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, but unfortunately we are not able to consider non-US applicants for this program. Since our funding for this program is from the NSF, participants must be U.S. citizens, U.S. nationals, or permanent residents of the United States.

Applicants should apply at NSF ETAP. The 2022 undergraduate summer internship program is scheduled to run from June 6 to August 12, 2022. Applications for Summer 2022 are currently closed. Please check back in Fall 2022 for details about the Summer 2023 program.

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.

A list of potential projects for Summer 2022 can be found here.

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 computer science, check out https://www.cs.umd.edu/projects/reucaar/.

Faculty mentors:

Useful information

University of Maryland COVID-19 guidelines

UMD Dept of Resident Life: Summer Housing

CBCB Wiki page: Getting started at CBCB

FAQs:

1. Do you provide any housing to interns? Are there any other benefits?

Students will receive a stipend of $600 per week for ten weeks. Travel expenses to the site ($500), meal costs ($140/week), and housing (set up by the program in UMD housing). If required, parking costs will also be covered.

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?

CBCB faculty have provided a list of potential projects for undergraduate students. Applicants should look over these projects and indicate the top three projects they are interested in on their applications, though this is not required. 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.

11. 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.

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

Former Students:

2021 (held virtually due to COVID-19)

  • 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 (held virtually due to COVID-19)

  • 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)

Attachment: