Center News
Computational Modeling & Machine Learning in Biology & Medicine Workshop 2024
December 11th - 12th, 2024
The workshop will focus on recent progress in mathematical and computational modeling of biological and biomedical systems, model translational predictions in biology and medicine, as well as data-driven and machine learning methodologies with applications to biology. The workshop will provide a follow up to an NSF sponsored conference on similar topics held at UCR in November of 2023 titled Predictive Modeling in Biology and Medicine.
The workshop is sponsored by the UCR Interdisciplinary Center for Quantitative Modeling in Biology (ICQMB) and UCR Artificial Intelligence Research and Education Institute (RAISE).
*Due to the limited capacity of the venue, registration is currently closed for this event.
Colloquium
April 3rd, 2024 - 4:00 - 5:00 p.m., Skye 284
Bjorn Birnir, UCSB
The Statistical Theory of Angiogenesis
Angiogenesis is a multiscale process by which a primary blood vessel issues secondary vessel sprouts that reach regions lacking oxygen. Angiogenesis can be a natural process of organ growth and development or a pathological one induced by a cancerous tumor. A mean-field approximation for a stochastic model of angiogenesis consists of a partial differential equation (PDE) for the density of active vessel tips. Addition of Gaussian and jump noise terms to this equation produces a stochastic PDE that defines an infinite-dimensional Lévy process and is the basis of a statistical theory of angiogenesis. The associated functional equation has been solved and the invariant measure obtained. The results of this theory are compared to direct numerical simulations of the underlying angiogenesis model. The invariant measure and the moments are functions of a Korteweg–de Vries-like soliton, which approximates the deterministic density of active vessel tips.
Dr. Finley ICQMB Talk 2/21/24
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Postdoc Earns Prestigious NIH Fellowship to Expand Prion Disease Research
Postdoctoral Scholar Mikahl Banwarth-Kuhn was awarded a $205,140 National Institutes of Health Ruth L. Kirschstein Postdoctoral Individual National Research Service Award (NIH-F32) to be distributed over three years.
The purpose of the fellowship is to enhance the research training of postdoctoral candidates who have the potential to become productive, independent investigators in scientific health-related research fields.
For her postdoctoral research, Banwarth-Kuhn is working with UC Merced Applied Mathematics Professor Suzanne Sindi and Tricia Serio, dean of the College of Natural Sciences at the University of Massachusetts Amherst.
“I am thrilled for what this means for Mikahl's research program,” Sindi said. “Mathematical biology is a tough area to receive funding for because you lie between two different fields. The fact that Mikahl received an F32 for a fully computational research program speaks to the strength of her research and the potential impact it will have on understanding proteostasis.”
BREAKING BIOFUEL BARRIERS: Researchers want to make it easier to convert plants into fuel
To optimize biocrop growth, The U.S. Department of Energy, or DOE, has prioritized research to develop a fundamental understanding of soil microbes and cell metabolism. “Poor growth of biocrops on marginal lands is one of the leading factors holding the biofuel industry back at the moment,” said the study’s co-author Dr. William Cannon, an adjunct math professor at UCR and computational scientist at Pacific Northwest National Laboratory.
Cannon and UCR researcher Dr. Mark Alber received a three-year, $2.1 million grant from the DOE to develop mathematical and computational modeling, artificial intelligence algorithms, and experiments to better understand the chemical reactions involved in cellular metabolism, the process that fuels life in cells in which enzymes break down and build fats, proteins, energy carriers, and genetic information. For example, the researchers employed mathematical control theory, a field of applied mathematics used to understand how systems control themselves, as well as machine learning to predict which enzymes needed to be controlled to prevent excessive buildup of metabolites.
“This way, the metabolite concentrations don’t get so high that the liquid inside the cell becomes thick and gooey like molasses, which could cause cell death,” Cannon said.
SMB Diversity Workshop 2021
We are enthusiastic to announce a virtual workshop on Diversity, Equity and Inclusion on March 26th, 2021.
The goal of our workshop is to collaborate toward building a welcoming and inclusive environment within the Society for Mathematical Biology (SMB) and the scientific community more broadly.
