Improving the performance of supervised deep learning for regulatory genomics using phylogenetic augmentation.

Motivation: Supervised deep learning is used to model the complex relationship between genomic sequence and regulatory function. Understanding how these models make predictions can provide biological insight into regulatory functions. Given the complexity of the sequence to regulatory function mapping (the cis-regulatory code), it has been suggested that the genome contains insufficient sequence variation to train models with suitable complexity.

A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells.

Transcriptional enhancers are critical for development and phenotype evolution and are often mutated in disease contexts; however, even in well-studied cell types, the sequence code conferring enhancer activity remains unknown. To examine the enhancer regulatory code for pluripotent stem cells, we identified genomic regions with conserved binding of multiple transcription factors in mouse and human embryonic stem cells (ESCs). Examination of these regions revealed that they contain on average 12.

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows.

As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S.

An instrument design for non-contact detection of biomolecules and minerals on Mars using fluorescence.

We discuss fluorescence as a method to detect polycyclic aromatic hydrocarbons and other organic molecules, as well as minerals on the surface of Mars. We present an instrument design that is adapted from the ChemCam instrument which is currently on the Mars Science Lander Rover Curiosity and thus most of the primary components are currently flight qualified for Mars surface operations, significantly reducing development costs. The major change compared to ChemCam is the frequency multipliers of the 1064 nm laser to wavelengths suitable for fluorescence excitation (266 nm, 355 nm, and 532 nm).