Transcription factor–DNA binding: beyond binding site motifs
S Inukai, KH Kock, ML Bulyk - Current opinion in genetics & development, 2017 - Elsevier
Sequence-specific transcription factors (TFs) regulate gene expression by binding to cis-
regulatory elements in promoter and enhancer DNA. While studies of TF–DNA binding have …
regulatory elements in promoter and enhancer DNA. While studies of TF–DNA binding have …
[HTML][HTML] Absence of a simple code: how transcription factors read the genome
Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …
Whole-genome and epigenomic landscapes of etiologically distinct subtypes of cholangiocarcinoma
Cholangiocarcinoma (CCA) is a hepatobiliary malignancy exhibiting high incidence in
countries with endemic liver-fluke infection. We analyzed 489 CCAs from 10 countries …
countries with endemic liver-fluke infection. We analyzed 489 CCAs from 10 countries …
Predicting the sequence specificities of DNA-and RNA-binding proteins by deep learning
Knowing the sequence specificities of DNA-and RNA-binding proteins is essential for
developing models of the regulatory processes in biological systems and for identifying …
developing models of the regulatory processes in biological systems and for identifying …
[HTML][HTML] Recurrent neural network for predicting transcription factor binding sites
Z Shen, W Bao, DS Huang - Scientific reports, 2018 - nature.com
It is well known that DNA sequence contains a certain amount of transcription factors (TF)
binding sites, and only part of them are identified through biological experiments. However …
binding sites, and only part of them are identified through biological experiments. However …
DNA mismatches reveal conformational penalties in protein–DNA recognition
Transcription factors recognize specific genomic sequences to regulate complex gene-
expression programs. Although it is well-established that transcription factors bind to specific …
expression programs. Although it is well-established that transcription factors bind to specific …
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models
IV Kulakovskiy, IE Vorontsov, IS Yevshin… - Nucleic acids …, 2016 - academic.oup.com
Abstract Models of transcription factor (TF) binding sites provide a basis for a wide spectrum
of studies in regulatory genomics, from reconstruction of regulatory networks to functional …
of studies in regulatory genomics, from reconstruction of regulatory networks to functional …
Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities
Motivation Deep learning architectures have recently demonstrated their power in predicting
DNA-and RNA-binding specificity. Existing methods fall into three classes: Some are based …
DNA-and RNA-binding specificity. Existing methods fall into three classes: Some are based …
[HTML][HTML] Fungal iron homeostasis with a focus on Aspergillus fumigatus
M Misslinger, P Hortschansky, AA Brakhage… - Biochimica et Biophysica …, 2021 - Elsevier
To maintain iron homeostasis, fungi have to balance iron acquisition, storage, and utilization
to ensure sufficient supply and to avoid toxic excess of this essential trace element. As …
to ensure sufficient supply and to avoid toxic excess of this essential trace element. As …