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Documents from 2022

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Invasive Species Identification and Monitoring using Computer Vision, Street View Imagery, and Community Science, Liam Megraw

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Identification of Essential Gene Relations For Lung Adenocarcinoma Therapy Targets by Cross-Referencing Literature-Mined and RNASeq Data, Mariel V. Pridmore

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Functional evolutionary adaptation of binding dynamics in the SARS-CoV-2/ACE2 interface from bats to humans, Madhusudan Rajendran

Documents from 2021

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Effects of Microplastic on Freshwater Benthic Ecosystems: toxicity and impacts on biogeochemical cycling, Kristina Chomiak

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Examining the Associations Between Neighborhood Socioeconomic Status and the Potential Distribution of Four Urban Ecosystem Services in Rochester, NY, Joshua Greene

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Literature-Assisted Validation of a Novel Causal Inference Graph in a Sparsely Sampled Multi-Regimen Exercise Data, Aditya Gupta

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Effects of wetland design and invasive species removal on carbon and microbial communities in restored wetlands, Benjamin Hamilton

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Controls on Denitrification and Nitrous Oxide Flux in Created Wetlands, Sonia Huang

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An Exploratory Assessment of Peer-reviewed Life Science Literature Statement Readability Used in Text-based Interpretive Analyses, Jeremy Jackson

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Deep Learning Models to Characterize Smooth Muscle Fibers in Hematoxylin and Eosin Stained Histopathological Images of the Urinary Bladder, Sridevi Kayyur Subramanya

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Modeling the mechanistic behavioral logic supporting adherence to hormone therapy in breast cancer patients, Gina Kersey

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Assembly and annotation of the genome of an invasive bush honeysuckle, Amur honeysuckle (Lonicera maackii), Erin R. Kesel

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Assessment and Deployment of Genetic Tools for North American River Otters (Lontra canadensis), Kelsey Lawton

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Conservation of the Ambystoma jeffersonianum Complex, Morgan Motherwell

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Development of a Novel Algorithm to Remove Spurious Edges from Biological Networks Through Functional Enrichment, Jeffrey Page

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Comparative DNA Degradation Automation for Identifinders, Jennifer Pfaff

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Methane Emissions from Stormwater Ponds, Brianna Pollard

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ProMOL: Updating the Template Based Structural Alignment Plugin, Mariah Robertson

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Biodegradation and microbial CO2 evolution of blended polymers in food-waste and coffee supplemented disposal environments, Abigail Rolston

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SecretePEPPr: Computational Prediction and Characterization of Effector-like Proteins Secreted from Vitis vinifera, Patrick Rynkiewicz

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Evaluating Electronic Pulse Generators for Cooling Tower Sanitation, Hannah Saxena

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Characterization and Proteolytic Maturation of Head Proteins in a Giant Salmonella Virus, Aaron Scheuch

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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

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The Influence of Herbivory on Macrophyte Community Structure and Nitrogen Retention in Created Wetlands, Evan Squier

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Analysis of nucleosomal DNA patterns around transcription factor binding sites, Sheethal Umesh Nagalakshmi

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Socio-ecological context matters for wetland project outcomes, Sydney VanWinkle

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Carbon Soil Amendment for Promotion of Native Species in Created Emergent Freshwater Wetlands, Taylor E. Williams

Documents from 2020

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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

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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

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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

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Effects of Prior Land Use, Carbon Availability, and Hydrology on Nitrogen Cycling in Created Freshwater Wetlands, Michael McGowan

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A Recent (2020) Comparative Analysis of Genome Aligners Shows HISAT2 and BWA are Among the Best Tools, Ryan J. Musich

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Interactive Video Vignettes (IVVs) to Help Students Learn Genetics Concepts, Dina L. Newman, Jean Cardinale, and L Kate Wright

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Applying Systems Pharmacology to the Treatment of Chronic Illness Using Novel Scoring and Translational Methods, Spencer Richman

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Regulation of Transposable Elements by Tumor Suppressor Protein 53, Andrew J. Rosato

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Ecological Impacts of Food Waste Digestate Management in an Agricultural Watershed, Shradha Shrestha

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Transcriptomic Analysis and Developmental Neural Transcript Identification in the Brittle Star Ophioplocus esmarki, Alexandria Shumway

