Category Archives: research

A multidimensional, web-based database for OMICs data

Project Start Date: Spring 2013
Project Title: A multidimensional, web-based database for OMICs data.
Project Contact: Giovanni Coppola <gcoppola@ucla.edu>

Project Description:

We have created and developed three web-based databases to host high-throughput data, which are becoming major tools for collaboration and data mining within our lab and among our collaborators. We are now working to compile them in a single suite of tools for web0based mining of OMICs data.

Required Experience: Experience with some programming language (preferred: Python, Perl, R, Java etc.), some background knowledge of biology or genetics

Possibility of Funding : Yes

Personalized risk evaluation in neurodegenerative dementia

Project Start Date: Spring 2013
Project Title: Personalized risk evaluation in neurodegenerative dementia
Project Contact: Giovanni Coppola <gcoppola@ucla.edu>

Project Description: Large-scale genome-wide association studies (GWAS) have identified a number of genetic risk factors for complex diseases. Since each of these factors confers a very small fraction of the overall genetic risk, considering them in the clinical practice is of very limited utility in both guiding clinical decisions and counseling. About 100 genetic risk factors have been identified in Alzheimer’s disease, mostly in Caucasian individuals. We have typed these risk variants in a large series of patients with neurodegenerative diseases (including African Americans and Latinos), and the aim of this project is to apply and test risk estimation algorithms, with the long-term goal of developing a personalized plan of attack – based on genetic and environmental risk factors – for patients at early stage of disease.

Required Experience: Experience with some programming language (preferred: Python, Perl, R, Java etc.), some background knowledge of genetics

Possibility of Funding : Yes

Transcriptomic and Genomic Analyses of Brain Development and Autism

Project Start Date: Winter 2013
Project Title: Transcriptomic and Genomic Analyses of Brain Development and Autism
Project Contact: Neelroop Parikshak <neelroop@ucla.edu>

Project Description:
Human brain development is a complex process that involves the precise regulation of thousands of genes. We are applying RNA sequencing combined with multiple other genomics methods (exome sequencing, genome sequencing, ChIP sequencing) to better understand how these genes work together at a quantitative and systems biology level. We hope that analyzing brain development from this perspective sheds light on the biology underlying brain development and its susceptibility to autism, schizophrenia, and multiple other brain disorders.

Required Experience: Experience with a programming language similar to MATLAB or R (though most work will be in R), and shell scripting. A basic understanding of statistics including p-values, multiple hypothesis testing, and correlation. A good background in biology and high-throughput sequencing is a major plus.

Possibility of Funding : Yes, particularly if involved over summer or for a longer period.

Development of a metabolomics and proteomics pipeline for high-throughput analysis of cancer biology and immunity samples

Project Start Date: Winter 2014
Project Title: Development of a metabolomics and proteomics pipeline for high-throughput analysis of cancer biology and immunity samples

Contact: Thomas Graeber <tgraeber@mednet.ucla.edu>, Ph.D.

Project Description:
Recent advances in cancer biology have shown massive changes in the transcriptome, proteome and metabolome of tumor specimen in response to drug treatment. Our lab aims to understand the governing principles that cause these global changes. To this end, we are conducting metabolomics and proteomics analyses of cancer cell lines and xenograft tumors using top-of-the-line mass spectrometry equipment.

This project will develop the bioinformatic tools necessary to establish a high-throughput pipeline for the mass spectrometry-based analysis of biological samples. The project includes creation of bioinformatic algorithms and pipelines for analyzing multi-omic data, and collaboration with biologists in the analysis and interpretation of the data.

Required Experience: Experience with programming (R, Python, Perl, C++ etc.). Background knowledge of mass spectrometry and biology helpful.

Possibility of Funding : Can evolve to a paid position.

Building and analyzing the fish tree of life

Project Title: Building and analyzing the fish tree of life
Project Contact: Michael Alfaro (michaelalfaro@ucla.edu)

We are currently assembling the largest phylogenetic tree of vertebrates based upon published gene sequences and seek one or more students to assist with scripting and analysis. This project involves creating multi gene alignments from genetic databases, reconciling Genbank taxonomy with published classifications, phylogenetic reconstruction, and macroevolutionary analyses.

Required skills:
experience with some programming languages (python especially helpful)

Possibility of Funding: No

contact Michael Alfaro (michaelalfaro@ucla.edu)

Crowdsourcing of phenotypic data

Project Title: Crowdsourcing of phenotypic data
Project Contact: Michael Alfaro (michaelalfaro@ucla.edu)

We are developing software tools through Amazon mechanical turk to enable crowdsourced collection of shape data on a massive scale. This project will involve development of software protocols for data collection and analysis of geometric morphometric data.

Required skills: experience with some programming languages (python especially helpful)

Possibility of Funding: No

Analysis of transcriptome complexity using deep RNA sequencing

Project Start Date: Summer 2013

Project Title: Analysis of transcriptome complexity using deep RNA sequencing.

Project Contact: Yi Xing (yxing@ucla.edu; http://www.mimg.ucla.edu/faculty/xing/)

Project Description:
Deep RNA sequencing has emerged as a powerful technology for transcriptome analysis. By generating massive amount of short sequence reads from a given RNA sample, one can use RNA-Seq to define and quantify patterns of gene expression and RNA processing on a genomic scale. This project will develop methods for analysis of transcriptome complexity (gene expression, RNA processing, non-coding RNA) using RNA-Seq data, and apply these methods to study transcriptome regulation and mRNA isoform expression in development and disease.

Required Experience: Experience with some programming language (C, C++, Python, Perl, etc.), some background knowledge of statistics. Prior experience in bioinformatics and high-throughput sequencing is desirable but not a must.

Possibility of Funding : Yes

Mapping genes to diseases in admixed populations through 1000 Genomes imputation

Project Start Date: Spring/Summer 2013

Project Title: Mapping genes to diseases in admixed populations through 1000 Genomes imputation.

Project Contact: Bogdan Pasaniuc (bpasaniuc@mednet.ucla.edu)

Project Description:
Recently developed sequencing technologies have allowed for the collection of large repositories of human variation (e.g. 1000 Genomes project) that can be used to increase power for novel disease-gene discoveries.

This project will develop methods for incorporation of 1000 Genomes imputation in disease mapping in admixed populations (e.g. African-American, Latinos)

Required Experience: Experience with some programming language (C, C++, Java etc.), some background knowledge of statistics.

Possibility of Funding : Yes

Construction of a genomics-based body atlas of drugs using microarray and RNA-sequencing data

Project start date: Winter 2013

Project title: Construction of a genomics-based body atlas of drugs using microarray and RNA-sequencing data

Project contact: Xia Yang (xyang123@ucla.edu)

Project description: Drug molecules’ genomic footprints can infer mechanisms of action. By measuring how a pharmacological agent affects the expression of genes of a cell or a tissue type, we can derive cell- or tissue-specific biological pathways involved in the therapeutic effects. This project aims to systematically analyze public microarray and RNA-sequencing data from different cells and tissues in mouse and human to identify genes and biological processes that correlate with the use of therapeutic drugs.

Required Experience: Good programming skills. Experience with R/Bioconductor and basic knowledge of microarrays and RNA sequencing technologies a plus.

Effect of DNA methylation on genomic stability

Project Start Date: Winter 2012

Project Title: Effect of DNA methylation on genomic stability

Project Contact: Guoping Fan (gfan@mednet.ucla.edu)

Project Description:
Dysregulated DNA methylation has been associated with many diseases including cancers, but for reasons that are not well understood. Our lab has developed a model system to assess genomic stability based on different levels of DNA methylation. This project will examine a variety of model systems ranging in yeast, embryonic stem cells, and cancer cells to precisely quantify how DNA methylation contributes to genome stability.

Required Experience: Experience with programming language (Python, Perl, R, Matlab, etc), some background on high-throughput sequencing and epigenetics.

Possibility of Funding: No