Big Data Biology Lab @ Fudan University

Big Data Biology Logo

This is the lab of Luis Pedro Coelho at Fudan University in Shanghai located at the Institute of Science and Technology for Brain-Inspired Intelligence.

We are interested both in developing novel computational methods and in applying them to large scale problems. Our focus is on the global microbiome and in exploiting publicly available data to gain understanding into microbial ecosystems.

Lab motto for 2021: “Everyone is an expert and everyone is a novice”

Blog updates

News & Upcoming

2021

20 March 2021 First release of S3N2Bin, 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.