Current challenges and best-practice protocols for microbiome analysis

R Bharti, DG Grimm - Briefings in bioinformatics, 2021 - academic.oup.com
Analyzing the microbiome of diverse species and environments using next-generation
sequencing techniques has significantly enhanced our understanding on metabolic …

Classification of intrinsically disordered regions and proteins

R Van Der Lee, M Buljan, B Lang, RJ Weatheritt… - Chemical …, 2014 - ACS Publications
Over the past decade, we have observed a massive increase in the amount of information
describing protein sequences from a variety of organisms. 1, 2 While this may reflect the …

COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning

E Ong, MU Wong, A Huffman, Y He - Frontiers in immunology, 2020 - frontiersin.org
To ultimately combat the emerging COVID-19 pandemic, it is desired to develop an effective
and safe vaccine against this highly contagious disease caused by the SARS-CoV-2 …

Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

A Rives, J Meier, T Sercu, S Goyal… - Proceedings of the …, 2021 - National Acad Sciences
In the field of artificial intelligence, a combination of scale in data and model capacity
enabled by unsupervised learning has led to major advances in representation learning and …

dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs

X Liu, C Li, C Mou, Y Dong, Y Tu - Genome medicine, 2020 - Springer
Whole exome sequencing has been increasingly used in human disease studies.
Prioritization based on appropriate functional annotations has been used as an …

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

IV Kulakovskiy, IE Vorontsov, IS Yevshin… - Nucleic acids …, 2018 - academic.oup.com
We present a major update of the HOCOMOCO collection that consists of patterns
describing DNA binding specificities for human and mouse transcription factors. In this …

The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution

H Liu, X Wang, G Wang, P Cui, S Wu, C Ai, N Hu, A Li… - Nature Plants, 2021 - nature.com
Gymnosperms are a unique lineage of plants that currently lack a high-quality reference
genome due to their large genome size and high repetitive sequence content. Here, we …

DeepGOPlus: improved protein function prediction from sequence

M Kulmanov, R Hoehndorf - Bioinformatics, 2020 - academic.oup.com
Motivation Protein function prediction is one of the major tasks of bioinformatics that can help
in wide range of biological problems such as understanding disease mechanisms or finding …

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

AD Rouillard, GW Gundersen, NF Fernandez… - Database, 2016 - academic.oup.com
Genomics, epigenomics, transcriptomics, proteomics and metabolomics efforts rapidly
generate a plethora of data on the activity and levels of biomolecules within mammalian …

pH-responsive high stability polymeric nanoparticles for targeted delivery of anticancer therapeutics

L Palanikumar, S Al-Hosani, M Kalmouni… - Communications …, 2020 - nature.com
The practical application of nanoparticles (NPs) as chemotherapeutic drug delivery systems
is often hampered by issues such as poor circulation stability and targeting inefficiency …