The main long-term goal of the UC Riverside Interdisciplinary Center for Quantitative Modeling in Biology (ICQMB) is to develop comprehensive predictive quantitative models of complex biological systems. All projects at this center combine quantitative experiments, novel image analysis, modeling and statistical approaches, and build upon the mutually complementary strength of the researchers at UC Riverside with support from collaborators at other institutions.
Skye Hall 268
11:00 - 11:50 a.m.
Womb to Tomb: Development Inspired Engineering for Aging Research
Dr. Joshua Morgan, Department of Bioengineering, UC Riverside
Abstract: Chronic aging associated disease (AAD) is the defining medical challenge of our time, representing 95% of direct health costs for seniors and driving expected Medicare spending to over $1.2 trillion by 2024. Aging is more than an accumulation of damage over the lifespan, but a failure or alteration of the homeostatic mechanisms that guide tissue maintenance. Unfortunately, current gaps in research tools and aging models have driven current research to focus on extrema and end-cases, rather than the subtle markers of emerging disease. In many cases, animal models have physiology that is poorly matched to human aging and genetic models of AAD often present key differences in progression. Human in vitromodels have been invaluable at elucidating detailed molecular pathways, however, these models are often conducted on short time periods and lack context given by tissue-scale and systemic cues. In this talk, I will describe our use of self-assembly, inspired by developmental processes, to create tissue-scale models that are accessible, customizable, and cost-effective for the study of AAD. Additionally, I will describe our research elucidating mechanisms leading to loss of homeostasis and its spread throughout tissue.
Bio: Dr. Joshua Morgan joined the UCR Bioengineering Program in 2017 as an Assistant Professor. He performed his doctoral work in Mechanical & Aeronautical Engineering at the University of California, Davis, focusing on mechanotransduction in the aging-associated disease atherosclerosis. Following this, he studied the blinding disease glaucoma at Davis’ School of Veterinary Medicine and developmentally inspired tissue engineering at the University of Delaware. His work with students at the University of Delaware was recently recognized with the “Best Postdoc Mentor of the Year”. His current research focus is on developing better models of chronic disease for the design of therapeutics capable of treating multi-morbidities that are common in aging.
March 2nd, 2020
Skye Hall 268
11:00 - 11:50 a.m.
Dr. Nan Hao, Division of Biological Sciences, UCSD
Dr. Russell Rockne Appointed Adjunct Assistant Professor in the Department of Mathematics, UC Riverside
Dr. Russell Rockne from the City of Hope was appointed Adjunct Assistant Professor in the Department of Mathematics, UC Riverside: https://www.cityofhope.org/people/rockne-russell He is an Assistant Professor in the Department of Computational and Quantitative Medicine within Beckman Research Institute of City of Hope. He also serves as director of the Division of Mathematical Oncology, with the goal of translating mathematics, physics and evolution-based research to clinical care. The division, a part of Irell & Manella Graduate School of Biological Sciences and the Beckman Research Institute of the City of Hope, uniquely combines clinical care, scientific research and mathematical expertise to enhance the overall understanding of cancer development, growth, evolution and reaction to treatment. This work ultimately helps the care team to predict, control and thwart malignancy on both a global scale by improving evidence-based standards of care and an individual level by personalizing treatment using quantifiable patient and disease factors.
The Center is Co-Sponsoring Three Conferences through 2021
1. 9th Annual SoCal System Biology Conference to be held at UCR on February 1, 2020: https://icqmb.ucr.edu/9th-annual-southern-california-regional-systems-biology-conference
2. Dimitrios Morikis Memorial Symposium to be held at UCR on February 10, 2020: https://morikis-symposium.engr.ucr.edu/
3. 2021 Annual Society for Mathematical Biology Meeting to be held at UCR from June 13-17, 2021. This year it will be held in Germany. https://www.smb.org/meetings/
DOE Supported Interdisciplinary Collaborative Project at UCR, PNNL and ORNL
Dr. Alber is a co-PI on just awarded three year (9/1/2019-8/31/2022) Department of Energy grant titled: "Elucidating Principles of Bacterial-Fungal Interactions" with total budget of $2,246,000 and with $556,229 for the subaward to UCR.
Interdisciplinary Team includes:
PI: William Cannon, Senior Scientist at the Pacific Northwest National Laboratory and Adjunct Professor, Department of Mathematics, UC Riverside
Co-PI: Mark Alber, Distinguished Professor, Department of Mathematics, UC Riverside
Co-PI: Dale A Pelletier, Senior Staff Scientist in the Biosciences Division at Oak Ridge National Laboratory (ORNL)
Co-PI: Jessy Labbé, Staff Researcher, lead of the Fungal Systems Genetics and Biology Lab in the Biosciences Division at Oak Ridge National Laboratory (ORNL)
Title: Elucidating Principles of Bacterial-Fungal Interactions
Abstract: In comparison to bacterial-bacterial interactions, there is very little known about bacterial-fungal interactions even though these interactions are thought to be fundamentally important to DOE missions in sustainability, crop biofuel development and biosystem design. In biofuel crops, many crop root systems live in mutualistic symbiosis with fungi and bacteria. Mycorrhiza helper bacteria (MHB) increase host root colonization by mycorrhizal fungi, which in turn act as a micro-root system to provide the plant with soil nutrients. Recent work on the Populus root microbiome has determined that the interactions between the mycorrhizal fungus Laccaria bicolor and the bacterium, Pseudomonas fluorescens are key to the fitness of the plant. These organisms, Laccaria and P. fluorescens, are the focus of this project to use combined mathematical and computational modeling and experiments to understand fundamental principles of interactions between fungi and bacteria from the perspective of material exchange and energetics, and how material and energetics are linked in inter- and intra-microbial subsystems.
