My google scholar profile

Selected Publications

  1. Luis Pedro Coelho, Joshua D. Kangas, Armaghan Naik, Elvira Osuna-Highley, Estelle Glory-Afshar, Margaret Fuhrman, Ramanuja Simha, Peter B. Berget, Jonathan W. Jarvik, and Robert F. Murphy, Determining the subcellular location of new proteins from microscope images using local features in Bioinformatics, 2013 [DOI] [Video Abstract] [preprint] [mendeley]
  2. Luis Pedro Coelho*, Tao Peng*, and Robert F. Murphy, Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing in Bioinformatics, vol. 26(12), pp. i7-i12 [online version] [mendeley]
  3. Luis Pedro Coelho, Amr Ahmed, Andrew Arnold, Joshua Kangas, Abdul-Saboor Sheikh, Eric P. Xing, William W. Cohen, and Robert F. Murphy, Structured Literature Image Finder: Extracting Information from Text and Images in Biomedical Literature in Lecture Notes in Bioinformatics vol. 6004 [PDF version] [mendeley]
  4. Luis Pedro Coelho, Aabid Shariff, and Robert F. Murphy; Nuclear segmentation in microscope cell images: A hand-segmented dataset and comparison of algorithms ISBI 2009 [online version]
  5. Luis Pedro Coelho and Arlindo Oliveira; Dotted Suffix Trees: A Structure for Approximate Text Indexing SPIRE (2006)

(Annotated list of selected publications)

Full List of Publications

In reverse chronological order

Also available as a BibTeX file.

Peer Reviewed Research Papers

  1. Ana C. Pena, Mafalda R. Pimentel, Helena Manso, Rita Vaz-Drago, Daniel Neves, Francisco Aresta-Branco, Filipa R. Ferreira, Fabien Guegan, Luis Pedro Coelho, Maria Carmo-Fonseca, Nuno L. Barbosa-Morais, Luisa M. Figueiredo Trypanosoma brucei histone H1 inhibits RNA polymerase I transcription and is important for parasite fitness in vivo in Molecular Microbiology [DOI].
  1. Kristoffer Forslund, Shinichi Sunagawa, Luis P. Coelho, Peer Bork, Metagenomic insights into the human gut resistome and the forces that shape it in Bioessays (2014). [DOI] [Preprint]

    One sentence summary: Metagenomics analysis of the microbiome can detect antibiotic resistance genes which correlate with environmental exposures to antibiotics, even if the specific mechanisms whereby this arises still need further study.

  1. 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, and Maria M Mota, Host-cell sensors for Plasmodium activate innate immunity against liver-stage infection in Nature Medicine 20, 47–53 (2014) [Abstract] [DOI]

    One sentence summary: Plasmodium liver-stage infections trigger a type-I Interferon response. Nature Medicine wrote up a short summary as well

  1. 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, Metagenomic species profiling using universal phylogenetic marker genes in Nature Methods 10, 1196–1199 (2013) [Abstract] [DOI] [Preprint]

    One sentence summary: Using marker genes and careful statistics, we can estimate abundance of sequenced and unsequenced microorganims in metagenomics samples.

  1. Luis Pedro Coelho, Joshua D. Kangas, Armaghan Naik, Elvira Osuna-Highley, Estelle Glory-Afshar, Margaret Fuhrman, Ramanuja Simha, Peter B. Berget, Jonathan W. Jarvik, and Robert F. Murphy, Determining the subcellular location of new proteins from microscope images using local features in Bioinformatics, 2013 [DOI] [Video Abstract] [preprint]

    One sentence summary: Recognition of an organelle is a harder problem than recognition of a fluorescent marker, but local features can improve performance.

    Learn more about generalizable classification

  1. Luis Pedro Coelho, Mahotas: Open source software for scriptable computer vision, Journal of Open Research Software, vol. 1 (2013) [DOI] [mendeley].

    One sentence summary: Python is great for computer vision and image processing using mahotas.

  1. Luis Pedro Coelho*, Tao Peng*, and Robert F. Murphy, Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing in Bioinformatics, vol. 26(12), pp. i7-i12 [online version]

    One sentence summary: We can perform subcellular pattern unmixing even when the basis patterns are unknown, which we called unsupervised unmixing. Learn more about unsupervised unmixing

  1. Luis Pedro Coelho, Amr Ahmed, Andrew Arnold, Joshua Kangas, Abdul-Saboor Sheikh, Eric P. Xing, William W. Cohen, and Robert F. Murphy, Structured Literature Image Finder: Extracting Information from Text and Images in Biomedical Literature in Lecture Notes in Bioinformatics vol. 6004 [PDF version] [mendeley]

    Two sentence summary (shared with paper below): SLIF extracts text and images from published scientific literature. Using computer vision [the focus of this paper] and text modeling, we can make inferences and the text and provide a navigation tool for users.

  1. Amr Ahmed, Andrew Arnold, Luis Pedro Coelho, Joshua Kangas, Abdul-Saboor Sheikk, Eric P. Xing, William W. Cohen, Structured Literature Image Finder: Parsing Text and Figures in Biomedical Literature in Web Semantics: Science, Services and Agents on the World Wide Web, 2010 [online version]

    Two sentence summary (shared with paper above): SLIF extracts text and images from published scientific literature. Using computer vision and text modeling [the focus of this paper], we can make inferences and the text and provide a navigation tool for users.