We recognize that structural barriers have and continue to limit voices within our field based on race, gender identity or expression, disability status, sexual orientation, and immigration status among others. These barriers marginalize individuals at all educational and career stages.
We invite our community to join us as we engage in a critical reflection of our practices in order to cultivate a culture in which all voices are heard, valued and validated. Together, by sharing stories and identifying concrete actions, we can make space for everyone.
Please check here for more information: https://icqmb.ucr.edu/smb-diversity-workshop-2021
SMB Education & REU Workshop 2021
This workshop will be held on April 1st & 2nd, in preparation for the 2021 Annual Meeting of the Society for Mathematical Biology (SMB2021) to be held from June 13th - 17th, 2021: https://www.smb2021.org This is a 2 day workshop, with the first day’s events focusing on Education and the second day on Research Experience for Undergraduates (REU).
Education Workshop Mission and Vision Statement
This half-day workshop will target math biologists at all levels, focusing on links between education, diversity and research. The goal of this workshop is to bring together researchers and educators to share and exchange experiences and ideas on education in the current rapidly changing environment of mathematical biology. We will look at the evidence regarding hypotheses, cutting across different levels of education and across different groups, to find common features, and characteristics of success and identify paths forward.
REU Workshop Mission and Vision Statement
This workshop aims to engage with faculty, undergraduate students, and high school students who are interested in learning more about REU programs. We will have speakers and interactive Question & Answer (Q&A) panel discussions to help give background information on REUs, and how students can learn about programs and prepare applications. We will also provide a forum for general discussions and answering any questions. We hope this workshop will be helpful in further engaging the community providing opportunities for learning more about how to participate in as well as organize REUs in Applied Mathematics and Biological Sciences. We look forward to you joining us at this event.
Please check here for more information: https://icqmb.ucr.edu/smb-education-reu-workshop-2021
Distinguished Lecture in Mathematical Biology UCR Interdisciplinary Center for Quantitative Modeling in Biology Mathematics Colloquium: A systems biology approach to understanding the immunobiology of tuberculosis infection and treatment
Abstract: Tuberculosis (TB) is one of the world’s deadliest infectious diseases. Caused by the pathogen Mycobacterium tuberculosis (Mtb), the standard regimen for treating TB consists of treatment with multiple antibiotics for at least six months. There are a number of complicating factors that contribute to the need for this long treatment duration and increase the risk of treatment failure. The structure of granulomas, lesions forming in lungs in response to Mtb infection, create heterogeneous antibiotic distributions that limit antibiotic exposure to Mtb. We can use a systems biology approach pairing experimental data from non-human primates with computational modeling to represent and predict how factors impact antibiotic regimen efficacy and granuloma bacterial sterilization. We utilize an agent-based, computational model that simulates granuloma formation, function and treatment, called GranSim. A goal in improving antibiotic treatment for TB is to find regimens that can shorten the time it takes to sterilize granulomas while minimizing the amount of antibiotic required. With the number of potential combinations of antibiotics and dosages, it is prohibitively expensive to exhaustively search all combinations to achieve these goals. We present a framework to search for optimal regimens using GranSim. Overall, we present a computational tool to evaluate antibiotic regimen efficacy while accounting for the complicating factors in TB treatment to strengthen our ability to predict new regimens that can improve the clinical treatment of TB.
Bio: Dr. Kirschner received her Bachelors, Masters and PhD in applied mathematics from Tulane University. She did graduate work also at Los Alamos National Labs and a postdoctoral fellowship at Vanderbilt University joint with the departments of Mathematics and Infectious Diseases. Over the past 25 years, Dr. Kirschner has focused on questions related to models of host-pathogen interactions in infectious diseases. Her main focus has been to build models of persistent infections (e.g. Helicobacter pylori and Mycobacterium tuberculosis and HIV-1). Her goal is to understand the complex dynamics involved, together with how perturbations to this interaction (via treatment with chemotherapies or immunotherapies) can lead to prolonged or permanent health. For the past 20 years, her research focus has been on building multi-scale models to describe the host immune response to M. tuberculosis at multiple spatial and time scales and in multiple physiological compartments including lung, lymph nodes and blood. To date, she has worked and collaborated with experimentalists generating data on TB with mouse, non-human primate and human studies. Denise has over 150 publications in top journals describing this work that spans topics from methodological to biological advancement. Dr. Kirschner currently serves (and has for the past 17 years) as Editor-in-Chief of the Journal of Theoretical Biology. She serves as the founding co-director of The Center for Systems Biology at the University of Michigan, an interdisciplinary center at the University of Michigan aimed to facilitate research and training between wet-lab and theoretical scientists. In 2016 she was elected as President-elect of the Society for Mathematical Biology and has served as its president from 2017-2020. Denise’s passion for mentoring students, postdoctoral fellows and junior faculty has been a major focus of her career, and her key mission is to promote both mathematics and family values in the scientific community.
