Robust mapping of spatiotemporal trajectories and cell–cell interactions in healthy and diseased tissues
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DOI: 10.1038/s41467-023-43120-6
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- Takahiro Masuda & Roman Sankowski & Ori Staszewski & Chotima Böttcher & Lukas Amann & Sagar & Christian Scheiwe & Stefan Nessler & Patrik Kunz & Geert Loo & Volker Arnd Coenen & Peter Christoph Reinac, 2019. "Author Correction: Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution," Nature, Nature, vol. 568(7751), pages 4-4, April.
- Ed S. Lein & Michael J. Hawrylycz & Nancy Ao & Mikael Ayres & Amy Bensinger & Amy Bernard & Andrew F. Boe & Mark S. Boguski & Kevin S. Brockway & Emi J. Byrnes & Lin Chen & Li Chen & Tsuey-Ming Chen &, 2007. "Genome-wide atlas of gene expression in the adult mouse brain," Nature, Nature, vol. 445(7124), pages 168-176, January.
- Mel Greaves & Carlo C. Maley, 2012. "Clonal evolution in cancer," Nature, Nature, vol. 481(7381), pages 306-313, January.
- Amos Tanay & Aviv Regev, 2017. "Scaling single-cell genomics from phenomenology to mechanism," Nature, Nature, vol. 541(7637), pages 331-338, January.
- Takahiro Masuda & Roman Sankowski & Ori Staszewski & Chotima Böttcher & Lukas Amann & Sagar & Christian Scheiwe & Stefan Nessler & Patrik Kunz & Geert Loo & Volker Arnd Coenen & Peter Christoph Reinac, 2019. "Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution," Nature, Nature, vol. 566(7744), pages 388-392, February.
- Mihriban Karaayvaz & Simona Cristea & Shawn M. Gillespie & Anoop P. Patel & Ravindra Mylvaganam & Christina C. Luo & Michelle C. Specht & Bradley E. Bernstein & Franziska Michor & Leif W. Ellisen, 2018. "Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
- Junyue Cao & Malte Spielmann & Xiaojie Qiu & Xingfan Huang & Daniel M. Ibrahim & Andrew J. Hill & Fan Zhang & Stefan Mundlos & Lena Christiansen & Frank J. Steemers & Cole Trapnell & Jay Shendure, 2019. "The single-cell transcriptional landscape of mammalian organogenesis," Nature, Nature, vol. 566(7745), pages 496-502, February.
- Lawrence Fourgeaud & Paqui G. Través & Yusuf Tufail & Humberto Leal-Bailey & Erin D. Lew & Patrick G. Burrola & Perri Callaway & Anna Zagórska & Carla V. Rothlin & Axel Nimmerjahn & Greg Lemke, 2016. "TAM receptors regulate multiple features of microglial physiology," Nature, Nature, vol. 532(7598), pages 240-244, April.
- Benoît Schmauch & Alberto Romagnoni & Elodie Pronier & Charlie Saillard & Pascale Maillé & Julien Calderaro & Aurélie Kamoun & Meriem Sefta & Sylvain Toldo & Mikhail Zaslavskiy & Thomas Clozel & Matah, 2020. "A deep learning model to predict RNA-Seq expression of tumours from whole slide images," Nature Communications, Nature, vol. 11(1), pages 1-15, December.
- Honglei Ren & Benjamin L. Walker & Zixuan Cang & Qing Nie, 2022. "Identifying multicellular spatiotemporal organization of cells with SpaceFlow," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
- Yahui Long & Kok Siong Ang & Mengwei Li & Kian Long Kelvin Chong & Raman Sethi & Chengwei Zhong & Hang Xu & Zhiwei Ong & Karishma Sachaphibulkij & Ao Chen & Li Zeng & Huazhu Fu & Min Wu & Lina Hsiu Ki, 2023. "Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
- Rui Hou & Elena Denisenko & Huan Ting Ong & Jordan A. Ramilowski & Alistair R. R. Forrest, 2020. "Predicting cell-to-cell communication networks using NATMI," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
- Marie F. A. Cutiongco & Bjørn Sand Jensen & Paul M. Reynolds & Nikolaj Gadegaard, 2020. "Predicting gene expression using morphological cell responses to nanotopography," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
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- Shijia Zhu & Naoto Kubota & Shidan Wang & Tao Wang & Guanghua Xiao & Yujin Hoshida, 2024. "STIE: Single-cell level deconvolution, convolution, and clustering in in situ capturing-based spatial transcriptomics," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
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