Staff Scientist I, Data Science
Description

  

A little about us:

The Lieber Institute for Brain Development (LIBD) was established in 2010 to plot a new course in biomedical research that would change the lives of individuals affected with developmental brain disorders. We are one of the only research institutions in the world focused specifically on understanding how genes and the environment influence the way our brains develop that lead to conditions such as schizophrenia, autism, bipolar disorder and related developmental brain disorders. Through our cutting-edge research, answers are emerging and being translated into a robust pipeline of new drugs in development. And, by focusing on genes and their dynamic interplay with the environment, we are getting even closer to the “holy grail” in medical research, the discovery of strategies for primary prevention.


We are a group of dedicated, multidisciplinary and optimistic researchers, working at the cutting edge of science, utilizing state-of-the-art tools to unlock the mystery of the brain and transform the way we approach the development of new treatments, and ultimately cures. LIBD is an independent 501(c)(3) medical research institute located in the Bioscience Park on the campus of the Johns Hopkins School of Medicine and Hospital in Baltimore, MD.


Job Summary:

The Neural Plasticity group, headed by Dr. Keri Martinowich, has a Staff Scientist I position available in genomics data science. The position is housed within a translational research setting where the scientist will focus on data management, creation of computational training resources, and analysis of spatial transcriptomics and single cell data in postmortem human brain tissue in a dynamic team-based environment. Projects aim to generate transcriptome-scale maps in the human brain to understand differences in spatial gene expression in neuropsychiatric disorders. We work closely with collaborators from LIBD as well as from Johns Hopkins University (JHU), which reflects the cross-disciplinary approach and diversity in expertise needed to further advance our understanding of high throughout biology. 


The Staff Scientist I will be responsible for managing multi-omic data across several projects as well as assisting with management of computational workflows across teams in a fast-paced environment. Specifically, they will be responsible for database generation and maintenance for multiple projects, as well as implementation of emerging computational technologies and tools. The scientist will also have the opportunity to participate in analysis for team projects that involve integration of single cell and spatial transcriptomics data. We are particularly interested in candidates that are passionate about working in team environments and motivated to work with us in determining how to apply genomics data science in the human brain to better understand complex neuropsychiatric and neurodegenerative disorders. Initiative to learn new methods and perform work efficiently and carefully are essential. 


Specific Duties and Responsibilities:

· Manage internal and external datasets as well as data transfers

· Manage required data deposits for consortia data generation across multiple projects

· Help create computational training resources for junior scientists

· Assist with onboarding new team members to computational workflows, databases and data management practices

· Maintain databases and repositories of newly generated multi-omic data

· Communicate with individuals with different expertise such as biologists, computational scientists, and biostatisticians

· Perform creative, rigorous, and reproducible analyses on multi-omics datasets generated from the human postmortem brain samples from technologies such as bulk RNA-seq, single cell/nuclei RNA-seq, and spatial transcriptomics

· Present research results at team meetings and contribute to peer-reviewed publications and grant applications

· Perform computational work within a high-performance computing environment (with helper tools like sgejobs), version control code with GitHub, and utilize asynchronous messaging applications for team communication

· Participate in continuous learning activities such as the LIBD rstats club and bootcamps

· Assist with development of open-source computational biology software such as R/Bioconductor packages with helper tools such as biocthis

· Other duties as assigned.  

Requirements

  

Minimum Qualifications:

· Master’s degree in computer science, computational biology, biostatistics, bioinformatics, biomedical engineering, or a related field PhD degree preferred

· A minimum of 2 years related experience is required


Special Knowledge, Skills, and Abilities:


Required

· Experience with data organization and management

· Experience with genomic data analysis using R/Bioconductor packages for one or more projects

· Evidence of computational skills and code version control through GitHub or similar options

· Strong organizational skills, attention to detail, excellent problem-solving skills, excellent written and verbal communication skills

· Understanding of statistical methods such as linear regression, interaction models, ANOVA, t-Student and F distributions, p-values and false discovery rate (FDR)

· Ability to generate training resources and teach junior scientists basic computational skills


Preferred

· Demonstrated leadership skills and participation in team-oriented activities

· Experience high-performance computing environments

· Experience using Linux and advanced Linux file permission settings, particularly Access Control Lists (ACLs)

· Experience using Globus, and uploading data to scientific and software repositories such as NCBI Sequence Read Archive, Synapse, ExperimentHub, etc.

· Experience with data management tools, particularly REDCap

· Experience performing computational analysis projects (exemplified with peer-reviewed publications and/or public GitHub repositories)

· Familiarity with bioinformatics methods used for analysis of single-cell and/or spatial RNA-seq data 

· Experience creating small reproducible examples when asking for help using tools such as reprex

· R/Bioconductor package development experience

· Advanced statistics knowledge including exponential family distributions and mixed effect models


** If accommodations are needed due to pregnancy or a disability, please contact jobs@libd.org 


The Lieber Institute has mandated COVID-19 and influenza vaccines, as applicable. All personnel must certify that they have obtained the necessary inoculations and to maintain a copy of that certification, which employees must provide at the Company's request. Exceptions to the COVID-19 and flu vaccine requirements may be provided, on a case-by-case basis, to individuals for either medical contraindications or sincerely held religious beliefs. Requests for a medical or religious exemption must be submitted in writing to jobs@libd.org. Personnel who do not receive the COVID-19 or flu vaccines due to an exemption must wear a mask in shared spaces. Personnel without documentation of vaccination or valid exemption will be considered noncompliant with coronavirus (COVID-19) vaccination requirements. The employee will receive a written warning from their supervisor that they are not in compliance with the coronavirus (COVID-19) vaccination policy and will then have 15 days to comply (either through vaccination or valid exemption).


For additional information, applicants should visit https://covidinfo.jhu.edu/   https://covidinfo.jhu.edu/health-safety/covid-vaccination-information/ 


EEOC Statement: At the Lieber Institute, we are committed to a work environment of mutual respect where employment decisions are based on merit. As an equal opportunity employer, the Lieber Institute does not discriminate in employment opportunities on the basis of race, color, religion, color, sex, gender identity/expression, sexual orientation, pregnancy, marital status, age, national origin or ancestry, citizenship, disability (physical or mental), genetic information, military service, or other non-merit based factors protected by state or federal law or local ordinance, with regard to any position or employment for which the applicant or employee is qualified.