10th annual Southern California Systems Biology Symposium
Dear Colleagues,
Please join us for the 10th annual Southern California Systems Biology Symposium! This Symposium is co-sponsored by the UCR Center for Quantitative Modeling in Biology.
The annual symposium, now in its 10th year, brings together researchers from across Southern California—from Santa Barbara to San Diego—to share research, build community, and stimulate collaborations. The symposium will be held virtually via zoom and poster session on the Gather Town platform Friday, March 5th and will include thematic sessions of talks and a poster session.
Select poster abstracts will be featured in a lightning talk format prior to the virtual poster session.
Learn more at: https://www.cityofhope.org/2021-systems-biology-symposium
New Multicampus Consortium to Study Assembly of Coronaviruses
The University of California, Riverside, is the recipient of a 2021 UC Multicampus Research Programs and Initiatives, or MRPI, award allowing the campus to put together a UC Coronavirus Assembly Research Consortium.
“This consortium will aim to understand the physical principles underlying the formation of coronaviruses,” said Roya Zandi, a professor of physics and astronomy at UC Riverside and the principal investigator of the four-year project that received funding of more than $1.75 million. “We will also explore the impact of some drugs on the assembly process.”
UCR will be joined by UC Merced and UC Davis in the consortium. The three campuses will work together to understand the factors contributing to the formation of SARS-COV-2.
UC Riverside Study Focused on How HIV Mutates to Escape the Immune System
A team co-led by a scientist at the University of California, Riverside, has developed a method to study how HIV mutates to escape the immune system in multiple individuals, which could inform HIV vaccine design.
HIV, which can lead to AIDS, evolves rapidly and attacks the body’s immune system. Genetic mutations in the virus can prevent it from being eliminated by the immune system. While there is no effective cure for the virus currently available, it can be controlled with medication.
“Understanding the genetic drivers of disease is important in the biomedical sciences,” said John P. Barton, an assistant professor of physics and astronomy at UCR, who co-led the study with Matthew R. McKay, a professor of electronic and computer engineering and chemical and biological engineering at the Hong Kong University of Science and Technology.
Study Reveals How Cells Control What They Produce After Eating
A new study reveals how bacteria control the chemicals produced from consuming ‘food.’ The insight could lead to organisms that are more efficient at converting plants into biofuels.The study, authored by scientists at UC Riverside and Pacific Northwest National Laboratory, has been published in the Journal of the Royal Society Interface.
LGBTQ+ Math Day
The Fields Institute for Research in Mathematical Sciences is hosting the first (but not last) LGBTQ+ Math Day. This virtual event is aimed at LGBTQ+ mathematicians and students in the mathematical sciences, and their allies. There will be four half-hour talks by LGBTQ+ mathematicians, followed by a panel discussion. Speakers will present their mathematical research, as well as their journey navigating their academic careers as a member of the LGBTQ+ community.
Registration is free and the event will be held on Wednesday, November 18th from 10:00 a.m. - 1:45 p.m. PST. Note that the times listed on the online schedule are in the Eastern time zone.
The Pacific Math Alliance (PMA) Outreach Committee: Mario Banuelos, Carmen Caprau, John Rock, Cristina Runnalls, Edouard Tchertchian, Khang Tran
Proposal of the Special Session titled "Coupled Experimental and Multiscale Modeling Study of the Environmental Microbiome" for the 2021 AAAS Annual Meeting
February 8th - 11th, 2021: https://meetings.aaas.org/ The proposal has just been accepted by the Program Committee.
The theme for the 2021 Annual AAAS Meeting is focused on understanding the complexities and dynamics of various ecosystems by drawing on a multitude of perspectives.
