My Photo Ruibang Luo (罗锐邦)

Department of Computer Science
The University of Hong Kong

Office:
  Rm422, Chow Yei Ching Bldg., HKU
  Pokfulam Rd., Hong Kong
Email:
  rbluo (at) cs (dot) hku (dot) hk

[CV]   [Google Scholar]

I'm an Assistant Professor of Computer Science, HKU. With both a bio-engineering and a computer science background, I work on bioinformatics algorithm development and biological, clinical and pharmaceutical projects. My interdisciplinary research results have been published in peer-reviewed journals such as Nature, Nature Biotechnology and Bioinformatics. My ongoing target is to build models and develop software with my students and other collaborators with the aim of better understanding the origins of life and developing cures for cancer. The lab is intensively working on Next-Generation Sequencing data, but meanwhile shifting to Single-Molecule Long Reads on Genome Assembly, Variation Detection and Pathogen Detection. Recruitment: I'm looking for dedicated and self-motivated students and postdocs with interest in bioinformatics. If you enjoy deciphering biological and medical big data by writing up your own code to target for the best speed, sensitivity and accuracy, you might be interested in working with me. Please contact me through email with your CV.


Publications

2018:
  • Skyhawk: An Artificial Neural Network-based discriminator for reviewing clinically significant genomic variants
    Preprint  [PDF]
  • Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing
    Preprint  [PDF]
  • Transcriptome Analysis of Acute Phase Liver Graft Injury in Liver Transplantation
    Biomedicines  [PubMed]
  • AC-DIAMOND v1: Accelerating large-scale DNA-protein alignment.
    Bioinformatics  [PubMed]
  • 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]

Awards


Hobbies

I like extreme sports. I am a Private Pilot License holder and I enjoy flying a single-engine Cessna or Arrow on a day with a breeze and clear sky for sightseeing at new places. Here is a photo I took on the day I passed my VFR check-ride with a Cessna 172SP tail numbered N615JA (pronounced skyhawk-six-one-five-juliet-alpha) at KESN (Easton Airport, MD). One of my dreams is to establish my own aviation school in Mainland China to teach youngsters recreational flying. I was also an amateur auto racer, but I stopped racing after married. Scuba diving is also one of my favorite sports to explore a new place.