On June 17, the appointment ceremony of scientific advisors of Analytical
Biosciences took place in the Beijing office. Analytical Biosciences invited
Professor Runsheng Chen from Institute of Biophysics of the Chinese Academy of
Sciences, Professor Fuchou Tang from Peking University, and Professor Zemin Zhang
from Peking University to join its Scientific Advisory Board. The goal of these
appointment is to advance the research and technology capacities and to enhance the
impact of single-cell sequencing and bioinformatics. The appointment ceremony was
hosted by Mr. Tao Hong, Chief Operating Officer of Analytical Biosciences. On behalf
of the company, he issued letters of appointment to the three advisors.
Prof. Runsheng Chen is one of the pioneering scholars in computational biology and
bioinformatics in China. Prof. Chen has led his bioinformatics group to a series of
paramount successes, including the whole genome assembly and annotation for T.
tengcongensis B4 (the first bacterium genome completely sequenced in China), the 1%
Human Genome Project, and the Draft Sequence of the Rice Genome. Since 2001, Prof.
Chen has rapidly expanded his interests to the investigation of noncoding RNAs and
has established multiple widely used noncoding RNA databases. Prof. Chen has
published more than 200 papers and has won the winner of "Kotani Prize". Prof. Chen
is a member of the Chinese National Academy of Sciences.
Prof. Fuchou Tang pioneered the development of single cell RNA sequencing in the world, and has guided his laboratory in developing multiple successful cutting-edge single cell genomics techonologies including single cell DNA methylome sequencing, single cell chromatin accessibility sequencing, and single cell multiple omics sequencing. His lab also studies the gene regulation network in human early embryos and germline cells. He has published numerous high-impact studies in Cell, Nature, and Science, and has been widely recognized as a leading single cell biologist in the world. His work has been awarded the “Top 10 Scientific and Technological Advances of China” for both 2014 and 2015.
At the ceremony, Prof. Zemin Zhang presented the company vision as well as the current state of the research and development capabilities to Profs. Chen and Tang, and outline how the new advisor might help the company. Both Prof. Chen and Prof. Tang expressed their enthusiastic view towards the scientific and business plan of the company and then stated their commitment to the future success of Analytical Biosciences. After the official signing of the scientific advisory agreements, all three advisors toured the computational and experimental facilities of the company, and each of them provided constructive feedbacks. Mr. Hong expressed how the entire company staff members were excited by the participation of all three scientific advisors and expected the successful partnership will propel the success of Analytical Biosciences.
On the June 10, Mr. Boxi Kang, head of the Bioinformatics Department of Analytical
Biosciences, gave a lecture entitled “A Framework for Real-time Analysis and
Visualization of Large Single-cell RNA-seq Data” on the Cold Spring Harbor Asia
Conference (Suzhou) on the Scientific and Technical Advances in Cancer
The rapid and accurate annotation of single-cell data is becoming an analytical
challenge. The current unsupervised-clustering-annotation approaches are time- and
labor- consuming, and also cannot based on a uniform analysis standard. Like the
human genome references that make re-sequencing possible, supervised projection of
newly-generated data onto annotated labels has become more efficient and practical
with the fast accumulation of single cell RNA sequencing data. Based on the
Gamma-Poisson distribution of single cell gene expression data, Chenwei Li, Boxi
Kang and colleagues established an entropy-test for the determine of single-cell
gene expression variability. Applying such entropy statistic, they built SciBet
(Single Cell Identifier Based on Entropy Test), a Bayesian classifier that
accurately predicts cell identity for any randomly sequenced cells. Boxi
demonstrated that SciBet outperforms existing tools in accuracy, robustness, speed
and scalability in the presentation.
Mr. Kang’s enthusiastic lecture attracted a wide range of interests from the audience, including the world's top immunologists and computational biologists, and triggered extensive discussion. This work was also presented as a poster during the meeting.
Cold Spring Harbor Laboratory (CSHL) is a private, not-for-profit research and education institution at the forefront of efforts in molecular biology and genetics. CSHL meetings and courses are widely praised for propelling the advancement of modern biology. Cold Spring Harbor Asia conferences are held at Suzhou Dushu Lake Conference Center in Suzhou, China. The series of conference has become one of the most influential forums on life science in China and Asia Pacific. This particular meeting was co-organized by Zemin Zhang, a co-founder of Analytical Biosciences.
Analytical BioSciences Limited, the single-cell big data company, has raised the
Series A funding led by IDG Capital, a leading investment firm specialized in TMT
& Healthcare. Dr. Zemin Zhang, the founder of the company, says that the fund
will be used to accelerate the development of single-cell genomic capabilities for
medicine research, especially the establishment of single-cell big data platform,
intelligent analysis pipeline and in-depth interpretation.
