Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
Ståhl, Patrik L., Salmén, Fredrik, Vickovic, Sanja, Lundmark, Anna, Navarro, José Fernández, Magnusson, Jens, Giacomello, Stefania, Asp, Michaela +13 more·2016·Science
Cited by (1,007)
Items 201–300 of 1,007
- Single-cell sequencing to multi-omics: technologies and applicationsWu, Xiangyu, Yang, Xin, Dai, Yunhan, Zhao, Zihan, Zhu, Junmeng, Guo, Hongqian, Yang, Rong · 2024 · Biomarker Research
- Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liverFranziska Hildebrandt, Alma Andersson, Sami Saarenpää, Ludvig Larsson, Noémi Van Hul, Sachie Kanatani, Jan Masek, Ewa C. S. Ellis, Antonio Barragán, Annelie Mollbrink et al. · 2021 · Nature Communications
- GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics dataYuan, Ye, Bar-Joseph, Ziv · 2020 · Genome Biology
- Spatial multimodal analysis of transcriptomes and metabolomes in tissuesMarco Vicari, Reza Mirzazadeh, Anna Nilsson, Mohammadreza Shariatgorji, Patrik Bjärterot, Ludvig Larsson, Hower Lee, Mats F. Nilsson, Julia Foyer, Markus Ekvall et al. · 2023 · Nature Biotechnology
- Spatially resolved transcriptomics: a comprehensive review of their technological advances, applications, and challengesMengnan Cheng, Yujia Jiang, Jiangshan Xu, Alexios‐Fotios A. Mentis, Shuai Wang, Huiwen Zheng, Sunil Kumar Sahu, Longqi Liu, Xun Xu · 2023 · Journal of genetics and genomics/Journal of Genetics and Genomics
- Tumour evolution and microenvironment interactions in 2D and 3D spaceChia-Kuei Mo, Jingxian Liu, Siqi Chen, Erik P. Storrs, André Luiz N. Targino da Costa, Andrew Houston, Michael C. Wendl, Reyka G. Jayasinghe, Michael D. Iglesia, Cong Ma et al. · 2024 · Nature
- Advances in spatial transcriptomics and related data analysis strategiesJun Du, Yuchen Yang, Zhi-Jie An, Minghui Zhang, Xue-Hang Fu, Zoufang Huang, Ye Yuan, Jian Hou · 2023 · Journal of Translational Medicine
- Identifying temporal and spatial patterns of variation from multimodal data using MEFISTOBritta Velten, Jana M. Braunger, Ricard Argelaguet, Damien Arnol, Jakob Wirbel, Danila Bredikhin, Georg Zeller, Oliver Stegle · 2022 · Nature Methods
- Integrative analyses of single-cell transcriptome and regulome using MAESTROChenfei Wang, Dongqing Sun, Xin Huang, Changxin Wan, Ziyi Li, Ya Han, Qian Qin, Jing‐Yu Fan, Xintao Qiu, Yingtian Xie et al. · 2020 · Genome biology
- Integration of spatial and single-cell transcriptomics localizes epithelial cell–immune cross-talk in kidney injuryRicardo Melo Ferreira, Angela R. Sabo, Seth Winfree, Kimberly S. Collins, Danielle Janosevic, Connor J. Gulbronson, Ying‐Hua Cheng, Lauren Casbon, Daria Barwinska, Michael J. Ferkowicz et al. · 2021 · JCI Insight
- Statistical and machine learning methods for spatially resolved transcriptomics data analysisZeng, Zexian, Li, Yawei, Li, Yiming, Luo, Yuan · 2022 · Genome Biology
- Mechanisms of Macrophage Plasticity in the Tumor Environment: Manipulating Activation State to Improve OutcomesTiffany D. Ricketts, Néstor Prieto‐Domínguez, Pramod S. Gowda, Eric Ubil · 2021 · Frontiers in Immunology
- Clinical application of advanced multi-omics tumor profiling: Shaping precision oncology of the futureDilara Akhoundova, Mark A. Rubin · 2022 · Cancer Cell
