OLD Category: CosMx SMI

May 9, 2023 / Nucleic Acids Res

  • Mohamed A, Bhuva DD, Lee S, Liu N, Tan CW, Davis MJ
Gene-set analysis (GSA) dominates the functional interpretation of omics data and downstream hypothesis generation. Despite its ability to summarise thousands of measurements into semantically interpretable components, GSA often results in…
May 1, 2023 / Front Oncol

  • Lee RY, Ng CW, Rajapakse MP, Ang N, Yeong JPS, Lau MC
Growing evidence supports the critical role of tumour microenvironment (TME) in tumour progression, metastases, and treatment response. However, the in-situ interplay among various TME components, particularly between immune and tumour…
April 8, 2023 / MEGA J Case Rep

  • Yang H, Jiang QH
Background: Non-alcoholic fatty liver disease (NAFLD) is a common type of liver disease and is showing a high prevalence worldwide. The liver fibrosis caused by NAFLD increase the risk of…
April 7, 2023 / Adv Sci (Weinh)

  • Park HE, Jo SH, Lee RH, Macks CP, Ku T, Park J, Lee CW, Hur JK, Sohn CH
Spatial transcriptomics is a newly emerging field that enables high-throughput investigation of the spatial localization of transcripts and related analyses in various applications for biological systems. By transitioning from conventional…
April 7, 2023 / Eur Heart J

  • de Winther MPJ, Bäck M, Evans P, Gomez D, Goncalves I, Jørgensen HF, Koenen RR, Lutgens E, Norata GD, Osto E, Dib L, Simons M, Stellos K, Ylä-Herttuala S, Winkels H, Bochaton-Piallat ML, Monaco C
The advent of single-cell biology opens a new chapter for understanding human biological processes and for diagnosing, monitoring, and treating disease. This revolution now reaches the field of cardiovascular disease…
March 22, 2023 / JID innovations

  • Houser AE, Abiha Kazmi, Arjun K. Nair, Andrew L. Ji
The development of multi-omic profiling tools has rapidly expanded in recent years, along with their use in profiling skin tissues in various contexts, including dermatologic diseases. Among these tools, single-cell…
March 3, 2023 / Genome Biol

  • Zhu J, Shang L, Zhou X
Spatially resolved transcriptomics (SRT)-specific computational methods are often developed, tested, validated, and evaluated in silico using simulated data. Unfortunately, existing simulated SRT data are often poorly documented, hard to reproduce,…
January 27, 2023 / BMC Bioinformatics

  • Pont F, Cerapio JP, Gravelle P, Ligat L, Valle C, Sarot E, Perrier M, Lopez F, Laurent C, Fournié JJ, Tosolini M
Background:: The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called ’spatial transcriptomics’. Currently…
January 16, 2023 / Comput Struct Biotechnol J

  • Yue L, Feng Liu, Jiongsong Hu, Pin Yang, Yuxiang Wang, Junguo Dong, Wenjie Shu, Xingxu Huang, Shengqi Wang
Advances in transcriptomic technologies have deepened our understanding of the cellular gene expression programs of multicellular organisms and provided a theoretical basis for disease diagnosis and therapy. However, both bulk…
December 30, 2022 / Nat Method

  • Bost P, Schulz D, Engler S, Wasserfall C, Bodenmiller B
Recent advances in multiplexed imaging methods allow simultaneous detection of dozens of proteins and hundreds of RNAs, enabling deep spatial characterization of both healthy and diseased tissues. Parameters for the…
December 21, 2022 / Brief Bioinform

  • Tang Z, Zhang T, Yang B, Su J, Song Q
December 13, 2022 / Genome Biol

  • Park J, Kim J, Lewy T, Rice CM, Elemento O, Rendeiro AF, Mason CE