IDG Capital says, “We have been closely focusing on the development of cutting-edge
technology in the field of life medicine and strongly supporting technology
transformation. Among which single-cell big data is one of the key areas we
invested. Dr. Zemin Zhang has rich experience in the pharmaceutical industry and
also has a large number of internationally leading research results. We are
optimistic about the scientific strength and commercial potential of the Analytical
Biosciences team. We will continue to support the company to become the leading
company in China and over the world. "
Emerging single-cell sequencing technologies can now readily profile thousands of cells, and data is accumulating rapidly. However, few biotech companies in China can efficiently process such mass data and interpret it with biological insights. At present, Analytical Biosciences is in the leading position in single-cell medical genomics with advanced bioinformatics technologies. The IDG Capital's funding will support us to sustain our leadership in this territory.
Analytical BioSciences Limited aims to unleash the power of genomics and bioinformatics in understanding major human diseases, providing capacities on (1) Single-cell sequencing, (2) Cancer genomics; (3) Bioinformatics and biological data mining; (4) Drug targets and biomarkers discovery. Target customers are mainly researchers and clinicians from biomedical research institutes, hospitals and international pharmaceutical companies. The company was founded in December 2018, and based in Beijing, China. For more information, please access to www.abiosciences.com or contact: +86 10 62566819, email@example.com.
The management team of Analytical Biosciences Limited has comprehensive backgrounds in genomics, bioinformatics, information technology and investment, and rich experiences in biotechnology and pharmaceuticals. Dr. Zemin Zhang, the founder of the company, spent over 16 years at Genentech/Roche, leading the cancer genomics and bioinformatics group to discover anticancer targets and. After Join in Peking University, his lab developed single-cell sequencing technologies to delineate the detailed composition and functional status of the tumor microenvironment, the related studies were published on Nature, Cell and Nature Genetics, Nature Biotechnology, etc. He is also an inventor for 60 issued US patents, and has directly contributed to the initial finding of the molecular targets of multiple cancer therapeutic agents in clinical trials.
Founded in 1992, IDG Capital is a leading investment firm focused on developing extraordinary companies through our expertise in private equity, venture capital and mergers & acquisitions. Since its inception, IDG Capital has expanded into thirteen cities around the world. Accumulated assets under management have grown from US$10 million in 1992 to approximately US$20 billion today. IDG Capital focuses on Technology, Media and Telecommunications (TMT), Consumer and Entertainment, Healthcare, Advanced Manufacturing/Clean-Tech and Energy. To date, IDG Capital has invested in more than 800 companies and made over 180 successful exits across the globe through IPOs and M&A. For more information, please visit http://www.idgcapital.com/
On June 29, 2019, the fifth precision medicine and gene sequencing conference was
held in the academic hall of Peking Union Medical College. The conference was
co-sponsored by seqChina, Peking Union Medical College Hospital and Beijing Medical
Award Foundation. Prof. Runsheng Chen and Prof. Zemin Zhang were invited to attend
the conference and presented the plenary lectures, which received extensive
attention, discussion and recognition from the participants.
As the President of the conference, Prof. Runsheng Chen, academician of Chinese
Academy of Sciences and scientific advisor of Analytical Biosciences, gave the
opening speech. Prof. Chen said that the development of precision medicine is bound
up with multiple categories of genomic information, and their application is playing
more essential role in life sciences. The medical research is stepping into accuracy
and concrete through changing individual-oriented genomics to cell-oriented
genomics. With the advancement of gene sequencing technology, precision medicine
will affect more widely on people's daily lives.
Zemin Zhang, professor of Peking University and founder of Analytical Biosciences, gave a report entitled "Dynamic properties of tumor-infiltrating immune cells revealed by single cell sequencing". Prof. Zhang introduced the his studies focus on cancer immunology using cutting-edge single-cell transcriptome and bioinformatics, including the T cell landscapes of liver cancer, lung cancer and colorectal cancer using smart-seq2 technology, and the landscape of total CD45+ immune cells in liver cancer combining smart-seq2 and 10x Genomics technology. These studies systematically characterized the functional groups of immune cells in cancer, paving a path to the immune classification of cancer patients and the discovery of novel immunotherapies.
Prof. Zemin Zhang also introduced the current state of Analytical Biosciences, underlined the achievements and advantages of bioinformatics development, and such tools have been utilized in the above cancer immunology studies. He said our bioinformatics toolkits can be applied on the expanding scope of single-cell genomic research, thus promoting single-cell sequencing to play an increasingly important role in the development of precision medicine.
