药用植物研究所

刘昶研究员

中国医学科学院药用植物研究所研究员，博士生导师，“协和学者”特聘教授，生物信息学中心副主任。南开大学理学学士，专业为微生物学；美国明尼苏达大学理学博士，专业为动物病理学；美国明尼苏达大学理学硕士，专业为计算机科学（第二学位）。曾任GlaxoSmithKline(Research Triangle Park, North Carolina, USA)研发部项目经理、香港大学李嘉诚医学院研究助理教授，耶鲁大学访问学者。

主持及参加国家自然科学基金项目、北京市自然科学基金项目、香港GeneralResearchFund、科技部科技基础资源调查项目、科技部重大新药创制项目、教育部长江学者和创新团队发展计划资助项目、人力资源和社会保障部留学人员科技活动项目择优资助项目、中国医学科学院医学与健康创新工程项目、中国医学科学院协和学者特聘教授资助项目、中国医学科学院中药资源学协和创新团队项目等科研项目30余项。获得中华中医药学会科学技术奖一等奖、教育部科学技术进步奖一等奖。

发表论文90余篇，载文刊物包括Nature Communication、Nucleic Acids Research、Science、PNAS、Molecular Ecology Resource、BMC Genomics等。科研论文总被引次数大于5000次，其中3篇为ESI高被引论文, 4篇引用次数》100。开发了一系列生物信息数据分析工具，其中叶绿体基因组注释与分析系列工具cpgavas及cpgavas2在全球范围内被广泛使用。目前作为主编出版专著两部，获得软件著作权10项，获得专利授权2项。

作为联络人推动中国医学科学院药用植物研究所（IMPLAD）与美国Illumina公司签署协议，启动国际千种药用植物基因组计划（1000 Medicinal Plant Genomes，简称1KMPG），创建世界首个药用植物参考基因库，并建立1KMPG国际联盟。

主持及参加国家自然科学基金项目、北京市自然科学基金项目、香港General ResearchFund、科技部科技基础资源调查项目、科技部重大新药创制项目、教育部长江学者和创新团队发展计划资助项目、人力资源和社会保障部留学人员科技活动项目择优资助项目、中国医学科学院医学与健康创新工程项目、中国医学科学院协和学者特聘教授资助项目、中国医学科学院中药资源学协和创新团队项目等科研项目30余项。获得中华中医药学会科学技术奖一等奖、教育部科学技术进步奖一等奖。

最近五年发表的文章：

1. Wang Y,Yao X, Liu R, Liu C*:DDQR (dynamic DNA QR coding): An efficientalgorithm to represent DNA barcodesequences. PLoS One 2023, 18(1):e0279994.

2. Liu S,Ni Y, Li J, Zhang X,Yang H, Chen H, Liu C*: CPGView: A package forvisualizing detailed chloroplastgenome structures. Mol Ecol Resour 2023,23(3):694-704.

3. Jiang M,Ni Y, Li J, Liu C*:Characterisation of the complete mitochondrial genomeof Taraxacum mongolicumrevealed five repeat-mediated recombinations. PlantCell Rep 2023.

4. Zhang H,Zheng Y, Zhang G,Miao Y, Liu C*, Huang L: A Bibliometric Study for PlantRNA Editing Research:Trends and Future Challenges. Mol Biotechnol 2022.

5. Yue J,Ni Y, Jiang M, Chen H,Chen P, Liu C*: Characterization of Codonopsispilosula subsp. tangshen plastomeand comparative analysis of Codonopsisspecies. PLoS One 2022, 17(8):e0271813.

6. Yue J,Lu Q, Ni Y, Chen P, LiuC*: Comparative analysis of the plastid and mitochondrialgenomes of Artemisiagiraldii Pamp. Sci Rep 2022, 12(1):13931.

7. Yang H,Chen H, Ni Y, Li J,Cai Y, Ma B, Yu J, Wang J, Liu C*: De novo hybridassembly of the Salviamiltiorrhiza mitochondrial genome provides the firstevidence of themulti-chromosomal mitochondrial DNA structure of Salviaspecies. Int J Mol Sci2022, 23(22).

8. Xu Y,Fang B, Li J, Wang Y,Liu J, Liu C*, Yu J: Phylogenomic analysis anddevelopment of molecular markersfor the determination of twelve plum cultivars(Prunus, Rosaceae). BMC Genomics2022, 23(1):745.

9. Ni Y, LiJ, Chen H, Yue J,Chen P, Liu C*: Comparative analysis of the chloroplastand mitochondrialgenomes of Saposhnikovia divaricata revealed the possibletransfer of plastomerepeat regions into the mitogenome. BMC Genomics 2022,23(1):570.

10. Miao Y,Chen H, Xu W, Liu C*,Huang L: Cistanche Species Mitogenomes SuggestDiversity and Complexity inLamiales-Order Mitogenomes. Genes (Basel) 2022,13(10).

11. Li J,Yang M, Li Y, Jiang M,Liu C*, He M, Wu B: Chloroplast genomes of twoPueraria DC. species: sequencing,comparative analysis and molecular markerdevelopment. FEBS Open Bio 2022,12(2):349-361.

