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The single-cell transcriptional landscape of mammalian organogenesis

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  1. Stefanie Kirchberger & Mohamed R. Shoeb & Daria Lazic & Andrea Wenninger-Weinzierl & Kristin Fischer & Lisa E. Shaw & Filomena Nogueira & Fikret Rifatbegovic & Eva Bozsaky & Ruth Ladenstein & Bernd Bo, 2024. "Comparative transcriptomics coupled to developmental grading via transgenic zebrafish reporter strains identifies conserved features in neutrophil maturation," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  2. Duy Pham & Xiao Tan & Brad Balderson & Jun Xu & Laura F. Grice & Sohye Yoon & Emily F. Willis & Minh Tran & Pui Yeng Lam & Arti Raghubar & Priyakshi Kalita-de Croft & Sunil Lakhani & Jana Vukovic & Ma, 2023. "Robust mapping of spatiotemporal trajectories and cell–cell interactions in healthy and diseased tissues," Nature Communications, Nature, vol. 14(1), pages 1-25, December.
  3. David G. Coffey & Francesco Maura & Edgar Gonzalez-Kozlova & J. Javier Diaz-Mejia & Ping Luo & Yong Zhang & Yuexin Xu & Edus H. Warren & Travis Dawson & Brian Lee & Hui Xie & Eric Smith & Amanda Ciard, 2023. "Immunophenotypic correlates of sustained MRD negativity in patients with multiple myeloma," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  4. Luc Francis & Daniel McCluskey & Clarisse Ganier & Treasa Jiang & Xinyi Du-Harpur & Jeyrroy Gabriel & Pawan Dhami & Yogesh Kamra & Sudha Visvanathan & Jonathan N. Barker & Catherine H. Smith & Frances, 2024. "Single-cell analysis of psoriasis resolution demonstrates an inflammatory fibroblast state targeted by IL-23 blockade," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  5. Kun Yin & Yiling Xu & Ye Guo & Zhong Zheng & Xinrui Lin & Meijuan Zhao & He Dong & Dianyi Liang & Zhi Zhu & Junhua Zheng & Shichao Lin & Jia Song & Chaoyong Yang, 2024. "Dyna-vivo-seq unveils cellular RNA dynamics during acute kidney injury via in vivo metabolic RNA labeling-based scRNA-seq," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  6. Mírian Romitti & Adrien Tourneur & Barbara Faria da Fonseca & Gilles Doumont & Pierre Gillotay & Xiao-Hui Liao & Sema Elif Eski & Gaetan Simaeys & Laura Chomette & Helene Lasolle & Olivier Monestier &, 2022. "Transplantable human thyroid organoids generated from embryonic stem cells to rescue hypothyroidism," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  7. Rong Xiao & Deshu Xu & Meili Zhang & Zhanghua Chen & Li Cheng & Songjie Du & Mingfei Lu & Tonghai Zhou & Ruoyan Li & Fan Bai & Yue Huang, 2024. "Aneuploid embryonic stem cells drive teratoma metastasis," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  8. Shicheng Sun & Ali Motazedian & Jacky Y. Li & Kevin Wijanarko & Joe Jiang Zhu & Kothila Tharmarajah & Kathleen A. Strumila & Anton Shkaruta & L. Rayburn Nigos & Jacqueline V. Schiesser & Yi Yu & Paul , 2024. "Efficient generation of human NOTCH ligand-expressing haemogenic endothelial cells as infrastructure for in vitro haematopoiesis and lymphopoiesis," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  9. Sivakamasundari Vijayakumar & Roberta Sala & Gugene Kang & Angela Chen & Michelle Ann Pablo & Abidemi Ismail Adebayo & Andrea Cipriano & Jonas L. Fowler & Danielle L. Gomes & Lay Teng Ang & Kyle M. Lo, 2023. "Monolayer platform to generate and purify primordial germ-like cells in vitro provides insights into human germline specification," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
  10. Umji Lee & Yadong Zhang & Yonglin Zhu & Allen Chilun Luo & Liyan Gong & Daniel M. Tremmel & Yunhye Kim & Victoria Sofia Villarreal & Xi Wang & Ruei-Zeng Lin & Miao Cui & Minglin Ma & Ke Yuan & Kai Wan, 2024. "Robust differentiation of human pluripotent stem cells into mural progenitor cells via transient activation of NKX3.1," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  11. Yueqi Wang & Simone Chiola & Guang Yang & Chad Russell & Celeste J. Armstrong & Yuanyuan Wu & Jay Spampanato & Paisley Tarboton & H. M. Arif Ullah & Nicolas U. Edgar & Amelia N. Chang & David A. Harmi, 2022. "Modeling human telencephalic development and autism-associated SHANK3 deficiency using organoids generated from single neural rosettes," Nature Communications, Nature, vol. 13(1), pages 1-25, December.
