Dr. rer. nat. Buqing Yi

Principal Investigator/Senior Researcher of Microbiology&Virology at the Institute of Medical Microbiology and Virology,

Universitätsklinikum Carl Gustav Carus Dresden,

Technische Universität Dresden, Fiedlerstr. 42, 01307 Dresden

buqing.yi@tu-dresden.de

bootsing.yi@gmail.com

Website/ LinkedIn/ GitHub/ Twitter

Funding source: Deutsche Forschungsgemeinschaft (DFG) - Project number 458912928

Scientific focus

Respiratory infectious diseases; Host-pathogen-commensal interaction; Infection and Inflammation treatement; Cystic fibrosis; Immunology; Genomic epidemiology of emerging pathogens;

Functional genomics; Big-data analysis deciphering the pathogenesis of bacterial or viral pathogens; Multi-omics data analysis; Microbiome; Next-Generation Sequencing (NGS);

Virus genomic epidemiology and virus mutation surveillance

Degrees

Ph.D. graduation at the University of Tuebingen, Germany.

Ph.D thesis in Genetics (Evolution and Development), Max-Planck Institute for Developmental Biology, Tuebingen, Germany, which was carried out through a combination of molecular biology, genetics, genomics, biochemistry and bioinformatics approaches.

Current running projects

1. Investigation of host-pathogen-commensal interaction in human lung diseases to develop novel therapies for inflammation and infection control (supported by funding from DFG and Mukoviszidose e.V.)

2. Emerging pathogens e.g. SARS-CoV-2 genomic epidemiology and variants surveillance to precisely evaluate pandemic or post-pandemic conditions (supported by University Hospital and Medical Faculty Carl-Gustav-Carus)

3. Comparative analysis of Streptococcus pathogens and commensals with a combination of computational biology and microbiology approaches to identify pathogen-related genetic elements

4. Molecular identification of Pseudomonas aeruginosa epidemic strains in clinical samples to prevent nosocomial infections

5. Antibiotic resistance of pathogenic and commensal bacteria in airway microbiome (to identify the comprehensive effects of antibiotics treatment on human microbiome)

6. Collabration projects with other teams by providing analyses with well-established methods, such as microbiome investigation, functional genomics analysis or deep sequencing data analysis

Methods

Both experimental approaches (e.g. Microbiology, Immunology methods) and computational biology/bioinformatics approaches are applied.

Experimental approaches (both Mice and Human cells are used in the investigations):

ex vivo organoid: precision cut lung sclices (Mice)

in vitro models: BEAS-2B (Human bronchial epithelial cell line); BLaER1 (Human monocyte cell line); CFBE41o- (Human CF Bronchial Epithelial Cell Line)

Microbiolgy/Virology methods: growth rate assay; pathogenicity assay; metabolism assay; antibiotics resistance measurement; infection experiment; antibody neutrolization assay, and others.

Immunology methods: multicolor flow cytometry; FACS sorting; qPCR; bead-based protein multiplex assay; ELISA; NGS; Single-cell sequencing, and others.

Computational approaches:

Functional genomic analysis (in particular with a focus on bacterium and virus)

Microbiome investigation (experiment design, sequencing, and data analysis and interpretation)

Transcriptome analysis (differntial gene expression analysis, function enrichment analysis, master regulator analysis, and other custimized analysis based on specific reseach goals) - in Human,Mouse,and Bacterium

Phylogenetic analysis to decipher evolution relationship of differnet organisms, e.g. bacterium, virus, fungus

Phylogeographic analysis and phylodynamic analysis to investigate the spreading of certain pathogen, eg. bacterium, virus, fungus.

Multi-omics data analysis, incorporating omics data from diverse laysers, such as transcriptome, proteome, metabolome.

Deep sequencing data analysis for CRISPR experiment, e.g. library establishement, choosing of postive clones.

Professional Memberships or Honorary Offices

• Member of the European Cystic Fibrosis Society.

• Member of the Federation of European Microbiological Societies (FEMS).

• Member of the International Union of Microbiological Societies (IUMS).

• Member of the German Society for Hygiene and Microbiology (DGHM).

