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Trajectory-based differential expression analysis for single-cell sequencing data
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- 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.
- 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.
- Guillem Sanchez Sanchez & Maria Papadopoulou & Abdulkader Azouz & Yohannes Tafesse & Archita Mishra & Jerry K. Y. Chan & Yiping Fan & Isoline Verdebout & Silvana Porco & Frédérick Libert & Florent Gin, 2022. "Identification of distinct functional thymic programming of fetal and pediatric human γδ thymocytes via single-cell analysis," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
- Yichi Niu & Jiayi Luo & Chenghang Zong, 2024. "Single-cell total-RNA profiling unveils regulatory hubs of transcription factors," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
- Jason I. Griffiths & Patrick A. Cosgrove & Eric F. Medina & Aritro Nath & Jinfeng Chen & Frederick R. Adler & Jeffrey T. Chang & Qamar J. Khan & Andrea H. Bild, 2025. "Cellular interactions within the immune microenvironment underpins resistance to cell cycle inhibition in breast cancers," Nature Communications, Nature, vol. 16(1), pages 1-23, December.
- Jeff DeMartino & Michael T. Meister & Lindy L. Visser & Mariël Brok & Marian J. A. Groot Koerkamp & Amber K. L. Wezenaar & Laura S. Hiemcke-Jiwa & Terezinha Souza & Johannes H. M. Merks & Anne C. Rios, 2023. "Single-cell transcriptomics reveals immune suppression and cell states predictive of patient outcomes in rhabdomyosarcoma," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
- Jeffrey M. Grimes & Sadashib Ghosh & Shamza Manzoor & Li X. Li & Monica M. Moran & Jennifer C. Clements & Sherrie D. Alexander & James M. Markert & Jianmei W. Leavenworth, 2025. "Oncolytic reprogramming of tumor microenvironment shapes CD4 T-cell memory via the IL6ra-Bcl6 axis for targeted control of glioblastoma," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
- Jarne Beliën & Stijn Swinnen & Robbe D’hondt & Laia Verdú de Juan & Nina Dedoncker & Patrick Matthys & Jan Bauer & Celine Vens & Sinéad Moylett & Bénédicte Dubois, 2024. "CHIT1 at diagnosis predicts faster disability progression and reflects early microglial activation in multiple sclerosis," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- 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.
- Zhijun Dong & Fanghan Wang & Yali Liu & Yongxue Li & Haiyan Yu & Saijun Peng & Tingting Sun & Meng Qu & Ke Sun & Lei Wang & Yuanqing Ma & Kai Chen & Jianmin Zhao & Qiang Lin, 2024. "Genomic and single-cell analyses reveal genetic signatures of swimming pattern and diapause strategy in jellyfish," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
- Fahad Paryani & Ji-Sun Kwon & Christopher W. Ng & Kelly Jakubiak & Nacoya Madden & Kenneth Ofori & Alice Tang & Hong Lu & Shengnan Xia & Juncheng Li & Aayushi Mahajan & Shawn M. Davidson & Anna O. Bas, 2024. "Multi-omic analysis of Huntington’s disease reveals a compensatory astrocyte state," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
- Hana Komic & Tessa Schmachtel & Catia Simoes & Marius Külp & Weijia Yu & Adrien Jolly & Malin S. Nilsson & Carmen Gonzalez & Felipe Prosper & Halvard Bonig & Bruno Paiva & Fredrik B. Thorén & Michael , 2025. "Continuous map of early hematopoietic stem cell differentiation across human lifetime," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
- Malosree Maitra & Haruka Mitsuhashi & Reza Rahimian & Anjali Chawla & Jennie Yang & Laura M. Fiori & Maria Antonietta Davoli & Kelly Perlman & Zahia Aouabed & Deborah C. Mash & Matthew Suderman & Nagu, 2023. "Cell type specific transcriptomic differences in depression show similar patterns between males and females but implicate distinct cell types and genes," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Isaac Dean & Colin Y. C. Lee & Zewen K. Tuong & Zhi Li & Christopher A. Tibbitt & Claire Willis & Fabrina Gaspal & Bethany C. Kennedy & Veronika Matei-Rascu & Rémi Fiancette & Caroline Nordenvall & Ul, 2024. "Rapid functional impairment of natural killer cells following tumor entry limits anti-tumor immunity," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
- Manvendra Singh & Ying Zhao & Vinicius Daguano Gastaldi & Sonja M. Wojcik & Yasmina Curto & Riki Kawaguchi & Ricardo M. Merino & Laura Fernandez Garcia-Agudo & Holger Taschenberger & Nils Brose & Dani, 2023. "Erythropoietin re-wires cognition-associated transcriptional networks," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
- Khanyisile Kgoadi & Prashant Bajpai & Chris C. Ibegbu & Hedwin Kitdorlang Dkhar & Ana Beatriz Enriquez & Stanzin Dawa & Sushma K. Cribbs & Jyothi Rengarajan, 2025. "Alveolar macrophages from persons with HIV mount impaired TNF signaling networks to M. tuberculosis infection," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
- Ingrid M. Saldana-Guerrero & Luis F. Montano-Gutierrez & Katy Boswell & Christoph Hafemeister & Evon Poon & Lisa E. Shaw & Dylan Stavish & Rebecca A. Lea & Sara Wernig-Zorc & Eva Bozsaky & Irfete S. F, 2024. "A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations," Nature Communications, Nature, vol. 15(1), pages 1-25, December.