  12. Egle Kvedaraite & Magda Lourda & Natalia Mouratidou & Tim Düking & Avinash Padhi & Kirsten Moll & Paulo Czarnewski & Indranil Sinha & Ioanna Xagoraris & Efthymia Kokkinou & Anastasios Damdimopoulos & , 2024. "Intestinal stroma guides monocyte differentiation to macrophages through GM-CSF," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  13. Martin Arostegui & R. Wilder Scott & Kerstin Böse & T. Michael Underhill, 2022. "Cellular taxonomy of Hic1+ mesenchymal progenitor derivatives in the limb: from embryo to adult," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
  14. Kensuke Miyake & Junya Ito & Jun Nakabayashi & Shigeyuki Shichino & Kenji Ishiwata & Hajime Karasuyama, 2023. "Single cell transcriptomics clarifies the basophil differentiation trajectory and identifies pre-basophils upstream of mature basophils," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  15. Ting Zhong & Xinyu Li & Kang Lei & Rong Tang & Qiaolin Deng & Paul E Love & Zhiguang Zhou & Bin Zhao & Xia Li, 2024. "TGF-β-mediated crosstalk between TIGIT+ Tregs and CD226+CD8+ T cells in the progression and remission of type 1 diabetes," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  16. Ji-Hye Choi & Bok-Soon Lee & Jeon Yeob Jang & Yun Sang Lee & Hyo Jeong Kim & Jin Roh & Yoo Seob Shin & Hyun Goo Woo & Chul-Ho Kim, 2023. "Single-cell transcriptome profiling of the stepwise progression of head and neck cancer," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  17. Min Kyung Lee & Nasim Azizgolshani & Joshua A. Shapiro & Lananh N. Nguyen & Fred W. Kolling & George J. Zanazzi & Hildreth Robert Frost & Brock C. Christensen, 2024. "Identifying tumor type and cell type-specific gene expression alterations in pediatric central nervous system tumors," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  18. Ryan G. Lim & Osama Al-Dalahmah & Jie Wu & Maxwell P. Gold & Jack C. Reidling & Guomei Tang & Miriam Adam & David K. Dansu & Hye-Jin Park & Patrizia Casaccia & Ricardo Miramontes & Andrea M. Reyes-Ort, 2022. "Huntington disease oligodendrocyte maturation deficits revealed by single-nucleus RNAseq are rescued by thiamine-biotin supplementation," Nature Communications, Nature, vol. 13(1), pages 1-23, December.
  19. Florence M. Chardon & Troy A. McDiarmid & Nicholas F. Page & Riza M. Daza & Beth K. Martin & Silvia Domcke & Samuel G. Regalado & Jean-Benoît Lalanne & Diego Calderon & Xiaoyi Li & Lea M. Starita & St, 2024. "Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  20. Francisco X. Galdos & Sidra Xu & William R. Goodyer & Lauren Duan & Yuhsin V. Huang & Soah Lee & Han Zhu & Carissa Lee & Nicholas Wei & Daniel Lee & Sean M. Wu, 2022. "devCellPy is a machine learning-enabled pipeline for automated annotation of complex multilayered single-cell transcriptomic data," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
  21. Rong Li & Tianyuan Wang & Ryan M. Marquardt & John P. Lydon & San-Pin Wu & Francesco J. DeMayo, 2023. "TRIM28 modulates nuclear receptor signaling to regulate uterine function," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
  22. Sergei Grebenyuk & Abdel Rahman Abdel Fattah & Manoj Kumar & Burak Toprakhisar & Gregorius Rustandi & Anja Vananroye & Idris Salmon & Catherine Verfaillie & Mark Grillo & Adrian Ranga, 2023. "Large-scale perfused tissues via synthetic 3D soft microfluidics," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
  23. Brian DeVeale & Leqian Liu & Ryan Boileau & Jennifer Swindlehurst-Chan & Bryan Marsh & Jacob W. Freimer & Adam Abate & Robert Blelloch, 2022. "G1/S restriction point coordinates phasic gene expression and cell differentiation," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  24. Yasuaki Uehara & Yusuke Tanaka & Shuyang Zhao & Nikolaos M. Nikolaidis & Lori B. Pitstick & Huixing Wu & Jane J. Yu & Erik Zhang & Yoshihiro Hasegawa & John G. Noel & Jason C. Gardner & Elizabeth J. K, 2023. "Insights into pulmonary phosphate homeostasis and osteoclastogenesis emerge from the study of pulmonary alveolar microlithiasis," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  25. Andrea Flesken-Nikitin & Coulter Q. Ralston & Dah-Jiun Fu & Andrea