- A roadmap for the Human Developmental Cell AtlasMuzlifah A. Haniffa, Deanne M. Taylor, Sten Linnarsson, Bruce J. Aronow, Gary D. Bader, Roger A. Barker, Pablo G. Cámara, J. Gray Camp, Alain Chédotal, Andrew J. Copp et al. · 2021 · Nature
- The tumor microenvironment’s role in the response to immune checkpoint blockadeKonstantinos Aliazis, Anthos Christofides, Rushil Shah, Yao Yu Yeo, Sizun Jiang, Alain Charest, Vassiliki A. Boussiotis · 2025 · Nature Cancer
- Noncoding RNAs in neurodegenerationSalta, Evgenia, De Strooper, Bart · 2017 · Nature Reviews Neuroscience
- Unravelling cellular relationships during development and regeneration using genetic lineage tracingChloé S. Baron, Alexander van Oudenaarden · 2019 · Nature Reviews Molecular Cell Biology
- Decoding the tumor microenvironment with spatial technologiesLogan A. Walsh, Daniela F. Quail · 2023 · Nature Immunology
- Digital microfluidic isolation of single cells for -OmicsJulian Lamanna, E. Scott, Harrison S. Edwards, Michael Dean Chamberlain, Michael D. M. Dryden, Jiaxi Peng, Barbara Mair, Adam Lee, Calvin C. H. Chan, Alexandros A. Sklavounos et al. · 2020 · Nature Communications
- BASS: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studiesZheng Li, Xiang Zhou · 2022 · Genome biology
- Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densitiesBrendan F. Miller, Dhananjay Bambah-Mukku, Catherine G. Dulac, Xiaowei Zhuang, Jean Fan · 2021 · Genome Research
- Beyond genetics: driving cancer with the tumour microenvironment behind the wheelShaopeng Yuan, Jorge Almagro, Elaine V. Fuchs · 2024 · Nature reviews. Cancer
- Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflowsSergio Marco Salas, Louis Benedikt Kuemmerle, Christoffer Mattsson Langseth, Sebastian Tiesmeyer, Christophe Avenel, Taobo Hu, Habib Rehman, Marco Grillo, Paulo Czarnewski, Saga Helgadóttir et al. · 2025 · Nature Methods
- A single-cell tumor immune atlas for precision oncologyPaula Nieto, Marc Elosua-Bayés, Juan L. Trincado, Doménica Marchese, Ramon Massoni-Badosa, Maria Salvany, Ana Raquel Henriques, Juan Camilo Nieto, Sergio Aguilar-Fernández, Elisabetta Mereu et al. · 2021 · Genome Research
- Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalkAlexander N. Combes, Belinda Phipson, Kynan T. Lawlor, Aude Dorison, Ralph Patrick, Luke Zappia, Richard Paul Harvey, Alicia Oshlack, Melissa Helen Little · 2019 · Development
- Deciphering the spatial landscape and plasticity of immunosuppressive fibroblasts in breast cancerHugo Croizer, Rana Mhaidly, Yann Kieffer, Géraldine Gentric, Lounes Djerroudi, Renaud Leclère, Floriane Pelon, Catherine Robley, Mylène Bohec, Arnaud Meng et al. · 2024 · Nature Communications
- Single-cell atlases: shared and tissue-specific cell types across human organsRasa Elmentaite, Cecilia Domínguez Conde, Lu Yang, Sarah Amalia Teichmann · 2022 · Nature Reviews Genetics
- A transcriptomic axis predicts state modulation of cortical interneuronsStéphane Bugeon, Joshua A. M. Duffield, Mario Dipoppa, Anne Ritoux, Isabelle Prankerd, Dimitris Nicoloutsopoulos, David Orme, Maxwell Shinn, Han Peng, Hamish Forrest et al. · 2022 · Nature
- Advances in spatial transcriptomics and its applications in cancer researchYang Jin, Yuanli Zuo, Gang Li, Wenrong Liu, Yitong Pan, Ting Fan, Xin Fu, Xiaojun Yao, Yong Peng · 2024 · Molecular Cancer
