Students

2011-2013 Trainees

Christopher Graves

B.S. Biological Sciences, University of Vermont

My interests are in directly testing predictions of evolutionary theory through controlled experimental studies of evolution in microbial populations. Much of our understanding of evolution comes from mathematical inference rather than empirical observation due to the time scale on which most evolutionary processes act. Bacteria and other microbes offer an exciting model system because their short generation time and small genomes allow evolutionary processes to be examined while they occur and enable quantitative predictions based on evolutionary theory to be experimentally tested in the lab.

Elizabeth Makrides

M.S. Applied Mathematics, Brown University
B.S. Biology, University of North Carolina at Chapel Hill

I am primarily interested in using dynamical systems techniques to study natural systems. My mathematical research focuses on localized coherent structures and pattern formation. In particular, I am interested in the effects of symmetry breaking terms on the bifurcation structure of the cubic-quintic Swift-Hohenberg equation, which models pattern formation in a variety of contexts, including binary fluid convection, optical systems, reaction-diffusion systems, and spatial structures in ecology.

Victor Schmidt

M.S. Marine Biology, University of North Carolina, Wilmington, 2009
B.S. Biology, St. Lawrence University, Canton, NY, 2006
 

I am interested in the influence community shifts within host microbiomes can have on disease development, pathogen transmission and environmental health. My current research examines the microbiomes associated with a single fish species across a range of environmental conditions, and looks to determine the relative influence of genotype versus environment on microbiome community structure.

2012-2014 Trainees

August Guang

B.S. Mathematics, Harvey Mudd College

I am interested in assembly and phylogenetic algorithms, and the reproducibility and accuracy of their results. Although the number of programs and algorithms for genome assembly and tree reconstruction expands every year, there is often no way to assess their benefits and drawbacks or to compare between specific programs, and the metrics that are out there are not well understood. Eventually I hope to develop methods that will address these issues.

Lillian Hancock

M.S. Biology, University of Rhode Island, 2010
B.S. Biology, Trinity College, 2008

Generally, I am interested in convergent evolution and the genetic and environmental mechanisms underlying adaptation and evolution in plants, ranging from green and red algae to angiosperms. My Master’s research focused on red algal organellar genome evolution as a model for understanding the process by which organisms become obligately parasitic. For my doctorate research, I will be investigating Crassulacean Acid Metabolism (CAM) photosynthesis evolution in the context of two lineages in the Portulacineae, Montiaceae and Anacampserotaceae. Through the phylogenetic resolution of these two clades, we aim to gain an understanding of the genetic and environmental enablers to the CAM syndrome and its evolutionary relationship to intermediate CAM-like phenotypes and succulence.

Emily Hollenbeck

B.A. Biology, University of Pennsylvania

Many species have been observed moving up in elevation as well as latitude in response to warmer climates. I am interested in altitudinal range shifts occurring under current and future climate change. Steep mountains provide a spatially rapid gradient of environmental conditions and community assemblages, which could potentially mean much shorter (and easier) shifts in order for species to reach an ideal climate. However, climate change in many locations is more complex than a simple rise in temperature, and both biotic and abiotic mismatches may impact species’ fitness in a new location. I hope to explore the fitness consequences of range shifts from various angles, including population genetics, local adaptation, and physiological ecology.

Yinhong Lang (Associate)

B.S. Biosciences, University of Science and Technology of China, Hefei, China, 2012

Horizontal gene transfer is recognized as one of the most important mechanisms in prokaryotic evolution, especially in shaping the structure and function of microbial communities. I’m generally interested in the factors that determine the tendency of genes to be transferred or the barriers against it and the effect of horizontal gene transfer on speciation and metabolic network. My research will focus on analyzing datasets of prokaryotic genomes using bioinformatics approaches with a modularity perspective on metabolic network and studying speciation from a genomic dynamics view.

2013-2015 Trainees

Kimberly Cohen Neil

B.A. in Biology from Colby College, 2009.

I'm broadly interested in disease ecology, conservation medicine, and wildlife biology. For my dissertation research I am investigating parasite/pathogen dynamics of New England's threatened and invasive rabbits, the New England cottontail and the Eastern cottontail.

Kealohanuiopuna Kinney

PhD Candidate: Brown University, Dept. of Ecology and Evolutionary Biology
M.A: University of Maryland at College Park, Dept. of Geographical Science
B.S. University of Hawaii at Hilo, Dept. of Geography and Environmental Science
NSF-IGERT Reverse Ecology Fellow
NSF EAPSI Fellow

My research addresses how fire regimes affect the long-term development of dryland ecosystems. I use airborne remote sensing, field biogeochemistry, ancient DNA, and ecosystem modeling to investigate how Hawaiian dryland ecosystems have varied over time in response to nutrient availability and disturbance from fire.

Wilson McKerrow

B.S. Mathematics, Haverford College

I work on probabilistic models in molecular biology. Under a certain of assumptions, a probabilistic will give the exact probability that a prediction is correct. In RNAseq, probabilistic models allow us to distinguish read errors from SNPs from RNA editing events. In RNA folding, the shortcomings of a model indicate that equilibrium secondary structure alone is not enough account for the fact that many RNA molecules form a single stable structure.

