Hu, Bo Lelek, Sara Spanjaard, Bastiaan El-Sammak, Hadil Simões, Mariana Guedes Mintcheva, Janita Aliee, Hananeh Schäfer, Ronny Meyer, Alexander M. Theis, Fabian
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Published in
Nature Genetics
Single-cell RNA sequencing and spatiotemporal analysis of the regenerating zebrafish heart identify transient proregenerative fibroblast-like cells that are derived from the epicardium and the endocardium. Wnt signalling regulates the endocardial fibroblast response.
Young, Alexander I Nehzati, Seyed Moeen Benonisdottir, Stefania Okbay, Aysu Jayashankar, Hariharan Lee, Chanwook Cesarini, David Benjamin, Daniel J Turley, Patrick Kong, Augustine
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Published in
Nature genetics
Effects estimated by genome-wide association studies (GWASs) include effects of alleles in an individual on that individual (direct genetic effects), indirect genetic effects (for example, effects of alleles in parents on offspring through the environment) and bias from confounding. Within-family genetic variation is random, enabling unbiased estim...
Lips, Esther H Kumar, Tapsi Megalios, Anargyros Visser, Lindy L Sheinman, Michael Fortunato, Angelo Shah, Vandna Hoogstraat, Marlous Sei, Emi Mallo, Diego
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Published in
Nature genetics
Ductal carcinoma in situ (DCIS) is the most common form of preinvasive breast cancer and, despite treatment, a small fraction (5-10%) of DCIS patients develop subsequent invasive disease. A fundamental biologic question is whether the invasive disease arises from tumor cells in the initial DCIS or represents new unrelated disease. To address this q...
Soskic, Blagoje Cano-Gamez, Eddie Smyth, Deborah J Ambridge, Kirsty Ke, Ziying Matte, Julie C Bossini-Castillo, Lara Kaplanis, Joanna Ramirez-Navarro, Lucia Lorenc, Anna
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Published in
Nature genetics
During activation, T cells undergo extensive gene expression changes that shape the properties of cells to exert their effector function. Understanding the regulation of this process could help explain how genetic variants predispose to immune diseases. Here, we mapped genetic effects on gene expression (expression quantitative trait loci (eQTLs)) ...
Howe, Laurence J Nivard, Michel G Morris, Tim T Hansen, Ailin F Rasheed, Humaira Cho, Yoonsu Chittoor, Geetha Ahlskog, Rafael Lind, Penelope A Palviainen, Teemu
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Published in
Nature genetics
Estimates from genome-wide association studies (GWAS) of unrelated individuals capture effects of inherited variation (direct effects), demography (population stratification, assortative mating) and relatives (indirect genetic effects). Family-based GWAS designs can control for demographic and indirect genetic effects, but large-scale family datase...
Fauser, Friedrich Vilarrasa-Blasi, Josep Onishi, Masayuki Ramundo, Silvia Patena, Weronika Millican, Matthew Osaki, Jacqueline Philp, Charlotte Nemeth, Matthew Salomé, Patrice A.
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Published in
Nature Genetics
Systematic phenotyping of 58,101 mutants of the model eukaryotic alga Chlamydomonas reinhardtii under 121 environmental and chemical stress conditions provides a large resource for characterizing gene function.
Danenberg, Esther Bardwell, Helen Zanotelli, Vito R. T. Provenzano, Elena Chin, Suet-Feung Rueda, Oscar M. Green, Andrew Rakha, Emad Aparicio, Samuel Ellis, Ian O.
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Published in
Nature Genetics
Imaging mass cytometry profiling of 693 breast tumors identified 10 recurrent tumor microenvironment spatial structures. These structures were enriched in different molecular subtypes and can be associated with genomic profiles and outcomes.
Ebler, Jana Ebert, Peter Clarke, Wayne E. Rausch, Tobias Audano, Peter A. Houwaart, Torsten Mao, Yafei Korbel, Jan O. Eichler, Evan E. Zody, Michael C.
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Published in
Nature Genetics
PanGenie is an alignment-free, k -mer-based tool that utilizes a haplotype-resolved pangenome reference to genotype a wide range of variants.
Bellenguez, Céline Küçükali, Fahri Jansen, Iris E Kleineidam, Luca Moreno-Grau, Sonia Amin, Najaf Naj, Adam C Campos-Martin, Rafael Grenier-Boley, Benjamin Andrade, Victor
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Published in
Nature genetics
Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 ris...
Horowitz, Julie E Kosmicki, Jack A Damask, Amy Sharma, Deepika Roberts, Genevieve H L Justice, Anne E Banerjee, Nilanjana Coignet, Marie V Yadav, Ashish Leader, Joseph B
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Published in
Nature genetics
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters human host cells via angiotensin-converting enzyme 2 (ACE2) and causes coronavirus disease 2019 (COVID-19). Here, through a genome-wide association study, we identify a variant (rs190509934, minor allele frequency 0.2-2%) that downregulates ACE2 expression by 37% (P = 2.7 × 10-8) a...