Paola VeraLicona, Ph.D.Assistant Professor/Basic Science

 Education & Training
 Committees & Organizations
 Research
 Research Opportunities
 Lab Rotations
 Publications
 Presentations
Degree  Institution  Major 

B.S.  Universidad Nacional Autonoma de Mexico (UNAM)  Mathematics 
M.S.  Virginia Polytechnic Institute and State University  Mathematics 
Ph.D.  Virginia Polytechnic Institute and State University  Mathematics 
PostGraduate 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 reverseengineering 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 

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 InSilico.  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 2000July 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 precollege 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 

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  Codirector  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, reverseengineering 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: Summer 2021, Fall 2021, and Spring 2022
We have available short and longterm projects including: development of modeling and analysis tools and algorithms of regulatory networks, the analysis of multiomics data in cancer such as triple negative breast cancer and acute myeloid leukemia and cellreprogramming event in induced pluripotent stem cells (iPSCs).
Journal Articles

Macrophage mediated recognition and clearance of Borrelia burgdorferi elicits MyD88dependent and independent phagosomal signals that contribute to phagocytosis and inflammation.
BMC immunology 2021 May;22(1):32

OCSANA+: optimal control and simulation of signaling networks from network analysis.
Bioinformatics (Oxford, England) 2020 Dec;36(19):49604962

Identification of a nerveassociated, lungresident interstitial macrophage subset with distinct localization and immunoregulatory properties.
Science immunology 2020 Mar;5(45):

OCSANA+: Optimal Control and Simulation of Signaling Networks from Network Analysi
Bioinformatics 2020 Jan;

Nerve associated lung resident interstitial macrophage subset exhibits distinct localization and polarization
Science Immunology 2019 Dec;

Benchmarking TimeSeries Data Discretization on Inference Methods.
Bioinformatics (Oxford, England) 2019 Jan;

Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin.
Scientific reports 2017 Oct;7(1):14466

CD169(+) macrophages orchestrate innate immune responses by regulating bacterial localization in the spleen.
Science immunology 2017 Oct;2(16):

The Minimal Hitting Set Generation Problem: Algorithms and Computation
SIAM Journal on Discrete Mathematics 2016 Oct;31(1):63–100

AlgoRun: a Dockerbased packaging system for platformagnostic implemented algorithms.
Bioinformatics (Oxford, England) 2016 Aug;32(15):23968

QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks.
PLoS computational biology 2016 Jun;12(6):e1004809

An algebrabased method for inferring gene regulatory networks.
BMC systems biology 2014 Mar;8(37):37

OCSANA: optimal combinations of interventions from network analysis.
Bioinformatics (Oxford, England) 2013 Jun;29(12):15713

TIGRESS: Trustful Inference of Gene REgulation using Stability Selection.
BMC systems biology 2012 Nov;6(145):145

Wisdom of crowds for robust gene network inference.
Nature methods 2012 Aug;9(8):796804

Discretization of time series data.
Journal of computational biology : a journal of computational molecular cell biology 2010 Jun;17(6):85368

Inference of ecological networks
Annales Zoologici Fennici 2008 Oct;45(5):459464

Model your genes the mathematical way: a mathematical biology workshop for secondary school teachers
Teaching Mathematics and its Applications 2008 Jan;27(2):91101

Comparison of reverseengineering methods using an in silico network.
Annals of the New York Academy of Sciences 2007 Dec;11157389
Book Chapters

Computational Systems Biology: Discrete Models of Gene Regulation Networks.
Undergraduate Mathematics for the Life Sciences. 2013 Nov;189200

Reverse Engineering of Molecular Networks from a Common
Combinatorial Approach
Computational Molecular Biology: Techniques, Approaches and Applications 2011 Jan;
Conference Papers

Systems Identification for discrete polynomial models of gene regulatory networks
15th IFAC Symposium on System Identification, St. Malo, France. 2009 Jan;
Dissertations

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;

A GeometricCombinatorial 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 

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 triplenegative breast cancer subtype  Talk  Center for Reproducible Biomedical Modeling  2020  Virtual 
Reversion of the attractor landscape of an intracellular regulatory networkfor triplenegative 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 LargeScale Signaling Networks  Talk  Algebraic and Combinatorial Approaches in Systems Biology (ACSB2015)  2015  Farmington CT 
Controllability of large scale networks  Talk  The Winter qbio 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 AlgebraBased 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 OverExpressed 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 Overexpressing Human Breast Cancer.  Talk  IBPAS 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 
ReverseEngineering 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 
ReverseEngineering of Biological Network Models from Noisy TimeCourse Data Using Evolutionary Algorithms and Computational Algebra Tools.  Talk  Mathematical Biosciences Institute (MBI)  2008  Ohio State University, Ohio 
Discrete Finite Dynamical Systems for the ReverseEngineering of Biochemical Networks.  Talk  Mathematical Biology Seminar  2007  Rutgers University, New Jersey 
ReverseEngineering of Biological Systems Using Discrete Mathematics.  Talk  2nd Research Mixer, Bell Laboratories  2007  Bell Laboratories, New Jersey 
ReverseEngineering of Biochemical Networks.  Talk  Dynamics of Infectious Diseases Meeting  2007  SAMSI, North Carolina, USA 
ReverseEngineering 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 nDimensional 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 