Dotted Suffix Trees A Structure for Approximate Text Indexing. - Luís Pedro Coelho; Arlindo L. Oliveira (SPIRE, 2006)

An Adaptive Multiresolution Approach to Fingerprint Recognition. - Amina Chebira; Luís Pedro Coelho; Aliaksei Sandryhaila; Stephen Lin; William G. Jenkinson; Jeremiah MacSleyne; Christopher Hoffman; Philipp Cuadra; Charles Jackson; Markus Püschel; Jelena Kovacevic (ICIP (1), 2007)

Identifying Subcellular Locations from Images of Unknown Resolution. - Luís Pedro Coelho; Robert F. Murphy (BIRD, 2008)

Structured Literature Image Finder: Extracting Information from Text and Images in Biomedical Literature. - Luís Pedro Coelho; Amr Ahmed 001; Andrew Arnold; Joshua D. Kangas; Abdul-Saboor Sheikh; Eric P. Xing; William W. Cohen; Robert F. Murphy (BioLINK@ISMB/ECCB, 2008)

Principles of Bioimage Informatics: Focus on Machine Learning of Cell Patterns. - Luís Pedro Coelho; Estelle Glory-Afshar; Joshua D. Kangas; Shannon Quinn; Aabid Shariff; Robert F. Murphy (BioLINK@ISMB/ECCB, 2008)

Nuclear Segmentation in Microscope Cell Images: A Hand-Segmented Dataset and Comparison of Algorithms. - Luís Pedro Coelho; Aabid Shariff; Robert F. Murphy (ISBI, 2009)

Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing. - Luís Pedro Coelho; Tao Peng 004; Robert F. Murphy (Bioinform., 2010)

Structured literature image finder: Parsing text and figures in biomedical literature. - Amr Ahmed 001; Andrew Arnold; Luís Pedro Coelho; Joshua D. Kangas; Abdul-Saboor Sheikh; Eric P. Xing; William W. Cohen; Robert F. Murphy (J. Web Semant., 2010)

Mahotas: Open source software for scriptable computer vision - Luís Pedro Coelho (CoRR, 2012)

Determining the subcellular location of new proteins from microscope images using local features. - Luís 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 (Bioinform., 2013)

Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images. - Luís Pedro Coelho; Catarina Pato; Ana Friães; Ariane Neumann; Maren von Köckritz-Blickwede; Mário Ramirez; João André Carriço (Bioinform., 2015)

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

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes. - 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; et al. (Nucleic Acids Res., 2020)

EXPERT: transfer learning-enabled context-aware microbial community classification. - Hui Chong; Yuguo Zha; Qingyang Yu; Mingyue Cheng; Guangzhou Xiong; Nan Wang; Xinhe Huang; Shijuan Huang; Chuqing Sun; Sicheng Wu; Wei-Hua Chen; Luís Pedro Coelho; et al. (Briefings Bioinform., 2022)

SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing. - Shaojun Pan; Xing-Ming Zhao; Luís Pedro Coelho (Bioinform., 2023)

ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics. - Rémi Gschwind; Svetlana Ugarcina perovic; Maja Weiss; Marie Petitjean; Julie Lao; Luís Pedro Coelho; Etienne Ruppé (Nucleic Acids Res., 2023)

For long-term sustainable software in bioinformatics. - Luís Pedro Coelho (PLoS Comput. Biol., 2024)