Research Students
Undergraduate researchers I’ve had the privilege to advise since 2010. Names link to a full profile where one exists. Honors theses are listed on Publications.
| Year | Student(s) | Project | Funding |
|---|---|---|---|
| 2025 | Jesse Gunn Cheu ’26 | Immunoglobulin gene annotation refinement with machine learning classifiers — faculty mentor Ken Field (Biology), with Ava Hendrix ’28; Kalman Research Symposium 2026 talk | Department of Biology |
| 2024 | Ryan Koes ’26 | Machine learning on sensor and cyclic-voltammetry data for unbiased coffee characterization (co-advised with K. Wakabayashi and Alan Marchiori) — honors thesis, defended spring 2026 | |
| 2023 | Brad Schultes ’24 & Austin Beal ’24 | Utilizing extended reality for healthcare education (with Dr. Tyler Wallen, Geisinger) | Ciffolillo Healthcare Technology Inventors Program |
| 2021 | Z. Zeng, B. Hatzinger, G. Torres | Hygroscopic Tandem Differential Mobility Analyzer for aerosol studies (with Dabrina Dutcher & Tim Raymond) | NSF RUI |
| 2020 | A. Murph | Comparing finite sequences of discrete events with non-uniform time intervals (with Abby Flynt) — published in Sequential Analysis | |
| 2019 | Taehwan Kim ’20 | Chaotic time series prediction using deep echo state networks — honors thesis; published in Neural Computing & Applications; Presidential Fellow | McKenna Environmental Internship (Summer 2019) |
| 2019 | Zilin Ma | Low-level image features and gaze behavior (with Vanessa Troiani and Evan Peck) | Bucknell Geisinger Healthcare Research Initiative |
| 2019 | Lily Romano ’20 | Software for aerosol analysis (LILAC), with Dabrina Dutcher | Clare Boothe Luce Research Scholars |
| 2019 | Kartikeya Sharma ’22 | Trajectory gaze path analysis on eye-tracking data for autism spectrum disorder (with Vanessa Troiani, Geisinger) — SVURS 2021 and Kalman Symposium 2022 | Ciffolillo Healthcare Technology Inventors Program |
| 2019 | Bhagawat Acharya ’20 | Automated handwriting recognition for Moravian memoirs transcription (with Katie Faull and Carrie Pirmann) — DH2020 | Emerging Scholars |
| 2019 | Yili Wang ’21 | Using deep learning to identify features of images with high interest from children with autism (with Vanessa Troiani, Geisinger) | Program for Undergraduate Research |
| 2019 | Will Snyder | Self-organizing-map models of resting-state fMRI — lead advisor Vanessa Troiani (Geisinger) | |
| 2018 | Brooke Bullek ’18 | Eye-tracking software for crowd-sourced eye-tracking analysis (with Evan Peck and Vanessa Troiani, Geisinger) | Bucknell Geisinger Healthcare Research Initiative |
| 2016 | Khai Nguyen | Chemics: open-source cloud condensation nuclei analysis software (with Dabrina Dutcher), the forerunner of LILAC; early webcam eye-tracking prototype | CS and Chemical Engineering |
| 2016 | Morgan Eckenroth ’17 | Application for assessing visual bias in children with autism, in virtual reality (with Vanessa Troiani, Geisinger) | Ciffolillo Healthcare Innovation Award |
| 2016 | Tongyu Yang ’18 | Deep learning on images with varying autism interest levels (with Vanessa Troiani, Geisinger) | Program for Undergraduate Research |
| 2015 | Son Pham ’17 | Deep learning for protein sequence classification | Program for Undergraduate Research |
| 2015 | Jason Hammett ’17 | Data mining to predict meteorological events in the Susquehanna Valley | Program for Undergraduate Research |
| 2015 | Robert Cowen ’17 | Word prediction for augmentative and alternative communication for children with autism, Android app (with Marissa Mitchel and Abby Hare-Harris, Geisinger) | CS Healthcare Engineering Fund (2015); Ciffolillo (2016) |
| 2014 | Matthew Rogge ’17 | Spike-timing-dependent neural networks for more efficient starting-state learning | Program for Undergraduate Research |
| 2014 | Stephanie Gonthier ’15 | Statistical learning to improve word prediction for AAC — SVURS 2014 oral presentation winner | Program for Undergraduate Research |
| 2014 | Kevin Thomas ’13 & Yifan Ge ’14 | Hardware-based sequence alignment system | Greater Susquehanna Keystone Innovation Zone |
