Cameron, Christopher J.

DOE OSTI2022

Assessing Gender Bias in Particle Physics and Social Science Recommendations for Academic Jobs

We investigated gender bias in letters of recommendation as a possible cause of the under-representation of women in Experimental Particle Physics (EPP), where about 15% of faculty are female-well below the 60% level in psychology and sociology. We analyzed 2206 letters in EPP and these two social sciences using standard lexical measures as well as two new measures: author status and an open-ended search for gendered language. In contrast to former studies, women were not depicted as more communal, less agentic, or less standout. Lexical measures revealed few gender differences in either discipline. The open-ended analysis revealed disparities favoring women in social science and men in EPP. However, female EPP candidates were characterized as “brilliant” in nearly three times as many letters as were men.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2021

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.

59 BASIC BIOLOGICAL SCIENCES↗