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Paola Vera-Licona, PhDAssistant Professor/Basic Science
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- Education & Training
- Committees & Organizations
- Research
- Research Opportunities
- Lab Rotations
- Publications
- Presentations
Education
Post-Graduate Training
Awards
| Degree | Institution | Major |
|---|---|---|
| BS | Universidad Nacional Autonoma de Mexico (UNAM) | Mathematics |
| MS | Virginia Polytechnic Institute and State University | Mathematics |
| PhD | Virginia Polytechnic Institute and State University | Mathematics |
Post-Graduate Training
| Training | Institution | Specialty |
|---|---|---|
| Postdoctoral | Rutgers University | Postdoctoral Research Fellow The Center for Discrete Mathematics and Theoretical Computer Science (DIMACS), The Biology at the Interface with the Mathematical and Physical Sciences (BioMaPS) Institute and the Mathematics Department. Project: Development and application of algorithms for the reverse-engineering of biological networks. |
| Postdoctoral | Institute Curie | Postdoctoral Research Fellow “Bioinformatics and Computational Systems Biology of Cancer”. Research collaboration between Institute Curie and French pharmaceutical company Servier for the discovery and development of triple negative breast cancer drug therapies. |
Awards
| Name of Award/Honor | Awarding Organization |
|---|---|
| Winner at the 2022 Interstellar Initiative Alumni Program Competition | New York Academy of Sciences & Japan Agency for Medical Research and Devel. |
| Outstanding Team Presentation at the 2017 Interstellar Initiative for Early Career Investigators | Japan Agency for Medical Research Development &New York Academy of Sciences |
| 2010 International Challenge “The DREAM 5 Network Inference". Honorable Mention, 2nd place, Challenge 4, Category In-Silico. | The DREAM (Dialogue for Reverse Eng Assessments and Methods) Initiative |
| Scholarship to pursue master’s degree in Mathematics at Virginia Polytechnic Institute and State University (August 2001- June 2003). | National Council for Science and Technology (CONACYT) |
| Scholarship for the completion of undergraduate thesis project (September 2000-July 2001). UNAM, Mexico. | General Directorate for Affairs of Academic Personnel, UNAM |
| Scholarship to pursue research internship at the Mathematics Institute, campus Morelia, UNAM, Mexico, Summer 1998. | National Council for Science and Technology (CONACYT) |
| Scholarship to pursue a summer research internship at the School of Marine Sciences and Limnology, Mazatlan, UNAM, Mexico, Summer 1996. | Scientific Research Coordination, UNAM |
| Nationwide honor award for outstanding pre-college performance with highest overall grades. Mexico, September 1996. | Universidad Nacional Autonoma de Mexico (UNAM) |
| Scholarship to pursue a summer research internship at the Chemistry School, UNAM. Mexico, Summer 1995. | Scientific Research Coordination, UNAM |
| Name & Description | Category | Role | Type | Scope | Start Year | End Year |
|---|---|---|---|---|---|---|
| The 22nd International Conference of Systems Biology (ICSB 2023) | Workshop/Conference | Organizing Committee and Chair of Miscellaneous Section | External | International | 2023 | 2023 |
| Nature Communications Journal | Professional/Scientific Journal | Reviewer | External | International | 2022 | 2022 |
| NCI P01 Program Project | Study Section | Reviewer | External | National | 2021 | 2021 |
| Nature | Professional/Scientific Journal | Reviewer | External | International | 2021 | 2022 |
| NSF Graduate Research Fellowship Program (GRFP) | Study Section | Reviewer | External | National | 2020 | 2020 |
| Panel reviewer at the 2020 NSF Graduate Research Fellowship Program (GRFP) Competition | Study Section | Reviewer | External | National | 2020 | 2020 |
| Neurogenesis and Cell Fate (NCF) NIH Study Section | Study Section | Reviewer | External | National | 2019 | 2019 |
| 21st International Conference for Systems Biology 2020 | Workshop/Conference | Member of Organizing Committee | External | International | 2019 | 2020 |
| NetSci 2017: International School and Conference on Network Science | Advisory Committee | Program Committee Member | External | International | 2017 | 2017 |
| 18th International Congress of Animal Reproduction: ICAR | Advisory Committee | Scientific program committee member | External | International | 2016 | 2016 |