On October 24, 2019, Analytical BioSciences Limited received the official notification of 10x
Genomics, and was approved as a 10x Genomics Certified Service Provider for the Chromium Single Cell
Immune Profiling Solution. Analytical BioSciences also obtained the official certification from 10x
Genomics for the Single Cell 5' gene expression and VDJ analysis. This was the first time that 10x
Genomics certified this technology to an institution in China. Therefore, Analytical BioSciences
becomes the only domestic institution that has been certified by 10x Genomics for single cell immune
10x Genomics is an internationally renowned single-cell sequencing company. In 2016, it launched the Chromium system which can get single cell level digital gene expression profile and analyze thousands or even tens of thousands of single cell groups through different sequence tags between different groups of cells. The system is based on microfluidic single-celled sequencing and water-in-oil micro reaction system. The Chromium system can be adapt to a wide range of fields, such as cancer, immunology and neuroscience. With the platform and technology of 10x Genomics, more than 300 single-cell transcriptome papers have been published so far. Among them, the number of high-score paper has been increasing year by year, the papers appear in many key journals like CNS.
As the leading company of single-cell sequencing and data analysis, Analytical BioSciences introduced 10x Genomics system at the beginning of its establishment. The certification obtained from 10x Genomics demonstrates that Analytical BioSciences has a professional and reliable experimental team, as well as strong and stable experimental ability, which allow Analytical BioSciences to produce stable and repeatable experimental results by using the ChromiumTM Single Cell V(D)J kit. It also demonstrates that Analytical BioSciences is capable of providing high-quality scientific research services represented by 10x Genomics 5' single-cell transcriptome + single-cell TCR/BCR immune profiling, meeting the needs of high quality results from researchers in biology and medicine.
Furthermore, Analytical BioSciences provides technical services of 10x Genomics 3' single-cell transcriptome, 10x Genomics single-cell ATAC-seq, 10x Genomics single-cell genome (CNV) and SMART-seq2 single-cell sequencing with rapid, accurate, one-on-one single-cell sequencing data analysis. Analytical BioSciences aims to provide comprehensive and integrated single-cell sequencing services, to provide strong and reliable technical support for scientific research, clinical and pharmaceutical applications and so on.
On December 17, 2019, Analytical Biosciences celebrates its first birthday.
During this year, Analytical Biosciences has grown rapidly and has made great progress, becoming the most shining star in the field of single-cell sequencing analysis.
Professor Zemin Zhang，the founder of Analytical Biosciences
At the anniversary celebration, Professor Zemin Zhang，the founder of Analytical Biosciences，reviewed the company's process of establishment and expressed thanks to the employees for their contributions. “The rapid development of Analytical Biosciences during this year owns to everyone’s hard work，and it has brought us to where we are today. In such pace, Analytical Biosciences will definitely make a difference.”
Tao Hong，the COO of Analytical Biosciences
Then，Tao Hong，the COO of Analytical Biosciences, summarized the company's operation state over the past year. “Since the establishment of Analytical Biosciences, it has had a first-class team and technology, and has received financial support from IDG Capital, a top investment institution. After one year of development, the company's structure has been completed and a preliminary business system has been established.” He said.
“Now, the company is operating very well, it has sufficient cash flow and has exceeded its business goals. These have laid a good foundation for the company's future development. Nevertheless, I still hope that all employees of the company will not forget their original intentions and always work hard to achieve the company's ultimate vision.“
Dr. Zixuan Pang, Investment Manager of IDG Capital
In addition, Dr. Zixuan Pang, Investment Manager of IDG Capital, also attended the anniversary celebration. He shows optimism to the single cell sequencing and analysis field，and he is confident of the success of Analytical Biosciences in the future.
Academician RunSheng Chen, Professor Fuchou Tang and main leaders of Analytical Biosciences
Analytical Biosciences is certified by 10x Genomics
Partner logo of Analytical Biosciences
Analytical Biosciences Obtained the Zhongguancun High-tech Enterprise Certification
As the leaders said, Analytical Biosciences did achieve a lot in this year. In terms of scientific research and academics, Academician Chen Runsheng from the Institute of Biophysics of the Chinese Academy of Sciences, Professor Fuxuan Tang from Peking University, and Professor Zemin Zhang from Peking University have become Scientific Advisors of Analytical Biosciences. Besides，Analytical Biosciences has been certified by 10x Genomics. In terms of funding, the company has received investment from IDG Capital. In terms of business, the company has established cooperation with Bayer, Pfizer, Genentech, Peking University, Shenzhen University, Hong Kong University, Peking Union Medical College and other well-known pharmaceutical companies, top universities and hospitals. In addition, Analytical Biosciences also obtained the Zhongguancun High-tech Enterprise Certification. All of the above have laid a solid foundation for the company's future development and it is a solid step for the company to achieve its final vision.
Now, Single cell sequencing and analysis product of Analytical Biosciences can meet the needs of various customers in scientific research, clinical and pharmaceutical applications, and provide stable, repeatable experimental results with rapid, accurate, one-to-one customized data analysis services.
Next, Analytical Biosciences will continually improve the level of experimental technology and data analysis, build a powerful team, promote the applications of single-cell genomics and bioinformatics in diagnosis and treatment of human disease, find new therapeutic and diagnostic targets, create accurate maps of human disease, and strive to become the new engine of drug research and development!