Brooke Osborne

M.S. in Ecology from Colorado State University, 2012
B.S. in Environmental Toxicology as well as International Studies and Spanish from Penn State University, 2008.

I am interested in terrestrial ecosystem ecology and biogeochemistry. I like thinking about microbial linkages between global change and ecosystem-scale processes and am especially interested in questions that will advance our understanding of nutrient cycling dynamics and address knowledge gaps for management and mitigation purposes in the face of global change. My current work is focused on understanding state factor controls on nutrient cycling in lowland tropical forests.

Adam Spierer

B.A. Biology: Biochemistry, Colby College, 2013 

I am interested in how microscale, intra-individual evolution can manifest itself at the whole organism level. My undergraduate work focused on DNA cross-linking agents (like compounds found in mustard gas and cigarette smoke) as a chemotherapy for cancer. Despite their efficacy and current use, these compounds' main side-effect is their propensity to induce cancers and encourage resistance in existing ones. My doctoral research was inspired by this work, leading me to transition my theme of micro-evolution and organismal phenotype to a more happy/less toxic subject: mitochondrial genetics in the context of exercise and aging. I use Drosophila models to answer my questions because they are cute and compliant, and unlike humans, they have a relatively short lifespan and are genetically manipulatable. Broadly, my research aims to understand the larger role that exercise and diet play in aging, healthspan, and athletic capacity. 

2014-2016 Trainees

Morgan Moeglein

B.S. in Plant Biology from the University of Vermont. 

I am interested in the relationship between ecologically relevant traits and their underlying genetic basis. My undergraduate work focused on the morphology and hybridization of ferns in the genus Polypodium. I then worked as a lab technician studying epigenetics and imprinting in the endosperm of flowering plants. For my graduate work, I hope to study the environmental and genetic factors governing leaf shape in Viburnum. 

Stephen Rong

B.A. Mathematics, Anthropology, Washington University in St. Louis

I am interested in applying mathematical and computational tools to understanding population genomics and to aiding theoretical understanding of underlying patterns and processes of ecology and evolution. Rapid advancements in sequencing technology, genomic databases, and bioinformatic tools will allow greater resolution and understanding of population structure, population history, and genomic evolution in model organisms such as  humans and also in increasingly many non-model organisms. I am interested in developing theory and methods and applying these tools to study human populations and the organisms most affected by human evolutionary history and human activities, such as domesticated, infectious, invasive, and endangered species.

William Longo

M.S. Earth, Environmental and Planetary Sciences, Brown University
B.S. Chemistry, Haverford College

I am interested in chemical biomarkers in the environment and discerning what their distributions can tell us about paleoclimate and paleoecology. Aquatic biomarkers such as alkenones can provide us with continuous and high-quality geologic records of climate change, however we still know relatively little about the species that biosynthesize these compounds and how genotypic differences influence their distributions. My doctorate aims to better understanding chemical biomarkers in the modern environment while concurrently applying them to reconstruct Holocene climate variability in Northern Alaska. 

Yinsui Zheng (Associate)

B. Eng in Environmental Science, University of Science and Technology of China, Hefei, China, 2012

I am generally interested in understanding how the biomarker producers respond to environment change and how to apply these fundamental mechanisms in studying climate change. Specifically, I am looking into the alkenone/alkenoate difference of Isochrysidales and how their transcriptome difference under different environmental conditions. I am also studying the climate change and ecology systems of the Northern Amazon and its sensitivity to large-scale Atlantic climate forcing.

2015-2016 Trainees

Joaquin Nunez 

Sc.B. from Rosenstiel School of Marine and Atmospheric Science, University of Miami, 2015

My main research goal is to understand how natural populations evolve and adapt to highly heterogeneous environments. My current projects use the northern acorn barnacle (Semibalanus balanoides) as a system  to address questions on ecological and evolutionary genomics.  

Rebecca Elyanow 

B.S. in Computational Biology, Carnegie Mellon University, 2014 

I am interested in developing algorithms and using computational tools to model and analyze biological data. As an undergraduate I worked on developing software to model the morphology of neuronal cells from an input of microscopy images. I continued this work at the Blue Brain Project where I focused on capturing the morphological features of different cell types and neuronal arbors in generative statistical models. In addition to cell modeling, I also have an interest in genetics and how computer science and statistics can be utilized to extract meaningful information from seemingly intractable amounts of data. 

John Capano 

B.S. Biology, Dickinson College, 2013

I am broadly interested in physiology, morphology and ecology within an evolutionary context. More specifically, I seek to understand the function of morphological characteristics within species and how those characteristics drive and influence the ecology and evolution of the organism. For my doctoral research, I am focusing on various mechanisms of ventilation in members of Sauropsida, with my primary interest being the biomechanics of locomotion, ventilation, and feeding in snakes.

Bianca Brown

B.S City University of New York , York College, 2014

I am interested in how species adapt to environmental stress on a genetic level.  Some of my research goals are to figure out what genes are responsible for certain plastic traits, and how are some species better able to adapt in high stress environment than others. How species respond to temperature is of particular interest to me because of the relationship between changing temperatures and climate change.