- Tumor battlefield within inflamed, excluded or desert immune phenotypes: the mechanisms and strategiesSiwei Zheng, Wenwen Wang, Lesang Shen, Yao Yao, Wenjie Xia, Chao Ni · 2024 · Experimental Hematology and Oncology
- Recording development with single cell dynamic lineage tracingAaron McKenna, James A. Gagnon · 2019 · Development
- Single-cell and spatial multi-omics in the plant sciences: Technical advances, applications, and perspectivesXiaole Yu, Zhixin Liu, Xuwu Sun · 2022 · Plant Communications
- Shaping the brain vasculature in development and disease in the single-cell eraThomas Wälchli, Jeroen Bisschop, Peter Carmeliet, Gelareh Mohammed Zadeh, Philippe Patrick Monnier, Katrien De Bock, Ivan Radovanovic · 2023 · Nature reviews. Neuroscience
- Reconstruction of the tumor spatial microenvironment along the malignant-boundary-nonmalignant axisZhenzhen Xun, Xinyu Ding, Yao Zhang, Benyan Zhang, Shujing Lai, Duowu Zou, Junke Zheng, Guoqiang Chen, Bing Su, Leng Han et al. · 2023 · Nature Communications
- Platforms for Single-Cell Collection and AnalysisLukáš Valihrach, Peter Androvic, Mikael Kubista · 2018 · International Journal of Molecular Sciences
- Technological advances in cancer immunity: from immunogenomics to single‐cell analysis and artificial intelligenceXu, Ying, Su, Guan-Hua, Ma, Ding, Xiao, Yi, Shao, Zhi-Ming, Jiang, Yi-Zhou · 2021 · Signal Transduction and Targeted Therapy
- Next-generation computational tools for interrogating cancer immunityFrancesca Finotello, Dietmar Rieder, Hubert Hackl, Zlatko Trajanoski · 2019 · Nature Reviews Genetics
- Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic painFu, Xiaonan, Sun, Li, Dong, Runze, Chen, Jane Y., Silakit, Runglawan, Condon, Logan F., Lin, Yiing, Lin, Shin, Palmiter, Richard D., Gu, Liangcai · 2022 · Cell
- Bystander IFN-γ activity promotes widespread and sustained cytokine signaling altering the tumor microenvironmentRonan Thibaut, Pierre Bost, Idan Milo, Marine Cazaux, Fabrice Lemaı̂tre, Zacarias Garcia, Ido Amit, Béatrice Bréart, Clémence Cornuot, Benno Schwikowski et al. · 2020 · Nature Cancer
- Evaluation of cell-cell interaction methods by integrating single-cell RNA sequencing data with spatial informationZhaoyang Liu, Dongqing Sun, Chenfei Wang · 2022 · Genome biology
- Combined Single‐Cell and Spatial Transcriptomics Reveal the Metabolic Evolvement of Breast Cancer during Early DisseminationYiming Liu, Jingyu Ge, Yufei Chen, Tong Liu, Lie Chen, Cui‐Cui Liu, Ding Ma, Yiyu Chen, Yuwen Cai, Yingying Xu et al. · 2023 · Advanced Science
- Myeloid cell heterogeneity in cancer: not a single cell alikeKiss, Mate, Van Gassen, Sofie, Movahedi, Kiavash, Saeys, Yvan, Laoui, Damya · 2018 · Cellular Immunology
- Integrating spatial transcriptomics data across different conditions, technologies and developmental stagesZhou, Xiang, Dong, Kangning, Zhang, Shihua · 2023 · Nature Computational Science
- Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injuryE. Floriddia, Tânia Lourenço, Shupei Zhang, D. van Bruggen, M. Hilscher, P. Kukanja, J. P. Gonçalves dos Santos, Müge Altınkök, C. Yokota, Enric Llorens-Bobadilla et al. · 2020 · Nature Communications
