Who am I?

I am the principal investigator (PI) of the Big Data Biology Lab at the Centre for Microbiome Research at the Queensland University of Technology (Brisbane, Australia) where we study the global microbiome.

Previously, my lab was hosted at Fudan University in Shanghai (2018–2023).

Before becoming a group leader, I worked at the European Molecular Biology Laboratory (EMBL) in Peer Bork's group. I have a PhD from Carnegie Mellon University (2011), where I worked on bioimage informatics for subcellular location analysis with Bob Murphy.

My Erdös-Bacon number is 7.

Outside of research, I made Uncommon Ground, a party game for teams where each team finds what they secretly have in common and the other teams pounce if they share it too. You can play it in your browser.

Publication list

Upcoming Travels & Talks

2026

Oct 8–11, 2026 Progress Conference 2026 in Berkeley, CA, USA

Email me if you want to set up meetings at any of these opportunities (or to invite me for other opportunities).

If you want to chat with me about science and such, you can use my cal.com link.

Research Interests

More technical version: I am interested in microbiomes. I wish to answer basic questions on what determines the structure of a microbial community in a given environment and what are the differences/similarities between different environments. Towards this, I pursue both method development (e.g. SemiBin or NGLess) and biologically-driven projects. Solving problems related to small proteins (those with fewer than 100 amino acids) is a particular interest of mine.

Not-so technical version: Microbes are all around us (including inside of us), what we call a microbiome. With modern technology, it is possible to sequence the DNA of all the microbes in a sample (be it from a soil sample or from a human gut sample). This allows us to answer questions such as: what are the microbes present in a given sample? How do they differ between samples? What are the functions of these microbes?

However, to achieve this, we need to develop computational methods to analyse these data. My work is focused on both developing these methods and applying them to answer biological questions.

Here is what o3 had to say about my research interests:

I work at the nexus of microbiology, big data, and machine learning: my group mines massively scaled metagenomic datasets—tens of thousands of environmental and host-associated samples—to build global gene catalogs such as GMGC v1, capturing both canonical proteins and the overlooked “small gene” universe of short open-reading frames. Leveraging these resources, we uncover new biology, most recently assembling AMPSphere, the world’s largest collection of candidate antimicrobial peptides, and experimentally validating their therapeutic promise. In parallel, we create open-source, high-performance tools like SemiBin and SemiBin 2, which use self-supervised neural networks to reconstruct high-quality metagenome-assembled genomes from short- and long-read data with minimal computational cost. Together, these efforts aim to chart the diversity, ecology, and functional capacity of the global microbiome—and translate that knowledge into novel antibiotics and other bioactive molecules.

Recent Publications

Recent(ish) publications (since 2024; see full list):

All publications... (Google Scholar profile)

Past News & Travels

2026

Aug 26 AusBiotech QLD BioBriefing: AI and Quantum Technologies in Biotech Discovery and Translation in Brisbane, Australia

Aug 16-21 20th International Symposium on Microbial Ecology (ISME20) in Auckland, New Zealand

Aug 4 Our paper Milk osteopontin alters the infant microbiome to drive DC hematopoiesis and disease tolerance is published in Cell.

Aug 2-7 Environmental Dimensions of Antimicrobial Resistance (EDAR8) in Brisbane, Australia

Aug 1 Our paper Micropollutants and the Restructuring of Microbial Resilience in the Anthropocene is published in Global Change Biology.

May 18 Talk at the 55th Annual Meeting of SBBq in Águas de Lindóia, SP, Brazil. "Big data and small genes. The small proteins of the global microbiome"

May 12 Our preprint The elusive resistome: a global comparison reveals large discrepancies among detection pipelines is posted on bioRxiv.

Apr 3 Our paper Unbinned contigs expand known diversity in the global microbiome is published in Nature Microbiology.

Apr 1 Our paper Storage and soil depth, in addition to wastewater treatment, govern microbiota, and mobile genetic element and antibiotic resistance markers during reclaimed water irrigation is published in Water Research.

Mar 21 Our preprint Long-read metagenomic sequencing reveals novel lineages and functional diversity in urban soil microbiome is posted on bioRxiv.

Mar 5 Our paper A gut microbiome-kidney-heart axis predictive of future cardiovascular diseases is published in Nature Communications.

Mar 1 Our paper Persistence of high-risk antimicrobial resistance genes in extracellular DNA along an urban wastewater-river continuum is published in Cell Reports.

