Understudied proteins: opportunities and challenges for functional proteomics

G Kustatscher, T Collins, AC Gingras, T Guo… - Nature …, 2022 - nature.com
Most research aiming at understanding the molecular foundations of life and disease has
focused on a limited set of increasingly well-known proteins while the biological functions of …

Genomics, convergent neuroscience and progress in understanding autism spectrum disorder

HR Willsey, AJ Willsey, B Wang… - Nature Reviews …, 2022 - nature.com
More than a hundred genes have been identified that, when disrupted, impart large risk for
autism spectrum disorder (ASD). Current knowledge about the encoded proteins—although …

DALI shines a light on remote homologs: One hundred discoveries

L Holm, A Laiho, P Törönen, M Salgado - Protein Science, 2023 - Wiley Online Library
Structural comparison reveals remote homology that often fails to be detected by sequence
comparison. The DALI web server (http://ekhidna2. biocenter. helsinki. fi/dali) is a platform …

[HTML][HTML] clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng… - The innovation, 2021 - cell.com
Functional enrichment analysis is pivotal for interpreting high-throughput omics data in life
science. It is crucial for this type of tool to use the latest annotation databases for as many …

[HTML][HTML] Functional unknomics: Systematic screening of conserved genes of unknown function

JJ Rocha, SA Jayaram, TJ Stevens, N Muschalik… - PLoS …, 2023 - journals.plos.org
The human genome encodes approximately 20,000 proteins, many still uncharacterised. It
has become clear that scientific research tends to focus on well-studied proteins, leading to …

Identifying biases and their potential solutions in human microbiome studies

JT Nearing, AM Comeau, MGI Langille - Microbiome, 2021 - Springer
Advances in DNA sequencing technology have vastly improved the ability of researchers to
explore the microbial inhabitants of the human body. Unfortunately, while these studies have …

Peptidomics

R Hellinger, A Sigurdsson, W Wu… - Nature Reviews …, 2023 - nature.com
Peptides are biopolymers, typically consisting of 2–50 amino acids. They are biologically
produced by the cellular ribosomal machinery or by non-ribosomal enzymes and …

Computational approach to molecular catalysis by 3d transition metals: challenges and opportunities

KD Vogiatzis, MV Polynski, JK Kirkland… - Chemical …, 2018 - ACS Publications
Computational chemistry provides a versatile toolbox for studying mechanistic details of
catalytic reactions and holds promise to deliver practical strategies to enable the rational in …

Beyond experiments

E Diener, R Northcott, MJ Zyphur… - Perspectives on …, 2022 - journals.sagepub.com
It is often claimed that only experiments can support strong causal inferences and therefore
they should be privileged in the behavioral sciences. We disagree. Overvaluing experiments …

AnnoTree: visualization and exploration of a functionally annotated microbial tree of life

K Mendler, H Chen, DH Parks, B Lobb… - Nucleic acids …, 2019 - academic.oup.com
Bacterial genomics has revolutionized our understanding of the microbial tree of life;
however, mapping and visualizing the distribution of functional traits across bacteria remains …