Integrating Machine Learning and Multiscale Modeling Position Paper
Integrating Machine Learning and Multiscale Modeling https://arxiv.org/abs/1910.01258 to be discussed at the Conference to be held at NIH, Bethesda, MD, from October 24-25:
AMS at UC Riverside - 2019
We invite you to participate in the American Mathematical Society (AMS) Fall Western Sectional Meeting to be held at the University of California, Riverside, from November 9-10, 2019 (Saturday - Sunday):
In particular, the Meeting will include three Special Sessions on applications to biology as well as the Special Session of the Association for Women in Mathematics (AWM).
The 2nd Annual Conference on Quantitative Approaches in Biology will be held October 4-5, 2019 at Northwestern University
This conference is a two-day event that includes a range of activities to stimulate the cross-fertilization of ideas, including guest speaker talks, lightning talks, poster sessions, an undergraduate research competition, a reception, and plenty of networking opportunities.
SPEAKERS Day 1 – October 4, 2019
Hana El-Samad, University of California-San Francisco
Daniel Fisher, Stanford University
Christine Heitsch, Georgia Tech
Madhav Mani, Northwestern University
Andy Oates, L’Ecole Polytechnique Fédérale de Lausanne
Day 2 – October 5, 2019
Nicole Creanza, Vanderbilt University
James Lee, University of Illinois-Chicago
Srividya Iyer-Biswas, Purdue University
Xin Li & Dave Shihai Zhao, University of Illinois-Urbana Champaign
Christian Petersen, Northwestern University
Jeremiah Zartman, University of Notre Dame
Recent Special Issue of the the Bulletin of Mathematical Biology Includes Papers by Participants of the Conference Held at UC Riverside in 2017
Special Issue on Multiscale Modelling of Tissue Growth and Shape of the Bulletin of Mathematical Biology, Volume 81, Issue 8, August 2019: 3214-3218, doi: 10.1007/s11538-019-00649-2 https://link.springer.com/journal/11538/81/8/page/1 Issue Editors: Mark Alber, Christophe Godin, Philip Maini, Roeland Merks, Eric Mjolsness Introduction: https://link.springer.com/article/10.1007/s11538-019-00649-2
This Special Issue consists of contributions from participants of three workshops with similar focus held in 2016–17: “Modelling of Tissue Growth and Form” held from March 6 to March 10, 2017, at the NSF Mathematical Biology Institute (MBI), Columbus, OH, USA, “Multi-scale Modeling of Complex Systems in Developmental and Plant Biology” held on December 15, 2017, at the Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, CA, USA, “Computing a Tissue: Modeling Multicellular Systems” at the 15th European Conference on Computational Biology held from September 3 to September 7, 2016, at The Hague, Netherlands. The Special Issue combines papers on recent advances in the field with review articles discussing in detail some open problems. Contributors were asked to describe the recent results on the application of the very latest mathematical and computational modeling and experimental approaches used for studying problems in morphogenesis and growth of plants and animals.
Dr. William Cannon Appointed Adjunct Professor in the Department of Mathematics, UC Riverside
Dr. William Cannon from the Pacific Northwest National Laboratory (PNNL) was appointed Adjunct Professor in the Department of Mathematics, UC Riverside: https://www.pnnl.gov/science/staff/staff_info.asp?staff_num=7055
Dr. Cannon's Research Interests include: Computational biophysics, biochemistry and proteomics; Modeling and simulation including deterministic and stochastic simulation of metabolism; simulations of state; microbial metabolism; statistics, statistical mechanics and statistical proteomics data analysis; Cloud computing and high performance.
Dr. Cannon is author of more than 50 technical publications in modeling and simulation, data analysis and proteomics. His graduate work was in statistical thermodynamics in the laboratory of J. Andrew McCammon studying molecular recognition proteins using molecular dynamics and Monte Carlo methods. His graduate work was in the laboratory of Steven J. Benkovic where he worked in both experimental and computational enzymology. Before joining PNNL, Dr. Cannon spent time at Monsanto working on high-throughput transcriptome data analysis and network inference. Since joining PNNL, Dr. Cannon has worked on statistical methods for integrating proteomics data with models, the use of supercomputers to maximize the identification of peptides and proteins from high throughput mass spectrometry assays, and the modeling and simulation of metabolic pathways. Researchgate: www.researchgate.net/profile/William_Cannon2
Samuel Britton of UCR Math D.O.E. Office of Science Graduate Student Fellowship
Graduate student Samuel Britton in Mathematics Department has been awarded the U.S. Department of Energy (DOE) Office of Science Graduate Student (SCGSR ) Fellowship to conduct research on the collaborative project at the Pacific Northwest National Laboratory (PNNL) titled “Data integration and multi-scale computational model of metabolism”. He will be co-advised on this project by Dr. William Cannon (PNNL) and Dr. Mark Alber (UCR).
The SCGSR Award Notification indicates that: "The selection of Samuel Britton for the SCGSR award is in recognition of outstanding academic accomplishments and the merit of the SCGSR research proposal, and reflects Samuel Britton’s potential to advance the Ph.D. studies and make important contributions to the mission of the DOE Office of Science".