Undergraduate Summer Research Internships
The Systems Biology community at Harvard invites interested undergraduates who
will not have graduated by June 2014 to apply for research internships in the
summer of 2014. Deadline for applications AND recommendation letters is February 21. The application will be available on this link on the second week of January 2014.
Starting on Monday June 9 the internship will last for ten weeks (until Aug 15). Interns will work on research projects in the
labs of the Bauer Fellows and Systems
Biology faculty whose work spans many fields of science, from biology
(including systems biology, biophysics, boinformatics and genomics)
to applied mathematics and computation. Interns will have the opportunity to learn a range of cutting-edge
genomics or bioinformatics techniques in the exciting and dynamic research environment at
the FAS Center for Systems Biology and the Department for Systems Biology at Harvard Medical School.
The internships will be offered to Harvard
students and students from other US universities. Underrepresented minority students and students from disadvantaged backgrounds are particularly encouraged to apply. We consider applications from rising sophomores, juniors and seniors. Unfortunately we cannot consider international students unless they are enrolled at US universities and have valid student or work visas.
Interns will receive a competitive stipend and Harvard housing (Harvard students can opt out if they have housing through PRISE). Harvard students are also encouraged to apply for PRISE and HCRP fellowships. In addition to the research program, the internship includes field trips to local research institutes, weekly seminars, lectures by distinguished faculty, and social and career events coordinated with other Harvard internship program.
Applicants can find the application forms here on the second week of January 2014. In addition to completing the online form, applicants will be asked to submit a resume, transcripts (inofficial transcripts ok), a research statement and an optional personal statement. Intern candidates can apply for up to 3 projects which are listed below. In your research statement please specify why you are particularly interested in the chosen projects. This description plays an important part in the selection process. You will also be asked to provide contact information for two referees who should know you from prior or current academic or research activities. They will be asked automatically to upload their recommendation letter AFTER you submitted your application material. Please make sure that they are willing to serve as a reference and share your application material with them well before the deadline so that they can prepare a recommendation letter before February 20. In fact, we advise applicants to upload their material at least a week before the deadline so that the referees have enough time to upload their letters.
Please have all required documents ready before you start filling out the forms since you will not be able to access an incomplete application at a later stage. For questions please contact Bodo Stern at agg "at" cgr.harvard.edu.
Internprojects in 2013 (New projects will be published in early January)
Project 1, Peter Turnbaugh
1.Getting to know our trillions of microbial partners
Project 2, Nicolas Chevrier
2. Dissecting How Immunity Starts
Project 3, John Calarco
3. Exploring RNA diversity in the nervous system
Project 4, Rachel Dutton
4. What are microbes doing in my cheese?
Project 5-6, Andrew Murray
5. Directing the evolution of plasmid 'species' in Escherichia coli
6. Evolving new behavior in budding yeast
Project 7, Pardis Sabeti
7. Visualization of large datesets using information design
Project 8, Lauren O'Connell
8. Genetic basis of phenotypic diversity in posion dart frogs
Project 9, Jeremy Gunawardena
9. Information processing in mammalian signal transduction networks
Project 10, Dan Needleman/Lauren O'Connell
Evolutionary Biology of Cell Division
Project 11, Roy Kishony
Genome Scanning: Large-scale systematic quantification of functional genomic elements in E. coli
Project 12-13, Michael Springer
12. Evolution of decision-making circuits in yeast
13. Are duplicated genes really the same?
Project 14, Angela dePace
14. Integration of transcription in the fly embryo
Project 1. Getting to know our trillions of microbial partners
We never dine alone. Human beings are super-organisms composed of our own human cells and trillions of microorganisms, most of which are found in our gut. These microbial co-conspirators play important roles in health and disease. In particular, they aid in the digestion of our diet, and may influence the efficacy and toxicity of orally administered drugs. We are looking for intrepid microbial explorers, who would like to use 'metagenomic' methods, such as DNA extraction, PCR amplification, and next-gen sequencing to characterize these microbes with the goal of understanding and manipulating key factors that shape this complex community. We are also looking for students who want to tackle some of biology's largest computational problems. We generate and analyze hundreds of millions of microbial DNA sequences, looking for patterns that might help us learn about how microbes influence human health and disease.
