Shared and distinct transcriptomic cell types across neocortical areas

Citations

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1. Angeles Arzalluz-Luque & Pedro Salguero & Sonia Tarazona & Ana Conesa, 2022. "acorde unravels functionally interpretable networks of isoform co-usage from single cell data," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
2. Zhiyuan Liu & Dafei Wu & Weiwei Zhai & Liang Ma, 2023. "SONAR enables cell type deconvolution with spatially weighted Poisson-Gamma model for spatial transcriptomics," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
3. Wenyi Yang & Pingping Wang & Shouping Xu & Tao Wang & Meng Luo & Yideng Cai & Chang Xu & Guangfu Xue & Jinhao Que & Qian Ding & Xiyun Jin & Yuexin Yang & Fenglan Pang & Boran Pang & Yi Lin & Huan Nie , 2024. "Deciphering cell–cell communication at single-cell resolution for spatial transcriptomics with subgraph-based graph attention network," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
4. Alicia Bedolla & Elliot Wegman & Max Weed & Messiyah K. Stevens & Kierra Ware & Aditi Paranjpe & Anastasia Alkhimovitch & Igal Ifergan & Aleksandr Taranov & Joshua D. Peter & Rosa Maria Salazar Gonzal, 2024. "Adult microglial TGFβ1 is required for microglia homeostasis via an autocrine mechanism to maintain cognitive function in mice," Nature Communications, Nature, vol. 15(1), pages 1-25, December.
5. Olga Gliko & Matt Mallory & Rachel Dalley & Rohan Gala & James Gornet & Hongkui Zeng & Staci A. Sorensen & Uygar Sümbül, 2024. "High-throughput analysis of dendrite and axonal arbors reveals transcriptomic correlates of neuroanatomy," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
6. Li Yuan & Xiaoyin Chen & Huiqing Zhan & Gilbert L. Henry & Anthony M. Zador, 2024. "Massive multiplexing of spatially resolved single neuron projections with axonal BARseq," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
7. Susanne Prokop & Péter Ábrányi-Balogh & Benjámin Barti & Márton Vámosi & Miklós Zöldi & László Barna & Gabriella M. Urbán & András Dávid Tóth & Barna Dudok & Attila Egyed & Hui Deng & Gian Marco Leggi, 2021. "PharmacoSTORM nanoscale pharmacology reveals cariprazine binding on Islands of Calleja granule cells," Nature Communications, Nature, vol. 12(1), pages 1-19, December.
8. Giuseppe Chindemi & Marwan Abdellah & Oren Amsalem & Ruth Benavides-Piccione & Vincent Delattre & Michael Doron & András Ecker & Aurélien T. Jaquier & James King & Pramod Kumbhar & Caitlin Monney & Ro, 2022. "A calcium-based plasticity model for predicting long-term potentiation and depression in the neocortex," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
9. Xinrui Zhou & Wan Yi Seow & Norbert Ha & Teh How Cheng & Lingfan Jiang & Jeeranan Boonruangkan & Jolene Jie Lin Goh & Shyam Prabhakar & Nigel Chou & Kok Hao Chen, 2024. "Highly sensitive spatial transcriptomics using FISHnCHIPs of multiple co-expressed genes," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
10. Zeinab Asgarian & Marcio Guiomar Oliveira & Agata Stryjewska & Ioannis Maragkos & Anna Noren Rubin & Lorenza Magno & Vassilis Pachnis & Mohammadmersad Ghorbani & Scott Wayne Hiebert & Myrto Denaxa & N, 2022. "MTG8 interacts with LHX6 to specify cortical interneuron subtype identity," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
11. Gavin J. Sutton & Daniel Poppe & Rebecca K. Simmons & Kieran Walsh & Urwah Nawaz & Ryan Lister & Johann A. Gagnon-Bartsch & Irina Voineagu, 2022. "Comprehensive evaluation of deconvolution methods for human brain gene expression," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
12. Leonardo D. Garma & Lisbeth Harder & Juan M. Barba-Reyes & Sergio Marco Salas & Mónica Díez-Salguero & Mats Nilsson & Alberto Serrano-Pozo & Bradley T. Hyman & Ana B. Muñoz-Manchado, 2024. "Interneuron diversity in the human dorsal striatum," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
13. Dehua Peng & Zhipeng Gui & Dehe Wang & Yuncheng Ma & Zichen Huang & Yu Zhou & Huayi Wu, 2022. "Clustering by measuring local direction centrality for data with heterogeneous density and weak connectivity," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
14. Jingyang Qian & Jie Liao & Ziqi Liu & Ying Chi & Yin Fang & Yanrong Zheng & Xin Shao & Bingqi Liu & Yongjin Cui & Wenbo Guo & Yining Hu & Hudong Bao & Penghui Yang & Qian Chen & Mingxiao Li & Bing Zha, 2023. "Reconstruction of the cell pseudo-space from single-cell RNA sequencing data with scSpace," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