From October 20th to 21st,the ‘Single Cell Omics Beijing 2019 Symposium’ co-sponsored by Beijing
Advanced Innovation Center for Genomics (ICG) and Biomedical Pioneering Innovation Center (BIOPIC),
was held in Qiulin lecture hall of Peking University. Analytical Biosciences participated in the
symposium as a major sponsor, attracting many teachers and students and promoted heated discussions by
its single cell sequencing and analysis technology.
The symposium had 24 experts in the field of single cell omicsand nine relevant topics, which
comprehensively introduced the latest progress of single cell sequencing and analysis technologies
along with their application results in various biological fields, including Genomics, Single-cell
transcriptomics, Single-cell epigenomics and three-dimensional structure of the genome, Single-cell
proteomics, New single-cell omics technology, Applications of Single-cell omics in Immunology,
Single-cell omics in cancer, and Single-cell omics in neuroscience. The conference provided a
high-quality academic communication platform to scientists in the field of single-cell genomes,
systematically presented the rapid development of this field in the world, and demonstrated China's
international influence in single-cell sequencing and bioinformatics research.
During the symposium, Professor Fushen Tang, advisor of Analytical Biosciences, gave a lecture entitled ‘Decoding the Gene Regulation Network in Human Germline Cells by Single-cell Functional Genomics Approaches’, which mainly discuss the development trajectory and heterogeneity of human germline cells. Professor Fushen Tang 's laboratory has performed single-cell transcriptome and DNA methylation sequencing studies on human germ cells in female and male human embryos spanning several critical developmental stages, gave important insight of key features in the process of meiosis and gamete development.
In addition, Professor Zemin Zhang, the founder of Analytical Biosciences, gave a lecture entitled ‘Application of Novel Single Cell Bioinformatics Methods in Cancer Immunology’ on the symposium. Currently, the complexity of single-cell sequencing data poses challenges to bioinformatics. The R & D team of Analytical Biosciences led by Professor Zemin Zhang developed various tools for single cell clustering, expression tag identification, cell lineage tracking and cell space inference, then applied these tools to single cell transcriptome data for tumor immunity, revealed new cell types, tumor-specific immune cell characteristics, cell-cell interactions, dynamic characteristics of cancer-related immune cells, and further explained the significance and value of these findings in cancer biology and immunotherapy.
Recently, a new subsidiary journal of Nature, Nature Cancer was officially launched. It invited 10
leading scientists who approach cancer from diverse perspectives to ask them about the key
developments in their fields and what their envision will be the next breakthroughs in cancer and
published the first issue “A roadmap for the next decade in cancer research”.
In the first issue, the founder of Analytical Biosciences，Professor Zemin Zhang was invited to give a
The early years of cancer research were once focused on the cellular level. In the 1850s, Rudolf Virchow first linked the origin of cancer cells to normal cells, which turned into the most well-accepted definition of cancer: a disease of mutant cells that exhibit uncontrolled proliferation and invasiveness. Morphology-based studies of cancer cells dominated the field for more than a century, before the advances in genetics and biochemistry empowered the biological study of cancer. The boom in the understanding of cellular pathways in the 1980s gave cancer research a much needed leap. Over the years, we have accumulated unprecedented knowledge of genes that drive carcinogenesis, cancer progression, metastasis and resistance to therapies, and the paradigm of cancer research gradually shifted from the cellular level to the molecular level. Despite the profound knowledge we have gained from molecular and pathway-centric studies, a huge gap remains between the molecular-level understanding of cancer pathways and the anticipated intervention solutions. One possible reason for such disparity between biological knowledge and therapeutic progress may be that we are accustomed to treating clinical tumor samples as a whole, working hard to identify aberrant pathways in tumors and‘silver bullets’ that target them. While this idea propelled the development of targeted therapies, it may obscure the fact that different biochemical reactions or signaling pathways occur in different cells. This perception bias has had a deep impact on how targets can be identified. For example, although genes upregulated in tumors may have target implications, we have learned now that many such genes are not expressed by cancer cells at all.
Instead, they are expressed by other cellular components in the TME. This intricate tumor ecosystem is so diverse that when we view it as a bulk, we lose not just the knowledge of expression heterogeneity but also vital information about cell types, cell states and intercellular communications. How different cell types work in conjunction with each other to maintain and remodel the microenvironment ultimately shapes therapeutic responses and resistance, as exemplified by the success of immunotherapy. If targeting cancer cells does not cure cancer, the indirect approach of targeting other cells in the TME might improve therapeutic efficacy.
Therefore, more than ever, we need to take up the view of individual cells. If the TME is a battlefield for all anticancer therapies, then surveying the field comprehensively is a prerequisite for winning the battle. The recent advances in single-cell sequencing techniques have given us the most powerful approach for this transition of methodology, allowing us to revisit the molecular and genetic processes, back at the cellular level. The ability to study and target any distinct component of the TME will enable us to change the rules of the game fundamentally, for cancer research and, eventually, for the study of all diseases.
