Publications

(2021). Transgenic refractory Aedes aegypti lines are resistant to multiple serotypes of dengue virus.. Scientific Reports.

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(2021). NK cell receptor and ligand composition influences the clearance of SARS-CoV-2. The Journal of Clinical Investigation.

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(2021). Connecting MHC-I-binding motifs with HLA alleles via deep learning.. Communications Biology.

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(2021). Termite Pest Identification Method Based on Deep Convolution Neural Networks.. Journal of Economic Entomology.

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(2021). iTARGEX analysis of yeast deletome reveals novel regulators of transcriptional buffering in S phase and protein turnover.. Nucleic Acids Research.

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(2021). Targeting KDM4B that coactivates c-Myc-regulated metabolism to suppress tumor growth in castration-resistant prostate cancer.. Theranostics.

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(2020). Inferring the transcriptional regulatory mechanism of signal-dependent gene expression via an integrative computational approach. FEBS Letters.

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(2020). H3K4 methylation at active genes mitigates transcription-replication conflicts during replication stress.. Nature communications.

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(2019). Setting boundaries for genome-wide heterochromatic DNA deletions through flanking inverted repeats in Tetrahymena thermophile. Nucleic Acids Research.

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(2018). CATANA: a tool for generating comprehensive annotations of alternative transcript events. Bioinformatics.

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(2018). Borders of Cis-Regulatory DNA Sequences Preferentially Harbor the Divergent Transcription Factor Binding Motifs in the Human Genome. Frontiers in Genetics.

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(2017). IsoPlot: a database for comparison of mRNA isoforms in fruit fly and mosquitoes.. Database : the journal of biological databases and curation.

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(2017). Comparative genomic analyses highlight the contribution of pseudogenized protein-coding genes to human lincRNAs. BMC Genomics.

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(2015). The CrdRS two-component system in Helicobacter pylori responds to nitrosative stress.. Molecular microbiology.

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(2015). Genome-wide analysis of enhancer RNA in gene regulation across 12 mouse tissues. Scientific Reports.

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(2013). Associations between intronic non-B DNA structures and exon skipping. Nucleic Acids Research.

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(2013). The impact of trans-regulation on the evolutionary rates of metazoan proteins.. Nucleic acids research.

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(2012). The Impact of Normalization and Phylogenetic Information on Estimating the Distance for Metagenomes. IEEE/ACM Trans. Comput. Biol. Bioinformatics.

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(2012). Evolution of cis-regulatory elements in yeast de novo and duplicated new genes. BMC Genomics.

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(2012). De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae. Bioinformatics.

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(2012). Analysis of the association between transcription factor binding site variants and distinct accompanying regulatory motifs in yeast.. Gene.

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(2011). MetaRank: a rank conversion scheme for comparative analysis of microbial community compositions. Bioinformatics.

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(2011). MetaABC—an integrated metagenomics platform for data adjustment, binning and clustering. Bioinformatics.

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(2011). Evidence of association between Nucleosome Occupancy and the Evolution of Transcription Factor Binding Sites in Yeast. BMC Evolutionary Biology.

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(2010). Genome-wide analysis of the cis-regulatory modules of divergent gene pairs in yeast.. Genomics.

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(2010). Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency.. BMC bioinformatics.

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(2009). Impact of DNA-binding position variants on yeast gene expression. Nucleic Acids Research.

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(2009). Co-expression of neighboring genes in the zebrafish (Danio rerio) genome.. International journal of molecular sciences.

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(2009). Roles of Trans and Cis Variation in Yeast Intraspecies Evolution of Gene Expression. Molecular Biology and Evolution.

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(2008). Evolutionary conservation of DNA-contact residues in DNA-binding domains.. BMC bioinformatics.

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(2008). Discovering gapped binding sites of yeast transcription factors.. Proceedings of the National Academy of Sciences of the United States of America.

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(2007). Co-expression of adjacent genes in yeast cannot be simply attributed to shared regulatory system.. BMC genomics.

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(2007). MYBS: a comprehensive web server for mining transcription factor binding sites in yeast.. Nucleic acids research.

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(2006). Method for identifying transcription factor binding sites in yeast.. Bioinformatics (Oxford, England).

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(2005). Statistical methods for identifying yeast cell cycle transcription factors.. Proceedings of the National Academy of Sciences of the United States of America.

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(2005). Cysteine separations profiles on protein sequences infer disulfide connectivity.. Bioinformatics (Oxford, England).

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(2004). An evolutionary algorithm for large traveling salesman problems. IEEE Transactions on Systems, Man, and Cybernetics, Part B (Cybernetics).

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(2004). An evolutionary approach for gene expression patterns.. IEEE transactions on information technology in biomedicine : a publication of the IEEE Engineering in Medicine and Biology Society.

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(2004). Some issues of designing genetic algorithms for traveling salesman problems. Soft Computing.

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(2004). Designing multiple-use primer set for multiplex PCR by using compact GAs. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).

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(2003). Heterogeneous selection genetic algorithms for traveling salesman problems. Engineering Optimization.

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(2002). GEM: a Gaussian Evolutionary Method for predicting protein side-chain conformations.. Protein science : a publication of the Protein Society.

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