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Modeling RNA degradation for RNA-Seq with applications.
- Published in:
- Biostatistics, 2012, v. 13, n. 4, p. 734, doi. 10.1093/biostatistics/kxs001
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- Article
Increasing prediction performance of colorectal cancer disease status using random forests classification based on metagenomic shotgun sequencing data.
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- Synthetic & Systems Biotechnology, 2022, v. 7, n. 1, p. 574, doi. 10.1016/j.synbio.2022.01.005
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- Article
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data.
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- Microbiome, 2017, v. 5, p. 1, doi. 10.1186/s40168-017-0283-5
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- Article
Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer.
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- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-32995-6
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- Article
Inference of domain-disease associations from domain-protein, protein-disease and disease-disease relationships.
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- BMC Systems Biology, 2016, v. 10, p. 63, doi. 10.1186/s12918-015-0247-y
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- Article
Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates.
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- BMC Systems Biology, 2011, v. 5, n. Suppl 2, p. 1, doi. 10.1186/1752-0509-5-S2-S15
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- Article
DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases.
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- BMC Systems Biology, 2011, v. 5, n. 1, p. 55, doi. 10.1186/1752-0509-5-55
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- Article
The effects of protein interactions, gene essentiality and regulatory regions on expression variation.
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- BMC Systems Biology, 2008, v. 2, p. 1, doi. 10.1186/1752-0509-2-54
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Prediction of virus-host infectious association by supervised learning methods.
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- BMC Bioinformatics, 2017, v. 18, p. 143, doi. 10.1186/s12859-017-1473-7
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- Article
DeepMicroClass sorts metagenomic contigs into prokaryotes, eukaryotes and viruses.
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- NAR Genomics & Bioinformatics, 2024, v. 6, n. 2, p. 1, doi. 10.1093/nargab/lqae044
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ARG-SHINE: improve antibiotic resistance class prediction by integrating sequence homology, functional information and deep convolutional neural network.
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- NAR Genomics & Bioinformatics, 2021, v. 3, n. 3, p. 1, doi. 10.1093/nargab/lqab066
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- Article
Comparative Study of the Effects of Drugs Targeting Adrenergic Receptors on the Early Life Stages of Zebrafish.
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- Toxics, 2024, v. 12, n. 8, p. 583, doi. 10.3390/toxics12080583
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Confidence intervals for Markov chain transition probabilities based on next generation sequencing reads data.
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- Quantitative Biology, 2020, v. 8, n. 2, p. 143, doi. 10.1007/s40484-020-0200-y
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- Article
International Workshop on Applications of Probability and Statistics to Biology, July 11–13, 2019: —In Honor of Professor Minping Qian's 80th Birthday.
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- Quantitative Biology, 2020, v. 8, n. 2, p. 177, doi. 10.1007/s40484-019-0182-9
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- Article
Identifying viruses from metagenomic data using deep learning.
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- Quantitative Biology, 2020, v. 8, n. 1, p. 64, doi. 10.1007/s40484-019-0187-4
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Meeting report on RECOMB 2013 (the 17th Annual International Conference on Research in Computational Molecular Biology).
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- Quantitative Biology, 2013, v. 1, n. 2, p. 175, doi. 10.1007/s40484-013-0015-1
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- Article
Reduced fecal short‐chain fatty acids in hispanic children with ulcerative colitis.
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- Physiological Reports, 2021, v. 9, n. 14, p. 1, doi. 10.14814/phy2.14918
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- Article
Metagenomic Analyses of Multiple Gut Datasets Revealed the Association of Phage Signatures in Colorectal Cancer.
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- Frontiers in Cellular & Infection Microbiology, 2022, v. 12, p. 1, doi. 10.3389/fcimb.2022.918010
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Decreased secondary faecal bile acids in children with ulcerative colitis and Clostridioides difficile infection.
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- Alimentary Pharmacology & Therapeutics, 2021, v. 54, n. 6, p. 792, doi. 10.1111/apt.16496
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Towards enhanced and interpretable clustering/classification in integrative genomics.
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- Nucleic Acids Research, 2017, v. 45, n. 20, p. 1, doi. 10.1093/nar/gkx767
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- Article
CAFE: aCcelerated Alignment-FrEe sequence analysis.
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- Nucleic Acids Research, 2017, v. 45, n. W1, p. W554, doi. 10.1093/nar/gkx351
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- Article
Alignment-free d*<sub>2</sub> oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences.
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- Nucleic Acids Research, 2017, v. 45, n. 1, p. 39, doi. 10.1093/nar/gkw1002
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DiseaseConnect: a comprehensive web server for mechanism-based disease–disease connections.
