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  1. National Center for Toxicological Research

Binsheng Gong Ph.D.

Binsheng Gong

Visiting Scientist — Division of Bioinformatics and Biostatistics

Binsheng Gong
Binsheng Gong, Ph.D.

(870) 543-7391
NCTRResearch@fda.hhs.gov  

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 About  |  Publications 


Background

Dr. Binsheng Gong received a bachelor’s degree in medicine in 2003, and a Ph.D. in biophysics from Harbin Medical University, China. In 2003, he joined Harbin Medical University as a teaching and research assistant, then lecturer and associated professor. During his earlier research career, Dr. Gong was involved as one of the main investigators in several projects funded by the National High Technology Research and Development Program of China (863 Program), the National Basic Research Program of China (973 Program), and the National Natural Science Foundation of China. His research aimed at obtaining novel and insightful understandings of complex diseases at molecular levels. Dr. Gong received several awards from Heilongjiang Province, China.

In March 2012, Dr. Gong started his research at NCTR as a postdoctoral research scholar and later in November 2015, a visiting scientist. Since starting at NCTR, he has been involved as one of the major investigators of the FDA-led Sequencing Quality Control (SEQC) project. The SEQC project assesses the technical performance of next-generation sequencing platforms by generating benchmark datasets with reference samples and evaluating advantages and limitations of various bioinformatics strategies in RNA and DNA analyses. The project has resulted in more than ten publications in scientific journals. Dr. Gong was the lead author in one Nature Biotechnology manuscript and co-authored several other manuscripts. As quoted in Nature Biotechnology, “these large-scale coordinated efforts signal that the RNA-seq field is moving one step closer to clinical application by establishing standards for assessing analytical validity” and “the studies from the SEQC Consortium provide an important milestone in a longer path to develop laboratory tests that have analytical and clinical utility.” Dr. Gong has also been involved in the LTKB project studying drug safety with specific emphasis on drug-induced liver injury (DILI). Building on the big success of SEQC project and other projects he has been involved in, Dr. Gong now continues his research on the second phase of the project (SEQC II) and small RNA toxicity studies. During his time at NCTR he has received the following awards:

  • FDA Scientific Achievement Award: Chief Scientist Publication Award for “Basic, Translational or Applied Science” (2015)
  • NCTR Special Act Award (2016)
  • NCTR Chief Scientist Publication Award for Data Methods, Analysis, and Study Design (2016)
  • NCTR Group Recognition Award (2017)
  • NCTR Special Act Award (2017)


Research Interests

Dr. Gong has more than 15 years of distinguished research and education experiences and a record of exceptional scientific accomplishments in the field of bioinformatics, with emphasis on investigating the next-generation sequencing (NGS) and microarray technologies and biological/medical “big data” mining and data interpretation. The biological/medical “big data” incorporates personal genomic/transcriptomic data, clinical data, and many other data generated from high-throughput technologies. Data mining and interpretation develops and performs methods, software, workflows to manage and analyze the “big data” and interpret the biological/clinical meanings by integrating data and knowledge bases. This research supports basic biological study and translational medicine as well as drug development and drug-safety investigation. His current research interests include:

  • Examining the emerging technologies, particularly on NGS, to understand the impact of technical issues and bioinformatics methods
  • Evaluating the utility of these emerging technologies and methods in clinical and safety assessments with quality-control matrix and procedures
  • Biomarker identification for DILI and predictive toxicity, using data-mining methodology and systems-biology strategies
  • Developing standard operating procedures for NGS applications, such as ultralow-frequency mutations detection by duplex sequencing, biomarker identification by RNA sequencing, and small RNA sequencing
  • Genome-wide identification and characterization of circular RNAs and novel microRNAs for human, monkey, mouse, and rat


Professional Societies/National and International Groups

Arkansas Bioinformatics Consortium
Member
2015 – Present

The MidSouth Computational Biology and Bioinformatics Society
Member
2012 – Present

International Society for Computational Biology
Member
2016 – 2017

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Select Publications

Publication titles are linked to text abstracts on PubMed.

The Concordance Between RNA-Seq and Microarray Data Depends on Chemical Treatment and Transcript Abundance.
Wang C., Gong B., Bushel P., Thierry-Mieg J., Thierry-Mieg D., Xu J., Fang H., Hong H., Shen J., Su Z., Meehan J., Li X., Yang L., Li H., Labaj P., Kreil D., Megherbi D., Gaj S., Caiment F., van Delft J., Kleinjans J., Scherer A., Devanarayan V., Wang J., Yang Y., Qian H., Lancashire L., Bessarabova M., Nikolsky Y., Furlanello C., Chierici M., Albanese D., Jurman G., Riccadonna S., Filosi M., Visintainer R., Zhang K., Li J., Hsieh J., Svoboda D., Fuscoe J., Deng Y., Shi L., Paules R., Auerbach S., and Tong W.
Nat Biotechnology. 2014, 32: 926-932.


A Comprehensive Assessment of RNA-Seq Accuracy, Reproducibility and Information Content by the Sequencing Quality Control Consortium.
SEQC/MAQC-III Consortium.
Nat Biotechnology. 2014, 32: 903-914.


An Investigation of Biomarkers Derived from Legacy Microarray Data for Their Utility in the RNA-Seq Era.
Su Z., Fang H., Hong H., Shi L., Zhang W., Zhang W., Zhang Y., Dong Z., Lancashire L.J., Bessarabova M., Yang X., Ning B., Gong B., Meehan J., Xu J., Ge W., Perkins R., Fischer M., and Tong W.
Genome Biology. 2014, 15(12):523.


Mechanistic Roles of MicroRNAs in Hepatocarcinogenesis: A Study of Thioacetamide with Multiple Doses and Time-Points of Rats.
Dweep H., Morikawa Y., Gong B., Yan J., Liu Z., Chen T., Bisgin H., Zou W., Hong H., Shi T., Gong P., Castro C., Uehara T., Wang Y., and Tong W.
Scientific Reports. 2017, 7(1):3054.


The FDA's Experience with Emerging Genomics Technologies-Past, Present, and Future.
Xu J., Thakkar S., Gong B., and Tong W.
AAPS Journal. 2016, 18(4):814-8.


Comprehensive Assessments of RNA-Seq by the SEQC Consortium: FDA-Led Efforts Advance Precision Medicine.
Xu J., Gong B., Wu L., Thakkar S., Hong H., and Tong W.
Pharmaceutics. 2016, 8(1)


Discovering Functional Modules by Topic Modeling RNA-Seq Based Toxicogenomic Data.
Yu K., Gong B., Lee M., Liu Z., Xu J., Perkins R., and Tong W.
Scientific Reports. 2014, 27(9):1528-36.
 

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Contact Information
Binsheng Gong
(870) 543-7391
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