Applications Programmer II - Statistical Analyst at Cornell University

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Applications Programmer II - Statistical Analyst, Plant Breeding and Genetics Section, School of Integrative Plant Science, CALS, Cornell
Position Summary:
We seek an applications programmer to provide statistical computational assistance for a research program studying rice genomic characteristics underlying iron toxicity tolerance in rice. The position is funded as part of an international initiative entitled “Rapid Mobilization of Alleles for Rice Cultivar Improvement in Sub-Saharan Africa” funded by a grant from the Bill & Melinda Gates Foundation. The successful candidate will serve as an integral member of the McCouch Research Lab within the Department of Plant Breeding & Genetics at Cornell. Recent research in the McCouch Lab includes multiple locus genome-wide association studies (GWAS), genomic prediction, mapping of quantitative trait loci (QTL), population structure analysis at both whole genome and sub-genomic levels, tracking of target haplotypes through breeding pedigrees, selective sweep mapping, and a variety of projects in the area of computational agricultural genomics. The group is dynamic and interactive, and most projects require close teamwork among students, post doctoral associates, staff, and close collaborators.
Responsibilities of this position include:  
1)Implement computational algorithms used in statistical genomics.  This includes implementing existing algorithms and software for analyzing genome-wide association (GWA) data and developing genomic predictions for breeding; running analysis programs in parallel on large compute clusters; and integrating, organizing, and analyzing program output.
2)Analyzing next generation sequencing data.  This includes developing pipelines and improving automatic methods for data processing, as well as developing scripts to parse, convert, and analyze these data using one or multiple reference genomes, and/or genomic statistical packages.
3)Working with international collaborators to design and develop querying capabilities and user interfaces to facilitate access and transfer of rice diversity data and analysis tools; maintaining general software and database infrastructure of the lab; documenting projects, developing tutorials and SOPs.
4)Travel to national and international meetings and workshops to make presentations about the project.


Bachelor’s degree in computer science, bioinformatics, engineering or related field; 2-3 years programming experience in C/C++, PERL, Python, R, SQL. Proficiency working in UNIX/Linux including software installation and maintenance. Familiarly with HPC environments (e.g. OGE). Familiarity with NGS and PacBio sequence assembly, experience developing bioinformatic analysis tools and pipelines, web-based user interfaces, and visualization tools. Familiarity with model organism genome databases (Arabidopsis, rice, yeast, fly, mouse, bacteria). Demonstrated ability to handle data securely. Strong interpersonal skills and ability to work as part of a diverse team, while contributing to a high-quality and respectful work environment.  Excellent oral and written communication skills.  Ability to manage multiple projects in a dynamic environment with changing priorities, to work independently and solve problems as they arise, to help establish realistic goals and deliver work on schedule. Interest in genomics, bioinformatics, genetics, and molecular biology, willingness to learn relevant concepts and terminology as needed. 


Knowledge of SQL/MYSQL, Python, and R strongly preferred.  Familiarity with data analysis and visualization, development of web graphical user interfaces, PERL, JAVA, Linux.  Experience working with very large data sets and compute clusters.  Coursework or job experience in genetics, molecular biology, or evolutionary biology.

Background check may be required. No relocation assistance is provided for this position.Visa sponsorship is not available for this position.

Cornell University is an innovative Ivy League university and a great place to work. Our inclusive community of scholars, students and staff impart an uncommon sense of larger purpose and contribute creative ideas to further the university's mission of teaching, discovery and engagement. Located in Ithaca, NY, Cornell's far-flung global presence includes the medical college's campuses on the Upper East Side of Manhattan and Doha, Qatar, as well as the new Cornell Tech campus to be built on Roosevelt Island in the heart of New York City. 
Diversity and Inclusion are a part of Cornell University’s heritage. We are a recognized employer and educator valuing AA/EEO, Protected Veterans, and Individuals with Disabilities.


To apply visit:


-Programming, Planning, Analysis and Development

Primary Location



-Agriculture & Life Sciences, College of





Job Type


Overtime Status


Contact Name

-Leslie Larsen

Number of Openings


University Job Title-Applications Programmer II



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