Besides，René Bernards, Elizabeth Jaffee, Johanna A. Joyce, Scott W. Lowe, Elaine R. Mardis, Sean J. Morrison, Kornelia Polyak, Cynthia L. Sears, Karen H. Vousden also gave their viewpoint about identifying novel cancer vulnerabilities, immunotherapy, TME, next-generation mouse cancer models, genomics-guided cancer precision medicine, tumor initiation, metastasis, microbiome and cancer metabolism.
Reference： Bernards, R., Jaffee, E., Joyce, J.A. et al. A roadmap for the next decade in cancer research. Nat Cancer 1, 12–17 (2020)
On February 5, the founder and scientific advisor of Analytical Biosciences, Professor Zemin Zhang and his research group published a paper on Nature entitled "Genomic basis for RNA alterations in cancer" ，together with Alvis Brazma, Angela Brooks, Gunnar Rätsch and other collaborating teams. The research paper reports major advances in the field of tumor transcriptome alteration.
The study systematically depicts the most comprehensive atlas of tumor transcriptome alteration up to now, covers 27 different cancers, reveals the causes of transcriptome alteration and their association with genomic changes, and provides valuable resources for identifying genes and mechanisms related to cancer.
This research project belongs to a large academic consortium called Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, whose members include an interdisciplinary team of scientists from 744 affiliates on 4 continents, aimed at collaborating on unified standards to achieve the ambitious goal of comprehensive genomic characterization of tumors.
Recently, the alliance has made great progress and published its results in the top academic journal Nature and its sub-issues. The study conducted the most comprehensive meta-analysis of cancer genomes up to now, conducted multiple studies of more than 2,600 tumor genomes from 38 human tissues, yielded rich insights into the genetic basis of cancer, and revealed the complexity of cancer on an unprecedented scale.
Nature attaches great importance to 6 series of work and published related editorials. Of these 6 papers, the first paper outlines the breadth and depth of the PCAWG dataset, the remaining 5 papers explore different aspects of this dataset in detail, including cancer drivers, non-coding changes, mutational signatures, structural variants, cancer evolution and RNA alterations.
Among them, the article entitled with “Genomic basis for RNA alterations in cancer”, published by Professor Zhang Zemin's group and Alvis Brazma, Angela Brooks, Gunnar Rätsch and so on, reported the great progress of PCAWG Transcriptome working group in tumor transcriptome alterations,
In this study, researchers integratedly analyzed the transcriptome and whole genome sequencing data of a total of 1,188 tumors in 27 cancer species, systematically described the most comprehensive tumor transcriptome alteration atlas up to date, and revealed the causes of transcriptome alteration and its association with genomic changes.
The study revealed multiple patterns of cancer gene and pathway alterations at the DNA and RNA levels, and RNA analysis revealed changes in cancer-related pathways that have not been discovered through the DNA pathway alone, illustrating the power of integrated transcriptome and whole-genome sequencing analysis for cancer studies.
Reference：Calabrese, C., Davidson, N.R., Demircioğlu, D. et al. Genomic basis for RNA alterations in cancer. Nature 578, 129–136 (2020).
On January 30, 2020, the scientific advisor of Analytical Biosciences, Prof. FuChou Tang and his research group published a cover article on Cell entitled “Single-Cell Transcriptomic Atlas of Primate Ovarian Aging”, together with Guanghui Liu’s group and other collaborative teams, revealed the aging mechanism of primate ovarian.
Previous studies have shown that the ovary is one of the organs that undergo early degenerative changes during aging. Its aging manifestations include decreased number and quality of oocytes, and a corresponding reduction in female fertility. In addition, disorders of sex hormone secretion associated with ovarian aging may also cause aging-related diseases such as cardiovascular disease.
This study used high-precision single-cell transcriptome sequencing technology to draw the single-cell aging atlas of cynomolgus monkey ovaries for the first time. It found that the decline in antioxidant capacity associated with aging is one of the main features caused by primate ovarian aging. It helps people to understand the specific mechanism of primate ovarian aging more accurately and comprehensively under single-cell resolution, identifying biomarkers of ovarian aging in human and other primates. it laid a theoretical foundation for developing intervention strategies for aging and related diseases.
Reference：Si Wang, Yuxuan Zheng, Jingyi Li, ..., Jing Qu*, Fuchou Tang*, Guang-Hui Liu*. Single-Cell Transcriptomic Atlas of Primate Ovarian Aging. Cell. 2020.
On Feb 23, 2020, the founder of Analytical Biosciences, Professor Zemin Zhang, was invited to attend the Hanhai BioTalk series of lectures, and was interviewed by Dr. Zhang Jian, the chief scientist of Hanhai, talking about "single cell research and application of disease tissue".
