Artificial intelligence in cancer target identification and drug discovery

Y You, X Lai, Y Pan, H Zheng, J Vera, S Liu… - … and Targeted Therapy, 2022 - nature.com
Artificial intelligence is an advanced method to identify novel anticancer targets and discover
novel drugs from biology networks because the networks can effectively preserve and …

Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences

C Manzoni, DA Kia, J Vandrovcova… - Briefings in …, 2018 - academic.oup.com
Advances in the technologies and informatics used to generate and process large biological
data sets (omics data) are promoting a critical shift in the study of biomedical sciences. While …

A reference map of the human binary protein interactome

K Luck, DK Kim, L Lambourne, K Spirohn, BE Begg… - Nature, 2020 - nature.com
Global insights into cellular organization and genome function require comprehensive
understanding of the interactome networks that mediate genotype–phenotype relationships …

[HTML][HTML] A proteome-scale map of the human interactome network

T Rolland, M Taşan, B Charloteaux, SJ Pevzner… - Cell, 2014 - cell.com
Just as reference genome sequences revolutionized human genetics, reference maps of
interactome networks will be critical to fully understand genotype-phenotype relationships …

Determinants of community structure in the global plankton interactome

G Lima-Mendez, K Faust, N Henry, J Decelle, S Colin… - Science, 2015 - science.org
Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the
Tara Oceans project, we studied the photic zone interactome using environmental factors …

Autoreactive CD8+ T cells are restrained by an exhaustion-like program that is maintained by LAG3

S Grebinoski, Q Zhang, AR Cillo, S Manne, H Xiao… - Nature …, 2022 - nature.com
Impaired chronic viral and tumor clearance has been attributed to CD8+ T cell exhaustion, a
differentiation state in which T cells have reduced and altered effector function that can be …

Uncovering disease-disease relationships through the incomplete interactome

J Menche, A Sharma, M Kitsak, SD Ghiassian, M Vidal… - Science, 2015 - science.org
INTRODUCTION A disease is rarely a straightforward consequence of an abnormality in a
single gene, but rather reflects the interplay of multiple molecular processes. The …

A travel guide to Cytoscape plugins

R Saito, ME Smoot, K Ono, J Ruscheinski, PL Wang… - Nature …, 2012 - nature.com
Cytoscape is open-source software for integration, visualization and analysis of biological
networks. It can be extended through Cytoscape plugins, enabling a broad community of …

Meta-research: evaluation and improvement of research methods and practices

JPA Ioannidis, D Fanelli, DD Dunne, SN Goodman - PLoS biology, 2015 - journals.plos.org
As the scientific enterprise has grown in size and diversity, we need empirical evidence on
the research process to test and apply interventions that make it more efficient and its results …

OmniPath: guidelines and gateway for literature-curated signaling pathway resources

D Türei, T Korcsmáros, J Saez-Rodriguez - Nature methods, 2016 - nature.com
Resources that capture information about signaling pathways from the literature are
essential for the experimental design and analysis of many biological studies. Multiple …