Claire E Otero, Sophia Petkova, Martin Ebermann, Husam Taher, Nessy John, Katja Hoffmann, Angel Davalos, Matilda J Moström, Roxanne M Gilbride, Courtney R Papen, Aaron Barber-Axthelm, Elizabeth A Scheef, Richard Barfield, Lesli M Sprehe, Savannah Kendall, Tabitha D Manuel, Teresa Beechwood, Linh Khanh Nguyen, Nathan H Vande Burgt, Cliburn Chan, Michael Denton, Zachary J Streblow, Daniel N Streblow, Alice F Tarantal, Scott G Hansen, Amitinder Kaur, Sallie Permar, Klaus Früh, Hartmut Hengel, Daniel Malouli, Philipp Kolb
{"title":"Rhesus Cytomegalovirus-encoded Fcγ-binding glycoproteins facilitate viral evasion from IgG-mediated humoral immunity.","authors":"Claire E Otero, Sophia Petkova, Martin Ebermann, Husam Taher, Nessy John, Katja Hoffmann, Angel Davalos, Matilda J Moström, Roxanne M Gilbride, Courtney R Papen, Aaron Barber-Axthelm, Elizabeth A Scheef, Richard Barfield, Lesli M Sprehe, Savannah Kendall, Tabitha D Manuel, Teresa Beechwood, Linh Khanh Nguyen, Nathan H Vande Burgt, Cliburn Chan, Michael Denton, Zachary J Streblow, Daniel N Streblow, Alice F Tarantal, Scott G Hansen, Amitinder Kaur, Sallie Permar, Klaus Früh, Hartmut Hengel, Daniel Malouli, Philipp Kolb","doi":"10.1038/s41467-025-56419-3","DOIUrl":"10.1038/s41467-025-56419-3","url":null,"abstract":"<p><p>Human cytomegalovirus (HCMV) encodes four viral Fc-gamma receptors (vFcγRs) that counteract antibody-mediated activation in vitro, but their role in infection and pathogenesis is unknown. To examine their in vivo function in an animal model evolutionarily closely related to humans, we identified and characterized Rh05, Rh152/151 and Rh173 as the complete set of vFcγRs encoded by rhesus CMV (RhCMV). Each one of these proteins displays functional similarities to their prospective HCMV orthologs with respect to antagonizing host FcγR activation in vitro. When RhCMV-naïve male rhesus macaques were infected with vFcγR-deleted RhCMV, peak plasma DNAemia levels and anti-RhCMV antibody responses were comparable to wildtype infections of both male and female animals. However, the duration of plasma DNAemia was significantly shortened in immunocompetent, but not in CD4 + T cell-depleted animals. Since vFcγRs were not required for superinfection of rhesus macaques, we conclude that these proteins can prolong lytic replication during primary infection by evading virus-specific adaptive immune responses, particularly antibodies.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"16 1","pages":"1200"},"PeriodicalIF":14.7,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066911","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Victorio Palacio, Anna Pancho, Angela Morabito, Jonas Malkmus, Zhisong He, Geoffrey Soussi, Rolf Zeller, Barbara Treutlein, Aimée Zuniga
{"title":"Single-cell profiling of penta- and tetradactyl mouse limb buds identifies mesenchymal progenitors controlling digit numbers and identities","authors":"Victorio Palacio, Anna Pancho, Angela Morabito, Jonas Malkmus, Zhisong He, Geoffrey Soussi, Rolf Zeller, Barbara Treutlein, Aimée Zuniga","doi":"10.1038/s41467-025-56221-1","DOIUrl":"https://doi.org/10.1038/s41467-025-56221-1","url":null,"abstract":"<p>The cellular interactions controlling digit numbers and identities have remained largely elusive. Here, we leverage the anterior digit and identity loss in <i>Grem1</i> tetradactyl mouse limb buds to identify early specified limb bud mesenchymal progenitor (LMP) populations whose size and distribution is governed by spatial modulation of BMP activity and SHH signaling. <u>D</u>istal-autopodial LMPs (dLMP) express signature genes required for autopod and digit development, and alterations affecting the dLMP population size prefigure the changes in digit numbers that characterize specific congenital malformations. A second, <u>p</u>eripheral LMP (pLMP) population is anteriorly biased and reduction/loss of its asymmetric distribution underlies the loss of middle digit asymmetry and identities in <i>Grem1</i> tetradactyl and pig limb buds. pLMPs depend on BMP activity, while dLMPs require GREM1-mediated BMP antagonism. Taken together, the spatial alterations in GREM1 antagonism in mouse mutant and evolutionarily diversified pig limb buds tunes BMP activity, which impacts dLMP and pLMP populations in an opposing manner.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"39 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143072837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mohammad Erfan Mowlaei, Chong Li, Oveis Jamialahmadi, Raquel Dias, Junjie Chen, Benyamin Jamialahmadi, Timothy Richard Rebbeck, Vincenzo Carnevale, Sudhir Kumar, Xinghua Shi
