{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T07:18:07Z","timestamp":1777879087606,"version":"3.51.4"},"publisher-location":"New York, NY","reference-count":17,"publisher":"Springer US","isbn-type":[{"value":"9781071650264","type":"print"},{"value":"9781071650271","type":"electronic"}],"license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026]]},"DOI":"10.1007\/978-1-0716-5027-1_8","type":"book-chapter","created":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T23:34:50Z","timestamp":1777592090000},"page":"119-127","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Mapping the Tumor Microenvironment with Integrative Single-Cell RNA Sequencing and Spatial Proteomics: Uncovering Mechanisms of Disease and Therapeutic Resistance"],"prefix":"10.1007","author":[{"given":"Ashley P.","family":"Tsang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ahmed M.","family":"Elhossiny","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marina Pasca","family":"Di Magliano","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arvind","family":"Rao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2026,5,1]]},"reference":[{"key":"8_CR1","doi-asserted-by":"crossref","unstructured":"Yuan Y (2016) Spatial heterogeneity in the tumor microenvironment. Cold Spring Harb Perspect Med 6(8):a026583","DOI":"10.1101\/cshperspect.a026583"},{"key":"8_CR2","doi-asserted-by":"crossref","unstructured":"Mi H, Ho WJ, Yarchoan M, Popel AS (2022) Multi-scale spatial analysis of the tumor microenvironment reveals features of cabozantinib and nivolumab efficacy in hepatocellular carcinoma. Front Immunol 13:892250","DOI":"10.3389\/fimmu.2022.892250"},{"key":"8_CR3","doi-asserted-by":"crossref","unstructured":"Hunter MV, Moncada R, Weiss JM, Yanai I, White RM (2021) Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface. Nat Commun 12(1):6278","DOI":"10.1038\/s41467-021-26614-z"},{"key":"8_CR4","doi-asserted-by":"crossref","unstructured":"Black S, Phillips D, Hickey JW, Kennedy-Darling J, Venkataraaman VG, Samusik N et al (2021) CODEX multiplexed tissue imaging with DNA-conjugated antibodies. Nat Protoc 16(8):3802\u20133835","DOI":"10.1038\/s41596-021-00556-8"},{"key":"8_CR5","doi-asserted-by":"crossref","unstructured":"Lundberg E, Borner GHH (2019) Spatial proteomics: a powerful discovery tool for cell biology. Nat Rev Mol Cell Biol 20(5):285\u2013302","DOI":"10.1038\/s41580-018-0094-y"},{"key":"8_CR6","doi-asserted-by":"crossref","unstructured":"Krishnan SN, Ji S, Elhossiny AM, Rao A, Frankel TL, Rao A (2024) Proximogram\u2014a multi-omics network-based framework to capture tissue heterogeneity integrating single-cell omics and spatial profiling. Comput Biol Med 182:109082","DOI":"10.1016\/j.compbiomed.2024.109082"},{"key":"8_CR7","doi-asserted-by":"crossref","unstructured":"Baddeley A, Rubak E, Turner R (2015) Spatial point patterns: methodology and applications with R, 1st ed. Chapman & Hall, New York","DOI":"10.1201\/b19708"},{"key":"8_CR8","unstructured":"Schafer J, Opgen-Rhein R, Zuber V, Ahdesmaki M, Silva APD, Strimmer K (2021) corpcor: efficient estimation of covariance and (partial) correlation [Internet]. 2021 [cited 2025 May 2]. Available from: https:\/\/cran.r-project.org\/web\/packages\/corpcor\/index.html"},{"key":"8_CR9","doi-asserted-by":"crossref","unstructured":"Jin S, Guerrero-Juarez CF, Zhang L, Chang I, Ramos R, Kuan CH et al (2021) Inference and analysis of cell-cell communication using CellChat. Nat Commun 12(1):1088","DOI":"10.1038\/s41467-021-21246-9"},{"key":"8_CR10","doi-asserted-by":"crossref","unstructured":"Jin S, Plikus MV, Nie Q (2025) CellChat for systematic analysis of cell\u2013cell communication from single-cell transcriptomics. Nat Protoc 20(1):180\u2013219","DOI":"10.1038\/s41596-024-01045-4"},{"key":"8_CR11","doi-asserted-by":"crossref","unstructured":"Dimitrov D, T\u00fcrei D, Garrido-Rodriguez M, Burmedi PL, Nagai JS, Boys C et al (2022) Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. Nat Commun 13(1):3224","DOI":"10.1038\/s41467-022-30755-0"},{"key":"8_CR12","doi-asserted-by":"crossref","unstructured":"Browaeys R, Saelens W, Saeys Y (2020) NicheNet: modeling intercellular communication by linking ligands to target genes. Nat Methods 17(2):159\u2013162","DOI":"10.1038\/s41592-019-0667-5"},{"key":"#cr-split#-8_CR13.1","doi-asserted-by":"crossref","unstructured":"Hagberg AA, Schult DA, Swart PJ (2008) Exploring network structure, dynamics, and function using NetworkX. In Pasadena, California","DOI":"10.25080\/TCWV9851"},{"key":"#cr-split#-8_CR13.2","unstructured":"2008 [cited 2025 May 2]. pp 11-15. Available from: https:\/\/doi.curvenote.com\/10.25080\/TCWV9851"},{"key":"8_CR14","unstructured":"CSIRO\u2019s Data61 (2018) StellarGraph machine learning library [Internet]. GitHub; 2018 (GitHub Repository). Available from: https:\/\/github.com\/stellargraph\/stellargraph"},{"key":"8_CR15","doi-asserted-by":"crossref","unstructured":"Zhang Y, Liu T, Hu X, Wang M, Wang J, Zou B, Tan P, Cui T, Dou Y, Ning L et al (2021) CellCall: integrating paired ligand\u2013receptor and transcription factor activities for cell\u2013cell communication. Nucleic Acids Res 49(15):8520\u20138534","DOI":"10.1093\/nar\/gkab638"},{"key":"8_CR16","unstructured":"Csardi G, Nepusz T (2006) The igraph software package for complex network research. InterJournal. 2006; Complex Systems: 1695"}],"container-title":["Methods in Molecular Biology","Cellular Spatial Characterization and Analysis"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-0716-5027-1_8","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T23:34:52Z","timestamp":1777592092000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-1-0716-5027-1_8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"ISBN":["9781071650264","9781071650271"],"references-count":17,"URL":"https:\/\/doi.org\/10.1007\/978-1-0716-5027-1_8","relation":{},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"value":"1064-3745","type":"print"},{"value":"1940-6029","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026]]},"assertion":[{"value":"1 May 2026","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"A.R. serves as a member for Voxel Analytics LLC and consults for Genophyll LLC, Tempus Inc, Telperian, and serves as faculty advisor to TCS Ltd. He also serves as an Affiliate Investigator for the Fred Hutch Cancr Center, and a Satish Dhawan Visiting Chair Professor at the Indian Institute of Science Bangalore, India. All other authors have no conflicts of interest to declare.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of Interest"}}]}}