Introduction to Omics: basics, development and future
COURSE INTRODUCTION
Introduction To Omics: Basics, Development And Future is a comprehensive course that provides students with an overview of the rapidly growing field of Omics. The course consists of five modules, each exploring a key aspect of Omics, ranging from general theory to specific human health and disease applications.
Module 1: Introduction to Genomics, Bioinformatics and Sequencing Technology
This module provides students with a fundamental understanding of Omics, introducing the fields of genomics, transcriptomics, proteomics, metabolomics, and other related fields. Students will learn about the basic principles of sequencing technology and its applications in Omics research.
Module 2: Animal and Plant Research
This module focuses on the application of Omics in animal and plant research. Students will learn about genome assembly, annotation, population genomics, comparative genomics of animals, and case studies on plant evolution and bird biology.
Module 3: Microbial Research
In this module, students will explore the application of Omics in studying human microbiota. Topics include the use of culture-based approaches in microbiota research, virology, symbiosis between microbes and their hosts, and mathematical foundations and applications of network analysis.
Module 4: Human Disease Research
This module provides an overview of Omics approaches to studying human diseases, including rare diseases, complex diseases, and cancer. Students will learn about state-of-the-art research methods in these areas and case studies on specific diseases.
Module 5: Advanced Technology
This module introduces students to the latest technologies in Omics, including DNA storage as a new paradigm for big data storage, single-cell omics, and future directions in genomics research, such as spatial and temporal genomics.
Introduction To Omics: Basics, Development And Future is designed to provide students with a comprehensive understanding of Omics and its potential impact on the future of human health and disease research. The course is ideal for students interested in biology, biotechnology, biomedicine, and related fields.
COURSE OUTLINE
Introduction to Genomics, Bioinformatics and Sequencing Technology
Introduction to Genomics
Introduction to Bioinformatics
Principle of Sequencing Technology
Animal and Plant Research
Genome Assembly
Genome Annotation
Population Genomics
Comparative Genomics of Animals
Case Study of Lettuce Genome
Case Study of Penguins Genome
Microbial Research
The Application of Cultured-based Approach in the Investigation of Human Symbiotic Microbiota
Virus Genomics and the Control of Infectious Diseases
The Human Microbiome at the Interface of Health and Disease
Mathematical Principles of Network Analysis and Its Applications
Human Disease Research
High-throughput Sequencing-based Studies on Inherited Diseases
The Genetics of Human Complex Traits: Advanced Concept and Methodology
How to Conduct Cancer Genome Research
Precision Oncology: Bring Omics into Cancer Clinical Practice
Advanced Technology
DNA Data Storage: A Promising Paradigm for Future Data Storage
Introduction to Single-cell Technology
Large-scale Population, Single-cell and Spatiotemporal Omics
AUDIENCE
All undergraduates, graduate students, and scientific researchers in the fields of biology and medicine.
INSTRUCTORS
Dr. Xiuqing Zhang
Personal Profile
Professor and Ph.D. supervisor at BGI College, University of Chinese Academy of Sciences, Director of Guangdong Provincial Key Laboratory of Human Disease Genomics.
Research Focus
Mainly engaged in the application development of second-generation sequencing technology and translational research in cancer genomics and immunogenomics.
Academic Achievements
Undertaken more than 10 scientific research projects such as the National '863' Major Project, National Key R&D Project, CAS Knowledge Innovation Project, and National Natural Science Foundation. During the 'Twelfth Five-Year Plan' period, as a member of the '863' project overall expert group and coordinator of the 'China Cancer Genome Project', he led the '863' major project 'Genome Technology for Major Diseases', which joined the 'International Cancer Genome Consortium (ICGC)' for international cooperation. Achieved good research results in non-invasive prenatal genetic testing technology development and clinical application, tumor single-cell research, viral genome integration research of tumor cells, and genomic research of esophageal cancer, bladder cancer, and kidney cancer, with related papers published in Cell, Nature, and Nature Genetics.
Dr. Zewei Song
Personal Profile
Ph.D. graduate from the University of Minnesota Twin Cities in Bioproducts and Biosystems Engineering. Currently responsible for the scientific research planning of the Environmental Ecology Laboratory.
Research Focus
Long-term research on microbial communities and ecosystem functions. Metagenomics of important ecological system microbial communities and comparative genomics of important resource microorganisms.
Academic Achievements
As a major participant, established the world's first fungal functional database FUNGuild. So far, 20 SCI articles have been published, including 8 articles as the first or corresponding author.
Dr. Guangyi Fan
Personal Profile
Researcher at BGI-Research Institute, graduate tutor at the University of Chinese Academy of Sciences.
