| 1 |
Zeng Y, Yin R, Luo M, Chen J, Pan Z, Lu Y, Yu W, Yang Y. Identifying spatial domain by adapting transcriptomics with histology through contrastive learning. Brief Bioinform 2023;24:bbad048. [PMID: 36781228 DOI: 10.1093/bib/bbad048] [Reference Citation Analysis]
|
| 2 |
Wirth J, Huber N, Yin K, Brood S, Chang S, Martinez-Jimenez CP, Meier M. Spatial transcriptomics using multiplexed deterministic barcoding in tissue. Nat Commun 2023;14:1523. [PMID: 36934108 DOI: 10.1038/s41467-023-37111-w] [Reference Citation Analysis]
|
| 3 |
Shankar V, Yang X, Krishna V, Tan BT, Silva O, Rojansky R, Ng AY, Valvert F, Briercheck EL, Weinstock DM, Natkunam Y, Fernandez-pol S, Rajpurkar P. LymphoML: An interpretable artificial intelligence-based method identifies morphologic features that correlate with lymphoma subtype.. [DOI: 10.1101/2023.03.14.23287143] [Reference Citation Analysis]
|
| 4 |
Heiser CN, Simmons AJ, Revetta F, Mckinley ET, Ramirez-solano MA, Wang J, Shao J, Ayers GD, Wang Y, Glass SE, Kaur H, Rolong A, Chen B, Vega PN, Drewes JL, Saleh N, Vandekar S, Jones AL, Washington MK, Roland JT, Sears CL, Liu Q, Shrubsole MJ, Coffey RJ, Lau KS. Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors.. [DOI: 10.1101/2023.03.09.530832] [Reference Citation Analysis]
|
| 5 |
Lee S, Devanney NA, Golden LR, Smith CT, Schwartz JL, Walsh AE, Clarke HA, Goulding DS, Allenger EJ, Morillo-Segovia G, Friday CM, Gorman AA, Hawkinson TR, MacLean SM, Williams HC, Sun RC, Morganti JM, Johnson LA. APOE modulates microglial immunometabolism in response to age, amyloid pathology, and inflammatory challenge. Cell Rep 2023;42:112196. [PMID: 36871219 DOI: 10.1016/j.celrep.2023.112196] [Reference Citation Analysis]
|
| 6 |
Vandereyken K, Sifrim A, Thienpont B, Voet T. Methods and applications for single-cell and spatial multi-omics. Nat Rev Genet 2023;:1-22. [PMID: 36864178 DOI: 10.1038/s41576-023-00580-2] [Reference Citation Analysis]
|
| 7 |
Li M, Liu H, Li M, Fang S, Kang Q, Zhang J, Teng F, Wang D, Cen W, Li Z, Feng N, Guo J, He Q, Wang L, Zheng T, Li S, Bai Y, Xie M, Bai Y, Liao S, Chen A, Xu X, Zhang Y, Li Y. StereoCell enables high accuracy single cell segmentation for spatial transcriptomic dataset.. [DOI: 10.1101/2023.02.28.530414] [Reference Citation Analysis]
|
| 8 |
Righelli D, Sottosanti A, Risso D. Designing spatial transcriptomic experiments. Nat Methods 2023;20:355-6. [PMID: 36864198 DOI: 10.1038/s41592-023-01801-6] [Reference Citation Analysis]
|
| 9 |
. Spatial Omics DataBase (SODB): increasing accessibility to spatial omics data. Nat Methods 2023;20:359-60. [PMID: 36797411 DOI: 10.1038/s41592-023-01772-8] [Reference Citation Analysis]
|
| 10 |
Fischer DS, Schaar AC, Theis FJ. Modeling intercellular communication in tissues using spatial graphs of cells. Nat Biotechnol 2023;41:332-6. [PMID: 36302986 DOI: 10.1038/s41587-022-01467-z] [Cited by in Crossref: 4] [Article Influence: 4.0] [Reference Citation Analysis]
|
| 11 |
Yuan Z, Pan W, Zhao X, Zhao F, Xu Z, Li X, Zhao Y, Zhang MQ, Yao J. SODB facilitates comprehensive exploration of spatial omics data. Nat Methods 2023;20:387-99. [PMID: 36797409 DOI: 10.1038/s41592-023-01773-7] [Reference Citation Analysis]
|
| 12 |
Karin J, Bornfeld Y, Nitzan M. scPrisma infers, filters and enhances topological signals in single-cell data using spectral template matching. Nat Biotechnol 2023. [PMID: 36849830 DOI: 10.1038/s41587-023-01663-5] [Reference Citation Analysis]
|
| 13 |
Mages S, Moriel N, Avraham-Davidi I, Murray E, Watter J, Chen F, Rozenblatt-Rosen O, Klughammer J, Regev A, Nitzan M. TACCO unifies annotation transfer and decomposition of cell identities for single-cell and spatial omics. Nat Biotechnol 2023. [PMID: 36797494 DOI: 10.1038/s41587-023-01657-3] [Reference Citation Analysis]
