I am currently looking for postdocs to join my group in Shanghai. Come work with me on metagenomics, antimicrobial resistance, algorithms, or just propose your own project.

Who am I?

I am the principal investigator of the Big Data Biology Lab at Fudan University (Shanghai) since September 2018. Our group works in computational biology, with a focus on the very large-scale.

Previously, I worked at the European Molecular Biology Laboratory (EMBL) in Peer Bork's group in microbial community analysis using metagenomics. 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.

Research Interests

More technical version: I am interested in combining meta\'omics (methods that obtain high-throughput information on microbial communities such as metagenomics and metatranscriptomics) analysis with machine learning approaches to learn about microbial communities in different environments. 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.

My work is a mix of of method and tool development with applications. In methodological terms, I worry a lot about correct evaluation of methods and avoiding over-inflated measures of performance. A large fraction of my time is spent scaling up algorithms and pipelines to work on very-large problems.

Not-so technical version: With modern technology, namely robotic instruments, it is easy to acquire a lot of microscopic pictures. It is also possible to acquire large sequence datasets with the DNA of many organisms. I use these two families of technologies to investigate what is happening in mixed microbial communities such as the one in our guts, the microbiome.

In order to be able to use these data, I also need to develop new computer methods (software) for these tasks. Thus my work is a mix of solving biological problems and tackling the software issues that stand in the way of doing so.

Upcoming Travels & Talks

2021 April 6-9: Keystone Symposium Micropeptides: Biogenesis and Function

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

Publications

Recent(ish) publications (last 5 years; updated 12 Oct 2021; see full list):

