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Bioinformatics (Oxford, England)
Oct 14, 2022
SUMMARY: Computational methods that track single cells and quantify fluorescent biosensors in time-lapse microscopy images have revolutionized our approach in studying the molecular control of cellular decisions. One barrier that limits the adoption ...
Bioinformatics (Oxford, England)
Oct 14, 2022
MOTIVATION: The medical data are complex in nature as terms that appear in records usually appear in different contexts. Through this article, we investigate various bio model's embeddings (BioBERT, BioELECTRA and PubMedBERT) on their understanding o...
Bioinformatics (Oxford, England)
Oct 14, 2022
MOTIVATION: Metagenomics is the study of microbiomes using DNA sequencing. A microbiome consists of an assemblage of microbes that is associated with a 'theater of activity' (ToA). An important question is, to what degree does the taxonomic and funct...
Bioinformatics (Oxford, England)
Oct 14, 2022
MOTIVATION: Inter-organ/inter-tissue communication is central to multi-cellular organisms including humans, and mapping inter-tissue interactions can advance system-level whole-body modeling efforts. Large volumes of biomedical literature have foster...
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...
Bioinformatics (Oxford, England)
Sep 30, 2022
MOTIVATION: Over the last decades, image processing and analysis have become one of the key technologies in systems biology and medicine. The quantification of anatomical structures and dynamic processes in living systems is essential for understandi...
Bioinformatics (Oxford, England)
Sep 30, 2022
MOTIVATION: Predicting pathological complete response (pCR) to neoadjuvant chemotherapy (NAC) in triple-negative breast cancer (TNBC) patients accurately is direly needed for clinical decision making. pCR is also regarded as a strong predictor of ove...
Bioinformatics (Oxford, England)
Sep 30, 2022
MOTIVATION: With the breakthrough of AlphaFold2, the protein structure prediction problem has made remarkable progress through deep learning end-to-end techniques, in which correct folds could be built for nearly all single-domain proteins. However, ...
Bioinformatics (Oxford, England)
Sep 30, 2022
MOTIVATION: In many biomedical studies, there arises the need to integrate data from multiple directly or indirectly related sources. Collective matrix factorization (CMF) and its variants are models designed to collectively learn from arbitrary coll...
Bioinformatics (Oxford, England)
Sep 30, 2022
MOTIVATION: Automatic recognition of chemical structures from molecular images provides an important avenue for the rediscovery of chemicals. Traditional rule-based approaches that rely on expert knowledge and fail to consider all the stylistic varia...