|
| 14 |
Jiang R, Li Z, Jia Y, Li S, Chen S. SINFONIA: Scalable Identification of Spatially Variable Genes for Deciphering Spatial Domains. Cells 2023;12. [PMID: 36831270 DOI: 10.3390/cells12040604] [Reference Citation Analysis]
|
| 15 |
Rittel MF, Schmidt S, Weis C, Birgin E, van Marwick B, Rädle M, Diehl SJ, Rahbari N, Marx A, Hopf C. Spatial omics imaging of fresh-frozen tissue and routine FFPE histopathology on a single cancer needle core biopsy: freezing device and multimodal workflow.. [DOI: 10.1101/2023.02.11.528125] [Reference Citation Analysis]
|
| 16 |
Wang L, Liu C, Liu Z. Unraveling Spatial Gene Associations with SEAGAL: a Python Package for Spatial Transcriptomics Data Analysis and Visualization. bioRxiv 2023:2023. [PMID: 36824948 DOI: 10.1101/2023.02.13.528331] [Reference Citation Analysis]
|
| 17 |
Malagoli Tagliazucchi G, Wiecek AJ, Withnell E, Secrier M. Genomic and microenvironmental heterogeneity shaping epithelial-to-mesenchymal trajectories in cancer. Nat Commun 2023;14:789. [PMID: 36774358 DOI: 10.1038/s41467-023-36439-7] [Reference Citation Analysis]
|
| 18 |
Lee S, Williams HC, Gorman AA, Devanney NA, Harrison DA, Walsh AE, Goulding DS, Tuck T, Schwartz JL, Zajac DJ, Macauley SL, Estus S, Julia T, Johnson LA, Morganti JM. APOE4 drives transcriptional heterogeneity and maladaptive immunometabolic responses of astrocytes. bioRxiv 2023:2023. [PMID: 36798317 DOI: 10.1101/2023.02.06.527204] [Reference Citation Analysis]
|
| 19 |
Cang Z, Zhao Y, Almet AA, Stabell A, Ramos R, Plikus MV, Atwood SX, Nie Q. Screening cell-cell communication in spatial transcriptomics via collective optimal transport. Nat Methods 2023;20:218-28. [PMID: 36690742 DOI: 10.1038/s41592-022-01728-4] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
|
| 20 |
Li G, Song B, Singh H, Surya Prasath VB, Leighton Grimes H, Salomonis N. Decision level integration of unimodal and multimodal single cell data with scTriangulate. Nat Commun 2023;14:406. [PMID: 36697445 DOI: 10.1038/s41467-023-36016-y] [Reference Citation Analysis]
|
| 21 |
Mennillo E, Kim YJ, Rusu I, Lee G, Dorman LC, Bernard-Vazquez F, Bain JL, Patel R, Andersen C, Rao A, Tamaki S, Tsui J, Shen A, Naser M, Eckalbar W, Cho SJ, Beck K, El-Nachef N, Lewin S, Selvig DR, Terdiman JP, Mahadevan U, Oh DY, Fragiadakis GK, Pisco A, Combes AJ, Kattah MG. Single-cell and spatial multi-omics identify innate and stromal modules targeted by anti-integrin therapy in ulcerative colitis. bioRxiv 2023:2023. [PMID: 36711576 DOI: 10.1101/2023.01.21.525036] [Reference Citation Analysis]
|
| 22 |
Mongia A, Saunders DC, Wang YJ, Brissova M, Powers AC, Kaestner KH, Vahedi G, Naji A, Schwartz GW, Faryabi RB. AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics. bioRxiv 2023:2023. [PMID: 36712052 DOI: 10.1101/2023.01.15.524135] [Reference Citation Analysis]
|
| 23 |
Cotechini T, Jones O, Hindmarch CCT. Imaging Mass Cytometry in Immuno-Oncology. Methods Mol Biol 2023;2614:1-15. [PMID: 36587115 DOI: 10.1007/978-1-0716-2914-7_1] [Reference Citation Analysis]
|
| 24 |
Ma S, Fang X, Yao Y, Li J, Morgan DC, Xia Y, Kwok CSM, Lo MCK, Siu DMD, Tsia KK, Yang A, Ho JWK. StarmapVis: An interactive and narrative visualisation tool for single-cell and spatial data. Comput Struct Biotechnol J 2023;21:1598-605. [PMID: 36874160 DOI: 10.1016/j.csbj.2023.02.023] [Reference Citation Analysis]
|
| 25 |
Ospina O, Soupir A, Fridley BL. A Primer on Preprocessing, Visualization, Clustering, and Phenotyping of Barcode-Based Spatial Transcriptomics Data. Methods Mol Biol 2023;2629:115-40. [PMID: 36929076 DOI: 10.1007/978-1-0716-2986-4_7] [Reference Citation Analysis]
