About
Professor
Biological Sciences
Undergraduate Program Director
Bioinformatics and Computational Biology
Member, Center for Stem Cell Biology & Regenerative Medicine
University of Maryland, School of Medicine
Member, Marlene and Stewart Greenebaum Comprehensive Cancer Center
University of Maryland, Medical System
Research interests
The Lobo Lab aims to understand the regulation and mechanisms of biological growth, shape, and pattern formation with a systems biology approach. We combine both molecular and computational methods to gain a mechanistic understanding of development and regeneration, find personalized treatments for cancer, and streamline regulatory designs in synthetic biology. We have developed new techniques for the acquisition and formalization of microscopy spatial data, the formulation of mechanistic models of genetic, metabolic, and signaling networks, and high-performance machine learning methods for inferring such models. We combine these computational methods with molecular assays at the bench for obtaining quantitative spatial and dynamic data, such as gene expression and morphological outcomes, and for prediction validation including genetic, surgical, and pharmacological perturbations and the engineering of synthetic circuits. This ambitious research plan will have a long-term payoff for the streamline of our ability to infer and design dynamic mechanisms, which will be essential for advancing fundamental understanding in biology and developing new medical and industrial applications.
Teaching interests
BIOL 737 - Research Seminar in Bioinformatics and Computational Biology
BIOL 615 - Systems Biology (graduate)
BIOL 415 - Systems Biology
BIOL 313 - Introduction to Bioinformatics and Computational Biology
Education
- Postdoc, Developmental, Regenerative, and Cancer Biology — Tufts University (2015)
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Ph D, Computer Science
— University of Malaga (2010) Evolutionary development based on genetic regulatory models for behavior-finding
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MS, Computer Science and Artificial Intelligence
— University of Malaga (2007) Automated design of complex structures using bio-inspired genetic methods
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BS, Computer Science and Computer Engineering
— University of Seville (2005) A repository of software components specified by functionality
Publications
- Emergent stable tissue shapes from the regulatory feedback between morphogens and cell growth 2025
- Predicting the regulatory dynamics of AML disease progression from longitudinal multi-modal clinical data 2025
- FROG analysis ensures the reproducibility of genome scale metabolic models 2024
- Mechanistic regulation of planarian shape during growth and degrowth 2024
- Automatic design of gene regulatory mechanisms for spatial pattern formation 2024
- mergem: merging, comparing, and translating genome-scale metabolic models using universal identifiers 2024
- Formalizing Phenotypes of Regeneration 2022
- Automatic Generation of Interactive Multidimensional Phase Portraits 2022
- In Situ Probe and Inhibitory RNA Synthesis Using Streamlined Gene Cloning with Gibson Assembly 2022
- Inference of Dynamic Spatial GRN Models with Multi-GPU Evolutionary Computation 2021
- Computational systems biology of morphogenesis 2021
- Kinetic modeling of microbial growth, enzyme activity, and gene deletions: an integrated model of β-glucosidase function in Cellvibrio japonicus 2020
- Fluxer: a web application to compute, analyze, and visualize genome-scale metabolic flux networks 2020
- Curation and annotation of planarian gene expression patterns with segmented reference morphologies 2020
- Continuous dynamic modeling of regulated cell adhesion: sorting, intercalation, and involution 2019
- Cross-inhibition of Turing patterns explains the self-organized regulatory mechanism of planarian fission 2019
- Modeling regenerative processes with Membrane Computing 2017
- Discovering novel phenotypes with automatically inferred dynamic models: a partial melanocyte conversion in Xenopus 2017
- Computing a Worm: Reverse-Engineering Planarian Regeneration 2017
- Computational discovery and in vivo validation of hnf4 as a regulatory gene in planarian regeneration 2016
- Physiological controls of large-scale patterning in planarian regeneration: a molecular and computational perspective on growth and form 2016
- Artificial neural networks as models of robustness in development and regeneration: stability of memory during morphological remodeling 2016
- MoCha: Molecular Characterization of Unknown Pathways 2016
- A dynamic architecture of life 2015
- Gap Junctional Blockade Stochastically Induces Different Species-Specific Head Anatomies in Genetically Wild-Type Girardia dorotocephala Flatworms 2015
- Serotonergic regulation of melanocyte conversion: A bioelectrically regulated network for stochastic all-or-none hyperpigmentation 2015