Crowdsourcing biomedical research: leveraging communities as innovation engines
The generation of large-scale biomedical data is creating unprecedented opportunities for
basic and translational science. Typically, the data producers perform initial analyses, but it …
basic and translational science. Typically, the data producers perform initial analyses, but it …
The Matthews correlation coefficient (MCC) is more informative than Cohen's Kappa and Brier score in binary classification assessment
Even if measuring the outcome of binary classifications is a pivotal task in machine learning
and statistics, no consensus has been reached yet about which statistical rate to employ to …
and statistics, no consensus has been reached yet about which statistical rate to employ to …
Inferring causal molecular networks: empirical assessment through a community-based effort
It remains unclear whether causal, rather than merely correlational, relationships in
molecular networks can be inferred in complex biological settings. Here we describe the …
molecular networks can be inferred in complex biological settings. Here we describe the …
Transcriptome data are insufficient to control false discoveries in regulatory network inference
Inference of causal transcriptional regulatory networks (TRNs) from transcriptomic data
suffers notoriously from false positives. Approaches to control the false discovery rate (FDR) …
suffers notoriously from false positives. Approaches to control the false discovery rate (FDR) …
Computational approaches to understand transcription regulation in development
M van der Sande, S Frölich… - Biochemical Society …, 2023 - portlandpress.com
Gene regulatory networks (GRNs) serve as useful abstractions to understand transcriptional
dynamics in developmental systems. Computational prediction of GRNs has been …
dynamics in developmental systems. Computational prediction of GRNs has been …
Learning causal biological networks with the principle of Mendelian randomization
Although large amounts of genomic data are available, it remains a challenge to reliably
infer causal (ie, regulatory) relationships among molecular phenotypes (such as gene …
infer causal (ie, regulatory) relationships among molecular phenotypes (such as gene …
Fast and accurate inference of gene regulatory networks through robust precision matrix estimation
Motivation Transcriptional regulation mechanisms allow cells to adapt and respond to
external stimuli by altering gene expression. The possible cell transcriptional states are …
external stimuli by altering gene expression. The possible cell transcriptional states are …
Structural properties of aqueous grown polydopamine thin films determined by neutron reflectometry
In this work, neutron reflectometry (NR) studies of the bio-mimetic polymer, polydopamine
(PDA), deposited from differing initial concentrations of precursor material dopamine …
(PDA), deposited from differing initial concentrations of precursor material dopamine …
Technologies for whole‐cell modeling: Genome‐wide reconstruction of a cell in silico
K Kaizu, K Takahashi - Development, Growth & Differentiation, 2023 - Wiley Online Library
With advances in high‐throughput, large‐scale in vivo measurement and genome
modification techniques at the single‐nucleotide level, there is an increasing demand for the …
modification techniques at the single‐nucleotide level, there is an increasing demand for the …
Robust network inference using response logic
T Gross, MJ Wongchenko, Y Yan, N Blüthgen - Bioinformatics, 2019 - academic.oup.com
Motivation A major challenge in molecular and cellular biology is to map out the regulatory
networks of cells. As regulatory interactions can typically not be directly observed …
networks of cells. As regulatory interactions can typically not be directly observed …