Bioinformatics Programmer

Department of Molecular and Human Genetics, Baylor College of Medicine
Job Location
One Baylor Plaza
Houston, TX 77030
Job Description

Role & Responsibilities:

1.    Maintain the existing Exome, Whole Genome and RNA Seq variant analysis pipelines and continually identify novel tools and annotation databases to improve the efficiency, sensitivity and functionality of the results
2.    Identify bioinformatics tools or develop, thoroughly test and deploy novel software in the absence of an existing alternative and automate workflows for various routine bioinformatics analysis tasks
3.    Provide high quality data analysis, generate publication quality reports and plots for a diverse variety of bioinformatics challenges while working with collaborators from diverse scientific research and clinical backgrounds
4.    Identify new analysis methods and suggest informatics solutions for various biological problems within the lab


Skills and Experience:

1.    Bachelors/Masters Degree in Bioinformatics, Computational Biology, Computer Science, Engineering or other related analytical discipline
2.    Two years of experience in scientific programming with applications to biomedical research, preferably in the area of genomics and next generation sequencing analysis
3.    Through understanding of bioinformatics concepts such as sequence alignment, duplication removal, sequence retrieval, variant calling, gene and functional annotation, isoform and gene expression is essential to succeed in this role
4.    Excellent programming skill in atleast one scripting language such as Perl (preferred), Python or Ruby is required, programming knowledge in at least one of Java, C, C++ and knowledge of SQL is useful
5.    Must maintain well documented and tested code and thoroughly document analysis results
6.    Ability to perform data wrangling, statistical analysis and plotting in R is essential
7.    Must be comfortable working in a Unix/Linux operating system and knowledge of command line tools is essential
8.    Strong knowledge of commonly used bioinformatics packages such as the Genome Analysis Tool Kit (GATK), BWA, Bowtie, SAMtools, Picard, IGV, Tophat, Cufflinks, Annovar, BEDtools etc and ability to apply them to regular Bioinformatics problems is necessary
9.    Knowledge of working with a high performance computing (HPC) cluster such as LSF, Sun Grid Engine (SGE) or MOAB is useful
10.    Familiarity with biological data repositories such as the UCSC Genome Browser, NCBI, 1000 genomes, dbNSFP, Exome Aggregation Consortium (ExAC), BioMart etc and their associated APIs to retrieve data is essential
11.    Baylor College of Medicine is a highly collaborative work environment and as such strong communication skills and ability to interact with other researchers from diverse scientific backgrounds is mandatory
12.    Ability to multi task while working independently and exercising good judgment in terms of meeting deadlines is essential
13.    Must be motivated to learn new technologies and contribute towards publications in peer reviewed journals

How to Apply

Send an e-mail with your CV, motivation letter and contact information of references to Dr. Penelope Bonnen (

About Our Organization

About the Lab:

The lab primarily utilizes data from Exome and Whole Genome sequencing experiments to identify SNPs, Indels, Copy Number variants and other genomic aberrations followed by mitochondrial functional profiling in patient cells to identify validated novel mitochondrial disease genes implicated in childhood-onset mitochondrial disorders.

For more information on the lab and previous publications:

At Nature, Johns Hopkins' Gundula Bosch describes her graduate program that aims to get doctoral students thinking about the big picture.

Patricia Fara writes about childcare funding, and women in science and science history at NPR.

National Institute of Environmental Health Sciences researchers have visualized the career paths of former postdocs.

A new survey from the Pew Research Center finds that half of women working in STEM have experienced gender discrimination at work.