Tag Archives: genetics

Research Opportunity: Genetics of pediatric epilepsy

Con­tact Name: Heather Mefford

Con­tact Email: hmefford[at]uw.edu

Depart­ment: Pediatrics, Genetic Medicine

Descrip­tion:

Our lab uses genomic technologies to discover genetic causes of pediatric epilepsy syndromes and other disorders. Opportunities for projects include candidate gene sequencing to identify mutations, chromosome microarrays for copy number variant discovery, setting up functional assays to study the function of new epilepsy genes and bioinformatics analysis of sequence data to explore different models of inheritance.

http://www.washington.edu/medicine/pediatrics/meflab/

 

Require­ments:

Background in biological sciences
Able to commit 10-15 hrs per week minimum
Previous lab experience helpful but not required

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Research Opportunity: A path to independent cell and molecular research

Con­tact Name: Alex Paredez

Con­tact Email: aparedez[at]uw.edu

Depart­ment: Biology

Descrip­tion:

There are four spots left in Bio402, my new laboratory course.  While Bio 355 is listed as a requirement, I am interested in recruiting a couple of sophomore students who could continue working on independent projects after the course.  If you are interested please send your unofficial transcript to aparedez[at]uw.edu.

New Laboratory Course – Biology 402 Functional Genomics

Since joining the Department in autumn 2012, Assistant Professor Alex Paredez has been crafting a lab course using Giardia lamblia where students will get the chance to perform authentic experiments.  The Paredez lab has identified a large list of proteins through their genomic and proteomic analysis of Giardia; students will focus on epitope tagging these proteins with the goal of facilitating protein localization. Although sub-cellular localization does not indicate function, this data has the potential to provide the first clues about what processes these proteins might participate in.  Ultimately, the students’ results will be uploaded to EupathDB, a public database that hosts Giardia’s genomic data, thereby sharing student’s findings with the larger cell biology community.  Biology 402, Spring Quarter (M 1:30-2:30 W,F 1:30-4:20).  Add code required.

Require­ments:

3.5 GPA
Introductory Bio series

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Research Opportunity: Genetic analysis of zebrafish nervous system development, damage and regeneration

Con­tact Name: David Raible

Con­tact Email: draible[at]uw.edu

Depart­ment: Biological Structure

Descrip­tion:

We use the zebrafish system, molecular genetics, advanced microscopy and small molecule screening to uncover mechanisms underlying development, cell death and regeneration in the peripheral nervous system. Undergraduates would partner with a senior graduate student or postdoctoral fellow to carry out research with the opportunity to take on independent projects.

Require­ments:

Background in Biological Sciences.
Minimum 3.0 GPA.
Schedule to dedicate 10-15 hours per week.

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Research Opportunity: Bioengineering with the Yeast Gene Regulatory Network 2.0

Con­tact Name: Samuel Danziger

Con­tact Email: sam.danziger[at]seattlebiomed.org

Depart­ment: Seattle Biomed

Descrip­tion:

We have a developed a predictive environment and gene regulatory influence network (EGRIN) for S. Cerevisiae.  This network uses publicly available and in-house gene expression data from microarrays to predict genetic regulation and cellular responses.  We intend to expand it to a stochastically robust EGRIN 2.0 that we will use to engineer yeast to produce economically relevant compounds in peroxisomes.

10-week Project #1:  Write a framework for generating multiple EGRINs so that the EGRIN 2.0 can be generated with additional processor time.  This project would involving using the gene biclustering program cMonkey in [R] or python and interacting with a Sun Grid Engine cluster. There would be plenty of opportunity to improve the cMonkey algorithm.

Require­ments:

Familiarity with the [R] statistical programming language or Python.
Familiarity with Unix shell scripting and cluster computing using the Sun Grid Engine (SGE) or similar system.