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The impact of herbivory on methane cycling in a created wetland, Briana B. Stringer

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Phenology-dependent cold exposure and thermal performance of Ostrinia nubilalis ecotypes, Crista B. Wadsworth, Yuta Okada, and Erik B. Dopman

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Undergraduate Textbook Representations of Meiosis Neglect Essential Elements, Leslie Kate Wright, Grace Elizabeth C. Dy, and Dina L. Newman

Documents from 2019

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Genetics and Molecular Dynamics of L,L-Diaminopimelate Aminotransferase (DapL): an Enzyme Involved in Lysine and Peptidoglycan Biosynthesis, Lily E.J. Adams

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Habitat and Conservation Suitability Assessment for Shrubland Birds in Monroe County, New York, Rachel Allen

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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

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Simulating Pathway-Based Steady States to Prevent Epithelial- Mesenchymal Transition in Ovarian Cancer, K Jeselle Clark

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A Close-Up Look at PCR, Callie J. Donahue, Ashley A. Adair, Leslie Kate Wright, and Dina Newman

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Decadal Changes in Salt Marsh Succession and Assessing Salt Marsh Vulnerability using High-Resolution Hyperspectral Imagery, Sarah Goldsmith

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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

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Functional Comparison of Current Software Tools for Genomic Assembly from High Throughput Sequencing Data, Lars J. Olsen

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Investigation of Cold Stress Induced Disease Resistance (SIDR) in Grapevines and Arabidopsis, Cal D. Palumbo

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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

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Investigation of nest predation as a cause of turtle population declines on the Sequoyah National Wildlife Refuge, Oklahoma, Alexandra M. Shipman

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Effects of grazer exclusion on carbon cycling in created freshwater wetlands, Delanie Spangler

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Factors Limiting Organic Carbon Degradation by Antibiotic-Resistant Heterotrophic Microorganisms in Wastewater Contaminated Sediments, Katelyn Whitburn

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The Nucleosome Position-Encoding WW/SS Sequence Pattern is Depleted in Mammalian Genes Relative to Other Eukaryotes, Gregory M. Wright and Feng Cui

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Characterizing bladder cancer cells by comparing general machine learning methods to convolutional neural network, Peng Nien Yin

Documents from 2018

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Effect of lead contaminated soils on lycopene and mineral contents of tomatoes (Solanum lycopersicum), Andrea T. Amati

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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

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A Habitat Suitability Model for Ruffed Grouse (Bonasa umbellus) in New York State Department of Environmental Conservation Region 8, Austin Groff

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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

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Analysis of Grape Berry Epiphytic Microbiomes via QIIME, Isabelle O'Bryon

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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

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Effects of fullerenes on a freshwater benthic community: toxicity and implications for ecological functions and services, Sarah Ponte Cabral

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Transcriptome-Wide Analysis of VSV Strains with Varying Ability to Block NF-κB, Thomas M. Russell

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Comparative Transcriptomics of Grapevine Powdery Mildew, Christopher Wayne Snyder

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Modeling the Health Effects and Economic Costs of Particulate Matter Emissions from High Volume Hydraulic Fracturing, Marissa Steinheimer

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Modeling Health Effects of Particulate Matter Emissions From Heavy Duty Diesel Trucks Involved in High Volume Hydraulic Fracturing with BenMAP-CE, Katelijn Van Munster

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Arrows in Biology: Lack of Clarity and Consistency Points to Confusion for Learners, Leslie Kate Wright, Jordan J. Cardenas, Phyllis Liang, and Dina L. Newman

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The DNA Triangle and Its Application to Learning Meiosis, Leslie Kate Wright, Christina M. Catavero, and Dina L. Newman

Documents from 2017

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Greenhouse Gas Fluxes from Created Wetlands: How Management Techniques Impact Emissions and Implications for Climate Change, Thulfiqar Ali Jasim Al-Graiti

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To Be or Not To Be T4: Evidence of a Complex Evolutionary Pathway of Head Structure and Assembly in Giant Salmonella Virus SPN3US, Bazla Ali, Maxim Desmond, Sara Mallory, Andrea Benitez, Larry J. Buckley, Susan T. Weintraub, Michael V. Osier, Lindsay W. Black, and Julie A. Thomas