{"title":"STICI: Split-Transformer with integrated convolutions for genotype imputation","authors":"Mohammad Erfan Mowlaei, Chong Li, Oveis Jamialahmadi, Raquel Dias, Junjie Chen, Benyamin Jamialahmadi, Timothy Richard Rebbeck, Vincenzo Carnevale, Sudhir Kumar, Xinghua Shi","doi":"10.1038/s41467-025-56273-3","DOIUrl":"https://doi.org/10.1038/s41467-025-56273-3","url":null,"abstract":"<p>Despite advances in sequencing technologies, genome-scale datasets often contain missing bases and genomic segments, hindering downstream analyses. Genotype imputation addresses this issue and has been a cornerstone pre-processing step in genetic and genomic studies. Although various methods have been widely adopted for genotype imputation, it remains challenging to impute certain genomic regions and large structural variants. Here, we present a transformer-based framework, named STICI, for accurate genotype imputation. STICI models automatically learn genome-wide patterns of linkage disequilibrium, evidenced by much higher imputation accuracy in regions with highly linked variants. Our imputation results on the human 1000 Genomes Project and non-human genomes show that STICI can achieve high imputation accuracy comparable to the state-of-the-art genotype imputation methods, with the additional capability to impute multi-allelic variants and various types of genetic variants. STICI can be trained for any collection of genomes automatically using self-supervision. Moreover, STICI shows excellent performance without needing any special presuppositions about the underlying patterns in collections of non-human genomes, pointing to adaptability and applications of STICI to impute missing genotypes in any species.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"50 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143071899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Maria-Eleni Xypolita, Mubeen Goolam, Elizabeth K. Bikoff, Elizabeth J. Robertson, Arne W. Mould
{"title":"The zinc-finger transcription factor Blimp1/Prdm1 is required for uterine remodelling and repair in the mouse","authors":"Maria-Eleni Xypolita, Mubeen Goolam, Elizabeth K. Bikoff, Elizabeth J. Robertson, Arne W. Mould","doi":"10.1038/s41467-025-56511-8","DOIUrl":"https://doi.org/10.1038/s41467-025-56511-8","url":null,"abstract":"<p>The zinc finger transcription factor Blimp1/PRDM1 regulates gene expression in diverse cell types. Its activity controls the maternal decidual response at early post-implantation stages of development. The present experiments demonstrate surprisingly that Blimp1 activity in the uterus is required for tissue remodelling at sites of embryonic failure. Moreover Blimp1 mutant females are refractory to RU486 induced decidual shedding. RNA-seq together with immunostaining experiments strongly suggest that the failure to up-regulate expression of the matrix metalloprotease Mmp10 in combination with insufficient suppression of BMP signalling, likely explain Blimp1-dependent phenotypic changes. In the post-partum uterus Blimp1 together with Mmp10 are highly upregulated at sites of tissue repair following placental detachment. Conditional Blimp1 removal significantly impairs the re-epithelization process and severely impacts involution of the endometrium and luminal epithelium. Overall these results identify Blimp1 as a master regulator of uterine tissue remodelling and repair.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"63 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143071902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Samra Husremović, Oscar Gonzalez, Berit H Goodge, Lilia S Xie, Zhizhi Kong, Wanlin Zhang, Sae Hee Ryu, Stephanie M Ribet, Shannon S Fender, Karen C Bustillo, Chengyu Song, Jim Ciston, Takashi Taniguchi, Kenji Watanabe, Colin Ophus, Chris Jozwiak, Aaron Bostwick, Eli Rotenberg, D Kwabena Bediako
