Machine Learning Engineer

Avenue Code is the leading software consultancy focused on delivering end-to-end development solutions for digital transformation across every vertical. We’re privately held, profitable, and have been on a solid growth trajectory since day one. We care deeply about our clients, our partners, and our people. We prefer the word ‘partner’ over ‘vendor’, and our investment in professional relationships is a reflection of that philosophy. We pride ourselves on our technical acumen, our collaborative problem-solving ability, and the warm professionalism of our teams.

Avenue Code has been believing in and promoting plurality actions for over 10 years, understanding that recognizing differences and fostering a safe environment, employment opportunities, representation, and support are the best ways to promote an increasingly equitable culture.

About the opportunity

Job Description

We are a team of highly experienced and collaborative bioinformaticians and we are seeking a qualified intern to help us leverage state of the art AI for healthcare. Your work will involve research and development of AI based bioinformatics applications for multiple kinds of biological data, particularly next-generation sequencing (NGS). Working on the crossroads of state of the art in AI and bioinformatics will equip you with the skills and experience of applying AI in improving patients’ lives. We are seeking a highly motivated and analytical Bioinformatics contractor to join our computational biology team. In this full-time role, you will be at the forefront of liquid biopsy research. Your work will directly contribute to the computational development of our next-gen NGS assays, helping push the boundaries of personalized medicine.

Key Responsibilities

• Pipeline Execution & Optimization: Assist in developing, testing, and optimizing bioinformatics pipelines for the identification and quantification of genetic mutations from cfDNA NGS datasets.
• Data Visualization: Create clear, clarifying visualizations of genomic data, coverage maps, biomarker characteristics, to present findings to the cross-functional R&D team.
• Data Analysis: Analyze genetic mutations identified in cfDNA; propose and explore novel biomarkers; build reproducible machine learning models to quantitatively assess and validate biomarkers.
• Collaboration: Work closely with senior bioinformaticians to troubleshoot analysis strategies and correlate computational findings with clinical data.

Minimum Qualifications

• Education: Bachelor’s or Master’s degree or higher in Bioinformatics, Computational Biology, Computer Science, Biostatistics, or a closely related field.
• Programming Skills: Strong proficiency in Python and Bash/shell scripting within a Linux/Unix environment and familiarity with good engineering practices including proper use of generative AI, version control, and documentation.
• High-performance computing: Proficient in scaling bioinformatics pipelines across HPC clusters using Slurm or equivalent to accelerate NGS data processing.
• Genomic Fundamentals: Solid understanding of Next-Generation Sequencing (NGS) technologies, sequence alignment, and structural variant detection.
• Machine learning: Familiarity with common machine learning concepts, models, metrics and frameworks (scikit-learn, pandas etc).

Preferred Qualifications

• Familiarity with workflow management systems (Nextflow, Snakemake) and containerization (Docker, Singularity or equivalent).
• Prior exposure to liquid biopsy data (cfDNA/ctDNA) or cancer genomics.
• Strong track record of data analysis and publication in relevant fields is a plus.

Note

Our absolute priority is finding someone who is exceptionally strong in machine learning and algorithm development. We need someone who can work independently and has a deep, solid grasp of machine learning algorithm development. Specifically, we are looking for candidates with a strong academic background from a top university, or experience working at a reputable institute or company, with a proven track record in ML/algorithm development.

Please prioritize technical depth and a strong professional and academic background over specific biology experience for the next batch of resumes. Candidates with good publications regarding novel computational biomarker discovery, and/or ML+AI will be given priority consideration for interviews.

Avenue Code reinforces its commitment to privacy and to all the principles guaranteed by the most accurate global data protection laws, such as GDPR, LGPD, CCPA and CPRA. The Candidate data shared with Avenue Code will be kept confidential and will not be transmitted to disinterested third parties, nor will it be used for purposes other than the application for open positions. As a Consultancy company, Avenue Code may share your information with its clients and other Companies from the CompassUol Group to which Avenue Code’s consultants are allocated to perform its services.

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