2020 was a tough year for many reasons, but there are still things to be excited about! Here are NCGAS’ staff picks of interesting or exciting news in 2020.

COVID-19 News

mRNA vaccines. The COVID-19 pandemic presented scientists and public health officials with a challenge to bring a new vaccine from design to production in record time. Subsequently, the scientific community introduced the world to messenger RNA (mRNA) vaccines. Whereas conventional vaccines elicit an immune response by introducing a weakened or inactivated virus, mRNA vaccines operate by instructing cells to make proteins that trigger a response. Although mRNA therapeutics have been in development over the past decade, the COVID-19 vaccines introduced at the end of 2020 represent the first FDA-approved mRNA vaccine. mRNA, this is your time to shine! Read more: https://www.cdc.gov/coronavirus/2019-ncov/vaccines/different-vaccines/mrna.html

A faint silver lining. There was a ~9% decrease in global CO2 emissions in the first half of 2020 as compared to 2019.  The timing corresponds to the lock-downs around the world and the effect is larger than previous downturns and even WWII.  Further evidence for the causation being the pandemic: as economies reopened, the CO2 levels started returning to normal.  An interesting article with some nice day-by-day graphs for data around the world can be found here: https://www.nature.com/articles/s41467-020-18922-7

Fugaku gets busy. Fugaku, the world’s fastest supercomputer, was promptly put to work for coronavirus defense after its debut in the summer of 2020. Researchers from the Riken Center for Computational Science in Japan modeled partition heights required between people to prevent the spread of coronavirus. Fugaku simulated the spread of droplets from a cough and determined that a safe partition should be at least head-height. Watch the simulation here: http://www.asahi.com/ajw/articles/13440482

A big thanks to XSEDE and the HPC Consortium for generously dedicating compute space to COVID-19 research efforts. Now, more than ever, XSEDE plays an important role in the community by connecting researchers and enabling discoveries as we continue to combat the coronavirus. Read more: https://www.xsede.org/-/xsede-joins-hpc-consortium-for-covid-19-research

Advancements in Genomics

“Calling” all biologists- a portable Nanopore sequencing device. It was only a matter of time before genomic analyses started moving to the computers we all have in our pockets.  2020 saw the release of Genopo, the first-ever smartphone application for nanopore sequencing analysis. Nanopore has long been aiming for ease and portability, which is unique among the third generation sequencing platforms.  Combining MinION’s handheld flow cell caller with Genopo running on a cell phone, researchers were able to sequence COVID patient isolates in 30 minutes.  Read more here: https://www.nature.com/articles/s42003-020-01270-z

Variant callers. PrecisionFDA’s 2020 ‘Truth Challenge V2‘ called on the HPC and research communities’ collective expertise to assess variant calling pipeline performance. One of the highest-performing pipelines across categories (Difficult-to-Map Regions, All Benchmark Regions, MHC) is Google’s DeepVariant. DeepVariant- which uses a deep neural network to call genetic variants- is accurate across various sequencing platforms and makes a noticeable difference for lower coverage samples. Read more: https://github.com/google/deepvariant

The protein folding problem. In November, DeepMind’s AlphaFold2 Algorithm made major strides toward solving the long-standing protein folding problem.  The AI software came close to being roughly equivalent to experimentally determined structure (determined by quality score).  “This is going to empower a new generation of molecular biologists to ask more advanced questions,” says Lupas, an evolutionary biologist at the Max Planck Institute for Developmental Biology in Tübingen, Germany. “It’s going to require more thinking and less pipetting.”  Read more: https://www.nature.com/articles/d41586-020-03348-4

ProgressiveCactus- prickly, like 2020. The past five years have seen an explosion of new genome assemblies, and last year was no exception. ProgressiveCactus, a brand-spankin’-new multiple-genome aligner, rose to meet the computational challenge of aligning thousands of large genomes. Progressive Cactus uses reconstructed ancestral assemblies to combine sub-alignments, resulting in shorter runtimes: https://www.nature.com/articles/s41586-020-2871-y

Noteworthy Research

Is it really a favorites list without CRISPR?  One particularly neat application of the technology used the CRISPR-Cas9 system to knockout a pigmentation gene in squid embryos, eliminating eye and skin (!!) pigmentation. This work by Crawford et al. represents exciting progress toward making squid genetically tractable, so let’s keep all eight arms crossed for more squid genetics work! Read more: https://www.sciencedirect.com/science/article/abs/pii/S0960982220309854?via%3Dihub

Genomic catalog of Earth’s microbiomes. Before the modern genomics era, a huge portion of microbial diversity was inaccessible to biologists and consequently biased toward cultivated microorganisms. Cultivation-independent molecular approaches were invaluable to accessing this organismal diversity but lacked scalability. In recent years, metagenomics applications gave researchers a scalable, cultivation-independent approach to microbiology. This year, Nayfach et al. used shotgun metagenomics to provide the scientific community with no less than 52,515 metagenome-assembled genomes, resulting in an unprecedented genomic catalog of bacteria and archaea diversity from all over planet earth. Read more: https://www.nature.com/articles/s41587-020-0718-6

A hunt for ancient Martians. NASA successfully launched the next rover mission to the Red Planet in the summer of 2020. The Perseverance rover is on a hunt for evidence of ancient life in the Jezero Crater, thought to have been a lake 3.5 billion years ago. Perseverance also carries a nifty instrument known as MOXIE (Mars Oxygen In-Situ Resource Utilization Experiment) that is used to turn Martian atmosphere into oxygen. MOXIE serves as a proof of concept and preparation for human crews in the future. Read more: https://www.nasa.gov/press-release/nasa-ula-launch-mars-2020-perseverance-rover-mission-to-red-planet