The special session was proposed by Mark Alber, Distinguished Professor, Department of Mathematics, Center for Quantitative Modeling in Biology, University of California, Riverside
Joel Sachs, Professor, Department of Evolution, Ecology and Organismal Biology, University of California, Riverside
William Cannon, Computational Scientist, Computational Mathematics, Pacific Northwest National Laboratory; Adjunct Professor, Department of Mathematics, University of California, Riverside
and nominated by the Mathematics section (primary) and Biology section (secondary).
Session description and with the abstracts of the talks
Virtual Public Lectures: Turing Patterns on Turing Machines - Video
August 27th was our kick-off of virtual public lectures. Thank you very much that you have been part of our very first virtual event.
If you didn't have the chance to join the live session yesterday or you want to watch the lecture again please find the link below:
https://video.leidenuniv.nl/media/1_gqixuilc
Annual Computational Neuroscience meeting (CNS*2020)
This year the Annual Computational Neuroscience meeting (CNS'2020) will be held online on July 18th - 22nd and will be FREE (usually ~$500 to register). As part of the meeting, we are organizing a Tutorial and 2 Workshops on brain multiscale modeling and machine learning tools and resources, including several NIH-funded projects. The events are organized by SUNY, Yale, UCL and the Allen Brain Institute. We have over 20 speakers, all leaders in their fields and representing a wide range of modeling tools/resources.
- CNS'2020 Tutorial: "Building mechanistic multiscale models, from molecules to networks, using NEURON and NetPyNE", July 18th; https://sites.google.com/neurosim.downstate.edu/cns2020-tutorial
- CNS'2020 Workshop: "Tools and resources for developing and sharing models in computational neuroscience", July 21st - 22nd; https://neuralensemble.github.io/Networks_SIG/CNS2020
- Workshop: "Machine learning and mechanistic modeling for understanding brain in health and disease", July 22nd, https://sites.google.com/view/cns-ml-msm-workshop-2020/
To register visit the links above or go directly to http://cnsorg.org/cns-2020
Co-sponsored by UCR Math’s Interdisciplinary Center for Quantitative Modeling in Biology and the Lorentz Center In Leiden, The Netherlands, Dr. Mark Alber co-organizes the Summer School “Modeling of Shape and Size in Biological Development”
Students are encouraged to participate in online activities including listening to review talks and working on introductory projects. These activities will culminate in intense training and exchange program from 24th to 28th August, 2020.
A follow-up Special Session to be held at the 2021 Annual SMB Meeting, June 13th - 17th, 2021 at UCR as well as a Workshop at the Lorentz Center sometime in 2021-22 are planned.
The Summer School focuses on mathematical multiscale models of animal and plant development and plant growth. School participants will work with models rooted in the cellular level, i.e., models making links between cellular processes such as cellular growth and division, cell movement and interaction with the extracellular matrix (ECM), mechanical or chemical signaling between cells, etc., leading to organ shape development and growth at higher spatial scales.
Graduate students will be exposed to state-of-the-art examples of multiscale modeling in development. They will get hands-on experience with the development of mathematical and computational models as well as model calibration using experimental data. They will also develop in teams simple, but novel example models to answer open scientific questions proposed by the speakers ahead of time. Students will be expected to already have some experience in modeling but will be asked to work with a method that is new to them.
https://www.lorentzcenter.nl/modeling-shape-and-size-in-biological-development.html
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 the 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 1st, 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 10th, 2020: https://morikis-symposium.engr.ucr.edu/
3. 2021 Annual Society for Mathematical Biology Meeting to be held at UCR from June 13th - 17th, 2021. This year it will be held in Germany.
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 24th - 25th:
https://www.imagwiki.nibib.nih.gov/msm-consortium/2019-ml-msm
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 9th - 10th, 2019 (Saturday - Sunday):
http://www.ams.org/meetings/sectional/2266_timetable.html
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 4th - 5th, 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 4th, 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 5th, 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 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 a 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 15th, 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 3rd to September 7th, 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 the growth of plants and animals.
Dr. William Cannon Appointed Adjunct Professor in the Department of Mathematics, UC Riverside
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 the 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.
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".