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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. Parashar Dhapola & Johan Rodhe & Rasmus Olofzon & Thomas Bonald & Eva Erlandsson & Shamit Soneji & Göran Karlsson, 2022. "Scarf enables a highly memory-efficient analysis of large-scale single-cell genomics data," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  3. Jolene S. Ranek & Wayne Stallaert & J. Justin Milner & Margaret Redick & Samuel C. Wolff & Adriana S. Beltran & Natalie Stanley & Jeremy E. Purvis, 2024. "DELVE: feature selection for preserving biological trajectories in single-cell data," Nature Communications, Nature, vol. 15(1), pages 1-26, December.
  4. 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.
  5. 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.
  6. Nancy Yanzhe Li & Weiruo Zhang & Daniel Haensel & Anna R. Jussila & Cory Pan & Sadhana Gaddam & Sylvia K. Plevritis & Anthony E. Oro, 2024. "Basal-to-inflammatory transition and tumor resistance via crosstalk with a pro-inflammatory stromal niche," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
  7. Jing-Ping Lin & Hannah M. Kelly & Yeajin Song & Riki Kawaguchi & Daniel H. Geschwind & Steven Jacobson & Daniel S. Reich, 2022. "Transcriptomic architecture of nuclei in the marmoset CNS," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
  8. 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.
  9. 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.
  10. Karina F. Rodriguez & Paula R. Brown & Ciro M. Amato & Barbara Nicol & Chia-Feng Liu & Xin Xu & Humphrey Hung-Chang Yao, 2022. "Somatic cell fate maintenance in mouse fetal testes via autocrine/paracrine action of AMH and activin B," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  11. Alexia Borelli & Jérémy C. Santamaria & Cloé Zamit & Cécile Apert & Jessica Chevallier & Philippe Pierre & Rafael J. Argüello & Lionel Spinelli & Magali Irla, 2024. "Lymphotoxin limits Foxp3+ regulatory T cell development from Foxp3lo precursors via IL-4 signaling," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  12. Ran Wang & Xianfa Yang & Jiehui Chen & Lin Zhang & Jonathan A. Griffiths & Guizhong Cui & Yingying Chen & Yun Qian & Guangdun Peng & Jinsong Li & Liantang Wang & John C. Marioni & Patrick P. L. Tam & , 2023. "Time space and single-cell resolved tissue lineage trajectories and laterality of body plan at gastrulation," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
  13. 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.
  14. Joachim Jonghe & Tomasz S. Kaminski & David B. Morse & Marcin Tabaka & Anna L. Ellermann & Timo N. Kohler & Gianluca Amadei & Charlotte E. Handford & Gregory M. Findlay & Magdalena Zernicka-Goetz & Sa, 2023. "spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
  15. Hugo Croizer & Rana Mhaidly & Yann Kieffer & Geraldine Gentric & Lounes Djerroudi & Renaud Leclere & Floriane Pelon & Catherine Robley & Mylene Bohec & Arnaud Meng & Didier Meseure & Emanuela Romano &, 2024. "Deciphering the spatial landscape and plasticity of immunosuppressive fibroblasts in breast cancer," Nature Communications, Nature, vol. 15(1), pages 1-28, December.
  16. Chien-Wen Chen & Bo-Jhih Guan & Mohammed R. Alzahrani & Zhaofeng Gao & Long Gao & Syrena Bracey & Jing Wu & Cheikh A. Mbow & Raul Jobava & Leena Haataja & Ajay H. Zalavadia & Ashleigh E. Schaffer & Hu, 2022. "Adaptation to chronic ER stress enforces pancreatic β-cell plasticity," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  17. Yang Liu & Shuang-Yan Ye & Shuai He & Dong-Mei Chi & Xiu-Zhi Wang & Yue-Feng Wen & Dong Ma & Run-Cong Nie & Pu Xiang & You Zhou & Zhao-Hui Ruan & Rou-Jun Peng & Chun-Ling Luo & Pan-Pan Wei & Guo-Wang , 2024. "Single-cell and spatial transcriptome analyses reveal tertiary lymphoid structures linked to tumour progression and immunotherapy response in nasopharyngeal carcinoma," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
  18. 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.
  19. 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.
  20. Qian-Yue Zhang & Xiao-Ping Ye & Zheng Zhou & Chen-Fang Zhu & Rui Li & Ya Fang & Rui-Jia Zhang & Lu Li & Wei Liu & Zheng Wang & Shi-Yang Song & Sang-Yu Lu & Shuang-Xia Zhao & Jian-Nan Lin & Huai-Dong S, 2022. "Lymphocyte infiltration and thyrocyte destruction are driven by stromal and immune cell components in Hashimoto’s thyroiditis," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  21. Wenpin Hou & Zhicheng Ji & Zeyu Chen & E. John Wherry & Stephanie C. Hicks & Hongkai Ji, 2023. "A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
  22. 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.
  23. Z. L. Liu & X. Y. Meng & R. J. Bao & M. Y. Shen & J. J. Sun & W. D. Chen & F. Liu & Y. He, 2024. "Single cell deciphering of progression trajectories of the tumor ecosystem in head and neck cancer," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  24. 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.
  25. Joyce B. Kang & Aparna Nathan & Kathryn Weinand & Fan Zhang & Nghia Millard & Laurie Rumker & D. Branch Moody & Ilya Korsunsky & Soumya Raychaudhuri, 2021. "Efficient and precise single-cell reference atlas mapping with Symphony," Nature Communications, Nature, vol. 12(1), pages 1-21, December.
  26. 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.
