SpaDiff denoises sequence-based spatial transcriptomics via diffusion process.

Συγγραφείς: Cai J; Department of Statistics, University of Georgia, Athens, GA, USA., Chen Y; Department of Statistics, Harvard University, Cambridge, MA, USA., Fang L; Department of Statistics, University of Georgia, Athens, GA, USA., Liu X; Department of Statistics, University of Georgia, Athens, GA, USA., Zhong W; Department of Statistics, University of Georgia, Athens, GA, USA. Electronic address: wenxuan@uga.edu., Yuan GC; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Electronic address: guo-cheng.yuan@mssm.edu., Ma P; Department of Statistics, University of Georgia, Athens, GA, USA. Electronic address: pingma@uga.edu.

Πηγή: Cell reports methods [Cell Rep Methods] 2026 Sep 21; Vol. 6 (9), pp. 101530. Date of Electronic Publication: 2026 Jul 17.

Τύπος έκδοσης: Journal Article

Στοιχεία περιοδικού: Publisher: Elsevier Inc Country of Publication: United States NLM ID: 9918227360606676 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2667-2375 (Electronic) Linking ISSN: 26672375 NLM ISO Abbreviation: Cell Rep Methods Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Spatial Transcriptomics*/methods , Gene Expression Profiling*/methods , Transcriptome*/genetics, Colorectal Neoplasms/genetics ; Animals ; Humans ; Mice ; Algorithms

Enhancing Super-Resolution Spatial Transcriptomics Data by Transfer Learning.

Συγγραφείς: Li X; School of Artificial Intelligence, Wuhan University, Wuhan, China.; School of Computer Science, Yunnan University, Kunming, China., Zhang L; School of Artificial Intelligence, Wuhan University, Wuhan, China., Min W; School of Computer Science, Yunnan University, Kunming, China.

Πηγή: Advanced science (Weinheim, Baden-Wurttemberg, Germany) [Adv Sci (Weinh)] 2026 Oct; Vol. 13 (56), pp. e76601. Date of Electronic Publication: 2026 Jul 20.

Τύπος έκδοσης: Journal Article

Στοιχεία περιοδικού: Publisher: WILEY-VCH Country of Publication: Germany NLM ID: 101664569 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2198-3844 (Electronic) Linking ISSN: 21983844 NLM ISO Abbreviation: Adv Sci (Weinh) Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Spatial Transcriptomics*/methods , Image Processing, Computer-Assisted*/methods , Gene Expression Profiling*/methods , Transcriptome*/genetics, Humans ; Animals

Opportunities and challenges for the application of single-cell RNA sequencing and spatial transcriptomics in ischemic stroke.

Συγγραφείς: Wang Z; The First Clinical Medical College, Yunnan University of Chinese Medicine, Kunming, China., Hao Z; The First Clinical Medical College, Yunnan University of Chinese Medicine, Kunming, China., Xu S; The First Clinical Medical College, Yunnan University of Chinese Medicine, Kunming, China., Wu H; The First Clinical Medical College, Yunnan University of Chinese Medicine, Kunming, China., Wu J; The First Clinical Medical College, Yunnan University of Chinese Medicine, Kunming, China., Zhao M; The First Clinical Medical College, Yunnan University of Chinese Medicine, Kunming, China., Wang R; College of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, China. Electronic address: wangrryucm@126.com., Xing L; The First Clinical Medical College, Yunnan University of Chinese Medicine, Kunming, China. Electronic address: 1791536722@qq.com., Wang J; The First Clinical Medical College, Yunnan University of Chinese Medicine, Kunming, China. Electronic address: laohaodiao@126.com.

Πηγή: Experimental neurology [Exp Neurol] 2026 Oct; Vol. 404, pp. 115901. Date of Electronic Publication: 2026 Jul 05.

Τύπος έκδοσης: Journal Article; Review

Στοιχεία περιοδικού: Publisher: Academic Press Country of Publication: United States NLM ID: 0370712 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1090-2430 (Electronic) Linking ISSN: 00144886 NLM ISO Abbreviation: Exp Neurol Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Ischemic Stroke*/metabolism , Single-Cell Gene Expression Analysis* , Spatial Transcriptomics*, Humans ; Animals ; Translational Science, Biomedical

A variational graph autoencoder guided by residual multi-head attention reveals heterogeneity in spatial transcriptomics.