• Reviewer of scientific journals (e.g. Microbiology Spectrum (American society of Microbiology), multiple Springer Nature journals, Infection and Immunity (American society of Microbiology))

Publication overview:

1. ORCID: https://orcid.org/0000-0003-4820-2560
2. Researchgate: https://www.researchgate.net/profile/Buqing-Yi
3. Google Scholar: https://scholar.google.ch/citations?user=06ENkiMAAAAJ&hl=en

Number of first and last author papers: 17

Total impact factors of first and last author papers: 141

h-index: 12

Selected Publications:

1. A. Tony-Odigie, A. H. Dalpke, S. Boutin, B. Yi (corresponding author) (2023). Commensal bacteria can inhibit the growth of P. aeruginosa in cystic fibrosis airway infections through a released metabolite. bioRxiv. DOI: 10.1101/2023.02.03.526996.
2. B. Yi (corresponding author), A. Laubner, M. Stadtmüller, E. Patrasová, L. Šimůnková, F. Rost, S. Winkler, S. Reinhardt, A. Dahl, A. H. Dalpke (2022). Investigating the cause of a 2021 winter wave of COVID-19 in a border region in Eastern Germany: a mixed-methods study, August to November 2021. medRxiv. DOI: 10.1101/2022.10.15.22281123.
3. C. M. Munz, H. Kreher, A. Erdbeer, S. Richter, D. Westphal, B. Yi, R. Behrendt, N. Stanke, F. Lindel, D. Lindemann (2022). Efficient production of inhibitor-free foamy virus glycoprotein-containing retroviral vectors by proteoglycan-deficient packaging cells. Molecular Therapy-Methods & Clinical Development. DOI: 10.1016/j.omtm.2022.07.004. (Impact factor: 5.85)
4. M. Stadtmüller, A. Laubner, F. Rost, S. Winkler, E. Patrasová, L. Šimůnková, S. Reinhardt, J. Beil, A. H. Dalpke, B. Yi (corresponding author) (2022). Emergence and spread of a sub-lineage of SARS-CoV-2 Alpha variant B.1.1.7 in Europe, and with further evolution of spike mutation accumulations shared with the Beta and Gamma variants. Virus Evolution. DOI: 10.1093/ve/veac010. (Impact Factor: 5.61)
5. A. Tony-Odigie, L. Wilke, S. Boutin, A. H. Dalpke, B. Yi (corresponding author) (2022). Commensal bacteria in the cystic fibrosis airway microbiome reduce P. aeruginosa induced inflammation. Frontiers in Cellular and Infection Microbiology. DOI: 10.3389/fcimb.2022.824101. (Impact Factor: 6.07)
6. B. Yi (corresponding author), A. H. Dalpke (2022). Revisiting the intrageneric structure of the genus Pseudomonas with complete whole genome sequence information: Insights into diversity and pathogen-related generic determinants. Infection, Genetics and Evolution. DOI: 10.1016/j.meegid.2021.105183. (Impact Factor: 4.40)
7. L. Muhandes, M. Chapsa, M. Pippel, R. Behrendt, Y. Ge, A. Dahl, B. Yi, A. H. Dalpke, S. Winkler, M. Hiller, S. Boutin, S. Beissert, R. Jessberger, P. G. Fallon, A. Roers (2021). Low Threshold for Cutaneous Allergen Sensitization but No Spontaneous Dermatitis or Atopy in FLG-Deficient Mice. Journal of Investigative Dermatology. DOI: 10.1016/j.jid.2021.02.763. (Impact Factor: 7.59, ranking 5 out of 68 in Dermatology)