| PLOS Computational Biology | Editorial Board | Guest Editor | External | International | 2016 | |
| ACSB 2015: A Conference on Algebraic and Combinatorial Approaches in Systems Biology | Workshop/Conference | Organizer | External | National | 2015 | 2015 |
| 12th Conference on Computational Methods in Systems Biology | Advisory Committee | Reviewer | External | International | 2014 | 2014 |
| NIH/NIGMS Panel Review | Professional/Scientific Organization | Panel Reviewer | External | National | 2014 | 2014 |
| Institute for Systems Genomics Networking Workshop | Other | Member of the organizing committee | UConn Health | University | 2014 | 2014 |
| Workshop "Software Development on Parameter Estimation for Boolean models of biological networks". The Center for Discrete Mathematics and Theoretical Computer Science (DIMACS), New Jersey, USA | Workshop/Conference | Organizer | External | National | 2009 | 2009 |
| Workshop "Model your genes the mathematical way II". The Institute for Advance Learning and Research (IARL), VA USA | Workshop/Conference | Co-director | External | National | 2006 | 2006 |
| The Society of Industrial and Applied Mathematics (SIAM) Student Chapter at Virginia Tech | Professional/Scientific Organization | President | External | University | 2005 | 2007 |
| Association for Women in Mathematics (AWM) Mentor Network | Professional/Scientific Organization | Mentor | External | National | 2005 | |
| IEE/ACM Transactions on Computational Biology and Bioinformatics journal | Professional/Scientific Journal | Reviewer | External | International | ||
| PLOS Computational Biology journal | Professional/Scientific Journal | Reviewer | External | International | ||
| Journal of Mathematical Biology | Professional/Scientific Journal | Reviewer | External | International | ||
| Journal of Theoretical Biology | Professional/Scientific Journal | Reviewer | External | International | ||
| IET Systems Biology journal | Professional/Scientific Journal | Reviewer | External | International | ||
| Biosystems journal | Professional/Scientific Journal | Reviewer | External | International | ||
| PLOS One journal | Professional/Scientific Journal | Reviewer | External | International | ||
| Bioinformatics journal | Professional/Scientific Journal | Reviewer | External | International | ||
| BMC Bioinformatics | Professional/Scientific Journal | Reviewer | External | International | ||
| BMC Systems Biology | Professional/Scientific Journal | Reviewer | External | International |
Our research group works on a variety of problems within the fields of computational systems medicine, computational systems biology, mathematical biology and bioinformatics. We focus on the design and application of mathematical algorithms for the modeling, simulation and control of biological networks such as gene regulatory networks, intracellular signaling networks and functional brain networks. While the mathematical and computational tools we employ are varied, many of the approaches we develop have a flavor of fields such as discrete mathematics (graph theory and combinatorics), algebra, computational algebra as well as machine learning and network science.
Mathematical and Computational Biology research interests: Computational Systems Biology of Cancer, reverse-engineering of biological networks, network science, development and application of algorithms for mathematical modeling and analysis of biological networks, and discovery and development of combinations of targeted therapies
Mathematics and computer science research interests: mathematical modeling, finite dynamical systems, polynomial dynamical systems, combinatorics, graph theory, computational algebra and machine learning.
We welcome students (undergraduate and graduate) for summer and semester rotations and internships under the several sponsored projects at UConn Health, UConn and other institutions. All available projects are in computational systems biology and systems medicine. The participation in the projects are tailored to the students' background and knowledge expertise although is expected that students are interested in projects with a quantitative, computational and/or programming related work. We also welcome students interested in pursuing their own ideas and where the expertise of our lab can serve as a launching platform.
