ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    facet.materialart.
    Unknown
    Model-based clustering for RNA-seq data (2014)
    Oxford University Press
    Details
    Publication Date: 2014-01-16
    Description: Motivation: RNA-seq technology has been widely adopted as an attractive alternative to microarray-based methods to study global gene expression. However, robust statistical tools to analyze these complex datasets are still lacking. By grouping genes with similar expression profiles across treatments, cluster analysis provides insight into gene functions and networks, and hence is an important technique for RNA-seq data analysis. Results: In this manuscript, we derive clustering algorithms based on appropriate probability models for RNA-seq data. An expectation-maximization algorithm and another two stochastic versions of expectation-maximization algorithms are described. In addition, a strategy for initialization based on likelihood is proposed to improve the clustering algorithms. Moreover, we present a model-based hybrid-hierarchical clustering method to generate a tree structure that allows visualization of relationships among clusters as well as flexibility of choosing the number of clusters. Results from both simulation studies and analysis of a maize RNA-seq dataset show that our proposed methods provide better clustering results than alternative methods such as the K-means algorithm and hierarchical clustering methods that are not based on probability models. Availability and implementation: An R package, MBCluster.Seq, has been developed to implement our proposed algorithms. This R package provides fast computation and is publicly available at http://www.r-project.org . Contact: sy@swufe.edu.cn ; pliu@iastate.edu Supplementary Information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 2
    facet.materialart.
    Unknown
    An H I view of galaxy conformity: H I-rich environment around H I-excess galaxies (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-27
    Description: Using data taken as part of the Bluedisk project, we study the connection between neutral hydrogen (H i ) in the environment of spiral galaxies and that in the galaxies themselves. We measure the total H i mass present in the environment in a statistical way by studying the distribution of noise peaks in the H i data cubes obtained for 40 galaxies observed with Westerbork Synthesis Radio Telescope. We find that galaxies whose H i mass fraction is high relative to standard scaling relations have an excess H i mass in the surrounding environment as well. Gas in the environment consists of gas clumps which are individually below the detection limit of our H i data. These clumps may be hosted by small satellite galaxies and/or be the high-density peaks of a more diffuse gas distribution in the intergalactic medium. We interpret this result as an indication for a picture in which the ${\rm H}\,{\small {I}}$ -rich central galaxies accrete gas from an extended gas reservoir present in their environment.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 3
    facet.materialart.
    Unknown
    Magnetic field structures in star-forming regions: mid-infrared imaging polarimetry of K3-50 (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-27
    Description: We report new imaging polarimetry observations of the Galactic compact H ii region K3-50 using CanariCam at the Gran Telescopio Canarias. We use a standard polarimetric analysis technique, first outlined by Aitken, to decompose the observed polarization images centred at 8.7, 10.3, and 12.5 μm into the emissive and absorptive components from silicate grains that are aligned with the local magnetic field. These components reveal the spatially resolved magnetic field structures across the mid-infrared emission area of K3-50. We examine these structures and show that they are consistent with previously observed features and physical models of K3-50, such as the molecular torus and the ionized outflow. We propose a 3D geometry for all the structures seen at different wavelengths. We also compute relevant physical quantities in order to estimate the associated magnetic field strengths that would be implied under various physical assumptions. We compare these results with magnetohydrodynamic simulations of protostar formation that predict the magnetic field strength and configuration. We find that the magnetic field may be dynamically important in the innermost 0.2 pc of the molecular torus, but that the torus is more likely to be rotationally supported against gravity outside this radius. Similarly, magnetic fields are unlikely to dominate the global physics of the ionized outflow, but they may be important in helping confine the flow near the cavity wall in some locations. Ours is the first application of the Aitken technique to spatially resolved magnetic field structures in multiple layers along the line of sight, effectively a method of ‘polarization tomography’.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 4
    facet.materialart.
    Unknown
    Blood RNA profiling in a large cohort of multiple sclerosis patients and healthy controls (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-25
    Description: Multiple sclerosis (MS) is the most common autoimmune disease of the central nervous system (CNS). It is characterized by the infiltration of autoreactive immune cells into the CNS, which target the myelin sheath, leading to the loss of neuronal function. Although it is accepted that MS is a multifactorial disorder with both genetic and environmental factors influencing its development and course, the molecular pathogenesis of MS has not yet been fully elucidated. Here, we studied the longitudinal gene expression profiles of whole-blood RNA from a cohort of 195 MS patients and 66 healthy controls. We analyzed these transcriptomes at both the individual transcript and the biological pathway level. We found 62 transcripts to be significantly up-regulated in MS patients; the expression of 11 of these genes was counter-regulated by interferon treatment, suggesting partial restoration of a ‘healthy’ gene expression profile. Global pathway analyses linked the proteasome and Wnt signaling to MS disease processes. Since genotypes from a subset of individuals were available, we were able to identify expression quantitative trait loci (eQTL), a number of which involved two genes of the MS gene signature. However, all these eQTL were also present in healthy controls. This study highlights the challenge posed by analyzing transcripts from whole blood and how these can be mitigated by using large, well-characterized cohorts of patients with longitudinal follow-up and multi-modality measurements.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 5
    facet.materialart.