|
| 26 |
Miranda L, Bordes J, Gasperoni S, Lopez JP. Increasing resolution in stress neurobiology: from single cells to complex group behaviors. Stress 2023;26:2186141. [PMID: 36855966 DOI: 10.1080/10253890.2023.2186141] [Reference Citation Analysis]
|
| 27 |
Townes FW, Engelhardt BE. Nonnegative spatial factorization applied to spatial genomics. Nat Methods 2023;20:229-38. [PMID: 36587187 DOI: 10.1038/s41592-022-01687-w] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
|
| 28 |
Lo YC, Liu Y, Kammersgaard M, Koladiya A, Keyes TJ, Davis KL. Single-cell technologies uncover intra-tumor heterogeneity in childhood cancers. Semin Immunopathol 2023;45:61-9. [PMID: 36625902 DOI: 10.1007/s00281-022-00981-1] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
|
| 29 |
Yue L, Liu F, Hu J, Yang P, Wang Y, Dong J, Shu W, Huang X, Wang S. A guidebook of spatial transcriptomic technologies, data resources and analysis approaches. Computational and Structural Biotechnology Journal 2023. [DOI: 10.1016/j.csbj.2023.01.016] [Reference Citation Analysis]
|
| 30 |
Wrobel J, Harris C, Vandekar S. Statistical Analysis of Multiplex Immunofluorescence and Immunohistochemistry Imaging Data. Methods Mol Biol 2023;2629:141-68. [PMID: 36929077 DOI: 10.1007/978-1-0716-2986-4_8] [Reference Citation Analysis]
|
| 31 |
Li JSY, Raghubar AM, Matigian NA, Ng MSY, Rogers NM, Mallett AJ. The Utility of Spatial Transcriptomics for Solid Organ Transplantation. Transplantation 2022. [PMID: 36584371 DOI: 10.1097/TP.0000000000004466] [Reference Citation Analysis]
|
| 32 |
Muzellec B, Teleńczuk M, Cabeli V, Andreux M. PyDESeq2: a python package for bulk RNA-seq differential expression analysis.. [DOI: 10.1101/2022.12.14.520412] [Reference Citation Analysis]
|
| 33 |
Liu J, Tran V, Vemuri VNP, Byrne A, Borja M, Kim YJ, Agarwal S, Wang R, Awayan K, Murti A, Taychameekiatchai A, Wang B, Emanuel G, He J, Haliburton J, Oliveira Pisco A, Neff NF. Concordance of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing. Life Sci Alliance 2023;6. [PMID: 36526371 DOI: 10.26508/lsa.202201701] [Reference Citation Analysis]
|
| 34 |
Park J, Kim J, Lewy T, Rice CM, Elemento O, Rendeiro AF, Mason CE. Spatial omics technologies at multimodal and single cell/subcellular level. Genome Biol 2022;23:256. [PMID: 36514162 DOI: 10.1186/s13059-022-02824-6] [Reference Citation Analysis]
|
| 35 |
Mou M, Pan Z, Lu M, Sun H, Wang Y, Luo Y, Zhu F. Application of Machine Learning in Spatial Proteomics. J Chem Inf Model 2022;62:5875-95. [PMID: 36378082 DOI: 10.1021/acs.jcim.2c01161] [Reference Citation Analysis]
|
| 36 |
Qiu X, Zhu DY, Yao J, Jing Z, Zuo L, Wang M, Min KH(, Pan H, Wang S, Liao S, Lai Y, Hao S, Lu YR, Hill M, Martin-rufino JD, Weng C, Riera-escandell AM, Chen M, Wu L, Zhang Y, Wei X, Li M, Huang X, Xiang R, Yang Z, Liu C, Xia T, Liang Y, Xu J, Hu Q, Hu Y, Zhu H, Li Y, Chen A, Esteban MA, Gu Y, Lauffenburger DA, Xu X, Liu L, Weissman JS, Liu S, Bai Y. Spateo: multidimensional spatiotemporal modeling of single-cell spatial transcriptomics.. [DOI: 10.1101/2022.12.07.519417] [Reference Citation Analysis]
|
| 37 |
Andersson A, Behanova A, Avenel C, Wählby C, Malmberg F. Points2Regions: Fast Interactive Clustering ofin SituTranscriptomics Data.. [DOI: 10.1101/2022.12.07.519086] [Reference Citation Analysis]
|
| 38 |
Su M, Pan T, Chen QZ, Zhou WW, Gong Y, Xu G, Yan HY, Li S, Shi QZ, Zhang Y, He X, Jiang CJ, Fan SC, Li X, Cairns MJ, Wang X, Li YS. Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications. Mil Med Res 2022;9:68. [PMID: 36461064 DOI: 10.1186/s40779-022-00434-8] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
