Selected Publications

Kratika Naskulwar, Lourdes Peña-Castillo (2021). sRNARFTarget: A fast machine-learning-based approach for transcriptome-wide sRNA Target Prediction. bioRxiv.

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Ruben Chevez-Guardado, Lourdes Peña-Castillo (2021). Promotech: A general tool for bacterial promoter recognition. bioRxiv.

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Marı́a Esther Nieto-Blázquez, Lourdes Peña-Castillo, Julissa Roncal (2021). Historical biogeography of Caribbean Podocarpus does not support the progression rule. Journal of Biogeography.

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Kratika Naskulwar, Ruben Chevez-Guardado, Lourdes Peña-Castillo (2021). Computational Methods for Elucidating Gene Expression Regulation in Bacteria. Methods Mol Biol.

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Hanieh Marvi Khorasani, Hamid Usefi, Lourdes Peña-Castillo (2020). Detecting ulcerative colitis from colon samples using efficient feature selection and machine learning. Sci Rep.

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Michaelina N Nartey, Lourdes Peña-Castillo, Megan LeGrow, Jules Doré, Sriya Bhattacharya, Andrea Darby-King, Samantha J Carew, Qi Yuan, Carolyn W Harley, John H McLean (2020). Learning-induced mRNA alterations in olfactory bulb mitral cells in neonatal rats. Learn Mem.

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Bonita McCuaig, Lourdes Peña-Castillo, Suzanne C Dufour (2020). Metagenomic analysis suggests broad metabolic potential in extracellular symbionts of the bivalve Thyasira cf. gouldi. Anim Microbiome.

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Bonita McCuaig, Lourdes Peña-Castillo, Suzanne C. Dufour (2020). Metagenomic analysis suggests broad metabolic potential in extracellular symbionts of the bivalve Thyasira cf. gouldi. Animal Microbiome.

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Erik J J Eppenhof, Lourdes Peña-Castillo (2019). Prioritizing bona fide bacterial small RNAs with machine learning classifiers. PeerJ.

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Pranjal Patra, Tatsuo Izawa, Lourdes Pena-Castillo (2018). REPA: Applying Pathway Analysis to Genome-Wide Transcription Factor Binding Data. IEEE/ACM Trans Comput Biol Bioinform.

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Zobayer Alam, Julissa Roncal, Lourdes Peña-Castillo (2018). Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis-idaea. BMC Genomics.

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Marc P Grüll, Lourdes Peña-Castillo, Martin E Mulligan, Andrew S Lang (2017). Genome-wide identification and characterization of small RNAs in Rhodobacter capsulatus and identification of small RNAs affected by loss of the response regulator CtrA. RNA Biol.

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Amit P Desai, Mehdi Razeghin, Oscar Meruvia-Pastor, Lourdes Peña-Castillo (2017). GeNET: a web application to explore and share Gene Co-expression Network Analysis data. PeerJ.

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Amit P. Desai, Lourdes Peña Castillo, Oscar Meruvia Pastor (2017). A Window to Your Smartphone: Exploring Interaction and Communication in Immersive VR with Augmented Virtuality. 14th Conference on Computer and Robot Vision, CRV 2017, Edmonton, AB, Canada, May 16-19, 2017.

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Amit P. Desai, Lourdes Peña Castillo, Oscar Meruvia Pastor (2017). A Window to Your Smartphone: Exploring Interaction and Communication in Immersive VR with Augmented Virtuality. 14th Conference on Computer and Robot Vision, CRV 2017, Edmonton, AB, Canada, May 16-19, 2017.

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Oscar Meruvia-Pastor, Pranjal Patra, Karen Andres, Creina Twomey, Lourdes Peña-Castillo (2016). OMARC: An online multimedia application for training health care providers in the assessment of respiratory conditions. Int J Med Inform.

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Nicole L Ferguson, Lourdes Peña-Castillo, Marcus A Moore, Dawn R D Bignell, Kapil Tahlan (2016). Proteomics analysis of global regulatory cascades involved in clavulanic acid production and morphological development in Streptomyces clavuligerus. J Ind Microbiol Biotechnol.

