News Archive
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
Dec 18 Our paper Functional and evolutionary significance of unknown genes from uncultivated taxa is published in Nature.
Nov 12-15: The 22nd International Conference on Bioinformatics (InCoB 2023) in Brisbane. I presented a highlight talk on SemiBin (including SemiBin2).
Oct 28 Our paper SPIRE: a Searchable, Planetary-scale mIcrobiome REsource is published in Nucleic Acids Research.
Oct 15-20: International Peptide Symposium 2023 in Brisbane. I presented the talk A survey of antimicrobial peptides from the global microbiome.
Sep 20 Our paper Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide is published in Nature Communications.
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
Jul 1 Our paper Towards Monitoring of Antimicrobial Resistance in the Environment: For what Reasons, How to Implement It, and What Are the Data Needs? is published in Environment International.
Jun 30 Our paper SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing is published in Bioinformatics.
June 15-18: Vibecamp
May 31-June 2: microProteins 2023 (Copenhagen, Denmark)
May 19 Our paper ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics is published in Nucleic Acids Research.
April 2-6: Paris (France) for EMBARK and visiting INRAE
Jan 9-13: At the University of Warwick
2022
April 6-9: Keystone Symposium Micropeptides: Biogenesis and Function
2021
(No travel)
2020
Jan 6-7 I was in Gotenburg, Sweden for the first meeting of the EMBARK project
2019
June 20-24 2019 I was in San Francisco for ASM Microbe 2019
April 10-11 2019 I was in Chengdu (China), visiting the University of Electronic Science and Technology of China.
April 16-18 2019 I was in Utrecht (Netherlands) for the International Conference on One Health Antimicrobial Resistance (ICOHAR) talking about our dog microbiome work
2018
Oct 4 2018 I was in Paris talking about single cell approaches
Sep 16-19 2018 I was in Heidelberg for the Human Microbiome Conference
June 26-29 2018: Ireland IHMC2018: International Human Microbiome Consortium
June 14 2018: I taught the Introduction to Python lecture at the Lisbon (Portugal) Machine Learning Summer School
2017
Nov 22-24 2017 I was in Schwarzenberg, Switzerland for the Autumn School "Machine Learning applied to Systems Biology". I also visited the University of Bern and presented my scientific work.
Oct 24-26 2017 I was in Copenhagen teaching people how to use ngless at the Microbiome data interpretation workshop (slides no longer online) and giving a scientific talk on my work.
Sept 12-13 2017 I was in Delft for a workshop on data-driven cell factory and community design
July 21-25 2017 I was in Prague for ECCB/ISMB 2017 with a poster on NGLess
July 20 2017 I was in Lisbon on July 20 for LxMLS 2017
July 9-13 2017 I was in Valencia for FEMS 2017
2016
21-28 July 2016 I was in Lisbon for the 2016 edition of the Lisbon Machine Learning Summer School, presenting a tutorial on the first day
23-25 November 2016 I visited Zurich (Switzerland) for the course Machine learning for bioinformatics and computational biology
26-29 April 2016 I attended the Sloan Early Career Workshop on the Microbiology of the Built Environment in Chicago.
17 April 2016 I gave an invited keynote in Florence at PYCON Sette
7 March 2016 I am now an Associate Editor of the Journal of Open Research Software
21-26 February 2016 I was New Orleans for the 2016 Ocean Sciences Meeting. I presented a poster on our metagenomics work and gave a talk on our environmental imaging work
2015
22-25 August 2015 Visiting Tallinn (Estonia)
17 August 2015 The project ngless is now open source
16 July 2015 I taught at the Lisbon Machine Learning School
15-17 June 2015 I was in beautiful San Sebastian (Spain) for a software carpentry workshop (and some holiday time).
2 June 2015 I attended the Science of TARA Oceans conference in Paris
22 May 2015 Paper out in Science
March 31-April 2 2015 I attended the International Human Microbiome Congress (IHMC) in Luxembourg
March 2015 Paper accepted in Bioinformatics
February 2015 I was in Granada for the 2015 Aquatic Sciences Meeting, giving a talk on the 26th on our metagenomics work
2014
November 2014 I was the lead organizer for a software carpentry workshop at EMBL.
October 22 2014 O'Reilly webcast on Penalised Regression in Python
September 2014 Keynote talk in Python San Sebastien [Online talk]
September 2014 Speaking at TCMM2014
July 2014 Progression (in which I played the character Luis) has been released at New Filmmakers in NYC. See the film at the Big Bear Film festival
July 2014 Speaking at Lisbon Machine Learning School (LxMLS) 2014.
July 2014 New paper: Pena et al., Trypanosoma brucei histone H1 inhibits RNA polymerase I transcription and is important for parasite fitness in vivo in Molecular Microbiology [DOI].
June 2014 I taught at a software carpentry workshop in Cyprus and Amman (Jordan).
April 2014 Traveling to University of Southern Denmark for a software carpentry bootcamp.
February 2014 I'm now a certified Software Carpentry instructor
January 2014 New publication: Kristoffer Forslund, Shinichi Sunagawa, Luis P. Coelho, Peer Bork, Metagenomic insights into the human gut resistome and the forces that shape it in Bioessays (2014). [DOI]
2013
December 2013 New publication: Peter Liehl et al., Host-cell sensors for Plasmodium activate innate immunity against liver-stage infection in Nature Medicine 20, 47--53 (2014) [DOI]
November 2013 I attended the CFAR New York workshop
November 2013 I'm a member of the programme committee for DILS 2014 (10th International Conference on Data Integration in the Life Sciences)
October 2013 New publication: Shinichi Sunagawa et al., Metagenomic species profiling using universal phylogenetic marker genes in Nature Methods 10, 1196--1199 (2013) [Abstract] [DOI]
July 2013 I got a prize in the ICSB Computational Biology Wikipedia Competition for work on the Bioimage Informatics page
July 2013 My book Building Machine Learning Systems with Python is now published
July 2013 I posted a video abstract of my recent paper on subcellular location generalization
July 2013 I have a new paper out: Luis Pedro Coelho, Joshua D. Kangas, Armaghan Naik, Elvira Osuna-Highley, Estelle Glory-Afshar, Margaret Fuhrman, Ramanuja Simha, Peter B. Berget, Jonathan W. Jarvik, and Robert F. Murphy, Determining the subcellular location of new proteins from microscope images using local features in Bioinformatics, 2013 [Advanced Access]
May 2013 I started a research blog: metarabbit.wordpress.com
May 2013 My talk submission for BOSC (Bioinformatics Open Source Conference) about jug was accepted (it will be a lightning talk)
April 2013 I moved to EMBL, where I joined Peer Bork's group.
March 2013 I am part of the organizing committee for the 2013 edition of the Lisbon Machine Learning School
2012
November 2012 I have a new manuscript up at the arXiv on my computer vision software, mahotas [Update in 2013: this is now a peer-reviewed journal paper]
September 2012 I am teaching two session of a Programming for Scientists Course at IMM.
May 2012 I am writing a book
January 2012 I am now based in Lisbon at IMM in Musa Mhlanga's lab.
2011
November 2011 I start work as a postdoctoral researcher at Musa Mhlanga's lab.
October 2011 I graduated from Carnegie Mellon University with a PhD in computational biology!
September 2011 I was chosen as a 2012 Siebel Scholar