Accepting Lab Rotation Students: Fall Block 2024, Spring 1 and 2 Block 2025
We have available short and long-term projects including: development of modeling and analysis tools and algorithms of regulatory networks, the analysis of multi-omics data in cancer such as triple negative breast cancer and acute myeloid leukemia and cell-reprogramming event in induced pluripotent stem cells (iPSCs).
Journal Articles
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Oscillatory hypoxia induced gene expression predicts low survival in human breast cancer patients.
Molecular carcinogenesis 2024 Aug;
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NETISCE: a network-based tool for cell fate reprogramming.
NPJ systems biology and applications 2022 Jun;8(1):21
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Macrophage mediated recognition and clearance of Borrelia burgdorferi elicits MyD88-dependent and -independent phagosomal signals that contribute to phagocytosis and inflammation.
BMC immunology 2021 May;22(1):32
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OCSANA+: optimal control and simulation of signaling networks from network analysis.
Bioinformatics (Oxford, England) 2020 Dec;36(19):4960-4962
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Identification of a nerve-associated, lung-resident interstitial macrophage subset with distinct localization and immunoregulatory properties.
Science immunology 2020 Mar;5(45):
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OCSANA+: Optimal Control and Simulation of Signaling Networks from Network Analysi
Bioinformatics 2020 Jan;
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Nerve associated lung resident interstitial macrophage subset exhibits distinct localization and polarization
Science Immunology 2019 Dec;
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Benchmarking Time-Series Data Discretization on Inference Methods.
Bioinformatics (Oxford, England) 2019 Jan;
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Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin.
Scientific reports 2017 Oct;7(1):14466
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CD169(+) macrophages orchestrate innate immune responses by regulating bacterial localization in the spleen.
Science immunology 2017 Oct;2(16):
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The Minimal Hitting Set Generation Problem: Algorithms and Computation
SIAM Journal on Discrete Mathematics 2016 Oct;31(1):63–100
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AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms.
Bioinformatics (Oxford, England) 2016 Aug;32(15):2396-8
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QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks.
PLoS computational biology 2016 Jun;12(6):e1004809
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An algebra-based method for inferring gene regulatory networks.
BMC systems biology 2014 Mar;8(37):37
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OCSANA: optimal combinations of interventions from network analysis.
Bioinformatics (Oxford, England) 2013 Jun;29(12):1571-3
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TIGRESS: Trustful Inference of Gene REgulation using Stability Selection.
BMC systems biology 2012 Nov;6(145):145
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Wisdom of crowds for robust gene network inference.
Nature methods 2012 Aug;9(8):796-804
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Discretization of time series data.
Journal of computational biology : a journal of computational molecular cell biology 2010 Jun;17(6):853-68
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Inference of ecological networks
Annales Zoologici Fennici 2008 Oct;45(5):459-464
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Model your genes the mathematical way: a mathematical biology workshop for secondary school teachers
Teaching Mathematics and its Applications 2008 Jan;27(2):91-101
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Comparison of reverse-engineering methods using an in silico network.
Annals of the New York Academy of Sciences 2007 Dec;111573-89
Book Chapters
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Computational Systems Biology: Discrete Models of Gene Regulation Networks.
Undergraduate Mathematics for the Life Sciences. 2013 Nov;189-200
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Reverse Engineering of Molecular Networks from a Common
Combinatorial Approach
Computational Molecular Biology: Techniques, Approaches and Applications 2011 Jan;
Conference Papers
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Systems Identification for discrete polynomial models of gene regulatory networks
15th IFAC Symposium on System Identification, St. Malo, France. 2009 Jan;
Dissertations
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Algorithms for Modeling and Simulation of Biological Systems; Applications to Gene Regulatory Networks
Thesis Dissertation, Ph.D. in Mathematics. Mathematics Department, Virginia Tech. 2007 Jan;
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A Geometric-Combinatorial Analysis of Pascal’s Mystic Hexagram.
