Mots-Clés

Ligandome Database Peptide Algorithms Python Benchmarking Cleavage Immunology

Description

Master 2 Internship - Enterome Company

Intership Title: Ligandome Unleashed, Refining the Ligandome Database and Benchmarking Cleavage Prediction Tools

Background and Introduction: The identification of mimics, particularly within Enterome's peptidic technology, hinges on pivotal information: the precise cleavage of the peptide and its presence within the microbiota. The realm of bioinformatics has seen a surge in algorithms and databases tailored for such identifications. While these tools offer promising avenues for understanding and predicting peptide behavior, there remains a need for periodic updates and evaluations to ensure the most accurate and comprehensive insights.

Intership Objectives:

This research internship encompasses two primary objectives:

1. Database Augmentation: Update Enterome's extant ligandome database, ensuring its alignment with the most contemporary and salient data in the discipline,
2. Algorithmic Benchmarking: Undertake a meticulous evaluation of the prevailing peptide cleavage prediction algorithms by benchmarking them against the augmented ligandome database. This endeavor seeks to enhance our molecular understanding of peptide cleavage dynamics and refine the mimic identification protocol.

Methodology:

Materials and Methods:

The intern will deploy advanced bioinformatics tools and databases, in conjunction with programming paradigms such as Python, to curate and analyze the ligandome database. A profound understanding of peptide-centric databases and cleavage prediction algorithms will be advantageous.

Work Plan:

1. Acquaint oneself with the nuances of Enterome's current ligandome database and its associated peptidic technology,
2. Curate and update the ligandome database, integrating the latest and most pertinent data,
3. Catalogue the extant cleavage prediction algorithms in the discipline,
4. Benchmark these algorithms against the updated ligandome database, assessing their predictive accuracy and comprehensiveness,
5. Synthesize the benchmarking outcomes to discern the most efficacious prediction algorithms,
6. Propose recommendations for the integration of optimal algorithms into Enterome's analytical workflow.

Expected Outcomes:

Upon the end of the internship, Enterome will be equipped with a meticulously curated and updated ligandome database. Concurrently, a comprehensive benchmarking report will elucidate the relative efficacies of current cleavage prediction algorithms, thereby informing future algorithmic selection and development endeavors.

From a skill acquisition perspective, beyond the project-specific expertise, the intern will have the opportunity to operate within a high-caliber bioinformatics environment. This setting integrates best practices in programming, structured and standardized team collaboration, and the utilization of cloud solutions for both storage and computation. Guidance will be provided by a multidisciplinary team comprising data scientist, data engineer, bioinformatician, and biostatistician profiles.

Required Skills:

• Proficiency in retrieving data from external sources,
• Demonstrable experience with programming paradigms, preferably Python,
• Ability to integrate data from diverse sources into a unified database (SQL, Athena…),
• An analytical acumen with the capability to evaluate and juxtapose the performance of diverse algorithms.
• R programming is a strong plus.

Practical Information:

• Internship Duration: 6 months, commencing in February/March,

• Location: 94-96 Av. Ledru Rollin, 75011 Paris,

• Supervisor and Contact: To Be Determined.

Note: This internship is tailored for Master's level students (Second year, a.k.a M2) with a keen interest in bioinformatics in the biotech domain.

About Enterome

Enterome is a clinical-stage biopharmaceutical company developing breakthrough immunomodulatory drugs for the treatment of cancer and immune diseases. Enterome’s pioneering approach to drug discovery is based on its unique and powerful bacterial Mimicry drug discovery platform, which allows it to analyze and uncover new biological insights from the millions of gut bacterial proteins in constant cross-talk with the human body.

Enterome’s first-in-class small protein and peptide drug candidates modulate the immune system by closely mimicking the structure, effect or actions of specific antigens, hormones, or cytokines.

The company’s two pipelines of drug candidates include:

• OncoMimics™ peptides, a pipeline of peptide-based immunotherapies. EO2401 is in Phase 2 clinical trials for patients with glioblastoma and adrenal tumors and has demonstrated clinical proof of concept. EO2463 is in a Phase 2 clinical trial for indolent non-Hodgkin lymphomas and has shown a good safety profile with first signs of efficacy. EO4010 is in clinical development for third-line colorectal cancer and EO2040 is in a Phase 2 trial in patients suffering from colorectal cancer with ctDNA-defined, minimal residual disease.
• EndoMimics™ peptides, a pipeline of next-generation bioactives that act like human hormones or cytokines, are being developed in collaboration with Nestlé Health Science for food allergies and inflammatory bowel disease (IBD). The lead candidate, EB1010, expected to enter the clinic in 2024, is designed to improve therapeutic outcomes for patients with IBD.