NIMBioS: National Institute for Mathematical and Biological Synthesis

Welcome to NIMBioS!

Established in 2008 with an award from the National Science Foundation, the National Institute for Mathematical and Biological Synthesis brings together researchers from around the world to collaborate across disciplinary boundaries to find creative solutions to today's complex biological problems. The NIMBioS process and its results have united the forces of diverse academic communities, transforming the landscape of scientific research and education in the United States and the world. Read more »

My most exciting current research work is probably a project that was started during a Working Group at NIMBioS in Tennessee, looking at how interactions between pathogens can be disentangled from survey data.

Nik Cunniffe, Mathematical Biology, University of Cambridge

FEATURED PUBLICATION

Classifying long transient dynamics. A new paper published in Science by the NIMBioS Working Group on Long Transients and Ecological Forecasting proposes a classification system for ecological dynamics that persist over ecologically relevant time scales—dozens of generations or longer. In this review, the authors turn to dynamical systems theory to develop a classification scheme that categorizes the mechanisms underlying transients. The study also links empirical observations to simple prototypical models. The systematic framework described in the review could be useful for ecosystem management.
Learn more about this publication » View more science features »

VIDEO SPOTLIGHT

Discover What's New at NIMBioS
The new Center for the Dynamics of Social Complexity is bringing new discoveries to UT and the world.
View more NIMBioS videos »

Opportunities and Announcements

XSEDE High Performance Computing Workshops are held monthly at NIMBioS on various topics. Register online.
Applications are currently being accepted for a targeted postdoctoral position in mathematical modeling of biological systems at NIMBioS and in the Fefferman Lab at the University of Tennessee at Knoxville. This is a full-time, one year position, with the potential for renewal. Review of applications will begin 1 May 2018 and continue until the position is filled. For full details and the online application, click here.
Register now for the Tenth Annual Undergraduate Research Conference at the Interface of Biology and Mathematics, to be held Oct 27-28, 2018, at the UT Conference Center, Knoxville. Deadline to register Oct 5.
Apply now for the DySoC/NIMBioS Investigative Workshop: Social Norms: Emergence, Persistence, and Effects, to be held April 23-25, 2019, at NIMBioS. Deadline to apply: Dec 1.
Register now for the NIMBioS Tutorial, Risk Assessment Calculator Training, to be held March 5-7, 2019, at NIMBioS. Deadline to register: Dec 10, 2018 (early-bird); Feb 15, 2019 (final) .
New! Check out our new Accelerator Tutorials and Innovator Workshops. We are looking for proposals for transformative research (Innovator Workshops) and proposals for innovative ideas for teaching new quantitative approaches (Accelerator Tutorials). The next deadline to submit a proposal is Nov 1.
Requests for Visits to NIMBioS. NIMBioS hosts short-term supported visitors and self-supported visitors. Applications for Short-term Visits are considered 4 times a year with the following deadlines for submitting the requests: Feb 1, May 1, Aug 1 and Nov 1.

Now at NIMBioS
Full Calendar »

Week of Sep 24-29, 2018

Mon 3:30 pm: DySoC/NIMBioS Seminar. Damian Ruck (Anthropology, UTK; DySoC). Topic: Cultural prerequisites for democracy and economic development. Refreshments at 3.

Wed-Fri: NIMBioS Working Group: Long Transients and Ecological Forecasting, 3rd mtg. Featured in Science last week!
Reception: Wed. 5:10 p.m.

Videos now available:
–NIMBioS seminar: Luc Doyen on Tragedy of Open Ecosystems`
–NIMBioS seminar: Climate change & tipping points for seabird colonies in the Pacific Northwest
– NIMBioS Investigative Workshop: Bio-acoustic Structure
– NIMBioS Tutorial: Search for Selection

News:
– New in Science: Classifying long transient dynamics
– Read the Jul/Aug NIMBioS Newsletter!
– Happy Birthday to a Great Mentor – honoring Professor Emeritus and NIMBioS progenitor Thomas Guy Hallam.
– How Will Species Adapt to Climate Change? g2p2pop Seeks Answers
– Save the Salamander: Epidemiological Modeling Deployed to Halt Killer Fungus

