Currently
NSF Postdoctoral Fellow at Newcastle University.
Education and Employment
2013 - 2021
North Carolina State University
PhD, Civil Engineering. Minor in Biotechnology.
2011 - 2013
North Carolina State University
MS, Environmental Engineering
2002 - 2011
Sonalysts, Inc
Programmer/Analyst
1997 - 2002
Cornell University
BS, Electrical Engineering
Awards and Fellowships
2021
Postdoctoral Research Fellowship in Biology, National Science Foundation. NSF
Award 2007151.
2020
W. Wesley Eckenfelder Graduate Research Award for 2020 from the American
Academy of Environmental Engineers and Scientists/Association of Environmental Engineering Scientists and Professors
2014-2017
GAANN Fellow, Microbial Biotechnology Training Program. (US Department of
Education Graduate Assistance in Areas of National Need Award # P200A140020)
Travel Grants
2023
Federation of European Microbiological Societies, travel to FEMS 2023.
2022
International Society for Microbial Ecology, travel award to ISME18.
2019
NCSU College of Engineering Travel Award. Covering travel to the IWA MEWE
2019 Conference, Hiroshima.
2019 NCSU Graduate Student Association Travel Award. Covering travel to the IWA
MEWE 2019 Conference, Hiroshima.
Poster Awards
2021
Runner-up Modeling environmental bioreactors treating wastewater by integrating biological processes, floc microenvironments, and computational fluid dynamics. EB Network Early Career Researcher Conference, online
2017
3rd place poster, What’s Driving Microbial Community
Assembly in Full-Scale Wastewater Treatment? NC-AWWA-WEA Annual
Conference, Raleigh, NC
2014
1st place poster, Effect of Variable Shear on the Formation
of Aerobic Granules in an Eccentric Couette Micro-reactor. CCEE WREE Annual
Symposium, Raleigh, NC
2012
2nd place poster, Anaerobic biodegradability
of plastics in laboratory-scale landfill reactors. Global Waste Management
Symposium, Phoenix, AZ
Publications
A list containing abstracts and links to fulltext is also available online.
2023 Weaver, JE. (2023) “Quantifying drift-selection balance using an agent-based model of identical heterotrophs under low nutrient conditions.” Royal Society Interface Focus. In press
2021
Weaver, JE. (2021) “From Floc to Reactor Scales: A Multi-Faceted Investigation Integrating Microbial Ecological Experiments and Computational Modeling to Understand Aerobic Wastewater Systems.” Under the direction of de los Reyes III, F.L., Ducoste, J.J., Call, D.E., and Goller, C.G. PhD Dissertation, North Carolina State University, Raleigh, NC.
2019
Wu L, Ning D, Zhang B, Li Y, Zhang P, Shan X, Zhang Q, Brown MR, Li Z, Van Nostrand JD, Ling F, Xiao N, Zhang Y, Vierheilig J, Wells GF, Yang Y, Deng Y, Tu Q, Wang A, Acevedo D, Agullo-Barcelo M, Andersen GL, de Araujo JC, Boehnke KF, Bond P, Bott CB, Bovio P, Brewster RK, Bux F, Cabezas A, Cabrol L, Chen S, Etchebehere C, Ford A, Frigon D, Gómez JS, Griffin JS, Gu AZ, Habagil M, Hale L, Hardeman SD, Harmon M, Horn H, Hu Z, Jauffur S, Johnson DR, Keucken A, Kumari S, Leal CD, Lebrun LA, Lee J, Lee M, Lee ZMP, Li M, Li X, Liu Y, Luthy RG, Mendonça-Hagler LC, de Menezes FGR, Meyers AJ, Mohebbi A, Noyola A, Oehmen A, Palmer A, Parameswaran P, Park J, Patsch D, Reginatto V, de los Reyes FL, Rossetti S, Sidhu J, Sloan WT, Smith K, de Sousa OV, Stephens K, Tian R, Tooker NB, De los Cobos Vasconcelos D, Wakelin S, Wang B, Weaver JE, West S, Wilmes P, Woo S-G, Wu J-H, Wu L, Xi C, Xu M, Yan T, Yang M, Young M, Yue H, Zhang Q, Zhang W, Zhang Y, Zhou H, Zhang T, He Z, Keller J, Nielsen PH, Alvarez PJJ, Criddle CS, Wagner M, Tiedje JM, He Q, Curtis TP, Stahl DA, Alvarez-Cohen L, Rittmann BE, Wen X and Zhou J. “Global diversity and biogeography of bacterial communities in wastewater treatment plants”. Nature Microbiology 4, 1183–1195 (2019) doi:10.1038/s41564-019-0426-5. [bib]
2019
Weaver, JE and Wang, L and de los Reyes III, FL and Barlaz MA “Systems and Methods for Studying Microbial Processes and Communities in Landfills” in Understanding Terrestrial Microbial Communities Hurst, CJ ed. Springer ISBN:978-3-030-10777-2 [bib]