See turnbaugh.openwetware.org for more info.
Project 2. Disecting how immunity starts
We study how immune responses arise in mammals using cellular and mouse models of infection and vaccination. Specifically, we are interested in dissecting the cellular circuits propagating information within the host during the initial hours and days upon immune activation. Understanding the rules governing how these circuits operate within and between organs will help designing new strategies for immune manipulation. We are looking for highly motivated students interested in helping develop new tools and approaches to characterize and manipulate the immune system. Depending on the candidate skills and interests, the project will involve mammalian cell culture, mouse work, molecular biology, and/or computational analyses (e.g., DNA or RNA sequencing, image processing, network analysis).
Project 3. Exploring RNA diversity in the nervous system
Our group uses C. elegans as a model system to investigate how cell-type specific regulation of gene expression is achieved, and to better understand the physiological consequences of given gene regulatory events in creating molecular and cellular diversity. We are particularly interested in understanding how a particular pre-mRNA processing step known as alternative splicing can influence the development and function of the nervous system. Using recently developed fluorescent reporters, we have identified a number of genes with mRNA transcripts that are differentially spliced in specific classes of neurons. We are now interested in identifying the factors responsible for this differential splicing regulation, and we also wish to determine how these splice variants contribute to the myriad of functions performed by the nervous system. Interested students would have the opportunity to learn and utilize classical and molecular genetic techniques, biochemical approaches, and microscopy to explore these questions. Experience in any of these areas will be helpful but not a prerequisite.
Project 4. Cheese as a model microbial ecosystem
In an effort to understand how microbes behave in complex environments, we are using cheese as a simplified model system. Our lab is characterizing the microbial communities found on a variety of cheeses, using deep sequencing, metagenomics, and microbial culturing. Summer interns would be involved in the study of the cheese microbiome using lab-based experimental communities, specifically with the goal of characterizing the functions and interactions of different species. Projects are also available to study the genetic diversity and evolution of cheese microbes through the analysis of sequencing data from the individual genomes of cheese microbes and the metagenomes of cheese communities. Students with interests and/or a background in microbiology or bioinformatics/programming are encouraged to apply.
Please visit our lab website for more information: https://sites.google.com/site/theduttonlab/home
Project 5. Do plasmids communicate with their bacterial host?
Plasmids, circular double stranded DNA molecules, are found in the majority of prokaryotic cells. They are classified into groups, or species, based on their ability to coexist within the same cell; those of the same species being incompatible with each other. The mechanism underlying compatibility is dictated in part by the particular segregation machinery encoded on the plasmid. This machinery ensures that when a bacteria cell divides, the mother and daughter cells faithfully obtain at least one copy of the plasmid. Currently we assume that plasmid segregation acts autonomously and conclude that plasmid incompatibility is not influenced by host factors. However, this has never been rigorously tested. Could plasmids indeed be communicating with their host during segregation, and if so, what might the molecular basis of this communication be? To begin to answer this question, the aim of this project is to determine the level of incompatibility between two plasmids in different strains on E. coli, and also potentially in different bacterial species. The project will draw on basic microbiological techniques in handling and culturing bacterial strains, and extensive DNA manipulation. Incompatibility assays are based on a simple LacZ reporter system which will be utilized for high-throughput screening of multiple strains in parallel.
Project 6. Evolving new behavior in budding yeast
We are interested in how regulatory behaviors, which allow organisms to match their activities to environmental conditions, arise in evolution. To this end, we are evolving a new connection between a stimulus, such as a change in an environmental variable, and a response in the yeast Saccharomyces cerevisiae. Our goal is to determine the genetic changes that give rise to the new connection and how the evolved mechanism depends on the parameters of the selection. The student intern will have the opportunity to work on several aspects of this project, including sequence analysis, evaluation of putative causal mutations, and running further evolution experiments. The student may also work on a related project testing the hypothesis that expression of genes located in sub-telomeric regions enable yeast to quickly adapt to new carbon substrates.
