AnniZ Lab

Our sevices

• Who are we?
• We are a team of microbiologists and software engineers previously from MIT and Google.
• We develop biology-informed AI models to predict how proteins interact with DNA and ligands in bacteria.
• We analyze 500,000+ to design the computational blueprints needed for precise microbial engineering.

• What can we do?
• Technical R&D partner for companies in fermentation, therapeutics, drug discovery, and agriculture.
• Our platform identifies the specific "genetic switches" (regulatory motifs and binding sites) required to control and optimize bacterial behavior.

• Core industrial domains
• Industrial fermentation: designing genetic circuits that respond to environmental triggers to improve production yield
• Live biotherapeutics: identifying "localization switches" to ensure engineered probiotics release medicine only at the target site
• Drug discovery: predicting how to activate "silent" genes in bacteria to discover new antibiotics
• Agricultural biotech: engineering soil microbes to remain active in diverse conditions for better plant growth and nitrogen fixation.

Our Research:

• Biology-informed AI models for precise bacterial engineering
• Protein-ligand binding prediction: to sense different molecules
• Protein-DNA binding prediction: to change bacterial behavior accordingly

• Microbiome druggable target design via knowledge graph link prediction
• LLM-powered microbiome knowledge graph: extracting existing knowledge
• Link prediction: generating new hypotheses
• Rule-based microbial gene/metabolite prioritization: identifying microbiome-derived drug leads

• Our tools

• More research and thoughts shared on bluesky!

One PhD Position Available!

Requirements

• A curiosity about microbes
• An interest in coding
• A dedication to research

What to expect as our teammate:

• Receive training in critical thinking and hypothesis testing
• Gain a solid foundation in statistics, microbiology, and AI computation
• Develop skills in coding, analysis, visualization, and public speaking
• Practice collaboration and communication
• More importantly, we care about your future! We are happy to mentor you in career development.

News!

• 2026 Jun Dr. Fatima Aysha Hussain at Tufts University visited our lab at NTU.
• 2026 May Anni is invited to give a talk on Microbiome R&D and Business Collaboration Congress Asia.
• 2026 Apr BIG NEWS: we are awarded SG$1M Singapore MOE Tier 2 grant for protein-DNA binding prediction!
• 2026 Apr Zhiqi talked about "Detection of HGT and selective sweeps in human gut microbiome via large data analysis and population genomics" in But seminars - great job.
• 2026 Mar Anni was invited as a working group member for National Infectious Disease Research Strategy, Singapore!
• 2026 Jan Dr. Xiaoqian Yu (University of Montreal) visited our lab at NTU.
• 2025 Dec Qiwen talked about "Biology-guided AI models to predict bacteria protein DNA binding" in BUG seminars - great job.
• 2025 Dec Dr. Klas Udekwu (University of Idaho & SLU) visited our lab at NTU.
• 2025 Nov Anni talked about "Uncovering diverse microbial mechanisms via computation" in SCELSE Retreat.
• 2025 Aug Jinxuan joined our lab as a PhD student. Welcome :)
• 2025 Aug Zhiqi switched to a PhD student. Congrats!
• 2025 July-Aug Aolin and Yifang transitioned to future paths. Good luck!
• 2025 July Anni gave a talk at Gordon Conference AEM 2025
• 2025 July Jeff presented work at Gordon Conference AEM 2025 :)
• 2025 July Anni presented work at Gordon Conference MPB 2025 :)
• 2025 June Anni gave a talk at MIT BE Seminar!
• 2025 March Aolin joined us as a research associate.
• 2025 Jan Qiwen joined us as a PhD student. Welcome to AnniZLab!
• 2025 Jan Zhiqi joined us as a research associate.
• 2024 Nov Yifang joined us as a research associate.

Contact us!