12. Jiang M,Xu SF, Tang TS, MiaoL, Luo BZ, Ni Y, Kong FD, Liu C*: Development andevaluation of a meatmitochondrial metagenomic (3MG) method for compositiondetermination of meatfrom fifteen mammalian and avian species. BMC Genomics2022, 23(1):36.

13. Du Q,Yang H, Zeng J, Chen Z,Zhou J, Sun S, Wang B, Liu C*: ComparativeGenomics and Phylogenetic Analysis ofthe Chloroplast Genomes in ThreeMedicinal Salvia Species for Bioexploration.Int J Mol Sci 2022, 23(20).

14. Du Q, LiJ, Wang L, Chen H,Jiang M, Chen Z, Jiang C, Gao H, Wang B, Liu C*:Complete chloroplast genomes oftwo medicinal Swertia species: the comparativeevolutionary analysis of Swertiagenus in the Gentianaceae family. Planta 2022,256(4):73.

15. Du Q,Jiang M, Sun S, Wang L,Liu S, Jiang C, Gao H, Chen H, Li Y, Wang B, Liu C*:The complete chloroplastgenome sequence of Clerodendranthus spicatus, a medicinalplant for preventingand treating kidney diseases from Lamiaceae family. MolBiol Rep 2022,49(4):3073-3083.

16. Chen H,Chen Z, Du Q, Jiang M,Wang B, Liu C*: Complete chloroplast genome ofCampsis grandiflora (Thunb.)schum and systematic and comparative analysiswithin the family Bignoniaceae.Mol Biol Rep 2022, 49(4):3085-3098.

17. Boqin H,Zhou Q, Wang L, JiangM, Gong G, Liu C*, Wei C: The complete chloroplastgenome sequence ofRhaponticum uniflorum, the first of the genus Rhaponticum.Mitochondrial DNA BResour 2022, 7(1):303-305.

18. Zhou J,Du Q, Jiang M, Liu S,Wang L, Chen H, Wang B, Liu C*: Characterizationand comparative analysis of theplastome sequence from Justicia ventricosa(Lamiales: Acanthaceae).Mitochondrial DNA B Resour 2021, 6(10):2896-2902.

19. Yu J, WuX, Liu C*, NewmasterS, Ragupathy S, Kress WJ: Progress in the use of DNAbarcodes in theidentification and classification of medicinal plants.Ecotoxicol Environ Saf2021, 208:111691.

20. Yang H,Wang L, Chen H, JiangM, Wu W, Liu S, Wang J, Liu C*: Phylogeneticanalysis and development ofmolecular markers for five medicinal Alpiniaspecies based on complete plastomesequences. BMC Plant Biol 2021, 21(1):431.

21. Wu W, LiJ, Liu Y, Jiang M, LanM, Liu C*: Peculiarities of the inverted repeatsin the complete chloroplastgenome of Strobilanthes bantonensis Lindau.Mitochondrial DNA B Resour 2021,6(4):1440-1447.

22. Tian L,Jiang M, Chen H, Li J,Huang L, Liu C*: Comparative analysis of thecomplete chloroplast genomes ofCirsium japonicum from China and Korea.Mitochondrial DNA B Resour 2021,6(4):1468-1470.

23. Ni Y,Jiang M, Chen H, Huang L,Chen P, Liu C*: Adaptation of a parasiticlifestyle by Cuscuta gronovii Willd.ex Roem. & Schult.: large scale gene deletion,conserved gene orders, andlow intraspecific divergence. Mitochondrial DNA BResour 2021, 6(4):1475-1482.

24. Ni Y,Chen H, Liu D, Zeng L,Chen P, Liu C*: Discovery of genes involved inanthocyanin biosynthesis from therind and pith of three sugarcane varietiesusing integrated metabolic profilingand RNA-seq analysis. BMC Plant Biol 2021,21(1):214.

25. Liu J,Jiang M, Chen H, Liu Y,Liu C*, Wu W: Comparative genome analysisrevealed gene inversions, boundaryexpansions and contractions, and gene lossin the Stemona sessilifolia (Miq.)Miq. chloroplast genome. PLoS One 2021,16(6):e0247736.

26. Liu J,Chen H, Newmaster S,Wang S, Liu C*: Global Trends in Cannabis andCannabidiol Research from the Year1940 to 2019. Curr Pharm Biotechnol 2021,22(5):579-591.

27. Li J, XuY, Shan Y, Pei X, YongS, Liu C*, Yu J: Assembly of the completemitochondrial genome of an endemicplant, Scutellaria tsinyunensis, revealedthe existence of two conformationsgenerated by a repeat-mediatedrecombination. Planta 2021, 254(2):36.

28. Li J,Jiang M, Wang L, Yu J,Chen H, Liu J, Liu C*: The complete chloroplastgenome of Photinia davidsoniae:molecular structures and comparative analysis.Mitochondrial DNA B Resour 2021,6(4):1431-1439.