Visiting scholars:
– Pamela Small (Professor Emeritus, Microbiology, Univ. of Tennessee) and Heather Jordan (Biology, Mississippi State) are collaborating on a project with Suzanne Lenhart and Christina Edholm to model Bureli Ulcer Disease in Benin. 9/23-27
– Luis Melara (Mathematics, Shippensburg Univ.). Optimal control models for treatment of eye disease. 8/17-12/16
– Olivia Prosper (Mathematics, Univ. of Kentucky). Epidemiological models that incorporate heterogeneity to study malaria and the opioid crisis. 8/22-12/16

Recent NIMBioS Publications
More Products »

Frequency-dependent feedback and plant community coexistence
Incorporating sub-organismal processes into dynamic energy budget models for ecological risk assessment
A guide to calculating habitat‐quality metrics to inform conservation of highly mobile species
Next‐generation conservation genetics and biodiversity monitoring
Correlation between E. coli levels and the presence of foodborne pathogens in surface irrigation water: Establishment of a sampling program
Examining conservation compliance with randomized response technique analyses
Cutaneous leishmaniasis in Peru using a vector‐host model: Backward bifurcation and sensitivity analysis
Linking models of human behavior and climate alters projected climate change
Split probabilities and species tree inference under the multispecies coalescent model
Electromechanical vortex filaments during cardiac fibrillation
Predators in the plant-soil feedback loop: Aboveground plant-associated predators may alter the outcome of plant-soil interactions
Computational and mathematical methods in cardiovascular diseases
The treatment of uncertainty and learning in the economics of natural resource and environmental management
Multivariate climate change may favor large herbivore body size in food webs
Handling overheads: Optimal multi-method invasive species control
Cultural multilevel selection suggests neither large or small cooperative agreements are likely to solve climate change without changing the game
What are the environmental determinants of phenotypic selection? A meta-analysis of experimental studies
Catch bonds at T cell interfaces: Impact of surface reorganization and membrane fluctuations
Climate seasonality, fire and global patterns of tree cover
A risk assessment framework for seed degeneration: Informing an integrated seed health strategy for vegetatively propagated crops. Phytopathology
The aliens among us: How invasive species are transforming the planet – and ourselves
Modeling virus coinfection to inform management of maize lethal necrosis in Kenya
Collective action and the evolution of social norm internalization
Defining and classifying migratory habitats as sources and sinks: The migratory pathway approach
Beyond nutrients: A meta-analysis of the diverse effects of arbuscular mycorrhizal fungi on plants and soils
Predicting human olfactory perception from chemical features of odor molecules
Selecting the best stable isotope mixing model to estimate grizzly bear diets in the Greater Yellowstone Ecosystem
The evolution of parasitic and mutualistic plant-virus symbioses through transmission-virulence trade-offs
Constraints on the Fst-heterozygosity outlier approach
Transit times and mean ages for nonautonomous and autonomous compartmental systems
The evolution of extreme cooperation via shared dysphoric experiences
The next frontier of plant-soil feedback research: unraveling context dependence across biotic and abiotic gradients
Inferring biomarkers for Mycobacterium avium subsp. paratuberculosis infection and disease progression in cattle using experimental data
Precipitation drives global variation on natural selection
Contrasting post-settlement selection results in many-to-one mapping of high performance phenotypes in the Hawaiian waterfall-climbing goby Sicyopterus stimpsoni
Optimization and control of agent-based models in biology: A perspective
Best practices for virtual participation in meetings: Experiences from synthesis centers
Genome-wide selection components analysis in a fish with male pregnancy
Mate quality and the temporal dynamics of breeding in a sex-role-reversed pipefish, S. typhle
Invasive plant alters community and ecosystem dynamics by promoting native predators
Maximizing diversity in biology and beyond
skeleSim: an extensible, general framework for population genetic simulation in R
The coevolution of economic institutions and sustainable consumption via cultural group selection
Phylogenetics and biogeography of the dung beetle genus Onthophagus inferred from mitochondrial genomes
Finding the genomic basis of local adaptation: Pitfalls, practical solutions, and future directions
Advancing microbial sciences by individual-based modelling
Public control of rational and unpredictable epidemics
Tail use improves soft substrate performance in models of early vertebrate land locomotors
Ranavirus could facilitate local extinction of rare amphibian species
Mathematical modeling of early cellular innate and adaptive immune responses to ischemia/reperfusion injury and solid organ allotransplantation
Renal medullary and urinary oxygen tension during cardiopulmonary bypass in the rat
Quantifying limits on replication of death, and quiescence of Mycobacterium tuberculosis in mice
