Postdoc positions Genomics, Genetics, Precision Medicine and Machine Learning : Cleveland, OH, United States

Interested in genomics, computational biology, clinical oriented data science or software engineering?

“Why did the patient develop this disease?” “Will the patient respond to this medication?” “Can we predict the disease prognosis?” “What is the underlying mechanism?”

The Genomic Medicine Institute (GMI) of the Cleveland Clinic serves as the expert base for the principles and practice of genomic medicine, including genetics and genomics research, clinical care, and outreach and education directed at genomics-based personalized healthcare. Research conducted at GMI focuses on both translational and clinical human genetics and genomic science, meaning discoveries made in the laboratory will advance the field of precision medicine and, ultimately, improve the quality of patient care. The Epilepsy Center at the Cleveland Clinic has one of the largest, most comprehensive programs in the world for the evaluation, medical and surgical treatment of epilepsy in children and adults. The Center diagnoses and treats more than 10,000 patients with epilepsy each year.

The Lal Research group at Cleveland Clinic studies large-scale genetic and clinical biomarkers from thousands of patients to improve our understanding of brain disorders and aims to subsequently translate the gained knowledge into clinical care. We seek new team members to lead projects in genetics, electronic health records, neurophysiology and brain imaging data science as well as software engineers and web developers for the development of computational infrastructure. The accepted applicants will work in the Genomic Medicine Institute and the Epilepsy Center of the Cleveland Clinic in close collaboration with other data scientists, neuroscientists and clinical researchers from related fields, to ultimately develop personalized medicine approaches. Besides local collaborations, the team will interact on a daily to weekly basis with collaboration partners and other members of the Lal Research Groups located at the Broad Institute of MIT and Harvard, Boston, US, and the Cologne Center for Genomics in Germany.

Data available

We are currently generating genotyping and whole exome sequencing data from >2000 epilepsy patients. For all 2000 patients and another 5000 patients electronic health records over many patient visits, pre and post surgery cognitive testing results, MRI, EEG and many more biomarker are available. Since the Lal Research Group is positioned in the largest epilepsy surgery center in the US, for >1000 patients brain tissue for single cell RNA sequencing is available. By end of 2018 we are expecting to have generated 30 patient data sets with >50000 cells as a pilot project. Besides the local data, the group is part of the largest epilepsy genetic consortium "Epi25" analysis group and performs rare and common variant analyses of globally aggregated genetic data from >15000 patients and >30000 controls. For specific missense variant interpretation projects, we are collaborating with individual gene-disorder molecular and clinical experts from across the globe and develop novel approaches based on each projects individual variants and functional data.

Selected research projects include:

1. Gene and risk loci discovery using genetic data from in-house and globally collected epilepsy patient cohorts in collaboration with international disease consortia and population biobanks.

2. Developing novel methods for missense variant interpretation in 3D protein structures including homology modeling or protein structure prediction at genome-scale.

3. Characterization of patient disease trajectories using electronic health records as well characterizing patient brain tissues by analysing single cell RNA sequencing, brain neurophysiology and imaging data sets.

4. We are interested in your ideas -> Talk to us and suggest your own project.

Infrastructure project:

· Design and development of a scalable integrated multi-omic data management for application of machine learning techniques to stratify patient subtypes and disease progression.

Web tool project:

· We are developing many novel computational tools and want to expose these to the community, that our colleagues can use these methods. The position focuses on back and front-end web application development in the context of the research tools the group develops.

Requirements

We are looking for talented, passionate individuals who want to transform brain disorder research. Demonstrated capability as highly organized, creative problem-solver, self-motivated and able to work independently as well as within in an interdisciplinary teams. Previous experience with laboratory scientists and clinicians is a plus.

Postdoctoral Fellow. Required: Doctorate in computational biology, biology, computer science, electrical engineering, statistics, or physics, obtained within the last five years. Submitted first-author or joint first-author papers in any of the project relevant fields. Experience of working in a Linux environment. Demonstrated proficiency in at least two of the following programming languages Python, Perl, Java, Matlab, R, bash, and C++. Not required, but preferred qualifications: First-author papers published in peer-reviewed journals or a preprint archive. Demonstrated research interaction with medical doctors or biologist. Basic training in genetics.

Software engineer. Required: BS or higher in computer science or related field. Previous work history in data-centric software engineering or data engineering roles. Skilled with database technologies: SQL, MongoDB, HiveQL, Spark SQL. Skilled with data transfer & serialization formats: XML, JSON, Avro, simple formats (CSV, TSV). Experience in working in the cloud environment. Not required, but preferred qualifications: Experience with electronic health records, genetics, brain imaging or neurophysiological data. Web programming skills to support the development of web applications.

Web Developer. Required: BS degree or above in computer-related sciences or equivalent experience. Strong knowledge of Linux and MySQL, and demonstrated experience designing web-based interfaces and visualization tools using PHP/HTML, Javascript libraries/frameworks and CSS. Additional knowledge of web frameworks including Django or Catalyst being an asset. Experience in working in the cloud environment. Not required, but preferred qualifications: Some Perl, R and/or Python experience is desired, with additional knowledge of web frameworks including Django or Catalyst being an asset. Any bioinformatics experience is beneficial but not essential for this position.

We are focused on providing our team members with opportunities to develop themselves as researchers, exposing them to cutting edge methodology and world leading collaborative science including national and international conferences. We have the capacities and emphasize the development of research skills for all lab members. Biological knowledge, machine learning techniques, genetic variant interpretation, programming, and soft skills like scientific project management, oral presentations, written communication, scientific publication, and grant writing, are examples. A carefully tailored meeting strategy, supported by modern media communication channels, is enabling an excellent and constant communication of research progress, training and personal needs between the group leader and all lab members….