Scientist

Location: Cambridge / AMA site
Candidates local to the Cambridge/AMA area who can support an on-site schedule and commit to the full assignment duration will be strongly preferred.
Schedule: on-site Standard business hours (~8 AM - 5 PM preferred)
• OT Expected: Minimal to none
• Weekend Work: Not expected
Assignment Length: 18 months


The ideal candidate will have a Master's degree or PhD in bioinformatics, computational biology, genomics, or a related discipline and will be comfortable supporting established bioinformatics workflows in a highly operational environment. This person should have experience working with computational pipelines, metadata handling, and QC-focused support work. Familiarity with UNIX/Linux infrastructure and some Python exposure are preferred. Benchling experience is helpful but not required. The team is looking for someone highly detail-oriented, organized, and reliable who can independently execute routine computational and metadata management tasks with consistency and accuracy. Strong candidates will be comfortable supporting established workflows rather than focusing solely on Client pipeline development or research ownership.


Candidates local to the Cambridge/AMA area who can support an on-site schedule and commit to the full assignment duration will be strongly preferred.


TD&B-Discovery Genomics


This Contract Scientist will report to a Principal Scientist in the Discovery Genomics team of Target Discovery & Biology (TD&B). This role will support higher throughput, improved data management, and faster turnaround for projects analyzed within the TD&B group.


What you will do:


• Support routine computational analysis of functional genomics and transcriptomics datasets using established internal pipelines and reporting systems.
• Assist with experimental registration, source sample tracking, and data management for NGS-based workflows to ensure data retention, visibility, and accessibility.
• Manage workflow and data entry in Benchling OEMS for pooled gene perturbation, amplicon-seq, bulk RNA-seq, and related NGS experiments.
• Process pooled genomic perturbation screen data, including raw FASTQ files, using established NextFlow pipelines and internal gene-edited reporting systems.
• Support future arrayed perturbation screening efforts by running established analytical pipelines once developed and implemented.
• Process Perturb-seq datasets by converting raw FASTQ files into count tables using established Cell Ranger workflows.
• Support bulk RNA-seq routine by downloading data from CROs, processing samples through the internal bulk RNA-seq pipeline and generating reports using established RNA-seq reporting workflows.
• Assist with transcriptomic assessment of edited clones using existing analysis pipelines.
• Partner closely with the manager and TD&B team members to prioritize analyses, troubleshoot routine issues, and ensure timely project completion.
• Maintain organized records of analyses, inputs, outputs, and reports to support reproducibility, data integrity, and downstream interpretation.


Preferred Qualifications:


• Degree or experience in bioinformatics, computational biology, genomics, genetics, biology, data science, or related discipline.
• Familiarity with NGS data types, including pooled gene perturbation screens, bulk RNA-seq, amplicon-seq, Perturb-seq, or other functional genomics workflows.
• Experience running established computational pipelines and working with structured data outputs.
• Familiarity with sequencing file formats and analysis outputs, including FASTQ files, count matrices, and standard NGS reports.
• Experience with Benchling, sample tracking systems, or other experimental registration/data management platforms.
• Experience working in Unix/Linux environments and cloud-based computing platforms, including AWS, is preferred.
• Basic programming or scripting experience in R, Python, or shell scripting is preferred.
• Strong attention to detail and commitment to data integrity, reproducibility, and documentation.
• Ability to work independently on routine analyses while communicating regularly with the manager and project teams.
• Strong written and verbal communication skills, with the ability to collaborate effectively in a cross-functional research environment.