Machine Learning Research Scientist

at St. Jude Children's Research Hospital in Memphis, Tennessee, United States

Job Description

Madan Babu’s Group and the Center for Data-Driven Discovery in the Department of Structural Biology is seeking a highly driven, full-time Machine Learning Research Scientist support the Kalodimos and Babu Groups on the Blue Sky Initiative"Seeing the Invisible in Protein Kinases." This project is supported by $35 million in institutional funding (more information in the St. Jude Strategic Plan 2022-2027, pp 62-63). This is a joint project between the Kalodimos Lab and the Babu Group at St Jude.

The project will extend the ultra-high field NMR spectroscopy and biochemistry approaches developed recently by the Kalodimos lab (Science, 2020) to study the human kinome. This is a large-scale project that aims to detect and structurally characterize the distinct conformational states populated by kinases, and to dissect the mechanisms of allosteric regulation and those underpinning oncogenic and drug-resistance mutations. This strategy will be integrated with and complemented by data-science and computational approaches developed by the Babu lab (Nature, 2020), to systematically characterize the conformational landscape of the human kinome.

This position is for an experienced Machine Learning Scientist who will employ a variety of data-driven techniques to develop, construct and test machine learning systems aimed at exploring the conformational landscape of human kinases. The ideal candidate will have strong experience working and developing state of the art Machine Learning methods for the prediction and analysis of protein structures by integrating and visualizing high-dimensional biological data and help scientists building testable structural hypotheses. This role requires a strong background in machine learning, computer science, statistical analysis and data integration. You will work with an interdisciplinary team of 40 scientists including biochemists, spectroscopists, data scientists and bioinformaticians; exceptional communication (written and verbal), training experience and critical thinking skills are a must. When submitting your application, please include your CV and a cover letter.

The Group believes strongly in providing excellent scope for career advancement to the candidate to develop themselves as a future leader in the field. There will be strong support and encouragement for developing mentoring abilities, “outside the box” scientific ideas and acquiring tangential scientific/technical skills. St Jude offers a well-defined career ladder with potential for growth and advancement. Salaries are highly competitive with Industry, and scale with your degree and years of experience.

St. Jude Children’s Research Hospital is consistently named as one of Fortune magazine and’s “Best Places to Work,” as well as “Best Workplace for Women” and “Best Workplace for Diversity.” We are in the heart of Memphis, Tennessee, a vibrant and friendly city at the historic American crossroads of music, trade, food, and culture. Mild winters and beautiful green outdoor spaces are part of the reasons why Forbes recently named Memphis the 4th happiest city in which to work. Low cost of living and high quality of life are other attractions; Money magazine listed Memphis as one of the least expensive cities in which to raise a child. St. Jude facilities and salaries are highly competitive. The Babu Group strives to build and maintain a culture of respect, diversity, and inclusion and we strongly feel these values directly contribute to the dynamic and intellectually stimulating scientific environment we can provide.

+ Employ and develop state of-the-art ML techniques to investigate conformational changes in proteins and identify key structural elements defining the conformational landscape of human kinases.

+ Autonomously develop, setup, test, and benchmark novel ML systems to investigate structural and functional aspects pertaining to protein kinases in the interest of the BSP initiative.

+ Perform AI-based kinome-wide analysis integrating structural, evolutionary, functional, and medical data to derive family-wide insights.

+ Interface with human health-related data and integrate various data types in the analysis pipeline to help better understand impact of variation in protein kinases on human diseases.

+ Work collaboratively on a diverse team. Candidate must be able to generate testable predictions from computational results, interpret, and explain ML methodologies and predictions to experimental members and use experimental results to drive further data-driven and machine learning analyses.

+ Bachelor’s degree is required

+ Master’s or PhD is preferred

+ In-depth knowledge of state-of-the art machine learning and AI methods to model biomolecules is strongly preferred.

+ In-depth knowledge of modern deep-learning architectures (ConvNets, RNNs, Transformers, Attention Models) is strongly preferred.

+ Hands-on experience in using machine-learning tools to perform structural predictions of protein structures and complexes strongly preferred.

+ Working knowledge of computational evolutionary biology is strongly preferred.

+ Experience working in HPC and parallel computing environments as well as familiarity using UNIX-like systems, shell scripting, and LSF workload manager preferred.

+ Deep programming experience in Python is strongly preferred. Knowledge of R and/or C/C++ is not required but preferred.

+ Working knowledge of modern ML and scientific packages in Python (Tensorflow, PyTorch, sklearn, pandas, numpy) required.

+ Hands-on experience of sequence-analysis bioinformatics tools (hmmer, hh-suite, BLAST).

+ Ability to model the structure of proteins using a variety of different methods, including recent AI-based methods (e.g. AlphaFold2, RosettaFold, MSA transformers).

+ A good understanding of basic protein biology and biochemistry is required. Familiarity with the broad biological aspects of protein kinases is strongly preferred.

+ Familiarity working with biological datasets including sequence data, structural models, and variant data.

+ Hands-on experience of sequence-analysis bioinformatics tools (hmmer, hh-suite, BLAST).

+ Experience using modern tools for scientific visualisation (e.g., seaborn, bokeh, plotly, D3.js, chimera, pymol, etc.) and analysis (e.g., interaction networks, contact heatmaps, directed graphs, etc.).

Bioinformatics Research Scientist

+ Seven (7) years of relevant post-degree work experience is required

+ Five (5) years of relevant post-degree work experience is required with a Master’s degree

+ Two (2) years of relevant post-degree work experience is required with a PhD

Lead Bioinformatics Analyst

+ Six (6) years of relevant experience is required.

+ Four (4) years of relevant experience may be acceptable with a Master’s degree.

+ No experience may be acceptable with a PHD in Computer Science or Bioinformatics, with a background in the biological sciences.

+ Experience in programming (Python, Java, C/C++, perl or other programming/scripting languages) under linux/unix environment is required.

+ Experience with and the ability to deal with a wide range of users is required.

+ Experience of independent data analyses and project management is required.

+ End user support and training experience is required.

COVID-19 vaccine:

As of September 10, 2021, St. Jude Children’s Research Hospital has mandated the COVID-19 vaccine for all employees, excluding those with an approved medical or religious accommodation, as a condition of employment.

EEO Statement: St. Jude is an Equal Opportunity Employer

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Job Posting: JC198436874

Posted On: Nov 25, 2021

Updated On: Dec 02, 2021