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Mathematical Biology Seminar

Rana Parshad, Zhijun Wu and I organize a weekly Mathematical Biology Seminar at Iowa State University.

Seminars take place every Wednesday at 3:10pm in Carver 401. In addition, we have a zoom link for people working from home (if you are interested just email me).

 

Future speakers:



September 29, 2021
Rana Parshad, Iowa State University (Mathematics)
Title TBA

October 06, 2021
Daniel Plaugher, University of Kentucky
Modeling the Pancreatic Cancer Microenvironment in Search of Control Targets
Pancreatic Ductal Adenocarcinoma is among the leading causes of cancer-related deaths globally due to its extreme difficulty to detect and treat. Recently, research focus has shifted to analyzing the microenvironment of pancreatic cancer to better understand its key molecular mechanisms. This microenvironment can be represented with a multi-scale model consisting of pancreatic cancer cells (PCCs) and pancreatic stellate cells (PSCs), as well as cytokines and growth factors which are responsible for intercellular communication between the PCCs and PSCs. We have built a stochastic Boolean network (BN) model, validated by literature and clinical data, in which we probed for intervention strategies that force this gene regulatory network (GRN) from a diseased state to a healthy state. To do so, we implemented methods from phenotype control theory to determine a procedure for regulating specific genes within the microenvironment. We identified target genes and molecules, such that the application of their control drives the GRN to the desired state by suppression (or expression) and disruption of specific signaling pathways that may eventually lead to the eradication of the cancer cells. After applying well-studied control methods such as stable motifs, feedback vertex sets, and computational algebra, we discovered that each produces a different set of control targets that are not necessarily minimal nor unique. Yet, we were able to gain more insight about the performance of each process and the overlap of targets discovered. Nearly every control set contains cytokines, KRas, and HER2/neu, which suggests they are key players in the system's dynamics. To that end, this model can be used to produce further insight into the complex biological system of pancreatic cancer with hopes of finding new potential targets.

October 20, 2021
Julie Spencer, Los Alamos National Laboratory
Distinguishing Viruses Responsible for Influenza-like Illness

November 03, 2021
Santosh Manicka, Tufts University
Title TBA

November 10, 2021
Lubna Pinky, Eastern Virginia Medical School
Title TBA

November 17, 2021
Anayse Miller, Iowa State University (Mathematics)
Title TBA

December 08, 2021
Adam Runions, University of Calgary
Title TBA


Past speakers:

September 15, 2021
Kristina Moen, Iowa State University (Mathematics)
Tracking the Molecular Evolution of SARS-CoV-2: A Topological Approach

September 08, 2021
Aniket Banerjee, Iowa State University (Mathematics)
Exploring the Dynamics of Virulent and Avirulent Aphids: A Case for a  "Within Plant" Refuge

September 01, 2021
Claus Kadelka, Iowa State University (Mathematics)
Evaluation of the United States COVID-19 vaccine allocation strategy

April 28, 2021
Ivana Bozic, University of Washington
Mathematical model of colorectal cancer initiation

April 21, 2021
Nancy Rodriguez, UC Boulder
The effect of directed movement on the Allee Effect

April 14, 2021
Adam Maclean, University of Southern California
Modeling gene regulatory network dynamics at single-cell resolution 

April 07, 2021
Moumita Das, Rochester Institute of Technology
Mechanics and fracture properties of articular cartilage and cartilage-inspired soft materials

March 31, 2021
Veronica Grieneisen, Cardiff University
Mathematical modelling of Morphogenesis in Plants and Animals, from cells to tissues

March 24, 2021
Andrew Krause, Oxford University
Recent Progress & Open Frontiers in Turing-Type Morphogenesis

March 17, 2021
Madhavan Rajagopal Padmanabhan, Iowa State University (Computer Science)
Applications of Submodular Optimization in Information Diffusion

March 10, 2021
Daniel Cruz, Georgia Tech
Agent-based Modeling of Emergent Patterns Within Stem Cell Colonies

March 03, 2021
Elena Dimitrova, Cal Poly
Algebraic design of experiments for network identification

February 24, 2021
Audrey McCombs, Iowa State University (Statistics)
Structure Matters: Network topology and disease dynamics

February 17, 2021
David Murrugarra, University of Kentucky
Improving RNA secondary structure prediction via state inference with machine learning and deep learning methods

February 10, 2021
Anastasios Matzavinos, Brown University
Bayesian uncertainty quantification for particle-based simulations

November 18, 2020
Lauren Childs, Virginia Tech
Modeling Malaria Dynamics within the Mosquito