Research Focus
Joined BGI in 2010, focusing on genomics, particularly in the development of bioinformatics tools and big data mining for animal and plant genomes, including de novo genome assembly, population genetics, transcriptomics, and cytomics. By integrating experimental, biological, mathematical, and computer knowledge, valuable information for scientific research and application is extracted from animal and plant genomes.
Academic Achievements
Led and designed major projects such as 10,000 fish genomes, 10,000 mollusk genomes, and marine mammal genomics, published over 100 scientific papers in internationally renowned academic journals such as Nature, Science, and Cell, with more than 30 papers as the first or corresponding author (including co-authors), and accumulated over 8,000 citations.
Hosted and participated in 9 national and provincial-level projects such as the National 863 Program and the National Key R&D Program, and presided over 1 National Natural Science Foundation project. Served as a reviewer for internationally renowned academic journals such as Molecular Biology and Evolution.
Dr. Linfeng Yang
Personal Profile
R&D Director and Senior Project Leader at BGI Genomics Shenzhen, China
Research Focus
Joined BGI Genomics in 2009, focusing on genomics big data collection, analysis, and information mining related to animal, plant, and microbial genomes. Familiar with the technical features and applications of next-generation high-throughput sequencing, and proficient in the data characteristics, analysis methods, and software of genomics big data, including de novo genome assembly, metagenomics, etc.
Academic Achievements
As the project leader at BGI, completed multiple collaborative research projects such as gecko genome and Riemerella anatipestifer genome, led several large-scale collaborative projects in genome assembly using second and third-generation sequencing technologies, and published more than 10 articles in top international academic journals.
Dr. Min Xie
Personal Profile
Dr. Xie received her Ph.D. degree in molecular biotechnology in 2019 from the Chinese University of Hong Kong. After graduation, she joined the R & D department of BGI Genomics as a senior engineer to develop tools and pipelines to facilitate bioinformatic analysis.
Research Focus
Her research interest lies primarily in fields such as molecular-assisted crop breeding and improvement, bioinformatics tools development and multi-omics applications.
Academic Achievements
She was the recipient of the 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.
Dr. Yang Zhou
Personal Profile
Special Scientist at the Digital Earth Research Institute, BGI-Research Institute
Research Focus
Engaged in the research of vertebrate sex chromosome evolution. Focusing on monotremes and primates, the research reveals the evolutionary history of sex chromosomes in mammals and the degeneration events of the Y chromosome.
Academic Achievements
Rich research experience in animal comparative genomics and sex chromosome evolution, with a total of 14 SCI articles published, including 3 articles as the first author in international mainstream academic journals such as Nature and GigaScience.
In January 2021, as the first author, published a paper titled "Platypus and echidna genomes reveal mammalian biology and evolution" in Nature. For the first time, the evolutionary history of multiple sex chromosomes in monotreme species was analyzed at the whole-genome level, and the ancestral karyotype of all living mammals' most recent common ancestor was reconstructed.
In April 2021, as a co-first author, published a paper titled "Evolutionary and biomedical insights from a marmoset diploid genome assembly" in Nature. For the first time, it was discovered that marmoset sex chromosomes experienced further recombination suppression compared to other catarrhines and produced a new sex chromosome evolutionary hierarchy.
Instructor: Dr. Tong Wei
Personal Profile
Researcher at BGI-Research Institute, Ph.D. supervisor at Digital Earth Research Institute, graduated from Peking University School of Life Sciences. He has worked on functional genomics of plants such as Arabidopsis, rice, and sorghum at Peking University Department of Biotechnology, Peking University Bioinformatics Center, University of California Davis Department of Plant Pathology, and US Bioenergy Joint Research Center.
Research Focus
Currently mainly engaged in plant variomics, and crop population genetics, with the goal of using resequencing technology to conduct in-depth research on crop domestication history, pan-genome assembly, molecular markers of important agronomic traits, and identification of associated genes.
Academic Achievements
Participated in or led projects such as the Ministry of Agriculture's rice disease and pest resistance transgenic project, the US NIH rice disease resistance research project, and the US DOE bioenergy crop project. Published 12 articles in journals such as Plant Cell, New Phytologist, Molecular Plant Pathology, applied for 3 patents, and has a comprehensive research background in multiple disciplines.
Dr. Chengran Zhou
Personal Profile
Associate researcher in bioinformatics at BGI-Research Institute Digital Earth Research Institute, Biodiversity Research Center, and Wutong Talent D Class in Yantian District, Shenzhen.
Research Focus
In recent years, the main research direction is polar organism genomics, using genomics technology to explore the evolutionary history of polar organisms mainly living in Antarctica and the world's third pole, the Qinghai-Tibet Plateau, and the impact of environmental changes on polar organisms.