Συγγραφείς: Li J; School of Data Science, Qingdao University of Science and Technology, Qingdao 266061, China; Artificial Intelligence and Biomedical Big Data Research Center, Qingdao University of Science and Technology, Qingdao 266061, China., Lv H; School of Data Science, Qingdao University of Science and Technology, Qingdao 266061, China; Artificial Intelligence and Biomedical Big Data Research Center, Qingdao University of Science and Technology, Qingdao 266061, China., Jiang F; Editorial Office of Journal of Qingdao University of Science and Technology (Natural Science Edition), Qingdao University of Science and Technology, Qingdao 266061, China. Electronic address: jfhict@qust.edu.cn., Yu B; School of Data Science, Qingdao University of Science and Technology, Qingdao 266061, China; Artificial Intelligence and Biomedical Big Data Research Center, Qingdao University of Science and Technology, Qingdao 266061, China. Electronic address: yubin@qust.edu.cn.

Πηγή: Computational biology and chemistry [Comput Biol Chem] 2026 Oct; Vol. 124 (Pt 1), pp. 109112. Date of Electronic Publication: 2026 May 06.

Τύπος έκδοσης: Journal Article

Στοιχεία περιοδικού: Publisher: Elsevier Country of Publication: England NLM ID: 101157394 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1476-928X (Electronic) Linking ISSN: 14769271 NLM ISO Abbreviation: Comput Biol Chem Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Spatial Transcriptomics*, Autoencoder ; Graph Neural Networks ; Animals ; Humans

Insights Into Spatial Transcriptomics: Exploring Recent Technical Developments and Their Diverse Applications.

Συγγραφείς: Li X; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Henan University, Kaifeng, China., Yang Z; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Henan University, Kaifeng, China., Li J; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Henan University, Kaifeng, China., Cao H; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Henan University, Kaifeng, China., Xu K; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Henan University, Kaifeng, China., Shen J; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Henan University, Kaifeng, China., Wang Y; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Henan University, Kaifeng, China., Gomaa SE; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Henan University, Kaifeng, China.; Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt., Cheng G; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Henan University, Kaifeng, China.; Department of Pathogen Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.; Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China., Teng T; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Henan University, Kaifeng, China., Li J; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Henan University, Kaifeng, China., Wang X; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Henan University, Kaifeng, China.; Department of Pathogen Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.; Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China., Dong X; Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Henan University, Kaifeng, China.

Πηγή: FASEB journal : official publication of the Federation of American Societies for Experimental Biology [FASEB J] 2026 Sep 30; Vol. 40 (18), pp. e72294.

Τύπος έκδοσης: Journal Article; Review

Στοιχεία περιοδικού: Publisher: Federation of American Societies for Experimental Biology Country of Publication: United States NLM ID: 8804484 Publication Model: Print Cited Medium: Internet ISSN: 1530-6860 (Electronic) Linking ISSN: 08926638 NLM ISO Abbreviation: FASEB J Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Gene Expression Profiling*/methods , Spatial Transcriptomics* , Transcriptome*, Single-Cell Analysis/methods ; Animals ; Humans ; Multiomics ; Single-Cell Gene Expression Analysis

Single-cell and spatial transcriptomics inform mechanistic physiology in non-model animals.

Συγγραφείς: Amin A; Department of Life Sciences, Yeungnam University, Gyeongsan, 38541, Republic of Korea., Zaman W; Department of Life Sciences, Yeungnam University, Gyeongsan, 38541, Republic of Korea. wajidzaman@yu.ac.kr.

Πηγή: Functional & integrative genomics [Funct Integr Genomics] 2026 Sep 23; Vol. 26 (1). Date of Electronic Publication: 2026 Sep 23.

Τύπος έκδοσης: Journal Article; Review

Στοιχεία περιοδικού: Publisher: Springer Country of Publication: Germany NLM ID: 100939343 Publication Model: Electronic Cited Medium: Internet ISSN: 1438-7948 (Electronic) Linking ISSN: 1438793X NLM ISO Abbreviation: Funct Integr Genomics Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Physiology, Comparative*/methods , Invertebrates*/classification , Invertebrates*/cytology , Invertebrates*/genetics , Single-Cell Gene Expression Analysis* , Spatial Transcriptomics*, Skates, Fish/classification ; Skates, Fish/genetics ; Animals ; Genome ; Molecular Sequence Annotation ; Atlases as Topic

From descriptive to generative: foundation-model approaches for spatial transcriptomics.

Συγγραφείς: Fan T; School of Intelligent Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, Liaoning Province, 110122, China., Leng Y; School of Stomatology, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, Liaoning Province, 110122, China., Zhang J; The First Clinical College, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, Liaoning Province, 110122, China., Zhang Z; School of Intelligent Medicine, China Medical University, No. 77 Puhe Road, Shenbei New District, Shenyang, Liaoning Province, 110122, China.

