Postdoc Bioinformatics / Plant-Microbe Genomics

Upton, New York
February 12 2021
Position Type
Full Time
Organization Type
Job Type

Brookhaven National Laboratory ( delivers discovery science and transformative technology to power and secure the nation’s future. Brookhaven Lab is a multidisciplinary laboratory with seven Nobel Prize-winning discoveries, 37 R&D 100 Awards, and more than 70 years of pioneering research. The Lab is primarily supported by the U.S. Department of Energy’s (DOE) Office of Science. Brookhaven Science Associates (BSA) operates and manages the Laboratory for DOE. BSA is a partnership between Battelle and The Research Foundation for the State University of New York on behalf of Stony Brook University.

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 the role of gene duplications that can enhance tolerance to stress or toxic environments, and how stress tolerant microbes provide benefits for host plants. 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 ( 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). Because this position is entirely computational, opportunities for working remotely are possible.

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 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.
  • Competitive salary will be commensurate with relevant experience and qualifications.
  • 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 research associate appointments may be made to individuals who have received their doctorate within the past five years.
  • Brookhaven National Laboratory is an equal opportunity employer committed to building and maintaining a diverse workforce.

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

Brookhaven National Laboratory (BNL) is an equal opportunity employer that values inclusion and diversity at our Lab.We are committed to ensuring that all qualified applicants receive consideration for employment and will not be discriminated against on the basis of race, color, religion, sex, sexual orientation, gender identity, national origin, age, status as a veteran, disability or any other federal, state or local protected class.

BNL takes affirmative action in support of its policy and to advance in employment individuals who are minorities, women, protected veterans, and individuals with disabilities.We ensure that individuals with disabilities are provided reasonable accommodation to participate in the job application or interview process, to perform essential job functions, and to receive other benefits and privileges of employment.Please contact us to request accommodation.

*VEVRAA Federal Contractor

Brookhaven employees are subject to restrictions related to participation in Foreign Government Talent Recruitment Programs, as defined and detailed in United States Department of Energy Order 486.1A. You will be asked to disclose any such participation at the time of hire for review by Brookhaven. The full text of the Order may be found at:

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