Complete List of Publications

In reverse chronological order

Recency

First/last Author (including co-first & co-last)

49. Drivers and Determinants of Strain Dynamics Following Faecal Microbiota Transplantation by Thomas SB Schmidt, Simone S Li, Oleksandr M Maistrenko, Wasiu Akkani, Luis Pedro Coelho, Sibasish Dolai, Anthony Fullam, Anna Glazek, Rajna Hercog, Hilde Herrema in bioRxiv (2021).

48. SemiBin: Incorporating information from reference genomes with semi-supervised deep learning leads to better metagenomic assembled genomes (MAGs) by Shaojun Pan, Chengkai Zhu, Xing-Ming Zhao, Luis Pedro Coelho in bioRxiv (2021).

47. metaMIC: reference-free Misassembly Identification and Correction of de novo metagenomic assemblies by Senying Lai, Shaojun Pan, Luis Pedro Coelho, Wei-hua Chen, Xing-Ming Zhao in bioRxiv (2021).

46. MACREL: antimicrobial peptide screening in genomes and metagenomes by Célio Dias Santos-Junior, Shaojun Pan, Xing-Ming Zhao, Luis Pedro Coelho in PeerJ (2020).

45. GUNC: detection of chimerism and contamination in prokaryotic genomes by Askarbek Orakov, Anthony Fullam, Luis Pedro Coelho, Supriya Khedkar, Damian Szklarczyk, Daniel R Mende, Thomas SB Schmidt, Peer Bork in Genome Biology (2021).

44. Metagenomic assessment of the global diversity and distribution of bacteria and fungi by Mohammad Bahram, Tarquin Netherway, Clémence Frioux, Pamela Ferretti, Luis Pedro Coelho, Stefan Geisen, Peer Bork, Falk Hildebrand in Environmental Microbiology (2021).

43. Voices of the new generation: science in a state of benign confusion by Luis Pedro Coelho in Nature Reviews Molecular Cell Biology (2020).

42. Statin therapy is associated with lower prevalence of gut microbiota dysbiosis by 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 in Nature (2020).

41. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity by Oleksandr M Maistrenko, Daniel R Mende, Mechthild Luetge, Falk Hildebrand, Thomas SB Schmidt, Simone S Li, João F Matias Rodrigues, Christian von Mering, Luis Pedro Coelho, Jaime Huerta-Cepas, Shinichi Sunagawa, Peer Bork in The ISME Journal (2020).

40. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome by 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, Margaux 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, Shinichi Sunagawa in Cell (2019).

39. Global trends in marine plankton diversity across kingdoms of life by 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 in Cell (2019).

38. proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes by Daniel R Mende, Ivica Letunic, Oleksandr M Maistrenko, Thomas SB 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 in Nucleic acids research (2020).

37. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer by Jakob Wirbel, Paul Theodor Pyl, Ece Kartal, Konrad Zych, Alireza Kashani, Alessio Milanese, Jonas S Fleck, Anita Y Voigt, Albert Palleja, Ruby 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 in Nature medicine (2019).

36. Microbial abundance, activity and population genomic profiling with mOTUs2 by 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 in Nature Communications (2019).

35. Community‐Level Responses to Iron Availability in Open Ocean Planktonic Ecosystems by Luigi Caputi, Quentin Carradec, Damien Eveillard, Amos Kirilovsky, Eric Pelletier, Juan J Pierella Karlusich, Fabio Rocha Jimenez Vieira, Emilie Villar, Samuel Chaffron, Shruti Malviya, Eleonora Scalco, Silvia G. Acinas, Adriana Alberti, Jean-Marc Aury, Anne-Sophie Benoiston, Alexis Bertrand, Tristan Biard, Lucie Bittner, Martine Boccara, Jennifer R. Brum, Christophe Brunet, Greta Busseni, Anna Carratalà, Hervé Claustre, Luis Pedro Coelho, Sébastien Colin, Salvatore D'Aniello, Corinne Da Silva, Marianna Del Core, Hugo Doré, Stéphane Gasparini, Florian Kokoszka, Jean-Louis Jamet, Christophe Lejeusne, Cyrille Lepoivre, Magali Lescot, Gipsi Lima-Mendez, Fabien Lombard, Julius Lukeš, Nicolas Maillet, Mohammed-Amin Madoui, Elodie Martinez, Maria Grazia Mazzocchi, Mario B. Néou, Javier Paz-Yepes, Julie Poulain, Simon Ramondenc, Jean-Baptiste Romagnan, Simon Roux, Daniela Salvagio Manta, Remo Sanges, Sabrina Speich, Mario Sprovieri, Shinichi Sunagawa, Vincent Taillandier, Atsuko Tanaka, Leila Tirichine, Camille Trottier, Julia Uitz, Alaguraj Veluchamy, Jana Veselá, Flora Vincent, Sheree Yau, Stefanie Kandels-Lewis, Sarah Searson, Céline Dimier, Marc Picheral, Tara Oceans Coordinators, Peer Bork, Emmanuel Boss, Colomban de Vargas, Michael J. Follows, Nigel Grimsley, Lionel Guidi, Pascal Hingamp, Eric Karsenti, Paolo Sordino, Lars Stemmann, Matthew B. Sullivan, Alessandro Tagliabue, Adriana Zingone, Laurence Garczarek, Fabrizio d'Ortenzio, Pierre Testor, Fabrice Not, Maurizio Ribera d'Alcalà, Patrick Wincker, Chris Bowler, Daniele Iudicone in Global Biogeochemical Cycles (2019).

