BGI Bioinformatics Training

Training objectives

The BGI bioinformatics training program provides an introduction to the field of bioinformatics, with a focus on important bioinformatic tools and resources. The program combines theoretical and practical sessions, allowing participants to gain practical experience using various tools and resources, including bioinformatics pipelines, databases, statistical analysis, and data visualization. 

Target trainees

The program aims at individuals from a Life Science background who have a basic understanding of Biology, Medicine, Computer Science, Statistics, and those would like to become basic Bioinformatics users. A baseline level of understanding of the central dogma of molecular biology (i.e. DNA to RNA to Protein) is a requirement.

Teaching methods

The courses combine theories with practices and are delivered by recorded videos. Hands-on exercises will be tutored through online webinars. 

Course contents

Session 1: The Advances in Genomics

Introduction of Genomics: History, Technological Innovation and Future Perspectives

Session 2: Introduction to Bioinformatics

Bioinformatics: Basic Concepts and Applications

Principle of the High Throughput Sequencing Technology

Overview of NGS & Detailed Understanding

Data Retrieval & Introduction to Data Types

Overview of the Biological Information Data Analysis Method and Process

 Session 3: Introduction to Linux for Bioinformatics Bootcamp

Introduction of Linux System

The Method to Log in to the High-Performance Computing Cluster

Commonly Used Linux Bash Shell Command Line Use Introduction

Session 4: Introduction to Python and R for Bioinformatics Bootcamp 

Introduction to Python and Setting up a Python Environment

Python Data Structures

String Processing

Reading and Writing Files

Writing Functions and Larger Scripts

Using External Resources

Introduction to the Basic Grammar and the Function of R Language

Introduce the Typical Application Cases of R Language

Session 5: Research Project Design

Project Design in Human Genome Researches

Session 6: Next Generation Sequencing (NGS)-DNA-Seq Data Analysis

Alignment of Reads Against Reference Genome (BWA)

Evaluation of Mapping Results (Itools, Samtools)

Variant Identification (GATK, Manta, etc.) and Annotation

Backgroud of the Genome Annotation Analysis

Repeat Annotation, Gene Structure Annotation and Gene Function Annotation

Genome Annotation Practice: Gene Repeat Annotation, Gene Structure-Function-Trnascan

Session 7: Next Generation Sequencing (NGS)–RNA-Seq Data Analysis

Acquisition, Interpretation and Analysis of Transcriptome and Multi-Omics Data

RNA-seq Data Analysis and Practices

Biogenesis and Biological Functions of Regulatory Noncoding RNAs

Long Noncoding RNA (LncRNA) Data Analysis and Practices


Course description

1.Introduction to Genomics

This course systematically introduces the basic concepts of genomics, the design ideas of genomics-related classic research projects, the scientific research strategies that are used to sequence and analyze the genomes, and the methods for different categories of genomic studies, based on the classical scientific research projects of genomics.

2.Introduction to the Bioinformatics

This course introduces the basic concepts and applications of bioinformatics. It covers the principles of different sequencing technologies, the data format and quality assessment of high-throughput sequencing, and an overview of the biological information data analysis method and process. Meanwhile, systematically introduce the latest research methods of genome-transcriptome-proteome and other multi-omics research, as well as the basic strategy of bioinformatics data analysis project design and protocol formulation.

3.Introduction to the Linux for Bioinformatics Bootcamp

This course introduces basic knowledge of Linux system, the method to log in to the high-performance computing cluster, highly used commands on Linux bash shell as well as VIM editor.

4.Introduction to Programming

Popular programming languages (Python and R)will be introduced in this course. The course introduces basic grammar and functions of R language through a series of typical application examples,such as Python data structures,String processing,Reading and Writing files,writing functions and larger scripts,and using external resources.

5.Research Project Design

Through studying classical research projects of Mendelian Genetic disease as cases, this course introduces the design process, implementation, difficulties, and solutions of the research projects related to applying high-throughput sequencing technology to study genetic diseases.

6.Next Generation Sequencing (NGS)-DNA-Seq Data Analysis

This course introduces the data storage format (such as FASTA/FASTQ/BAM/SAM /VCF and so on) and the bioinformatics pipeline of the resequencing (Raw Data Quality Control - Mapping to the Reference Genome - Variant Detection - Visualization of Mapping and Variation - Annotation and Variant Effect Prediction, etc.). 

