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Article
Open AccessZero-shot prediction of mutation effects with multimodal deep representation learning guides protein engineering
Mutations in amino acid sequences can provoke changes in protein function. Accurate and unsupervised prediction of mutation effects is critical in biotechnology and biomedicine, but remains a fundamental chall...
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Article
Dynamically monitoring cellular γ-H2AX reveals the potential of carcinogenicity evaluation for genotoxic compounds
Amongst all toxicological endpoints, carcinogenicity might pose the greatest concern. Genetic damage has been considered an important underlying mechanism for the carcinogenicity of chemical substances. The de...
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Article
Open AccessDeep learning methods improve linear B-cell epitope prediction
B-cell epitopes play important roles in vaccine design, clinical diagnosis, and antibody production. Although some models have been developed to predict linear or conformational B-cell epitopes, their performa...
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Article
Open AccessImmune receptor repertoires in pediatric and adult acute myeloid leukemia
Acute myeloid leukemia (AML), caused by the abnormal proliferation of immature myeloid cells in the blood or bone marrow, is one of the most common hematologic malignancies. Currently, the interactions between...
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Article
Open AccessPredicting the regrowth of clinically non-functioning pituitary adenoma with a statistical model
Compared with clinically functioning pituitary adenoma (FPA), clinically non-functioning pituitary adenoma (NFPA) lacks of detectable hypersecreting serum hormones and related symptoms which make it difficult ...
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Article
Open AccessDetecting RNA-RNA interactions in E. coli using a modified CLASH method
Bacterial small regulatory RNAs (sRNAs) play important roles in sensing environment changes through sRNA-target mRNA interactions. However, the current strategy for detecting sRNA-mRNA interactions usually com...
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Article
Open AccessPredicting linear B-cell epitopes using amino acid anchoring pair composition
Accurate identification of linear B-cell epitopes plays an important role in peptide vaccine designs, immunodiagnosis, and antibody productions. Although several prediction methods have been reported, unsatisf...
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Article
A modified visual loop-mediated isothermal amplification method for diagnosis and differentiation of main pathogens from Mycobacterium tuberculosis complex
This study was aimed to rapidly identify and differentiate two main pathogens of the Mycobacterium tuberculosis complex: Mycobacterium tuberculosis subsp. tuberculosis and Mycobacterium bovis by a...
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Chapter
Computational Tools for Predicting sRNA Targets
Bacterial sRNAs are an emerging class of small regulatory RNAs of 40 to 500 nucleotides in length. They play a wide variety of important roles in many biological processes through binding to their mRNA or prot...
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Article
Generate gene expression profile from high-throughput sequencing data
This work presents two methods, the Least-square and Bayesian method, to solve the multiple map** problem in extracting gene expression profiles through the next-generation sequencing. We parallel the tag se...
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Article
Open AccessBioSunMS: a plug-in-based software for the management of patients information and the analysis of peptide profiles from mass spectrometry
With wide applications of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TO...
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Article
Identification and verification of microRNA in wheat (Triticum aestivum)
MicroRNAs (miRNAs) are small, endogenous RNAs that regulate gene expression in both plants and animals. A large number of miRNAs has been identified from various animals and model plant species such as Arabidopsi...
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Article
How many genes are needed for early detection of breast cancer, based on gene expression patterns in peripheral blood cells?
