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Transcriptor: a comprehensive platform for annotation of the enzymatic functions of transcripts

期刊: BIOINFORMATICS, 2021; 37 (3)

Motivation: Rapid advances in sequencing technology have resulted huge increases in the accessibility of sequencing data. Moreover, researchers are fo......

RabbitQC: high-speed scalable quality control for sequencing data

期刊: BIOINFORMATICS, 2021; 37 (4)

Motivation: Modern sequencing technologies continue to revolutionize many areas of biology and medicine. Since the generated datasets are error-prone,......

HiSCF: leveraging higher-order structures for clustering analysis in biological networks

期刊: BIOINFORMATICS, 2021; 37 (4)

Motivation: Clustering analysis in a biological network is to group biological entities into functional modules, thus providing valuable insight into ......

RNA inter-nucleotide 3D closeness prediction by deep residual neural networks

期刊: BIOINFORMATICS, 2021; 37 (8)

Motivation: Recent years have witnessed that the inter-residue contact/distance in proteins could be accurately predicted by deep neural networks, whi......

CRAFT: Compact genome Representation toward large-scale Alignment-Free daTabase

期刊: BIOINFORMATICS, 2021; 37 (2)

Motivation: Rapid developments in sequencing technologies have boosted generating high volumes of sequence data. To archive and analyze those data, on......

IsoResolve: predicting splice isoform functions by integrating gene and isoform-level features with domain adaptation

期刊: BIOINFORMATICS, 2021; 37 (4)

Motivation: High resolution annotation of gene functions is a central goal in functional genomics. A single gene may produce multiple isoforms with di......

Particle Gibbs sampling for Bayesian phylogenetic inference

期刊: BIOINFORMATICS, 2021; 37 (5)

Motivation: The combinatorial sequential Monte Carlo (CSMC) has been demonstrated to be an efficient complementary method to the standard Markov chain......

SOAPMetaS: profiling large metagenome datasets efficiently on distributed clusters

期刊: BIOINFORMATICS, 2021; 37 (7)

Rapid increase of the data size in metagenome researches has raised the demand for new tools to process large datasets efficiently. To accelerate the ......

Robust and ultrafast fiducial marker correspondence in electron tomography by a two-stage algorithm considering local constraints

期刊: BIOINFORMATICS, 2021; 37 (1)

Motivation: Electron tomography (ET) has become an indispensable tool for structural biology studies. In ET, the tilt series alignment and the project......

ProteomeExpert: a Docker image-based web server for exploring, modeling, visualizing and mining quantitative proteomic datasets

期刊: BIOINFORMATICS, 2021; 37 (2)

A Summary: The rapid progresses of high-throughput sequencing technology-based omics and mass spectrometry-based proteomics, such as data-independent ......

Genetic source completeness of HIV-1 circulating recombinant forms (CRFs) predicted by multi-label learning

期刊: BIOINFORMATICS, 2021; 37 (6)

Motivation: Infection with strains of different subtypes and the subsequent crossover reading between the two strands of genomic RNAs by host cells' r......

SARS2020: an integrated platform for identification of novel coronavirus by a consensus sequence-function model

期刊: BIOINFORMATICS, 2021; 37 (8)

Motivation: The 2019 novel coronavirus outbreak has significantly affected global health and society. Thus, predicting biological function from pathog......

SMI-BLAST: a novel supervised search framework based on PSI-BLAST for protein remote homology detection

期刊: BIOINFORMATICS, 2021; 37 (7)

Motivation: As one of the most important and widely used mainstream iterative search tool for protein sequence search, an accurate Position-Specific S......

A network-based deep learning methodology for stratification of tumor mutations

期刊: BIOINFORMATICS, 2021; 37 (1)

Motivation: Tumor stratification has a wide range of biomedical and clinical applications, including diagnosis, prognosis and personalized treatment. ......

VirPreNet: a weighted ensemble convolutional neural network for the virulence prediction of influenza A virus using all eight segments

期刊: BIOINFORMATICS, 2021; 37 (6)

Motivation: Influenza viruses are persistently threatening public health, causing annual epidemics and sporadic pandemics. The evolution of influenza ......

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