Documents from 2025
Systematic Evaluation of Regression Models for the Prediction of Influenza Cases, Mukul Kandwal
Defining transcriptional signatures of susceptibility for ceftriaxone and tetracycline in Neisseria gonorrhoeae, Sanjana Logu
Urban Heat Island Mitigation: A GIS Based Analysis of Cool Roofing, Canopy Cover, and Imperviousness in Rochester, New York, Benjamin Lyon
ProtPen: A pipeline that combines sequence- and structure-based approaches to predict protein functions, Diya Mathai
EVALUATING LEATHERBACK TURTLE CONSERVATION USING THE IUCN RED LIST, Hannah McGuiness-Piasecki
Bioinformatics Pipeline for Gene Regulatory Network Discovery: A Case Study with Exercise Response, Nadia Moore
Interspecific sources of resistance for Neisseria gonorrhoeae: Investigating horizontally transferred antimicrobial resistance markers, Makenna Swartz
A Computational Framework for Investigating Novel Bacterial Conjugation Inhibitors, Serena Tuytschaevers
Documents from 2024
Input of Anthropogenic Debris Across a Rural to Urban Gradient in the Lake Ontario Watershed, Paige Arieno
Identifying Functional and Potential Therapeutic Sites in Reverse Transcriptase Using Comparative Short-term Molecular Dynamics, Richmond Asare-Bediako
Quantifying Landscape Change Using Different Spectrometers, Spectral Unmixing, and UAS Imagery, Bianca Cilento
Modeling Stormwater Driven Plastic Debris in the Lake Ontario Watershed, Jayson A. Kucharek
Integrative approaches to evaluate challenges faced by songbirds during migration and associated physiological trade-offs, Gabriella L. Orfanides
Effects of Soil Amendments on Community Structure and Function in Created Wetlands, Lauren Saggese
Genomic analysis of virulence loci that enable growth of Plasmopara viticola on resistant Vitis spp., Sarah Teeter
Plastic Abundance and Degradation in the Anaerobic Digestion of Food Waste, Abbey Whitney
Documents from 2023
Characterization of microbial communities on post-consumer polymers in water bodies of the Lake Ontario watershed: Environment determines community structure on post-consumer plastic, Carmella M. Bangkong
Unsupervised Multi-resolution Analysis of Protein-Protein Abundance Patterns in Infectious Exacerbation of COPD, Eric Everingham
BioDOV: A Tool Used to Encourage Discovery in Bioinformatics Through Gamification, Gregory D. Johnson Jr.
Degradation of biodegradable products in simulated home compost environments, Jaclyn Neubauer
Visual Literacy of Molecular Biology Revealed through a Card-Sorting Task, Dina L. Newman, Hannah Spector, Anna Neuenschwander, Anna J. Miller, Lauren Trumpore, and Leslie Kate Wright
Multimodal AI for Prediction of Distant Metastasis in Carcinoma Patients, Isaac Olatunji
Antibiotics and Secondary Metabolites Analysis SHell (antiSMASH) as a tool to detect putative novel antibiotics, Rajiv Snape
Documents from 2022
Invasive Species Identification and Monitoring using Computer Vision, Street View Imagery, and Community Science, Liam Megraw
Impacts of Spatial Resolution and Viewing Angle on Remotely Sensed Estimates of Spartina alterniflora Aboveground Biomass, Avery Miller
Identification of the conserved genes required to form large tailed virus particles, Sara Moran
Development of soil microbial community structure in created and natural wetlands, Wendy A. Owens
Bioinformatics Analyses of New Genes of Focus in the Research of Autism with Dogs, Rats, and a Variety of Other Model Organisms, Aaron Pennington
Identification of Essential Gene Relations For Lung Adenocarcinoma Therapy Targets by Cross-Referencing Literature-Mined and RNASeq Data, Mariel V. Pridmore
Evolutionary paths to macrolide resistance in a Neisseria commensal converge on ribosomal genes through short sequence duplications, Jordan C. Raisman, Michael A. Fiore, Lucille Tomin, Joseph K. O. Adjei, Virginia X. Aswad, Jonathan Chu, Christina J. Domondon, Ben A. Donahue, Claudia A. Masciotti, Connor G. McGrath, Jo Melita, Paul A. Podbielski, Madelyn R. Schreiner, Lauren J. Trumpore, Peter C. Wengert, Emalee A. Wrightstone, André O. Hudson, and Crista B. Wadsworth
Functional evolutionary adaptation of binding dynamics in the SARS-CoV-2/ACE2 interface from bats to humans, Madhusudan Rajendran
Whole genome duplication analysis of the invasive Lonicera maackii (Amur honeysuckle), Gaochan Wang