Bachelor’s Degree in Mathematics. Sciences School, UNAM 2001 Jan;
| Title or Abstract | Type | Sponsor/Event | Date/Year | Location |
|---|---|---|---|---|
| Environmental and signaling factors regulating transcriptional dynamics of HIF-1 within a tumor microenvironment | Talk | 2024 | American Mathematical Society (AMS) Joint Mathematics Meetings, San Francisco, CA | |
| Network-Based cell reprogramming: tools and applications | Talk | Mexican Biology and Mathematics Network (RedMexBiomate) | 2023 | Mexican Biology and Mathematics Network (RedMexBiomate), Cuernavaca, Mexico |
| Constructing an encyclopedia of cancer cell reversion mechanisms | Talk | The International Conference of Systems Biology 2023 (ICSB 2023) | 2023 | The International Conference of Systems Biology 2023 (ICSB 2023), Hartford, CT |
| Model checking for inferred static networks | Talk | Thematic workshop on networks and biological models inference | 2023 | Thematic workshop on networks and biological models inference, CIRM, Marseille, France |
| NETISCE: A Network-Based Tool for Cell Fate Reprogramming | Poster | NetBioMed 2022 | 2022 | NetBioMed 2022, Online |
| NETISCE: A dynamical systems and control theory approach to cell reprogramming | Talk | International Conference of Systems Biology (ICSB 2022) | 2022 | ICSB 2022, Berlin, Germany |
| Rescuing cellular alterations in aged pancreatic beta cells to restore insulin-secretion function | Talk | The Interstellar Initiative | 2022 | Interstellar InitiativeOnline |
| A dynamical systems and control theory approach to cell reprogramming | Talk | 2022 | Paris, France | |
| A dynamical systems and control theory approach to cell reprogramming | Talk | NetBioMed 2021 | 2021 | Online |
| A dynamical systems and control theory approach to cell reprogramming | Talk | ISG Virtual Networking Event | 2020 | Virtual |
| A computational systems biology pipeline for the reversion of resistance to cisplatin in a triple-negative breast cancer subtype | Talk | Center for Reproducible Biomedical Modeling | 2020 | Virtual |
| Reversion of the attractor landscape of an intracellular regulatory networkfor triple-negative breast cancer | Talk | Joint Mathematics Meetings (JMM) 2019 | 2019 | Baltimore, USA |
| The Minimal Hitting Set Problem and Its Applications | Lecture | Mexican Mathematicians in the World | 2018 | Casa Matemática Oaxaca (CMO) |
| Optimal Control Based on the Structure of the Dynamical System | Lecture | XIV National Meeting on Mathematical Biology (ENBM) | 2018 | Mathematics Research Center (CIMAT), Guanajuato, Mexico |
| Predicting patient response to immune checkpoint therapies through deep immune profiling | Talk | Interstellar Initiative Workshop sponsor by AMED and NYAS | 2017 | New York Academy of Sciences (NYAS), New York |
| On the minimal hitting set generation problem and its applications | Talk | Discrete Math Day of the Northeast | 2016 | Smith College, Northampton MA, USA |
| On the minimal hitting set generation problem and its applications | Talk | SIGMA Seminar at the Mathematics Department at UConn | 2016 | Mathematics Department at UConn |
| Combinatorial Interventions for Control Tasks in Large-Scale Signaling Networks | Talk | Algebraic and Combinatorial Approaches in Systems Biology (ACSB2015) | 2015 | Farmington CT |
| Controllability of large scale networks | Talk | The Winter q-bio Meeting 2015 | 2015 | Maui, HI |
| A Signaling Pathway Rationale for the Design of Combination Therapies for Cancer. | Talk | 6th International Moscow Conference on Computational Molecular Biology | 2013 | Moscow, Russia |
| An Algebra-Based Method to Infer the Structure and Dynamics of Gene Regulatory Networks. Workshop: Algebraic Methods in Systems and Evolutionary Biology. | Talk | Workshop: Algebraic Methods in Systems and Evolutionary Biology | 2012 | MBI, Ohio, USA |
