An Affiliate of Colossal is seeking a talented computational biologist with strong analytical skills to tackle challenging genotype-to-phenotype questions. The successful candidate will collaborate with scientists and engineers to design and perform bioinformatics analyses and integrate genomic, epigenomic, transcriptomic, and proteomic datasets to support de-extinction efforts. The candidate must have experience in bioinformatics, computational biology, statistics, or comparative genomics.
Preference will be given to candidates with a PhD who have demonstrated experience leveraging and interpreting machine learning / artificial intelligence frameworks to link genotype and phenotype using diverse comparative or functional genomic data and information in data-sparse or non-model organisms.**This position will be based on-site in our Dallas, TX headquarters. Relocation assistance is available**
Duties and Responsibilities:- Build machine learning or artificial intelligence models using diverse, integrative datasets
- Run comparative, functional, and statistical genomics analysis
- Run data analysis with biological data
- Develop new tools in R/Python for data analysis and visualization
- Curate and document raw and intermediate data and analysis software
- Prepare reports and presentations to communicate findings to wet-bench biologists and leadership
Required Skills and Abilities:- Two years of bioinformatics experience in the following areas: Applied Statistics or Machine Learning / Artificial Intelligence in Genomics, Comparative Genomics, Functional Genomics / Multi-Omics, or Molecular Evolution.
- Demonstrated ability building and training ML/AI models linking genotype and phenotype (e.g., sequence-to-function models) and experience with the popular libraries like Pytorch, Tensorflow, or OpenCV.
- Capable of leveraging and integrating knowledge across multiple levels of biological organization to validate the outputs of complex analyses.
- Demonstrated 2 years of experience with scripting languages, including but not limited to: Python, R, Perl, Ruby, Java, and BASH.
- Ability to write and run custom bioinformatics scripts using existing published tools and occasionally tools developed to summarize the results in a digestible manner and deliver the information using established reporting procedures.
- Proficiency with handling large-scale genomic data in an HPC (SGE, SLURM, PBS) Linux and/or cloud environment (e.g. AWS, Google Cloud, Azure).
- Experience in using GIT version control software and maintaining well-documented, reproducible notebooks and workflows.
- Ability to design and maintain databases (MySQL, PostgreSQL, MongoDB) and connect with visual platforms to curate and share data with non-bioinformatics team members.
Preferred Skills and Abilities:- Developing or implementing AI/ML frameworks and systems biology networks (e.g., interpretable aka visible deep neural networks like GenNet) for genotype-to-phenotype and functional predictions
- Executing rigorous analyses of diverse functional epigenomics approaches (e.g., RNA-seq and ATAC-seq) and integrating multi-omics datasets to aid in understanding of gene expression regulation
- Performing evolutionary and statistical genomics analyses, including population genetics analysis (e.g., runs of homozygosity and association mapping), genome-wide scans for evolutionary signatures and selective sweeps, and comparative genomics analyses associating genotype and phenotype (e.g., PAML inference of molecular evolution and phylogenetic regression)
- Constructing, interpreting, and utilizing pangenome graphs, whole genome alignments, and gene homology relationships
- Calling germline and somatic sequence variants from high-coverage WGS, low-coverage WGS with imputation, and sequencing libraries from degraded or ancient DNA
- Statistical planning and collaboration with laboratory scientists on designing well-powered experiments to generate useful multi-omics data sets
- Understanding of precision gene editing technologies like CRISPR/Cas9 systems
Education and Experience:- Masters with 2 years of relevant post-graduation work experience or PhD in quantitative or basic science (computer science, computational biology, bioinformatics, chemistry, physics, or mathematics/statistics preferred) is required
What Colossal Offers Full-Time Employees:- Medical, dental, and vision coverage
- Excellent paid time off and company holidays so you can rest and recharge
- Flexible spending accounts (FSA)
- Company matched 401k retirement plan
- Paid parental leave at 100% salary for up to 12 weeks
- Education reimbursement
- An opportunity to help us return the Earth to a healthier state