Home-field advantage? evidence of local adaptation among plants, soil, and arbuscular mycorrhizal fungi through meta-analysis
A management-oriented framework for selecting metrics used to assess habitat- and path-specific quality in spatially structured populations
The costs of avoiding environmental impacts from shale gas surface infrastructure
MycoDB, a global database of plant response to mycorrhizal fungi
Self-harm to preferentially harm the pathogens within: Non-specific stressors in innate immunity
Root-disentangling canid howls across multiple species and subspecies: Structure in a complex communication
Re-examination of the relationship between marine virus and microbial cell abundances
Can immune response mechanisms explain the fecal shedding patterns of cattle infected with Mycobacterium avium subspecies paratuberculosis?
Dominance of the suppressed: Power-law size structure in tropical forests
Leading indicators of mosquito-borne disease elimination
The evolution of antievolution policies after Kitzmiller v. Dover.
Assessing local population vulnerability with branching process models: an application to wind energy development
Broad CTL response in early HIV infection drives multiple concurrent CTL escapes
Predicting the role of IL-10 in the regulation of the adaptive immune responses in Mycobacterium avium subsp. paratuberculosis infections using mathematical models
Comparative limb bone loading in the humerus and femur of the tiger salamander Ambystoma tigrinum
Leadership in mammalian societies: Emergence, distribution, power, and payoff
Social feedback and the emergence of rank in animal society
Interspecific contact and competition may affect the strength and direction of disease-diversity relationships for directly transmitted microparasites
Genetic variation, simplicity and evolutionary constraints for function-valued traits
Genetic and ecological data reveal species boundaries between viviparous and oviparous lizard lineages
Bayesian analysis of a morphological supermatrix sheds light on controversial fossil hominin relationships
Loci under selection during multiple range expansions of an invasive plant are mostly population‐specific, but patterns are associated with climate
Mainstreaming early warning systems in development and planning processes: Multilevel implementation of Sendai Framework in Indus and Sahel
Effects of light, nutrients, and food chain length on trophic efficiencies in simple stoichiometric aquatic food chain models
Decreased water limitation under elevated CO2 amplifies potential for forest carbon sinks
A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes
Topological effects of network structure on long-term social network dynamics in a wild mammal
Ex situ seed collections will benefit from considering spatial sampling design and species' reproductive biology
A theory of human warfare: group-structured cultural selection
Exploring the benefits of antibody immune response in HIV-1 infection using a discrete model
Using ABC and microsatellite data to detect multiple introductions of invasive species from a single source
Shared genetic diversity across the global invasive range of the monk parakeet suggests a common restricted geographic origin and the possibility of convergent selection
Stochastic dynamics of a warmer Great Barrier Reef
Estimating vocal repertoire size is like collecting coupons: A theoretical framework with heterogeneity in signal abundance
Chloroplast haplotypes suggest preglacial differentiation and separate postglacial migration paths for the threatened North American forest tree Juglans cinerea L.
A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes
Acoustic sequences in non-human animals: a tutorial review and prospectus
Internet and Free Press Are Associated with Reduced Lags in Global Outbreak Reporting
Non-timber forest product harvest does not affect the genetic diversity of a tropical tree despite negative effects on population fitness
A comparison of elasticities of viral levels to specific immune response mechanisms in human immunodeficiency virus infection
Model selection in historical biogeography reveals that founder-event speciation is a crucial process in island clades
The socioecology of Monk Parakeets: Insights into parrot social complexity
Conservation paleobiology needs phylogenetic methods
Quantifying the impact of decay in bed-net efficacy on malaria transmission
Model selection in historical biogeography reveals that found-event speciation is a crucial process in island clades
Impacts of an interdisciplinary research center on participant publication and collaboration patterns: A case study of the National Institute for Mathematical and Biological Synthesis
A theoretical mathematical assessment of the effectiveness of coartemether in the treatment of Plasmodium falciparum malaria infection
Male hyraxes increase song complexity and duration in the presence of alert individuals
A theoretical mathematical assessment of the effectiveness of coartemether in the treatment of Plasmodium falciparum malaria infection
Comparative evaluation of potential indicators and temporal sampling protocols for monitoring genetic erosion
Optimal sampling of seeds from plant populations for ex-situ conservation of genetic biodiversity…
Persistent oscillations and backward bifurcation in a malaria model with varying human and mosquito populations…
