Who Am I?

Hi, my name is Duo Peng, I am a biologist with training in Genetics (B.S.), Bioinformatics (M.S.), Cellular Biology (Ph.D.), Medical Entomology (Postdoc) and machine learning (Harvard certificate).

Currently, I am working at the Chan Zuckerberg Biohub as a bioinformatics data scientist II.

My research interests:
  1. Develop scalable computation pipelines to automate the design and validation of CRISPR experiments.
  2. Data mine public bio-sequence repositories at the petabase-scale.
  3. Unraveling complex host-pathogen interaction using machine learning with high-throughput omics and imaging data.

Vector biology

Parasitology

Bench research

Machine learning

Education

University of Georgia, Athens, Georgia, U.S.A.

2012-2017

Dissertation: Developing CRISPR/Cas9 for Genome-Wide Gene Editing in the Human Pathogen Trypanosoma cruzi

University of Georgia, Athens, Georgia, U.S.A.

2012-2016

Dissertation: Frequent Intra-Family Recombination in the Largest Repository of Antigen Variants in The Protozoan Pathogen Trypanosoma cruzi

Wuhan University, Wuhan, Hubei, P.R.China

2006-2010

Thesis: Predicting Trans-splicing by Analysis of RNA-seq Sequencing Data

Selected Publications

1.  D. Peng, E.G. Kakani, E.Mameli, C. Vidoudez, S.N. Mitchell, G.E. Merrihew, M.J. MacCoss, K. Adams, T.A. Rinvee, W.R Shaw, F. Catteruccia. (2022) A male steroid controls female sexual behaviour in the malaria mosquito. Nature

2.  D. Peng, R. Tarleton. (2015) EuPaGDT: A Web Tool Tailored to Design CRISPR Guide RNAs for Eukaryotic Pathogens. Microbial Genomics

3.  D. Peng, S.P. Kurup, P.Y. Yao, T.A. Minning, R.L. Tarleton. (2014) CRISPR-Cas9-mediated Single-gene and Gene Family Disruption in Trypanosoma cruzi. mBio

4.  D. Peng, X. Gu, L.J. Xue, J.H. Leebens-Mack, C.J. Tsai. (2014) Bayesian phylogeny of sucrose transporters: Ancient Origins, Differential Expansion and Convergent Evolution in Monocots and Dicots. Frontiers in Plant Science

5.  D.B. Weatherly*, D. Peng*, RL Tarleton. (2016) Recombination-driven Generation of the Largest Pathogen Repository of Antigen Variants in the Protozoan Trypanosoma cruzi. BMC Genomics (* equal contribution)

6.  Z. Zuo*, D. Peng*, X. Yin, X. Zhou, H. Cheng, R. Zhou. (2013) Genome-wide Analysis Reveals Origin of Transfer RNA Genes From tRNA Halves. Molecular Biology and Evolution (* equal contribution)

8.  K. Werling, R. Shaw, M. Itoe, K. Westervelt, P. Marcenac, D. Paton, D. Peng, N. Singh, A. Smidler, A. South, A. Deik, L. Mancio-Silva, A. Demas, E. Calvo, S. Bhatia, C. Clish, F. Catteruccia (2018) Steroid Hormone Function Controls Non-competitive Plasmodium Development in Anopheles. Cell

9.  W. Wang, D. Peng, RP Baptista, Y Li, JC Kissinger, RL Tarleton. (2021) Strain-specific genome evolution in Trypanosoma cruzi, the agent of Chagas disease. PLOS Pathogens

Work Experience

Bioinformatics scientist
2021.11-present

1. Develop computational pipelines for genome-wide CRISPR experiments:
    (i) Target design, (ii) editing validation and (iii) genotyping.
2. Unsupervised phenotyping of infection at the single-cellular level using high-content imaging.

Software developed

1.  Webserver: Eukaryotic Pathogen gRNA design tool (This webserver had 24,907 users, 49,267 visits, 17,972 job requests from 91 countries [Google Analytics, 2021])
    online access

2.  Automated Image Preprocessing and Malaria-oocyst Recognition Tool
    online access
    code base:
        Preprocessing
        Recognition