Research Experience for Undergraduates (REU) Summer Internships
Every summer from 2014–2024, the Center for Bioinformatics and Computational Biology (CBCB) hosted a cohort of summer undergraduate researchers supported by the National Science Foundation (NSF). The Research Experiences for Undergraduates (REU) program called BRIDGE (Bioinformatics Research In Data science for Genomics) is now inactive as a result of federal funding cuts to NSF. Many of our former interns have gone on to have successful careers in industry and academia.
- Erick Alvarez (Utah Valley University), "Analysis of data on treatment for drug abuse", Mentor: Michael Cummings
- Anning Cui (University of Maryland, College Park), "Resolving containments in assembly graphs", Mentor: Mihai Pop
- Jake Jasmer (Carleton College), "Discovering new phage plasmids", Mentor: Mihai Pop
- Genelle Jenkins (Arizona State University), "Discovering new phage plasmids", Mentor: Mihai Pop
- Kashir Khan (UT Dallas), "Lineage tracing from single cell RNA-seq data", Mentor: Heng Huang
- Amara McGowan (St. Lawrence University), "Lineage tracing from single cell RNA-seq data", Mentor: Heng Huang
- James Mwihaki (MidAmerica Nazarene University), "Determining host range of bacterial plasmids", Mentor: Seth Commichaux
- Jay Rangarajan (UC San Diego), "Determining host range of bacterial plasmids", Mentor: Seth Commichaux
- Skylar Rinderknecht (Colorado School of Mines), "Indexing the CHESS transcript database", Mentor: Rob Patro
- Sophie Robertson (University of Washington), "Indexing the CHESS transcript database", Mentor: Rob Patro
- Ryan Schuenke (Drake University), "Analysis of data on treatment for drug abuse", Mentor: Michael Cummings
- Vivek Agarwal (University of Maryland, College Park), "Identifying shared genomic segments across metagenomic samples", Mentor: Mihai Pop
- Sarah Blankespoor (California Polytechnic State University San Luis Obispo), "Improving sequence polishing for Nanopore reads", Mentor: Mihai Pop
- Madeline Bonanno (Tulane University), "Evaluating fast phylogenetic methods for reconstructing the evolution of SARS-CoV-2 lineages", Mentor: Erin Molloy
- John Bridgers (University of Maryland, College Park), "Improving Species Tree Estimation with Missing Data", Mentor: Erin Molloy
- Noah Cape (Williams College), “Developing a General Purpose, High Performance, Sequence pre-processor”, Mentor: Rob Patro
- Junyan Dai (University of Maryland, College Park), "Leveraging Constraints and Dynamic Programming for the Large Dollo parsimony Problem", Mentor: Erin Molloy
- Olivia Davis (Rose-Hulman Institute of Technology), “Developing an efficient algorithm for determining orthologous and paralogous relationships in a phylogeny”, Mentor: Michael Cummings
- Carola Gonzales Lebron (University of Dayton), "Evaluating multiple sequence alignment methods in light of taxonomic diversity and sampling", Mentor: Erin Molloy
- Natalia Quintana Parilla (University of Puerto Rico Mayaguez), “Investigating the splicing status of sequenced molecules from single-cell RNA-seq data”, Mentor: Rob Patro
- Charlotte Ravel (University of Maryland, College Park), "Firmware development for low-power wearable devices enabling time-tracking and low-power data transmission using Bluetooth Low Energy", Mentor: Brantley Hall
- Ashley Tien (University of Maryland, College Park), "Firmware development for low-power wearable devices enabling time-tracking and low-power data transmission using Bluetooth Low Energy", Mentor: Brantley Hall
- Gaoussou Touré (Montgomery College), “Developing an efficient algorithm for determining orthologous and paralogous relationships in a phylogeny”, Mentor: Michael Cummings
- Raunak Vijay (University of New Hampshire at Manchester), "Improving sequence polishing for Nanopore reads", Mentor: Mihai Pop
- David Zhan (University of Pennsylvania), "Firmware development for low-power wearable devices enabling time-tracking and low-power data transmission using Bluetooth Low Energy", Mentor: Brantley Hall
- Esmma Almousa (University of Wisconsin Madison), "Machine learning and model interpretation for longitudinal data with applications to Parkinson's disease", Mentor: Michael Cummings
- Shria Arcot (University of California San Diego), "Improved detection of worn state in a wearable sensor", Mentor: Brantley Hall
