Harnessing regulatory networks in Actinobacteria for natural product discovery

HE Augustijn, AM Roseboom… - Journal of Industrial …, 2024 - academic.oup.com
Microbes typically live in complex habitats, where they need to rapidly adapt to continuously
changing growth conditions. To do so, they produce an astonishing array of natural products …

A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery

M Moazzzam Jazi, SM Seyedi, E Ebrahimie… - BMC genomics, 2017 - Springer
Abstract Background Pistachio (Pistacia vera L.) is one of the most important commercial nut
crops worldwide. It is a salt-tolerant and long-lived tree, with the largest cultivation area in …

Predicting the impact of promoter variability on regulatory outputs

NN Kreamer, R Phillips, DK Newman, JQ Boedicker - Scientific Reports, 2015 - nature.com
The increased availability of whole genome sequences calls for quantitative models of
global gene expression, yet predicting gene expression patterns directly from genome …

ChIPulate: A comprehensive ChIP-seq simulation pipeline

V Datta, S Hannenhalli… - PLoS computational …, 2019 - journals.plos.org
ChIP-seq (Chromatin Immunoprecipitation followed by sequencing) is a high-throughput
technique to identify genomic regions that are bound in vivo by a particular protein, eg, a …

Synthetic enhancers reveal design principles of cell state specific regulatory elements in hematopoiesis

R Fromel, J Ruhle, A Bernal Martinez, C Szu-Tu… - bioRxiv, 2024 - biorxiv.org
During cellular differentiation, enhancers transform overlapping gradients of transcription
factors (TFs) to highly specific gene expression patterns. However, the vast complexity of …

Protein target search diffusion-association/dissociation free energy landscape around DNA binding site with flanking sequences

B Wan, J Yu - bioRxiv, 2024 - biorxiv.org
Proteins including transcription factors (TFs) and regulating enzymes search DNA for
specific sites by alternating 3D diffusion in cell nucleus space and 1D diffusion on DNA. The …

Prediction and Analysis of Transcription Factor Binding Sites: Practical Examples and Case Studies Using R Programming

VY Muley - Reverse Engineering of Regulatory Networks, 2023 - Springer
Transcription factors (TFs) bind to specific regions of DNA known as transcription factor
binding sites (TFBSs) and modulate gene expression by interacting with the transcriptional …

MotifGP: DNA motif discovery using multiobjective evolution

M Belmadani - 2016 - ruor.uottawa.ca
The motif discovery problem is becoming increasingly important for molecular biologists as
new sequencing technologies are producing large amounts of data, at rates which are …

A computational model for predicting integrase catalytic domain of retrovirus

S Wu, J Han, X Zhang, D Zhong, R Liu - Journal of Theoretical Biology, 2017 - Elsevier
Integrase catalytic domain (ICD) is an essential part in the retrovirus for integration reaction,
which enables its newly synthesized DNA to be incorporated into the DNA of infected cells …

Aproximación a la medicina personalizada mediante el desarrollo de nuevas metodologías en inteligencia artificial

C Navarro Luzón - 2017 - digibug.ugr.es
Los últimos años han visto florecer y consolidarse a un extenso catálogo de metodologías
experimentales, las cuales han dado lugar a vastas cantidades de información biológica. La …