| Computational Systems Biology: Discrete Models of Gene Regulatory Networks. | Talk | 8th European Conference on Mathematical and Theoretical Biology and Annual | 2011 | Krakow, Poland |
| An Integrative Signaling Pathway Analysis for Determining Master Regulators and Dysregulated Pathways in Her2 Over-Expressed Human Breast Cancer. | Talk | Journées Ouvertes en Biologie, Informatique et Mathématiques | 2011 | Institut Pasteur. Paris, France |
| Integrative Analysis for Determining Key Molecular Players Involved in Her2 Over-expressing Human Breast Cancer. | Talk | IB-PAS 2010: Internat. Workshop on Integrative PathwayAnalysis and Simulati | 2010 | Bielefeld, Germany. |
| On the Inverse Problem for Molecular Regulatory Networks. | Talk | Department of Mathematical Sciences | 2009 | University of Delaware, Delaware |
| Inference of Molecular Regulatory Networks Using Evolutionary Computation. | Talk | Institut Curie | 2009 | Institut Curie, Paris, France |
| System Identification for Discrete Polynomial Models of Gene Regulatory Networks. | Talk | 15th International Federation of Automatic Control (IFAC) Symposium on Syst | 2009 | Saint Malo, France. |
| Inference of Molecular Regulatory Networks. | Talk | Department of Neurology | 2009 | Mount Sinai School of Medicine, New York |
| Reverse-Engineering of Molecular Regulatory Networks. | Talk | Department of Pathology Informatics | 2009 | Yale School of Medicine, Connecticut |
| Inference of Brain Connectivity Networks. | Talk | Minority Biomedical Research Support Seminars | 2008 | Rutgers University, New Jersey |
| Reverse-Engineering of Biological Network Models from Noisy Time-Course Data Using Evolutionary Algorithms and Computational Algebra Tools. | Talk | Mathematical Biosciences Institute (MBI) | 2008 | Ohio State University, Ohio |
| Discrete Finite Dynamical Systems for the Reverse-Engineering of Biochemical Networks. | Talk | Mathematical Biology Seminar | 2007 | Rutgers University, New Jersey |
| Reverse-Engineering of Biological Systems Using Discrete Mathematics. | Talk | 2nd Research Mixer, Bell Laboratories | 2007 | Bell Laboratories, New Jersey |
| Reverse-Engineering of Biochemical Networks. | Talk | Dynamics of Infectious Diseases Meeting | 2007 | SAMSI, North Carolina, USA |
| Reverse-Engineering of Biological Systems Using Discrete Mathematics | Talk | Department of Mathematical Sciences | 2007 | Florida Atlantic University, Florida |
| Algorithms for the Modeling and Simulation of Gene Regulatory Networks. | Talk | Gene Network Sciences, Inc. | 2007 | Gene Network Sciences, Inc., Boston, MA |
| Dynamical Modeling of Gene Regulatory Networks. | Talk | Center for Multiscale Analysis of Genetic Networks | 2007 | Columbia University, New York |
| An Evolutionary Algorithm for the Identification of Biochemical networks. | Talk | Society for Industrial and Applied Mathematics (SIAM) Annual Meeting | 2006 | Boston, MA |
| Nonlinear Dynamics of Structured Populations: Theory and Applications of Matrix Models | Talk | Park City Math Institute (PCMI) and the Institute of Advanced Studies (IAS) | 2005 | Park City, Utah |
| Cycles of the State Space of n-Dimensional Dynamical Systems. | Talk | Mathematics Department | 2003 | Virginia Tech, Virginia |
| The Mystic Hexagram: A Combinatorial Approach. | Talk | Mathematics Department, Sciences School, UNAM | 2001 | Mexico City, Mexico |
| Secrets Among Prime Numbers: An Introduction to Cryptography. | Talk | Mathematics Month at the Museum of Sciences “Universum”, | 1999 | Universum, UNAM, Mexico |
| Pascal’s Mystic Hexagram: Combinatorial and algebraic aspects. | Talk | National Conference for the “Summer with a Scientist” Research Program | 1998 | Veracruz, Mexico |