2019
Weaver, JE and Williams, JC and Ducoste, JJ and de los Reyes III, FL “Measuring the Shape and Size of Activated Sludge Particles Immobilized in Agar with an Open Source Software Pipeline” Journal of Visualized Experiments v143, e58963. doi:10.3791/58963 [bib]
2018
Weaver, JE and Hong, H and Ducoste, JJ and de los Reyes III, FL “Controlling
aerobic biological floc size using Couette-Taylor bioreactors” Water Research v147, pp 177-183. doi:10.1016/j.watres.2018.09.060 [bib]
2016
Weaver, JE and Ducoste, JJ and de los Reyes III, FL “Fluid shear variation
potentially plays a role in aerobic granular sludge formation” Proceedings of
the Water Environment Federation, WEFTEC 2016, v2016 i11 pp 5737-5744. doi:10.2175/193864716819706734) [bib]
2015
de los Reyes III, FL and Weaver, JE and Wang, L “A methodological framework for
linking bioreactor function to microbial communities and environmental
conditions.” Current Opinion in Biotechnlogy v33, pp 112-118. doi:10.1016/j.copbio.2015.02.002 [bib]
2013
Weaver, JE, “Effect of Inoculum Source on the Rate and Extent of Anaerobic
Biodegradation” Under the direction of Barlaz, MA and de los Reyes III, FL. MS Thesis, North Carolina State University, Raleigh, NC. [bib]
In Submission
Weaver, JE and Zuliani, P and Chen, J. and Mcgough, S and Li, B and Ofiteru, ID and Wipa, A and Davenport, R and Swailes, D and Curtis, TP “Accelerating environmental bioreactor design: Why your care and phone are getting faster than your sewage works and anaerobic digester” Environmental Science and Technology (viewpoint)
Haq, A and Malik, A and Khan, A and Weaver, JE and Wang, L and Khan, H and Shah, S and Ahmed, AA and de los Reyes III, FL and Badshah, M “Effect of removal of inhibitors on microbial communities and biogas yield of Jatropha curcas during continuous anaerobic digestion.” Reneweable Sustainable Energy Reviews
In Preparation
Weaver, JE and Ducoste, JJ and de los Reyes III, FL “Stochastic and niche-driven community assembly between two full-scale wastewater treatment plants With initially identical microbial communities”
Weaver, JE and Ducost, JJ and de los Reyes III, FL “A combined computational fluid dynamics and biokinetic framework for simulating aerobic wastewater treatment using loosely coupled sequential components”
Presentations and Conference Invitations
Presented
2023
Weaver, J.E. Understanding the balance between drift and selection in biofilm formation using agent-based biofilm modelling. Association of Environmental Engineering Scientists and Professors (AEESP) Conference 2023, Boston, US.
2023
Weaver, J.E. Illuminating the balance between drift and kinetics in biofilm formation using an agent-based model to maniuplate luck. Federation of European Microbial Societies (FEMS) Conference 2023. Hamburg, Germany (poster)
2022
Weaver, J.E. Fit or just luck? Using agent-based biofilm models to quantify the selection advantage required to overcome negative selection via random drift. 1St Annual Microbiology Oylmpiad Symposium, Newcastle, UK
2021
Weaver, J.E. Drift Matters, Until it Doesn’t: Quantifying the Fitness Advantage Necessary to Overcome Negative Drift Selection using an Agent-Based Model of Spatially Competing Heterotrophic Bacteria, 9th IWA Microbial Ecology and Water Engineering Specialist Conference (MEWE2021), Delft, Netherlands. (presented virtually)
2021
Weaver, J.E., de los Reyes III, F.L. and Ducoste J.J. Implementing a Single Modeling Approach that Combines Computational Fluid Dynamics (CFD), Biokinetics, Micro-floc Scale Diffusion, and Particle Sizes. WEFTEC, Chicago IL. (n.b. J. Ducoste presented on Weaver’s behalf due to conference schedule conflicts)
2019
Weaver, J.E., and de los Reyes III, F.L. Microbial Community Assembly in Two Full Scale Aerobic Basins Containing Identical Starting Populations: Drivers and Implications, 8th IWA Microbial Ecology and Water Engineering Specialist Conference (MEWE2019), Hiroshima, Japan.
