Category Archives: research

Database construction for skin metagenomic data

Project Start Date: Winter 2012

Project Title: Database construction for skin metagenomic data

Project Contact: Huiying Li (huiying@mednet.ucla.edu)

Project Description:
The human microbiome plays important roles in human physiology and has become a new exciting research field in recent years. Our group studies the human skin microbiome and oral microbiome and their associations with diseases. This project will develop a database for the metagenomic data and genome data that we obtained to study the disease associations.

Required Experience: Experience with some programming language (C, C++, Perl, Python, etc.), databases (eg. MySQL), and some general background knowledge of high throughput sequencing.

Possibility of Funding: No

Genetics of Neuropsychiatric disorders

Project Start Date: Winter 2012
Project Title: Genetics of Neuropsychiatric disorders
Project Contact: Roel Ophoff (rophoff@mednet.ucla.edu)

Project Description:
Neuropsychiatric disorders are common and can severely disrupt normal life. Despite their high heritability estimates, only a small part of the genetic basis of these disorders has been uncovered. Our lab focuses mostly on schizophrenia, bipolar disorder and amyotrophic lateral sclerosis (ALS). We have begun applying sequencing techniques on different types of human tissue to be able to study different layers of genetic information, including microRNAs, mRNAs, methylation profiles and exomes. The aim of this research direction is shedding light on genetic architecture of neuropsychiatric disorders. These large datasets offer the opportunity to apply either existing methods or develop novel methods and strategies.

Required Experience: Some programming experience.

Possibility of Funding : No

Computational Challenges in Cardiovascular Systems Biology

Project Start Date: Summer 2011
Project Title: Computational Challenges in Cardiovascular Systems Biology

Contact: Tom Vondriska (tvondriska@mednet.ucla.edu)
Project Description:
Our group uses proteomics and genomics to study complex phenotypes in animal models of cardiovascular disease. We are interested in understanding the basic principles by which chromatin structure underlies gene expression patterns. Available projects involve bioinformatic analysis of proteomics, microarray and DNA/RNA sequencing data with the goals of annotation, hierarchical comparison and analysis of emergent properties. Additional projects involve image analysis/recognition and challenges in evolutionary genomics.

Required experience:
Extensive experience with some programming language(s); basic knowledge of molecular biology; basic knowledge of genomics; Individuals with interest/experience in mathematical modeling are also encouraged to inquire.
Funding:
Yes; to be determined by level of student commitment; course credit also available

Effect of copy number variation on mammalian gene expression

Project Start Date: Summer/Fall 2011
Project Title: Effect of copy number variation on mammalian gene expression
Project Contact: Mete Civelek (mcivelek@mednet.ucla.edu) (Jake Lusis’ laboratory)

Project Description:
Structural variation occurs in roughly 2-3% of the genome and can range in size from several kilobases to several megabases. These variations, termed Copy Number Variation (CNV), have been associated with disease, such as autism and schizophrenia. Human aortic endothelial cells (HAECs) that line inside the blood vessels play key roles in the initiation and progression of atherosclerosis. Our lab has been studying the effects of oxidized phospholipids on endothelial cell gene expression. We have recently cultured HAECs from approximately 150 human donors in control media or media containing oxidized phospholipids. We have genotyped the donors using

Affymetrix SNP 6.0 arrays and measured the gene expression levels using Affymetrix Human HT-HG133A arrays. Previous publication from our lab (Romanoski et al. Am J Hum Genet. 86(3):399-410) identified single nucleotide polymorphisms that control gene expression locally and distally.
For this project, we want to understand how CNVs affect gene expression and gene-by-environment interactions by performing an association study using the CNV information of the ~150 donors. This will be the first study that looks at affect of CNVs on a molecular phenotype in mammalian cells. CNV information and expression data have already been collected.

Required Experience: Interested student will use an association algorithm, such as PLINK, R and/or python for downstream analysis.

Possibility of Funding : No

Defining human cardiac protein half-life in healthy man and heart failure patients

Project Start Date: Summer 2011
Project Title: Defining human cardiac protein half-life in healthy man and heart failure patients.