- Spatial transcriptomics: paving the way for tissue-level systems biologyAndreas E. Moor, Shalev Itzkovitz · 2017 · Current Opinion in Biotechnology
- Interplay between genetics and epigenetics in osteoarthritisSarah J. Rice, Frank Beier, David Alan Young, John A. Loughlin · 2020 · Nature Reviews Rheumatology
- spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics dataBrenda Pardo, Abby Spangler, Lukas M. Weber, Stephanie C. Page, Stephanie C. Hicks, Andrew E. Jaffe, Keri Martinowich, Kristen R. Maynard, Leonardo Collado‐Torres · 2022 · BMC Genomics
- Integrating next-generation sequencing into clinical oncology: strategies, promises and pitfallsPeter Horak, Stefan Fröhling, Hanno Glimm · 2016 · ESMO Open
- LifeTime and improving European healthcare through cell-based interceptive medicineNikolaus Rajewsky, Geneviève Almouzni, Stanislaw A. Gorski, Stein Aerts, Ido Amit, Michela Giulia Bertero, Christoph Bock, Annelien L. Bredenoord, Giacomo Cavalli, Susanna Chiocca et al. · 2020 · Nature
- Multi-domain translation between single-cell imaging and sequencing data using autoencodersKarren Yang, Anastasiya Belyaeva, Saradha Venkatachalapathy, Karthik Damodaran, Abigail Katcoff, Adityanarayanan Radhakrishnan, G. V. Shivashankar, Caroline Uhler · 2021 · Nature Communications
- Mapping the physical network of cellular interactionsJean-Charles Boisset, Judith Vivié, Dominic Grün, Mauro J. Muraro, Anna Lyubimova, Alexander van Oudenaarden · 2018 · Nature Methods
- A chromatin integration labelling method enables epigenomic profiling with lower inputAkihito Harada, Kazumitsu Maehara, Tetsuya Handa, Yasuhiro Arimura, Jumpei Nogami, Yoko Hayashi‐Takanaka, Katsuhiko Shirahige, Hitoshi Kurumizaka, Hiroshi Kimurâ, Yasuyuki Ohkawa · 2018 · Nature Cell Biology
- ZipSeq: barcoding for real-time mapping of single cell transcriptomesKenneth H. Hu, John Paul Eichorst, Christopher S. McGinnis, David M. Patterson, Eric D. Chow, Kelly Kersten, Stephen C. Jameson, Zev J. Gartner, Arjun Arkal Rao, Matthew F. Krummel · 2020 · Nature Methods
- The orchestrated cellular and molecular responses of the kidney to endotoxin define a precise sepsis timelineDanielle Janosevic, Jered Myslinski, Thomas W. McCarthy, Amy Zollman, Farooq Syed, Xiaoling Xuei, Hongyu Gao, Yunlong Liu, Kimberly S. Collins, Ying‐Hua Cheng et al. · 2021 · eLife
- Deciphering the state of immune silence in fatal COVID-19 patientsPierre Bost, Francesco De Sanctis, Stefania Canè, Stefano Ugel, Katia Donadello, Monica Castellucci, Eyal David, Alessandra Fiore, Cristina Anselmi, Roza Maria Barouni et al. · 2021 · Nature Communications
- Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays.Ao Chen, Sha Liao, Mengnan Cheng, Kailong Ma, Liang Li Wu, Yiwei Lai, Xiaojie Qiu, Yang, Jin, Jiangshan Xu, Shijie Hao et al. · 2022 · Apollo (University of Cambridge)
- scDesign3 generates realistic in silico data for multimodal single-cell and spatial omicsDongyuan Song, Qingyang Wang, Guanao Yan, Tianyang Liu, Tianyi Sun, Jingyi Jessica Li · 2023 · Nature Biotechnology
- Spatial Transcriptomic TechnologiesTsai-Ying Chen, Li You, José A. Hardillo, Miao‐Ping Chien · 2023 · Cells