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Darren D O'Rielly, Mohammed Uddin, Dianne Codner, Michael Hayley, Jiayi Zhou, Lourdes Pena-Castillo, Ahmed A Mostafa, S M Mahmudul Hasan, William Liu, Nigil Haroon, Robert Inman, Proton Rahman (2016). Private rare deletions in SEC16A and MAMDC4 may represent novel pathogenic variants in familial axial spondyloarthritis. Ann Rheum Dis.

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Lourdes Peña-Castillo, Gwenael Badis (2016). Systematic Determination of Transcription Factor DNA-Binding Specificities in Yeast. Methods Mol Biol.

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Lourdes Peña-Castillo, Marc Grüell, Martin E Mulligan, Andrew S Lang (2016). DETECTION OF BACTERIAL SMALL TRANSCRIPTS FROM RNA-SEQ DATA: A COMPARATIVE ASSESSMENT. Pac Symp Biocomput.

Lourdes Peña-Castillo, Ryan G Mercer, Anastasia Gurinovich, Stephen J Callister, Aaron T Wright, Alexander B Westbye, J Thomas Beatty, Andrew S Lang (2014). Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides. BMC Genomics.

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Mark B Stead, Sarah Marshburn, Bijoy K Mohanty, Joydeep Mitra, Lourdes Pena Castillo, Debashish Ray, Harm van Bakel, Timothy R Hughes, Sidney R Kushner (2011). Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays. Nucleic Acids Res.

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Jeffrey Fillingham, Pinay Kainth, Jean-Philippe Lambert, Harm van Bakel, Kyle Tsui, Lourdes Peña-Castillo, Corey Nislow, Daniel Figeys, Timothy R Hughes, Jack Greenblatt, Brenda J Andrews (2009). Two-color cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression. Mol Cell.

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Debashish Ray, Hilal Kazan, Esther T Chan, Lourdes Peña Castillo, Sidharth Chaudhry, Shaheynoor Talukder, Benjamin J Blencowe, Quaid Morris, Timothy R Hughes (2009). Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nat Biotechnol.

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Trevis M Alleyne, Lourdes Peña-Castillo, Gwenael Badis, Shaheynoor Talukder, Michael F Berger, Andrew R Gehrke, Anthony A Philippakis, Martha L Bulyk, Quaid D Morris, Timothy R Hughes (2009). Predicting the binding preference of transcription factors to individual DNA k-mers. Bioinformatics.

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Gwenael Badis, Esther T Chan, Harm van Bakel, Lourdes Pena-Castillo, Desiree Tillo, Kyle Tsui, Clayton D Carlson, Andrea J Gossett, Michael J Hasinoff, Christopher L Warren, Marinella Gebbia, Shaheynoor Talukder, Ally Yang, Sanie Mnaimneh, Dimitri Terterov, David Coburn, Ai Li Yeo, Zhen Xuan Yeo, Neil D Clarke, Jason D Lieb, Aseem Z Ansari, Corey Nislow, Timothy R Hughes (2008). A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell.

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Fiona E Lovegrove, Lourdes Peña-Castillo, W Conrad Liles, Timothy R Hughes, Kevin C Kain (2008). Plasmodium falciparum shows transcriptional versatility within the human host. Trends Parasitol.

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Michael F Berger, Gwenael Badis, Andrew R Gehrke, Shaheynoor Talukder, Anthony A Philippakis, Lourdes Peña-Castillo, Trevis M Alleyne, Sanie Mnaimneh, Olga B Botvinnik, Esther T Chan, Faiqua Khalid, Wen Zhang, Daniel Newburger, Savina A Jaeger, Quaid D Morris, Martha L Bulyk, Timothy R Hughes (2008). Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell.

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Fiona E Lovegrove, Sina A Gharib, Lourdes Peña-Castillo, Samir N Patel, John T Ruzinski, Timothy R Hughes, W Conrad Liles, Kevin C Kain (2008). Parasite burden and CD36-mediated sequestration are determinants of acute lung injury in an experimental malaria model. PLoS Pathog.

