Results 41 to 50 of about 5,375,401 (399)

De novo design of insulated cis-regulatory elements based on deep learning-predicted fitness landscape. [PDF]

Nucleic Acids Res
Wang H, Xiang Y, Liu Z, Yin W, Li B, Qian L, Wang X, Lou C.   +7 more
europepmc   +3 more sources

The transcriptome dynamics of single cells during the cell cycle

Molecular Systems Biology, 2020
The cell cycle is among the most basic phenomena in biology. Despite advances in single‐cell analysis, dynamics and topology of the cell cycle in high‐dimensional gene expression space remain largely unknown.
Daniel Schwabe, Sara Formichetti, Jan Philipp Junker, Martin Falcke, Nikolaus Rajewsky   +4 more
doaj   +1 more source

Computational prediction of splicing regulatory elements shared by Tetrapoda organisms [PDF]

, 2009
Background: auxiliary splicing sequences play an important role in ensuring accurate and efficient splicing by promoting or repressing recognition of authentic splice sites.
Churbanov, Alexander, Hicks, Chindo, Vořechovský, Igor   +2 more
core   +3 more sources

DeepRegFinder: deep learning-based regulatory elements finder [PDF]

Bioinformatics Advances, 2021
Abstract Summary Enhancers and promoters are important classes of DNA regulatory elements (DREs) that govern gene expression. Identifying them at a genomic scale is a critical task in bioinformatics.
Aarthi Ramakrishnan, George Wangensteen, Sarah Kim, Eric J. Nestler, Li Shen   +4 more
openaire   +2 more sources

Expression Profiling of Salt-Responsive Genes and Transcription Factors in Leaf Transcriptome of Arabidopsis thaliana

Diversity, 2023
This investigation discerns the expression profiles of genes within the leaf transcriptome of Arabidopsis thaliana subjected to salt stress (200 mM NaCl).
Nahaa M. Alotaibi, Aala A. Abulfaraj
doaj   +1 more source

Theoretical analysis of the role of chromatin interactions in long-range action of enhancers and insulators [PDF]

, 2011
Long-distance regulatory interactions between enhancers and their target genes are commonplace in higher eukaryotes. Interposed boundaries or insulators are able to block these long distance regulatory interactions.
A. M. Sengupta, Arya, Banzhaf, Blackwood, Bondarenko, Bushey, Bustin, Capelson, Carter, Chodaparambil, Corces, Cremer, Cui, Dekker, Dorsett, Gerasimova, Geyer, Geyer, Hahnfeldt, Langowski, Luger, Moore, Nielsen, Nobrega, P. Schedl, Phair, Polikanov, Rochman, S. Mukhopadhyay, Savitskaya, Schermelleh, Simonis, Tolhuis, V. M. Studitsky, Valenzuela, van den Engh, Wallace, West, Zheng, Zhou   +39 more
core   +3 more sources

Regression trees for regulatory element identification [PDF]

Bioinformatics, 2004
Abstract Motivation: The transcription of a gene is largely determined by short sequence motifs that serve as binding sites for transcription factors. Recent findings suggest direct relationships between the motifs and gene expression levels. In this work, we present a method for identifying regulatory motifs.
Phuong T.M., Lee D. Lee, Doheon, Lee K.H. Lee, Kwang-Hyung   +2 more
openaire   +3 more sources

Identification of proteins and miRNAs that specifically bind an mRNA in vivo

Nature Communications, 2019
The entire mRNA interactome capture has been established but identification of specific mRNA-binding proteins has been challenging. Here, the authors developed an in vivo RNA–protein crosslinking and RNA pulldown approach and characterized novel ...
Kathrin Theil, Koshi Imami, Nikolaus Rajewsky   +2 more
doaj   +1 more source

Analysis of Intron Sequences Reveals Hallmarks of Circular RNA Biogenesis in Animals

Cell Reports, 2015
Circular RNAs (circRNAs) are a large class of animal RNAs. To investigate possible circRNA functions, it is important to understand circRNA biogenesis. Besides human ALU repeats, sequence features that promote exon circularization are largely unknown. We
Andranik Ivanov, Sebastian Memczak, Emanuel Wyler, Francesca Torti, Hagit T. Porath, Marta R. Orejuela, Michael Piechotta, Erez Y. Levanon, Markus Landthaler, Christoph Dieterich, Nikolaus Rajewsky   +10 more
doaj   +1 more source

Multilevel evolution shapes the function of NB-LRR encoding genes in plant innate immunity

Frontiers in Plant Science, 2022
A sophisticated innate immune system based on diverse pathogen receptor genes (PRGs) evolved in the history of plant life. To reconstruct the direction and magnitude of evolutionary trajectories of a given gene family, it is critical to detect the ...
Maria Raffaella Ercolano, Daniela D’Esposito, Giuseppe Andolfo, Luigi Frusciante   +3 more
doaj   +1 more source