  27. Won Kyung Kim & Alyssa J. Buckley & Dong-Hoon Lee & Alex Hiroto & Christian H. Nenninger & Adam W. Olson & Jinhui Wang & Zhuo Li & Rajeev Vikram & Yao Mawulikplimi Adzavon & Tak-yu Yau & Yigang Bao & , 2024. "Androgen deprivation induces double-null prostate cancer via aberrant nuclear export and ribosomal biogenesis through HGF and Wnt activation," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  28. 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.
  29. Mohammad Faujul Kabir & Adam L. Karami & Ricardo Cruz-Acuña & Alena Klochkova & Reshu Saxena & Anbin Mu & Mary Grace Murray & Jasmine Cruz & Annie D. Fuller & Margarette H. Clevenger & Kumaraswamy Nai, 2022. "Single cell transcriptomic analysis reveals cellular diversity of murine esophageal epithelium," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  30. 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.
  31. 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.
  32. Hyeon-Jin Kim & Greg Booth & Lauren Saunders & Sanjay Srivatsan & José L. McFaline-Figueroa & Cole Trapnell, 2022. "Nuclear oligo hashing improves differential analysis of single-cell RNA-seq," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
  33. 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.
  34. 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.
  35. 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.
  36. P. Bielefeld & A. Martirosyan & S. Martín-Suárez & A. Apresyan & G. F. Meerhoff & F. Pestana & S. Poovathingal & N. Reijner & W. Koning & R. A. Clement & I. Veen & E. M. Toledo & O. Polzer & I. Durá &, 2024. "Traumatic brain injury promotes neurogenesis at the cost of astrogliogenesis in the adult hippocampus of male mice," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
  37. 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.
  38. 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.
  39. 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.
  40. Rebecca Sebastian & Kang Jin & Narciso Pavon & Ruby Bansal & Andrew Potter & Yoonjae Song & Juliana Babu & Rafael Gabriel & Yubing Sun & Bruce Aronow & ChangHui Pak, 2023. "Schizophrenia-associated NRXN1 deletions induce developmental-timing- and cell-type-specific vulnerabilities in human brain organoids," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  41. Fangfang Qu & Wenjia Li & Jian Xu & Ruifang Zhang & Jincan Ke & Xiaodie Ren & Xiaogao Meng & Lexin Qin & Jingna Zhang & Fangru Lu & Xin Zhou & Xi Luo & Zhen Zhang & Minhan Wang & Guangming Wu & Duanqi, 2023. "Three-dimensional molecular architecture of mouse organogenesis," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
  42. Anissa Fries & Fanny Saidoune & François Kuonen & Isabelle Dupanloup & Nadine Fournier & Ana Cristina Guerra de Souza & Muzlifah Haniffa & Feiyang Ma & Johann E. Gudjonsson & Lennart Roesner & Yang Li, 2023. "Differentiation of IL-26+ TH17 intermediates into IL-17A producers via epithelial crosstalk in psoriasis," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  43. 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.
  44. 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.
  45. 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.
  46. 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.
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  49. 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.
  50. 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.
  51. Suijuan Zhong & Mengdi Wang & Luwei Huang & Youqiao Chen & Yuxin Ge & Jiyao Zhang & Yingchao Shi & Hao Dong & Xin Zhou & Bosong Wang & Tian Lu & Xiaoxi Jing & Yufeng Lu & Junjing Zhang & Xiaoqun Wang , 2023. "Single-cell epigenomics and spatiotemporal transcriptomics reveal human cerebellar development," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  52. Francesco Panariello & Onelia Gagliano & Camilla Luni & Antonio Grimaldi & Silvia Angiolillo & Wei Qin & Anna Manfredi & Patrizia Annunziata & Shaked Slovin & Lorenzo Vaccaro & Sara Riccardo & Valenti, 2023. "Cellular population dynamics shape the route to human pluripotency," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
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  54. Greg Holmes & Ana S. Gonzalez-Reiche & Madrikha Saturne & Susan M. Motch Perrine & Xianxiao Zhou & Ana C. Borges & Bhavana Shewale & Joan T. Richtsmeier & Bin Zhang & Harm Bakel & Ethylin Wang Jabs, 2021. "Single-cell analysis identifies a key role for Hhip in murine coronal suture development," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
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  60. Zhen Zuo & Xuesen Cheng & Salma Ferdous & Jianming Shao & Jin Li & Yourong Bao & Jean Li & Jiaxiong Lu & Antonio Jacobo Lopez & Juliette Wohlschlegel & Aric Prieve & Mervyn G. Thomas & Thomas A. Reh &, 2024. "Single cell dual-omic atlas of the human developing retina," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
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  65. Seongryong Kim & Ji Hyang Jeon & Myeonghwan Kim & Yeji Lee & Yun-Ho Hwang & Myungsun Park & C. Han Li & Taeyoung Lee & Jung-Ah Lee & You-Me Kim & Dokeun Kim & Hyukjin Lee & You-Jin Kim & V. Narry Kim , 2024. "Innate immune responses against mRNA vaccine promote cellular immunity through IFN-β at the injection site," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  66. Zachary A. Hing & Janek S. Walker & Ethan C. Whipp & Lindsey Brinton & Matthew Cannon & Pu Zhang & Steven Sher & Casey B. Cempre & Fiona Brown & Porsha L. Smith & Claudio Agostinelli & Stefano A. Pile, 2023. "Dysregulation of PRMT5 in chronic lymphocytic leukemia promotes progression with high risk of Richter’s transformation," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
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  72. 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.
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