|
| 39 |
Moreno M, Vilaça R, Ferreira PG. Scalable transcriptomics analysis with Dask: applications in data science and machine learning. BMC Bioinformatics 2022;23:514. [PMID: 36451115 DOI: 10.1186/s12859-022-05065-3] [Reference Citation Analysis]
|
| 40 |
Yuan Z, Li Y, Shi M, Yang F, Gao J, Yao J, Zhang MQ. SOTIP is a versatile method for microenvironment modeling with spatial omics data. Nat Commun 2022;13:7330. [PMID: 36443314 DOI: 10.1038/s41467-022-34867-5] [Reference Citation Analysis]
|
| 41 |
Wu Z, Wang R, Sun Z, Su Y, Xiao L. A mass spectrometry imaging approach on spatiotemporal distribution of multiple alkaloids in Gelsemium elegans. Front Plant Sci 2022;13. [DOI: 10.3389/fpls.2022.1051756] [Reference Citation Analysis]
|
| 42 |
Rovira-Clavé X, Drainas AP, Jiang S, Bai Y, Baron M, Zhu B, Dallas AE, Lee MC, Chu TP, Holzem A, Ayyagari R, Bhattacharya D, McCaffrey EF, Greenwald NF, Markovic M, Coles GL, Angelo M, Bassik MC, Sage J, Nolan GP. Spatial epitope barcoding reveals clonal tumor patch behaviors. Cancer Cell 2022;40:1423-1439.e11. [PMID: 36240778 DOI: 10.1016/j.ccell.2022.09.014] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
|
| 43 |
Mallick H, Porwal A, Saha S, Svetnik V, Paul E. An integrated Bayesian framework for multi-omics prediction and classification.. [DOI: 10.1101/2022.11.06.514786] [Reference Citation Analysis]
|
| 44 |
Jones DC, Danaher P, Kim Y, Beechem JM, Gottardo R, Newell EW. An information theoretic approach to detecting spatially varying genes.. [DOI: 10.1101/2022.11.02.514777] [Reference Citation Analysis]
|
| 45 |
Zhao J, Liu Y, Wang M, Ma J, Yang P, Wang S, Wu Q, Gao J, Chen M, Qu G, Wang J, Jiang G. Insights into highly multiplexed tissue images: A primer for Mass Cytometry Imaging data analysis. TrAC Trends in Analytical Chemistry 2022. [DOI: 10.1016/j.trac.2022.116794] [Reference Citation Analysis]
|
| 46 |
Summers HD, Wills JW, Rees P. Spatial statistics is a comprehensive tool for quantifying cell neighbor relationships and biological processes via tissue image analysis. Cell Reports Methods 2022;2:100348. [DOI: 10.1016/j.crmeth.2022.100348] [Reference Citation Analysis]
|
| 47 |
Su J, Reynier J, Fu X, Zhong G, Jiang J, Escalante RS, Wang Y, Izar B, Knowles DA, Rabadan R. A Unified Modular Framework to Incorporate Structural Dependency in Spatial Omics Data.. [DOI: 10.1101/2022.10.25.513785] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
|
| 48 |
Ding J, Wen H, Tang W, Liu R, Li Z, Venegas J, Su R, Molho D, Jin W, Zuo W, Wang Y, Yang R, Xie Y, Tang J. DANCE: A Deep Learning Library and Benchmark Platform for Single-Cell Analysis.. [DOI: 10.1101/2022.10.19.512741] [Reference Citation Analysis]
|
| 49 |
Quintanal-Villalonga Á, Chan JM, Masilionis I, Gao VR, Xie Y, Allaj V, Chow A, Poirier JT, Pe'er D, Rudin CM, Mazutis L. Protocol to dissociate, process, and analyze the human lung tissue using single-cell RNA-seq. STAR Protoc 2022;3:101776. [PMID: 36313536 DOI: 10.1016/j.xpro.2022.101776] [Reference Citation Analysis]
|
| 50 |
Dufour A, Das N, de Almeida L, Derakhshani A, Young D, Salo P, Rezansoff A, Jay G, Sommerhoff C, Schmidt T, Krawetz R. Tryptase β regulation of joint lubrication and inflammation via proteoglycan-4 in osteoarthritis.. [DOI: 10.21203/rs.3.rs-2105857/v1] [Reference Citation Analysis]
|
| 51 |
Xu C, Jin X, Wei S, Wang P, Luo M, Xu Z, Yang W, Cai Y, Xiao L, Lin X, Liu H, Cheng R, Pang F, Chen R, Su X, Hu Y, Wang G, Jiang Q. DeepST: identifying spatial domains in spatial transcriptomics by deep learning. Nucleic Acids Res 2022;50:e131. [PMID: 36250636 DOI: 10.1093/nar/gkac901] [Reference Citation Analysis]
|