Πηγή: Briefings in bioinformatics [Brief Bioinform] 2026 Sep 01; Vol. 27 (5).

Τύπος έκδοσης: Journal Article; Review

Στοιχεία περιοδικού: Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Spatial Transcriptomics* , Transcriptome*, Large Language Models ; Humans ; Animals ; Generative Artificial Intelligence

spMosaic: multi-sample integration for scalable spatial domain discovery based on spatial transcriptomics.

Συγγραφείς: Fu S; Department of Statistics, University of California, Riverside, 900 University Ave., Riverside, CA 92521, United States., Li H; Department of Computer Science and Engineering, University of California, Riverside, 900 University Ave., Riverside, CA 92521, United States., Li WV; Department of Statistics, University of California, Riverside, 900 University Ave., Riverside, CA 92521, United States.

Πηγή: Briefings in bioinformatics [Brief Bioinform] 2026 Sep 01; Vol. 27 (5).

Τύπος έκδοσης: Journal Article

Στοιχεία περιοδικού: Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Gene Expression Profiling*/methods , Computational Biology*/methods , Spatial Transcriptomics* , Transcriptome* , Software*, Animals ; Autoencoder ; Mice ; Clustering Algorithms ; Algorithms ; Humans

ST-ConMa: a multimodal foundation framework for spatial transcriptomics via image-gene contrastive and matching learning.

Συγγραφείς: Yeom T; Department of AI, College of Artificial Intelligence, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea., Choi D; Department of AI, College of Artificial Intelligence, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea., Lee H; Department of AI, College of Artificial Intelligence, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea.

Πηγή: Briefings in bioinformatics [Brief Bioinform] 2026 Sep 01; Vol. 27 (5).

Τύπος έκδοσης: Journal Article

Στοιχεία περιοδικού: Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Gene Expression Profiling*/methods , Image Processing, Computer-Assisted*/methods , Spatial Transcriptomics* , Deep Learning* , Transcriptome*, Humans ; Algorithms

Decoding cell-cell communication in spatial transcriptomics: mechanistic insights, modeling constraints, and analytical caveats.

Συγγραφείς: Wu Y; Department of Statistics and Probability, Michigan State University, 619 Red Cedar Road, East Lansing 48824, MI, United States., Su H; Department of Statistics and Probability, Michigan State University, 619 Red Cedar Road, East Lansing 48824, MI, United States., Cui Y; Department of Statistics and Probability, Michigan State University, 619 Red Cedar Road, East Lansing 48824, MI, United States.

Πηγή: Briefings in bioinformatics [Brief Bioinform] 2026 Sep 01; Vol. 27 (5).

Τύπος έκδοσης: Journal Article; Review

Στοιχεία περιοδικού: Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Cell Communication*/genetics , Spatial Transcriptomics* , Transcriptome* , Models, Biological*, Computational Biology/methods ; Humans ; Signal Transduction ; Animals

SANNO: A Graph-Transformer Enhanced Optimal Transport Tool for Spatial Transcriptomic Annotation.

Συγγραφείς: Zeng Y; School of Big Data and Software Engineering, Chongqing University, Chongqing, 400000, China. zengys@cqu.edu.cn.; Jinfeng Laboratory, Chongqing, 400000, China. zengys@cqu.edu.cn., Chen Y; Department of Pathology, Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China., Shangguan N; School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, 510000 , China., Li W; School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, 510000 , China., Cai X; School of Big Data and Software Engineering, Chongqing University, Chongqing, 400000, China., Zhang H; School of Big Data and Software Engineering, Chongqing University, Chongqing, 400000, China., Wang Z; Jinfeng Laboratory, Chongqing, 400000, China. biowz@mail.ustc.edu.cn., Zhao H; Department of Pathology, Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China. zhaohy8@mail.sysu.edu.cn.

Πηγή: Interdisciplinary sciences, computational life sciences [Interdiscip Sci] 2026 Sep; Vol. 18 (3), pp. 1113-1127. Date of Electronic Publication: 2025 Aug 11.

Τύπος έκδοσης: Journal Article

Στοιχεία περιοδικού: Publisher: Springer-Verlag Country of Publication: Germany NLM ID: 101515919 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1867-1462 (Electronic) Linking ISSN: 18671462 NLM ISO Abbreviation: Interdiscip Sci Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Computational Biology*/methods , Spatial Transcriptomics*, Software ; Algorithms ; Single-Cell Analysis ; Humans

Φ-Space ST: A platform-agnostic method to identify cell states in spatial transcriptomics studies.

Συγγραφείς: Mao J; Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia., Choi J; Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia., Lê Cao KA; Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia. Electronic address: kimanh.lecao@unimelb.edu.au.

