Forthcoming

2025

Aug 17-22 Luis will be a speaker at the Decoding Microproteins Across Evolution and Disease GRC.

Feel free to get in touch if you will be at any of these events (actually, feel free to get in touch even if you will not).

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Recent News

See our publications page for recent publications.

2025

Jan 14 Updates for January 2025

2024

Dec 10 & 12: Open office hours.

Dec 3-5 Vedanth presented argNorm at the Microbiome Virtual International Forum along with Svetlana.

Nov 11-15 Luis 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 7 - Dec 15 Yiqian visited Brisbane.

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

Oct 14-24 Luis visited Fudan University in Shanghai.

Sep 24 Luis presented 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). Click here to learn more and register.

Oct 10: A manuscript detailing argNorm has been made available as a preprint at QUT ePrints. You can find the preprint here

Sep 24 Luis 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). Click here to learn more and register.

Aug 31 Yiqian's manuscript on the GMSC was published in Nature Communications.

Aug 18-23 Anna and Luis will be at the ISME19 in Cape Town, South Africa.

July 31: Farewell to Shaojun who recently graduated with his PhD. He will be missed!

July 26: argNorm now included in nf-core/funcscan (part of the git version, will included in next release)

July 12-17: Luis was at ISMB2024, followed by the Quest for Orthologs meeting in Montreal, Canada. His BOSC talk is available on YouTube

July 4 Luis presented at the Australian Society for Microbiology on the AMPSphere

July 1 Anna gave a talk at the Applied Hologenomics conference in Copenhagen. You can find it on YouTube here

Jun 28 We updated the webserver to report AMPSphere matches.

Jun 27 Macrel v1.4.0 released which includes a new subcommand for query-ampsphere to match against the AMPSphere database.

Jun 14 Anna presented at the Oxford Nanopore event within ASM Microbe in Atlanta. You can watch it on YouTube here

Jun 12 Updates for June 2024

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 10 ArgNorm v0.4.0 released with improved mappings for MegaRes

Jun 5 AMPSphere manuscript published in Cell

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

Apr 27 argNorm v0.3.0 has been released

Apr 19 Luis posted a SemiBin2 tutorial

Apr 17 Yiqian presented at mVIF, describing the GMSC and AMPSphere projects.

Mar 29 Luis will hold two Zoom open office hour sessions on April 24 and May 9.

Mar 15 Luis published a perspective piece on maintaining open source research software at PLoS Computational Biology

Mar 8 Luis, Célio, and César de la Fuente published a review paper on mining bioactive peptides in Proteomics.

Mar 5 Marija's paper on HGT was published at Nature Ecology & Evolution.

Jan 29 Start of Extremely Open Science 2024

Jan 23-25 Luis will be in Berlin for the SEARCHER kickoff meeting.

Jan 14: Extremely open science project for 2024 announced

2023

Dec 18: New collaborative paper out! del Río et al. describes finding novel families from the global microbiome! We were happy to play a role.

Dec 4-8: ABACBS 2023 in Brisbane. Luis presented a poster on SemiBin

Nov 12-15: incob23. Luis presented on SemiBin

Nov 6: Jug tutorial.

Nov 5: Jug 2.3.1 adds support for Python 3.12

Oct 29: SPIRE manuscript out!

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

Oct 23: SemiBin tutorial. Signup free, but required

Oct 20 SemiBin 2.0.0 released

Aug 31 AMPSphere preprint posted.

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

12 Aug We are looking for PhD students!

23-27 Jul Luis was at ISMB/ECCB 2023 in Lyon. On the 25th, he presented SemiBin2 [talk slides] and [YouTube re-recording of the presentation].

9-13 Jul Anna was at #FEMS2023 in Hamburg.

30 Jun. The SemiBin2 manuscript is online!

26 Jun. New logo (see above)!

23 May The ResFinderFG2 manuscript is published in NAR WebServer Issue.

12 Apr. The SemiBin2 manuscript has been accepted at ISMB Proceeding (Bioinformatics). See you in Lyon!

18/20 Jan. We published a couple of tutorials on how to use NGLess and SemiBin to build MAGs from a metagenome on our YouTube channel (available in English, Portuguese, French, and German).