15. Yanjie Wang & Zhaonan Chen & Guofen Ma & Lizhao Wang & Yanmei Liu & Meiling Qin & Xiang Fei & Yifan Wu & Min Xu & Siyu Zhang, 2023. "A frontal transcallosal inhibition loop mediates interhemispheric balance in visuospatial processing," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
16. Jia-Ru Wei & Zhao-Zhe Hao & Chuan Xu & Mengyao Huang & Lei Tang & Nana Xu & Ruifeng Liu & Yuhui Shen & Sarah A. Teichmann & Zhichao Miao & Sheng Liu, 2022. "Identification of visual cortex cell types and species differences using single-cell RNA sequencing," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
17. Yuqiu Zhou & Wei He & Weizhen Hou & Ying Zhu, 2024. "Pianno: a probabilistic framework automating semantic annotation for spatial transcriptomics," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
18. Yoav Ben-Simon & Karola Kaefer & Philipp Velicky & Jozsef Csicsvari & Johann G. Danzl & Peter Jonas, 2022. "A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
19. Kiya W. Govek & Patrick Nicodemus & Yuxuan Lin & Jake Crawford & Artur B. Saturnino & Hannah Cui & Kristi Zoga & Michael P. Hart & Pablo G. Camara, 2023. "CAJAL enables analysis and integration of single-cell morphological data using metric geometry," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
20. Daniel G. Taub & Qiufen Jiang & Francesca Pietrafesa & Junfeng Su & Aloe Carroll & Caitlin Greene & Michael R. Blanchard & Aakanksha Jain & Mahmoud El-Rifai & Alexis Callen & Katherine Yager & Clara C, 2024. "The secondary somatosensory cortex gates mechanical and heat sensitivity," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
21. Gregory J. Salimando & Sébastien Tremblay & Blake A. Kimmey & Jia Li & Sophie A. Rogers & Jessica A. Wojick & Nora M. McCall & Lisa M. Wooldridge & Amrith Rodrigues & Tito Borner & Kristin L. Gardiner, 2023. "Human OPRM1 and murine Oprm1 promoter driven viral constructs for genetic access to μ-opioidergic cell types," Nature Communications, Nature, vol. 14(1), pages 1-24, December.
22. Yuzhou Chang & Jixin Liu & Yi Jiang & Anjun Ma & Yao Yu Yeo & Qi Guo & Megan McNutt & Jordan E. Krull & Scott J. Rodig & Dan H. Barouch & Garry P. Nolan & Dong Xu & Sizun Jiang & Zihai Li & Bingqiang , 2024. "Graph Fourier transform for spatial omics representation and analyses of complex organs," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
23. Daniel J. Lodge & Hannah B. Elam & Angela M. Boley & Jennifer J. Donegan, 2023. "Discrete hippocampal projections are differentially regulated by parvalbumin and somatostatin interneurons," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
24. Ravneet Jaura & Ssu-Yu Yeh & Kaitlin N. Montanera & Alyssa Ialongo & Zobia Anwar & Yiming Lu & Kavindu Puwakdandawa & Ho Sung Rhee, 2022. "Extended intergenic DNA contributes to neuron-specific expression of neighboring genes in the mammalian nervous system," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
25. Xiaomeng Wan & Jiashun Xiao & Sindy Sing Ting Tam & Mingxuan Cai & Ryohichi Sugimura & Yang Wang & Xiang Wan & Zhixiang Lin & Angela Ruohao Wu & Can Yang, 2023. "Integrating spatial and single-cell transcriptomics data using deep generative models with SpatialScope," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
26. Nelson Johansen & Hongru Hu & Gerald Quon, 2023. "Projecting RNA measurements onto single cell atlases to extract cell type-specific expression profiles using scProjection," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
27. Rongbo Shen & Lin Liu & Zihan Wu & Ying Zhang & Zhiyuan Yuan & Junfu Guo & Fan Yang & Chao Zhang & Bichao Chen & Wanwan Feng & Chao Liu & Jing Guo & Guozhen Fan & Yong Zhang & Yuxiang Li & Xun Xu & Ji, 2022. "Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
28. Yina Wei & Anirban Nandi & Xiaoxuan Jia & Joshua H. Siegle & Daniel Denman & Soo Yeun Lee & Anatoly Buchin & Werner Geit & Clayton P. Mosher & Shawn Olsen & Costas A. Anastassiou, 2023. "Associations between in vitro, in vivo and in silico cell classes in mouse primary visual cortex," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
29. Oren Amsalem & Hidehiko Inagaki & Jianing Yu & Karel Svoboda & Ran Darshan, 2024. "Sub-threshold neuronal activity and the dynamical regime of cerebral cortex," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
30. Vincent Geldhof & Laura P. M. H. Rooij & Liliana Sokol & Jacob Amersfoort & Maxim Schepper & Katerina Rohlenova & Griet Hoste & Adriaan Vanderstichele & Anne-Marie Delsupehe & Edoardo Isnaldi & Naima , 2022. "Single cell atlas identifies lipid-processing and immunomodulatory endothelial cells in healthy and malignant breast," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