- Nicholas Arellano (Community College of Baltimore County), "Machine learning and model interpretation for longitudinal data with applications to Parkinson's disease", Mentor: Michael Cummings
- Aditya Girish (Rutgers University), "FastMulRFS (phylogenetic inference with multi-copy genes) optimization", Mentor: Erin Molloy
- Nathan Jacobi (University of Georgia), "Single cell RNA-seq transcript quantification", Mentor: Rob Patro
- Adam Levav (University of Maryland), "Sequence alignment to detect structural variants" , Mentor: Mihai Pop
- Luiz Mata Lopez (Montgomery College), "FastMulRFS (phylogenetic inference with multi-copy genes) optimization", Mentor: Erin Molloy
- Sean Markey (University of Maryland), "Single cell RNA-seq transcript quantification", Mentor: Rob Patro
- Lucy Mettee (The University of Texas at Dallas), "Sequence alignment to detect structural variants" , Mentor: Mihai Pop
- Olivia Miskala-Dinc (University of Maryland), "Improved detection of worn state in a wearable sensor", Mentor: Brantley Hall
- Alexander Lee (UMD), "Testing Averages for Binnacle Coverage Estimation", Mentors: Jacquelyn Michaelis, Mihai Pop
- Sho Takeshita (UMD), "Testing Averages for Binnacle Coverage Estimation", Mentors: Jacquelyn Michaelis, Mihai Pop
- Alyssa Pratt (Oregon State Univ), "Improving Taxonomic Classifications by Guarding Against Bad Data", Mentors: Jacquelyn Michaelis, Mihai Pop
- Celestine Zhao (UMD), "Improving Taxonomic Classifications by Guarding Against Bad Data", Mentors: Jacquelyn Michaelis, Mihai Pop
- Shiva Mehravaran (Morgan State University), Mentors: Jacquelyn Meisel, Mihai Pop
- Chatonya Brown (Morgan State University), Mentors: Jacquelyn Meisel, Mihai Pop
- Subhadra Paudel (Morgan State University), Mentors: Jacquelyn Meisel, Mihai Pop
- Aya Kutbi (Morgan State University), Mentors: Jacquelyn Meisel, Mihai Pop
- Somayeh Moslehi (Morgan State University ), Mentors: Jacquelyn Meisel, Mihai Pop
- Christian Yovo (Towson University), Mentors: Jacquelyn Meisel, Mihai Pop
- Camilo Calvo-Alcaniz (UMD), "Characterizing Synthetic Lethality Using Single- and Double-Knockout Experiments", Mentor: Sridhar Hannenhalli
- Hyeyun Chae, (Swarthmore College), "Visualizing Results from Galaxy Workflows Using Epiviz", Mentors: Jayaram Kancherla, Hector Corrada Bravo
- Marie Crane (Macalester College), "Analysis of metagenomic assembly graphs", Mentors: Jacquelyn Meisel, Mihai Pop
- Jessica Pan (Yale), "Characterizing Synthetic Lethality Using Single- and Double-Knockout Experiments", Mentor: Sridhar Hannenhalli
- Kassie Wang (high school student), "Analysis of metagenomic assembly graphs", Mentors: Jacquelyn Meisel, Mihai Pop
- Larry Feldman (UMD), "CONSERVE Project and its Significant Findings", Mentor: Mihai Pop
- Kay Htut (UMD), "Application of NMF on Mutational Signatures", Mentors: Hector Corrada Bravo and Max Leiserson
- Yousef Khan (UMD), "Identification and Classification of Biothreats Case Study: Staphylococcus aureus", Mentor: Jeremy Selengut
- Nupur Pandya (UMD), "Identification and Classification of Biothreats Case Study: Staphylococcus aureus", Mentor: Jeremy Selengut
- Shilpa Roy (UMD), "Identification and Classification of Biothreats Case Study: Staphylococcus aureus", Mentor: Jeremy Selengut
- Kassie Wang (high school student), "Evaluating Refinded 16S Taxonomic Assignments", Mentor: Mihai Pop
- Quinn Doubet (Wells College) - "Bacterial gene family modeling", Mentor: Jeremy Selengut
- Brian Gottfried (UMD) - "Interactive genomic visualizations", Mentor: Héctor Corrada Bravo
- Rachel Hammelman (University of Rochester)
- Ayub Khan (Virginia Commonwealth University) - "Intron retention during raspberry fruit development", Mentors: Zhongchi Liu, Sridhar Hannenhalli, Haley Wight
- Alex Lugo (UMD) - "Genetic mapping with RNA-seq data", Mentor: Steve Mount
- Reilly Thate (Rochester Institute of Technology) - "Critical assessment of metagenome interpretation", Mentors: Todd Treangen, Mihai Pop
- Michelle Tu (UMD) - "Bacterial gene family modeling", Mentor: Jeremy Selengut
- Min Geol Joo (Johns Hopkins University) - "Hunt for tiny RNAs", Mentor: Sridhar Hannenhalli / Anthony Jose
- Ankita Acharya (UMD) - "Biomarkers of Healthy Human Aging", Mentor: Zia Khan
- Christopher Zawora (Georgetown University) - "Strawberry development", Mentor: Steve Mount / Zongchi Liu