Professor Zemin Zhang is an expert in bioinformatics, a national “overseas high-level talent” distinguished expert, “Chang Jiang Scholar” of the Ministry of Education, researcher of the Biomedical Pioneering Innovation Center in Peking University (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Chair Professor of School of Life Sciences, Peking University, Senior Researcher of Peking University Tsinghua United Center. He has published papers in Cell, Nature, Nature Genetics, Nature Biotechnology, Nature Medicine and other internationally renowned magazines, and served as the editorial board of several professional magazines, including Cell Systems, Genome Medicine and Cell Reports.
In this interview, Professor Zemin Zhang introduced his recent research work for being chosen as the "Top Ten Applications of Chinese Informatics in 2019" and "Top Ten Advances of Chinese Informatics in 2019", and explained the single-cell sequencing technology and its related bioinformatics technologies. Professor Zhang pointed out that the difficulty of single-cell sequencing has shifted from the initial experiments to the bioinformatics analysis of a large number of single-cell sequencing data in the later stage. In addition, Professor Zemin Zhang also introduced how basic research based on single-cell sequencing technology has promoted cancer treatment, and emphasized the role of single-cell technology in cancer research-only in the precision of single cells can avoid being misled when selecting targets.
Finally, talking about the original intention of the establishment of Analytical Biosciences, Professor Zemin Zhang said that Analytical Biosciences is committed to promoting science with technology and then promoting the development of the pharmaceutical industry. On the one hand, the company fills the market demand through international advanced bioinformatics analysis technology. On the other hand, it begins to develop mature databases and analysis software, so that single cell sequencing technology, an advanced biological tool, can be used by more researchers and applied in more fields of biology. In addition, through the mining of single-cell sequencing data, Analytical Biosciences can found disease targets and biomarkers for the development of new drugs.
The research group of Professor Zemin Zhang, the founder and scientific consultant of Analytical Biosciences, has made a pioneering breakthrough of hepatocellular carcinoma. On February 16, 2020, the research was recognized in Top Ten Advances in Bioinformatics of China 2019 recognized by the peer reviewers organized by Genomics, Proteomics and Bioinformatics (GPB) journal.
This study used single-cell sequencing technology to draw hepatocellular carcinoma immune map, revealing the dynamic characteristics of hepatocellular carcinoma tumor microenvironment, and was published in Cell in November 2019, entitled "Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma".
The reasons for the selection given by GPB as follows:
Single-cell transcriptome sequencing technology provides a powerful experimental tool for
systematically analyzing the composition and characteristics of tumor microenvironment, but how to
infer the dynamic behavior of immune cells in tumor microenvironment is an urgent bioinformatics
The team of Zemin Zhang and Xianwen Ren of Peking University, the team of Jirun Peng of Beijing Shijitan Hospital, and the team of Kang Liu of Boehringer Ingelheim Pharmaceutical Co., Ltd, revealed the source of ascites immune cells and the dynamic behavior of tumor dendritic cells in hepatocellular carcinoma patients by systematically integrating the current cell dynamic behavior inference algorithm and establishing a matching statistical test method.
By integrating the advantages of different algorithms for high universality of the similarity inference algorithm based on gene expression profiles, the high reliability of the mitochondrial mutation inference algorithm, the analysis of RNA splicing dynamics to indicated the direction of cell dynamic behavior, and performing hypothesis tests, the research revealed that ascites lymphoid immune cells of patients with hepatocellular carcinoma are mainly derived from peripheral blood, while myeloid immune cells are mainly derived from tumors and adjacent tissues. A group of LAMP3 + dendritic cells in tumors has the ability to migrate from tumors to lymph nodes, and can regulate the infiltration and phenotype of T lymphocytes by expressing multiple ligands and receptors.
These findings are of great significance for understanding the immune escape mechanism of hepatocellular carcinoma and developing new immunotherapy methods.
On March 16th, 2020, 8 companies, including Analytical BioSciences, MGI, Geneplus, iGeneTech, WeGene, NextOmics, TSINGKE, IGENECODE, form the Domestic Sequencing Platform Application Ecological Alliance. By the alliance, members will provide the more competitive products and services to customers in various segments of the industry by cooperation, creating a new ecology for the Chinese gene industry.
As the first batch of domestic sequencing platform application alliance companies, these 8 companies cover the upstream and downstream of the gene sequencing industry chain. Regarding the establishment idea and future development of the alliance, all enterprise representatives expressed their views:
MGI CEO Feng Mou:
The implementation of technology results in diversified applications, and the application also spurs technological innovation. Through the application of the ecological alliance， we will give full play to the strength of China's upstream and downstream linkages in the industry, and promote the breadth and depth of global development.
