Literature DB >> 34845373

Super-resolved spatial transcriptomics by deep data fusion.

Ludvig Bergenstråhle1, Bryan He2, Joseph Bergenstråhle1, Xesús Abalo1, Reza Mirzazadeh1, Kim Thrane1, Andrew L Ji3, Alma Andersson1, Ludvig Larsson1, Nathalie Stakenborg4, Guy Boeckxstaens4, Paul Khavari3, James Zou2, Joakim Lundeberg5, Jonas Maaskola1,6.   

Abstract

Current methods for spatial transcriptomics are limited by low spatial resolution. Here we introduce a method that integrates spatial gene expression data with histological image data from the same tissue section to infer higher-resolution expression maps. Using a deep generative model, our method characterizes the transcriptome of micrometer-scale anatomical features and can predict spatial gene expression from histology images alone.
© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.

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Year:  2021        PMID： 34845373     DOI： 10.1038/s41587-021-01075-3

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


  25 in total

1.  Genome-wide atlas of gene expression in the adult mouse brain.

Authors:  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; Mei Chi Chin; Jimmy Chong; Brian E Crook; Aneta Czaplinska; Chinh N Dang; Suvro Datta; Nick R Dee; Aimee L Desaki; Tsega Desta; Ellen Diep; Tim A Dolbeare; Matthew J Donelan; Hong-Wei Dong; Jennifer G Dougherty; Ben J Duncan; Amanda J Ebbert; Gregor Eichele; Lili K Estin; Casey Faber; Benjamin A Facer; Rick Fields; Shanna R Fischer; Tim P Fliss; Cliff Frensley; Sabrina N Gates; Katie J Glattfelder; Kevin R Halverson; Matthew R Hart; John G Hohmann; Maureen P Howell; Darren P Jeung; Rebecca A Johnson; Patrick T Karr; Reena Kawal; Jolene M Kidney; Rachel H Knapik; Chihchau L Kuan; James H Lake; Annabel R Laramee; Kirk D Larsen; Christopher Lau; Tracy A Lemon; Agnes J Liang; Ying Liu; Lon T Luong; Jesse Michaels; Judith J Morgan; Rebecca J Morgan; Marty T Mortrud; Nerick F Mosqueda; Lydia L Ng; Randy Ng; Geralyn J Orta; Caroline C Overly; Tu H Pak; Sheana E Parry; Sayan D Pathak; Owen C Pearson; Ralph B Puchalski; Zackery L Riley; Hannah R Rockett; Stephen A Rowland; Joshua J Royall; Marcos J Ruiz; Nadia R Sarno; Katherine Schaffnit; Nadiya V Shapovalova; Taz Sivisay; Clifford R Slaughterbeck; Simon C Smith; Kimberly A Smith; Bryan I Smith; Andy J Sodt; Nick N Stewart; Kenda-Ruth Stumpf; Susan M Sunkin; Madhavi Sutram; Angelene Tam; Carey D Teemer; Christina Thaller; Carol L Thompson; Lee R Varnam; Axel Visel; Ray M Whitlock; Paul E Wohnoutka; Crissa K Wolkey; Victoria Y Wong; Matthew Wood; Murat B Yaylaoglu; Rob C Young; Brian L Youngstrom; Xu Feng Yuan; Bin Zhang; Theresa A Zwingman; Allan R Jones
Journal:  Nature       Date:  2006-12-06       Impact factor: 49.962

2.  In situ sequencing for RNA analysis in preserved tissue and cells.

Authors:  Rongqin Ke; Marco Mignardi; Alexandra Pacureanu; Jessica Svedlund; Johan Botling; Carolina Wählby; Mats Nilsson
Journal:  Nat Methods       Date:  2013-07-14       Impact factor: 28.547

3.  Visualization of single RNA transcripts in situ.

Authors:  A M Femino; F S Fay; K Fogarty; R H Singer
Journal:  Science       Date:  1998-04-24       Impact factor: 47.728

4.  Proteomics. Tissue-based map of the human proteome.

Authors:  Mathias Uhlén; Linn Fagerberg; Björn M Hallström; Cecilia Lindskog; Per Oksvold; Adil Mardinoglu; Åsa Sivertsson; Caroline Kampf; Evelina Sjöstedt; Anna Asplund; IngMarie Olsson; Karolina Edlund; Emma Lundberg; Sanjay Navani; Cristina Al-Khalili Szigyarto; Jacob Odeberg; Dijana Djureinovic; Jenny Ottosson Takanen; Sophia Hober; Tove Alm; Per-Henrik Edqvist; Holger Berling; Hanna Tegel; Jan Mulder; Johan Rockberg; Peter Nilsson; Jochen M Schwenk; Marica Hamsten; Kalle von Feilitzen; Mattias Forsberg; Lukas Persson; Fredric Johansson; Martin Zwahlen; Gunnar von Heijne; Jens Nielsen; Fredrik Pontén
Journal:  Science       Date:  2015-01-23       Impact factor: 47.728

5.  Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution.

Authors:  Samuel G Rodriques; Robert R Stickels; Aleksandrina Goeva; Carly A Martin; Evan Murray; Charles R Vanderburg; Joshua Welch; Linlin M Chen; Fei Chen; Evan Z Macosko
Journal:  Science       Date:  2019-03-28       Impact factor: 47.728

6.  Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.