{"title":"Tailored topotactic chemistry unlocks heterostructures of magnetic intercalation compounds.","authors":"Samra Husremović, Oscar Gonzalez, Berit H Goodge, Lilia S Xie, Zhizhi Kong, Wanlin Zhang, Sae Hee Ryu, Stephanie M Ribet, Shannon S Fender, Karen C Bustillo, Chengyu Song, Jim Ciston, Takashi Taniguchi, Kenji Watanabe, Colin Ophus, Chris Jozwiak, Aaron Bostwick, Eli Rotenberg, D Kwabena Bediako","doi":"10.1038/s41467-025-56467-9","DOIUrl":"10.1038/s41467-025-56467-9","url":null,"abstract":"<p><p>The construction of thin film heterostructures has been a widely successful archetype for fabricating materials with emergent physical properties. This strategy is of particular importance for the design of multilayer magnetic architectures in which direct interfacial spin-spin interactions between magnetic phases in dissimilar layers lead to emergent and controllable magnetic behavior. However, crystallographic incommensurability and atomic-scale interfacial disorder can severely limit the types of materials amenable to this strategy, as well as the performance of these systems. Here, we demonstrate a method for synthesizing heterostructures comprising magnetic intercalation compounds of transition metal dichalcogenides (TMDs), through directed topotactic reaction of the TMD with a metal oxide. The mechanism of the intercalation reaction enables thermally initiated intercalation of the TMD from lithographically patterned oxide films, giving access to a family of multi-component magnetic architectures through the combination of deterministic van der Waals assembly and directed intercalation chemistry.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"16 1","pages":"1208"},"PeriodicalIF":14.7,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Iason-Zois Gazis, Henko de Stigter, Jochen Mohrmann, Karl Heger, Melanie Diaz, Benjamin Gillard, Matthias Baeye, Mario E. Veloso-Alarcón, Kaveh Purkiani, Matthias Haeckel, Annemiek Vink, Laurenz Thomsen, Jens Greinert
{"title":"Monitoring benthic plumes, sediment redeposition and seafloor imprints caused by deep-sea polymetallic nodule mining","authors":"Iason-Zois Gazis, Henko de Stigter, Jochen Mohrmann, Karl Heger, Melanie Diaz, Benjamin Gillard, Matthias Baeye, Mario E. Veloso-Alarcón, Kaveh Purkiani, Matthias Haeckel, Annemiek Vink, Laurenz Thomsen, Jens Greinert","doi":"10.1038/s41467-025-56311-0","DOIUrl":"https://doi.org/10.1038/s41467-025-56311-0","url":null,"abstract":"<p>A deep-sea (4500 m) trial of a pre-prototype polymetallic nodule collector with independent scientific monitoring revealed that a gravity current formed behind the collector channeled through steeper seafloor sections and traveled 500 m downslope. The prevailing bottom currents dominated sediment dispersion up to the end of the monitoring area at 4.5 km distance. The maximum suspended particle concentration recorded 50 m from mining lanes was up to four orders of magnitude higher than ambient values but decreased rapidly with increasing time, distance, and altitude. Most of the plume remained close to the seafloor, with the highest concentrations at 1 m monitoring altitude and reaching background concentrations at 50 m. Rapid particle flocculation was followed by fast and substantial sediment redeposition. A mm-scale photogrammetric seafloor reconstruction allowed quantitative estimates of the thickness of redeposited sediment next to mining lanes of ≈ 3 cm and a minimum erosional depth of 5 cm.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"2 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143072839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Selim Terhzaz, David Kerrigan, Floriane Almire, Agnieszka M. Szemiel, Joseph Hughes, Jean-Philippe Parvy, Massimo Palmarini, Alain Kohl, Xiaohong Shi, Emilie Pondeville
