Recent advancements in transcriptomics and its application in basic medical and clinical sciences

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Cao J, Li C, Cui Z, Deng S, Lei T, Liu W, Yang H, Chen P. 2024. Spatial Transcriptomics: A Powerful Tool in Disease Understanding and Drug Discovery. Theranostics 14(7), 2946.

Cheng XY, Zhang YS, Cao ZF. 2023. Applications and advances of spatial transcriptomics in oncology research. Zhonghua bing li xue za zhi Chinese Journal of Pathology 52(6), 643-646.

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Drakos SG, Badolia R, Makaju A, Kyriakopoulos CP, Wever-Pinzon O, Tracy CM, Bakhtina A, Bia R, Parnell T, Taleb I, Ramadurai DK. 2023. Distinct transcriptomic and proteomic profile specifies patients who have heart failure with potential of myocardial recovery on mechanical unloading and circulatory support. Circulation 147(5), 409-424.

Fan J, Slowikowski K, Zhang F. 2020. Single-cell transcriptomics in cancer: computational challenges and opportunities. Experimental & Molecular Medicine 52, 1452–1465.

Fan Y, Andrusivová Ž, Wu Y, Chai C, Larsson L, He M, Luo L, Lundeberg J, Wang B. 2023. Expansion spatial transcriptomics. Nature Methods 20(8), 1179-82.

Glodzik D, Selenica P, Rogge RA, Silverman IM, Mandelker D, Harris S, Zhao J, Zinda M, Veloso A, Malani N, Riaz N. 2023. Detection of biallelic loss of DNA repair genes in formalin-fixed, paraffin-embedded tumor samples using a novel tumor-only sequencing panel. The Journal of Molecular Diagnostics 25(5), 295-310.

Herwanto V, Tang B, Wang Y, Shojaei M, Nalos M, Shetty A, Lai K, McLean AS, Schughart K. 2021. Blood transcriptome analysis of patients with uncomplicated bacterial infection and sepsis. BMC Research Notes 14, 1-3.

Hibi M, Katada S, Kawakami A, Bito K, Ohtsuka M, Sugitani K, Muliandi A, Yamanaka N, Hasumura T, Ando Y, Fushimi T. 2023. Assessment of Multidimensional Health Care Parameters Among Adults in Japan for Developing a Virtual Human Generative Model: Protocol for a Cross-sectional Study. JMIR Research Protocols 12(1), e47024.

Hoogstrate Y, Draaisma K, Ghisai SA, van Hijfte L, Barin N, de Heer I, Coppieters W, van den Bosch TP, Bolleboom A, Gao Z, Vincent AJ. 2023. Transcriptome analysis reveals tumor microenvironment changes in glioblastoma. Cancer Cell 41(4), 678-92.

Imle R, Blosel D, Kommoss F, Zhao E, Autry R, Blume C, Lupar D, Schmitt L, Winter C, Wagner L, Placke S. 2024. Somatic gene delivery for flexible in vivo modeling of high-risk sarcoma. bioRxiv 2024, 2024-01.

Jang MJ, Coughlin GM, Jackson CR, Chen X, Chuapoco MR, Vendemiatti JL, Wang AZ, Gradinaru V. 2023. Spatial transcriptomics for profiling the tropism of viral vectors in tissues. Nature Biotechnology 41(9), 1272-86.

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Li H, Wang X, Yang Q, Cheng L, Zeng HL. 2023. Identification of iron metabolism-related genes as diagnostic signatures in sepsis by blood transcriptomic analysis. Open Life Sciences 18(1), 20220549.

Li H, Zhou J, Li Z, Chen S, Liao X, Zhang B, Zhang R, Wang Y, Sun S, Gao X. 2023. A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics. Nature Communication 14(1), 1548.

Long X, Yuan X, Du J. 2023. Single-cell and spatial transcriptomics: Advances in heart development and disease applications. Computational and Structural Biotechnology Journal 21, 2717-31.

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Moufarrej MN, Quake SR. 2023. An inexpensive semi-automated sample processing pipeline for cell-free RNA extraction. Nature Protocols 18(9), 2772-93.

Mundi PS, Dela Cruz FS, Ortiz MV, Grunn A, Diolaiti D, Alvarez MJ, Kung AL, Califano A. 2023. Evaluation of a transcriptomics-based precision oncology platform for patient-therapy alignment in treatment resistant malignancies. Cancer Research 83(7_Supplement), 849.

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Parola M, Pinzani M. 2024. Invited review: liver fibrosis in NAFLD/NASH: from pathophysiology towards diagnostic and therapeutic strategies. Molecular Aspects of Medicine 95, 101231.

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Yoshida T, Latt KZ, Rosenberg AZ, Shrivastav S, Heymann J, Halushka MK, Winkler CA, Kopp JB. 2023. Transcriptomic analysis of human podocytes in vitro: effects of differentiation and APOL1 genotype. Kidney International Reports 8(1), 164-78.

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Zhao S, Zhu K, Li X, Zhong X, Zhao Y, Le Z, Liu Z, Xiao Y, Lai D, Jiao N, Shu Q. 2024. Co-expression and interaction network analysis reveals dysregulated neutrophil and T-cell activation as the core mechanism associated with septic shock. Frontiers in Genetics 14, 1132361.

Zhao Y, Wang T, Liu Z, Ke Y, Li R, Chen H, You Y, Wu G, Cao S, Du Z, Bai F. 2023. Single-cell transcriptomics of immune cells in lymph nodes reveals their composition and alterations in functional dynamics during the early stages of bubonic plague. Science China Life Sciences 66(1), 110-26.

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