J. Micheli & Daryl J. Phuong & Blaine A. Harlan & Christopher S. Ashe & Amanda P. Armstrong & David W. McKellar & Sangeeta Ghuwalewal, 2024. "Pre-ciliated tubal epithelial cells are prone to initiation of high-grade serous ovarian carcinoma," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  26. Hongchun Lin & Hui Peng & Yuxiang Sun & Meijun Si & Jiao Wu & Yanlin Wang & Sandhya S. Thomas & Zheng Sun & Zhaoyong Hu, 2023. "Reprogramming of cis-regulatory networks during skeletal muscle atrophy in male mice," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  27. Han-Ying Huang & Yan-Zhou Chen & Chuang Zhao & Xin-Nan Zheng & Kai Yu & Jia-Xing Yue & Huai-Qiang Ju & Yan-Xia Shi & Lin Tian, 2024. "Alternations in inflammatory macrophage niche drive phenotypic and functional plasticity of Kupffer cells," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  28. Nicola A. Kearns & Artemis Iatrou & Daniel J. Flood & Sashini Tissera & Zachary M. Mullaney & Jishu Xu & Chris Gaiteri & David A. Bennett & Yanling Wang, 2023. "Dissecting the human leptomeninges at single-cell resolution," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  29. Sophie G. Kellaway & Sandeep Potluri & Peter Keane & Helen J. Blair & Luke Ames & Alice Worker & Paulynn S. Chin & Anetta Ptasinska & Polina K. Derevyanko & Assunta Adamo & Daniel J. L. Coleman & Naee, 2024. "Leukemic stem cells activate lineage inappropriate signalling pathways to promote their growth," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
  30. Arthur S. Lee & Lauren J. Ayers & Michael Kosicki & Wai-Man Chan & Lydia N. Fozo & Brandon M. Pratt & Thomas E. Collins & Boxun Zhao & Matthew F. Rose & Alba Sanchis-Juan & Jack M. Fu & Isaac Wong & X, 2024. "A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders," Nature Communications, Nature, vol. 15(1), pages 1-26, December.
  31. J. McClatchy & R. Strogantsev & E. Wolfe & H. Y. Lin & M. Mohammadhosseini & B. A. Davis & C. Eden & D. Goldman & W. H. Fleming & P. Conley & G. Wu & L. Cimmino & H. Mohammed & A. Agarwal, 2023. "Clonal hematopoiesis related TET2 loss-of-function impedes IL1β-mediated epigenetic reprogramming in hematopoietic stem and progenitor cells," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  32. Sudha Sunil Rajderkar & Kitt Paraiso & Maria Luisa Amaral & Michael Kosicki & Laura E. Cook & Fabrice Darbellay & Cailyn H. Spurrell & Marco Osterwalder & Yiwen Zhu & Han Wu & Sarah Yasmeen Afzal & Ma, 2024. "Dynamic enhancer landscapes in human craniofacial development," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  33. Indranil Paul & Dante Bolzan & Ahmed Youssef & Keith A. Gagnon & Heather Hook & Gopal Karemore & Michael U. J. Oliphant & Weiwei Lin & Qian Liu & Sadhna Phanse & Carl White & Dzmitry Padhorny & Sergei, 2023. "Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
  34. Ci Fu & Xiang Zhang & Amanda O. Veri & Kali R. Iyer & Emma Lash & Alice Xue & Huijuan Yan & Nicole M. Revie & Cassandra Wong & Zhen-Yuan Lin & Elizabeth J. Polvi & Sean D. Liston & Benjamin VanderSlui, 2021. "Leveraging machine learning essentiality predictions and chemogenomic interactions to identify antifungal targets," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
  35. Junyi Chen & Xiaoying Wang & Anjun Ma & Qi-En Wang & Bingqiang Liu & Lang Li & Dong Xu & Qin Ma, 2022. "Deep transfer learning of cancer drug responses by integrating bulk and single-cell RNA-seq data," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  36. Ke Song & Xinyan Yang & Geng An & Xinyu Xia & Jiexiang Zhao & Xiaoheng Xu & Cong Wan & Tianyuan Liu & Yi Zheng & Shaofang Ren & Mei Wang & Gang Chang & Shane J. F. Cronin & Josef M. Penninger & Tao Ji, 2022. "Targeting APLN/APJ restores blood-testis barrier and improves spermatogenesis in murine and human diabetic models," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  37. Hussein A. Abbas & Dapeng Hao & Katarzyna Tomczak & Praveen Barrodia & Jin Seon Im & Patrick K. Reville & Zoe Alaniz & Wei Wang & Ruiping Wang & Feng Wang & Gheath Al-Atrash & Koichi Takahashi & Jing , 2021. "Single cell T cell landscape and T cell receptor repertoire profiling of AML in context of PD-1 blockade therapy," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
