Toxicity testing in the 21st century: progress in the past decade and future perspectives

D Krewski, ME Andersen, MG Tyshenko… - Archives of …, 2020 - Springer
Advances in the biological sciences have led to an ongoing paradigm shift in toxicity testing
based on expanded application of high-throughput in vitro screening and in silico methods …

The Perseus computational platform for comprehensive analysis of (prote) omics data

S Tyanova, T Temu, P Sinitcyn, A Carlson, MY Hein… - Nature …, 2016 - nature.com
A main bottleneck in proteomics is the downstream biological analysis of highly multivariate
quantitative protein abundance data generated using mass-spectrometry-based analysis …

Systemic immunity is required for effective cancer immunotherapy

MH Spitzer, Y Carmi, NE Reticker-Flynn, SS Kwek… - Cell, 2017 - Elsevier
Immune responses involve coordination across cell types and tissues. However, studies in
cancer immunotherapy have focused heavily on local immune responses in the tumor …

Mass spectrometry‐based protein–protein interaction networks for the study of human diseases

AL Richards, M Eckhardt, NJ Krogan - Molecular systems biology, 2021 - embopress.org
A better understanding of the molecular mechanisms underlying disease is key for
expediting the development of novel therapeutic interventions. Disease mechanisms are …

[PDF][PDF] An approach to spatiotemporally resolve protein interaction networks in living cells

BT Lobingier, R Hüttenhain, K Eichel, KB Miller… - Cell, 2017 - cell.com
Cells operate through protein interaction networks organized in space and time. Here, we
describe an approach to resolve both dimensions simultaneously by using proximity …

The coral microbiome: Towards an understanding of the molecular mechanisms of coral–microbiota interactions

AR Mohamed, MA Ochsenkühn… - FEMS Microbiology …, 2023 - academic.oup.com
Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms,
some of which are implicated in vital functions, such as those related to resilience against …

Constraint-based models predict metabolic and associated cellular functions

A Bordbar, JM Monk, ZA King, BO Palsson - Nature Reviews Genetics, 2014 - nature.com
The prediction of cellular function from a genotype is a fundamental goal in biology. For
metabolism, constraint-based modelling methods systematize biochemical, genetic and …

Network biology concepts in complex disease comorbidities

JX Hu, CE Thomas, S Brunak - Nature Reviews Genetics, 2016 - nature.com
The co-occurrence of diseases can inform the underlying network biology of shared and
multifunctional genes and pathways. In addition, comorbidities help to elucidate the effects …

Connecting omics signatures and revealing biological mechanisms with iLINCS

M Pilarczyk, M Fazel-Najafabadi, M Kouril… - Nature …, 2022 - nature.com
There are only a few platforms that integrate multiple omics data types, bioinformatics tools,
and interfaces for integrative analyses and visualization that do not require programming …

Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review

P Csermely, T Korcsmáros, HJM Kiss, G London… - Pharmacology & …, 2013 - Elsevier
Despite considerable progress in genome-and proteome-based high-throughput screening
methods and in rational drug design, the increase in approved drugs in the past decade did …