Geneplus CTO XinYi:
The era of biotechnology based on multi-omics big data is rapidly coming. The speed of its development depends on two key factors, namely the cost of getting data and the depth of our understanding to the data. The rapid development of domestic MPS (Massively parallel sequencing) technology has provided us with platform support. Based on this platform, we will definitely build a better business ecosystem, thus promote the development of the industry and serve customers better.
Analytical Biosciences VP XueDa Hu:
Currently, we are fortunate to witness and participate in the historical transition from individual genomics to cellular genomics. Single-cell genomics and its bioinformatics are important cornerstones of future biomedicine, and will also become the main engine for digitizing biomedicine. Analytical Biosciences’ bioinformatics analysis and big data mining capabilities can provide global medical institutions and pharmaceutical companies with a deep understanding of diseases and their diagnosis and treatment from a single-cell perspective. The establishment of this alliance will help us obtain extremely important basic data output capabilities. I believe that this alliance can combine our technical means, give full play to our respective advantages, thus promote the rapid development of China's biological industry.
iGeneTech CEO XingYi Hang:
As a domestic supplier of reagents upstream of the gene detection industry, iGeneTech will use two independent intellectual property rights of gene capture technology -- TargetSeq® liquid probe gene capture and MultipSeq® multiple PCR gene capture to actively develop reagents suitable for domestic sequencers, accelerating the adaptation of domestic reagents to domestic sequencers, promoting the development of the national industry.
WeGene Co-founder GuoQing Li:
WeGene is one of the major C-terminal gene detection suppliers in China, with about 1 million genetic data and phenotypic databases. The database can not only provide users with accurate interpretation and suggestions, but also be of great value to Chinese population characteristics analysis and genetic disease research. The maturity of domestic sequencing equipment, especially the establishment of an ecological alliance for domestic sequencing applications, is a long-awaited opportunity for us. We hope that this alliance can promote cooperation, complement each other's advantages, integrate more comprehensive, deeper, and more cost-effective products, provide customers with satisfactory services.
About Analytical Biosciences
Analytical Biosciences aims to create and harness the human disease precision atlas through cutting-edge single-cell genomics and bioinformatics.
By partnering with researchers and clinicians from biomedical research institutes, hospitals and pharmaceutical companies, we strive to unleash the power of genomics and bioinformatics in understanding major human diseases.
We hope to identify novel therapeutic targets and develope innovative therapeutic strategies through navigating our comprehensive disease single-cell atlas, performing intelligent big data mining, and enabling our partners across the wide biotechnology discipline.
April 17, 2020: Biopharmaceutical expert Nathan Siemers, Ph.D. joins Abiosciences as Senior Vice President and Head of US Operations, leading the work of the company's American branch.
Dr. Siemers has 28 years of experience in the pharmaceutical and diagnostics industries, most recently as Director of Research and Development at the US biopharmaceutical company Bristol-Myers Squibb, where he co-founded the genomics, bioinformatics, and translational medicine groups. His teams at BMS contributed to small-molecule and biologics drug development in oncology, immunology, cardiovascular, metabolic, neuroscience, and infectious disease areas. The efforts covered the spectrum of pharmaceutical R&D activities, from genomic and in-silico based target discovery, to translational research identifying mechanistic, pharmacodynamic, and predictive biomarkers, to identifying optimal patient populations and endpoints in late-stage clinical trials. During his tenure at BMS, Nathan’s teams contributed to the successful development and launch of a dozen new therapies.
Dr. Siemers received his Ph.D. degree in Chemistry from Cornell University and his B.S. degree in Chemistry from the Massachusetts Institute of Technology. He was a visiting scientist at the Whitehead Institute, working in the laboratories of Eric Lander, a famous biologist and pioneer of genome sequencing.
April 17, 2020: Dr. Yuelan Wang joined Abiosciences as the Vice President, leading the research and development of the company's bioinformatics software department.
Dr. Yuelan Wang has more than 20 years of experience in bioinformatics, nearly ten years of experience in high-throughput sequencing data analysis software development and big data genomic mutation database development, and many years of experience in company management. Her research fields cover eukaryotic expression regulation, phylogenetics and microbial genomics, etc.
Dr. Yuelan Wang engaged in bioinformatics research at the Beijing Institute of Bioengineering from 2000 to 2011. She undertook or participated as a main researcher in dozens of research projects, including national key projects. Most recently, Dr. Yuelan Wang has served as the vice president and the COO of two biotechnology companies, where she take responsibility of R&D, operation and management, and obtained two patents on sequencing techniques.
The bioinformatics department of Abiosciences is focusing on the development of single-cell omics database and interactive single-cell data display platform. The joining of Dr. Yuelan Wang will add strength to the software development and data mining capabilities of Abiosciences, thereby facilitating the discovery of new drug targets and the identification of new human therapeutics, helping the company quickly realize it vision.