2016
Weaver, J.E., de los Reyes III, F.L. and Ducoste J.J. Inducing aerobic granular sludge formation through unevenly distributed hydrodynamic shear rates NC AWWA-WEA, Raleigh, NC.
2016
Weaver, J.E., de los Reyes III, F.L. and Ducoste J.J. Fluid shear variation potentially plays a role in aerobic granular sludge formation. WEFTEC, New Orleans, LA.
2015
Weaver, J.E., and de los Reyes III, F.L. Microbial Ecology of Aerobic Wastewater Treatment: Community assembly during full scale startup and dynamics of bench scale granulation. NCSU MBTP Symposium, Raleigh, NC.
2015
Weaver, J.E., and Barlaz, M.A. Effect of Inoculum source on the rate and extent of anaerobic biodegradation AWMA National Conference, Raleigh, NC.
Invited Seminars and Conferences
2022
Weaver, J.E. Inferring Drift Prevalence Using Agent-Based Biofilm Models and Its Implications in Environmental Biotechnology Les Ecologistes Seminar Series, Simon Fraser University, Burnaby, CA (presented remotely)
2022
Session Chair. Microbial ecology for engineering biology, the Theo Murphy international scientific meeting of The Royal Society, Buckinghamshire UK.
2021
Weaver, J.E. From Floc to Reactor Scales: A Multi-Faceted Investigation Integrating Microbial Ecological Experiments and Computational Modeling to Understand Aerobic Wastewater Systems. Environmental Engineering Research Group Seminar Series, Newcastle University, Newcastle UK
Pedagocial training
2022
Data and Software Carpentries Instructor Training Program
2019
Completed the NCSU Teaching and Communication Certificate.
Teaching
Teaching assistant
Spring 2021
CE 774 - Environmental Biotechnology
Spring 2019
CE 481 - Senior Design Project
Spring 2019
CE 774 - Environmental Biotechnology
Fall 2019
CE 484 - Water Supply and Wastewater Systems
Spring 2018
CE 497/596 - Global WASH
Fall 2017
CE 484 - Water Supply and Wastewater Systems.
Fall 2014
CE 573 - Biological Principles of Environmental Engineering.
Course Guest lectures
Spring 2023
CEG 8110 - Project skills and professional development. Efficiently conducting a literature review.
Spring 2023
CEG 8110 - Project skills and professional development. Introduction to coding in Python.
Spring 2023
CEG 8104 - Wastewater Engineering. Solving wastewater design problems via Python. (Computer lab practical)
Spring 2015 - Fall 2018
BIT 495 - Metagenomics. Guest lectures on ordination and data visualization.
Falls 2014-2017
CE 378 - Environmental chemistry and microbiology. Facilitated lab on identifying problem orgranisms in wastewater via microscopy.
Internal Workshops Organized
2022
Peer and Expert MSc Oral Defense Feedback Session, Newcastle University Environmental Engineering MSc Program
2022
Performing an Effective Literature Search, Newcastle University Environmental Engineering MSc Professional Development, special workshop
2022
Constructing an Individual Development Plan Newcastle Environmental Engineering Early Career Researcher Development
2014
Laziness, Levers, and Literature. How to search and manage the literature. NCSU CCEE Department Seminar.
Formal Mentoring
2023 - present
PhD Co-Supervisor to Xiaoqi Yu, working title Spatio-temporal antimicrobial resistance (AMR) patterns in catchments and AMR attenuation within green infrastructure
2023 - present
MSc Supervisor to Hongze Li, working title Screening competition between bacteria relevant to environmnetal biotechnology
2022
MSc Supervisor to Xiaoqi Yu, Creation of a Pairwise Interaction Database of Antibacterial Type VI Secretion Systems
Summer 2016 - 2018
Research Internship Summer Experience (RISE) Program. Responsible for training and mentoring undergraduate researchers while they performed their own summer research culuminating in poster presentation.
2017
Formed and coordinated prelim study group for graduate student cohort.