7.Next Generation Sequencing (NGS)–RNA-Seq Data Analysis

This course introduces the acquisition, interpretation, and analysis of transcriptome and multi-omics data, the bioinformatics pipeline of the RNA-seq data analysis and practices, biogenesis and biological functions of regulatory noncoding RNAs, and long noncoding RNA (LncRNA) data analysis and practices, etc.

Instructors


 Prof. Lars Bolund

 Professor of Clinical Genetics, Institute of Human Genetics, Aarhus University. Lifetime Appointment as Professor by the Queen of Denmark. Adjunct Professor, Institute of Biology, Copenhagen University

Research Supervision

Supervision of more than 30 pre-graduate researchers, Ph.D. students and doctorate candidates from Medical as well as Natural Science Faculties in Sweden, Denmark, Poland and China (more than 15 Ph.D.-students from China only).

Scientific Evaluation

Chairman/member of numerous evaluation committees regarding Ph.D.-exams, doctorates, research positions and professorships in Denmark, Finland, Norway, Sweden and U.S.A.

Evaluation (since 1983) of research grant applications for the Danish Medical Research Council, Novo's Fund and the European Commission. Referee for a number of international scientific journals.

Scientific Production

393 scientific articles (including 18 in Cell, Science, and Nature Series), database submissions and patents in the fields of genome/gene structure and function in cell biology and clinical genetics, molecular cell pathology of complex diseases, development of genetically designed animal model complex disease processes and somatic cell/gene therapy (see separate list of publications).


Dr.Xiaodong Fang

Ph.D. in Bioinformatics, University of Copenhagen, Denmark Titles

Vice-president, BGI Institute of Life Sciences

CTO, BGI Institute of Life Sciences

Researcher, Guangzhou University of Traditional Chinese Medicine

Adjunct Professor, Northwest University

Ph.D. Supervisor

Research Interests

Cancer Genome

Intestinal Flora

Publication

More than 30 papers in Nature, Science, Nature Genetics, etc., including 10 papers published as the first or corresponding author

Personal Webpage

http://www.bgi-college.cn/UpLoadFiles/file/2020042018161797.pdf


Dr. Zewei Song

Dr. Song received his Ph.D. degree in 2014 from the University of Minnesota, Twin Cities, at the department of Bioproducts and Biosystems Engineering. At 2017, he joined Institute of Metagenomics of BGI as a senior scientist leading the new track on environmental microbiology.

Research Field

His research focuses on Metagenomics.

Major Achievements

Dr. Song has established long-term collaborations with various institute across China and overseas, including Chinese Agricultural Academy of Sciences, University of Minnesota, University of Ljubljana, and many others. 

Teaching Experience

Dr. Song also dedicated himself in teach principles of metagenomics to students and researchers with various background. The series course on metagenomics developed by Dr. Song has a wide range of audience, from graduate student of U of M, Chinese Academy of Sciences, to researchers of main research institutes, such as CIAT at Vietnam.


Dr.Xinming Liang

Core R&D Senior Manager of Sequencer R&D Center, MGI Tech Co., Ltd.

Research Field

He has 12 years’ experience in bioinformatics analysis, participated in several animal and plant genome projects, familiar with evolution, population resequencing analysis. Currently, he is mainly engaged in data performance evaluation of domestic high-throughput sequencers, application kits and research and development of bioinformatics software products.


Dr.Tong Wei

Dr. Tong Wei works as a Bioinformatics Scientist of State Key Laboratory of Agricultural Genomics at BGI-Research in Shenzhen, China. After graduation in 2009 from the School of Life Sciences in Peking University, Dr. Wei carried out his postdoctoral research in the University of California, Davis, and the Joint Bioenergy Institute in USA. He has been engaged in functional genomic research of Arabidopsis, rice, sorghum, switchgrass, and other crop species. In 2017, Dr. Wei joined the BGI-Research as Team Lead of Crop Genomics.

Research Field

His research interests lie primarily in the fields of crop pangenome, population genetics, multi-omics approaches, genome selection and editing technology.


 Dr.Mingyan Fang

Dr. Fang’s main interest lies in human disease research using multi-omics approach, she has strong expertise in applying multi-omics and bioinformatics technologies on disease study. She uses machine learning and other data mining technologies to explore the synergistic effect between genes, and to identify new disease biomarkers. She is also committed to translating research findings into disease screening, diagnosis and therapeutics.