| 52 |
Zheng Y, Chen Y, Ding X, Wong KH, Cheung E. Aquila: a spatial omics database and analysis platform. Nucleic Acids Res 2023;51:D827-34. [PMID: 36243967 DOI: 10.1093/nar/gkac874] [Reference Citation Analysis]
|
| 53 |
Atkins TK, Song T, Kuang R. FIST-nD: A tool forn-dimensional spatial transcriptomics data imputation via graph-regularized tensor completion.. [DOI: 10.1101/2022.10.12.511928] [Reference Citation Analysis]
|
| 54 |
Mantri M, Hinchman MM, Mckellar DW, Wang MFZ, Cross ST, Parker JSL, De Vlaminck I. Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis. Nat Cardiovasc Res 2022;1:946-960. [DOI: 10.1038/s44161-022-00138-1] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
|
| 55 |
Zuo C, Zhang Y, Cao C, Feng J, Jiao M, Chen L. Elucidating tumor heterogeneity from spatially resolved transcriptomics data by multi-view graph collaborative learning. Nat Commun 2022;13:5962. [PMID: 36216831 DOI: 10.1038/s41467-022-33619-9] [Reference Citation Analysis]
|
| 56 |
Overbey EG, Das S, Cope H, Madrigal P, Andrusivova Z, Frapard S, Klotz R, Bezdan D, Gupta A, Scott RT, Park J, Chirko D, Galazka JM, Costes SV, Mason CE, Herranz R, Szewczyk NJ, Borg J, Giacomello S. Challenges and considerations for single-cell and spatially resolved transcriptomics sample collection during spaceflight. Cell Reports Methods 2022. [DOI: 10.1016/j.crmeth.2022.100325] [Reference Citation Analysis]
|
| 57 |
Ali A, Davidson S, Fraenkel E, Gilmore I, Hankemeier T, Kirwan JA, Lane AN, Lanekoff I, Larion M, McCall LI, Murphy M, Sweedler JV, Zhu C. Single cell metabolism: current and future trends. Metabolomics 2022;18:77. [PMID: 36181583 DOI: 10.1007/s11306-022-01934-3] [Cited by in Crossref: 2] [Article Influence: 2.0] [Reference Citation Analysis]
|
| 58 |
Sardoo AM, Zhang S, Ferraro TN, Keck TM, Chen Y. Decoding brain memory formation by single-cell RNA sequencing. Brief Bioinform 2022;23. [PMID: 36156112 DOI: 10.1093/bib/bbac412] [Reference Citation Analysis]
|
| 59 |
Krieger TG, Sudy A, Schicktanz F, Tosti L, Liebig J, Konukiewitz B, Rouault M, Niesnerová A, Qian X, Weichert W, Eils R, Steiger K, Conrad C. Transcriptionally defined morphological subtypes of pancreatic ductal adenocarcinoma.. [DOI: 10.1101/2022.09.23.509133] [Reference Citation Analysis]
|
| 60 |
Chao Y, Xiang Y, Xiao J, Zhang S, Zheng W, Wan X, Li Z, Gao M, Wang G, Chen Z, Ebrahimkhani M, Yang C, Wu AR, Liu P, Huang Y, Sugimura R. Organoid-based single-cell spatiotemporal gene expression landscape of human embryonic development and hematopoiesis.. [DOI: 10.1101/2022.09.02.505700] [Reference Citation Analysis]
|
| 61 |
Martin PCN, Kim H, Lövkvist C, Hong BW, Won KJ. Vesalius: high-resolution in silico anatomization of spatial transcriptomic data using image analysis. Mol Syst Biol 2022;18:e11080. [PMID: 36065846 DOI: 10.15252/msb.202211080] [Reference Citation Analysis]
|
| 62 |
Xi J, Lee JH, Kang HM, Jun G. STtools: A Comprehensive Software Pipeline for Ultra-high Resolution Spatial Transcriptomics Data. Bioinform Adv 2022;2:vbac061. [PMID: 36284674 DOI: 10.1093/bioadv/vbac061] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
|
| 63 |
Wirth J, Compera N, Yin K, Brood S, Chang S, Martinez-jimenez CP, Meier M. Spatial Transcriptomics Using Multiplexed Deterministic Barcoding in Tissue.. [DOI: 10.1101/2022.08.30.505834] [Reference Citation Analysis]
|
| 64 |
Ruiz-moreno C, Salas SM, Samuelsson E, Brandner S, Kranendonk ME, Nilsson M, Stunnenberg HG. Harmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastoma.. [DOI: 10.1101/2022.08.27.505439] [Reference Citation Analysis]
|
| 65 |