{"title":"NSm is a critical determinant for bunyavirus transmission between vertebrate and mosquito hosts","authors":"Selim Terhzaz, David Kerrigan, Floriane Almire, Agnieszka M. Szemiel, Joseph Hughes, Jean-Philippe Parvy, Massimo Palmarini, Alain Kohl, Xiaohong Shi, Emilie Pondeville","doi":"10.1038/s41467-024-54809-7","DOIUrl":"https://doi.org/10.1038/s41467-024-54809-7","url":null,"abstract":"<p><i>Bunyavirales</i> is a very large order including viruses infecting a variety of taxonomic groups such as arthropods, vertebrates, plants, and protozoa. Some bunyaviruses are transmitted between vertebrate hosts by blood-sucking arthropods and cause major diseases in humans and animals. It is not understood why only some bunyaviruses have evolved the capacity to be transmitted by arthropod vectors. Here we show that only vector-borne bunyaviruses express a non-structural protein, NSm, whose function has so far remained largely elusive. Using as experimental system Bunyamwera virus (BUNV) and its invertebrate host, <i>Aedes aegypti</i>, we show that NSm is dispensable for viral replication in mosquito cells in vitro but is absolutely required for successful infection in the female mosquito following a blood meal. More specifically, NSm is required for cell-to-cell spread and egress from the mosquito midgut, a known barrier to viral infection. Notably, the requirement for NSm is specific to the midgut; bypassing this barrier by experimental intrathoracic infection of the mosquito eliminates the necessity of NSm for virus spread in other tissues, including the salivary glands. Overall, we unveiled a key evolutionary process that allows the transmission of vector-borne bunyaviruses between arthropod and vertebrate hosts.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"54 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143071872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mengzhu Sun, Laure Garnier, Romane Chevalier, Martin Roumain, Chen Wang, Julien Angelillo, Julien Montorfani, Robert Pick, Dale Brighouse, Nadine Fournier, David Tarussio, Stéphanie Tissot, Jean-Marc Lobaccaro, Tatiana V. Petrova, Camilla Jandus, Daniel E. Speiser, Manfred Kopf, Caroline Pot, Christoph Scheiermann, Krisztian Homicsko, Giulio G. Muccioli, Abhishek D. Garg, Stéphanie Hugues
{"title":"Lymphatic-derived oxysterols promote anti-tumor immunity and response to immunotherapy in melanoma","authors":"Mengzhu Sun, Laure Garnier, Romane Chevalier, Martin Roumain, Chen Wang, Julien Angelillo, Julien Montorfani, Robert Pick, Dale Brighouse, Nadine Fournier, David Tarussio, Stéphanie Tissot, Jean-Marc Lobaccaro, Tatiana V. Petrova, Camilla Jandus, Daniel E. Speiser, Manfred Kopf, Caroline Pot, Christoph Scheiermann, Krisztian Homicsko, Giulio G. Muccioli, Abhishek D. Garg, Stéphanie Hugues","doi":"10.1038/s41467-025-55969-w","DOIUrl":"https://doi.org/10.1038/s41467-025-55969-w","url":null,"abstract":"<p>In melanoma, lymphangiogenesis correlates with metastasis and poor prognosis and promotes immunosuppression. However, it also potentiates immunotherapy by supporting immune cell trafficking. We show in a lymphangiogenic murine melanoma that lymphatic endothelial cells (LECs) upregulate the enzyme Ch25h, which catalyzes the formation of 25-hydroxycholesterol (25-HC) from cholesterol and plays important roles in lipid metabolism, gene regulation, and immune activation. We identify a role for LECs as a source of extracellular 25-HC in tumors inhibiting PPAR-γ in intra-tumoral macrophages and monocytes, preventing their immunosuppressive function and instead promoting their conversion into proinflammatory myeloid cells that support effector T cell functions. In human melanoma, LECs also upregulate Ch25h, and its expression correlates with the lymphatic vessel signature, infiltration of pro-inflammatory macrophages, better patient survival, and better response to immunotherapy. We identify here in mechanistic detail an important LEC function that supports anti-tumor immunity, which can be therapeutically exploited in combination with immunotherapy.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"60 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143071900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Luozhijie Jin, Zijian Du, Le Shu, Yan Cen, Yuanfeng Xu, Yongfeng Mei, Hao Zhang