  38. Kotaro Shimizu & Junichi Kikuta & Yumi Ohta & Yutaka Uchida & Yu Miyamoto & Akito Morimoto & Shinya Yari & Takashi Sato & Takefumi Kamakura & Kazuo Oshima & Ryusuke Imai & Yu-Chen Liu & Daisuke Okuzak, 2023. "Single-cell transcriptomics of human cholesteatoma identifies an activin A-producing osteoclastogenic fibroblast subset inducing bone destruction," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  39. Marta Losa & Iros Barozzi & Marco Osterwalder & Viviana Hermosilla-Aguayo & Angela Morabito & Brandon H. Chacón & Peyman Zarrineh & Ausra Girdziusaite & Jean Denis Benazet & Jianjian Zhu & Susan Macke, 2023. "A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
  40. Monika Graf & Marta Interlandi & Natalia Moreno & Dörthe Holdhof & Carolin Göbel & Viktoria Melcher & Julius Mertins & Thomas K. Albert & Dennis Kastrati & Amelie Alfert & Till Holsten & Flavia de Far, 2022. "Single-cell transcriptomics identifies potential cells of origin of MYC rhabdoid tumors," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
  41. Young Hee Lee & Yu-Been Kim & Kyu Sik Kim & Mirae Jang & Ha Young Song & Sang-Ho Jung & Dong-Soo Ha & Joon Seok Park & Jaegeon Lee & Kyung Min Kim & Deok-Hyeon Cheon & Inhyeok Baek & Min-Gi Shin & Eun, 2023. "Lateral hypothalamic leptin receptor neurons drive hunger-gated food-seeking and consummatory behaviours in male mice," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  42. Yu Xia & Sierra Duca & Björn Perder & Friederike Dündar & Paul Zumbo & Miaoyan Qiu & Jun Yao & Yingxi Cao & Michael R. M. Harrison & Lior Zangi & Doron Betel & Jingli Cao, 2022. "Activation of a transient progenitor state in the epicardium is required for zebrafish heart regeneration," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  43. Maša Alečković & Simona Cristea & Carlos R. Gil Del Alcazar & Pengze Yan & Lina Ding & Ethan D. Krop & Nicholas W. Harper & Ernesto Rojas Jimenez & Donghao Lu & Anushree C. Gulvady & Pierre Foidart & , 2022. "Breast cancer prevention by short-term inhibition of TGFβ signaling," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
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  49. María-Jesús Lobón-Iglesias & Mamy Andrianteranagna & Zhi-Yan Han & Céline Chauvin & Julien Masliah-Planchon & Valeria Manriquez & Arnault Tauziede-Espariat & Sandrina Turczynski & Rachida Bouarich-Bou, 2023. "Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
  50. Seung-Hyun Jung & Byung-Hee Hwang & Sun Shin & Eun-Hye Park & Sin-Hee Park & Chan Woo Kim & Eunmin Kim & Eunho Choo & Ik Jun Choi & Filip K. Swirski & Kiyuk Chang & Yeun-Jun Chung, 2022. "Spatiotemporal dynamics of macrophage heterogeneity and a potential function of Trem2hi macrophages in infarcted hearts," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
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  54. Takayoshi Matsumura & Haruhito Totani & Yoshitaka Gunji & Masahiro Fukuda & Rui Yokomori & Jianwen Deng & Malini Rethnam & Chong Yang & Tze King Tan & Tadayoshi Karasawa & Kazuomi Kario & Masafumi Tak, 2022. "A Myb enhancer-guided analysis of basophil and mast cell differentiation," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
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  64. Bobby Ranjan & Wenjie Sun & Jinyu Park & Kunal Mishra & Florian Schmidt & Ronald Xie & Fatemeh Alipour & Vipul Singhal & Ignasius Joanito & Mohammad Amin Honardoost & Jacy Mei Yun Yong & Ee Tzun Koh &, 2021. "DUBStepR is a scalable correlation-based feature selection method for accurately clustering single-cell data," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
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  71. Andrea Lauria & Guohua Meng & Valentina Proserpio & Stefania Rapelli & Mara Maldotti & Isabelle Laurence Polignano & Francesca Anselmi & Danny Incarnato & Anna Krepelova & Daniela Donna & Chiara Levra, 2023. "DNMT3B supports meso-endoderm differentiation from mouse embryonic stem cells," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
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