Cang Z, Zhao Y, Almet AA, Stabell A, Ramos R, Plikus M, Atwood SX, Nie Q. Screening cell-cell communication in spatial transcriptomics via collective optimal transport.. [DOI: 10.1101/2022.08.24.505185] [Reference Citation Analysis]
|
| 66 |
Vallejo AF, Harvey K, Wang T, Wise K, Butler LM, Polo J, Plummer J, Swarbrick A, Martelotto LG. snPATHO-seq: unlocking the FFPE archives for single nucleus RNA profiling.. [DOI: 10.1101/2022.08.23.505054] [Cited by in F6Publishing: 2] [Reference Citation Analysis]
|
| 67 |
Pechuan-jorge X, Li X, Risom T, Zubkov A, Tabatsky E, Prilipko A, Ye X, Shi Z, Nowicka M, Peale F, Hibar D, Ziai J, Jesudason R, Orlova D. SPEX: A modular end-to-end analytics tool for spatially resolved omics of tissues.. [DOI: 10.1101/2022.08.22.504841] [Reference Citation Analysis]
|
| 68 |
Creason A, Watson C, Gu Q, Persson D, Sargent L, Chen Y, Lin J, Sivagnanam S, Wünnemann F, Nirmal AJ, Chin K, Feiler HS, Coussens LM, Schapiro D, Grüning B, Sorger PK, Sokolov A, Goecks J. A Web-based Software Resource for Interactive Analysis of Multiplex Tissue Imaging Datasets.. [DOI: 10.1101/2022.08.18.504436] [Reference Citation Analysis]
|
| 69 |
Pont F, Cerapio JP, Gravelle P, Ligat L, Valle C, Sarot E, Perrier M, Lopez F, Laurent C, Fournié JJ, Tosolini M. Single-cell Spatial Explorer: Easy exploration of spatial and multimodal transcriptomics.. [DOI: 10.1101/2022.08.04.502890] [Reference Citation Analysis]
|
| 70 |
Chiu C, Clack N; the napari community. napari: a Python Multi-Dimensional Image Viewer Platform for the Research Community. Microsc Microanal 2022;28:1576-7. [DOI: 10.1017/s1431927622006328] [Reference Citation Analysis]
|
| 71 |
Tran M, Yoon S, Teoh M, Andersen S, Lam P, Purdue BW, Raghubar A, Hanson S, Devitt K, Jones K, Walters S, Monkman J, Kulasinghe A, Tuong Z, Soyer H, Frazer IH, Nguyen Q. A robust experimental and computational analysis framework at multiple resolutions, modalities and coverages. Front Immunol 2022;13:911873. [DOI: 10.3389/fimmu.2022.911873] [Reference Citation Analysis]
|
| 72 |
Sztanka-Toth TR, Jens M, Karaiskos N, Rajewsky N. Spacemake: processing and analysis of large-scale spatial transcriptomics data. Gigascience 2022;11:giac064. [PMID: 35852420 DOI: 10.1093/gigascience/giac064] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
|
| 73 |
Suwalska A, Zientek L, Polanska J, Marczyk M. Quantifying Spatial Heterogeneity of Tumor-Infiltrating Lymphocytes to Predict Survival of Individual Cancer Patients. JPM 2022;12:1113. [DOI: 10.3390/jpm12071113] [Reference Citation Analysis]
|
| 74 |
Parreno-centeno M, Malagoli Tagliazucchi G, Withnell E, Pan S, Secrier M. A deep learning and graph-based approach to characterise the immunological landscape and spatial architecture of colon cancer tissue.. [DOI: 10.1101/2022.07.06.498984] [Reference Citation Analysis]
|
| 75 |
Biermann J, Melms JC, Amin AD, Wang Y, Caprio LA, Karz A, Tagore S, Barrera I, Ibarra-arellano MA, Andreatta M, Fullerton BT, Gretarsson KH, Sahu V, Mangipudy VS, Nguyen TT, Nair A, Rogava M, Ho P, Koch PD, Banu M, Humala N, Mahajan A, Walsh ZH, Shah SB, Vaccaro DH, Caldwell B, Mu M, Wünnemann F, Chazotte M, Berhe S, Luoma AM, Driver J, Ingham M, Khan SA, Rapisuwon S, Slingluff CL, Eigentler T, Röcken M, Carvajal R, Atkins MB, Davies MA, Agustinus A, Bakhoum SF, Azizi E, Siegelin M, Lu C, Carmona SJ, Hibshoosh H, Ribas A, Canoll P, Bruce JN, Bi WL, Agrawal P, Schapiro D, Hernando E, Macosko EZ, Chen F, Schwartz GK, Izar B. Dissecting the treatment-naive ecosystem of human melanoma brain metastasis. Cell 2022;185:2591-2608.e30. [DOI: 10.1016/j.cell.2022.06.007] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
|
| 76 |
