Lourdes Pena-Castillo

Professor

Memorial University

Biography

Dr. Peña-Castillo is a Professor at the Departments of Biology and Computer Science (jointly appointed) at Memorial University Faculty of Science. Her current main area of research is the application of statistical- and machine learning-based methods to decipher bacterial gene regulation. Throughout her academic career, she has developed and/or applied artificial intelligence or machine learning methods in various areas such as biomedical sciences, games, and augmented virtuality.

Interests

Bioinformatics
Machine Learning
Transcriptomics
Gene regulation
Microbiology

Education

Postdoc in Bioinformatics

University of Toronto, Canada
Ph.D. in Computer Science (Doktoringenieurin)

Otto von Guericke Universitaet Magdeburg, Germany
M.Sc. in Computer Science

University of Alberta, Canada
BSc in Information Systems Engineering

Technological Institute of Monterrey (ITESM), Mexico

Selected Publications

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Historical biogeography of Caribbean Podocarpus does not support the progression rule

Abstract Aim The Progression Rule, that older lineages inhabit older islands and colonize newer ones as they emerge, has seldom been …

Marı́a Esther Nieto-Blázquez, Lourdes Peña-Castillo, Julissa Roncal

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Promotech: A general tool for bacterial promoter recognition

Promoters are genomic regions where the transcription machinery binds to initiate the transcription of specific genes. Computational …

Ruben Chevez-Guardado, Lourdes Peña-Castillo

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sRNARFTarget: A fast machine-learning-based approach for transcriptome-wide sRNA Target Prediction

Bacterial small regulatory RNAs (sRNAs) are key regulators of gene expression in many processes related to adaptive responses. A …

Kratika Naskulwar, Lourdes Peña-Castillo

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Computational Methods for Elucidating Gene Expression Regulation in Bacteria

Research over the past two decades has uncovered an unexpected complexity and intricacy of gene expression regulation in bacteria. …

Kratika Naskulwar, Ruben Chevez-Guardado, Lourdes Peña-Castillo

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Detecting ulcerative colitis from colon samples using efficient feature selection and machine learning

Ulcerative colitis (UC) is one of the most common forms of inflammatory bowel disease (IBD) characterized by inflammation of the …

Hanieh Marvi Khorasani, Hamid Usefi, Lourdes Peña-Castillo

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Learning-induced mRNA alterations in olfactory bulb mitral cells in neonatal rats

In the olfactory bulb, a cAMP/PKA/CREB-dependent form of learning occurs in the first week of life that provides a unique mammalian …

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

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Metagenomic analysis suggests broad metabolic potential in extracellular symbionts of the bivalve Thyasira cf. gouldi

BACKGROUND: Next-generation sequencing has opened new avenues for studying metabolic capabilities of bacteria that cannot be cultured. …

Bonita McCuaig, Lourdes Peña-Castillo, Suzanne C Dufour

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Metagenomic analysis suggests broad metabolic potential in extracellular symbionts of the bivalve Thyasira cf. gouldi

Next-generation sequencing has opened new avenues for studying metabolic capabilities of bacteria that cannot be cultured. Here, we …

Bonita McCuaig, Lourdes Peña-Castillo, Suzanne C. Dufour

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Prioritizing bona fide bacterial small RNAs with machine learning classifiers

Bacterial small (sRNAs) are involved in the control of several cellular processes. Hundreds of putative sRNAs have been identified in …

Erik J J Eppenhof, Lourdes Peña-Castillo

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Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis-idaea

BACKGROUND: Lingonberry (Vaccinium vitis-idaea L.), one of the least studied fruit crops in the Ericaceae family, has a dramatically …

Zobayer Alam, Julissa Roncal, Lourdes Peña-Castillo

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REPA: Applying Pathway Analysis to Genome-Wide Transcription Factor Binding Data

Pathway analysis has been extensively applied to aid in the interpretation of the results of genome-wide transcription profiling …

Pranjal Patra, Tatsuo Izawa, Lourdes Pena-Castillo

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Genome-wide identification and characterization of small RNAs in Rhodobacter capsulatus and identification of small RNAs affected by loss of the response regulator CtrA

Small non-coding RNAs (sRNAs) are involved in the control of numerous cellular processes through various regulatory mechanisms, and in …

Marc P Grüll, Lourdes Peña-Castillo, Martin E Mulligan, Andrew S Lang

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A Window to Your Smartphone: Exploring Interaction and Communication in Immersive VR with Augmented Virtuality

Amit P. Desai, Lourdes Peña Castillo, Oscar Meruvia Pastor

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A Window to Your Smartphone: Exploring Interaction and Communication in Immersive VR with Augmented Virtuality