1. Thomas SB Schmidt*, Simone S Li*, Oleksandr M Maistrenko, Wasiu Akanni, Luis Pedro Coelho, Sibasish Dolai, Anthony Fullam, Anna M Glazek, Rajna Hercog, Hilde Herrema, Ferris Jung, Stefanie Kandels, Askarbek Orakov, Thea Van Rossum, Vladimir Benes, Thomas J Borody, Willem M de Vos, Cyriel Y Ponsioen, Max Nieuwdorp, Peer Bork Drivers and Determinants of Strain Dynamics Following Faecal Microbiota Transplantation bioRxiv preprint (2021)
2. Shaojun Pan, Chengkai Zhu, Xing-Ming Zhao, and Luis Pedro Coelho SemiBin: Incorporating information from reference genomes with semi-supervised deep learning leads to better metagenomic assembled genomes (MAGs) BioRxiv preprint (2021)
3. Senying Lai, Shaojun Pan, Luis Pedro Coelho, Wei-Hua Chen, Xing-Ming Zhao, metaMIC: reference-free Misassembly Identification and Correction of de novo metagenomic assemblies BioRXiv preprint (2021)
4. Askarbek Orakov*, Anthony Fullam*, Luis Pedro Coelho, Supriya Khedkar, Damian Szklarczyk, Daniel R Mende, Thomas SB Schmidt† and Peer Bork† GUNC: Detection of Chimerism and Contamination in Prokaryotic Genomes at Genome Biology (2021)
5. Célio Dias Santos-Junior, Shaojun Pan, Xing-Ming Zhao, Luis Pedro Coelho MACREL: antimicrobial peptide screening in genomes and metagenomes at PeerJ (2020)
6. Mohammad Bahram, Tarquin Netherway, Clémence Frioux, Pamela Ferretti, Luis Pedro Coelho, Stefan Geisen, Peer Bork, and Falk Hildebrand Metagenomic assessment of the global diversity and distribution of bacteria and fungi at Environmental Microbiology (2020)
7. Luis Pedro Coelho Voices of the New Generation Nature Reviews Molecular Cell Biology (2020)
8. Sara Vieira-Silva, Gwen Falony, Eugeni Belda, Trine Nielsen, Judith Aron-Wisnewsky, Rima Chakaroun, Sofia K. Forslund, Karen Assmann, Mireia Valles-Colomer, Thi Thuy Duyen Nguyen, Sebastian Proost, Edi Prifti, Valentina Tremaroli, Nicolas Pons, Emmanuelle Le Chatelier, Fabrizio Andreelli, Jean-Phillippe Bastard, Luis Pedro Coelho, Nathalie Galleron, Tue H. Hansen, Jean-Sébastien Hulot, Christian Lewinter, Helle K. Pedersen, Benoit Quinquis, Christine Rouault, Hugo Roume, Joe-Elie Salem, Nadja B. Søndertoft, Sothea Touch, MetaCardis Consortium, Marc-Emmanuel Dumas, Stanislav Dusko Ehrlich, Pilar Galan, Jens P. Gøtze, Torben Hansen, Jens J. Holst, Lars Køber, Ivica Letunic, Jens Nielsen, Jean-Michel Oppert, Michael Stumvoll, Henrik Vestergaard, Jean-Daniel Zucker, Peer Bork, Oluf Pedersen, Fredrik Bäckhed, Karine Clément & Jeroen Raes Statin therapy is associated with lower prevalence of gut microbiota dysbiosis, Nature 581, 310--315 (2020).
9. Oleksandr M Maistrenko*, Daniel R Mende*, Mechthild Luetge, Falk Hildebrand, Thomas SB Schmidt, Simone S Li, Luis Pedro Coelho, Jaime Huerta-Cepas, Shinichi Sunagawa, Peer Bork Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity, ISME Journal 2020
10. Federico M. Ibarbalz, Nicolas Henry, Manoela C. Brandão, Séverine Martini, Greta Busseni, Hannah Byrne, Luis Pedro Coelho, Hisashi Endo, Josep M. Gasol, Ann C. Gregory, Frédéric Mahé, Janaina Rigonato, Marta Royo-Llonch, Guillem Salazar, Isabel Sanz-Sáez, Eleonora Scalco, Dodji Soviadan, Ahmed A. Zayed, Adriana Zingone, Karine Labadie, Joannie Ferland, Claudie Marec, Stefanie Kandels, Marc Picheral, Céline Dimier, Julie Poulain, Sergey Pisarev, Margaux Carmichael, Stéphane Pesant, Tara Oceans Coordinators, Marcel Babin, Emmanuel Boss, Daniele Iudicone, Olivier Jaillon, Silvia G. Acinas, Hiroyuki Ogata, Eric Pelletier, Lars Stemmann, Matthew B. Sullivan, Shinichi Sunagawa, Laurent Bopp, Colomban de Vargas, Lee Karp-Boss, Patrick Wincker, Fabien Lombard, Chris Bowler#, and Lucie Zinger# Global Trends in Marine Plankton Diversity across Kingdoms of Life31124-9), Cell 2019
11. Guillem Salazar*, Lucas Paoli*, Adriana Alberti, Jaime Huerta-Cepas, Hans-Joachim Ruscheweyh, Miguelangel Cuenca, Christopher M. Field, Luis Pedro Coelho, Corinne Cruaud, Stefan Engelen, Ann C. Gregory, Karine Labadie, Claudie Marec, Eric Pelletier, Marta Royo-Llonch, Simon Roux, Pablo Sánchez, Hideya Uehara, Ahmed A. Zayed, Georg Zeller,1Margaux Carmichael, Céline Dimier, Joannie Ferland, Stefanie Kandels, Marc Picheral, Sergey Pisarev, Julie Poulain, Tara Oceans Coordinators, Silvia G. Acinas, Marcel Babin, Peer Bork, Chris Bowler, Colomban de Vargas, Lionel Guidi, Pascal Hingamp, Daniele Iudicone, Lee Karp-Boss, Eric Karsenti, Hiroyuki Ogata, Stephane Pesant, Sabrina Speich, Matthew B. Sullivan, , Patrick Wincker, and Shinichi Sunagawa,* Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome31164-X), Cell 2019
12. Daniel R Mende, Ivica Letunic, Oleksandr M Maistrenko, Thomas S B Schmidt, Alessio Milanese, Lucas Paoli, Ana Hernández-Plaza, Askarbek N Orakov, Sofia K Forslund, Shinichi Sunagawa, Georg Zeller, Jaime Huerta-Cepas, Luis Pedro Coelho, Peer Bork proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes, Nucleic Acids Research, 2020
13. Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language, Microbiome (2019)
14. Jakob Wirbel*, Paul Theodor Pyl*, Ece Kartal, Konrad Zych, Alireza Kashani, Alessio Milanese, Jonas S Fleck, Anita Y Voigt, Albert Palleja, Ruby P Ponnudurai, Shinichi Sunagawa, Luis Pedro Coelho, Petra Schrotz-King, Emily Vogtmann, Nina Habermann, Emma Niméus, Andrew M Thomas, Paolo Manghi, Sara Gandini, Davide Serrano, Sayaka Mizutani , Hirotsugu Shiroma, Satoshi Shiba, Tatsuhiro Shibata, Shinichi Yachida, Takuji Yamada, Levi Waldron, Alessio Naccarati, Nicola Segata, Rashmi Sinha, Cornelia M. Ulrich, Hermann Brenner, Manimozhiyan Arumugam, Peer Bork, Georg Zeller Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer, Nature Medicine (2019)