Project 7. Visualization of large datasets using Information Design
This project consists in creating a software tool for systematic visualization and analysis of biomedical data. This tool will help researchers to quickly explore patterns in the data and to make hypothesis about novel associations between phenotypes, genetic information, and causes of disease. It incorporates views that allow to interactively visualize large datasets with several hundreds of variables.
The software is being tested with data from the National Health and Nutrition Examination Survey (NHANES, http://www.cdc.gov/nchs/nhanes.htm). This survey is conducted continuously since 1999 in biannual cycles. Each NHANES cycle includes approximately 10,000 respondents, and around 2,000 variables encompassing demographic, examination and interview parameters. Although the focus at this moment is to study the NHANES dataset, the software is of general applicability and we plan to use it with other datasets as well.
This project is carried out in collaboration with Fathom Information Design, a Boston-based design studio specialized in information visualization. This collaboration is a very exciting opportunity to create a new tool that could have a significant impact in the medical community, by integrating techniques from information and interaction design with algorithms for automated pattern discovery.
Requirements: Knowledge of basic statistical techniques for analysis (hypothesis testing, linear regression) and graphics (scatter plots, histograms) is required. Previous experience with statistical and math tools (R, SAS, Matlab, etc.) would be helpful but not required.
Project 8. Genetic basis of phenotypic diversity in poison dart frogs
Our group uses poison dart frogs to understand how the genome contributes to diversity within ecologically relevant traits. In the large family of dart frogs (family Dendrobatidae), there are many between and within species differences in toxicity, color morphology, and behavior. Our group focuses on two main research aims: (1) We use a comparative approach to learn more about the genetic and neural basis of parental care by comparing species where only the males care for offspring to other species where only females care for offspring. (2) We use molecular tools to better understand how the genome of a single species can produce such diversity in phenotypes, as many species have over thirty different color patterns advertising their toxicity to potential predators. Interns will have the opportunity to work with the frogs and learn molecular techniques at the lab bench, including RNA sequencing, immunohistochemistry and microscopy.
Project 9. Information processing in mammalian signal transduction networks
The Gunawardena Lab is interested in how mammalian cells process information and make decisions (http://vcp.med.harvard.edu/). We take two broad approaches to this. From the “inside out”, we look at specific molecular mechanisms like post-translational modification or gene regulation and try to understand how they encode regulatory information. From the “outside in”, we interrogate cells by using complex environments to learn more about the architecture of their molecular networks. We use a combination of experimental methods (biochemistry, fluorescence microscopy, microfluidic devices, mass spectrometry), mathematical theory (dynamical systems, algebraic geometry, graph theory, Bayesian approaches) and computation. We have a number of projects on the mathematical side that are suitable for short (two to three month) summer research internships. Experimental projects may also be possible, depending on background and interest, but, typically, it is harder to make progress on these in a short time. We have a long-standing interest in undergraduate research. Our students participate in current research projects and several have become authors, and even first authors, on published papers (available on our website). Our group has a wide mixture of skills from cell biology and biochemistry to string theory and electronic engineering. If you have some knowledge of mathematics, a deep interest in modern biology and a willingness to work really hard for a couple of months, you could have a lot of fun.
Dan Needleman/Lauren O'Connell
Project 10: Evolutionary Biology of Cell Division
The architecture of cells and subcellular structures can show remarkable variability between tissues and organisms, but there is currently little understanding of the evolutionary basis of this diversity. Thus it is unclear why metaphase spindles in different eukaryotes exhibit a range of morphologies and dynamics, or why the volumes of these spindles vary over one thousand fold. We will seek to gain insight into these issues by exploring the within and between species variation in egg morphology and cell division in poison dart frogs. Dart frogs (family Dendrobatidae) display extreme variation in color patterning and behavior and are useful animal model for understanding mechanisms that govern phenotypic diversity. This project will utilize the eggs of different dart frog color morphs within a species as well as comparisons between closely related dart frog species. Summer interns involved in this project will learn to work with dart frogs, perform high resolution microscopy, quantitative image processing, and quantitative genetic and comparative analysis.