Feb 25 Talk at BRISJAMS in Brisbane, Australia. "AI and big data in microbiology: the hype, the promise, and the disappointments"

2025

Dec 15-18 Keynote at the 19th International Conference on Data and Text Mining in Biomedical Informatics (DTMBIO 2025) in Muju, Republic of Korea.

Nov 20 Our paper proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes is published in Nucleic Acids Research.

Oct 23-24 I attended the Queensland Immunology Networking Symposium

Oct 13-15 I was in Houston for the SMBE Satellite Meeting: Evolutionary Biochemistry of Insect Antimicrobial Peptides.

Sep 17 Our preprint Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort is posted on bioRxiv.

Sep 16-19 I was at the EMBL Human Microbiome Symposium.

Aug 17-22, 2025 Decoding Microproteins Across Evolution and Disease GRC in Barcelona, Spain

Aug 1 Our preprint AEMB: a computationally efficient abundance estimation method for metagenomic binning is posted on bioRxiv.

Jul 15-24 I was in London and then in Liverpool for the ISMB/ECCB 2025 – Intelligent Systems for Molecular Biology & European Conference on Computational Biology

Jun 3 Our review AI-Driven Antimicrobial Peptide Discovery: Mining and Generation is published in Accounts of Chemical Research.

Apr 15-18 I was at the Pakistan Society for Microbiology Conference.

Apr 15 argNorm published at Bioinformatics

2024

Dec 10 & 12: Open office hours. Two sessions at different times of the day, so it works for all timezones. Attendance is free, but registration is required:

• Dec 10 @ 9.30am UTC (find your local time): Register now
• Dec 12 @ 9.30pm UTC (find your local time): Register now

Nov 11-15 I co-taught a 1 week course on state-of-the-art bioinformatic approaches to analyze metagenomic data. Click here to learn more and register.

Nov 3-6 I will be in Sydney. On the 4th, I will present at the Symposium on Bioinformatics Excellence and Innovation which is part of the ABACBS conference.

Oct 14-24 I will be in Shanghai

Oct 15 Our paper Quest for Orthologs in the Era of Biodiversity Genomics is published in Genome Biology and Evolution.

Sep 24 I will be presenting online at APBioNet on using machine learning to find antimicrobial peptides in the global microbiome. The talk will be on September 24, 2024 at 5am UTC (1pm SGT). Learn more and register

Aug 31 Our paper A catalog of small proteins from the global microbiome is published in Nature Communications.

Aug 18-23 I was in Cape Town, South Africa for ISME19. I will present at the Night of the Microbes event.

July 19-22: I was in San Francisco

July 12-17: ISMB2024, followed by the Quest for Orthologs meeting in Montreal, Canada. I presented a talk on AMPSphere and on long term sustainable research software (YouTube version).

July 4: ASM (the Australian one), in Brisbane, QLD, Australia

Jun 11 The AMPSphere manuscript was featured in several news outlets, including the BBC (Science in Action), Deutsche Welle, Guardian, El País, Folha de São Paulo as well as mentions as a Nature Research Highlight and in the Science Adviser.

Jun 5 AMPSphere manuscript published in Cell

May 14 New Season of Extremely Open Science. See episode 1 and the sardyne github repository

May 9 open office hours (Zoom)

Apr 27 argNorm v0.3.0 has been released

Apr 24 open office hours (Zoom)

Mar 8 Our review Challenges in computational discovery of bioactive peptides in ’omics data is published in PROTEOMICS.

Mar 5 Our paper A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer is published in Nature Ecology & Evolution.

Feb 12 Our preprint Ubiquity of inverted ’gelatinous’ ecosystem pyramids in the global ocean is posted on bioRxiv.

Jan 23-25 Berlin, Germany

2023

Nov 12-15: The 22nd International Conference on Bioinformatics (InCoB 2023) in Brisbane. I presented a highlight talk on SemiBin (including SemiBin2).

Oct 15-20: International Peptide Symposium 2023 in Brisbane. I presented the talk A survey of antimicrobial peptides from the global microbiome.

Aug 21-24: Quadram Institute in Norwich (UK).

July 27: I was awarded an ARC Future Fellowship to work on small proteins of the global microbiome at QUT.

July 23-27: ISMB (Lyon, France) - talk

June 15-18: Vibecamp

May 31-June 2: microProteins 2023 (Copenhagen, Denmark)

April 2-6: Paris (France) for EMBARK and visiting INRAE

Jan 9-13: At the University of Warwick

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