Selected Publications
- 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]
- 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]
- 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]
- Luis Pedro Coelho and Arlindo Oliveira; Dotted Suffix Trees: A Structure for Approximate Text Indexing SPIRE (2006)
Submitted or In Preparation
- 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, Local Features for Determining Subcellular Location with Better Generalization (submitted)
- Luis Pedro Coelho, Shannon Quinn, Hagit Shatkay and Robert F. Murphy Waldo: A Python Library for Unifying Location Databases (submitted)
- Luis Pedro Coelho, mahotas: Open source software for scriptable computer vision, Journal of Open Research Software (forthcoming) [preprint].
- Luis Pedro Coelho, Joshua D. Kangas, Armaghan Naik, Elvira Osuna-Highley, Estelle Glory-Afshar, Margaret Fuhrman, Ramanuja Simha, Peter B. Berget, Jonathan W. Jarvik, Hagit Shatkay, and Robert F. Murphy, Loto: Location Topics for Modeling Subcellular Location Space in Mammalian Cells (in preparation)
Full List of Publications
In chronological order
Also available as a BibTeX file.
Peer Reviewed Journal Articles
- 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]
- 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]
- 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]
Review Articles
- 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].
- 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).
Peer Reviewed Conference Papers
- Luis Pedro Coelho and Arlindo Oliveira; Dotted Suffix Trees: A Structure for Approximate Text Indexing SPIRE (2006)
- 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)
- 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)
- 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).
- 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]
- 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.
Technical Reports
- 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].
Invited Talks
- Proteome-scale analysis and modeling of subcellular location, Luis Pedro Coelho, 4th CeBiTec Symposium BioImaging, Bielefeld, Germany 25-27 August 2009
- Unsupervised Mixture Pattern Unmixing, University of Bielefeld International Graduate School of Bioinformatics and Genome Research, July 2008.
- Studying the subcellular location space with bioimages and other data modalities, University of Delaware, Computer and Information Sciences Department, September 2011
- Bioimage Informatics: Computer Vision for Biology, EMBO Practical Course on Microscopy: from single molecules to animals, Pretoria, November 2011
- Learning Subcellular Location from Images and Other Sources of Information, KDBIO (Knowledge Discovery and Bioinformatics) seminar, Lisbon, February 2012
- Modeling Subcellular Location from Images and Other Sources of Information, EAO Seminar (Instituto Gulbenkian da Ciência), Oeiras, March 2012
- Modeling Subcellular Location from Images and Other Sources of Information, Luxembourg Center for Systems Biology, University of Luxembourg, July 2012
Other Talks
- Determining Resolvable Subcellular Location Categories as a Function of Image Resolution, Luis Pedro Coelho and Robert F. Murphy, 24th ISAC Congress, Budapest, May 2008.
- 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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