Project 11. Genome Scanning: Large-scale systematic quantification of functional genomic elements in E. coli
Although many species have sequenced genomes, we don't know enough about genome function to design whole new genomes, for two reasons. First, there are functional elements within genomes that are undiscovered. Second, for the known functional elements, we don't understand all the rules that determine which potential sequence variants are good and which are bad. For example, given the amino acid sequence of a protein, many possible RNA sequences will poorly produce proteins due to inefficient choices of synonymous codons. To better understand these fitness rules we are developing a method for “genome scanning”, where we make libraries of mutants within a small genomic region of E. coli, and quantify the fitness of these mutants using next-generation sequencing. By scanning the mutational window along the genome we can measure the effects of mutations across functional elements like promoters, genes, other regulatory motifs. From this data we will be able to characterize the general rules that determine function, as well as discover the presence of new functional elements.
The aims for this project are ambitious, but if we are successful it will lead to understanding a bacterial genome at an unprecedented level of detail. We want to use genome scanning to generate a huge systematic mutant library across a portion of the E. coli genome. Your goal in this project would be to specialize in making targeted libraries of mutant genomes, to use these methods to scan a large number of genomic sites, then to help us prepare libraries for next-generation sequencing and to help analyze the first portion of the resulting data. You should be comfortable with very basic molecular biology lab techniques (pipetting, bacterial culture), or at least be able to learn the basics very quickly! We will teach you how to make mutant libraries, how to do next-generation sequencing, and techniques for high-throughput experiments. We are looking for motivated, organized and responsible students who can rise to the challenge of a working with a team to complete a ‘marathon-style’ experiment. Many projects in our lab involve generating and analyzing data from large-scale experiments, so students with quantitative interests are encouraged to apply. If you choose to accept this challenge, please describe how this project matches your general interests in systems biology, your experiences working on teams or group projects, and your biological lab experience.
Project 12. Evolution of decision-making circuits in yeast
Signaling pathways can perform complex computations, but unlike man-made circuits, all biological networks had to evolve from other pre-existing networks. In order to understand how signaling pathways evolve and function, we are comparing cellular responses to complex environments in a number of related yeast species. Specifically, the project will involve creating yeast strains with fluorescent reporter constructs and monitoring metabolic gene expression by flow cytometry and microscopy. The project may also involve a theoretical/computation component to understand how quantitative features of decision-making circuits affect their output. Preference will be given to candidates with knowledge or experience in microbiology, programming, and quantitative methods.
Project 13. Are duplicated genes really the same?
Gene duplication creates a duplicate copy of a gene that may relieve many of the selective constraints on a gene’s function and thus plays a major role in biological innovation. 10% of yeast genes are duplicated. In this project, we aim to explore the role of post-translational modification in the evolution of duplicate genes in the budding yeast S. cerevisiae . We hope to determine how these modification contribute to the new roles that duplicate genes may acquire to confer a selective advantage to a given species.
Project 14. Integration of transcription in the fly embryo
As cells differentiate in a developing embryo it is essential that they activate the proper genes at the proper times. In fruit flies, gene expression is controlled by transcription factors binding to enhancers, which are regions of regulatory DNA that can be distantly located upstream or downstream of a promoter. We are interested in how information from many bound transcription factors is integrated together. Mediator is a large protein complex that transfers information from transcription factors to the polymerase and might be involved in this integration. This project will look at what subunits of mediator interact with different transcription factors. The project will include modern genetic screening with RNA interference, two photon microscopy, and data analysis in MatLab. All levels of experience are welcome to apply.