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Lourdes Peña-Castillo, Murat Tasan, Chad L Myers, Hyunju Lee, Trupti Joshi, Chao Zhang, Yuanfang Guan, Michele Leone, Andrea Pagnani, Wan Kyu Kim, Chase Krumpelman, Weidong Tian, Guillaume Obozinski, Yanjun Qi, Sara Mostafavi, Guan Ning Lin, Gabriel F Berriz, Francis D Gibbons, Gert Lanckriet, Jian Qiu, Charles Grant, Zafer Barutcuoglu, David P Hill, David Warde-Farley, Chris Grouios, Debajyoti Ray, Judith A Blake, Minghua Deng, Michael I Jordan, William S Noble, Quaid Morris, Judith Klein-Seetharaman, Ziv Bar-Joseph, Ting Chen, Fengzhu Sun, Olga G Troyanskaya, Edward M Marcotte, Dong Xu, Timothy R Hughes, Frederick P Roth (2008). A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol.

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Lourdes Peña-Castillo, Timothy R Hughes (2007). Why are there still over 1000 uncharacterized yeast genes?. Genetics.

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Fiona E Lovegrove, Lourdes Peña-Castillo, Naveed Mohammad, W Conrad Liles, Timothy R Hughes, Kevin C Kain (2006). Simultaneous host and parasite expression profiling identifies tissue-specific transcriptional programs associated with susceptibility or resistance to experimental cerebral malaria. BMC Genomics.

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Lisa Yu, Lourdes Peña Castillo, Sanie Mnaimneh, Timothy R Hughes, Grant W Brown (2006). A survey of essential gene function in the yeast cell division cycle. Mol Biol Cell.

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Maria de Lourdes Peña Castillo (2004). Search improvements in multirelational learning.

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Lourdes Peña Castillo, Stefan Wrobel (2004). A comparative study on methods for reducing myopia of hill-climbing search in multirelational learning. Machine Learning, Proceedings of the Twenty-first International Conference (ICML 2004), Banff, Alberta, Canada, July 4-8, 2004.

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Lourdes Peña Castillo, Stefan Wrobel (2004). A comparative study on methods for reducing myopia of hill-climbing search in multirelational learning. Machine Learning, Proceedings of the Twenty-first International Conference (ICML 2004), Banff, Alberta, Canada, July 4-8, 2004.

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Lourdes Peña Castillo, Stefan Wrobel (2003). Learning Minesweeper with Multirelational Learning. IJCAI-03, Proceedings of the Eighteenth International Joint Conference on Artificial Intelligence, Acapulco, Mexico, August 9-15, 2003.

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Lourdes Peña Castillo, Stefan Wrobel (2003). Learning Minesweeper with Multirelational Learning. IJCAI-03, Proceedings of the Eighteenth International Joint Conference on Artificial Intelligence, Acapulco, Mexico, August 9-15, 2003.

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Lourdes Peña Castillo, Stefan Wrobel (2002). Macro-Operators in Multirelational Learning: A Search-Space Reduction Technique. Machine Learning: ECML 2002, 13th European Conference on Machine Learning, Helsinki, Finland, August 19-23, 2002, Proceedings.

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Lourdes Peña Castillo, Stefan Wrobel (2002). Macro-Operators in Multirelational Learning: A Search-Space Reduction Technique. Machine Learning: ECML 2002, 13th European Conference on Machine Learning, Helsinki, Finland, August 19-23, 2002, Proceedings.

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Maria de Lourdes Peñ̃a-Castillo (2001). Probabilities and simulations in poker..

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Darse Billings, Lourdes Peña Castillo, Jonathan Schaeffer, Duane Szafron (1999). Using Probabilistic Knowledge and Simulation to Play Poker. Proceedings of the Sixteenth National Conference on Artificial Intelligence and Eleventh Conference on Innovative Applications of Artificial Intelligence, July 18-22, 1999, Orlando, Florida, USA.

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Darse Billings, Lourdes Peña Castillo, Jonathan Schaeffer, Duane Szafron (1999). Using Probabilistic Knowledge and Simulation to Play Poker. Proceedings of the Sixteenth National Conference on Artificial Intelligence and Eleventh Conference on Innovative Applications of Artificial Intelligence, July 18-22, 1999, Orlando, Florida, USA.

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