- Spatial metatranscriptomics resolves host–bacteria–fungi interactomesSami Saarenpää, Or Shalev, Haim Ashkenazy, Vanessa Carlos, Derek S. Lundberg, Detlef Weigel, Stefania Giacomello · 2023 · Nature Biotechnology
- Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosisLovisa Franzén, Martina Olsson Lindvall, Michael H. Hühn, Victoria Ptasinski, Laura C. Setyo, Benjamin P. Keith, Astrid Collin, Steven Oag, Thomas Volckaert, Annika Borde et al. · 2024 · Nature Genetics
- Novel research and future prospects of artificial intelligence in cancer diagnosis and treatmentZhang, Chaoyi, Xu, Jin, Tang, Rong, Yang, Jianhui, Wang, Wei, Yu, Xianjun, Shi, Si · 2023 · Journal of Hematology & Oncology
- RNA Sequencing Data: Hitchhiker's Guide to Expression AnalysisKoen Van den Berge, Katharina Hembach, Charlotte Soneson, Simone Tiberi, Lieven Clement, Michael I. Love, Rob Patro, Mark D. Robinson · 2019 · Annual Review of Biomedical Data Science
- Degenerative and regenerative pathways underlying Duchenne muscular dystrophy revealed by single-nucleus RNA sequencingFrancesco Chemello, Zhaoning Wang, Hui zi Li, John McAnally, Ning Liu, Rhonda Bassel‐Duby, Eric N. Olson · 2020 · Proceedings of the National Academy of Sciences
- Nrf1 promotes heart regeneration and repair by regulating proteostasis and redox balanceMiao Cui, Ayhan Atmanli, María Gabriela Morales, Wei Hong Tan, Kenian Chen, Xue Xiao, Lin Xu, Ning Liu, Rhonda Bassel‐Duby, Eric N. Olson · 2021 · Nature Communications
- Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tissue with Automated Sample Transfer to NanodropletsZhu, Ying, Dou, Maowei, Piehowski, Paul D., Liang, Yiran, Wang, Fangjun, Chu, Rosalie K., Chrisler, William B., Smith, Jordan N., Schwarz, Kaitlynn C., Shen, Yufeng et al. · 2018 · Molecular & Cellular Proteomics
- Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLARJeremy L. Muhlich, Yu‐An Chen, Clarence Yapp, Douglas Russell, Sandro Santagata, Peter Karl Sorger · 2022 · Bioinformatics
- Characterizing the ecological and evolutionary dynamics of cancerNastaran Zahir, Ruping Sun, Daniel Gallahan, Robert A. Gatenby, Christina N. Curtis · 2020 · Nature Genetics
- Next-Generation Morphometry for pathomics-data mining in histopathologyDavid Laurin Hölscher, Nassim Bouteldja, Mehdi Joodaki, María Luisa Russo, Yu-Chia Lan, Alireza Vafaei Sadr, Mingbo Cheng, Vladimı́r Tesař, Saskia Freifrau von Stillfried, Barbara M. Klinkhammer et al. · 2023 · Nature Communications
- Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamicsCamilla Engblom, Kim Thrane, Qirong Lin, Alma Andersson, Hosein Toosi, Xinsong Chen, Embla Steiner, Chang Lu, Giulia Mantovani, Michael Hagemann-Jensen et al. · 2023 · Science
- Systemic Immunometabolism: Challenges and OpportunitiesAlexander Lercher, Hatoon Baazim, Andreas Bergthaler · 2020 · Immunity
- Design principles of microneedles for drug delivery and sampling applicationsZhicheng Le, Jinming Yu, Ying Jie Quek, Bingyu Bai, Xianlei Li, Yufeng Shou, Ba Myint, Chenjie Xu, Andy Kah Ping Tay · 2022 · Materials Today
- Spatial landscapes of cancers: insights and opportunitiesJulia Chen, Ludvig Larsson, Alexander Swarbrick, Joakim Lundeberg · 2024 · Nature Reviews Clinical Oncology
- SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using BioconductorDario Righelli, Lukas M. Weber, Helena Lucia Crowell, Brenda Pardo, Leonardo Collado‐Torres, Shila Ghazanfar, Aaron T. L. Lun, Stephanie C. Hicks, Davide Risso · 2022 · Bioinformatics
- Deep learning applications in single-cell genomics and transcriptomics data analysisNafiseh Erfanian, A. Ali Heydari, Adib Miraki Feriz, Pablo Iáñez Picazo, Afshin Derakhshani, Mohammad GhasemiGol, Mohsen Farahpour, Seyyed Mohammad Razavi, Saeed Nasseri, Hossein Safarpour et al. · 2023 · Biomedicine & Pharmacotherapy
- Crosstalk among podocytes, glomerular endothelial cells and mesangial cells in diabetic kidney disease: an updated reviewShiwan Hu, Xing Hang, Yu Wei, Han Wang, Lili Zhang, Linhua Zhao · 2024 · Cell Communication and Signaling
- A systematic capsid evolution approach performed in vivo for the design of AAV vectors with tailored properties and tropismDavidsson, Marcus, Wang, Gang, Aldrin-Kirk, Patrick, Cardoso, Tiago, Nolbrant, Sara, Hartnor, Morgan, Mudannayake, Janitha, Parmar, Malin, Björklund, Tomas · 2019 · Proceedings of the National Academy of Sciences
- Single‐Nucleus RNA Sequencing and Spatial Transcriptomics Reveal the Immunological Microenvironment of Cervical Squamous Cell CarcinomaZhihua Ou, Shitong Lin, Jiaying Qiu, Wencheng Ding, Peidi Ren, Dongsheng Chen, Jiaxuan Wang, Yihan Tong, Di Wu, Ao Chen et al. · 2022 · Advanced Science
- Resolving the immune landscape of human prostate at a single-cell level in health and cancerZewen Kelvin Tuong, Kevin W. Loudon, Brendan Berry, Nathan Richoz, Julia L. Jones, Xiao Tan, Quan Hoang Nguyen, Anne George, Satoshi Hori, Sarah Field et al. · 2021 · Cell Reports
- Transcriptional profiling of microglia; current state of the art and future perspectivesGerrits, Emma, Heng, Yang, Boddeke, Erik W. G. M., Eggen, Bart J. L. · 2020 · Glia
- Spatial and single-cell transcriptomics decipher the cellular environment containing HLA-G+ cancer cells and SPP1+ macrophages in colorectal cancerYuki Ozato, Yasuhiro Kojima, Yuta Kobayashi, Yuuichi Hisamatsu, Takeo Toshima, Yusuke Yonemura, Takaaki Masuda, Kouichi Kagawa, Yasuhiro Goto, Mitsuaki Utou et al. · 2023 · Cell Reports
- From whole-mount to single-cell spatial assessment of gene expression in 3DLisa N. Waylen, Hieu Tri Nim, Luciano Gastón Martelotto, Mirana Ramialison · 2020 · Communications Biology
- Estimation of cell lineages in tumors from spatial transcriptomics dataBeibei Ru, Jinlin Huang, Yu Zhang, Kenneth Aldape, Peng Jiang · 2023 · Nature Communications
- Spatial host–microbiome sequencing reveals niches in the mouse gutBritta Lötstedt, Martin Stražar, Ramnik J. Xavier, Aviv Regev, Sanja Vicković · 2023 · Nature Biotechnology
- Spatial transcriptomics in health and diseaseSanjay R. Jain, Michael T. Eadon · 2024 · Nature Reviews Nephrology
- Microglia-astrocyte crosstalk in the amyloid plaque niche of an Alzheimer’s disease mouse model, as revealed by spatial transcriptomicsMallach, Anna, Zielonka, Magdalena, van Lieshout, Veerle, An, Yanru, Khoo, Jia Hui, Vanheusden, Marisa, Chen, Wei-Ting, Moechars, Daan, Arancibia-Carcamo, I. Lorena, Fiers, Mark et al. · 2024 · Cell Reports
- Spatial omics: Navigating to the golden era of cancer researchYingcheng Charles Wu, Yifei Cheng, Xiangdong Wang, Jia Fan, Qiang Gao · 2022 · Clinical and Translational Medicine