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Research Opportunity: Exon Array for Disease Classification

Con­tact Name: Samuel Danziger

Con­tact Email: sam.danziger[at]seattlebiomed.org

Depart­ment: Seattle Biomed

Descrip­tion:

We are exploring exon arrays on serum response cells to detect alternative splicing events that act as disease biomarkers and possibly give clues to the mechanism of disease progression.  We are currently applying this technology to investigate ALS (i.e. Lou-Gehrig Disease) in mice and Alzheimer’s Disease in humans.  We expect these techniques to transition from exon arrays to RNA-seq as the technology progresses. The idea is to train a discriminating classifier to predict ALS on the basis of features derived from the exon array.  We have currently used the FIRMA algorithm to predict alternative splicing events and an ensemble of classifiers to make predictions. Techniques developed in this project are also applied to HIV related data sets.

10-week Project #1:   For this project, the student would expand a deep learning module written in [R] (or other language) with an eye to using the hidden layer(s) to improve the classifier and possibly identify gene network pathways. There would be plenty of opportunity to apply / develop / expand machine learning and analysis techniques for both disease classification and biomarker discovery.

 

Require­ments:

Experience with [R] statistical programming language.

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Research Opportunity: Studies of the biology and pathogenesis of a bacterial carcinogen

Con­tact Name: Nina Salama

Con­tact Email: nsalama[at]fhcrc.org

Depart­ment: Microbiology

Descrip­tion:

The bacterial pathogen Helicobacter pylori chronically colonizes the stomach of 50% of the human population. While many remain asymptomatic, this infection is the major risk factor for development of ulcers and stomach cancer. The Salama is interested in the mechanisms by which this bacterium can establish and maintain a chronic infection in the unusual environment of the human stomach and the molecular cross talk between the host and the bacteria during the decades long infection. Current lab projects include studies on the cause and consequence of genetic variation during chronic infection and the molecular mechanism underlying this bacterium’s unique helical morphology.
We are presently seeking an undergraduate with a strong interest in microbiology and molecular biology and who is looking to gain experience working in a lab. Specifically, we are looking for someone to perform routine PCR, DNA sequencing and bacterial transformations. This person will also have the opportunity to assist and interact with all members of the lab and learn additional techniques. Over time and with experience, this person may be able to work on a dedicated project of their own. We are looking for someone available for ~10-15 hours each week. This is an unpaid position but is an outstanding opportunity to participate in engaging and important research.

Require­ments:

10-15 hours a week
Course work/familiarity in some of the following: molecular biology, genetics, microbiology, biochemistry

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Research Opportunity: Statistical analysis of large genetic data sets

Con­tact Name: Sharon Browning

Con­tact Email: sguy[at]uw.edu

Depart­ment: Biostatistics

Descrip­tion:

Our group, led by Dr. Sharon Browning in Biostatistics and Dr. Brian Browning in Medical Genetics, develops statistically-powerful, computationally-efficient methods for analyzing large genetic data sets such as those from whole genome sequencing of large cohorts.

This project involves using software developed by our group to analyze a unique, cutting-edge genetic data set from a large dairy cow population.  The goal will be to assess the quality of the results under different settings and approaches to make recommendations for best practices.  Ultimately, this work will help dairy breeders to improve the herds.

Require­ments:

A strong background in computing and/or statistics is required.  Usually we will consider only Juniors and Seniors with a GPA of at least 3.7.  Please include a copy of your unofficial transcript with your e-mail inquiry.

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Research Opportunity: Zebrafish stem cell analyses by mutagenesis and transgenic line production

Con­tact Name: Professor David Parichy

Con­tact Email: dparichy[at]uw.edu

Depart­ment: Biology

Descrip­tion:

The laboratory studies various aspects of post-embryonic development in zebrafish, focusing on adult pigment stem cells. Current projects include a forward genetic mutant screen to identify new genes required for stem cell development and maintenance as well as the production of transgenic reporter lines for observing these cells in vivo. For a fuller description of on-going projects visit the lab website (http://faculty.washington.edu/dparichy/Index.html).

Require­ments:

No previous biology lab experience is required but applicants should have some real-world work experience (e.g., retail, restaurant, construction, military). Preference will be given to given to applicants of freshman or sophomore standing who are able to work at least 12 hours per week and are interested in continuing research for multiple quarters. Exceptional applicants with junior standing may be considered as well.

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