Cengnata, A., Rahman, T. H. A., Ismail, A. M., Lim, R. L. H., Xu, S., & Hoh, B. (2025) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2025.02.003 · Cited by 7 · see citing works

Chromatin accessibility variation provides insights into missing regulation underlying immune-mediated diseasesPreprint

Jeong, R., & Bulyk, M. L. (2024) · eLife · doi:10.7554/elife.98289 · Cited by 7 · see citing works

Are complex traits underpinned by polygenic molecular traits? A reflection on the complexity of gene expression

Hajheidari, M., Sunyaev, S. R., & de Meaux, J. (2024) · Plant and Cell Physiology · doi:10.1093/pcp/pcae140 · Cited by 6 · see citing works

Exon-variant interplay and multi-modal evidence identify endocrine dysregulation in severe psychiatric disorders impacting excitatory neurons

Worf, K., Matosin, N., Gerstner, N., Fröhlich, A. S., Koller, A. C., Degenhardt, F., Thiele, H., Rietschel, M., Udawela, M., Scarr, E., et al. (2025) · Translational Psychiatry · doi:10.1038/s41398-025-03366-8 · Cited by 9 · see citing works

CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer’s disease

Green, N. F. O., Sutton, G. J., Pérez‐Burillo, J., Wang, J., Bagot, S., Danon, H. G., Walsh, K., Gokoolparsadh, A., Miles, S. A., Yang, G., et al. (2025) · Nature Neuroscience · doi:10.1038/s41593-025-02154-3 · Cited by 6 · see citing works

Large-scale mapping of environmental-genetic interactions illustrates the dynamic nature of cell-cycle and DNA repair regulation

Herken, B. W., Wong, G. T., Mäkiniemi, A., Lundberg, E. K., Norman, T. M., & Gilbert, L. A. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.01.025 · Cited by 6 · see citing works

Reimagining research papers as interactive and reliable AI agents

Miao, J.-C., Davis, J. R., Zhang, Y.-H., Pritchard, J. K., & Zou, J. (2026) · Nature · doi:10.1038/s41586-026-11044-y · Cited by 16 · see citing works

Chromatin accessibility variation provides insights into missing regulation underlying immune-mediated diseases

Jeong, R., & Bulyk, M. L. (2025) · eLife · doi:10.7554/elife.98289.3 · Cited by 9 · see citing works

Limited overlap of eQTLs and GWAS hits due to systematic differences in discoveryPreprint

Mostafavi, H., Spence, J. P., Naqvi, S., & Pritchard, J. K. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.07.491045 · Cited by 86 · see citing works

Advanced ALK-positive lung cancer with lorlatinib versus crizotinib in Asian patients with brain metastases

Hung, S. (2021) · European Journal of Hospital Pharmacy · doi:10.1136/ejhpharm-2021-003018

A meta-analysis of chromatin-associated loci provides insights into mechanistic interpretations of trait heritabilityPreprint

Dudek, M. F., Wenz, B. M., Voight, B. F., Almasy, L. A., & Grant, S. F. A. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.19.712994 · Cited by 1 · see citing works

From genome to function by studying eQTLs

Westra, H.-J., & Franke, L. (2014) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2014.04.024 · Cited by 166 · see citing works

Candidate Causal Regulatory Effects by Integration of Expression QTLs with Complex Trait Genetic Associations

Nica, A. C., Montgomery, S. B., Dimas, A. S., Stranger, B. E., Beazley, C., Barroso, I., & Dermitzakis, E. T. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000895 · Cited by 423 · see citing works