Zhi-Luo Deng


Gender: Male
Nationality: Chinese
E-mail: dawnmsg(at)gmail.com
Online CV: https://dawnmy.github.io/CV/
Address: Braunschweig, Germany
Research interests: Complex diseases, Microbiome, Evolutionary biology, Bioinformatics

Education

Postdoctoral researcher (2018-present)

Research area: Bioinformatics, Human microbiome, Virome, NGS diagnosis
Helmholtz Centre for Infection research, Germany
Group: Prof. Dr. Alice McHardy (Computational biology)

Doctor of Science (2014-2018)

Research area: Human microbiome, Periodontitis, IBD
Helmholtz Centre for Infection research, Germany
Supervisor: Prof. Dr. Irene Wagner-Döbler
Thesis: Activity profiling of human microbiota in health and disease using metatranscriptomics. (Excellent defense)

Master of Science (2010-2013)

Major: Biochemistry and Molecular Biology
Research area: Bioinformatics, Cheminformatics
College of Life Sciences & Technology, Huazhong Agricultural University
Supervisor: Prof. Hong-Yu Zhang & Prof. De-Xin Kong

Bachelor of Engineering (2006-2010)

Major: Biological Engineering
College of Life Sciences & Technology, Huazhong Agricultural University

Research Skills

Bioinformatics techniques

(meta-)transcriptomics, (meta-)genomics, proteomics, Hi-C, scRNA-seq, phylogenetics, machine and deep learning, (Bayesian) statistics

Programing skills

Proficient in Linux shell, Python, R. Experienced in Golang, Pytorch, Snakemake, Docker, Web, Shiny APP and database development

Projects

1. Deep neural networks optimized for genomic datasets (2020-present)

2. Pathogen discovery and disease diagnosis using metagenomics (2021-present)

3. CoVerage: SARS-Cov-2 lineage, spike protein mutation dynamics tracking (2021-present)

4. Second round of challenges for Critical Assessment of Metagenome Interpretation (CAMI) (2018-2021)

5. QuasiModo: benchmarking of strain-resolved analysis for population of large DNA-viruses (2018-2020)

6. The impact of fecal microbiota transplantation treatment of pouchitis on human gut microbiome (2017-2022)

7. Study of the activity shifts of the oral microbiota in periodontitis driven by key microbial players using metatranscriptomics (2014-2017)

8. The alterations of microbiome in bacterial vaginosis (BV) contribute to antibiotic resistance during treatment (2015-2017)

9. Explore biologically relevant chemical space for drug discovery (2011-2013)


Publications

  1. Deng ZL, Münch PC, Mreches R, McHardy AC. RiboDetector: Rapid and accurate detection of ribosomal RNA sequences using deep learning. Nucleic Acids Research. 2022. (Corresponding author)
  2. Deng ZL, Dhingra A, Fritz A, Götting J, Münch PC, Steinbrück L, Schulz T, Ganzenmueller T, McHardy AC. Quasimodo: Evaluating assembly and variant calling software for strain-resolved analysis of large DNA-viruses. Briefings in Bioinformatics. 2020:7.
  3. Meyer F, Fritz A, Deng ZL, Koslicki D, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, ..., All CAMI consortium. Critical Assessment of Metagenome Interpretation-the second round of challenges CAMI community. Critical Assessment of Metagenome Interpretation - the second round of benchmarking challenges. Nature Methods. 2022.
  4. Deng ZL, Gottschick C, Bhuju S, Masur C, Abels C, Wagner-Doebler I. Metatranscriptome analysis of the vaginal microbiota reveals potential mechanisms for protection against metronidazole in bacterial vaginosis. mSphere. 2018:3. (Corresponding author)
  5. Deng ZL, Sztajer H, Jarek M, Bhuju S, Wagner-Doebler I. Worlds apart - transcriptome profiles of key oral microbes in the periodontal pocket compared to single laboratory culture reflect synergistic interactions. Frontiers in Microbiology. 2018:9. (Corresponding author)
  6. Deng ZL, Szafranski SP, Jarek M, Bhuju S, Wagner-Döbler I. Dysbiosis in chronic periodontitis: Key microbial players and interactions with the human host. Scientific Reports. 2017:7.
  7. Deng ZL, Du CX, Li X, Hu B, Kuang ZK., Wang R, Feng SY, Zhang HY and Kong DX. Exploring the biologically relevant chemical space for drug discovery. Journal of chemical information and modeling. 2013:53.
  8. Gottschick C, Deng ZL, Vital M, Masur C, Abels C, Pieper DH, Rohde M, Mendling W, Wagner-Doebler I. Treatment of biofilms in bacterial vaginosis by an amphoteric tenside pessary-clinical study and microbiota analysis. Microbiome. 2017:5.
  9. Gottschick C, Deng ZL, Vital M, Masur C, Abels C, Pieper DH, Wagner-Doebler I. The urinary microbiome of men and women and its changes in women during bacterial vaginosis and antibiotic treatment. Microbiome. 2017:5.
  10. Szafrański SP, Deng ZL, Tomasch J, Jarek M, Bhuju S, Rohde M, Sztajer H, Wagner-Döbler I. Quorum sensing of Streptococcus mutans is activated by Aggregatibacter actinomycetemcomitans and by the periodontal microbiome. BMC genomics. 2017:18.
  11. Wang C, Deng ZL, Xie ZM, Chu XY, Chang JW, Kong DX, Li BJ, Zhang HY and Chen LL. Construction of a genome-scale metabolic network of the plant pathogen Pectobacterium carotovorum provides new strategies for bactericide discovery. FEBS Letters. 2014:893 (co-first author)
  12. Fritz A, Bremges A, Deng ZL, Lesker LR, Ganzenmüller T, Klawonn F, Dilthey A, McHardy A. Haploflow: strain-resolved de novo assembly of viral genomes. Genome Biology. 2021:212
  13. Yang XX, Deng ZL, Liu R. RBRDetector: Improved prediction of RNA-binding residues from protein structures using complementary feature- and template-based strategies. Proteins. 2014:82
  14. Szafranski SP, Deng ZL, Tomasch J, Jarek M, Bhuju S, Meisinger C, Kühnisch J, Sztajer H, Wagner-Döbler I. Functional biomarkers for chronic periodontitis and insights into the roles of Prevotella nigrescens and Fusobacterium nucleatum; a metatranscriptome analysis. npj Biofilms and Microbiomes. 2015:1.
  15. Milici M, Deng ZL, Tomasch J, Decelle J, Wos-Oxley ML, Wang H, Jáuregui R, Plumeier I, Giebel HA, Badewien TH, Wurst M. Co-occurrence analysis of microbial taxa in the Atlantic Ocean reveals high connectivity in the free-living bacterioplankton. Frontiers in microbiology. 2016:7.
  16. Reck M, Tomasch J, Deng ZL, Jarek M, Husemann P, Wagner-Döbler I. Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation. BMC genomics. 2015:4.
  17. Peng C, Fu LY, Dong PF, Deng ZL, Li JX, Wang XT and Zhang HY. The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling. Nucleic Acids Research. 2013:41.

    18. Not yet published

  18. Deng ZL, Pieper DH, Stallmach A, Vital M, Reck M, Wagner-Döbler I. Metatranscriptome analysis of fecal microbiota transplantation in chronic antibiotic resistant pouchitis: Remission is triggered by multiple transfers of essential functions. Microbiome. 2022. (Corresponding author) (Under revision)