Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders

NN Parikshak, MJ Gandal, DH Geschwind - Nature Reviews Genetics, 2015 - nature.com
Genetic and genomic approaches have implicated hundreds of genetic loci in
neurodevelopmental disorders and neurodegeneration, but mechanistic understanding …

Improving fatty acids production by engineering dynamic pathway regulation and metabolic control

P Xu, L Li, F Zhang, G Stephanopoulos… - Proceedings of the …, 2014 - pnas.org
Global energy demand and environmental concerns have stimulated increasing efforts to
produce carbon-neutral fuels directly from renewable resources. Microbially derived …

ChIP–seq: advantages and challenges of a maturing technology

PJ Park - Nature reviews genetics, 2009 - nature.com
Chromatin immunoprecipitation followed by sequencing (ChIP–seq) is a technique for
genome-wide profiling of DNA-binding proteins, histone modifications or nucleosomes …

Gene regulatory network inference resources: A practical overview

D Mercatelli, L Scalambra, L Triboli, F Ray… - Biochimica et Biophysica …, 2020 - Elsevier
Transcriptional regulation is a fundamental molecular mechanism involved in almost every
aspect of life, from homeostasis to development, from metabolism to behavior, from reaction …

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

P Kheradpour, M Kellis - Nucleic acids research, 2014 - academic.oup.com
Recent advances in technology have led to a dramatic increase in the number of available
transcription factor ChIP-seq and ChIP-chip data sets. Understanding the motif content of …

MEME: discovering and analyzing DNA and protein sequence motifs

TL Bailey, N Williams, C Misleh, WW Li - Nucleic acids research, 2006 - academic.oup.com
Abstract MEME (Multiple EM for Motif Elicitation) is one of the most widely used tools for
searching for novel 'signals' in sets of biological sequences. Applications include the …

Quantifying similarity between motifs

S Gupta, JA Stamatoyannopoulos, TL Bailey… - Genome biology, 2007 - Springer
A common question within the context of de novo motif discovery is whether a newly
discovered, putative motif resembles any previously discovered motif in an existing …