{"title":"Transformer-generated atomic embeddings to enhance prediction accuracy of crystal properties with machine learning.","authors":"Luozhijie Jin, Zijian Du, Le Shu, Yan Cen, Yuanfeng Xu, Yongfeng Mei, Hao Zhang","doi":"10.1038/s41467-025-56481-x","DOIUrl":"10.1038/s41467-025-56481-x","url":null,"abstract":"<p><p>Accelerating the discovery of novel crystal materials by machine learning is crucial for advancing various technologies from clean energy to information processing. The machine-learning models for prediction of materials properties require embedding atomic information, while traditional methods have limited effectiveness in enhancing prediction accuracy. Here, we proposed an atomic embedding strategy called universal atomic embeddings (UAEs) for their broad applicability as atomic fingerprints, and generated the UAE tensors based on the proposed CrystalTransformer model. By performing experiments on widely-used materials database, our CrystalTransformer-based UAEs (ct-UAEs) are shown to accurately capture complex atomic features, leading to a 14% improvement in prediction accuracy on CGCNN and 18% on ALIGNN when using formation energies as the target, based on the Materials Project database. We also demonstrated the good transferability of ct-UAEs across various databases. Based on the clustering analysis for multi-task ct-UAEs, the elements in the periodic table can be categorized with reasonable connections between atomic features and targeted crystal properties. After applying ct-UAEs to predict formation energy in hybrid perovskites database, we realized an improvement in accuracy, with a 34% boost in MEGNET and 16% in CGCNN, showcasing their potential as atomic fingerprints to address the data scarcity challenges.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"16 1","pages":"1210"},"PeriodicalIF":14.7,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yunfan Li, Hancong Li, Yijie Lin, Dan Zhang, Dezhong Peng, Xiting Liu, Jie Xie, Peng Hu, Lu Chen, Han Luo, Xi Peng
{"title":"MetaQ: fast, scalable and accurate metacell inference via single-cell quantization.","authors":"Yunfan Li, Hancong Li, Yijie Lin, Dan Zhang, Dezhong Peng, Xiting Liu, Jie Xie, Peng Hu, Lu Chen, Han Luo, Xi Peng","doi":"10.1038/s41467-025-56424-6","DOIUrl":"10.1038/s41467-025-56424-6","url":null,"abstract":"<p><p>To overcome the computational barriers of analyzing large-scale single-cell sequencing data, we introduce MetaQ, a metacell algorithm that scales to arbitrarily large datasets with linear runtime and constant memory usage. Inspired by cellular development, MetaQ conceptualizes each metacell as a collective ancestor of biologically similar cells. By quantizing cells into a discrete codebook, where each entry represents a metacell capable of reconstructing the original cells it quantizes, MetaQ identifies homogeneous cell subsets for efficient and accurate metacell inference. This approach reduces computational complexity from exponential to linear while maintaining or surpassing the performance of existing metacell algorithms. Extensive experiments demonstrate that MetaQ excels in downstream tasks such as cell type annotation, developmental trajectory inference, batch integration, and differential expression analysis. Thanks to its superior efficiency and effectiveness, MetaQ makes analyzing datasets with millions of cells practical, offering a powerful solution for single-cell studies in the era of high-throughput profiling.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"16 1","pages":"1205"},"PeriodicalIF":14.7,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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