- Progression from ductal carcinoma in situ to invasive breast cancer: molecular features and clinical significanceJing Wang, Baizhou Li, Meng Luo, Jia Huang, Kun Zhang, Shu Zheng, Suzhan Zhang, Jiaojiao Zhou · 2024 · Signal Transduction and Targeted Therapy
- Spatial transcriptomics reveals substantial heterogeneity in triple-negative breast cancer with potential clinical implicationsXiaoxiao Wang, David Venet, Frédéric Lifrange, Denis Larsimont, Mattia Rediti, Linnea Stenbeck, Floriane Dupont, Ghizlane Rouas, Andrea Joaquin Garcia, Ligia Craciun et al. · 2024 · Nature Communications
- Giotto, a toolbox for integrative analysis and visualization of spatial expression dataRuben Dries, Qian Zhu, Rui Dong, Chee-Huat Linus Eng, Huipeng Li, Kan Liu, Yuntian Fu, Tianxiao Zhao, Arpan Sarkar, Feng Bao et al. · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
- Qualifying antibodies for image-based immune profiling and multiplexed tissue imagingZiming Du, Jia‐Ren Lin, Rumana Rashid, Zoltan Maliga, Shu Wang, Jon Christopher Aster, Benjamin Izar, Peter Karl Sorger, Sandro Santagata · 2019 · Nature Protocols
- Modern venomics—Current insights, novel methods, and future perspectives in biological and applied animal venom researchBjörn M. von Reumont, Gregor Anderluh, Agostinho Antunes, Naira M. Ayvazyan, Dimitris Beis, Figen Çalışkan, Ana Crnković, Maik Damm, Sébastien Dutertre, Lars Ellgaard et al. · 2022 · GigaScience
- Spatial oncology: Translating contextual biology to the clinicDennis H. Gong, Jeanna M Arbesfeld-Qiu, Ella N. Perrault, Jung Woo Bae, William L. Hwang · 2024 · Cancer Cell
- Identification of early neurodegenerative pathways in progressive multiple sclerosisMax Kaufmann, Anna-Lena Schaupp, Rosa Sun, Fabian Coscia, Calliope Athena Dendrou, Adrián Cortés, Gurman Kaur, Hayley G. Evans, Annelie Mollbrink, José Fernández Navarro et al. · 2022 · Nature Neuroscience
- Molecular and cellular mechanisms of selective vulnerability in neurodegenerative diseasesMartin Kampmann · 2024 · Nature reviews. Neuroscience
- Genome-wide spatial expression profiling in formalin-fixed tissuesGracia Villacampa, Eva, Larsson, Ludvig, Mirzazadeh, Reza, Kvastad, Linda, Andersson, Alma, Mollbrink, Annelie, Kokaraki, Georgia, Monteil, Vanessa, Schultz, Niklas, Appelberg, Karin Sofia et al. · 2021 · Cell Genomics
- Gut-associated lymphoid tissue: a microbiota-driven hub of B cell immunityMats Bemark, Michael J. Pitcher, Chiara Dionisi, Jo Spencer · 2024 · Trends in Immunology
- SPACEL: deep learning-based characterization of spatial transcriptome architecturesHao Xu, Shuyan Wang, Minghao Fang, Songwen Luo, Chunpeng Chen, Siyuan Wan, Rirui Wang, Meifang Tang, Tian Xue, Bin Li et al. · 2023 · Nature Communications
- Cancer cell states: Lessons from ten years of single-cell RNA-sequencing of human tumorsItay Tirosh, Mario L. Suvà · 2024 · Cancer Cell
- Leveraging information in spatial transcriptomics to predict super-resolution gene expression from histology images in tumorsPang, Minxing, Su, Kenong, Li, Mingyao · 2021
- THItoGene: a deep learning method for predicting spatial transcriptomics from histological imagesJia, Yuran, Liu, Junliang, Chen, Li, Zhao, Tianyi, Wang, Yadong · 2023 · Briefings in Bioinformatics