34. Extensive transmission of microbes along the gastrointestinal tract by Thomas Sebastian Benedikt Schmidt, Matthew Robert Hayward, Luis Pedro Coelho, Simone S Li, Paul Igor Costea, Anita Yvonne Voigt, Jakob Wirbel, Oleksandr M Maistrenko, Renato JC Alves, Emma Bergsten, Carine de Beaufort, Iradj Sobhani, Anna Heintz-Buschart, Shinichi Sunagawa, Georg Zeller, Paul Wilmes, Peer Bork in eLife (2019).

33. Recovery of gut microbiota of healthy adults following antibiotic exposure by 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 in Nature microbiology (2018).

32. Structure and function of the global topsoil microbiome by 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 in Nature (2018).

31. NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language by Luis Pedro Coelho, Renato Alves, Paulo Monteiro, Jaime Huerta-Cepas, Ana Teresa Freitas, Peer Bork in Microbiome (2019).

30. Similarity of the dog and human gut microbiomes in gene content and response to diet by Luis Pedro Coelho, Jens Roat Kultima, Paul Igor Costea, Coralie Fournier, Yuanlong Pan, Gail Czarnecki-Maulden, Matthew Robert Hayward, Sofia K Forslund, Thomas Sebastian Benedikt Schmidt, Patrick Descombes, Janet R. Jackson, Qinghong Li, Peer Bork in Microbiome (2018).

29. Selective maternal seeding and environment shape the human gut microbiome by Katri Korpela, Paul Igor Costea, Luis Pedro Coelho, Stefanie Kandels-Lewis, Gonneke Willemsen, Dorret I Boomsma, Nicola Segata, Peer Bork in Genome Research (2018).

28. Subspecies in the global human gut microbiome by Paul I Costea, Luis Pedro Coelho, Shinichi Sunagawa, Robin Munch, Jaime Huerta‐Cepas, Kristoffer Forslund, Falk Hildebrand, Almagul Kushugulova, Georg Zeller, Peer Bork in Molecular Systems Biology (2017).

27. Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes by Sebastien Colin, Luis Pedro Coelho, Shinichi Sunagawa, Chris Bowler, Eric Karsenti, Peer Bork, Rainer Pepperkok, Colomban de Vargas in eLife (2017).

26. Jug: Software for Parallel Reproducible Computation in Python by Luis Pedro Coelho in Journal of Open Research Software (2017).

25. Towards standards for human fecal sample processing in metagenomic studies by 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, Peer Bork in Nature biotechnology (2017).

24. metaSNV: A tool for metagenomic strain level analysis by Paul Igor Costea, Robin Munch, Luis Pedro Coelho, Lucas Paoli, Shinichi Sunagawa, Peer Bork in PloS one (2017).

23. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper by Jaime Huerta-Cepas, Kristoffer Forslund, Luis Pedro Coelho, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering, Peer Bork in Mol Biol Evol (2017).

22. Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients by Janis R Bedarf, Falk Hildebrand, Luis P Coelho, Shinichi Sunagawa, Mohammad Bahram, Felix Goeser, Peer Bork, Ullrich Wüllner in Genome medicine (2017).

21. MOCAT2: a metagenomic assembly, annotation and profiling framework by Jens Roat Kultima, Luis Pedro Coelho, Kristoffer Forslund, Jaime Huerta-Cepas, Simone S Li, Marja Driessen, Anita Yvonne Voigt, Georg Zeller, Shinichi Sunagawa, Peer Bork in Bioinformatics (2016).

20. Plankton networks driving carbon export in the oligotrophic ocean by Lionel Guidi, Samuel Chaffron, Lucie Bittner, Damien Eveillard, Abdelhalim Larhlimi, Simon Roux, Youssef Darzi, Stephane Audic, Léo Berline, Jennifer Brum in Nature (2016).

19. Gene expression changes in the salivary glands of Anopheles coluzzii elicited by Plasmodium berghei infection by Renato Pinheiro-Silva, Lara Borges, Luis Pedro Coelho, Alejandro Cabezas-Cruz, James J Valdés, Virgilio Do Rosario, José De La Fuente, Ana Domingos in Parasites & vectors (2015).

18. Structure and function of the global ocean microbiome by 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 in Science (2015).

17. Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images by Luis Pedro Coelho, Catarina Pato, Ana Friães, Ariane Neumann, Maren von Köckritz-Blickwede, Mário Ramirez, Joao Andre Carrico in Bioinformatics (2015).