Amit P. Desai, Lourdes Peña Castillo, Oscar Meruvia Pastor

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GeNET: a web application to explore and share Gene Co-expression Network Analysis data

Gene Co-expression Network Analysis (GCNA) is a popular approach to analyze a collection of gene expression profiles. GCNA yields an …

Amit P Desai, Mehdi Razeghin, Oscar Meruvia-Pastor, Lourdes Peña-Castillo

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OMARC: An online multimedia application for training health care providers in the assessment of respiratory conditions

OBJECTIVES: OMARC, a multimedia application designed to support the training of health care providers for the identification of common …

Oscar Meruvia-Pastor, Pranjal Patra, Karen Andres, Creina Twomey, Lourdes Peña-Castillo

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Private rare deletions in SEC16A and MAMDC4 may represent novel pathogenic variants in familial axial spondyloarthritis

OBJECTIVE: Axial spondyloarthritis (AxSpA) represents a group of inflammatory axial diseases that share common clinical and …

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

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Proteomics analysis of global regulatory cascades involved in clavulanic acid production and morphological development in Streptomyces clavuligerus

The genus Streptomyces comprises bacteria that undergo a complex developmental life cycle and produce many metabolites of importance to …

Nicole L Ferguson, Lourdes Peña-Castillo, Marcus A Moore, Dawn R D Bignell, Kapil Tahlan

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DETECTION OF BACTERIAL SMALL TRANSCRIPTS FROM RNA-SEQ DATA: A COMPARATIVE ASSESSMENT

Small non-coding RNAs (sRNAs) are regulatory RNA molecules that have been identified in a multitude of bacterial species and shown to …

Lourdes Peña-Castillo, Marc Grüell, Martin E Mulligan, Andrew S Lang

Systematic Determination of Transcription Factor DNA-Binding Specificities in Yeast

Understanding how genes are regulated, decoding their “regulome”, is one of the main challenges of the post-genomic era. …

Lourdes Peña-Castillo, Gwenael Badis

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Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides

BACKGROUND: The genus Rhodobacter contains purple nonsulfur bacteria found mostly in freshwater environments. Representative strains of …

Lourdes Peña-Castillo, Ryan G Mercer, Anastasia Gurinovich, Stephen J Callister, Aaron T Wright, Alexander B Westbye, J Thomas Beatty, Andrew S Lang

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Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays

Tiling microarrays have proven to be a valuable tool for gaining insights into the transcriptomes of microbial organisms grown under …

Mark B Stead, Sarah Marshburn, Bijoy K Mohanty, Joydeep Mitra, Lourdes Pena Castillo, Debashish Ray, Harm van Bakel, Timothy R Hughes, Sidney R Kushner

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Two-color cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression

We describe a fluorescent reporter system that exploits the functional genomic tools available in budding yeast to systematically …

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

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Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

Metazoan genomes encode hundreds of RNA-binding proteins (RBPs) but RNA-binding preferences for relatively few RBPs have been well …

Debashish Ray, Hilal Kazan, Esther T Chan, Lourdes Peña Castillo, Sidharth Chaudhry, Shaheynoor Talukder, Benjamin J Blencowe, Quaid Morris, Timothy R Hughes

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Predicting the binding preference of transcription factors to individual DNA k-mers

MOTIVATION: Recognition of specific DNA sequences is a central mechanism by which transcription factors (TFs) control gene expression. …

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

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A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters

The sequence specificity of DNA-binding proteins is the primary mechanism by which the cell recognizes genomic features. Here, we …

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

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Plasmodium falciparum shows transcriptional versatility within the human host

In a recent study published in Nature, Daily et al. profiled parasite gene expression in Plasmodium falciparum infections and …

Fiona E Lovegrove, Lourdes Peña-Castillo, W Conrad Liles, Timothy R Hughes, Kevin C Kain

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Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences

Most homeodomains are unique within a genome, yet many are highly conserved across vast evolutionary distances, implying strong …

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

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Parasite burden and CD36-mediated sequestration are determinants of acute lung injury in an experimental malaria model

Although acute lung injury (ALI) is a common complication of severe malaria, little is known about the underlying molecular basis of …

Fiona E Lovegrove, Sina A Gharib, Lourdes Peña-Castillo, Samir N Patel, John T Ruzinski, Timothy R Hughes, W Conrad Liles, Kevin C Kain

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A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

BACKGROUND: Several years after sequencing the human genome and the mouse genome, much remains to be discovered about the functions of …

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

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