31. Koun Onodera & Hiroyuki K. Kato, 2022. "Translaminar recurrence from layer 5 suppresses superficial cortical layers," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
32. April R. Kriebel & Joshua D. Welch, 2022. "UINMF performs mosaic integration of single-cell multi-omic datasets using nonnegative matrix factorization," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
33. Wei Zhao & Kevin G. Johnston & Honglei Ren & Xiangmin Xu & Qing Nie, 2023. "Inferring neuron-neuron communications from single-cell transcriptomics through NeuronChat," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
34. Ian Covert & Rohan Gala & Tim Wang & Karel Svoboda & Uygar Sümbül & Su-In Lee, 2023. "Predictive and robust gene selection for spatial transcriptomics," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
35. Ariel Madrigal & Tianyuan Lu & Larisa M. Soto & Hamed S. Najafabadi, 2024. "A unified model for interpretable latent embedding of multi-sample, multi-condition single-cell data," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
36. Luis Flores Horgue & Alexis Assens & Leon Fodoulian & Leonardo Marconi & Joël Tuberosa & Alexander Haider & Madlaina Boillat & Alan Carleton & Ivan Rodriguez, 2022. "Transcriptional adaptation of olfactory sensory neurons to GPCR identity and activity," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
37. Kazuhiro Kon & Koji L. Ode & Tomoyuki Mano & Hiroshi Fujishima & Riina R. Takahashi & Daisuke Tone & Chika Shimizu & Shinnosuke Shiono & Saori Yada & Kyoko Matsuzawa & Shota Y. Yoshida & Junko Yoshida, 2024. "Cortical parvalbumin neurons are responsible for homeostatic sleep rebound through CaMKII activation," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
38. Stefano Berto & Alex H. Treacher & Emre Caglayan & Danni Luo & Jillian R. Haney & Michael J. Gandal & Daniel H. Geschwind & Albert A. Montillo & Genevieve Konopka, 2022. "Association between resting-state functional brain connectivity and gene expression is altered in autism spectrum disorder," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
39. Dmitry Kobak & Yves Bernaerts & Marissa A. Weis & Federico Scala & Andreas S. Tolias & Philipp Berens, 2021. "Sparse reduced‐rank regression for exploratory visualisation of paired multivariate data," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 70(4), pages 980-1000, August.
40. Jonathan P. Ling & Alexei M. Bygrave & Clayton P. Santiago & Rogger P. Carmen-Orozco & Vickie T. Trinh & Minzhong Yu & Yini Li & Ying Liu & Kyra D. Bowden & Leighton H. Duncan & Jeong Han & Kamil Tane, 2022. "Cell-specific regulation of gene expression using splicing-dependent frameshifting," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
41. Christopher T. Rhodes & Joyce J. Thompson & Apratim Mitra & Dhanya Asokumar & Dongjin R. Lee & Daniel J. Lee & Yajun Zhang & Eva Jason & Ryan K. Dale & Pedro P. Rocha & Timothy J. Petros, 2022. "An epigenome atlas of neural progenitors within the embryonic mouse forebrain," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
42. Ziqi Zhang & Haoran Sun & Ragunathan Mariappan & Xi Chen & Xinyu Chen & Mika S. Jain & Mirjana Efremova & Sarah A. Teichmann & Vaibhav Rajan & Xiuwei Zhang, 2023. "scMoMaT jointly performs single cell mosaic integration and multi-modal bio-marker detection," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
43. Shan Shen & Xiaolong Jiang & Federico Scala & Jiakun Fu & Paul Fahey & Dmitry Kobak & Zhenghuan Tan & Na Zhou & Jacob Reimer & Fabian Sinz & Andreas S. Tolias, 2022. "Distinct organization of two cortico-cortical feedback pathways," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
44. Ying Lei & Mengnan Cheng & Zihao Li & Zhenkun Zhuang & Liang Wu & Yunong sun & Lei Han & Zhihao Huang & Yuzhou Wang & Zifei Wang & Liqin Xu & Yue Yuan & Shang Liu & Taotao Pan & Jiarui Xie & Chuanyu L, 2022. "Spatially resolved gene regulatory and disease-related vulnerability map of the adult Macaque cortex," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
45. Prateek Kumar & Annie M. Goettemoeller & Claudia Espinosa-Garcia & Brendan R. Tobin & Ali Tfaily & Ruth S. Nelson & Aditya Natu & Eric B. Dammer & Juliet V. Santiago & Sneha Malepati & Lihong Cheng & , 2024. "Native-state proteomics of Parvalbumin interneurons identifies unique molecular signatures and vulnerabilities to early Alzheimer’s pathology," Nature Communications, Nature, vol. 15(1), pages 1-26, December.
46. Wendy Xueyi Wang & Julie L. Lefebvre, 2022. "Morphological pseudotime ordering and fate mapping reveal diversification of cerebellar inhibitory interneurons," Nature Communications, Nature, vol. 13(1), pages 1-21, December.