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Analytical Flood Risk Models for First Responder Use: Obstruction Detection and Risk Assessment, Brett Edmond Carlock

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Revising a Habitat Suitability Model for Spotted Turtles (Clemmys guttata) in Upstate New York, Caitlin Dailey

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Evasion of Host Innate Immunity by Emerging Viruses: Antagonizing Host RIG-I Pathways, Maureen Ferran and Gary Skuse

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Identification of Differential Expression of p53 associated RNAs at 3 Different Treatment Timepoints, and Association with ChIP-seq Identified p53 Genes., Julia Freewoman

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Hydrology, nutrient availability, and herbivory interacting to control ecosystem functions and services in created emergent freshwater wetlands, Kimberly A. Lodge

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Development of the Central Dogma Concept Inventory (CDCI) Assessment Tool, Dina L. Newman, Christopher W. Snyder, J. Nick Fisk, and Leslie Kate Wright

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Meiosis: A Play in Three Acts, Starring DNA Sequence, Dina L. Newman and Leslie Kate Wright

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Degradation of cyclic ethers by microorganisms isolated from contaminated groundwater, Rowan Thompson

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Exploring GRIA2 Sequence Variations Using Virtual Reality, Jimmy Fan Zhang

Documents from 2016

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Developing a Prototype System for Syndromic Surveillance and Visualization Using Social Media Data., Anup Aryal

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Determining the Impact of Latitude on Parturition Timing in Captive North American River Otters: A Statistical Analysis of AZA Studbook Records, Jordan I. Bailey

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Computational analysis in vivo p53 binding sites in the context of chromatin and repeat regions, Feifei Bao

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Analyses of amber mutants of Salmonella phage SPN3US, Andrea Denisse Benítez Quintana

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Investigating the Role of Anaerobic Bacteria in Colorectal Carcinoma, Oluwadara Coker

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Oh Deer! Analyzing the Impact of RIT Expansion and Development on White-tailed Deer (Odocoileus Virginianus) and Vehicle Collisions from 1993-2014, Gina De Naples

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Killing Two Birds with One Stone: The Concurrent Development of the Novel Alignment Free Tree Building Method, Scrawkov-Phy, and the Extensible Phyloinformatics Utility, EMU-Phy., J. Nick Fisk

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Development of a Data Management System for Grape Breeding Programs, Connor Fortin

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Isolation of Pharmaceutical-Degrading Bacteria from Lake Sediments Associated with Wastewater Effluents, Noreen Anne Gallagher

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Improving the Performance of ProMOL by Integrating Communal Database Access, Alexander Grier

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Investigation of methods for machine learning associations between genetic variations and phenotype, Amanda M. Hartung

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Limitation of Invasive Plant Colonization by Native Shrubs During Forested Wetland Restoration, Kaitlyn E. Moranz

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Using Geographic Information Systems to Identify Habitat for the Golden-winged Warbler (Vermivora chrysoptera) in Western New York, Jesse Michael Rubenstein

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The influences of different socioeconomic scenarios in bioinformatics and biotechnology research: The ethical issues arising from technological advances, Marcia Miki Sato

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Estimates of Emissions from Heavy Duty Diesel Vehicles (HDDV) and Control Strategies Related to Transport Activities Supporting High Volume Hydraulic Fracturing Wells in the Marcellus Shale Formation, Rachel M. Zoyhofski

Documents from 2015

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Homology Based Motif Generation, Cameron Baker

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Computational identification of conserved haustorial-expressed genes in the grapevine powdery mildew fungus Erysiphe necator, Miriam E. Barnett

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Effect of Simulated Canopy Cover on Created Vernal Pools in the Northeastern US, Elizabeth Anne Bruen

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Novel nucleosomal particles containing core histones and linker DNA but no histone H1, Hope A. Cole, Feng Cui, Tara L. Burke, Tatiana Nikitina, Vivekananthan Nargarajavel, Naoe Kotomura, Victor B. Zhurkin, and David J. Clark

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Assessment of Alignment Algorithms, Variant Discovery and Genotype Calling Strategies in Exome Sequencing Data, Anthony Corbett

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Developing an algal biofilm filtration system for the remediation of nutrient pollution in freshwater ponds, Danielle Delp