9 Jan. Preprint describing improvements to SemiBin is published: SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing

1 Jan. Accepting intern applications for Spring 2023. Deadline: 5 Feb 2023.

2022

15 Dec. SemiBin v1.4.0 released. This includes support for binning long-read contigs.

4 Nov. SemiBin v1.3.0 released

2 Nov. Svetlana will give a seminar Challenges in metagenomic annotation of antibiotic resistome invited by Serbian Society of Bioinformatics and Computational Biology.

27 Oct @ 11AM UTC. Luis online office hours — open, but registration required (check your local time)

20 Oct. SemiBin v1.2.0 released

22-27 Sep. Svetlana and Luis attended in September the EDAR6 conference and annual EMBARK meeting in Gothenburg (Sweden).

17-21 Sep. Luis was at ECCB 2022, presenting in the Quest for Orthologs workshop (Spain).

13-15 Sep. Anna gave a talk Exploring the pet gut microbiome within a large-scale investigation of animal gut metagenomes at the Applied Hologenomics conference in Bilbao (Spain).

14-19 Aug. Marija presented the poster A global survey of the contribution of ecological factors to rates of horizontal gene transfer at the ISME18 in Lausanne (Switzerland).

30 June. Svetlana gave a talk on challenges in the metagenomic annotation of antibiotic resistome at the main session Antimicrobial Resistance - Challenges and Perspectives of the #FCOM22

28 June Summer 2022 update

14 June @ Noon UTC SemiBin tutorial (sign up required)

9 June Luis presented in Copenhagen at NNF Prize Symposium

2 June @ Noon UTC Open Office Hours (registration required)

9 May macrel v1.2.0 released

9 May SemiBin v1.0.1 released

28 April SemiBin manuscript published

22 March BDB-Lab Spring 2022 Update

3 March SemiBin version 0.7 released with better support for Mac OS X.

28 February Deadline for remote internship applications.

13 January Online office hours

2021

15 December The paper Towards the biogeography of prokaryotic genes by LP. Coelho et al. was published in Nature.

15 December (1pm UTC) Svetlana presented at the EMBARK Webinar

14 December The preprint on EXPERT by Hui Chong et al. was posted

14 December First online release of the AMPSphere website (still a WIP).

10 December We posted a preprint with a proposal on how to solve collective action problems in academia: conditional pledges

8 December A collaborative manuscript on how drugs and the human gut microbiome interact was published in Nature

2 November (Noon UTC) SemiBin tutorial (SIGN UP LINK)

21 September Our Autumn 2021 update

August 16 SemiBin manuscript is online

21 June Our Summer 2021 update

25 June & 5 July 2021 (Noon UTC): Two hour tutorial on NGLess. Registration is required

27 May 2021 SemiBin v0.2 released (used to be called S3N2Bin).

20 March 2021 First release of SemiBin, our new genome binning tool (releases on pyPI. Also, see the introductory blogpost.

14 March 2021 We started a quarterly newsletter. If the blog is too high-frequency for you, the newsletter will come out (exactly) four times a year. The first edition will come later this month, but you can subscribe now.

6 March 2021 AMPSphere (AMP catalog) posted

26 February 2021 New call for remote interns posted posted!

2020

20 December 2020 The macrel paper is published at PeerJ. We also released Macrel 1.0 to coincide with the publication.

17 December 2020 GUNC preprint available

21 August 2020 We are looking for a remote intern.

15 July 2020 We present two abstracts at the ISMB 2020 Microbiome Track: one on macrel and another on a project on smORFs (small ORFs).

26 April 2020: We updated the Macrel preprint.

14 April 2020: NGLess 1.1.1 released

23 March 2020: Macrel 0.4.0 available online

24 February 2020: NGLess 1.1 released

21 February 2020: We are looking for students who want to participate in the Google Summer of Code or Tweag Fellowship.

14 February 2020: We published our commitments for software tools.

January 2020 We are looking for a postdoc who is interested in antimicrobial resistance.

2019

December 2019 Our newest preprint is online: FACS: antimicrobial peptide screening in genomes and metagenomes by Dias Santos-Júnior et al.

November 2019 Two Tara papers published (featured on the cover of the journal Cell): Longitudinal diversity gradients across the whole spectrum of life and Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

September 2019 Amy Houseman joined our group!

July 2019: NGLess was presented at BOSC 2019, part of ISMB/ECCB 2019.

June 2019: Célio Dias Santos Júnior joined our group!

June 2019: NGLess manuscript published: NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language in Microbiome

March 2019: Our dog microbiome work was presented at the International Conference on One Health Antimicrobial Resistance (ICOHAR) conference in Utrecht.