15. Alessio Milanese*, Daniel R Mende*, Lucas Paoli, Guillem Salazar, Hans-Joachim Ruscheweyh, Miguelangel Cuenca, Pascal Hingamp, Renato Alves, Paul I Costea, Luis Pedro Coelho, Thomas S B Schmidt, Alexandre Almeida, Alex L Mitchell, Robert D Finn, Jaime Huerta-Cepas, Peer Bork, Georg Zeller# & Shinichi Sunagawa#. Microbial abundance, activity and population genomic profiling with mOTUs2 Nature Communications 10, Article number: 1014 (2019).
16. Thomas SB Schmidt*, Matthew R Hayward*, Luis Pedro Coelho, Simone S Li, Paul I Costea, Anita Y Voigt, Jakob Wirbel, Oleksandr M Maistrenko, Renato J Alves, Emma Bergsten, Carine de Beaufort, Iradj Sobhani, Anna Heintz-Buschart, Shinichi Sunagawa, Georg Zeller, Paul Wilmes, Peer Bork Extensive Transmission of Microbes along the Gastrointestinal Tract in eLife (2019) [DOI]
17. Luigi Caputi*, Quentin Carradec*, Damien Eveillard*, Amos Kirilovsky*, Eric Pelletier*, ..., Luis Pedro Coelho, ..., Chris Bowler*, Daniele Iudicone* Community‐Level Responses to Iron Availability in Open Ocean Planktonic Ecosystems in Global Biogeochemical Cycles (2019) [DOI]
18. Albert Palleja*, Kristian H. Mikkelsen*, Sofia K. Forslund*, Alireza Kashani, Kristine H. Allin, Trine Nielsen, Tue H. Hansen, Suisha Liang, Qiang Feng, Chenchen Zhang, Paul Theodor Pyl, Luis Pedro Coelho, Huanming Yang, Jian Wang, Athanasios Typas, Morten F. Nielsen, Henrik Bjorn Nielsen, Peer Bork, Jun Wang, Tina Vilsbøll, Torben Hansen, Filip K. Knop, Manimozhiyan Arumugam & Oluf Pedersen Recovery of gut microbiota of healthy adults following antibiotic exposure in Nature Microbiology (2018) [DOI]
19. Mohammad Bahram*, Falk Hildebrand*, Sofia K Forslund, Jennifer L Anderson, Nadejda A Soudzilovskaia, Peter M Bodegom, Johan Bengtsson-Palme, Sten Anslan, Luis Pedro Coelho, Helery Harend, Jaime Huerta-Cepas, Marnix H Medema, Mia R Maltz, Sunil Mundra, Pål Axel Olsson, Mari Pent, Sergei Põlme, Shinichi Sunagawa, Martin Ryberg, Leho Tedersoo, Peer Bork Structure and function of the global topsoil microbiome in Nature (2018) [DOI]
20. Luis Pedro Coelho, Jens Kultima, Paul Costea, Coralie Fournier, Yuanlong Pan, Gail Czarnecki-Maulden, Matthew Hayward, Sofia K. Forslund, Patrick Descombes, Janet Jackson, Qinghong Li, and Peer Bork Similarity of the dog and human gut microbiomes in gene content and response to diet in Microbiome (2018) [DOI]
21. Katri Korpela, Paul Igor Costea, Luis Pedro Coelho, Stefanie Kandels-Lewis, Gonneke Willemsen, Dorret I Boomsma, Nicola Segata, and Peer Bork Selective maternal seeding and environment shape the human gut microbiome in Genome Research (2018) [DOI]
22. Paul I Costea, Luis Pedro Coelho, Shinichi Sunagawa, Robin Munch, Jaime Huerta‐Cepas, Kristoffer Forslund, Falk Hildebrand, Almagul Kushugulova, Georg Zeller, Peer Bork Subspecies in the global human gut microbiome in Molecular Systems Biology (2017) [DOI]
23. Luis Pedro Coelho Jug: Software for parallel reproducible computation in Python in the Journal for Open Research Software (2017) [DOI]
24. Sebastien Colin*, Luis Pedro Coelho*, Shinichi Sunagawa, Chris Bowler, Eric Karsenti, Peer Bork, Rainer Pepperkok, Colomban de Vargas, Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes in eLife (2017) [DOI]
25. Paul I Costea, Georg Zeller, Shinichi Sunagawa, Eric Pelletier, Adriana Alberti, Florence Levenez, Melanie Tramontano, Marja Driessen, Rajna Hercog, Ferris-Elias Jung, Jens Roat Kultima, Matthew R Hayward, Luis Pedro Coelho, Emma Allen-Vercoe, Laurie Bertrand, Michael Blaut, Jillian R M Brown, Thomas Carton, Stéphanie Cools-Portier, Michelle Daigneault, Muriel Derrien, Anne Druesne, Willem M de Vos, B Brett Finlay, Harry J Flint, Francisco Guarner, Masahira Hattori, Hans Heilig, Ruth Ann Luna, Johan van Hylckama Vlieg, Jana Junick, Ingeborg Klymiuk, Philippe Langella, Emmanuelle Le Chatelier, Volker Mai, Chaysavanh Manichanh, Jennifer C Martin, Clémentine Mery, Hidetoshi Morita, Paul W O\'Toole, Céline Orvain, Kiran Raosaheb Patil, John Penders, Søren Persson, Nicolas Pons, Milena Popova, Anne Salonen, Delphine Saulnier, Karen P Scott, Bhagirath Singh, Kathleen Slezak, Patrick Veiga, James Versalovic, Liping Zhao, Erwin G Zoetendal, S Dusko Ehrlich, Joel Dore, and Peer Bork Towards standards for human fecal sample processing in metagenomic studies in Nature Biotechnology (2017) [DOI] [PDF]
26. Paul Igor Costea*, Robin Munch*, Luis Pedro Coelho, Lucas Paoli, Shinichi Sunagawa, Peer Bork metaSNV: A tool for metagenomic strain level analysis in PLoS One (2017) [DOI]
27. Jaime Huerta-Cepas*, Kristoffer Forslund*, Luis Pedro Coelho, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering, and Peer Bork Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper in Molecular Biology & Evolution (2017) [DOI]
28. Janis Rebecca Bedarf, Falk Hildebrand, Luis Pedro Coelho, Shinichi Sunagawa, Mohammad Bahram, Felix Goeser, Peer Bork, Ullrich Wüllner Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA naive Parkinson\'s Disease patients in Genome Medicine (2017) [DOI]

