Baecher lab @ Emory

Quest lab at Emory

Baecher CV Quest lab publications
Research
Forecasting ecological dynamics and disease
Forecasting ecological dynamics and disease

Understanding the pattern and process behind ecological phenomena, including population changes, invasive species, and vector-borne disease.

Mar 15, 2025
Integrated population modeling
Integrated population modeling

Integrated field data with semi-structured citizen science data to model population dynamics

Feb 15, 2025
Spatiotemporal statistics
Spatiotemporal statistics

Developing spatial and spatiotemporal models using stochastic partial differential equations

Feb 15, 2024
Landscape connectivity
Landscape connectivity

Estimating how the landscape influences movement

Mar 15, 2023
Biodiversity redistribution
Biodiversity redistribution

Understanding the ecology of climate-induced range shifts

Jan 15, 2023
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Publications (since 2024)
V a Askshay, J Alex Baecher, Nathan Burkett-Cadena, James T Thorson, Yesenia Sánchez, Yasmin N Tavares, Amely M Bauer, Robert Guralnick, Lindsay P Campbell (2025). Linking hosts, landscapes, and climate to advance zoonotic arbovirus forecasting. EcoEvoRxiv.
Preprint Cite Code Project DOI
J Alex Baecher, V a Askshay, Robert Guralnick, Amely M Bauer, Yasmin N Tavares, Yesenia Sánchez, James T Thorson, Lindsay P Campbell (2025). Toward ecological forecasting of West Nile virus in Florida: Insights from two decades of sentinel chicken surveillance. Science of the Total Environment.
Preprint PDF Cite Code Project DOI PRESS: FMNH
Luke J Evans, J Alex Baecher, Brett R Scheffers (2024). Invasion risk posed by the pet trade. As a Research Communication in Frontiers in Ecology and the Environment.
PDF Cite DOI Project
J Alex Baecher (2024). The environmental filtering paradigm and non-filtering community assembly processes. Journal of Biogeography.
PDF Cite DOI Slides Project Supplimental Figure
David H Klinges, J Alex Baecher, Jonas J Lembrechts, Ilya M D Maclean, Jonathan Lenoir, Caroline Greiser, Michael Ashcroft, Luke J Evans, Michael R. Kearney, Juha Aalto, Isabel C Barrio, Pieter De Frenne, Joannès Guillemot, Kristoffer Hylander, Tommaso Jucker, Martin Kopecký, Miska Luoto, Martin Macek, Ivan Nijs, Josef Urban, Liesbeth Van Den Brink, Pieter Vangansbeke, Jonathan Von Oppen, Jan Wild, Julia Boike, Rafaella Canessa, Marcelo Nosetto, Alexey Rubtsov, Jhonatan Sallo-Bravo, Brett R Scheffers (2024). Proximal microclimate: Moving beyond spatiotemporalresolution improves ecological predictions. Global Ecology and Biogeography.
PDF Cite Code Dataset DOI David Klinges Supplimental Info
Jake a Lawlor, Lise Comte, Gaël Grenouillet, Jonathan Lenoir, J Alex Baecher, R M W J Bandara, Romain Bertrand, I-Ching Chen, Sarah E Diamond, Lesley T Lancaster, Nikki a Moore, Jerome Murienne, Brunno F Oliveira, Gretta T Pecl, Malin L Pinsky, Jonathan Rolland, Madeleine Rubenstein, Brett R Scheffers, Laura M Thompson, Brit Van Amerom, Fabricio Villalobos, Sarah R Weiskopf, Jennifer Sunday (2024). Mechanisms, detection and impacts of species redistribution under climate change. Nature Reviews Earth & Environment.
PDF Cite DOI Project Jake Lawlor
Lise Comte, Romain Bertrand, Sarah Diamond, Lesley T Lancaster, Malin L Pinsky, Brett R Scheffers, J Alex Baecher, R M W J Bandara, I-Ching Chen, Jake a Lawlor, Nikki a Moore, Brunno F Oliveira, Jerome Murienne, Jonathan Rolland, Madeleine a Rubenstein, Jennifer Sunday, Laura M Thompson, Fabricio Villalobos, Sarah R Weiskopf, Jonathan Lenoir (2024). Bringing traits back into the equation, A roadmap to understand species redistribution. Global Change Biology.
PDF Cite Code Dataset DOI Project Lise Comte Supplimental Info
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R sandbox: 📊 Coding Tutorials
Mixed effects models in R
Mixed effects models in R

Decision tool for creaing mixed models in R

Dec 11, 2025
Spatial Structures in Ecological Models
Spatial Structures in Ecological Models

A tutorial for incoporating Gaussian processes, spatial smoothers, or other features into ecological GLM(M)s or hierarchical models

Nov 22, 2025
Intro to R (part 1): The basics
Intro to R (part 1): The basics

A tutorial for base R usage and functions

Aug 12, 2022
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Teaching & Mentoring

Whether in a classroom or lab, teaching must be student-centered, holistic, and equitable. By fostering a supportive, engaging environment and recognizing all of students’ needs (educational, emotional, and biological), I empower students to demonstrate mastery or seek additional support as needed—an approach known to increase success and enhance well-being.

Teaching Philosophy:

Evidence-based strategies:

  • inquiry-based learning through real-world problem-solving

  • hands-on, experiential activities (in the classroom, lab, or field)

  • active learning exercises (e.g., case studies and debates)

Mentoring Philosophy:

Key practices:

  • align students’ academic progress with personal goals and well-being

  • foster independent problem-solving by providing space to explore and reflect

  • encourage outside collaboration and/or mentorship

Student Outcomes

My students have gone on to pursue careers in academia, state/federal agencies, and the private sector:

  • Career progression: 7 students pursued or completed MS (5) and PhD (2) programs and credit my mentorship in shaping their career trajectory
  • Academic output: 15 conference presentations, 2 undergraduate theses, and 4 peer-reviewed publications

Recent courses

Environmental Science | University of Florida

Senior-level course | 2022 – 2024 EVS 3000L collage

A course covering population ecology, habitat management, and conservation strategies for wildlife species. Students learn to apply quantitative methods to real conservation problems.

  • Topics: Land management, Climate science, social-ecological systems, environmental justice, sustainability, invasive species
  • Methods: R programming, GIS analysis, field techniques, technical writing, science communication
  • Enrollment: 12 students

Syllabus (PDF) | Teaching R: pt 1 & pt 2

Landscape Connectivity Modeling | Professional workshop

Intensive workshop | Spring 2024

Hands-on workshop teaching cutting-edge methods for modeling animal movement and landscape connectivity using circuit theory and spatial absorbing Markov chains.

  • Software: R, Circuitscape, SAMC package
  • Participants: 40 researchers from 15 institutions
  • Focus: Theory, implementation, and interpretation

Workshop Materials | Video Lectures | Practice Datasets

Select Guest Lectures & Workshops

  • Salamander Conservation in the Southeastern USA - University of Florida (Spring 2020)
  • Connectivity for Species Redistribution - University of Florida (Spring 2020)
  • Expert Elicitation for Invasive Species Management - University of Florida (2023)
  • SAMC Connectivity Modeling - Species on the Move Conference (2023)

Resources:

See my R sandbox for a 2-part tutorial on R coding:

  • Part 1:
    • Using functions
    • Help functions
    • Vectors
    • Sequences
    • Data frames
  • Part 2:
    • read data from a csv file
    • manipulate a data set
    • join multiple data sets
    • plot data
    • animate figures
    • create for loops