8. B. Yi, A. H. Dalpke and S. Boutin (2021). Changes in the Cystic Fibrosis Airway Microbiome in Response to CFTR Modulator Therapy. Frontiers in Cellular and Infection Microbiology. DOI: 10.3389/fcimb.2021.548613. (Impact Factor: 6.07)
9. A. Tony-Odigie, S. Boutin, A. H. Dalpke, B. Yi (corresponding author) (2021). WS01. 1 Commensal bacteria in cystic fibrosis airway infections modulate growth and inflammation of P. aeruginosa. Journal of Cystic Fibrosis. DOI: 10.1016/S1569-1993(21)00915-2. (Impact Factor: 5.527)
10. B. Yi (corresponding author), A. Poetsch, M. Stadtmüller, F. Rost, S. Winkler, A. H. Dalpke (2021). Phylogenetic analysis of SARS-CoV-2 lineage development across the first and second waves in Eastern Germany in 2020: insights into the cause of the second wave. Epidemiology & Infection. DOI: 9.1017/S0950268821001461. (Impact Factor: 4.43)
11. U. Kolbe, B. Yi, T. Poth, A. Saunders, S. Boutin and A. H. Dalpke (2020). Early cytokine induction upon Pseudomonas aeruginosa infection in murine precision cut lung slices depends on sensing of bacterial viability. Frontiers in Immunology. DOI: 10.3389/fimmu.2020.598636. (Impact Factor: 8.79)
12. M. Sörensen, B. Khakimov, D. Nurjadi, S. Boutin, B. Yi, A. H. Dalpke, T. Eigenbrod (2020). Comparative evaluation of the effect of different growth media on in vitro sensitivity to azithromycin in multi-drug resistant Pseudomonas aeruginosa isolated from cystic fibrosis patients. Antimicrobial Resistance & Infection Control. DOI: 10.1186/s13756-020-00859-7. (Impact Factor: 6.46)
13. B. Yi (corresponding author), I. Nichiporuk, M. Nicolas, S. Schneider, M. Feuerecker, G. Vassilieva, D. Thieme, G. Schelling, A. Choukèr (2016). Reductions in circulating endocannabinoid 2-arachidonoylglycerol levels in healthy human subjects exposed to chronic stressors. Progress in Neuro-Psychopharmacology and Biology Psychiatry. 67:92-7; DOI: 10.1016/ j.pnpbp.2016.01.004. (Impact Factor: 5.20)
14. B. Yi, M. Rykova, G. Jäger, M. Feuerecker, M. Hörl, S. Matzel, S. Ponomarev, G. Vassilieva, I. Nichiporuk, A. Choukèr (2015). Influences of large sets of environmental exposures on immune responses in healthy adult men. Scientific Reports. 5:13367; DOI: 10.1038/srep13367 (Impact Factor: 5.00).
15. A. Jacubowski, V. Abeln, T. Vogt, B. Yi, A. Choukèr, E. Fomina, H. Strüder, S. Schneider (2015). The impact of long-term confinement and exercise on central and peripheral stress markers. Physiology & Behavior. 152:106-11; DOI: 10.1016/j.physbeh.2015.09.017. (Impact Factor: 3.74)
16. B. Yi (corresponding author), J. Titze, A. Choukèr (2015). Dietary Sodium Intake and Risk of Cardiovascular Disease. JAMA Internal Medicine. 175(9):1578-9; DOI: 10.1001/jamainternmed.2015.2558. (Impact Factor: 44.460, ranking 7 out of 169 journals in "Medicine, General & Internal")
17. B. Yi, J. Titze, M. Rykova, M. Feuerecker, G. Vassilieva, I. Nichiporuk, G. Schelling, B. Morukov, A. Choukèr (2015). Effects of dietary salt levels on monocytic cells and immune responses in healthy human subjects: a longitudinal study. Translational Research. 166(1):103-10; DOI: 10.1016/j.trsl.2014.11.007. (Impact Factor: 10.17, ranking 2 out of 29 in Medical Laboratory Technology)