Academic Achievements
Research mainly focuses on the system evolution and environmental adaptability of polar organisms (such as penguins, pikas, etc.), using multidisciplinary research methods to construct the evolutionary relationships of related groups and reveal the molecular mechanisms of some groups adapting to polar environments. Major research results have been published as first and corresponding authors (including co-authors) in international academic journals such as Nature Communications, Zoological Research, and Conservation Genetics; participated in the writing of a professional book. Other early genomic project results have been published in journals such as Nature, Science, and GigaScience.
Dr. Yuanqiang Zou
Personal Profile
Associate Researcher in Genomics, Deputy Director of Shenzhen Human Intestinal Microecology Detection and Intervention Engineering Laboratory, Graduate Supervisor of BGI College, China Academy of Sciences, and Graduate Supervisor of Zhengzhou University.
Joined BGI-Research Institute in 2010, participated in the construction of intestinal microbial culture platform, intestinal microbial identification, analysis of intestinal bacterial genomes, and functional analysis and evaluation of probiotics as the project leader of metagenomics direction. He has been invited to give presentations at several microecology-related conferences. He is the principal investigator of a National Natural Science Foundation for Young Scientists and has participated in several key national research projects, National Natural Science Foundation projects, Guangdong Province key projects, and Shenzhen City science and technology projects as core members.
Research Focus
Microbial culture genomics, genomic research, microbial classification and evolution, and functional research of probiotics.
Academic Achievements
Constructed the largest intestinal bacterial strain library and intestinal reference genome database in the field so far, with related results published in the top international journal Nature Biotechnology in 2019. Also, ongoing research and application transformation on probiotics' functional mining and their intervention in various diseases such as intestinal inflammatory diseases, metabolic diseases, neurodegenerative diseases, and reproductive tract infections.
Currently leading the clinical transformation of intestinal microbiome functional mining and novel probiotics for obesity, diabetes, inflammatory bowel disease, Alzheimer's disease, and bacterial vaginosis-related disease intervention.
Published more than 20 SCI articles in top journals such as Nature Biotechnology, Nature Genetics, Nature Communications, Trends in Microbiology, and Cell Discovery as the first author and co-author, with 10 articles as the first author or corresponding author, and applied for more than 30 patents.
Dr. Zhihua Ou
Personal Profile
Doctor of Virology from the University of Hong Kong; Associate Researcher in Bioinformatics at BGI-Research Institute in Shenzhen, Project Leader of Infection Spatiotemporal Omics Research; Shenzhen Overseas High-level Talent Class C, Shenzhen Yantian District 'Wutong Talent' Class C.
Research Focus
Combining cutting-edge genomics, single-cell transcriptomics, and spatial transcriptomics technologies to explore the pathogenic mechanisms of acute/chronic infectious pathogens (such as HPV infection and cervical cancer, COVID-19 infection and respiratory diseases, Echinococcus infection and hydatid disease, etc.), elucidating the interactions between pathogens and host cell proliferation, immunity, and metabolic pathways at different stages of disease progression, providing new insights for the prevention, diagnosis, and treatment of acute/chronic infectious diseases.
Academic Achievements
Participated in the genetic tracing of H7N9 avian influenza virus in 2013, with related results published in Nature. In recent years, research on the genetic variation and pathogenic mechanisms of COVID-19 and human papillomavirus has been carried out, with more than ten papers published in high-level journals such as Advanced Science, Cellular & Molecular Immunology, Genomics, and Genome Biology and Evolution.
Dr. Ruijin Guo
Personal Profile
Associate researcher of bioinformatics at the Precision Health Research Institute of BGI-Research Institute, and Ph.D. from the University of Macau. Joined BGI-Research Institute in 2014, serving as the project leader for skin microbiome metagenomics, schizophrenia gut microbiota, and probiotics for rheumatoid arthritis. Guided students to obtain the Enthusiastic Intestine Scholarship.
He has participated in multiple scientific projects funded by the National Natural Science Foundation, Macau Science and Technology Development Fund, and Shenzhen Science and Innovation Commission. Academic part-time positions include Enthusiastic Intestine Think Tank Expert, Standing Committee Member of the Chinese Microcirculation Society-Neurodegenerative Disease Professional Committee-Alzheimer's Disease Biomarker [AT(N)-C] Branch, Member of the World Federation of Chinese Medicine Societies-Traditional Chinese Medicine Immunology Professional Committee, and Member of the Chinese Biophysical Society Intestinal Microbiota Branch.
Research Focus
He mainly focuses on the "bacteria-brain" axis, construction of human symbiotic bacteria reference set, and precision medicine multi-omics.