On April 14th, Analytical BioSciences and Professor Zemin Zhang's research group published a bioinformatics methodology paper on Nature Communications, titled "SciBet as a portable and fast single cell type identifier ", officially released SciBet, a new tool for fast and supervised cell type annotation based on single-cell transcriptome data.
SciBet makes full use of existing data as a reference and annotates newly generated data sets with a supervised method, which can greatly speed up the progress of research that is based on single-cell transcriptome sequencing. Compared with the existing tools, scmap and Seurat3, SciBet not only outperforms in accuracy, but also achieves a computing speed a thousand times faster. Hence, users can run SciBet to achieve supervised cell type prediction on the order of 100,000 cells per second using only their personal computers. When dealing with large-scale data sets with hundreds of millions of cells such as Human Cell Atlas, SciBet will become one of the best tools for researchers in the future.
In practical applications, SciBet was evaluated in multiple scenarios such as cross-datasets, cross-sequencing platforms and cross-species, and was proved to be able to robustly and accurately complete supervised cell type annotation tasks. For the cell types that are not covered by the training set, SciBet can correctly identify them and maintain accurate annotations of other cells at the same time.
In addition, SciBet-trained models are also very efficient in terms of storage and it only depends on the number of cell types. For example, a common SciBet model with a dataset of dozens of cell types has a size of less than 1MB. Based on the portability feature, we released SciBet pre-trained models with nearly one hundred high-quality data sets, which can be directly imported into SciBet's R software package.
References : Chenwei Li，Baolin liu，Boxi Kang，... , Xianwen Ren*, Zemin Zhang*. SciBet as a portable and fast single cell type identifier. Nature Communications. 2020.
On April 16, the founder and scientific adviser of Analytical BioSciences, Professor Zemin Zhang and his research group published an article on Cell with collaborators，titled "Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies In Colon Cancer", which systematically characterized the tumor microenvironment of patients with colorectal cancer by using single-cell transcriptome sequencing，especially the infiltrating myeloid cell group for the first time. Meanwhile, it uses a mouse model to explain the potential mechanism of immunotherapeutic strategies of anti-CD40 agonists and anti-CSF1R inhibitor targeting myeloid cells.
The study establishes a paradigm to study tumor immunotherapy by combining single-cell transcriptome of tumor patients and mouse models, it provides insights for studying immune cells in other diseases and develop new therapeutics.
Professor Bing Su，the director of Shanghai Institute of Immunology, spoke highly of the study: this work has comprehensively analyzed the tumor microenvironment cell atlas of colon cancer and has clarified the interaction between cells. It provides a detailed theoretical basis for tumor therapy based on the targeted tumor immune microenvironment, and provides assistance for the precise treatment targeting myeloid cells in the future. It has great significance on clinical transformation.
Lei Z. et al., Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer. Cell. 2020.
On June 15, 2020, the founder and scientific adviser of Analytical Biosciences，Professor Zemin Zhang and his group published a paper on Cell Research, title with "Reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor". The paper present a new algorithm for cell spatial relationships based on cell interaction, CSOmap.
Schematics of single-cell spatial reconstruction by CSOmap
The paper shows that CSOmap can successfully recapitulate the spatial organization of multiple organs of human and mouse including tumor microenvironments for multiple cancers in pseudo-space, and reveal molecular determinants of cellular interactions. Further, CSOmap readily simulates perturbation of genes or cell types to gain novel biological insights, especially into how immune cells interact in the tumor microenvironment.
Hence, CSOmap can be a widely applicable tool to interrogate cellular organizations based on scRNA-seq data for various tissues in diverse systems. Overall, this method is of great significance for further digging the rich biomedical knowledge contained in data of single cell transcriptome sequencing .
On June 22th, Analytical BioSciences and Professor Zemin Zhang's research group published a bioinformatics methodology paper on Nature Communications, titled " An entropy-based metric for assessing the purity of single cell populations ", officially released ROGUE, a new tool for unsupervised gene selection and cell group purity assessment based on single-cell transcriptome data.
The tool uses the expression entropy model to describe the relationship between differential entropy and the mean value of gene expression, which can accurately and effectively identify highly variable genes，thereby assessing the purity of a given cell population. In various tests, ROGUE performed significantly better than other unsupervised gene selection methods. In practical applications, ROGUE can quantify cell type purity and guide clustering robustly and accurately without affecting by sequencing depth.
Schematics of single-cell spatial reconstruction by CSOmap
With the rapid development of single-cell sequencing technology, new cell types are constantly being discovered. The credibility of the classification of these new cell groups is challenging. ROGUE can be a potential criteria for guiding clustering and judge the quality of cell groups.
At present, the R software package of the tool is available online (https://github.com/PaulingLiu/ROGUE), which can provide users with unsupervised gene selection and cell purity assessment.
References：Baolin Liu et al. An entropy-based metric for assessing the purity of single cell populations. Nat. Commun. (2020).
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