The controversial role of human gut lachnospiraceae

M Vacca, G Celano, FM Calabrese, P Portincasa… - Microorganisms, 2020 - mdpi.com
The complex polymicrobial composition of human gut microbiota plays a key role in health
and disease. Lachnospiraceae belong to the core of gut microbiota, colonizing the intestinal …

Big data and artificial intelligence modeling for drug discovery

H Zhu - Annual review of pharmacology and toxicology, 2020 - annualreviews.org
Due to the massive data sets available for drug candidates, modern drug discovery has
advanced to the big data era. Central to this shift is the development of artificial intelligence …

The genome sequence archive family: toward explosive data growth and diverse data types

T Chen, X Chen, S Zhang, J Zhu, B Tang… - Genomics …, 2021 - academic.oup.com
Abstract The Genome Sequence Archive (GSA) is a data repository for archiving raw
sequence data, which provides data storage and sharing services for worldwide scientific …

BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database

T Brůna, KJ Hoff, A Lomsadze, M Stanke… - NAR genomics and …, 2021 - academic.oup.com
The task of eukaryotic genome annotation remains challenging. Only a few genomes could
serve as standards of annotation achieved through a tremendous investment of human …

RESCRIPt: Reproducible sequence taxonomy reference database management

MS Robeson, DR O'Rourke, BD Kaehler… - PLoS computational …, 2021 - journals.plos.org
Nucleotide sequence and taxonomy reference databases are critical resources for
widespread applications including marker-gene and metagenome sequencing for …

MetaboLights: a resource evolving in response to the needs of its scientific community

K Haug, K Cochrane, VC Nainala… - Nucleic acids …, 2020 - academic.oup.com
MetaboLights is a database for metabolomics studies, their raw experimental data and
associated metadata. The database is cross-species and cross-technique and it covers …

Dynamic genome evolution in a model fern

DB Marchant, G Chen, S Cai, F Chen, P Schafran… - Nature Plants, 2022 - nature.com
The large size and complexity of most fern genomes have hampered efforts to elucidate
fundamental aspects of fern biology and land plant evolution through genome-enabled …

Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells

TCT Lan, MF Allan, LE Malsick, JZ Woo, C Zhu… - Nature …, 2022 - nature.com
SARS-CoV-2 is a betacoronavirus with a single-stranded, positive-sense, 30-kilobase RNA
genome responsible for the ongoing COVID-19 pandemic. Although population average …

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

DH Parks, C Rinke, M Chuvochina, PA Chaumeil… - Nature …, 2017 - nature.com
Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently
available microbial genomes. This is being addressed by advances in sequencing …

RefSeq: an update on prokaryotic genome annotation and curation

DH Haft, M DiCuccio, A Badretdin, V Brover… - Nucleic acids …, 2018 - academic.oup.com
Abstract The Reference Sequence (RefSeq) project at the National Center for Biotechnology
Information (NCBI) provides annotation for over 95 000 prokaryotic genomes that meet …