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Briefings in bioinformatics
Nov 22, 2023
Accurate identification of replication origins (ORIs) is crucial for a comprehensive investigation into the progression of human cell growth and cancer therapy. Here, we proposed a computational approach Ori-FinderH, which can efficiently and precise...
Briefings in bioinformatics
Sep 20, 2023
Silencers are noncoding DNA sequence fragments located on the genome that suppress gene expression. The variation of silencers in specific cells is closely related to gene expression and cancer development. Computational approaches that exclusively r...
Bioinformatics (Oxford, England)
Sep 2, 2023
MOTIVATION: Cancer heterogeneity drastically affects cancer therapeutic outcomes. Predicting drug response in vitro is expected to help formulate personalized therapy regimens. In recent years, several computational models based on machine learning a...
Briefings in bioinformatics
Jan 19, 2023
With the improvement of single-cell measurement techniques, there is a growing awareness that individual differences exist among cells, and protein expression distribution can vary across cells in the same tissue or cell line. Pinpointing the protein...
Briefings in bioinformatics
Jan 19, 2023
Drug response prediction is an important problem in personalized cancer therapy. Among various newly developed models, significant improvement in prediction performance has been reported using deep learning methods. However, systematic comparisons of...
Bioinformatics (Oxford, England)
Jan 1, 2023
MOTIVATION: Protein essentiality is usually accepted to be a conditional trait and strongly affected by cellular environments. However, existing computational methods often do not take such characteristics into account, preferring to incorporate all ...
Endocrine, metabolic & immune disorders drug targets
Jan 1, 2023
BACKGROUND: Mitochondrial morphology reversibly changes between fission and fusion. As these changes (mitochondrial dynamics) reflect the cellular condition, they are one of the simplest indicators of cell state and predictors of cell fate. However, ...
Briefings in bioinformatics
Nov 19, 2022
Identifying synergistic drug combinations (SDCs) is a great challenge due to the combinatorial complexity and the fact that SDC is cell line specific. The existing computational methods either did not consider the cell line specificity of SDC, or did...
Bioinformatics (Oxford, England)
Sep 30, 2022
MOTIVATION: Three-dimensional (3D) genome organization is of vital importance in gene regulation and disease mechanisms. Previous studies have shown that CTCF-mediated chromatin loops are crucial to studying the 3D structure of cells. Although variou...
Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
Jul 1, 2022
Cellular Thermal Shift Assay (CETSA) has been widely used in drug discovery, cancer cell biology, immunology, etc. One of the barriers for CETSA applications is that CETSA experiments have to be conducted on various cell lines, which is extremely tim...