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131 papers found.
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Kinetics of transcription initiation directed by multiple cis-regulatory elements on the glnAp2 promoter

Transcription initiation is orchestrated by dynamic molecular interactions, with kinetic steps difficult to detect. Utilizing a hybrid method, we aim to unravel essential kinetic steps of transcriptional regulation on the glnAp2 promoter, whose regulatory region includes two enhancers (sites I and II) and three low-affinity sequences (sites III-V), to which the transcriptional ...

Circulating histones for predicting prognosis after cardiac surgery: a prospective study

OBJECTIVES The objective of this study was to assess the perioperative changes in circulating histones and their relationships with other biomarkers and clinical outcomes after cardiac surgery with cardiopulmonary bypass (CPB) in patients.

FastHap: fast and accurate single individual haplotype reconstruction using fuzzy conflict graphs

Motivation: Understanding exact structure of an individual’s haplotype plays a significant role in various fields of human genetics. Despite tremendous research effort in recent years, fast and accurate haplotype reconstruction remains as an active research topic, mainly owing to the computational challenges involved. Existing haplotype assembly algorithms focus primarily on ...

Regulation of flowering time by the miR156-mediated age pathway

Precise flowering time is critical to reproductive success. In response to diverse exogenous and endogenous cues including age, hormones, photoperiod, and temperature, the floral transition is controlled by a complex regulatory network, which involves extensive crosstalks, feedback, or feedforward loops between the components within flowering time pathways. The newly identified age ...

YUCCA-mediated auxin biogenesis is required for cell fate transition occurring during de novo root organogenesis in Arabidopsis

Many plant organs have the ability to regenerate a new plant after detachment or wounding via de novo organogenesis. During de novo root organogenesis from Arabidopsis thaliana leaf explants, endogenic auxin is essential for the fate transition of regeneration-competent cells to become root founder cells via activation of WUSCHEL-RELATED HOMEOBOX 11 (WOX11). However, the molecular ...

Upregulation of microRNA-98 increases radiosensitivity in esophageal squamous cell carcinoma

Although radiation resistance is a common challenge in the clinical treatment of esophageal squamous cell carcinoma (ESCC), an effective treatment strategy has yet to be developed. Aberrant expression of microRNAs (miRNAs) is responsible for cancer sensitivity to radiation. In this study, we aimed to identify the miRNAs that are associated with radioresistance in ESCC. We used a ...

RNA-Skim: a rapid method for RNA-Seq quantification at transcript level

Zhaojun Zhang 1 Wei Wang 0 0 Department of Computer Science, University of California , Los Angeles, CA, USA 1 Department of Computer Science, University of North Carolina at Chapel Hill , Chapel

Copy number variation of a gene cluster encoding endopolygalacturonase mediates flesh texture and stone adhesion in peach

Texture is an important attribute affecting consumer perception of fruit quality. Peach melting flesh and flesh adhesion to stone (endocarp) are simply inherited and controlled by the F-M locus on linkage group (LG) 4. Here, we report that two genes encoding endopolygalacturonase (endoPG) in the F-M locus, designated PpendoPGF and PpendoPGM, are associated with the melting flesh ...

Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution

RNA polymerase II (pol II) utilizes a complex interaction network to select and incorporate correct nucleoside triphosphate (NTP) substrates with high efficiency and fidelity. Our previous ‘synthetic nucleic acid substitution’ strategy has been successfully applied in dissecting the function of nucleic acid moieties in pol II transcription. However, how the triphosphate moiety of ...

A change-point model for identifying 3′UTR switching by next-generation RNA sequencing

A change-point model for identifying 30UTR switching by next-generation RNA sequencing Wei Wang 1 Zhi Wei 1 Hongzhe Li 0 Associate Editor: Inanc Birol 0 Department of Biostatistics and Epidemiology

piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing

Motivation: PIWI-interacting RNAs (piRNAs), 23–36 nt small silencing RNAs, repress transposon expression in the metazoan germ line, thereby protecting the genome. Although high-throughput sequencing has made it possible to examine the genome and transcriptome at unprecedented resolution, extracting useful information from gigabytes of sequencing data still requires substantial ...

PtrABF of Poncirus trifoliata functions in dehydration tolerance by reducing stomatal density and maintaining reactive oxygen species homeostasis

Abscisic acid-responsive element (ABRE)-binding factors (ABFs) play important roles in abiotic stress responses; however, the underlying mechanisms are poorly understood. In this study, it is reported that overexpression of Poncirus trifoliata PtrABF significantly enhanced dehydration tolerance. The transgenic lines displayed smaller stomatal apertures, reduced stomatal ...

Allele-specific copy-number discovery from whole-genome and whole-exome sequencing

Copy-number variants (CNVs) are a major form of genetic variation and a risk factor for various human diseases, so it is crucial to accurately detect and characterize them. It is conceivable that allele-specific reads from high-throughput sequencing data could be leveraged to both enhance CNV detection and produce allele-specific copy number (ASCN) calls. Although statistical ...

The surgical management of hypertrophic obstructive cardiomyopathy with the concomitant mitral valve abnormalities

OBJECTIVES The purpose of this retrospective study was to analyse the pathogenesis and the treatment strategies of hypertrophic obstructive cardiomyopathy (HOCM) with the concomitant mitral valve abnormalities.

Normalization and noise reduction for single cell RNA-seq experiments

based on spike-in ERCC molecules. Availability and implementation: The software is implemented by R and the download version is available at http://wanglab.ucsd.edu/star/GRM. Contact: wei-wang{at}ucsd.edu

DriverDBv2: a database for human cancer driver gene research

We previously presented DriverDB, a database that incorporates ∼6000 cases of exome-seq data, in addition to annotation databases and published bioinformatics algorithms dedicated to driver gene/mutation identification. The database provides two points of view, ‘Cancer’ and ‘Gene’, to help researchers visualize the relationships between cancers and driver genes/mutations. In the ...

Long-term hard X-ray monitoring of 2S 0114+65 with INTEGRAL/IBIS

We present the results of the long-term hard X-ray monitoring of the high-mass X-ray binary 2S 0114+65 with INTEGRAL/IBIS from 2003 to 2008. 2S 0114+65 is a variable hard X-ray source with X-ray luminosities of 1035–4 × 1036 erg s−1 from 20 to 100 keV due to accretion rate changes in different orbital phases. In several observations when 2S 0114+65 was bright, we found a pulse ...

Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data

Background: Fusion transcripts are formed by either fusion genes (DNA level) or trans-splicing events (RNA level). They have been recognized as a promising tool for diagnosing, subtyping and treating cancers. RNA-seq has become a precise and efficient standard for genome-wide screening of such aberration events. Many fusion transcript detection algorithms have been developed for ...

Impact of template backbone heterogeneity on RNA polymerase II transcription

Variations in the sugar component (ribose or deoxyribose) and the nature of the phosphodiester linkage (3′-5′ or 2′-5′ orientation) have been a challenge for genetic information transfer from the very beginning of evolution. RNA polymerase II (pol II) governs the transcription of DNA into precursor mRNA in all eukaryotic cells. How pol II recognizes DNA template backbone ...

Graph-regularized dual Lasso for robust eQTL mapping

Motivation: As a promising tool for dissecting the genetic basis of complex traits, expression quantitative trait loci (eQTL) mapping has attracted increasing research interest. An important issue in eQTL mapping is how to effectively integrate networks representing interactions among genetic markers and genes. Recently, several Lasso-based methods have been proposed to leverage ...