Profile Picture LUO, Ruibang
B.Eng.(SCUT), Ph.D.(HKU), Postdoc(JHU)

Academic CV, Apr 2017

Email: rbluo (at) connect (dot) hku (dot) hk   
Website with reference links: http://i.cs.hku.hk/~rbluo/
Linkedin: View Ruibang Luo's profile on LinkedIn
Google Scholar: Ruibang Luo


Education

The University of Hong Kong, Hong Kong
2011 - 2015
Doctor of Philosophy (Ph.D.) in Computer Science
Research areas: Computational Biology and High Performance Computing

Dissertation: An all-purpose genome assembler for next-generation sequencing reads


Supervised by Prof. Tak-Wah Lam


Co-supervisors: Dr. Siu-Ming Yiu and Dr. Ruiqiang Li


Hong Kong and China Gas Company Limited Postgraduate Scholarship (2012)


Hong Kong Postgraduate Fellowship (2011)

South China University of Technology, Guangzhou
2007 - 2010
B. E. , Bioengineering, Graduated 1 year ahead of time

Excellent Thesis Award (2010)


Director of Public Relationship Department of Student Union of SCUT (2008)

Hobbies and Certificates

  • Stanford Genetics and Genomics Certificate
  • Advanced Open Water Diver (PADI)
  • Automobile Sports Competition License, Level E (FASC)

Experience

Johns Hopkins University, MD
08 / 2016 - Present
Postdoctoral Fellow
  • Salzberg Lab and Schatz Lab

United Electronics Co. Limited, Beijing
08 / 2015 - 08 / 2016
Director of Bio-Cloud Computing, Lead Scientist
  • I led the new business preparation of the Bio-Cloud Computing Department.
  • I facilitated the acquisition of L3 Bioinformatics Limited’s products and technologies.

L3 Bioinformatics Limited, Hong Kong
04 / 2014 - Present
Co-founder, Director (08/2015-)
CEO (04/2014-08/2015)
  • I was the mastermind of L3 Bioinformatics, with a mission to provide solutions that make working with genomic data fast, accurate, and easy.
  • I led the R&D on platforms supporting automated sequencing data analysis for local institutes including the Department of Health and HKSH
  • We provide software outsourcing service to large companies such as Beijing Genomics Institutes.

Products:

  • BALSA / ELSA
    BALSA / ELSA is a clinical-context enabling, ultra fast and accurate solution for the secondary analysis of next generation sequencing data on single node. It can process a 50-fold whole genome sequence (WGS) sample from raw reads to variants, including single nucleotide polymorphism (SNP), and insertion and deletion (INDEL), in about 4 hours, or just 10 minutes for a 200-fold whole exome sequence (WES) sample. Validation of the final results with the NIST Genome In A Bottle standard demonutrates that BALSA / ELSA's analysis pipeline has the highest combined sensitivity and precision.
    http://www.l3-bioinfo.com/products/balsa_elsa.html

  • database.bio
    database.bio is a web application that combines variant annotation, prioritization, and visualization so as to support fast hypothesis making and insights into precision medicine.
    http://database.bio

  • BGI-Online
    BGI-Online is a HIPAA-compliant cloud platform that helps with genome sequencing and analysis projects, while eliminating software setup and file transfer logistics.
    https://www.bgionline.com/

  • Helicube
    Helicube is an integrated solution for managing and analyzing Next Generation Sequencing (NGS) data. Preinstalled with state-of-the-art software BALSA and database.bio, and common pipelines such as BWA+GATK and TopHat, Helicube supports heterogeneous workloads, ranging from data analysis to results visualization. Helicube can serve multiple users via web browser. Helicube is designed to be HIPAA compliant; it allows users to share projects and data using carefully designed privileges, while strictly protecting private data. Helicube can scale up to multiple units to support the workloads of larger institutes; workload scheduling and balancing is also automatic, giving users convenience and efficiency.
    http://l3-bioinfo.com/products/Helicube/index.html
HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Hong Kong
09 / 2012 - 08 / 2015

I led a team of 10 bioinformaticians and graduate students to focus on algorithm design and implementation for genome analysis. Grants:

  • Hong Kong ITF Grant ITS/155/15FP: HK$ 6.805M
    中國人群基因組數據庫與精密醫學的應用
    A Genomic Database for the Chinese Population with Applications to Precision Medicine
    1/12/2015 - 30/11/2017, as Co-Investigator and Project Manager

  • Hong Kong ITF Grant GHP/011/12: HK$ 5.82M
    融合基因和藥物知識庫的臨床診斷及案例系統
    A Genomic and Pharmaceutical Knowledge-based System for Clinical Diagnosis and Case Repository
    3/1/2013 - 2/28/2015, as Co-Investigator and Project Manager

Selected leading works and open source projects:
Selected collaborating works:
  • Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber.
    Published in Plant Cell, 2015
  • Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression.
    Published in BMC Genomics, 2012

Works in consortium:
  • An integrated map of genetic variation from 1,092 human genome.
    Published in Nature, 2012
  • Assemblathon 1: A competitive assessment of de novo short read assembly methods.
    Published in Genome Research, 2011
  • Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.
    Published in BMC GigaScience, 2013

Beijing Genomics Institute, Shenzhen
09 / 2010 - 09 / 2011
Director of Bioinformatics Algorithm Research Laboratory

Job description: 1. Manage a team of 15 to develop and maintain BGI's staring tools including SOAPdenovo, SOAPaligner and etc. 2. Design and implement new algorithms and pipelines for NGS data analysis and management. Leading works:

  • Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly.
    Published in Nature Biotechnology, 2011

Collaborating works:
  • Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude.
    Published in Science, 2010
  • Mapping copy number variation by population-scale genome sequencing.
    Published in Nature, 2011

Works in consortium:
  • International network of cancer genome projects.
    Published in Nature, 2010

Patents:
Beijing Genomics Institute, Shenzhen
03 / 2008 - 08 / 2010
Bioinformatics Analyst
Leading works:
Collaborating works:
  • The DNA Methylome of Human Peripheral Blood Mononuclear Cells.
    Published in PLoS Biology, 2010

Works in consortium:
  • A map of human genome variation from population scale sequencing.
    Published in Nature, 2010
JHU Sapientia et Virtus

Shang Shan Ruo Shui Dont worry be happy