18. B. Yi (corresponding author), S. Matzel, M. Feuerecker, M. Hörl, C. Ladinig, V. Abeln, A. Choukèr, S. Schneider (2015). The impact of chronic stress burden of 520-d isolation and confinement on the physiological response to subsequent acute stress challenge. Behavioural Brain Research. 281:111-5; DOI: 10.1016/j.bbr.2014.12.011. (Impact Factor: 3.35)
19. B. Yi, I. Nichiporuk, M. Feuerecker, G. Schelling, A. Choukèr (2015). Chronic stress decreases circulating endocannabinoid 2-arachidonoylglycerol in healthy human subjects. Endocrine Abstracts. DOI: 10.1530/endoabs.37.GP.18.01.
20. C. Strewe, F. Muckenthaler, M. Feuerecker, B. Yi, M. Rykova, I. Kaufmann, I. Nichiporuk, G. Vassieva, M. Hörf, S. Matzel, G. Schelling, M. Thiel, B. Morukov, A. Choukèr (2015). Functional changes in neutrophils and psychoneuroendocrine responses during 105 days of confinement. Journal of Applied Physiology. 118(9): 1122-27; DOI: 10.1152/japplphysiol.00755.2014. (Impact Factor: 3.88)
21. B. Yi (2015). Kinetics of stress-induced trafficking of blood immune cells and alterations of viral shedding under the exposure of acute stressors in healthy human subjects. Psychoneuroendocrinology. 61:78; DOI: 10.1016/j.psyneuen.2015.07.607. (Impact Factor: 4.69)
22. B. Yi, M. Rykova, M. Feuerecker, B. Jäger, C. Ladinig, M. Basner, M. Hörl, S.Matzel, I. Kaufmann, I. Nichiporuk, G. Vassilieva, K. Rinas, S. Baatout, G. Schelling, M. Thiel, D. F. Dinges, B. Morukov, A. Choukèr (2014). 520-d isolation and confinement simulating a flight to Mars reveals heightened immune responses and alterations of leukocyte phenotype. Brain Behavior and Immunity. 40:203-10; DOI: 10.1016/j.bbi.2014.03.018. (Impact Factor: 19.23, ranking 6 out of 274 in Neurosciences)
23. M. Feuerecker, W. Mayer, I. Kaufmann, M. Gruber, F. Muckenthaler, B. Yi, AP. Salam, J. Briegel, G. Schelling, M. Thiel, A. Choukèr (2013). A corticoid-sensitive cytokine release assay for monitoring stress-mediated immune modulation. Clinical & Experimental Immunology. 172(2):290-9; DOI: 10.1111/cei.12049. (Impact Factor: 5.73)
24. B. Yi, D. Bumbarger, RJ. Sommer (2009). Genetic evidence for pax-3 function in myogenesis in the nematode Pristionchus pacificus. Evolution & Development. 11(6):669-79; DOI: 10.1111/j.1525-142X.2009.00374.x. (Impact Factor: 2.84)
25. B. Yi, RJ. Sommer (2007). The pax-3 gene is involved in vulva formation in Pristionchus pacificus and is a target of the Hox gene lin-39. Development. 134(17):3111-9; DOI: 10.1242/dev.008375 (Impact Factor: 6.86).
26. Z. Jiang, R. Li, J. Xi, B.Yi (1999). Determination of trace amounts of manganese by β-cyclodextrin polymer solid phase spectrophotometry using 2-(5-bromo-2-pyridylazo)-5-diethylaminophenol. Analytica chimica acta. 392(2-3):247-53; DOI: 10.1016/S0003-2670(99)00175-0 (Impact Factor: 6.91)

