Summer Internships

2022 Undergraduate Summer Internship Program at CBCB

Updates will be posted here when available. Typically the application process begins in early January and ends March 1st. Notifications of acceptance are usually made by the third week of March.

The program is open to university level undergrad students (including graduating seniors).

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.

Program Overview:

The goal of this program is to give young scientists at the undergraduate level hands-on research experience in bioinformatics as part of ongoing research projects within CBCB. The program involves full-time research (40 hours/week). During the first week you will choose your primary project for the summer from among several projects offered by faculty 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.

At the end of the summer you will put together a report outlining the results of your project and give a short presentation describing your project and what you have achieved.

In addition to research, there will be other seminars and research presentations, both at CBCB and elsewhere on campus. We will announce any seminars that might be of interest to you. In the past there have been weekly talks given by visiting faculty and graduate students on their research.

The 2022 undergraduate summer internship program is tentatively scheduled to run from June 7 to August 16, 2022.

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.

Applicants should email the following documents to blewis12 [at]

  • an up-to-date resume
  • a one page essay indicating their objectives for this internship
  • current transcripts (unofficial transcripts are fine)
These application materials must be emailed in PDF format (no Word documents please!).

In addition, applications should have a teacher or mentor send a recommendation letter to blewis12 [at]

Useful information

University of Maryland COVID-19 guidelines

Housing at UMD

UMD Dept of Resident Life: Summer Housing

Off-Campus Housing

CBCB Wiki page: Getting started at CBCB


June 7 to August 16, 2022


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

Housing allowances will be provided if funds are available. We can point the interns to various resources on and off campus, but we do not directly provide or assist in finding housing. Additional benefits include funds to support campus parking costs during ten week program.

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 specific mentor. The students are expected to attend various relevant seminars in 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 will provide a list of potential projects (coming soon) for undergraduate students before applications open. 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. Typically, each intern will work on a different project, but joint projects may be possible if two interns are assigned to the same PI.

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.

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

They should expect to receive very close guidance from the mentors.

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

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

Former Students:


  • Alexander Lee (UMD)...
  • Alyssa Pratt (Oregon State Univ)...
  • Sho Takeshita (UMD)...
  • Celestine Zhao (UMD)...


  • Not held due to Covid-19


  • 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", Mentor: 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

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)