Ishita Mandhan who is working on a project evaluating the impact of loss-of-function mutations on gene transcription receives the ECEN Undergraduate Research Award. The purpose of this one-time scholarship is to encourage and support research for undergraduate students. Donor representative of the program is Dr. Chanan Singh, Regents Professor, Irma Runyon Chair Professor at the Electrical and Computer Engineering Department, TAMU. 

The 1000 genomes toxicity screening project is led by Prof. Ivan Rusyn. The goals of this project are to (i) develop toxicogenetic expression quantitative trait loci (eQTL) mapping tools, perform transcription factor network inference and integrative pathway assessment; (ii) perform toxicogenetic modeling of liver toxicity in cultured mouse hepatocytes; (iii) discover chemical-induced regulatory networks using population-based toxicity phenotyping in human cells.

Increasing evidence suggests that the variance (as opposed to the mean) among phenotypes may be genotype-dependent. Conventional eQTL analysis focuses on the mean, instead of the variance, of gene expression. In a paper published in Genetics, Amanda Hulse and James Cai perform an analysis that identifies what we describe as evQTL—loci associated with the variances of gene expression among three possible genotypes of a biallelic SNP. The discovered evQTL provide orthogonal information, unavailable in existing eQTL literature, on genetic control of gene expression. The evQTL can act in single-SNP and multiple-SNP effects. Detecting evQTL may represent a novel method for effectively screening for genetic interactions. [Read on...]

Ishita Mandhan is an undergraduate student of the Departments of Electrical & Computer Engineering, TAMU. She is interested in application of computational approaches in processing large-scale genomics data. Thanks to the Undergraduate Research Scholars Program. Her scholars application has been accepted on Sep. 27, 2012. Congratulations and welcome to the 2012-13 class of Undergraduate Research Scholars! She will be participating Scholars Orientation and Welcome Bar B Q on October 10th in the Interdisciplinary Life Sciences Building.  After the kick-off, Ishita will start working on a population-level evaluation of the impact of loss-of-function mutations and GWAS mutations on human transcriptomes.

We present SBEToolbox (Systems Biology and Evolution Toolbox), an open-source Matlab toolbox for biological network analysis. It takes a network file as input, calculates a variety of centralities and topological metrics, clusters nodes into modules, and interactively displays the network using different graph layout algorithms. Efficient lightweight design allows large-scale networks to be handled. Straightforward implementation and the inclusion of high-level functions allow the functionality to be easily extended or tailored. SBEGUI, a menu-driven Graphical User Interface (GUI) of SBEToolbox, is highly interactive, enabling easy usage of most network and graph algorithms without prior knowledge of programming. The stand-alone executable SBEGUI, running on all major operating systems, does not require the installation of Matlab system. Availability: Pre-compiled stand-alone executable for all major operating systems and source code are freely available at http://sbetoolbox.sourceforge.net.

The Chowdhary & Cai lab (http://vetmed.tamu.edu/labs/cytogenics-genomics & http://www.genomezoo.net) is seeking a joint appointment post-doc that will apply the latest bioinformatics tools towards understanding equine diseases (including laminitis, recurrent airway obstruction, and stallion subfertility) and phenotypes. The Chowdhary lab is focusing on characterizing genetic factors involved in major equine diseases, sexual development, and reproductive disorders. The approaches applied include genetic association analysis using the equine SNP chip, microsatellites, copy number variation tiling array, re-sequencing of candidate genes, gene expression microarrays, next-generation sequencing, protein expression analysis, RT-PCR, RH mapping, karyotyping, and FISH. In addition, the lab is also working on describing the PAR and the MSY of the equine Y chromosome including gene loss, gain, function, and the roles Y genes play in stallion fertility. The Cai lab focuses on the interaction between the genotype and phenotype using computational genomics to identify the causal variants underlying genetic disorders and complex traits of different organisms. Projects will focus on applying next-generation sequencing to follow up associations found with more traditional methods. The work is funded by USDA-CREES, USDA-NIFA, American Quarter Horse Foundation, and Morris Animal Foundation. We seek a motivated postdoc that is interested in applying the latest bioinformatics tools to understand the genomic factors that play a role in diseases and phenotypes of horses, and other important domestic, agricultural, and wild animals. The post-doc will be required to write manuscripts and proposals, and will have opportunities to develop additional projects in line with their areas of interest. The successful applicant will work as part of a multidisciplinary team and will develop skills in bioinformatics, genomics, and translational medicine. REQUIREMENTS: Ph.D. in a relevant biological discipline with previous research experience using genomic bioinformatics tools. Knowledge of both genomics and computational analysis of genomic data is required, as is familiarity with Linux, Python, Matlab, and Perl, and the ability to write scripts. Excellent writing, communication skills, and the ability work as part of a team are also required. Previous work with large data sets, SNP analysis, and next-generation sequencing data is preferred. Knowledge and experience with horses, other domestic animals, or wildlife is also preferred. TO APPLY: For inquiries or to apply, email Dr. Jan Janecka (jjanecka@cvm.tamu.edu) a (1) a 1-page cover letter with as summary of your primary research experience and interests, (2) your CV, (3) and contact information for three references.