Senior Bioinformatics Scientist

1 month ago

Watertown, Massachusetts, United States Acrivon Therapeutics Full time

Acrivon is a clinical stage biopharmaceutical company developing precision oncology medicines that it matches to patients whose tumors are predicted to be sensitive to each specific medicine by utilizing Acrivon's proprietary proteomics-based patient responder identification platform, Acrivon Predictive Precision Proteomics, or AP3. The AP3 platform is engineered to measure compound-specific effects on the entire tumor cell protein signaling network and drug-induced resistance mechanisms in an unbiased manner. These distinctive capabilities enable AP3's direct application for drug design optimization for monotherapy activity, the identification of rational drug combinations, and the creation of drug-specific proprietary OncoSignature companion diagnostics that are used to identify the patients most likely to benefit from Acrivon's drug candidates.

Acrivon is currently advancing its lead candidate, ACR-368 (also known as prexasertib), a selective small molecule inhibitor targeting CHK1 and CHK2 in a potentially registrational Phase 2 trial across multiple tumor types. The company has received Fast Track designation from the Food and Drug Administration, or FDA, for the investigation of ACR-368 as monotherapy based on OncoSignature-predicted sensitivity in patients with platinum-resistant ovarian or endometrial cancer. Acrivon's ACR-368 OncoSignature test, which has not yet obtained regulatory approval, has been extensively evaluated in preclinical studies, including in two separate, blinded, prospectively-designed studies on pretreatment tumor biopsies collected from past third-party Phase 2 trials in patients with ovarian cancer treated with ACR-368. The FDA has granted Breakthrough Device designation for the ACR-368 OncoSignature assay for the identification of ovarian cancer patients who may benefit from ACR-368 treatment. In addition to ACR-368, Acrivon is also leveraging its proprietary AP3 precision medicine platform for developing its co-crystallography-driven, internally-discovered preclinical stage pipeline programs. These include ACR-2316, a potent, selective WEE1/PKMYT1 inhibitor designed for superior single-agent activity as demonstrated in preclinical studies against benchmark inhibitors, and a cell cycle program with an undisclosed target.

Our global team operates out of two leading life science clusters, Watertown, MA and Medicon Village in Lund, Sweden.

Position Overview:

The Senior Bioinformatics Scientist will be a key member of Acrivon Therapeutics' Data Science Team and will leverage their bioinformatics and computational biology expertise to provide innovative solutions for our drug discovery and development efforts, leveraging Acrivon's AP3 platform. The ideal candidate will possess hands-on experience in developing, implementing, and deploying data analytics tools and models, with a particular emphasis on AI/ML algorithms. Additionally, the candidate will have a track record integrating multi-omics datasets to generate actionable biological insights, including the identification and validation of targets, elucidation of mechanisms of action, and discovery of biomarkers. This position will be based in Watertown, MA.

Duties and Responsibilities:

Contribute to evaluation and fine-tuning of AI foundation models by leveraging AP3 and multi-omics data.
Extract and curate external multi-omics data, enabling integration with AI/ML methodologies.
Contribute to the advancement of innovative computational methods for analyzing large-scale proteomics and phosphoproteomics datasets.
Provide customized computational analyses in collaboration with proteomics, biology, and biomarker development teams.
Design and maintain interactive web-based applications that integrate internal and external data within a cloud environment.
Use data mining, text mining, network visualization and AI/ML techniques to identify potential biomarkers.

Requirements and Qualifications:
Demonstrated proficiency of 2-6 years in applying bioinformatics or computational biology methodologies preferably within an industry environment, with a preference for experience in oncology and immunology.
Hands on experience in the development and implementation of AI/ML methodologies, including deep learning, large language models (LLMs), or protein language models (pLMs).
Hands on experience in developing computational workflows and conducting data analyses for multi-omics datasets, with a particular emphasis on proteomics/phosphoproteomics.

Qualifications include:
Ph.D. or M.S. in Computational biology, Bioinformatics, Engineering, Computer Sciences, or a related field.
Proficient coding skills, especially in Python and R, alongside proficiency in other scripting languages.
Experience with machine learning frameworks such as TensorFlow, PyTorch, or scikit-learn.
Hands-on experience in constructing and deploying web-based applications utilizing web development frameworks, such as R Shiny, Python Django/Flask/Streamlit.
Familiarity with cloud computing platforms such as AWS, Google Cloud, or Azure.
Familiarity with cancer biology in a drug discovery and development setting is preferred.
Excellent communication and presentation skills with demonstrated record of peer-reviewed publication.
Team player with ability to nurture productive collaborative relationship with internal and external partner.

Acrivon Therapeutics is proud to be an equal opportunity employer and to provide equal opportunities to all employees and applicants for employment without regard to race, color, religion, sex or gender identity, national origin, age, disability, sexual orientation or genetics. In addition to federal law requirements, Acrivon Therapeutics complies with applicable state and local laws governing nondiscrimination in employment.

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