The DNA Landscape: Development and Application of a New Framework for Visual Communication about DNA, Leslie Kate Wright, Emalee Wrightstone, Lauren Trumpore, Julia Steele, Deanna M. Abid, and Dina L. Newman
Documents from 2021
Effects of Microplastic on Freshwater Benthic Ecosystems: toxicity and impacts on biogeochemical cycling, Kristina Chomiak
Literature-Assisted Validation of a Novel Causal Inference Graph in a Sparsely Sampled Multi-Regimen Exercise Data, Aditya Gupta
Effects of wetland design and invasive species removal on carbon and microbial communities in restored wetlands, Benjamin Hamilton
Controls on Denitrification and Nitrous Oxide Flux in Created Wetlands, Sonia Huang
An Exploratory Assessment of Peer-reviewed Life Science Literature Statement Readability Used in Text-based Interpretive Analyses, Jeremy Jackson
Deep Learning Models to Characterize Smooth Muscle Fibers in Hematoxylin and Eosin Stained Histopathological Images of the Urinary Bladder, Sridevi Kayyur Subramanya
Modeling the mechanistic behavioral logic supporting adherence to hormone therapy in breast cancer patients, Gina Kersey
Assembly and annotation of the genome of an invasive bush honeysuckle, Amur honeysuckle (Lonicera maackii), Erin R. Kesel
Assessment and Deployment of Genetic Tools for North American River Otters (Lontra canadensis), Kelsey Lawton
Conservation of the Ambystoma jeffersonianum Complex, Morgan Motherwell
Punnett Square or Protein Production? The Expert-Novice Divide for Conceptions of Genes and Gene Expression, Dina L. Newman, Aeowynn Coakley, Aidan Link, Korinne Mills, and Leslie Kate Wright
Development of a Novel Algorithm to Remove Spurious Edges from Biological Networks Through Functional Enrichment, Jeffrey Page
Comparative DNA Degradation Automation for Identifinders, Jennifer Pfaff
Methane Emissions from Stormwater Ponds, Brianna Pollard
ProMOL: Updating the Template Based Structural Alignment Plugin, Mariah Robertson
Biodegradation and microbial CO2 evolution of blended polymers in food-waste and coffee supplemented disposal environments, Abigail Rolston
SecretePEPPr: Computational Prediction and Characterization of Effector-like Proteins Secreted from Vitis vinifera, Patrick Rynkiewicz
Evaluating Electronic Pulse Generators for Cooling Tower Sanitation, Hannah Saxena
Characterization and Proteolytic Maturation of Head Proteins in a Giant Salmonella Virus, Aaron Scheuch
The effect of roadside mowing and road traffic on bumble bee abundance and pollinating insect habitat quality in New York highway rights-of-way., Alyssa Schoenfeldt
The Influence of Herbivory on Macrophyte Community Structure and Nitrogen Retention in Created Wetlands, Evan Squier
Analysis of nucleosomal DNA patterns around transcription factor binding sites, Sheethal Umesh Nagalakshmi
Socio-ecological context matters for wetland project outcomes, Sydney VanWinkle
Carbon Soil Amendment for Promotion of Native Species in Created Emergent Freshwater Wetlands, Taylor E. Williams
Teaching meiosis with the DNA triangle framework: A classroom activity that changes how students think about chromosomes, Leslie Kate Wright, Paulina Cortez, Margaret A. Franzen, and Dina L. Newman
Documents from 2020
Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing, Karel Břinda, Alanna Callendrello, Kevin C. Ma, Derek R. MacFadden, Themoula Charalampous, Robyn S. Lee, Lauren Cowley, Crista B. Wadsworth, Yonatan H. Grad, Gregory Kucherov, Justin O'Grady, Michael Baym, and William P. Hanage
An Online Interactive Video Vignette that Helps Students Learn Key Concepts of Fermentation and Respiration, Jean A. Cardinale, Dina L. Newman, and L. Kate Wright
Exploration of the Neisseria Resistome Reveals Resistance Mechanisms in Commensals That May Be Acquired by N. gonorrhoeae through Horizontal Gene Transfer, Michael A. Fiore, Jordan C. Raisman, Narayan H. Wong, André O. Hudson, and Crista B. Wadsworth
Effects of Prior Land Use, Carbon Availability, and Hydrology on Nitrogen Cycling in Created Freshwater Wetlands, Michael McGowan
A Recent (2020) Comparative Analysis of Genome Aligners Shows HISAT2 and BWA are Among the Best Tools, Ryan J. Musich
Interactive Video Vignettes (IVVs) to Help Students Learn Genetics Concepts, Dina L. Newman, Jean Cardinale, and L Kate Wright
Applying Systems Pharmacology to the Treatment of Chronic Illness Using Novel Scoring and Translational Methods, Spencer Richman
Regulation of Transposable Elements by Tumor Suppressor Protein 53, Andrew J. Rosato
