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ATP, Mg2+, nuclear phase separation, and genome accessibility
(Elsevier, 2019)
Misregulation of the processes controlling eukaryotic gene expression can result in disease. Gene expression is influenced by the surrounding chromatin; hence the nuclear environment is also of vital ...
The plant noncoding transcriptome: a versatile environmental sensor
(EMBO Press, 2023)
Plant noncoding RNA transcripts have gained increasing attention in recent years due to growing evidence that they can regulate developmental plasticity. In this review article, we comprehensively analyze ...
Derivation of nearest-neighbor DNA parameters in magnesium from single molecule experiments
(Oxford University Press, 2017)
DNA hybridization is an essential molecular reaction in biology with many applications. The nearest-neighbor (NN) model for nucleic acids predicts DNA thermodynamics using energy values for the different ...
Identification of key sequence features required for microRNA biogenesis in plants
(Springer Nature, 2020)
MicroRNAs (miRNAs) are endogenous small RNAs of ∼21 nt that regulate multiple biological pathways in multicellular organisms. They derive from longer transcripts that harbor an imperfect stem-loop ...
LoxTnSeq: random transposon insertions combined with cre/lox recombination and counterselection to generate large random genome reductions
(John Wiley & Sons, 2021)
The removal of unwanted genetic material is a key aspect in many synthetic biology efforts and often requires preliminary knowledge of which genomic regions are dispensable. Typically, these efforts are ...
Statistical properties of metastable intermediates in DNA unzipping
(American Physical Society, 2009)
We unzip DNA molecules using optical tweezers and determine the sizes of the cooperatively unzipping and zipping regions separating consecutive metastable intermediates along the unzipping pathway. Sizes ...
Identification of new microRNA-regulated genes by conserved targeting in plant species
(Oxford University Press, 2012)
MicroRNAs (miRNAs) are major regulators of gene expression in multicellular organisms. They recognize their targets by sequence complementarity and guide them to cleavage or translational arrest. It is ...
comTAR: a web tool for the prediction and characterization of conserved microRNA targets in plants
(Oxford University Press, 2014)
Motivation: MicroRNAs (miRNAs) are major regulators of gene expression in plants and animals. They recognize their target messenger RNAs (mRNAs) by sequence complementarity and guide them to cleavage ...
SURE editing: combining oligo-recombineering and programmable insertion/deletion of selection markers to efficiently edit the Mycoplasma pneumoniae genome
(Oxford University Press, 2022)
The development of advanced genetic tools is boosting microbial engineering which can potentially tackle wide-ranging challenges currently faced by our society. Here we present SURE editing, a ...
Iron Regulation and the Cell Cycle: identification of an iron-responsive element in the 3′-untranslated region of human cell division cycle 14a mrna by a refined microarray-based screening strategy
(Elsevier, 2006)
Iron regulatory proteins (IRPs) 1 and 2 post-transcriptionally control mammalian iron homeostasis by binding to iron-responsive elements (IREs), conserved RNA stem-loop structures located in the 5′- or ...