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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.

Seminar: Computational Modeling of Dense Bacterial Colonies Growing on Hard Agar
October 27, 2020 @ 2:00 pm
Zoom Meeting
Hui Sun, Department of Mathematics and Statistics, California State University, Long Beach Abstract: The physical interactions of growing bacterial cells with each other and with their surroundings significantly affect the structure and dynamics of biofilms. Here a 3D agent-based model is formulated to describe the establishment…
Seminar: Dr. Robyn Shuttleworth, University of Saskatchewan
November 03, 2020 @ 2:00 pm
Zoom Meeting
Robyn Shuttleworth, University of Saskatchewan Title/Abstract: TBA *For zoom meeting information of the seminars, please contact Dr. Qixuan Wang
Colloquium: Modeling cell migration: from 2D to 3D
November 04, 2020 @ 4:00 pm
Zoom Meeting - Link TBP
Alex Mogilner, Courant Institute, New York University Cell migration is a fundamentally important phenomenon underlying wound healing, tissue development, immune response and cancer metastasis. Understanding basic physics of the cell migration presented a great challenge until, in the last three decades, a combination of…
Seminar: Skin patterns in zebrafish: agent-based modeling and public-science projects
November 10, 2020 @ 2:00 pm
Zoom Meeting
Alexandria Volkening, Northwestern University Abstract: Wild-type zebrafish (Danio rerio) are characterized by black and yellow stripes, which form on their body and fins due to the self-organization of thousands of pigment cells. Mutant zebrafish and sibling species in the Danio genus, on the other hand, feature altered,…

Center News

Proposal of the Special Session titled "Coupled Experimental andMultiscale Modeling Study of the Environmental Microbiome" for the2021 AAAS Annual Meeting

February 8-11, 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). Please find here the file with the session description and with the abstracts of the talks. The exact date and time of the special session will be provided later.

 

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 had 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)

CNS 2020

 

This year the Annual Computational Neuroscience meeting (CNS'2020) will be held online on July 18-22 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.

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”

Lorentz Center


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 24 to 28 August, 2020.

A follow up Special Session to be held at the 2021 Annual SMB Meeting, June 13-17, 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

Russell Rockne

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:

https://www.imagwiki.nibib.nih.gov/msm-consortium/2019-ml-msm

https://www.imagwiki.nibib.nih.gov/msm-consortium/agenda

 

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):

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 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

Register Here

 

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

William Cannon

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

Samuel Britton

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".