Bioinformatician - Lotterhos Lab

NU USA Northeastern University; Nahant (MA); On-site; USD 68,000 - 96,000; Full time

Job summary

Northeastern University’s Lotterhos Lab at the Marine Science Center in Nahant, MA, seeks a Bioinformatician to build scalable pipelines for large genomic datasets, including whole-genome and RADseq, to assemble a database of 5,000 genomes from 100 species.

The role emphasizes short-read alignment, population inference, reproducible workflows, collaboration with wet lab and computational teams, and documentation. This is an in‑person, on‑site position with a competitive salary and benefits.

Qualifications

• Master's degree in biology, ecology and evolution, bioinformatics, computational biology, genetics, or related field.
• 2–5 years of hands-on experience in bioinformatics with genomics work.
• Proficiency in short-read alignment tools such as BWA, Bowtie2, and STAR.
• Experience with SAMtools, GATK, and Picard; pipelines with Snakemake or Nextflow; Python, R, Bash.
• Comfort with Unix/Linux, HPC/HTCondor environments and SLURM/HTCondor; data transfer via APIs.

Responsibilities

• Collaborate with network members to define data standards and reproducibility.
• Design and maintain scalable bioinformatics pipelines for large population genomic datasets.
• Align short-read data to reference genomes and assess mapping quality.
• Perform downstream population genomic analyses including variant calling and QC.
• Document pipelines and analyses for internal use and publication.
• Develop educational tutorials and assist with website development.

Skills

Short-read alignment

Python

R

Unix/Linux

Workflow expertise (Snakemake/Nextflow

Scripting (Bash)

HPC/HTC environments (SLURM/HTCondor)

Data transfer APIs

Education

Master's degree in Biology, Ecology and Evolution, Bioinformatics, Computational Biology, Genetics, or related field

Tools

SAMtools

GATK

Picard

Snakemake

Nextflow

Docker/Singularity

Job description

About the Opportunity

About the Center for Marine Ecological Genomics The successful candidate will be based at the Lotterhos Lab and the Center for Marine Ecological Genomics at Northeastern Marine Science Center in Nahant, Massachusetts. This is an in‑person position.

Job Summary

We are seeking a skilled Bioinformatician to join our consortium in Marine Macrogenomics, which seeks to create a database of interoperable population genomic data for 5,000 genomes from 100 species. The successful candidate will play a central role in developing and maintaining scalable computational pipelines for the analysis of large‑scale genomic datasets, with a focus on short‑read alignment and population‑level inference. This is an exciting opportunity to contribute to cutting‑edge research in ecological and conservation genomics.

Minimum Qualifications Required

• Master's degree in Biology, Ecology and Evolution, Bioinformatics, Computational Biology, Genetics, or a related field
• 2-5 years of hands‑on experience in bioinformatics, with demonstrated work in genomics
• Proficiency in short‑read alignment tools such as BWA, Bowtie2, and STAR
• Familiarity with downstream processing tools such as SAMtools, Genome Analysis Toolkit (GATK), and Picard
• Experience writing pipelines using workflow management systems such as Snakemake or Nextflow
• Solid scripting skills in Python, R, and Bash
• Comfort working on the command line, including in a Unix/Linux environment
• Familiarity with high‑performance computing (HPC) and high‑throughput computing (HTC) environments and job schedulers such as SLURM and HTCondor
• Experience using application programming interfaces (APIs) to send and receive data and/or experience using tools to transfer large amounts of data between remote servers

Preferred

• PhD or 3 years of post‑Master's experience preferred
• Experience with population genomic analyses and tools such as ANGSD, PLINK, ADMIXTURE, TreeMix, or similar platforms
• Familiarity with handling non‑model organism genomes or low‑coverage sequencing data
• Experience with version control systems such as Git and containerization technologies including Docker and Singularity/Apptainer
• Track record of contributing to published research

Key Responsibilities & Accountabilities

• Collaborate and coordinate with members of the network, including wet lab and computational team members, to define data standards, ensure analytical reproducibility, and assist with project goals
• Design, build, and maintain reproducible bioinformatics pipelines capable of scaling across many population genomic datasets
• Align short‑read sequencing data, including whole-genome and Restriction Site Associated DNA Sequencing (RADseq) datasets, to reference genomes using standard and emerging tools, and evaluate mapping quality across diverse datasets
• Perform downstream population genomic analyses, including variant calling, filtering, and quality control
• Document pipelines and analyses clearly for internal use and publication
• Develop educational tutorials and assist with website development
• Collate publicly available data and metadata, corresponding with authors as necessary to ensure data standards
• Position Type: Research

Additional Information

Northeastern University considers factors such as candidate work experience, education and skills when extending an offer. Northeastern has a comprehensive benefits package for benefit eligible employees. This includes medical, vision, dental, paid time off, tuition assistance, wellness & life, retirement- as well as commuting & transportation. Visit https://hr.northeastern.edu/benefits/ for more information. All qualified applicants are encouraged to apply and will receive consideration for employment without regard to race, religion, color, national origin, age, sex, sexual orientation, disability status, or any other characteristic protected by applicable law.

Compensation

Grade/Pay Type: 109S Expected Hiring Range: $67,855.00 - $95,845.00 With the pay range(s) shown above, the starting salary will depend on several factors, which may include your education, experience, location, knowledge and expertise, and skills as well as a pay comparison to similarly-situated employees already in the role. Salary ranges are reviewed regularly and are subject to change.

Founded in 1898, Northeastern is a global research university and the recognized leader in experiential lifelong learning. Our approach of integrating real-world experience with education, research, and innovation empowers our students, faculty, alumni, and partners to create worldwide impact. Our global university system provides our community and academic, government, and industry partners with unique opportunities to think locally and act globally. The system—which includes 14 campuses across the U.S., U.K., and Canada, 300,000-plus alumni, and 3,000 partners worldwide—serves as a platform for scaling ideas, talent, and solutions. The university’s residential campuses for undergraduate and graduate degrees are located in Boston, London, and Oakland, California. Our research and graduate campuses are in the Massachusetts communities of Burlington and Nahant; Arlington, Virginia; Charlotte, North Carolina; Miami; Portland, Maine; Seattle; Silicon Valley, California; Toronto; and Vancouver. Northeastern’s personalized, experiential undergraduate and graduate programs lead to degrees through the doctorate in 10 colleges and schools across our campuses. Learning emphasizes the intersection of data, technology, and human literacies, uniquely preparing graduates for careers of the future and lives of fulfillment and accomplishment. Our research enterprise, with an R1 Carnegie classification, is solutions oriented and spans the world. Our faculty scholars and students work in teams that cross not just disciplines, but also sectors—aligned around solving today’s highly interconnected global challenges and focused on transformative impact for humankind.