- Jia-Yuan Zhang & Fiona Hamey & Dominik Trzupek & Marius Mickunas & Mercede Lee & Leila Godfrey & Jennie H. M. Yang & Marcin L. Pekalski & Jane Kennet & Frank Waldron-Lynch & Mark L. Evans & Timothy I., 2022. "Low-dose IL-2 reduces IL-21+ T cell frequency and induces anti-inflammatory gene expression in type 1 diabetes," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
- Maxime Brunner & David Lopez-Rodriguez & Judith Estrada-Meza & Rafik Dali & Antoine Rohrbach & Tamara Deglise & Andrea Messina & Bernard Thorens & Federico Santoni & Fanny Langlet, 2024. "Fasting induces metabolic switches and spatial redistributions of lipid processing and neuronal interactions in tanycytes," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
- Kensuke Miyake & Junya Ito & Kazufusa Takahashi & Jun Nakabayashi & Frank Brombacher & Shigeyuki Shichino & Soichiro Yoshikawa & Sachiko Miyake & Hajime Karasuyama, 2024. "Single-cell transcriptomics identifies the differentiation trajectory from inflammatory monocytes to pro-resolving macrophages in a mouse skin allergy model," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
- Sarah Cappuyns & Gino Philips & Vincent Vandecaveye & Bram Boeckx & Rogier Schepers & Thomas Van Brussel & Ingrid Arijs & Aurelie Mechels & Ayse Bassez & Francesca Lodi & Joris Jaekers & Halit Topal &, 2023. "PD-1- CD45RA+ effector-memory CD8 T cells and CXCL10+ macrophages are associated with response to atezolizumab plus bevacizumab in advanced hepatocellular carcinoma," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
- Henry Quach & Spencer Farrell & Ming Jia Michael Wu & Kayshani Kanagarajah & Joseph Wai-Hin Leung & Xiaoqiao Xu & Prajkta Kallurkar & Andrei L. Turinsky & Christine E. Bear & Felix Ratjen & Brian Kali, 2024. "Early human fetal lung atlas reveals the temporal dynamics of epithelial cell plasticity," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
- Kensuke Shibata & Chihiro Motozono & Masamichi Nagae & Takashi Shimizu & Eri Ishikawa & Daisuke Motooka & Daisuke Okuzaki & Yoshihiro Izumi & Masatomo Takahashi & Nao Fujimori & James B. Wing & Takahi, 2022. "Symbiotic bacteria-dependent expansion of MR1-reactive T cells causes autoimmunity in the absence of Bcl11b," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
- Jan Kueckelhaus & Simon Frerich & Jasim Kada-Benotmane & Christina Koupourtidou & Jovica Ninkovic & Martin Dichgans & Juergen Beck & Oliver Schnell & Dieter Henrik Heiland, 2024. "Inferring histology-associated gene expression gradients in spatial transcriptomic studies," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
- Ihab Ansari & Llorenç Solé-Boldo & Meshi Ridnik & Julian Gutekunst & Oliver Gilliam & Maria Korshko & Timur Liwinski & Birgit Jickeli & Noa Weinberg-Corem & Michal Shoshkes-Carmel & Eli Pikarsky & Era, 2023. "TET2 and TET3 loss disrupts small intestine differentiation and homeostasis," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Hyun Kim & Won Chang & Seok Joo Chae & Jong-Eun Park & Minseok Seo & Jae Kyoung Kim, 2024. "scLENS: data-driven signal detection for unbiased scRNA-seq data analysis," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- Meilin Xue & Youwei Zhu & Yongsheng Jiang & Lijie Han & Minmin Shi & Rui Su & Liwen Wang & Cheng Xiong & Chaofu Wang & Ting Wang & Shijie Deng & Dong Wu & Yizhi Cao & Lei Dong & Fan Bai & Shulin Zhao , 2023. "Schwann cells regulate tumor cells and cancer-associated fibroblasts in the pancreatic ductal adenocarcinoma microenvironment," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Hiroki Furuya & Yosuke Toda & Arifumi Iwata & Mizuki Kanai & Kodai Kato & Takashi Kumagai & Takahiro Kageyama & Shigeru Tanaka & Lisa Fujimura & Akemi Sakamoto & Masahiko Hatano & Akira Suto & Kotaro , 2024. "Stage-specific GATA3 induction promotes ILC2 development after lineage commitment," Nature Communications, Nature, vol. 15(1), pages 1-16, December.