van Dam S, Baars MJD, Vercoulen Y. Multiplex Tissue Imaging: Spatial Revelations in the Tumor Microenvironment. Cancers 2022;14:3170. [DOI: 10.3390/cancers14133170] [Reference Citation Analysis]
|
| 77 |
Chen J, Liu W, Luo T, Yu Z, Jiang M, Wen J, Gupta GP, Giusti P, Zhu H, Yang Y, Li Y. A comprehensive comparison on cell-type composition inference for spatial transcriptomics data. Brief Bioinform 2022;23. [PMID: 35753702 DOI: 10.1093/bib/bbac245] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 2.0] [Reference Citation Analysis]
|
| 78 |
Williams CG, Lee HJ, Asatsuma T, Vento-Tormo R, Haque A. An introduction to spatial transcriptomics for biomedical research. Genome Med 2022;14:68. [PMID: 35761361 DOI: 10.1186/s13073-022-01075-1] [Cited by in Crossref: 5] [Cited by in F6Publishing: 5] [Article Influence: 5.0] [Reference Citation Analysis]
|
| 79 |
Peng L, Wang F, Wang Z, Tan J, Huang L, Tian X, Liu G, Zhou L. Cell-cell communication inference and analysis in the tumour microenvironments from single-cell transcriptomics: data resources and computational strategies. Brief Bioinform 2022:bbac234. [PMID: 35753695 DOI: 10.1093/bib/bbac234] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 2.0] [Reference Citation Analysis]
|
| 80 |
Mah CK, Ahmed N, Lam D, Monell A, Kern C, Han Y, Cesnik AJ, Lundberg E, Zhu Q, Carter H, Yeo GW. Bento: A toolkit for subcellular analysis of spatial transcriptomics data.. [DOI: 10.1101/2022.06.10.495510] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
|
| 81 |
Pardo B, Spangler A, Weber LM, Page SC, Hicks SC, Jaffe AE, Martinowich K, Maynard KR, Collado-Torres L. spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data. BMC Genomics 2022;23:434. [PMID: 35689177 DOI: 10.1186/s12864-022-08601-w] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
|
| 82 |
Hilscher MM, Langseth CM, Kukanja P, Yokota C, Nilsson M, Castelo-Branco G. Spatial and temporal heterogeneity in the lineage progression of fine oligodendrocyte subtypes. BMC Biol 2022;20:122. [PMID: 35610641 DOI: 10.1186/s12915-022-01325-z] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 2.0] [Reference Citation Analysis]
|
| 83 |
Cheng M, Wu L, Han L, Huang X, Lai Y, Xu J, Wang S, Li M, Zheng H, Feng W, Huang Z, Jiang Y, Hao S, Li Z, Chen X, Peng J, Guo P, Zhang X, Lai G, Deng Q, Yuan Y, Yang F, Wei X, Liao S, Chen A, Volpe G, Esteban MA, Hou Y, Liu C, Liu L. A Cellular Resolution Spatial Transcriptomic Landscape of the Medial Structures in Postnatal Mouse Brain. Front Cell Dev Biol 2022;10:878346. [DOI: 10.3389/fcell.2022.878346] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
|
| 84 |
Suo C, Dann E, Goh I, Jardine L, Kleshchevnikov V, Park JE, Botting RA, Stephenson E, Engelbert J, Tuong ZK, Polanski K, Yayon N, Xu C, Suchanek O, Elmentaite R, Domínguez Conde C, He P, Pritchard S, Miah M, Moldovan C, Steemers AS, Mazin P, Prete M, Horsfall D, Marioni JC, Clatworthy MR, Haniffa M, Teichmann SA. Mapping the developing human immune system across organs. Science 2022;:eabo0510. [PMID: 35549310 DOI: 10.1126/science.abo0510] [Cited by in Crossref: 12] [Cited by in F6Publishing: 15] [Article Influence: 12.0] [Reference Citation Analysis]
|
| 85 |
Spitzer H, Berry S, Donoghoe M, Pelkmans L, Theis FJ. Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps.. [DOI: 10.1101/2022.05.07.490900] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
|
| 86 |
Dhainaut M, Rose SA, Akturk G, Wroblewska A, Nielsen SR, Park ES, Buckup M, Roudko V, Pia L, Sweeney R, Le Berichel J, Wilk CM, Bektesevic A, Lee BH, Bhardwaj N, Rahman AH, Baccarini A, Gnjatic S, Pe'er D, Merad M, Brown BD. Spatial CRISPR genomics identifies regulators of the tumor microenvironment. Cell 2022;185:1223-1239.e20. [PMID: 35290801 DOI: 10.1016/j.cell.2022.02.015] [Cited by in Crossref: 9] [Cited by in F6Publishing: 17] [Article Influence: 9.0] [Reference Citation Analysis]