November 11, 2020
Fusun Akman, Illinois State University
Symmetries of nested canalizing functions and of phase spaces of gene regulatory networks

November 04, 2020
Thomas Woolley, Cardiff University
Patterns, cellular movement and brain tumours

October 28, 2020
Samantha Erwin, Oak Ridge National Laboratory
Monitoring and Forecasting COVID-19 Disease Progression

October 21, 2020
Ruoyu Wu, Iowa State University (Mathematics)
Mean field interaction on random graphs: Erdos—Renyi and multi-color graphs

October 14, 2020
T.M. Murali, Virginia Tech
How to build regulatory networks from single-cell gene expression data

October 07, 2020
Md Rafiul Islam, Iowa State University (Mathematics)
Mathematical modeling of infectious diseases using ordinary and fractional differential equations 

September 30, 2020
Laura Strube, Virginia Tech
The role of repeat infection in the dynamics of a simple model of waning and boosting immunity

September 23, 2020
Manoj Srinivasan, Ohio State University
Theories of human locomotion: How healthy humans walk stably and efficiently

September 16, 2020
Eric Takyi, Iowa State University (Mathematics)
Diffusion induced extinction and recovery in a Female Harvesting Male Stocking (FHMS) model with weak Allee effects

September 09, 2020
Davit Potoyan, Iowa State University (Chemistry)
Multi-scale modeling of nuclear organization and regulation

September 02, 2020
Zhijun Wu, Iowa State University (Mathematics)
Social Distancing amid Social Living 

May 06, 2020
Leonid Rubchinsky, Indiana University Purdue University Indianapolis
In and Out of Synch: Intermittent Synchronization of Living Systems

April 29, 2020
Claus Kadelka, Iowa State University (Mathematics)
A model-based evaluation of the efficacy of COVID-19 social distancing testing and hospital triage policies

April 08, 2020
Ivair Valmorbida, Iowa State University (Entomology)
Soybean aphid (Hemiptera: Aphididae) response to lambda-cyhalothrin varies with its virulence status to aphid-resistant soybean

April 01, 2020
Matthew ONeal, Iowa State University (Entomology)
Soybean aphids - an invasive pest that changed soybean production in the US.

March 11, 2020
Zhijun Wu, Iowa State University (Mathematics)
Why Multilingual, and How to Keep It -- An Evolutionary Dynamics Perspective

March 04, 2020
Amy Toth, Iowa State University (EEOB and Entomology)
Building a super organism: Social insects as models for studying the evolution of biological complexity

February 26, 2020
Eric Takyi, Iowa State University (Mathematics)
On large and small data blow-up solutions in the Classical Trojan Y- Chromosome Model

February 19, 2020
Shofi Andari, Iowa State University (Statistics)
Paired-end reads merging using pair-hidden Markov model

February 12, 2020
Rana Parshad, Iowa State University (Mathematics)
Indirect Effects of Invasive Species

February 05, 2020
Claus Kadelka, Iowa State University (Mathematics)
Understanding the Rules of Life: Design Principles of Gene Regulatory Networks

January 29, 2020
Kushani da Silva, Iowa State University (Mathematics)
The higher status language doesn’t always win: The fall of English in India and the rise of Hindi 

January 22, 2020
Audrey McCombs, Iowa State University (Statistics)
Community stability of ecological networks

December 11, 2019
Oyeyemi Oyebola, Iowa State University (Mathematics)
Extra Polyloops and their Applications to Biological Inheritance

December 04, 2019
Karin Dorman, Iowa State University (Statistics)
Denoising Illumina Amplicon Data

November 06, 2019
Bob Jernigan, Iowa State University (Biochemistry, Biophysics and Molecular Biology)
Looking for complexity - when pairs are not enough

October 30, 2019
Tom Sappington, USDA
"It's not easy to be me…": Bridging the worlds of applied ecologists and modelers to change the world of pest management

October 23, 2019
Ian Braun, Iowa State University (GDCB)
Automated methods enable direct computation on phenotypic descriptions for novel candidate gene prediction

October 16, 2019
Haldre Rogers, Iowa State University (EEOB)
What is the fate of an empty forest?

October 09, 2019
Zhijun Wu, Iowa State University (Mathematics)
When Do Cheaters Lose?

September 25, 2019
Kushani da Silva, Iowa State University (Mathematics)
Dynamics of Endangered Languages of the World

September 18, 2019
Eric Takyi, Iowa State University (Mathematics)
The Trojan Y Chromosome strategy