Job Opportunities

There are no current faculty openings at the Institute.

There are no staff openings at present.

The SemAnTICA (Semantic Analysis of Text for Informing Clinical Action) Lab, housed in the Department of Biostatistics, Epidemiology, & Informatics (DBEI), is led by Danielle Mowery PhD, Assistant Professor of Informatics at the University of Pennsylvania and Chief Research Information Officer of Penn Medicine through the Institute for Biomedical Informatics (IBI). Our mission is to develop technologies, primarily natural language processing (NLP) solutions, which support clinical and translational research studies for improving patient care by learning and/or promoting actionable knowledge from electronic health records.

Job Summary
We are currently seeking a postdoctoral fellow. An ideal candidate will develop novel natural language processing and computational methods for extracting study variables and inferring actionable knowledge from clinical text-based resources including clinical notes, transcripts, free-texts, and more. These methods could address one or more use cases from a diverse set of clinical specialties e.g., cancer, pathology, neurology, genetics, psychiatry, pulmonary, palliative care, infectious disease, etc. As a member of the SemAnTICA Lab, the candidate will primarily participate in NLP research. The candidate may also collaborate with clinical data scientists from the IBI Clinical Research Informatics Core (CIC) within the Institute for Biomedical Informatics that serve the needs of clinical investigators throughout Perelman School of Medicine.

Core Duties & Responsibilities
• Collaborate with students, CIC staff, clinical domain experts, and biostatisticians
• Participate in group CIC and SemAnTICA lab meetings as well as department and institute seminars
• Write manuscripts for peer-reviewed conferences and academic journals
• Present salient findings to their academic peers via conferences and seminars
• Contribute to grant writing efforts for National Institute of Health and foundation announcements

Qualifications & Skills
We seek a self-motivated candidate with a Ph.D. in computer science, biomedical informatics, computational linguistics, or related field. This position requires proficient skills in Python or Java, machine learning, natural language processing, knowledge representations, and ontologies. Some experience using deep learning is a plus. The candidate should have 1 or more first author papers in a peer-reviewed journal. The candidate will receive professional mentorship and protected time towards the development of a K award application. This position is supported for 2 years.

Qualified applicants should send their cover letter and curriculum vitae of their work to Dr. Mowery at dlmowery@pennmedicine.upenn.edu.


Postdoctoral Fellow, Faryabi Lab

About the lab:
Faryabi Lab is part of Institute for Biomedical Informatics (IBI) and Abramson
Cancer Center (ACC) of the University of Pennsylvania. The primary focus of the lab is on
combining novel computational and experimental methods to explore how oncogenic cell
signalings impact tumors epigenome.

About the position:
The primary research focus of an ideal candidate will be on developing novel computational
methods for the integration of genomics, epigenomics and chromatin conformation data sets
within the context of tumor biology. Specifically, we are using single cell technologies to probe
cancer epigenomics to investigate tumor heterogeneity and development. As a member of the
Center for Personalized Diagnostics, a potential candidate will have opportunity to participate in
both basic and translational research while collaborating with scientists across the Perelman
School of Medicine.

A qualified candidate will be strongly motivated individual with following qualifications: a Ph.D. in
computational sciences, engineering, physics, bioinformatics, or related field. Ability to program
in Python/Perl and R in Unix environment, knowledge of SQL, C++ and/or Java is a plus.
Demonstrated applied bioinformatics/computational proficiency evidenced by relevant
publications in peer-reviewed journals is required.

Further information about the lab could be found at https://faryabib.github.io

Interested applicants should send cover letter and CV to faryabiLab@gmail.com.