- Brian Liu (UMD) - "Contamination in ancient DNA", Mentor: Philip Johnson
- Steffan Cornwell (University of Pennsylvania) - "Improving transcript quantification methods", Mentor: Steve Mount / Hector Corrada Bravo
- Marcus Fedarko (UMD) - "Metagenomic assembly", Mentor: Mihai Pop
- Morgan Walter (UMD) - "Epigenomic visualization", Mentor: Hector Corrada Bravo
- Pranaya Terse (UMD) - "Comparative genomics of fruitfly to understand their development", Mentor: Zia Khan
- Kymberlee McMaster (UMD) - "Resolving haplotypes in turtle from sequencing data on multiple progeny", Mentor: Steve Mount
- Matthew Myers (UMD) - "Characterization of genomic variants in metagenomic assemblies", Mentor: Mihai Pop
- Morgan Walter (UMD) - "Protocols for interactive, collaborative, genomic visualization", Mentor: Hector Corrada-Bravo
- Teressa Chambers (University of Pittsburgh) - "Deconvolving signaling pathways from cancer data", Mentor: Sridhar Hannenhalli
- Taylor Gavin (Drake University) - 2014, "Positional effects of Enhancers", Mentor: Sridhar Hannenhalli
- Michelle Hwang (University of Michigan) - 2014, "Regulatory Rewiring of engrailed gene in insects", Mentor: Leslie Pick
- Yanhong Alice Lu (UMD) - 2014, "Biosimulation of Vocal Fold Wound Healing Response to Mechanical Stress", Mentor: Nicole Li
- Kevin Nguyen (University of Maryland Baltimore County) - 2014, "Genome Assembly", Mentor: Mihai Pop
- Rama Atitkar (UMD) - 2013, "RNA-seq analysis of strawberry development", Mentor: Zhongchi Liu
- Julien Buchbinder (UMD) - 2013, "K-mer based gene segment expression analysis", Mentor: Steve Mount
- Howard Huang (Johns Hopkins) - 2013, "Assembly algorithm correctness testing", Mentors: Atif Memon, Mihai Pop
- Emily Jones (UMD) - 2013, "Evolution of Intrinsically disordered proteins", Mentor: Sridhar Hannenhalli
- Llwellyn Smith (Williams College) - 2013, "Interactive Visualization of RNA-Seq Experiments with EpiViz", Mentor: Hector Corrada-Bravo
- Mary Allison Abad (UMD) - 2012, "Motif-based and protein interaction-based sequence similarity tools", Mentor: Hannenhalli
- Elfalem Alemu (UMD) - 2012, "Epigenetic correlates of inter-tissue differences in expression variability", Mentors: Hannenhalli, Corrada-Bravo
- Jakub Bialas (UMD) - 2012, "Compression of DNA sequences from sequencing machines", Mentors: Cummings, Kingsford
- Naomi Goldstein (Wash U) - 2012, "DNA methylation genome context analysis", Mentors: Corrada-Bravo
- Michael Kleyman (UMD) - 2012, "Alternative splicing and gene expression", Mentors: Mount
- Scott Rome - 2011 - UMD - Analysis of cancer demthylation (Mentor: Hector Corrada-Bravo)
- Michele Pondlick - 2011 - UMD - (Mentor: Hector Corrada-Bravo)
- Cara Treglio - 2011 - UMD - Determination of chromatin structure from 3C data (Mentor: Carl Kingsford)
- Rachel Blythe - 2010 - Graph-based detection of genetic reassortment and rearrangement (Mentor: Carl Kingsford)
- Aashish Gadani - 2010 - Graph clustering and visualization (Mentor: Carl Kingsford)
- Nicholas Jacobs - 2010 - Gene function prediction via clustering by co-evolution (Mentor: Liliana Florea)
- JaeYoung Kwak - 2010 - Detection of variation in human genes (Mentor: Steven Salzberg)
- Joseph Paulson - 2010 - Statistics for comparing clinical data; and identification of variation in assembly graphs (Mentor: Mihai Pop)
- Megan Riordan - 2010 - Graph clustering and visualization (Mentor: Carl Kingsford)
- Joshua Wetzel - 2009 - Genome assembly complexity (Mentors: Carl Kingsford, Mihai Pop)
- Govin Vatsan (highschool)- 2009 - Visualization of assembly graphs (Mentor: Carl Kingsford)
- Petar Stojanov - 2009 - Transcriptome alignment (Mentor: Liliana Florea)
REU BRIDGE in the News
REU Bioinformatics Program Immerses Students into Interdisciplinary Research
Sponsored by NSF, the program exposes visiting undergraduates to interdisciplinary training needed to process and analyze large scale genomic datasets.
REU Interns Learn to Navigate Complexities of Health Research
From exploring the mysteries of the gut microbiome to researching the complexities of the COVID-19 virus, 14 undergraduate students from across the country…
REU Summer Interns Tackle Big Problems in Bioinformatics
The 10 undergraduate students are part of an internship funded by NSF and run by faculty in CBCB.