Ecological effects and human use of commercial mosquito insecticides in aquatic communities
The elemental composition of virus particles: implications for marine biogeochemical cycles
Investigating the performance of AIC in selecting phylogenetic models
Effects of animal movement strategies and costs on the distribution of active subsidies across simple landscapes
An overview of the utility of population simulation software in molecular ecology
Spatial genetic structure in 21 populations of butternut, a temperate forest tree (Juglans cinerea L.), is correlated to spatial arrangement, habitat, and land-use history
Competition for antigen between Th1 and Th2 responses determines the timing of the immune response switch during Mycobacterium avium subspecies paratuberculosis infection in ruminants
Three keys to the radiation of angiosperms into freezing environments
Effects of subsidy quality on reciprocal subsidies: How leaf litter species changes frog biomass
An image processing based paradigm for the extraction of tonal sounds in cetacean communications
Water stress strengthens mutualism among ants, trees, and scale insects
Behavioral refuges and predator-prey coexistence
Mighty small: Observing and modeling individual microbes becomes big science
The encoding of individual identity in dolphin signature whistles: how much information is needed?
Entropy rate as a measure of animal vocal complexity
Evaluation of the "Iceberg Phenomenon" in Johne's Disease through mathematical modeling
Evaluating the significance of paleophylogeographic species distribution models in reconstructing quaternary range-shifts of Nearctic Chelonians
Carryover effects in amphibians: How much complexity is needed to predict survival?
Demographic network and multi-season occupancy modeling of Rana sylvatica reveal spatial and temporal patterns of connectivity
War, space, and the evolution of Old World complex societies
Strong species-environment feedback shapes plant community assembly along environmental gradients
Modeling the forest
Latent tuberculosis: Models, computational efforts and the pathogen's regulatory mechanisms during dormancy
Cellular and population plasticity of helper CD4(+) T cell responses
Defoliaton and bark harvesting affect life history traits of a tropical tree
Homosexuality via canalized sexual development: A testing protocol for a new epigenetic model
Asymmetric selection and the evolution of extraordinary defences. Nature Communications
Analysis and simulation of propagule dispersal and salinity intrusion from storm surge on the movement of a marsh–mangrove ecotone in south Florida
Evolution of mate choice and the so called magic traits in ecological speciation
Demographic network and multi-season occupancy modeling of Rana sylvatica reveal spatial and temporal patterns of population connectivity and persistence
The ability of landowners and their cooperatives to leverage payments greater than opportunity costs from conservation contract
Structural balance in the social networks of a wild mammal
Spatial subsidies, trophic state, and community structure: Examining the effects of leaf litter input on ponds
The impact of bed-net use on malaria prevalence
Understanding TB latency using computational and dynamic modelling procedures
Species tree inference by the STAR method and its generalizations
Understanding TB latency using computational and dynamic modelling procedures
Global mapping of infectious disease
Optimal control in individual-based models: Implications from aggregated methods
Behavioural changes and the adaptive diversification of pigeons and doves
On the role of screening and educational campaigns on controlling HCV in correctional institutions
Fatal or harmless: Extreme bistability induced by sterilizing, sexually transmitted pathogens
Identifying Transmission Cycles at the Human-Animal Interface: The role of animal reservoirs in maintaining Gambiense human African trypanosomiasis
Homosexuality as a consequence of epigenetically canalized sexual development
Mathematical modeling of viral zoonoses in wildlife
Stochastic models for competing species with a shared pathogen
Understanding TB latency using computational and dynamic modelling procedures
Incentives in the family II: Behavioral dynamics and the evolution of non-costly signaling
Communicating science through music: A case study from mathematics and biology
Multiple merger genes genealogies in two species: Monophyly, paraphyly, and polyphyly for two examples of Lambda coalescents
Modeling stabilizing selection: Expanding the Ornstein-Uhlenbeck model of adaptive evolution
Coevolution in multidimensional trait space favors escape from parasites and pathogens
Human origins and the transition from promiscuity to pair-bonding
On the evolutionary origins of the egalitarian syndrome
Using optimal control theory to identify network structures that foster synchrony
How facilitation may interfere with ecological speciation
Genetic evidence for hybridization in red oaks (Quercus sect. Lobatae, Fagaceae)
Beyond Lyme: Aeitology of tick-borne human diseases with emphasis on the south-eastern United States
How a hurricane disturbance influences extreme CO2 fluxes and variance in a tropical forest
Optimal control of integrodifference equations with growth-harvesting-dispersal order
Data-driven models for regional coral-reef dynamics