Πηγή: Cell reports methods [Cell Rep Methods] 2026 Aug 17; Vol. 6 (8), pp. 101483. Date of Electronic Publication: 2026 Jun 12.

Τύπος έκδοσης: Journal Article

Στοιχεία περιοδικού: Publisher: Elsevier Inc Country of Publication: United States NLM ID: 9918227360606676 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2667-2375 (Electronic) Linking ISSN: 26672375 NLM ISO Abbreviation: Cell Rep Methods Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Spatial Transcriptomics*/methods , Transcriptome*/genetics, Humans ; Single-Cell Gene Expression Analysis

Cross-Propagative Graph Learning Reveals Spatial Tissue Domains in Multi-Modal Spatial Transcriptomics.

Συγγραφείς: Guo Y; School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, Shannxi, China., Liu S; School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, Shannxi, China., Zhang Z; School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, Shannxi, China., Zhang S; School of Mathematical Sciences, Fudan University, Shanghai, China., Li L; School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, Shannxi, China.

Πηγή: Small methods [Small Methods] 2026 Aug; Vol. 10 (15), pp. e70851. Date of Electronic Publication: 2026 Jul 12.

Τύπος έκδοσης: Journal Article

Στοιχεία περιοδικού: Publisher: WILEY-VCH Verlag GmbH & Co. KGaA Country of Publication: Germany NLM ID: 101724536 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2366-9608 (Electronic) Linking ISSN: 23669608 NLM ISO Abbreviation: Small Methods Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Spatial Transcriptomics*/methods , Gene Expression Profiling*/methods , Transcriptome*, Algorithms ; Graph Neural Networks ; Humans ; Animals ; Clustering Algorithms

ResolVI: addressing noise and bias in spatial transcriptomics.

Συγγραφείς: Ergen C; Center for Computational Biology, University of California, Berkeley, CA, USA. ergenbehr@gmail.com.; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA. ergenbehr@gmail.com.; Würzburg Institute of Systems Immunology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany. ergenbehr@gmail.com., Yosef N; System Immunology, Weizmann Institute of Science, Rehovot, Israel. nir.yosef@weizmann.ac.il.

Πηγή: Nature methods [Nat Methods] 2026 Oct; Vol. 23 (10), pp. 2003-2014. Date of Electronic Publication: 2026 Sep 24.

Τύπος έκδοσης: Journal Article

Στοιχεία περιοδικού: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Spatial Transcriptomics*/methods , Gene Expression Profiling*/methods , Software* , Transcriptome*, Algorithms ; Animals ; Humans

Spatial Transcriptomics Open a New Era of Pan-Cancer Analysis.

Συγγραφείς: Sheng Y; State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China., Yang Y; State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China., Zhang R; 2011 College, Nanjing Tech University, Nanjing, China., Li M; State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China., Ge Q; State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.

Πηγή: Cancer investigation [Cancer Invest] 2026 Oct; Vol. 44 (9), pp. 966-983. Date of Electronic Publication: 2026 Jun 07.

Τύπος έκδοσης: Journal Article; Review

Στοιχεία περιοδικού: Publisher: Taylor & Francis Country of Publication: England NLM ID: 8307154 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1532-4192 (Electronic) Linking ISSN: 07357907 NLM ISO Abbreviation: Cancer Invest Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Neoplasms*/genetics , Neoplasms*/pathology , Spatial Transcriptomics* , Transcriptome*, Tumor Microenvironment/genetics ; Gene Expression Profiling/methods ; Humans ; Animals ; Gene Expression Regulation, Neoplastic

OT-knn: A neighborhood-aware optimal transport framework for aligning spatial transcriptomics data.

Συγγραφείς: Song J; Department of Statistics, The Pennsylvania State University, University Park, Pennsylvania, United States of America., Li Q; Department of Statistics, The Pennsylvania State University, University Park, Pennsylvania, United States of America.

Πηγή: PLoS computational biology [PLoS Comput Biol] 2026 Sep 22; Vol. 22 (9), pp. e1014041. Date of Electronic Publication: 2026 Sep 22 (Print Publication: 2026).

Τύπος έκδοσης: Journal Article

Στοιχεία περιοδικού: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Spatial Transcriptomics*/methods , Gene Expression Profiling*/methods, Computational Biology/methods ; Brain/metabolism ; Transcriptome/genetics ; Animals ; Humans ; Mice ; Algorithms

Ten quick tips for spatial transcriptomics analysis.

Συγγραφείς: Kurogi N; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan., Shimbara K; BaraPhaSilico, Ibaraki, Japan., Koreeda T; CLINIC FOR Group, Tokyo, Japan., Tsuyuzaki K; Data Science Core, Chiba University, Chiba, Japan.

