Organizational Overview
Researchers in the Biology Department at Brookhaven National Laboratory seek to unravel and fully describe the complexities of biological systems from how plants make oils and other products to the role of proteins in disease. Our work helps to develop and makes use of the tools and techniques of biochemistry, molecular genetics, and structural biology. We also leverage the unique capabilities of Brookhaven’s National Synchrotron Light Source-II and Center for Functional Nanomaterials, major research facilities open to scientists from around the world. Our research makes important contributions to fulfilling the missions of the U.S. Department of Energy’s Office of Basic Energy Sciences and Office of Biological and Environmental Research. In addition, together with the Collider-Accelerator Department, the Biology Department manages the NASA Space Radiation Laboratory (NSRL) at Brookhaven, which is used by radiobiologists and physicists to study the effects of space radiation on both living and non-living systems with the aim of protecting future astronauts.

Position Description

We are seeking a bioinformatician to analyze genome wide transcriptomic responses to stress in plants and microbes for functional genomic studies. The post doc will be involved in many exciting projects using newly assembled reference genomes of host plants and nitrogen-fixing symbiotic microbes. We are particularly interested in genes that can enhance tolerance to stress or toxic environments. Incorporation of evolutionary and/or ecological aspects and analyses into this research is highly encouraged. The research is essential to meet the DOE’s Biological and Environmental Research (BER) mission to use genome-enabled approaches to understand the relationship between soil biogeochemistry, nutrient cycling by plants, and the movement or transport of metals ions from soils into plant biomass. (https://www.energy.gov/science/ber/biological-and-environmental-research)

This position has a high level of interaction with an international and multicultural scientific community, including the Joint Genome Institute (JGI) and the Environmental Molecular Sciences Laboratory (EMSL), both DOE run facilities. The research will support two JGI funded community science awards (New Investigator and Functional Genomics).

Position Requirements

Essential Duties and Responsibilities:

• Quantify gene expression changes in response to stress treatments such as heavy metals, temperature, drought.
• Assess the role of gene duplications on expression level.
• Identify candidate genes that provide greater tolerance to stress.
• Develop statistical pipelines to identify differentially expressed genes and co-expression networks.
• Integrate genome wide association study (GWAS) candidates with transcriptomics data to identify target genes for functional studies.

Required Knowledge, Skills, and Abilities:

• Requires a Ph.D. in bioinformatics or biology with focus on genomics, or computational biology, evolutionary genomics, plant genomics/agricultural genomics or related field.
• Experience mapping and analyzing RNA-seq data, including differential expression analysis (e.g. DeSEQ, edgeR).
• Ability to install and use bioinformatics software (i.e., samtools, BWA, GATK, plink) in a Linux framework.
• Proficient in one or more programming languages such as python or perl, and ability to write and modify scripts in R.
• A proven track record of experimental design, execution and data analysis as reflected in manuscript writing and successful publication in peer-reviewed journals.
• Demonstrated track record of poster presentations and/or oral presentations at scientific meetings.

Preferred Knowledge, Skills, and Abilities: 

• Standard genome annotation software experience with genome assembly and annotation using RNA-seq data.
• Gene co-expression network analysis using WCGNA or other tools.
• Single gene alignment software and PCR primer design.

Other information:

• Review of applications begins immediately. Applications will be accepted until the position is filled.
• Initial 1-year appointment subject to annual renewal contingent on performance and funding.
• Research is under the direction of Dr. Tim Paape.
• BNL policy requires that after obtaining their PhD, eligible candidates for research associate appointments may not exceed a combined total of 5 years of relevant work experience as a post-doc and/or in an R&D position, excluding time associated with family planning, military service, illness or other life-changing events.

At Brookhaven National Laboratory we believe that a comprehensive employee benefits program is an important and meaningful part of the compensation employees receive. Our benefits program includes, but is not limited to:

• Medical Plans
• Dental Plans
• Vacation
• Holidays
• Life Insurance
• 401(k) Plan
• Paid Parental Leave
• Swimming Pool, Weight Room, Tennis Courts, and many other employee perks and benefits