2013 Graduate mentor for ungraduate research to Ally Patrick. Thermal Acclimation of Mesosphilic Inocula for Thermophilic Biochemical Methane
Potential Tests
2011 thru 2018
Multiple undergraduate research assistants.
Community
Peer Review
2013-203
Articles reviewed for multiple journals, including Water Science & Technology, Waste Managment, and Journal of Environmental Engineering, Royal Society Interface Focus.
Outreach
2017 - 2018
Girl Scouts of America engineering day
2013 - 2016
Boy Scouts of America engineering day
Service
2023-present
Postgrad member of Newcastle University environemntal engineering seminar committee.
2019-2020
Lab group representative, Environmental Engineering Lab Condition and Safety Committee
2019
Invited panel member, “Tell It Like It Is”: Teaching Assistant Discussion Panel for the NCSU campuswide New TA workshop
2015
Chair, program committee. NCSU CCEE WREE Graduate Research Symposium.
Current Professional Organizations
- International Water Association
- International Society for Microbial Ecology
Grantwriting
As Primary Investigator or Fellow
2019
Weaver, Joseph E. Individual Based Modelling of Chemically Mediated Microbial Interactions in Biofilms. NSF-Postdoctoral Research Fellowship in Biology (Awarded NSF 2007151)
2014
Weaver, Joseph E. Microbial Biotechnology Training Program, Graduate Assistance in Areas of National Need. US Department of Education (Awarded DoE GANN P200A140020)
As mentor for undergraduate research
2013
Joseph E., Patrick, Ally Thermal Acclimation of Mesosphilic Inocula for Thermophilic Biochemical Methane Potential Tests. (Awarded)
Contributing writer
2022
Zuliani, P., Li, B., and Curtis, T.P. NUFEB: Microbial Communities Simulation for the (Biologists) Masses EPSRC
2021
Zuliani, P, Li. B., Allen, B., and Curtis, T.P. BIOHPC: Simulating Microbial Communities on High-Performance Computers EPSRC IAA (Awarded)
2021
Curtis, T.P., Allen, B., and Zuliani, P. Accelerating Innovation By Designing Water Treatment Biofilm Media in silico. NBIC PoC (Awarded)
2017
de los Reyes III, Francis L. and Ducoste, Joel J. Using Microbial Ecology Theory to Understand Microbial Community Dynamics and Improve Function of Anaerobic Bioreactors. NSF.(Awarded)
2017
de los Reyes III, Francis L. Understanding substrate-community interactions to develop resilient anaerobic digestion of food waste. EREF. (Awarded)
2016
de los Reyes III, Francis L. and Ducoste, Joel J. WERF: Microbial ecology theory as a framework for understanding and improving anaerobic co-digestion. NSF.
Professional Development
Certificates
2022
EBNET Metabolic Modelling
2019
NCSU Teaching and Communication Certificate
Microbial Biotechnololgy Training Program, US Department of Education Graduate Assistance in Areas of National Need
2016
BIT Professional Development Seminar.
2015
BIT Capstone Seminar.
2015
BIT Research Ethics Seminar.
Pedagogy
2017
Introduction to Teaching.
2017
Responding to Student Writing.
2017
Teaching Portfolio.
2017
Avoiding Death By Powerpoint.
2017
How to Engage with Diverse Learning Styles.
2017
Managing Conflict in the Classroom.
2017
Teaching Assistant Orientation Symposium.
2017
Moodle Essentials, DELTA workshop.
2017
AEESP Strategies, Tools, and Tips for Teaching in Environmental Engineering and Sciences.
Grant writing
2019
September mini-course on grant identification, drafting, and submission
2018
Broadening the Impacts of Your Research workshop.
Other
2019
Composing Cover Letters for Academic Jobs
2019
How to deliver a Job Talk
2019
3D Scanning Studio Orientation
2019
How to Write Concise Sentences
2018
Best Practices in Software Citation seminar.
2017
Title IX Training Certificate.
(2016 - Present)
American Association for the Advancement of Science Individual Development Planning
2017
Developing Arduino Projects.
2016
Makerspace Orientation.
2015
AEESP Case Studies in Project Based Learning.
2014
COMSOL Multiphysics and Chemical Engineering Workshop.
2013
Writing Research Introductions in the Sciences.
2012
Bioinformatics Databases and Tools: The Basics.
2011
Finding Information While you Sleep
2011
Managing Your Research Using the Libraries