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- Nucleic Acids Research, 2014, v. 42, n. W1, p. W137, doi. 10.1093/nar/gku412
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- Article
A global overview of genetically interpretable multimorbidities among common diseases in the UK Biobank.
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- Genome Medicine, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13073-021-00927-6
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Sparse generalized linear model with L<sub>0</sub> approximation for feature selection and prediction with big omics data.
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- BioData Mining, 2017, v. 10, p. 1, doi. 10.1186/s13040-017-0159-z
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- Article
Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes.
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- ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2015, v. 9, n. 12, p. 2573, doi. 10.1038/ismej.2015.76
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- Article
Marine bacterial, archaeal and protistan association networks reveal ecological linkages.
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- ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2011, v. 5, n. 9, p. 1414, doi. 10.1038/ismej.2011.24
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- Article
Deep sequencing of HBV pre-S region reveals high heterogeneity of HBV genotypes and associations of word pattern frequencies with HCC.
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- PLoS Genetics, 2018, v. 14, n. 2, p. 1, doi. 10.1371/journal.pgen.1007206
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Phage–bacterial contig association prediction with a convolutional neural network.
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- Bioinformatics, 2022, v. 38, p. i45, doi. 10.1093/bioinformatics/btac239
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- Article
HiFine: integrating Hi-C-based and shotgun-based methods to refine binning of metagenomic contigs.
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- Bioinformatics, 2022, v. 38, n. 11, p. 2973, doi. 10.1093/bioinformatics/btac295
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KIMI: Knockoff Inference for Motif Identification from molecular sequences with controlled false discovery rate.
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- Bioinformatics, 2021, v. 37, n. 6, p. 759, doi. 10.1093/bioinformatics/btaa912
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- Article
CRAFT: Compact genome Representation toward large-scale Alignment-Free daTabase.
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- Bioinformatics, 2021, v. 37, n. 2, p. 155, doi. 10.1093/bioinformatics/btaa699
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- Article
New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing.
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- Briefings in Bioinformatics, 2014, v. 15, n. 3, p. 343, doi. 10.1093/bib/bbt067
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- Article
Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains.
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- Scientific Reports, 2016, p. 37243, doi. 10.1038/srep37243
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- Article
Effective binning of metagenomic contigs using contrastive multi-view representation learning.
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- Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-023-44290-z
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- Article
MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data.
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- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-41209-6
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- Article
HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps.
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- Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02626-w
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- Article
Comparison of Metatranscriptomic Samples Based on <i>k-</i>Tuple Frequencies.
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- PLoS ONE, 2014, v. 9, n. 1, p. 1, doi. 10.1371/journal.pone.0084348
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Accurate Genome Relative Abundance Estimation Based on Shotgun Metagenomic Reads.
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- PLoS ONE, 2011, v. 6, n. 12, p. 1, doi. 10.1371/journal.pone.0027992
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Sparse logistic regression revealed the associations between HBV PreS quasispecies and hepatocellular carcinoma.
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- Virology Journal, 2022, v. 19, n. 1, p. 1, doi. 10.1186/s12985-022-01836-9
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- Article
The Machine-Learning-Mediated Interface of Microbiome and Genetic Risk Stratification in Neuroblastoma Reveals Molecular Pathways Related to Patient Survival.
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- Cancers, 2022, v. 14, n. 12, p. 2874, doi. 10.3390/cancers14122874
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- Article
Somatic, germline and sex hierarchy regulated gene expression during Drosophila metamorphosis.
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- BMC Genomics, 2009, v. 10, p. 1, doi. 10.1186/1471-2164-10-80
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A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila.
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- BMC Genomics, 2009, v. 10, p. 1, doi. 10.1186/1471-2164-10-220
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Further understanding human disease genes by comparing with housekeeping genes and other genes.
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- BMC Genomics, 2006, v. 7, p. 31, doi. 10.1186/1471-2164-7-31
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Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains.
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- BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-015-0732-8
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- Article
Network tuned multiple rank aggregation and applications to gene ranking.
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- BMC Bioinformatics, 2015, v. 16, p. S6, doi. 10.1186/1471-2105-16-S1-S6
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- Article
Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach.
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- BMC Bioinformatics, 2011, v. 12, n. Suppl 1, p. 1, doi. 10.1186/1471-2105-12-S1-S11
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- Article
Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny.
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- BMC Bioinformatics, 2011, v. 12, n. 1, p. 118, doi. 10.1186/1471-2105-12-118
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- Article
Testing gene set enrichment for subset of genes: Sub-GSE.
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- BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-362
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- Article
Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis.
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- BMC Bioinformatics, 2007, v. 8, p. 453, doi. 10.1186/1471-2105-8-452
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- Article