Contact: Peipei Ping (pping@mednet.ucla.edu)

Project Description:
Cell synthesizes proteins and degrades proteins; the half-life of proteins is the key to biological function of all cells. Understanding protein turnover and protein dynamics is essential to developing novel therapies in diseases, including the treatment of heart failure. Using experimental data, this project will develop computational models for predicting the half-life of proteins in healthy individuals and how these protein half-lives maybe impacted in patients suffering from heart failure.

Required Experience: Experience with some programming language (C, C++, Java etc.), some background knowledge of proteins and their half-lives are preferred but not essential.

Possibility of Funding : Yes.

Analysis of mitochondrial protein expression profiles using four large protein data sets

Project Start Date: Summer/Fall 2011
Project Title: Analysis of mitochondrial protein expression profiles using four large protein data sets.
Contact: Peipei Ping (pping@mednet.ucla.edu)

Project Description:
Mitochondrion produces ATP and is the energy source of all cells. A mitochondrial proteome may contain up to 2000 distinct proteins with various abundance and they form up to 100 networks/pathways. We have obtained four large protein datasets on four types of mitochondria: the human heart mitochondria; the mouse heart mitochondria; the mouse liver mitochondria; and the fly muscle mitochondria. The analyses of these four datasets will inform what are the core proteins essential to all mitochondrial proteomes, which proteins are unique and contribute to the specificities in function for heart, liver, and muscle, and which proteins are fundamental to the human heart mitochondrial proteome. These information will be essential for our understanding of human cardiac mitochondrial function.

Required Experience: Experience with some programming language (C, C++, Java etc.), some background knowledge of cell biology are preferred but not essential.

Possibility of Funding : Yes

Internet Services for Collaborative Data Sharing (ISCDS)

Project Start Date: Summer 2011

Project Title: Internet Services for Collaborative Data Sharing (ISCDS)

Contact: Ivo Dinov (dinov@loni.ucla.edu)

Project Description: The ISCDS project aims to develop a system enabling the examination of research grant proposals data (specifically reviewer’s and study section’s (panel’s) tendency to deliver a constructive (positive, negative or neutral) evaluation of grant applications). The project will collect and mine all publicly available information and construct a set of metrics characterizing research grants based on applicant/application-topic. Specifically, ISCDS will provide a webservice enabling: Community Entry of Data, Community Export of Data, Exploratory Data Analysis/Graphics, Model Estimation/Model Fitting, and Outcome Prediction.

Required Experience:
1. Excellent database, web-technologies, design and web-services skills.
2. Bachelor’s, Master’s or PhD degree in computer science, engineering or a related field.
3. Solid experience with HTML, JavaScript, Ruby, Java, JSP, PHP, JSON development.
4. Knowledge of UNIX, LINUX, Mac and PC.
5. Experience with virtualization technology.
6. Excellent team and independent environment working skills.
7. Experience with Data Mining.
8. Excellent analytical skills and the ability to quickly gain an understanding of complex systems and tools.
9. Strong written and verbal communication.
10. Experience with building and maintaining social networks and collaborative web resources.

Possibility of Funding: Yes

Graphical Pipeline Workflow Environment for Visual Informatics and Genomics

Project Start Date: Summer 2011

Project Title: Graphical Pipeline Workflow Environment for Visual Informatics and Genomics

Contact: Ivo Dinov (dinov@loni.ucla.edu)

Project Description: Informatics and genomics research require efficient, flexible and robust management of large heterogeneous data, advanced computational tools, powerful visualization, reliable hardware infrastructure, interoperability of computational resources, and detailed protocol provenance.

This project will extend the Pipeline Environment (http://pipeline.loni.ucla.edu), a client-server distributed computational infrastructure, to enable the visual graphical construction, execution, monitoring, validation and dissemination of advanced informatics and genomics data analysis protocols. Examples of diverse genomics tools and the interoperability of informatics tools include EMBOSS, mrFAST, GWASS, PLINK, MAQ, SAMtools, Bowtie, CNVer, etc.

Required Experience: Java and web-services programming experience and strong motivation to contribute to a large scale research project development

Possibility of Funding: Yes