Selected presentations at national or international conferences:

27. B. Yi (presenting author), et al.: Sars-CoV-2 community transmissions in a border region between Germany and the Czech Republic in autumn 2021. Presentation at the 31st Annual Meeting of the Society for Virology, virtual meeting, March, 2022.
28. B. Yi (presenting author), et al.: Emergence and spread of a SARS-CoV-2 B.1.1.7 sub-lineage in Europe. Presentation at the 7th JOINT CONFERENCE OF DGHM & VAAM, virtual meeting, September 12-14, 2021.
29. B. Yi (presenting author) et al.: The impact of Streptococcus on immune response triggered by Pseudomonas aeruginosa infection in the context of cystic fibrosis. Presentation at the 7th JOINT CONFERENCE OF DGHM & VAAM, virtual meeting, September 12-14, 2021.
30. B. Yi (presenting author) et al.: Commensal bacteria in cystic fibrosis airway infections modulate growth and inflammation of P. aeruginosa. Presentation at the 44th European Cystic Fibrosis Conference, virtual meeting, June 09-12, 2021.
31. B. Yi (presenting author), et al.: A systematic analysis of genomic diversity of Pseudomonas species in the human microbiome. Presentation at the 6th JOINT CONFERENCE OF DGHM & VAAM, Leipzig, March 08-11, 2020.
32. B. Yi (presenting author) et al.: Dietary salt consumption induces a specific proinflammatory response in the macrophage compartment. Presentation at the 10th International Symposium of IFReC, Bonn, November 5-6, 2018.
33. B. Yi (presenting author): Kinetics of stress-induced trafficking of blood immune cells and alterations of viral shedding under the exposure of acute stressors in healthy human subjects. Presentation at the 45th Annual Meeting of the International Society of Psychoneuroendocrinology (ISPNE), Edinburgh, September 2015.
34. B. Yi (presenting author) et al.: Effects of gravity stress on the efficiency of immune responses displayed as changes in immune cell migration performances and altered expression of cell adhesion molecules. Presentation at the 6th China-Germany Workshop on Microgravity and Space Life Sciences, Hangzhou, September 2015.
35. B. Yi (presenting author): Acute stress during parabolic flight induces redistribution of immune cells and changes of immune activity. Presentation at the International Academy of Astronautics’ 20th Humans in Space Symposium (HIS), Prague, Jun 29 to July 3, 2015.
36. B. Yi (presenting author) et al.: Re-adaptation of the immune system after interplanetary spaceflight. Presentation at the 6th International Congress of Medicine in Space and Extreme Environments (ICMS), Berlin, September 16-19, 2014.
37. B. Yi (presenting author) et al.: Molecular analyses of stress and immune responses. Presentation at the 6th International Congress of Medicine in Space and Extreme Environments (ICMS), Berlin, September 16-19, 2014.
38. B. Yi (presenting author) et al.: Influence of a high-salt diet on monocytes in healthy male subjects. Presentation at the 11th International Conference on Innate Immunity, Rhodes, June 1-6, 2014.
39. B. Yi (presenting author) et al.: Effect of salt intake levels on human immunity. Presentation at the 9th International Congress on Autoimmunity, Nice, March 26-30, 2014.
40. B. Yi (presenting author) et al.: Influence of long-term spaceflight simulation: from chronic to acute stress responses. Presentation at the 64th International Astronautical Congress, Beijing, September 23-27 2013.
41. B. Yi (presenting author) et al.: Immune responses to the long-term stressed conditions: immune dysfunction and long-lasting effect. Presentation at the IAA Humans in Space Symposium 2013, Cologne, July 2013.
42. B. Yi (presenting author) et al.: The Hox gene lin-39 is involved in different regulatory networks between C. elegans and P. pacificus. Presentation at the East Asia Worm Meeting 2009, Shanghai Jiaotong University, Medical School Campus, Shanghai, April 18 - 21, 2009.
43. B. Yi (presenting author) et al.: The pax-3 gene is involved in vulva formation in Pristionchus pacificus and is a target of the Hox gene lin-39. Presentation at the 16th International C. elegans Meeting, University of California, Los Angeles, California, June 27 – July 1, 2008.

BOOK CHAPTERS:

44. B. Yi, A. Choukèr. The immune system and man-environment interaction: A general understanding. In: The Immune System in Space – Are We Prepared? Edited by A. Choukèr and O. Ullrich. Springer 2016.

45. B. Yi, S. Tauber, O. Ullrich, A. Choukèr. Immune dysfunction in space - an integrative view. In: Effect of Spaceflight and Analogue Culture on Human and Microbial Cells: Novel Insights into Disease Mechanisms. Edited by Cheryl A. Nickerson, Neal R. Pellis, C. Mark Ott, Springer 2016.

46. S. Tauber, B. Yi, A. Choukèr, O. Ullrich. Use of in vitro cell culture models to understand the cellular and molecular basis of immune dysfunction during spaceflight. In: Effect of Spaceflight and Analogue Culture on Human and Microbial Cells: Novel Insights into Disease Mechanisms. Edited by Cheryl A. Nickerson, Neal R. Pellis, C. Mark Ott, Springer 2016.

47. B. Yi, M. Thiel, A. Choukèr. The immune system in evolution. In: The Immune System in Space – Are We Prepared? Edited by A. Choukèr and O. Ullrich. Springer 2016.

48. N. R. Pellis, A. Choukèr, B. Yi, S. Tauber, O. Ullrich, A. Sundaresan. Overview and translational impact of space cell biology research. In: Effect of Spaceflight and Analogue Culture on Human and Microbial Cells: Novel Insights into Disease Mechanisms. Edited by Cheryl A. Nickerson, Neal R. Pellis, C. Mark Ott, Springer 2016.