[HTML][HTML] Absence of a simple code: how transcription factors read the genome

M Slattery, T Zhou, L Yang, ACD Machado… - Trends in biochemical …, 2014 - cell.com
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 …

The significant other: splicing by the minor spliceosome

JJ Turunen, EH Niemelä, B Verma… - Wiley Interdisciplinary …, 2013 - Wiley Online Library
The removal of non‐coding sequences, introns, from the mRNA precursors is an essential
step in eukaryotic gene expression. U12‐type introns are a minor subgroup of introns …

Logomaker: beautiful sequence logos in Python

A Tareen, JB Kinney - Bioinformatics, 2020 - academic.oup.com
Sequence logos are visually compelling ways of illustrating the biological properties of DNA,
RNA and protein sequences, yet it is currently difficult to generate and customize such logos …

[HTML][HTML] Dissecting the role of PfAP2-G in malaria gametocytogenesis

GA Josling, TJ Russell, J Venezia, L Orchard… - Nature …, 2020 - nature.com
In the malaria parasite Plasmodium falciparum, the switch from asexual multiplication to
sexual differentiation into gametocytes is essential for transmission to mosquitos. The …

A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium

A Sinha, KR Hughes, KK Modrzynska, TD Otto… - Nature, 2014 - nature.com
Commitment to and completion of sexual development are essential for malaria parasites
(protists of the genus Plasmodium) to be transmitted through mosquitoes. The molecular …

pLogo: a probabilistic approach to visualizing sequence motifs

JP O'shea, MF Chou, SA Quader, JK Ryan… - Nature …, 2013 - nature.com
Methods for visualizing protein or nucleic acid motifs have traditionally relied upon residue
frequencies to graphically scale character heights. We describe the pLogo, a motif …

Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two …

MCF Thomsen, M Nielsen - Nucleic acids research, 2012 - academic.oup.com
Seq2Logo is a web-based sequence logo generator. Sequence logos are a graphical
representation of the information content stored in a multiple sequence alignment (MSA) and …

[HTML][HTML] FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription

M Lupien, J Eeckhoute, CA Meyer, Q Wang, Y Zhang… - Cell, 2008 - cell.com
Complex organisms require tissue-specific transcriptional programs, yet little is known about
how these are established. The transcription factor FoxA1 is thought to contribute to gene …

GLK Transcription Factors Coordinate Expression of the Photosynthetic Apparatus in Arabidopsis

MT Waters, P Wang, M Korkaric, RG Capper… - The Plant …, 2009 - academic.oup.com
Chloroplasts of photosynthetic organisms harness light energy and convert it into chemical
energy. In several land plants, GOLDEN2-LIKE (GLK) transcription factors are required for …

[HTML][HTML] Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome

TH Kim, ZK Abdullaev, AD Smith, KA Ching… - Cell, 2007 - cell.com
Insulator elements affect gene expression by preventing the spread of heterochromatin and
restricting transcriptional enhancers from activation of unrelated promoters. In vertebrates …