Summer Internships

This Research Experiences for Undergraduates (REU) program is open to university level undergrad students. You do not need to be a University of Maryland student to apply; applicants from other universities are encouraged. Applicants must be U.S. citizens, U.S. nationals, or permanent residents of the United States.

Applicants should apply at NSF ETAP. The 2024 undergraduate summer internship program is scheduled to run from June 3 to August 9, 2024. Applications for summer 2024 will be accepted until March 1, 2024.

See HERE for advice on how to strengthen your application

Program Overview:

Following the genome revolution, bioinformatics has arisen as an essential field of research. There is a critical need for scientists with interdisciplinary training to process and analyze large scale genomic datasets. This REU establishes a program called BRIDGE (Bioinformatics Research In Data science for Genomics) that exposes students to research within bioinformatics and computational biology. Ten students will receive training and mentorship for ten weeks each summer and will be jointly advised by members of the UMD Center for Bioinformatics and Computational Biology (CBCB).

Throughout this experience, students will work in pairs to learn about a research problem, propose a plan to tackle a specific research question, and implement their plan. With the guidance of experienced mentors, undergraduate students will research real world problems in cutting-edge areas of bioinformatics, including metagenomics, machine learning, single-cell RNA sequencing, parallel computing, and phylogenomics. Students will address novel problems with unknown answers. By the end of the summer, each team will produce a paper and give an oral presentation on their project. Students’ findings will advance knowledge and understanding of the field.

BRIDGE aims to build a diverse cohort of exceptional undergraduates from across the country and provide research opportunities for women, underrepresented minorities, and non-traditional students. In order to build a solid foundation in bioinformatics and computational biology, students will take a week-long intensive course and attend seminars and panel discussions on various professional development topics. BRIDGE will provide students with a valuable, enjoyable research experience that will encourage them to pursue interdisciplinary graduate studies and eventually expand and diversify the biomedical research field.

Given the short duration and intensive work schedule of the internship, interns are expected to plan their vacations around the internship dates. Exceptions will be made in case of emergencies.

For another program at the University of Maryland focused on combinatorics and computer science, check out https://www.cs.umd.edu/projects/reucaar/.

Financial information

The following are provided to participants in the program:

• Costs of travel to/from the University of Maryland
• Housing in student dorms (double occupancy)
• Stipend: $600/week
• Meal card: $140/week. The meal card can be used at multiple cafeterias on campus.
• Parking (if needed)

Faculty mentors:

• Michael Cummings
• Seth Commichaux (FDA)
• Heng Huang
• Rob Patro
• Mihai Pop

Useful information

University of Maryland COVID-19 guidelines

UMD Dept of Resident Life: Summer Housing

CBCB Wiki page: Getting started at CBCB

FAQs:

1. My school is on the quarter system and my final exams conflict with the start date of the program. Can I still apply?

Yes. The program dates were selected based on housing availability, which unfortunately conflicts with the end of the year for schools on quarter systems. We are happy to work with students to get them up to speed if their exam schedule would require a later starting date.

2. What are the times of day that the intern is expected to be at work?

We expect interns to be at work 9:30 to 5, but it will depend on the specific mentor. The students are expected to attend various relevant seminars on campus.

3. Is the intern expected to dress professionally each day or is business causal okay for this type of work environment?

There is no dress code.

4. I realize that topics will be chosen the first week of the internship, but what sort of projects are available for the intern to choose to work on?

A list of general topics provided by faculty last year is available here. This list will be updated closer to the start of the internship. A list of research projects completed by summer interns in prior years can be found below the FAQ to give potential interns an idea of the types of projects being worked on.

5. How many other interns are there expected to be? Will the interns have the chance to work with other interns?

We are aiming to have 10 interns each summer. Interns will work in teams to address novel problems in computational biology.

6. Is there any chance that an intern could work at the CBCB during the school year, or possibly in future summers?

Yes, depending on mentor's funding and availability.

7. What do the intern's responsibilities entail? Will the intern work at a desk or in a lab?

All research at CBCB is purely computational, i.e., on a computer. The program involves full-time research (40 hours/week).

8. Will CBCB provide computers?

Students are encouraged to bring and use their own computers, but some computers will be available if requested.

9. How much guidance will the interns have from mentors?

They should expect to receive very close guidance from the mentors. You will also get to meet graduate students and postdocs in the Center who work on related projects. They will help co-mentor you throughout the duration of your project.

10. Do the interns work on campus daily, or is it possible for the interns to telecommute?

Interns are expected to be on campus. Specific exceptions can be made by the intern's mentor.

Have additional questions? Please reach out to info-cbcb@umiacs.umd.edu

Former Students:

2023 REU BRIDGE

• 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

2022 REU BRIDGE

• 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

2021 (virtual)

• 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

2020 (virtual)

• 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

2019

• 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

2018

• 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

2017

• 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

2016

• 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

2015

• 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

2014 and before

• 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)