16. Trypanosoma brucei histone H1 inhibits RNA polymerase I transcription and is important for parasite fitness in vivo by Ana C Pena, Mafalda R Pimentel, Helena Manso, Rita Vaz‐Drago, Daniel Pinto‐Neves, Francisco Aresta‐Branco, Filipa Rijo‐Ferreira, Fabien Guegan, Luis Pedro Coelho, Maria Carmo‐Fonseca, Nuno L. Barbosa-Morais, Luisa M. Figueiredo in Molecular microbiology (2014).

15. Metagenomic insights into the human gut resistome and the forces that shape it by Kristoffer Forslund, Shinichi Sunagawa, Luis P Coelho, Peer Bork in BioEssays (2014).

14. Host-cell sensors for Plasmodium activate innate immunity against liver-stage infection by Peter Liehl, Vanessa Zuzarte-Luís, Jennie Chan, Thomas Zillinger, Fernanda Baptista, Daniel Carapau, Madlen Konert, Kirsten K Hanson, Céline Carret, Caroline Lassnig, Mathias Müller, Ulrich Kalinke, Mohsan Saeed, Angelo Ferreira Chora, Douglas T Golenbock, Birgit Strobl, Miguel Prudêncio, Luis P Coelho, Stefan H Kappe, Giulio Superti-Furga, Andreas Pichlmair, Ana M Vigário, Charles M Rice, Katherine A Fitzgerald, Winfried Barchet, Maria M Mota in Nature medicine (2014).

13. Metagenomic species profiling using universal phylogenetic marker genes by Shinichi Sunagawa, Daniel R Mende, Georg Zeller, Fernando Izquierdo-Carrasco, Simon A Berger, Jens Roat Kultima, Luis Pedro Coelho, Manimozhiyan Arumugam, Julien Tap, Henrik Bjørn Nielsen, Simon Rasmussen, Søren Brunak, Oluf Pedersen, Francisco Guarner, Willem M de Vos, Jun Wang, Junhua Li, Joël Doré, S Dusko Ehrlich, Alexandros Stamatakis, Peer Bork in Nature methods (2013).

12. Determining the subcellular location of new proteins from microscope images using local features by Luis Pedro Coelho, Joshua D Kangas, Armaghan W Naik, Elvira Osuna-Highley, Estelle Glory-Afshar, Margaret Fuhrman, Ramanuja Simha, Peter B Berget, Jonathan W Jarvik, Robert F Murphy in Bioinformatics (2013).

11. Mahotas: Open source software for scriptable computer vision by Luis Pedro Coelho in Journal of Open Research Software (2013).

10. Dotted suffix trees: a structure for approximate text indexing by Luis Coelho, Arlindo Oliveira in String Processing and Information Retrieval (2006).

9. Identifying Subcellular Locations from Images of Unknown Resolution by Luis Pedro Coelho, Robert F Murphy in International Conference on Bioinformatics Research and Development (2008).

8. Structured literature image finder: extracting information from text and images in biomedical literature by Luis Pedro Coelho, Amr Ahmed, Andrew Arnold, Joshua Kangas, Abdul-Saboor Sheikh, Eric P Xing, William W Cohen, Robert F Murphy in Linking Literature, Information, and Knowledge for Biology (2010).

7. Structured literature image finder: Parsing text and figures in biomedical literature by Amr Ahmed, Andrew Arnold, Luis Pedro Coelho, Joshua Kangas, Abdul-Saboor Sheikh, Eric Xing, William Cohen, Robert F Murphy in Web Semantics: Science, Services and Agents on the World Wide Web (2010).

6. Cell cycle dependence of protein subcellular location inferred from static, asynchronous images by Taráz E Buck, Arvind Rao, Luis Pedro Coelho, Margaret H Fuhrman, Jonathan W Jarvik, Peter B Berget, Robert F Murphy in 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (2009).

5. Automated image analysis for high-content screening and analysis by Aabid Shariff, Joshua Kangas, Luis Pedro Coelho, Shannon Quinn, Robert F Murphy in Journal of biomolecular screening (2010).

4. Principles of bioimage informatics: focus on machine learning of cell patterns by Luis Pedro Coelho, Estelle Glory-Afshar, Joshua Kangas, Shannon Quinn, Aabid Shariff, Robert F Murphy in Linking Literature, Information, and Knowledge for Biology (2010).

3. Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing by Luis Pedro Coelho, Tao Peng, Robert F Murphy in Bioinformatics (2010).

2. An adaptive multiresolution approach to fingerprint recognition by Amina Chebira, Luis P Coelho, Aliaksei Sandryhaila, Stephen Lin, William G Jenkinson, Jeremiah MacSleyne, Christopher Hoffman, Philipp Cuadra, Charles Jackson, Markus Püschel in Image Processing, 2007. ICIP 2007. IEEE International Conference on (2007).

1. Nuclear segmentation in microscope cell images: a hand-segmented dataset and comparison of algorithms by Luis Pedro Coelho, Aabid Shariff, Robert F Murphy in Biomedical Imaging: From Nano to Macro, 2009. ISBI09. IEEE International Symposium on (2009).


Copyright (c) 2009-2021. Luis Pedro Coelho and other group members. All rights reserved.