|
| 87 |
Zhang Y, Miller JA, Park J, Lelieveldt BP, Long B, Abdelaal T, Aevermann BD, Biancalani T, Comiter C, Dzyubachyk O, Eggermont J, Langseth CM, Petukhov V, Scalia G, Vaishnav ED, Zhao Y, Lein ES, Scheuermann RH. Reference-based cell type matching of spatial transcriptomics data.. [DOI: 10.1101/2022.03.28.486139] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
|
| 88 |
Moses L, Pachter L. Museum of spatial transcriptomics. Nat Methods 2022. [PMID: 35273392 DOI: 10.1038/s41592-022-01409-2] [Cited by in Crossref: 28] [Cited by in F6Publishing: 41] [Article Influence: 28.0] [Reference Citation Analysis]
|
| 89 |
Liu J, Tran V, Vemuri VNP, Byrne A, Borja M, Kim YJ, Agarwal S, Wang R, Awayan K, Murti A, Taychameekiatchai A, Wang B, Emanuel G, He J, Haliburton J, Pisco AO, Neff N. Concordance of MERFISH Spatial Transcriptomics with Bulk and Single-cell RNA Sequencing.. [DOI: 10.1101/2022.03.04.483068] [Cited by in Crossref: 3] [Cited by in F6Publishing: 4] [Article Influence: 3.0] [Reference Citation Analysis]
|
| 90 |
Jin S, Ramos R. Computational exploration of cellular communication in skin from emerging single-cell and spatial transcriptomic data. Biochem Soc Trans 2022:BST20210863. [PMID: 35191953 DOI: 10.1042/BST20210863] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 3.0] [Reference Citation Analysis]
|
| 91 |
Kleino I, Frolovaitė P, Suomi T, Elo LL. Computational solutions for spatial transcriptomics. Computational and Structural Biotechnology Journal 2022;20:4870-84. [DOI: 10.1016/j.csbj.2022.08.043] [Reference Citation Analysis]
|
| 92 |
Liu I, Jiang L, Samuelsson ER, Marco Salas S, Beck A, Hack OA, Jeong D, Shaw ML, Englinger B, LaBelle J, Mire HM, Madlener S, Mayr L, Quezada MA, Trissal M, Panditharatna E, Ernst KJ, Vogelzang J, Gatesman TA, Halbert ME, Palova H, Pokorna P, Sterba J, Slaby O, Geyeregger R, Diaz A, Findlay IJ, Dun MD, Resnick A, Suvà ML, Jones DTW, Agnihotri S, Svedlund J, Koschmann C, Haberler C, Czech T, Slavc I, Cotter JA, Ligon KL, Alexandrescu S, Yung WKA, Arrillaga-Romany I, Gojo J, Monje M, Nilsson M, Filbin MG. The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location. Nat Genet 2022;54:1881-94. [PMID: 36471067 DOI: 10.1038/s41588-022-01236-3] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 2.0] [Reference Citation Analysis]
|
| 93 |
Mantri M, Hinchman MM, Mckellar DW, Wang MFZ, Cross ST, Parker JSL, De Vlaminck I. Spatiotemporal transcriptomics reveals pathogenesis of viral myocarditis.. [DOI: 10.1101/2021.12.07.471659] [Cited by in Crossref: 4] [Cited by in F6Publishing: 4] [Article Influence: 2.0] [Reference Citation Analysis]
|
| 94 |
Preibisch S, Karaiskos N, Rajewsky N. Image-based representation of massive spatial transcriptomics datasets.. [DOI: 10.1101/2021.12.07.471629] [Cited by in F6Publishing: 1] [Reference Citation Analysis]
|
| 95 |
Tippani M, Divecha HR, Catallini JL, Kwon SH, Weber LM, Spangler A, Jaffe AE, Hicks SC, Martinowich K, Collado-torres L, Page SC, Maynard KR. VistoSeg: processing utilities for high-resolution Visium/Visium-IF images for spatial transcriptomics data.. [DOI: 10.1101/2021.08.04.452489] [Cited by in Crossref: 3] [Cited by in F6Publishing: 3] [Article Influence: 1.5] [Reference Citation Analysis]
|
| 96 |
Chidester B, Zhou T, Alam S, Ma J. SPICEMIX: Integrative single-cell spatial modeling of cell identity.. [DOI: 10.1101/2020.11.29.383067] [Cited by in Crossref: 7] [Cited by in F6Publishing: 7] [Article Influence: 2.3] [Reference Citation Analysis]
|