Πηγή: PLoS computational biology [PLoS Comput Biol] 2026 Sep 15; Vol. 22 (9), pp. e1014757. Date of Electronic Publication: 2026 Sep 15 (Print Publication: 2026).

Τύπος έκδοσης: Journal Article; Review; Research Support, Non-U.S. Gov't

Στοιχεία περιοδικού: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Spatial Transcriptomics*/methods , Gene Expression Profiling*/methods, Computational Biology/methods ; Software ; Animals ; Humans ; Proteomics

Spatially guided translation from histology images to transcriptomic profiles using foundation model-driven contrastive learning.

Συγγραφείς: Huang ZH; Department of Biochemistry, Western University, London, Canada., Xu Z; Department of Biochemistry, Western University, London, Canada., Hu P; Department of Biochemistry, Western University, London, Canada.; Department of Computer Sciences, Western University, London, Canada.; Division of Biostatistics, University of Toronto, Toronto, Canada.

Πηγή: PLoS computational biology [PLoS Comput Biol] 2026 Sep 08; Vol. 22 (9), pp. e1014762. Date of Electronic Publication: 2026 Sep 08 (Print Publication: 2026).

Τύπος έκδοσης: Journal Article; Research Support, Non-U.S. Gov't

Στοιχεία περιοδικού: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Graph Neural Networks* , Spatial Transcriptomics*, Breast Neoplasms/genetics ; Breast Neoplasms/pathology ; Breast Neoplasms/diagnostic imaging ; Computational Biology/methods ; Female ; Humans ; Deep Learning

Benchmarking copy number alteration inference methods for spatial transcriptomics.

Συγγραφείς: Han S; Department of Mathematics, The Hong Kong University of Science and Technology, Hong Kong SAR, China., Xiong Z; Department of Mathematics, The Hong Kong University of Science and Technology, Hong Kong SAR, China., Zhou Y; School of Biomedical Engineering, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China., Yang C; Department of Mathematics, The Hong Kong University of Science and Technology, Hong Kong SAR, China. macyang@ust.hk.; State Key Laboratory of Nervous System Disorders, The Hong Kong University of Science and Technology, Hong Kong SAR, China. macyang@ust.hk.; Big Data Bio-Intelligence Lab, The Hong Kong University of Science and Technology, Hong Kong SAR, China. macyang@ust.hk.; IAS Center for AI for scientific discoveries, The Hong Kong University of Science and Technology, Hong Kong SAR, China. macyang@ust.hk.

Πηγή: Nature communications [Nat Commun] 2026 Sep 05; Vol. 17 (1). Date of Electronic Publication: 2026 Sep 05.

Τύπος έκδοσης: Journal Article; Research Support, Non-U.S. Gov't

Στοιχεία περιοδικού: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Spatial Transcriptomics*/methods , DNA Copy Number Variations*/genetics , Neoplasms*/genetics, Computational Biology/methods ; Gene Expression Profiling/methods ; Humans ; Benchmarking ; Algorithms

Weighted sliced inverse regression for scalable supervised dimensionality reduction of spatial transcriptomics data.

Συγγραφείς: Woollard M; School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia.; Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia.; Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia., Panwar P; School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia.; Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia.; Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia., Harland LTG; Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.; Department of Haematology, University of Cambridge, Cambridge, UK.; Wolfson College, University of Cambridge, Cambridge, UK., Mo J; Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.; Faculty of Medicine & Health, School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia.; Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW, Australia., Zhang H; Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.; Faculty of Medicine & Health, School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia., Swarbrick A; Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.; Faculty of Medicine & Health, School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia., Gottgens B; Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.; Department of Haematology, University of Cambridge, Cambridge, UK., Ghazanfar S; School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia. shila.ghazanfar@sydney.edu.au.; Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia. shila.ghazanfar@sydney.edu.au.; Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia. shila.ghazanfar@sydney.edu.au., Nghiem LH; School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia. linh.nghiem@sydney.edu.au.; Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia. linh.nghiem@sydney.edu.au.

Πηγή: Nature communications [Nat Commun] 2026 Sep 03; Vol. 17 (1). Date of Electronic Publication: 2026 Sep 03.

Τύπος έκδοσης: Journal Article

Στοιχεία περιοδικού: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

Ιατρικοί όροι (MeSH): Gene Expression Profiling*/methods , Spatial Transcriptomics* , Transcriptome*, Breast Neoplasms/genetics ; Animals ; Dimensionality Reduction ; Mice ; Humans ; Female ; Algorithms ; Regression Analysis