EGSB News

Previous work on microbial mats had primarily relied on culturing virus and host pairs in the laboratory to study their interactions. In The ISME Journal, a team co-led by JGI postdoctoral researcher Mária Džunková used single-cell sequencing to sequence both a cell’s genome and detect accompanying viral sequences, which would suggest the virus had been infecting the cell. Read the full story on the JGI website.

For the past several months, teams of bioscientists have utilized Berkeley Lab’s world-class research facilities to contribute to the national response to COVID-19, resulting in a wide range of promising research. Four videos showcase researcher contributions from across the Biosciences Area, which aim to help address some of the many scientific challenges posed by the pandemic.

University of California San Francisco (UCSF), UC Davis, and Lawrence Berkeley National Laboratory (Berkeley Lab) have formed a Tri-Institutional Partnership in Microbiome Research (TrIP Microbiome) to catalyze and fund novel, bold, and potentially transformative collaborative microbiome research projects. A unique aspect of the partnership is its data-driven focus and data infrastructure, brought through the participation of the Berkeley Lab-led National Microbiome Data Collaborative (NMDC). The NMDC is working with TrIP Microbiome researchers to catalyze experimental co-design between biologists and computational scientists, adoption of data management best practices, and open science to enable cross-study comparison and machine learning.

The Encyclopedia of DNA Elements (ENCODE) collaboration was launched 17 years ago by the National Human Genome Research Institute with the goal of developing the tools and expertise needed to shed light on the 98% of our genome that does not code for proteins. Now in its final year, ENCODE has made huge advances thanks to the combined scientific and technological prowess of several hundred researchers at dozens of institutions. Leading the project for Berkeley Lab are Diane Dickel, Len Pennacchio, and Axel Visel, co-PIs of the Mammalian Functional Genomics Laboratory in Biosciences’ Environmental Genomics and Systems Biology (EGSB) Division. They are co-authors on 4 of the 15 new ENCODE papers published this week as part of a special collection in Nature.

Under a special project launched in May, a Berkeley Lab–led team of computing and bioinformatics experts is developing a platform that consolidates disparate COVID-19 data sources and uses the unified library to make predictions—about potential drug targets, for example.