All publications... (Google Scholar profile)

Other News

(See above for papers)

2020

Jan 6-7 I was in Gotenburg, Sweden for the first meeting of the EMBARK project

2019

November 21-27 I was in Sydney, Australia

July 21-25 2019 I was in Basel for ECCB/ISMB 2019

June 21-26 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

Sep 16-19 2018 I was in Heidelberg for the Human Microbiome Conference

Oct 4 2018 I was in Paris talking about single cell approaches

June 26-29: Ireland IHMC2018: International Human Microbiome Consortium

June 14: I taught the Introduction to Python lecture at the Lisbon (Portugal) Machine Learning Summer School

2017

Nov 22-24 I was in Schwarzenber, 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 I was in Copenhagen teaching people how to use ngless at the Microbiome data interpretation workshop (slides here) and giving a scientific talk on my work.

Sept 12-13 I was in Delft 12-13** for a workshop on data-driven cell factory and community design

July 21-25 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

23-25 November 2016 I visited Zurich (Switzerland) for the course Machine learning for bioinformatics and computational biology

7 March 2016 I am now an Associate Editor of the Journal of Open Research Software

22-25 August 2015 Visiting Tallinn (Estonia)

17 August 2015 The project ngless is now open source

16 July 2015 I will be teaching at the Lisbon Machine Learning School

15-17 June 2015 I will be in beautiful San Sebastian (Spain) for a software carpentry workshop (and some holiday time).

March 31-April 2 I attended the International Human Microbiome Congress (IHMC) in Luxembourg

February 2015 I was in Granada for the 2015 Aquatic Sciences Meeting, giving a talk on the 26th on our metagenomics work

November 2014 I am the lead organizer for a software carpentry workshop at EMBL.

September 2014 Keynote talk in Python San Sebastien [Online talk]

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

February 2014 I\'m now a certified Software Carpentry instructor

November 2013 I\'m a member of the programme committee for DILS 2014 (10th International Conference on Data Integration in the Life Sciences)

July 2013 I got a prize in the ICSB Computational Biology Wikipedia Competition for work on the Bioimage Informatics page

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