29. Jiang M,Li Y, Chen H, Wang B,Liu C*: Comparative and phylogenetic analysis ofthe complete chloroplast genomesequences of Lactuca raddeana and Lactucasativa. Mitochondrial DNA B Resour2021, 6(4):1498-1506.

30. Jiang M,Chen H, Liu J, Du Q,Lu S, Liu C*: Genome-wide identification and functionalcharacterization ofnatural antisense transcripts in Salvia miltiorrhiza. SciRep 2021, 11(1):4769.

31. Jiang M,Chen H, Du Q, Wang L,Liu X, Liu C*: Genome-Wide Identification ofCircular RNAs Potentially Involvedin the Biosynthesis of Secondary Metabolitesin Salvia miltiorrhiza. Front Genet2021, 12:645115.

32. Zhou Y,Wu M, Zhu H, Shao J,Liu C*, Cui Y: Identification of LincRNA fromDermatophagoides farinae (Acari:Pyroglyphidae) for Potential Allergen-RelatedTargets. Genet Mol Biol 2020,43(1):e20190243.

33. Zhou Q,Li J, Jiang M, Wang L,Liu C*, Wang Y: The complete chloroplast genome ofAristolochia kwangsiensi.Mitochondrial DNA Part B 2020, 5(2):1184-1185.

34. Wang L,Zhang H, Wu X, Wang Z,Fang W, Jiang M, Chen H, Huang L, Liu C*: Phylogeneticrelationships ofAtractylodes lancea, A. chinensis and A. macrocephala,revealed by completeplastome and nuclear gene sequences. PLoS One 2020,15(1):e0227610.

35. Sun X, LiL, Pei J, Liu C*,Huang LF: Metabolome and transcriptome profilingreveals quality variation andunderlying regulation of three ecotypes forCistanche deserticola. Plant MolBiol 2020, 102(3):253-269.

36. Shao J,Wang L, Liu Y, Qi Q,Wang B, Lu S, Liu C*: Identification of milRNAs andtheir target genes inGanoderma lucidum by high-throughput sequencing anddegradome analysis. FungalGenet Biol 2020, 136:103313.

37. Li J,Jiang M, Chen H, Yu J,Liu C*: Intraspecific variations among thechloroplast genomes of Artemisiascoparia (asteraceae) from Pakistan and China.Mitochondrial DNA Part B 2020,5(3):3182-3184.

38. Jiang M, Xu Y, Wang L, Liu J,Yu J, Chen H: High level of intraspecific divergence andlow frequency of RNAediting in the chloroplast genome sequence of Tageteserecta. Mitochondrial DNAB Resour 2020, 5(3):2948-2953.

39. 吴茜, 姜梅, 陈海梅, 王立强, 黄林芳, 刘昶*: 旋覆花,湖北旋覆花和线叶旋覆花的叶绿体基因组比较分析和系统发育研究. 药学学报 2020, 55(5):8.

40. 刘蕤, 陈紫雯, 华桂丰, 王立强, 萨翼, 刘昶*: 基于层次分析法（AHP）的保健食品原料评价体系构建及分析. 中草药 2020, 51(18):4829-4836.

41. Zhou Q,Pei J, Poon J, Lau AY,Zhang L, Wang Y, Liu C*, Huang L: Worldwideresearch trends on aristolochicacids (1957-2017): Suggestions for researchers.PLoS One 2019, 14(5):e0216135.

42. Wang L,Zhang H, Jiang M, ChenH, Huang L, Liu C*: Complete plastome sequence ofIodes cirrhosa Turcz., thefirst in the Icacinaceae, comparative genomicanalyses and possible split ofIdoes species in response to climate changes.PeerJ 2019, 7:e6663.

43. Shi L,Chen H, Jiang M, Wang L,Wu X, Huang L, Liu C*: CPGAVAS2, an integratedplastome sequence annotator andanalyzer. Nucleic Acids Res 2019,47(W1):W65-w73.

44. Shao J,Wang L, Liu X, Yang M,Chen H, Wu B, Liu C*: Identification andcharacterization of circular RNAs inGanoderma lucidum. Sci Rep 2019,9(1):16522.

45. Liu J,Jiang M, Wang L, HuangL, Chen H, Liu C*: The complete chloroplast genomesequence of the medicinalplant Siegesbeckia orientalis L., the first in thegenus Siegesbeckia.Mitochondrial DNA B Resour 2019, 5(1):145-146.

46. Jiang M,Chen H, Wang L, You J,Liu C*: The complete chloroplast genome sequenceof Cosmos bipinnatus, the firstof the genus Cosmos. Mitochondrial DNA B Resour2019, 4(2):4204-4206.

47. Chen H,Jiang M, Wang L, You J,Liu C*: Complete plastome of Leucanthemummaximum, the first in genusLeucanthemum. Mitochondrial DNA B Resour 2019,5(1):19-20.

48. 杨俏俏, 姜梅, 王立强, 陈海梅, 刘昶*, 黄林芳: 药食两用藠头叶绿体基因组解析、比较基因组学及系统发育研究. 药学学报 2019, 54(1):9.