Franklin & Marshall College

Hughes Bioinformatics Scholars have the unique opportunity to pursue research in partnership with a faculty member.

A minimum of 16 student scholars will receive salary and research funds to work on bioinformatics project each summer.  Six more students will receive funds during the academic year. Many of our research opportunities have launched students into careers involving bioinformatics.

For more information about the funding for the bioinformatics project and research please see our grants page.  

Interested student should also see the recommended course list.  

Research opportunities in bioinformatics at Franklin and Marshall College take place in the follow areas:

Computational Biology

Jing Hu (Computer Science): Professor Jing Hu's research lab mainly focuses on developing computational tools to solve specific Bioinformatics problems like the prediction of protein structures or functions, the identification of protein functional sites, and the discovery of genes. Students working in Professor Jing's lab will have the opportunity to participate in multiple research projects, through which they will gain experience in processing large biological datasets, maintaining biological databases, working in a collaborative and interdisciplinary environment, as well as applying Bioinformatics tools such as alignment, clustering and BLAST. Students may even develop their own Bioinformatics tools.

Christina Weaver (Computer Science): Students working with Professor Weaver have the opportunity to explore two areas of interest.  The first deals with the sensitivity analysis of synaptic parameters.  Synapses are the electrical junctions between two neurons, and are often affected by aging and disease.  Using the mathematical model of neurons that are involved in memory tasks and a tool called sensitivity analysis, students will quantify how parameters controlling the synapses affect the output of the model.  The second area of study deals with the parameter fitting of model neurons. A crucial step in developing mathematical models is to identify combinations of model parameters so that the model output matches some data recorded experimentally.  A protocol to do parameter fitting for mathematical models of neurons has already been developed, but there is room for improvement.  Students will find a way to optimize the steps of the parameter fitting protocol to identify models which best fit the experimental data, in the least amount of time.

Genomics

Jaime Blair (Biology):  Students in Professor Blair's lab will use a variety of bioinformatics tools to study the evolution of pathogenicity within the Oomycetes, a group of eukaryotes that includes a number of devastating plant and animal pathogens.  Several complete genome sequences are currently available, which provide a wealth of data for comparative genomics.  Experimental approaches will also be used to explore the phylogenetic relationships among different genomic groups, and to associate changes in certain genomic elements with patterns of host specificity, virulence, and speciation.

Pablo Jenik (Biology ): Professor Jenik's research focuses on the connections between gene regulation at various levels, cell identity, and tissue patterning during development. Projects that students will work on in the lab include the use of DNA microarrays, Genevestigator, and other bioinformatics tools available at The Arabidopsis Information Resource to compare gene expression patterns in wild-type and mutant Arabidopsis plants to better understand the mutations and the developmental pathways that the genes affect.

Clara Moore (Biology ): Students in Professor Moore's lab will work with gene expression microarrays and quantitative PCR to measure gene expression patterns in a trisomic mouse model for Down syndrome. Analysis of RNA samples from critical stages during cardiogenesis will identify the signaling pathways and differentiation patterns disrupted by elevated expression of triplicated genes.

Proteomics

Peter Fields (Biology): The student-oriented research conducted in Professor Fields' lab employs a number of bioinformatics components. Studies focusing on changes in osmolyte composition in tissues in response to environmental stress employ HPLC-MS, followed by examination of metabolic pathways (via the KEGG database, for example) to determine likely modes of synthesis for further research. The proteomics work is bioinformatics-intensive, relying on gel data analysis software (Delta 2D) to quantify changes in protein expression in tissues, as well as MASCOT software to identify proteins via access to both online (NCBI, EMBL, SwissProt) and in-house protein sequence databases. Students pursuing research in the Fields lab thus will have the opportunity to combine classical "wet-bench" biochemical techniques with the use of bioinformatics tools.

Robert Jinks (Biology):  Students in Professor Jinks' lab investigate how the brain regulates the daily metabolism of the retina using the horseshoe crab Limulus as a simple model system. Each day rod photoreceptors in our retinas shed and renew a portion of the light sensitive membrane of their outer segments. In humans, this process is regulated by the circadian clock, and triggered by light. This daily renewal is vital for healthy normal vision. Photoreceptors in the horseshoe crab retina also undergo daily shedding and renewal of a portion of their light-sensitive membrane; here again, the process is regulated by the circadian clock and triggered by dawn.

Professor Jinks' students have determined (1) the metabotrophic signaling cascade that the circadian clock uses to prime the photoreceptors for daily shredding and renewal, and (2) the signaling cascade through which light triggers shedding. We are now using proteomic and bioinformatics techniques and tools to probe the point(s) of convergence of these two signaling cascades. From the bioinformatics perspective, we are designing small-interfering RNAs (siRNAs) that we can microinject directly into photoreceptor cells to disrupt the translation of key proteins that may serve as targets for the clock and light in driving daily shedding and renewal of the light-sensitive membrane. Knocking down (reducing the abundance) of these proteins with the siRNAs provides us an opportunity to study the roles of these proteins in normal retinal metabolism.

Applied Bioinformatics

Daniel Ardia (Biology):  Student research in Professor Ardia's lab will use  computational and statistical tools to test hypotheses about life history evolution or to understand how environmental variation affects geographic distribution of animals using Geographic Information Systems (GIS). Examples include estimating cooling and heating rates of eggs and nestling birds; modeling growth of nestling birds; molecular screening of parasites in wild birds along a gradient from the Tropics to the Temperate Zone; and the effect of microclimate on deer habitat use at Millport Conservancy. 

Jorge Mena-Ali (Biology ):  Students in Professor Mena-Ali's lab apply several genomic, mathematical and GIS-based methods in combination with field- and greenhouse-based experiments to investigate the factors controlling the reproductive success of invasive weeds. Studies focus on a variety of problems, including: comparative proteomics of S-RNases with contrasting patterns of strength during the self-incompatibility (SI) response; genomic and phylogenetic analysis of S-alleles of natural weed populations from their native and invaded ranges; GIS-based model generation of the invasion process of weeds and comparative community structure as a factor in invasiveness in the continental USA; functional genomics (microarrays) and chemical ecology (secondary volatile compounds) of the response to herbivory in plants with contrasting breeding histories and the role of herbivores on the success of invasion; development and analysis of microsatellite markers for the study of population structures and past evolutionary history of plants and zooplankton species; evolutionary, geographical and phylogenetic analysis of host-pathogen interactions and the evolution of variable virulence and host-driven speciation in a fungal venereal disease in plants.

Medical Genomics

The Clinic for Special Children:  Students who participate in research at The Clinic for Special Children will work with biochemical disorders such as glutaric aciduria (GA1), maple syrup urine disease (MSUD), Crigler-Najjar syndrome, medium-chain acyl-CoA dehydrogenase deficiency (MCADD), and other disorders that occur in the Old Order Amish and Old Order Mennonite communities in Pennsylvania. Students may perform clinical, patient-centered research with Drs. Morton and Strauss and/or they may concentrate on laboratory-based research projects involving molecular genetics and bioinformatics.