Recent NIMBioS Awards
More Awards »

Integrating Structural Theories of Revolution with Evolutionary Models to Predict Societal Resilience and (In)stability

Modeling Risk Perception, Vector-borne Diseases and Environmental Integrity: Understanding Impacts of Policy Decisions for Vector Control

Optimal Spatial Targeting of Payments for Forest-based Ecosystem Services Under Climate and Market Risks

Building Capacity for the DOI Southeast Climate Science Center to Co-produce Actionable Science Focused on Global Change Impacts to Natural Resources

Predicting the Evolution of Vector-borne Disease Dynamics in a Changing World

ABR: Melding and Mathematical Theoretical Models of Stress

NRT INFEWS: Computational data science to advance research at the energy-environment nexus

Radford HHMI Inclusive Excellence Project

The 2017 Undergraduate Research Conference at the Interface of Biology & Mathematics

Increasing STEM Education Retention with Intrusive Advising and Learning (I-SERIAL)

High-performance Computing for Agent-based Modeling of Between-group Conflicts (2 awards)

Gains from Synchronizing Top-down and Bottom-up Conservation Activities within Agricultural Landscapes

Collaborative Research: NSF INCLUDES: South East Alliance for Persons with Disabilities in STEM (SEAPD-STEM)

External Evaluation of the Quantitative Undergraduate Biology Education and Synthesis Project

Biology Undergraduate Mathematics Anxiety and Attitudes Project (BioMAAP)

DCL: NSF INCLUDES Conference on Multi-Scale Evaluation in STEM Education

Modeling the Emergence of Leaders in Self-organizing Social Networks

Mathematics Support for Spatio-temporal Population and Population Dynamics Modeling and Simulation (4 awards)

Forestry Multicultural Scholar Program (MSP)

Modeling Zika Control Effectiveness with Feedback in Risk Perception and Associated Demand Across Scales of Intervention

NIMBioS Communication

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NIMBioS Seminars

NIMBioS and DySoC are hosting a series of seminars on topics related to social complexity.

Next: Monday, Sep 24, 3:30 (refreshments at 3)
Speaker: Damian Ruck, Anthropology, Univ. of Tennessee, Knoxville; Center for the Dynamics of Social Complexity (DySoC)
Topic: Cultural prerequisites for democracy and economic development. Flyer (PDF)
Location: Room 206, Claxton Bldg, 1122 Volunteer Blvd.
Most seminars are streamed live. Watch previously recorded seminars online.

Report Your Results!

The results produced from NIMBioS research activities are important in measuring our success.
• Report your publications and other products resulting from NIMBioS activities.
• Acknowledging NIMBioS

NIMBioS
1122 Volunteer Blvd., Suite 106
University of Tennessee
Knoxville, TN 37996-3410
PH: (865) 974-9334
FAX: (865) 974-9300
Contact NIMBioS

NIMBioS is supported by the National Science Foundation through NSF Award #DBI-1300426, with additional support from The University of Tennessee, Knoxville. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

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