Ecological Impacts of Food Waste Digestate Management in an Agricultural Watershed, Shradha Shrestha
Transcriptomic Analysis and Developmental Neural Transcript Identification in the Brittle Star Ophioplocus esmarki, Alexandria Shumway
The impact of herbivory on methane cycling in a created wetland, Briana B. Stringer
Phenology-dependent cold exposure and thermal performance of Ostrinia nubilalis ecotypes, Crista B. Wadsworth, Yuta Okada, and Erik B. Dopman
Undergraduate Textbook Representations of Meiosis Neglect Essential Elements, Leslie Kate Wright, Grace Elizabeth C. Dy, and Dina L. Newman
Documents from 2019
Genetics and Molecular Dynamics of L,L-Diaminopimelate Aminotransferase (DapL): an Enzyme Involved in Lysine and Peptidoglycan Biosynthesis, Lily E.J. Adams
Habitat and Conservation Suitability Assessment for Shrubland Birds in Monroe County, New York, Rachel Allen
Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen, Brian Arnold, Mashaal Sohail, Crista B. Wadsworth, Jukka Corander, William P. Hanage, Shamil Sunyaev, and Yonatan H. Grad
Simulating Pathway-Based Steady States to Prevent Epithelial- Mesenchymal Transition in Ovarian Cancer, K Jeselle Clark
A Close-Up Look at PCR, Callie J. Donahue, Ashley A. Adair, Leslie Kate Wright, and Dina Newman
Decadal Changes in Salt Marsh Succession and Assessing Salt Marsh Vulnerability using High-Resolution Hyperspectral Imagery, Sarah Goldsmith
GNE: A Deep Learning Framework for Gene Network Inference by Aggregating Biological Information, Kishan KC, Rui Li, Feng Cui, Qi Yu, and Anne R. Haake
An examination of students' perceptions of the Kekulé resonance representation using a perceptual learning theory lens, Thomas Kim, Leslie Kate Wright, and Kathryn Miller
Functional Comparison of Current Software Tools for Genomic Assembly from High Throughput Sequencing Data, Lars J. Olsen
Investigation of Cold Stress Induced Disease Resistance (SIDR) in Grapevines and Arabidopsis, Cal D. Palumbo
Near-Complete Genome Sequences of Vesicular Stomatitis Virus Indiana Laboratory Strains HR and T1026R1 and Plaque Isolates 22-20 and 22-25, Thomas M. Russell, Evan E. Santo, Lisa Golebiewski, Nathan S. Haseley, and Maureen Ferran
Investigation of nest predation as a cause of turtle population declines on the Sequoyah National Wildlife Refuge, Oklahoma, Alexandra M. Shipman
Effects of grazer exclusion on carbon cycling in created freshwater wetlands, Delanie Spangler
Factors Limiting Organic Carbon Degradation by Antibiotic-Resistant Heterotrophic Microorganisms in Wastewater Contaminated Sediments, Katelyn Whitburn
The Nucleosome Position-Encoding WW/SS Sequence Pattern is Depleted in Mammalian Genes Relative to Other Eukaryotes, Gregory M. Wright and Feng Cui
Characterizing bladder cancer cells by comparing general machine learning methods to convolutional neural network, Peng Nien Yin
Documents from 2018
Effect of lead contaminated soils on lycopene and mineral contents of tomatoes (Solanum lycopersicum), Andrea T. Amati
Using Microalgae to Remediate Food and Bio-Digester Effluents from Western New York Agro Industries and Prospecting Harvested Algae Biomass for Biofuel Feedstocks, Daniel Anini Baah
Physical Models Can Provide Superior Learning Opportunities Beyond the Benefits of Active Engagements, Dina L. Newman, Megan Stefkovich, Catherine Clasen, Margaret A. Franzen, and Leslie Kate Wright
Analysis of Grape Berry Epiphytic Microbiomes via QIIME, Isabelle O'Bryon
A Community-Building Framework for Collaborative Research Coordination across the Education and Biology Research Disciplines, Nancy Pelaez, Trevor R. Anderson, Stephanie M. Gardner, Yue Yin, Joel K. Abraham, Edward L. Bartlett, Cara Gormally, Carol A. Hurney, Tammy M. Long, Dina L. Newman, Karen Sirum, and Michael T. Stevens
Effects of fullerenes on a freshwater benthic community: toxicity and implications for ecological functions and services, Sarah Ponte Cabral
Transcriptome-Wide Analysis of VSV Strains with Varying Ability to Block NF-κB, Thomas M. Russell
Comparative Transcriptomics of Grapevine Powdery Mildew, Christopher Wayne Snyder
Modeling the Health Effects and Economic Costs of Particulate Matter Emissions from High Volume Hydraulic Fracturing, Marissa Steinheimer
Modeling Health Effects of Particulate Matter Emissions From Heavy Duty Diesel Trucks Involved in High Volume Hydraulic Fracturing with BenMAP-CE, Katelijn Van Munster