Academic Achievements
Led and participated in the construction of the human gut microbiome reference gene set, rat gut microbiome reference gene set, and human nasal cavity symbiotic microbial genome set. In the past five years, as the first author, corresponding author, and co-author, published 11 high-level scientific research papers in journals such as Cell Systems, Nature Communication, Molecular Psychiatry, Microbiome, Nature Biotechnology. Served as guest editor for Frontiers in Microbiome, reviewer for Journal of Neuroinflammation, BMC Microbiology, and Frontiers in Microbiology. Also authorized/applied for 11 patents, 5 software copyrights, and 3 technology transfers.
Dr. Mingyan Fang
Personal Profile
Dr. Fang’s main interest lies in human disease research using the multi-omics approach, she has strong expertise in applying multi-omics and bioinformatics technologies to 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 oligogenic mechanisms 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 Focus
Multi-omics study of human disease, disease translational research, immunogenetics.
Academic Achievements
She has published more than 50 papers in this field (h-index 29, more than 2000 citations according to Google Scholar), 17 of which were published as the first or corresponding author. She is the inventor of 15 patents (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. Yan Li
Personal Profile
Li Yan is a Senior Scientist at the Precision Health Research Department of BGI Research. She obtained her Ph.D. in Statistical Genetics from the Department of Psychiatry, Li Ka Shing Faculty of Medicine at the University of Hong Kong.
Research Focus
She specializes in genetic analysis of complex traits, genetic risk prediction for human complex diseases, and the construction of genetic statistical models for multiple disease comorbidities.
Academic Achievements
She has published 14 SCI papers, including 6 as first author or corresponding author, in journals such as Molecular Biology and Evolution, Aging Cell, Cell Reports, and The Spine Journal. Her research has proposed two pathogenic genetic mechanisms for back pain.
Dr. Zhi Ping
Personal Profile
Dr. Zhi Ping currently serves as the Chief Scientist at the Institute of Biochemistry of BGI-Research, Shenzhen. He earned both his B.Sc. and Ph.D. from Nanyang Technological University of Singapore.
Research Focus
His research currently focuses on the development of transcoding algorithms and integrated systems of DNA data storage, bioinformatics analysis of synthetic biology, and other BT-IT converging directions.
Academic Achievements
He has published 8 related papers in prestigious journals including Nature Computational Science, Advanced Science, National Science Review, GigaScience, etc.
Dr. Chuanyu Liu
Personal Profile
Ph.D. in Genomics, currently responsible for single-cell genomics 'reading' tool research at the Super Cell BGI-Research Institute. Previously received first-class funding from the China Postdoctoral Science Foundation and is a high-level talent in Shenzhen.
Research Focus
Development and application of ultra-high-throughput single-cell multi-omics sequencing technology (including species cell atlas, large population cohort studies of diseases, etc.).
Academic Achievements
As a core member, participated in the development of the domestic high-throughput single-cell microfluidic system DNBeLab C4 and completed industrial transformation. In recent years, published more than 20 papers in journals such as Nature, Nature Communications, Cellular & Molecular Immunology, Frontiers in Cell and Developmental Biology, with a cumulative impact factor of 201.4 as the first or corresponding author (including co-authors), applied for 5 invention patents, and authorized 1.
Dr. Xun Xu
Personal Profile
Currently serves as the Executive Director of BGI Group, Dean of BGI-Research Institute, Vice Chairman of International Organization for Standardization/Biotechnology Committee (ISO/TC276), ISBER (International Society for Biological and Environmental Repositories) China Chairman, World Economic Forum Future Council Member, Expert Member of National Biological Sample Standardization Committee (SAC/TC559), Vice President of the Third Council of Shenzhen Life Science and Biotechnology Association, and Deputy Director of the First Basic Medical Expert Committee of Shenzhen Medical Association.
Research Focus
Including the development of sequencers and related technologies, single-cell sequencing technology, spatiotemporal omics sequencing technology (stereo-seq), and the translational application of sequencing technology in disease and agriculture.
Academic Achievements
So far, 242 SCI-indexed papers have been published in top international scientific journals, including Nature, Science, and Cell, with more than 30,000 citations in the past five years. He has presided over or participated in several major projects, including the National 863 Sequencer Development Project, the National Development and Reform Commission's Industrial Agglomeration Project, etc. He has won awards such as the "Ministry of Science and Technology's Big Challenge Young Scientist", "Pengcheng Outstanding Talent Award", "Guangdong Provincial Science and Technology Award" First Prize, and "Ministry of Education Natural Science Award" Second Prize. In July 2020, he was selected for the National Hundred, Thousand, and Million Talent Project and awarded the honorary title of "Outstanding Young and Middle-aged Expert with Outstanding Contributions".
COURSE FEES
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