| 2013 | Brigitte Hofmeister ’14 | ngPhylo: n-gram modeled proteins for phylogenetic analysis — ACM BCB 2013 | |
| 2013 | Elizabeth Dwornik ’14 | Named-entity recognition with regular expressions | Program for Undergraduate Research |
| 2013 | Chuqiao (Rachel) Ren ’15 | Ensemble classification for protein contact map prediction — honors thesis; ACM BCB 2014 | Program for Undergraduate Research |
| 2012 | Charles Cole ’14 | Machine learning to predict the health of HIV-infected patients — honors thesis; ACM BCB 2013; SVURS 2013 oral presentation winner | Program for Undergraduate Research |
| 2012 | Marc Burian ’12 | Twitter sentiment and stock market performance | |
| 2011 | Phil Stahlfeld ’13 | Installation and deployment of caBIG for cancer research (with Gerard Tromp, Geisinger) | Geisinger Research Center |
| 2011 | Alex Barteau ’13 | ngLOC software for subcellular localization prediction (with Chittibabu Guda, University of Nebraska Medical Center) — BMC Research Notes 2012 | University of Nebraska Medical Center |
| 2011 | Matthew Segar ’12 | De novo genome assembly for next-generation sequencing — honors thesis (Harold W. Miller Prize); ISMB 2012 | Program for Undergraduate Research |
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Profiles and updates (2011–2016)
| Year | Profile / update | Description |
|---|---|---|
| 2016 | Summer 2016 | It has been quite some time since I’ve updated current events. Thanks to our students, we have had a pretty active summer… |
| 2015 | Son Pham, ’17 |
Project: Using Deep Learning to Automatically Learn Feature Representation and Build a Better Classification Model on Protein Sequential Data Started: Summer 2015 Funding… |
| 2015 | Chuqiao Ren, ’15 |
Project: A novel ensemble classifier for protein contact map prediction Duration: Summer 2013 – Spring 2015 Funding: Bucknell University Program for Undergraduate Research… |
| 2015 | Summer 2015 | We have an active summer in store. Three students are working on entirely different research projects, while Rachel Ren is wrapping up her work. |
| 2015 | Spring 2015 | Rachel Ren successfully defended her honors thesis, titled, “Predicting Protein Contact Maps by Bagging Decision Trees”. Congratulations, Rachel! Additionally, Rachel will… |
| 2014 | Stephanie Gonthier, ’15 |
Project: Using statistical learning to improve word prediction for augmentative and alternative communication Duration: Summer 2014 Funding: Bucknell University Program for… |
| 2014 | Elizabeth Dwornik, ’14 |
Project: Named-Entity Recognition Duration: Summer 2013 – Spring 2014 Funding: Bucknell University Program for Undergraduate Research |
| 2014 | Matthew Rogge, ’17 |
Project: Analysis of Spike Timing Dependent Neural Networks for More Efficient Starting State Learning Duration: Summer 2014 Funding: Bucknell University Program for… |
| 2014 | Charles Cole ’14 |
Project: Using Machine Learning to Predict the Health of HIV-Infected Patients Duration: Summer 2012 – Spring 2014 Funding: Bucknell University PUR, Biology Dept. and CS… |
| 2014 | Brigitte Hofmeister ’14 |
Project: Modeling the Evolution of Influenza Duration: Summer 2013 – Fall 2013 Funding: Bucknell University Program for Undergraduate Research, CS Dept. Funding |
| 2012 | Alex Barteau, ’13 |
Project: Development of protein sequence analysis software Duration: Summer 2011 – Spring 2012 Funding: University of Nebraska Medical Center Collaboration: Dr. Chittibabu… |
| 2012 | Matthew Segar, ’12 |
Project: A probabilistic method for assembly of next generation sequencing instrumentation Duration: Summer 2011 – Spring 2012 Funding: Bucknell PUR, Provost’s Office, CS.… |
| 2012 | Marc Burian ’12 |
Project: Twitter sentiment and stock market performance Duration: Spring 2012 – Summer 2012 Funding: None |
| 2011 | Phil Stahlfeld ’13 |
Project: Installation and deployment of caBIG – an information management network for cancer research Duration: Summer 2011 – Spring 2012 Funding: Geisinger Research Collabor… |
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