Engineers' interest and contributions to molecular biology have sparked a completely new research field: synthetic biology. Despite no commercial applications so far, the prospects for basic research are exciting
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http://dx.doi.org/10.1038/sj.embor.7400607 | DOI Listing |
Brief Bioinform
November 2024
State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou, Xuanwu District, Nanjing 210096, China.
Spatial transcriptomics technologies have been extensively applied in biological research, enabling the study of transcriptome while preserving the spatial context of tissues. Paired with spatial transcriptomics data, platforms often provide histology and (or) chromatin images, which capture cellular morphology and chromatin organization. Additionally, single-cell RNA sequencing (scRNA-seq) data from matching tissues often accompany spatial data, offering a transcriptome-wide gene expression profile of individual cells.
View Article and Find Full Text PDFBrief Bioinform
November 2024
School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Buk-gu, Gwangju 61005, Republic of Korea.
Combination therapies have emerged as a promising approach for treating complex diseases, particularly cancer. However, predicting the efficacy and safety profiles of these therapies remains a significant challenge, primarily because of the complex interactions among drugs and their wide-ranging effects. To address this issue, we introduce DD-PRiSM (Decomposition of Drug-Pair Response into Synergy and Monotherapy effect), a deep-learning pipeline that predicts the effects of combination therapy.
View Article and Find Full Text PDFBrief Bioinform
November 2024
Department of Electronic Engineering, Tsinghua University, 100084 Beijing, China.
Single-cell multi-omics techniques, which enable the simultaneous measurement of multiple modalities such as RNA gene expression and Assay for Transposase-Accessible Chromatin (ATAC) within individual cells, have become a powerful tool for deciphering the intricate complexity of cellular systems. Most current methods rely on motif databases to establish cross-modality relationships between genes from RNA-seq data and peaks from ATAC-seq data. However, these approaches are constrained by incomplete database coverage, particularly for novel or poorly characterized relationships.
View Article and Find Full Text PDFJ Econ Entomol
January 2025
College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan 466001, China.
Species distribution modeling is extensively used for predicting potential distributions of invasive species. However, an ensemble modeling approach has been less frequently used particularly pest species. The bird cherry-oat aphid Rhopalosiphum padi L.
View Article and Find Full Text PDFWorld J Microbiol Biotechnol
January 2025
School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing, 210023, People's Republic of China.
Organic acids constitute a vital category of chemical raw materials. They have extensive applications in industries such as polymers, food, and pharmaceuticals. Currently, industrial production predominantly relies on microbial fermentation.
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