Resumé

A long-form CV is available as a PDF Version.

A narrative version is available as my scientific biography.

Luis Pedro Coelho

Education

Ph.D. in Computational Biology, 2006–2011 Carnegie Mellon University, Pittsburgh.

Dissertation topic: Modeling the Space of Subcellular Location Patterns Using Images and Other Sources of Information, advised by Prof. Robert F. Murphy.

MS in computer science, Instituto Superior Técnico (Technical University Lisbon), 2006

Dissertation topic: Bayesian Network Parameter Estimation Using Noisy Observations or Soft Evidence, advised by Prof. Arlindo Oliveira.

BS in computer science, Instituto Superior Técnico (Technical University Lisbon), 2004. Finished top of my class.

Spent one year at Technical University of Vienna (Austria) as international exchange student.

Postgraduate Experience

Currently (since 2023) Associate Professor and group leader at the Centre for Microbiome Research, Queensland University of Technology

2018-2023 Junior Principal Investigator at Fudan University

2013-2018 Postdoctoral researcher at the European Molecular Biology Laboratory (EMBL) with Peer Bork.

2012 Postdoctoral researcher at the Institute for Molecular Medicine (IMM), Lisbon, with Musa Mhlanga.

Scholarships & Awards

  • QUT Faculty of Health Researcher of the Year (2024)
  • ARC Future Fellowship (2023), to work on the small proteins of the global microbiome
  • Highly Cited Researcher (Cross-field category), since 2022
  • Zhicheng Teaching Award, first prize (Fudan University, 2021)
  • Siebel Scholar 2012.
  • Portugal's Science and Research Foundation Ph.D. scholarship 2007-2011
  • Outstanding Research Accomplishment Award for Research Excellence in the Joint CMU-University of Pittsburgh Ph.D. Program in Computational Biology (2007).
  • Academic Excellence Diploma of Merit from Instituto Superior Técnico for academic excellence in the academic year 1999/2000.
  • Award for Academic Excellence in the Joint CMU-University of Pittsburgh Ph.D. Program in Computational Biology (2007).
  • Fulbright Fellowship for Ph.D. Study in the US, 2006/07.
  • Portugal's Science and Research Foundation research scholarship from December 2004 through July 2006.

Selected Publications

  1. Célio Dias Santos-Júnior*, Marcelo D.T. Torres*, Yiqian Duan, Álvaro Rodríguez del Río, Thomas S.B. Schmidt, Hui Chong, Anthony Fullam, Michael Kuhn, Chengkai Zhu, Amy Houseman, Jelena Somborski, Anna Vines, Xing-Ming Zhao, Peer Bork, Jaime Huerta-Cepas, Cesar de la Fuente-Nunez⁺, Luis Pedro Coelho⁺ Discovery of antimicrobial peptides in the global microbiome with machine learning in Cell (2024).
  2. Yiqian Duan, Célio Dias Santos-Júnior, Thomas Sebastian Schmidt, Anthony Fullam, Breno L. S. de Almeida, Chengkai Zhu, Michael Kuhn, Xing-Ming Zhao⁺, Peer Bork, Luis Pedro Coelho⁺ A catalog of small proteins from the global microbiome in Nature Communications (2024).
  3. Luis Pedro Coelho, Renato Alves, Álvaro Rodríguez del Río, Pernille Neve Myers, Carlos P. Cantalapiedra, Joaquín Giner-Lamia, Thomas Sebastian Schmidt, Daniel R. Mende, Askarbek Orakov, Ivica Letunic, Falk Hildebrand, Thea Van Rossum, Sofia K. Forslund, Supriya Khedkar, Oleksandr M. Maistrenko, Shaojun Pan, Longhao Jia, Pamela Ferretti, Shinichi Sunagawa, Xing-Ming Zhao, Henrik Bjørn Nielsen, Jaime Huerta-Cepas⁺, Peer Bork⁺ Towards the biogeography of prokaryotic genes in Nature (2022) [Open Access version].
  4. Shaojun Pan, Chengkai Zhu, Xing-Ming Zhao⁺, and Luis Pedro Coelho ⁺ A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments in Nature Communications (2022).
  5. Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, and Peer Bork NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language in Microbiome (2019)
  6. 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]
  7. Shinichi Sunagawa,* Luis Pedro Coelho*, Samuel Chaffron*, Jens Roat Kultima, Karine Labadie, Guillem Salazar, Bardya Djahanschiri, Georg Zeller, Daniel R. Mende, Adriana Alberti, Francisco M. Cornejo-Castillo, Paul I. Costea, Corinne Cruaud, Francesco d'Ovidio, Stefan Engelen, Isabel Ferrera, Josep M. Gasol, Lionel Guidi, Falk Hildebrand, Florian Kokoszka, Cyrille Lepoivre, Gipsi Lima-Mendez, Julie Poulain, Bonnie T. Poulos, Marta Royo-Llonch, Hugo Sarmento, Sara Vieira-Silva, Céline Dimier, Marc Picheral, Sarah Searson, Stefanie Kandels-Lewis, Tara Oceans coordinators, Chris Bowler, Colomban de Vargas, Gabriel Gorsky, Nigel Grimsley, Pascal Hingamp, Daniele Iudicone, Olivier Jaillon, Fabrice Not, Hiroyuki Ogata, Stephane Pesant, Sabrina Speich, Lars Stemmann, Matthew B. Sullivan, Jean Weissenbach, Patrick Wincker, Eric Karsenti, Jeroen Raes, Silvia G. Acinas, Peer Bork, Structure and function of the global ocean microbiome in Science (2015) [DOI]

See also my full annotated list of publications or my full length CV.

Languages

  • Bilingual: Portuguese and English
  • Fluent oral and good written German (attended a German-speaking school, grades 5 through 12; spent a year at the Technical University of Vienna).
  • Fluent oral and good written French
  • Basic knowledge of Spanish and Luxembourgish

Teaching

Designed and taught a course in computer programming for the sciences (Programming for Scientists). This was a semester-long course taught at Carnegie Mellon University in Spring 2009 (as a student-taught course). In 2012, I taught a shortened version of this at IMM as a two-and-a-half day workshop. I am a certified Software Carpentry instructor

Teaching Assistant for Decision Support Systems at Technical University of Lisbon (Spring 2005). Co-designed and co-taught a Computer Initiation Course for Adults in a social housing project (pro-bono). Teaching Assistant for Laboratory Methods for Computational Biology at Carnegie Mellon University (Spring 2008).

Local Committee for Portuguese-American Postgraduate Society National Forum

I headed the local organising committee for the 2010 edition of this annual event. It took place in Pittsburgh and included, as speakers, cabinet-level Portuguese government officials, renowned researchers, artists, as well as participants from all around the US.

Open Source Programming

I publish and maintain many open source projects of interest to my research, including SemiBin (metagenomic binning), NGLess (a domain-specific language for sequence processing), Jug (parallel reproducible computation), and mahotas, a computer vision library in Python.

See my software page for a summary, or the full list of projects in my github page.