She received the Overseas High-Caliber Personnel in Shenzhen and Phoenix Tree Talent in Shenzhen Yantian. She is the principal investigator of a National Natural Science Foundation of China (NSFC) funded project, which is to explore of oligogenic mechanism in Primary Immunodeficiency. She is also the principal investigator of a project that investigates the genetic basis of systemic lupus erythematosus, and the project was funded by Science, Technology and Innovation Commission of Shenzhen Municipality. At the same time, she is the recipient (collaborator) of a number of national, provincial or municipal research grants.

Research Field

Multi-omics study of human disease, disease translational research, immunogenetics.

Scientific Production

She has published more than 50 papers in this fields (h-index 29, more than 2000 citations according to Google scholar), 17 of which were published as first or corresponding author. She is the inventor of 15patents (12 have been granted, seven of which she was the first inventor), she has applied for 4 software copyrights, and participated in the writing of one book.


Dr.Quan Shi

Dr. Shi received his Ph.D. degree in molecular biology from the University of Copenhagen and joined BGI Research as a bioinformatician in 2013. He is a core member of the BGI single-cell team.

Research Field

His primary research field is computational biology in single-cell omics and spatial transcriptome. In addition, he is an open-source software developer and developed algorithms and software for TF and gene regulatory network analysis and trajectory analysis during mammalian organ development and regeneration. 

Scientific Production

He has published 12 papers in multiple research journals.


 Dr. Min Xie

Dr. Xie received her Ph.D. degree in molecular biotechnology in 2019 from the Chinese University of Hong Kong. After graduation, she joined R & D department of BGI Genomics as a senior engineer to develop tools and pipelines to facilitate bioinformatic analysis.

Research Field

Her research interest lies primarily in fields such as molecular-assisted crop breeding and improvement, bioinformatics tools development and multi-omics applications.

Scientific Production

She was the receipt of Young Scholars Thesis Award (the Chinese University of Hong Kong) in 2019. To date, she has published 18 papers in multiple research journals, including but not limited to Science, Nature Biotechnology, Nature communications, etc. 

Teaching Experience

Dr. Xie also dedicated herself in teach principles of genomics to students and researchers with various background. The course on bioinformatics developed by Dr. Xie has a wide range of audience, from graduate student of Chinese Academy of Sciences, to researchers of main research institutes, such as China Tobacco.


Dr. Haixi Sun

Dr. Sun received his PhD degree in Bioinformatics in 2013 from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences. From 2013 to 2015, he entered the Rockefeller University in the United States for post-doctoral research, mainly focused on the identification and functional characterization of long non-coding RNAs. From 2015 to 2017, he worked as a research scientist in R&D department of Wilmar International Limited, mainly focused on gene mining in different organisms, flavor peptides and metagenomic analysis of fermented foods. In September 2017, he joined BGI-Shenzhen as an associate investigator and was awarded as "Overseas High-Caliber Personnel" of Shenzhen municipality and "Phoenix Tree Talent" of Yantian district of Shenzhen.

Research Field

His research focuses on the regulatory networks in the competition of pluripotent stem cells from different species, functions and regulatory mechanisms of non-coding RNAs, and the development of bioinformatics tools for better interpretation of omics data, etc.

Scientific Production

He has rich experience in both academic and industrial research, and have published 28 papers, 2 chapters regarding bioinformatics methodology, applied for 6 patents and obtained 6 software copyright.

Teaching Experience

Dr. Sun also dedicated herself in teach principles of transcriptomics to students and researchers with various background Every year. The series course on transcriptomics developed by Dr. Sun has a wide range of audience, from graduate student of Chinese Academy of Sciences, to researchers of main research institutes.


Dr. Shangjin Tan

Shangjin obtained master of philosophy degree in Life Science from The Hong Kong Unversity of Science and Technology. After graduation, he moved to BGI-research and continued research in microbial ecology. 

Research Field

His current projects are mainly concerned with 1) the roles of holobionts of corals and sponges in the adaptation and fitness of the hosts and 2)  understanding the diversity, distribution and controlling factors of the microbiome in Greenland under the context of global warming.

Scientific Production

Up to now, he has published or co-authored a total of 16 papers in influential scientific journals, including Nature, the ISME Journal, Limnology and Oceanography, etc.

Course fees

For course purchases or group discounts, please contact us at bgi-college@genomics.cn for inquiries.