Tailblazing deeper and scalable cellular biology.

Hi! I'm Duo Peng, a computational biologist at the Chan Zuckerberg Biohub San Francisco.
I manage a team that builds open-source tools and computational methods to:

  • Map the human subcellular proteome from organellar mass spectrometry data, and build a software ecosystem for spatial proteomics analysis and visualization.
  • Automate high-throughput CRISPR informatics pipelines to accelerate cell-biology discovery at scale.
  • Mine, integrate, and model omics datasets at repository scale—spanning whole species and large perturbation screens.

Selected Publications

† corresponding author
* equal contribution

1.  M.Y. Hein*†, D. Peng*†, V. Todorova*, F. McCarthy*, K. Kim*, C. Liu*, ..., J.E. Elias†, M.D. Leonetti† (2025) Global organelle profiling reveals subcellular localization and remodeling at proteome scale. Cell [link] [webapp]

2.  D. Peng†, E. Marrogi, E. Nelson, Q. Liu, T.A. Rinvee, L.E. de Vries, K. Thornburg, N. Singh, W.R. Shaw, F. Catteruccia† (2025) OocystMeter, a machine-learning algorithm to count and measure Plasmodium oocysts, reveals clustering patterns in the Anopheles midgut bioRxiv [link]

2.  D. Peng†, M. Vangipuram, J. Wong, M.D. Leonetti† (2024) protoSpaceJAM: an open-source, customizable and web-accessible design platform for CRISPR/Cas insertional knock-in. Nucleic Acids Research [link] [webapp]

3.  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 [link]

4.  D. Peng, R. Tarleton. (2015) EuPaGDT: A Web Tool Tailored to Design CRISPR Guide RNAs for Eukaryotic Pathogens. Microbial Genomics [link] [webapp] cited 327 times

5.  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 [link] cited 231 times

6.  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 [link]

7.  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 [link]

8.  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 [link]

See Google Scholar for a complete list

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

Work Experience

Team manager, computational biology
2025.10-present

1. Oversee the development of a software ecosystem for spatial proteomics analysis and visualization.
2. Co-steer the development of computational pipelines to validate CRISPR-edited cells and perform quality control using long-read sequencing.
3. Guide and engage in data-driven understanding of the landscape of cellular responses from multimodal assays.

Senior computational biologist
2024.07-2025.09

1. Coordinate a team to mine, integrate, and model omics datasets at repository scale spanning whole species.
2. Build computational pipelines to validate CRISPR-edited cells and perform quality control using long-read sequencing.

Bioinformatics data scientist II
2023.01-2024.06

1. Develop analysis approaches to map the human subcellular proteome from organellar mass spectrometry data (paper, app ).
2. Led design and prototyping of species-scale pipelines to mine and analyze expression datasets for paired host and nonhost gene expression.

Bioinformatics data scientist I
2021.11-2022.12

1. ProtoSpaceJAM: Genome-wide CRISPR knock-in design at scale using biologically informed algorithms (paper, webapp).
2. DeepGenotype: Calculate frequencies of protein-level mutations from deep-sequencing reads of CRISPR-edited cells (codebase).

Software developed

1.  Data portal for: Global organelle profiling reveals the human proteome’s subcellular landscape and its dynamic remodeling
    online access (hosted by the Chan Zuckerberg Biohub San Francisco)

2.  Web-based App: ProtoSpaceJAM - CRISPR knock-in design at scale
    online access (hosted by the Chan Zuckerberg Biohub San Francisco)
    code base

3.  Web-based App: 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 (hosted by the University of Georgia)

4.  Automated Image Preprocessing and Malaria-oocyst Recognition Tool
    online access (hosted by AWS cloud)
    code base:    Preprocessing    Recognition