  1. Taraz Buck, Arvind Rao, Luis Pedro Coelho, Margaret Fuhrman, Jonathan W. Jarvik, Peter B. Berget, and Robert F. Murphy; Cell Cycle Dependence of Protein Subcellular Location Inferred from Static, Asynchronous Images EMBC 2009.

    One sentence summary: We can infer cell-cycle (or other) dynamics from static images of cells by looking at many cells and putting them "in order".

  1. Amr Ahmed, Andrew Arnold, Luis Pedro Coelho, Joshua Kangas, Abdul-Saboor Sheikk, Eric P. Xing, William W. Cohen, and Robert F. Murphy; Structured Literature Image Finder, Proceedings of BioLINK (ISMB Special Interest Group 2009).
  1. Luis Pedro Coelho, Aabid Shariff, and Robert F. Murphy; Nuclear segmentation in microscope cell images: A hand-segmented dataset and comparison of algorithms ISBI 2009 [online version]

    One-n-a-half sentence summary: We created a hand-segmented dataset (which we make available to everyone) to test different nuclear segmentation algorithms; a model based method from Lin et al. was deemed the best (note that follow up work on this same dataset has claimed better results). Learn more about my nuclear segmentation project

  1. Luis Pedro Coelho and Robert Murphy; Identifying Subcellular Locations from Images of Unknown Resolution Bioinformatics Research and Development, LNCS, Springer, Volume 13, Vienna, Austria (2008)
  1. Amina Chebira, Luis Pedro Coelho, Aliaksei Sandryhaila, Stephen Lin, William G. Jenkinson, Jeremiah MacSleyne, Christopher Hoffman, Philipp Cuadra, Charles Jackson, Markus Püschel, Jelena Kovacevick; An Adaptive Multiresolution Approach to Fingerprint Recognition, International Conference on Image Processing, (2007) [DOI] [PDF]

    One sentence summary multi-resolution systems achieve good results for fingerprint recognition.

  1. Luis Pedro Coelho and Arlindo Oliveira; Dotted Suffix Trees: A Structure for Approximate Text Indexing SPIRE (2006) [DOI] [PDF]

    One sentence summary: we show how to build an extended suffix tree (the dotted suffix tree) in O(N log N) which supports approximate queries.

Review Articles

  1. Luis Pedro Coelho, Estelle Glory-Afshar, Joshua Kangas, Shannon Quinn, Aabid Shariff, and Robert F. Murphy; Principles of Bioimage Informatics: Focus on machine learning of cell patterns in Lecture Notes in Computer Science [PDF Version].
  2. Aabid Shariff, Joshua Kangas, Luis Pedro Coelho, Shannon Quinn, and Robert F. Murphy; Automated Image Analysis for High Content Screening and Analysis, Journal Biomolecular Screening (2010) [online version] This was the 2013 JBS Authors' Choice Award winner (reflects number of citations throughout 2012).

Technical Reports

  1. Abdul-Saboor Sheikh, Amr Ahmed, Andrew Arnold, Luis Pedro Coelho, Joshua Kangas, Eric P. Xing, William Cohen, Robert F. Murphy; Structured Literature Image Finder: Open Source Software for Extracting and Disseminating Information from Text and Figures in Biomedical Literature, Technical Report, School of Computer Science, Lane Center for Computational Biology, Carnegie Mellon University, October 2009 [PDF version].

    One sentence summary: Everything about SLIF which could not be fit into the papers (because of page limits).

Invited Talks

  1. Proteome-scale analysis and modeling of subcellular location, Luis Pedro Coelho, 4th CeBiTec Symposium BioImaging, Bielefeld, Germany 25-27 August 2009
  2. Unsupervised Mixture Pattern Unmixing, University of Bielefeld International Graduate School of Bioinformatics and Genome Research, July 2008.
  3. Studying the subcellular location space with bioimages and other data modalities, University of Delaware, Computer and Information Sciences Department, September 2011
  4. Bioimage Informatics: Computer Vision for Biology, EMBO Practical Course on Microscopy: from single molecules to animals, Pretoria, November 2011
  5. Learning Subcellular Location from Images and Other Sources of Information, KDBIO (Knowledge Discovery and Bioinformatics) seminar, Lisbon, February 2012
  6. Modeling Subcellular Location from Images and Other Sources of Information, EAO Seminar (Instituto Gulbenkian da Ciência), Oeiras, March 2012
  7. Modeling Subcellular Location from Images and Other Sources of Information, Luxembourg Center for Systems Biology, University of Luxembourg, July 2012

Other Talks

  1. Determining Resolvable Subcellular Location Categories as a Function of Image Resolution, Luis Pedro Coelho and Robert F. Murphy, 24th ISAC Congress, Budapest, May 2008.
  2. Rita Reis and Luis Pedro Coelho Using Theatre to Fight HIV/AIDS in Mozambique, National Conference of the Association for Theatre in Higher Education, Chicago 2011

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