Authors:  Patrik L Ståhl; Fredrik Salmén; Sanja Vickovic; Anna Lundmark; José Fernández Navarro; Jens Magnusson; Stefania Giacomello; Michaela Asp; Jakub O Westholm; Mikael Huss; Annelie Mollbrink; Sten Linnarsson; Simone Codeluppi; Åke Borg; Fredrik Pontén; Paul Igor Costea; Pelin Sahlén; Jan Mulder; Olaf Bergmann; Joakim Lundeberg; Jonas Frisén
Journal:  Science       Date:  2016-07-01       Impact factor: 47.728

7.  RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells.

Authors:  Kok Hao Chen; Alistair N Boettiger; Jeffrey R Moffitt; Siyuan Wang; Xiaowei Zhuang
Journal:  Science       Date:  2015-04-09       Impact factor: 47.728

8.  Highly multiplexed subcellular RNA sequencing in situ.

Authors:  Je Hyuk Lee; Evan R Daugharthy; Jonathan Scheiman; Reza Kalhor; Joyce L Yang; Thomas C Ferrante; Richard Terry; Sauveur S F Jeanty; Chao Li; Ryoji Amamoto; Derek T Peters; Brian M Turczyk; Adam H Marblestone; Samuel A Inverso; Amy Bernard; Prashant Mali; Xavier Rios; John Aach; George M Church
Journal:  Science       Date:  2014-02-27       Impact factor: 47.728

9.  Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH.

Authors:  Chee-Huat Linus Eng; Michael Lawson; Qian Zhu; Ruben Dries; Noushin Koulena; Yodai Takei; Jina Yun; Christopher Cronin; Christoph Karp; Guo-Cheng Yuan; Long Cai
Journal:  Nature       Date:  2019-03-25       Impact factor: 49.962

10.  High-definition spatial transcriptomics for in situ tissue profiling.

Authors:  Gökcen Eraslan; Fredrik Salmén; Johanna Klughammer; Linnea Stenbeck; Sanja Vickovic; Denis Schapiro; Tarmo Äijö; Richard Bonneau; Ludvig Bergenstråhle; José Fernandéz Navarro; Joshua Gould; Gabriel K Griffin; Åke Borg; Mostafa Ronaghi; Jonas Frisén; Joakim Lundeberg; Aviv Regev; Patrik L Ståhl
Journal:  Nat Methods       Date:  2019-09-09       Impact factor: 28.547
View more
  9 in total

Review 1.  Emerging artificial intelligence applications in Spatial Transcriptomics analysis.

Authors:  Yijun Li; Stefan Stanojevic; Lana X Garmire
Journal:  Comput Struct Biotechnol J       Date:  2022-06-02       Impact factor: 6.155

2.  Modeling zero inflation is not necessary for spatial transcriptomics.

Authors:  Peiyao Zhao; Jiaqiang Zhu; Ying Ma; Xiang Zhou
Journal:  Genome Biol       Date:  2022-05-18       Impact factor: 17.906

Review 3.  Research Techniques Made Simple: Spatial Transcriptomics.

Authors:  Arianna J Piñeiro; Aubrey E Houser; Andrew L Ji
Journal:  J Invest Dermatol       Date:  2022-04       Impact factor: 8.551

4.  Efficient prediction of a spatial transcriptomics profile better characterizes breast cancer tissue sections without costly experimentation.

Authors:  Taku Monjo; Masaru Koido; Satoi Nagasawa; Yutaka Suzuki; Yoichiro Kamatani
Journal:  Sci Rep       Date:  2022-03-08       Impact factor: 4.379

Review 5.  Recent advances in spatially resolved transcriptomics: challenges and opportunities.

Authors:  Jongwon Lee; Minsu Yoo; Jungmin Choi
Journal:  BMB Rep       Date:  2022-03       Impact factor: 4.778

Review 6.  The Multi-Dimensional Biomarker Landscape in Cancer Immunotherapy.

Authors:  Jing Yi Lee; Bavani Kannan; Boon Yee Lim; Zhimei Li; Abner Herbert Lim; Jui Wan Loh; Tun Kiat Ko; Cedric Chuan-Young Ng; Jason Yongsheng Chan
Journal:  Int J Mol Sci       Date:  2022-07-16       Impact factor: 6.208

Review 7.  An introduction to spatial transcriptomics for biomedical research.

Authors:  Cameron G Williams; Hyun Jae Lee; Takahiro Asatsuma; Roser Vento-Tormo; Ashraful Haque
Journal:  Genome Med       Date:  2022-06-27       Impact factor: 15.266

8.  Spatial Transcriptomic Analysis Reveals Associations between Genes and Cellular Topology in Breast and Prostate Cancers.

Authors:  Lujain Alsaleh; Chen Li; Justin L Couetil; Ze Ye; Kun Huang; Jie Zhang; Chao Chen; Travis S Johnson
Journal:  Cancers (Basel)       Date:  2022-10-04       Impact factor: 6.575

Review 9.  Statistical and machine learning methods for spatially resolved transcriptomics data analysis.

Authors:  Zexian Zeng; Yawei Li; Yiming Li; Yuan Luo
Journal:  Genome Biol       Date:  2022-03-25       Impact factor: 13.583
  9 in total

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