Summer Internships

2019 Undergraduate Summer Internship Program at CBCB


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.

The program will run from June 10 to August 16, 2019. Wages will be $12.50/hour. Due to the nature of the funding source, interns are not eligible for overtime.

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.

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.

How to apply:

This summer the program is open to university level students ONLY (including graduating seniors). You do not need to be a University of Maryland student to apply; applicants from other universities are encouraged, but we are not able to consider non-US applicants.

In addition, applications should have:

  • one recommendation letter from a teacher or mentor
emailed to cbcb-internships [at], or submitted via the Google Form. If the person who recommends you would prefer to mail a hard copy of their letter, please send to: Summer Internship Program, The Center for Bioinformatics and Computation Biology, 8314 Paint Branch Drive, 3121 Biomolecular Sciences Bldg, University of Maryland, College Park, MD 20742.

For full consideration, applications must be received by March 15, 2019 (applications will be considered until the positions are filled). Incomplete applications will not be considered.


This program is supported in part by various NIH and NSF grants to various faculty, and by Illumina

Faculty mentors:


Useful information

Housing at UMD

UMD Dept of Resident Life: Summer Housing

Off-Campus Housing

CBCB Wiki page: Getting started at CBCB


To be announced


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

There are no additional benefits. We can point the interns to various resources on and off campus, but we do not directly provide or assist in finding housing.

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?

It will depend on the specific mentor that the intern will be assigned to. Please look at CBCB faculty pages to get an idea of types of problems that interns may work 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 6 interns. Typically, each intern will work on a different project, but joint project 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.

Current Students (Summer 2019):

  • Camilo Calvo-Alcaniz
  • Hyeyun Chae
  • Marine Crane
  • Jessica Pan
  • Kassie Wang

Former Students:


  • Larry Feldman (University of Maryland), "CONSERVE Project and its Significant Findings", Mentor: Mihai Pop
  • Kay Htut (University of Maryland), "Application of NMF on Mutational Signatures", Mentor: Hector Corrada Bravo and Max Leiserson
  • Yousef Khan (University of Maryland), "Identification and Classification of Biothreats Case Study: Staphylococcus aureus", Mentor: Jeremy Selengut
  • Nupur Pandya (University of Maryland), "Identification and Classification of Biothreats Case Study: Staphylococcus aureus", Mentor: Jeremy Selengut
  • Shilpa Roy (University of Maryland), "Identification and Classification of Biothreats Case Study: Staphylococcus aureus", Mentor: Jeremy Selengut
  • Kassie Wang, "Evaluating Refinded 16S Taxonomic Assignments", Mentor: Mihai Pop


  • Quinn Doubet (Wells College) - "Bacterial gene family modeling", Mentor: Jeremy Selengut
  • Brian Gottfried (University of Maryland) - "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 (University of Maryland) - "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 (University of Maryland) - "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)