Publications

2019:
  • RENET: A Deep Learning Approach for Extracting Gene-Disease Associations from Literature
    RECOMB 2019.  [Springer]
  • Skyhawk: An Artificial Neural Network-based discriminator for reviewing clinically significant genomic variants
    ICIBM 2019.  [PDF] [GitHub]
  • Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
    Nature Communications.  [Nat. Comm.] [GitHub]
2018:
  • Transcriptome Analysis of Acute Phase Liver Graft Injury in Liver Transplantation
    Biomedicines.  [PubMed]
  • AC-DIAMOND v1: Accelerating large-scale DNA-protein alignment
    Bioinformatics.  [PubMed] [GitHub]
  • MegaPath: Low-Similarity Pathogen Detection from Metagenomic NGS Data
    ICCABS 2018.  [IEEE]
  • Restricted Boltzmann Machine and its Potential to Better Predict Cancer Survival
    Biomed J Sci & Tech Res.  [PDF]
2017:
  • First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (formerly Scedosporium prolificans)
    G3: Genes, Genomes, Genetics.  [PubMed]
  • Serine peptidase inhibitor Kazal type 1 (SPINK1) as novel downstream effector of the cadherin-17/β-catenin axis in hepatocellular carcinoma
    Cellular Oncology.  [PubMed]
  • LRSim: a Linked Reads Simulator generating insights for better genome partitioning
    Computational and Structural Biotechnology Journal.  [PubMed] [GitHub]
  • 16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model
    GigaScience.  [PubMed] [GitHub]
  • MegaGTA: a sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs
    BMC Bioinformatics.  [PubMed]
2016:
  • MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices
    Methods.  [PubMed]
  • AC-DIAMOND: Accelerating Protein Alignment via Better SIMD Parallelization and Space-Efficient Indexing
    IWBBIO.  [Springer]
  • BASE: a practical de novo assembler for large genomes using long NGS reads
    BMC Genomics.  [PubMed]
2015:
  • database.bio: a web application for interpreting human variations
    Bioinformatics.  [PubMed]
  • De novo assembly of a haplotype-resolved human genome
    Nature Biotechnology.  [PubMed]
  • MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
    Bioinformatics.  [PubMed] [GitHub]
  • MICA: A fast short-read aligner that takes full advantage of Intel Many Integrated Core Architecture (MIC)
    BMC Bioinformtics.  [PubMed] [SourceForge] [GitHub]
  • Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber
    Plant Cell.  [PubMed]
2014:
  • SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads
    Bioinformatics.  [PubMed] [SourceForge] [GitHub]
  • Exome sequencing of tumor cell lines: Optimizing for cancer variants
    Cancer Research.  [AACR]
  • GPU-Accelerated BWT Construction for Large Collection of Short Reads
    ArXiv.  [PDF]
  • BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU
    PeerJ.  [PubMed] [SourceForge]
2013:
  • SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner
    PLoS ONE.  [PubMed] [GitHub]
  • Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
    GigaScience.  [PubMed]
2012:
  • SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler
    GigaScience.  [PubMed] [SourceForge] [GitHub]
  • COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
    Bioinformatics.  [PubMed] [SourceForge]
  • The oyster genome reveals stress adaptation and complexity of shell formation
    Nature.  [PubMed]
  • Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression
    BMC Genomics.  [PubMed]
  • An integrated map of genetic variation from 1,092 human genome
    Nature.  [PubMed]
2011:
  • Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly
    Nature Biotechnology.  [PubMed]
  • Mapping copy number variation by population-scale genome sequencing
    Nature.  [PubMed]
  • Assemblathon 1: A competitive assessment of de novo short read assembly methods
    Genome Research.  [PubMed]
2010:
  • Building the sequence map of the human pan-genome
    Nature Biotechnology.  [PubMed]
  • Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude
    Science.  [PubMed]
  • The DNA Methylome of Human Peripheral Blood Mononuclear Cells
    PLoS Biology.  [PubMed]
  • International network of cancer genome projects
    Nature.  [PubMed]
  • A map of human genome variation from population scale sequencing
    Nature.  [PubMed]