    Unknown
    CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model (2013)
    Oxford University Press
    Details
    Publication Date: 2013-04-02
    Description: Thousands of novel transcripts have been identified using deep transcriptome sequencing. This discovery of large and ‘hidden’ transcriptome rejuvenates the demand for methods that can rapidly distinguish between coding and noncoding RNA. Here, we present a novel alignment-free method, Coding Potential Assessment Tool (CPAT), which rapidly recognizes coding and noncoding transcripts from a large pool of candidates. To this end, CPAT uses a logistic regression model built with four sequence features: open reading frame size, open reading frame coverage, Fickett TESTCODE statistic and hexamer usage bias. CPAT software outperformed (sensitivity: 0.96, specificity: 0.97) other state-of-the-art alignment-based software such as Coding-Potential Calculator (sensitivity: 0.99, specificity: 0.74) and Phylo Codon Substitution Frequencies (sensitivity: 0.90, specificity: 0.63). In addition to high accuracy, CPAT is approximately four orders of magnitude faster than Coding-Potential Calculator and Phylo Codon Substitution Frequencies, enabling its users to process thousands of transcripts within seconds. The software accepts input sequences in either FASTA- or BED-formatted data files. We also developed a web interface for CPAT that allows users to submit sequences and receive the prediction results almost instantly.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 6
    facet.materialart.
    Unknown
    Modeling structural and functional deficiencies of RBM20 familial dilated cardiomyopathy using human induced pluripotent stem cells (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-09
    Description: Dilated cardiomyopathy (DCM) is a leading cause of heart failure. In families with autosomal-dominant DCM, heterozygous missense mutations were identified in RNA-binding motif protein 20 ( RBM20 ), a spliceosome protein induced during early cardiogenesis. Dermal fibroblasts from two unrelated patients harboring an RBM20 R636S missense mutation were reprogrammed to human induced pluripotent stem cells (hiPSCs) and differentiated to beating cardiomyocytes (CMs). Stage-specific transcriptome profiling identified differentially expressed genes ranging from angiogenesis regulator to embryonic heart transcription factor as initial molecular aberrations. Furthermore, gene expression analysis for RBM20- dependent splice variants affected sarcomeric ( TTN and LDB3 ) and calcium (Ca 2+ ) handling ( CAMK2D and CACNA1C ) genes. Indeed, RBM20 hiPSC-CMs exhibited increased sarcomeric length ( RBM20 : 1.747 ± 0.238 µm versus control: 1.404 ± 0.194 µm; P 〈 0.0001) and decreased sarcomeric width ( RBM20 : 0.791 ± 0.609 µm versus control: 0.943 ± 0.166 µm; P 〈 0.0001). Additionally, CMs showed defective Ca 2+ handling machinery with prolonged Ca 2+ levels in the cytoplasm as measured by greater area under the curve ( RBM20 : 814.718 ± 94.343 AU versus control: 206.941 ± 22.417 AU; P 〈 0.05) and higher Ca 2+ spike amplitude ( RBM20 : 35.281 ± 4.060 AU versus control:18.484 ± 1.518 AU; P 〈 0.05). β-adrenergic stress induced with 10 µ m norepinephrine demonstrated increased susceptibility to sarcomeric disorganization ( RBM20 : 86 ± 10.5% versus control: 40 ± 7%; P 〈 0.001). This study features the first hiPSC model of RBM20 familial DCM. By monitoring human cardiac disease according to stage-specific cardiogenesis, this study demonstrates RBM20 familial DCM is a developmental disorder initiated by molecular defects that pattern maladaptive cellular mechanisms of pathological cardiac remodeling. Indeed, hiPSC-CMs recapitulate RBM20 familial DCM phenotype in a dish and establish a tool to dissect disease-relevant defects in RBM20 splicing as a global regulator of heart function.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 7
    facet.materialart.
    Unknown
    Subunit cell-level measurement of polarization in an individual polar vortex (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉Recently, several captivating topological structures of electric dipole moments (e.g., vortex, flux closure) have been reported in ferroelectrics with reduced size/dimensions. However, accurate polarization distribution of these topological ferroelectric structures has never been experimentally obtained. We precisely measure the polarization distribution of an individual ferroelectric vortex in PbTiO〈sub〉3〈/sub〉/SrTiO〈sub〉3〈/sub〉 superlattices at the subunit cell level by using the atomically resolved integrated differential phase contrast imaging in an aberration-corrected scanning transmission electron microscope. We find, in vortices, that out-of-plane polarization is larger than in-plane polarization, and that downward polarization is larger than upward polarization. The polarization magnitude is closely related to tetragonality. Moreover, the contribution of the PbO bond to total polarization is highly inhomogeneous in vortices. Our precise measurement at the subunit cell scale provides a sound foundation for mechanistic understanding of the structure and properties of a ferroelectric vortex and lattice-charge coupling phenomena in these topological ferroelectric structures.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 8
    facet.materialart.
    Unknown
    AIBP-mediated cholesterol efflux instructs hematopoietic stem and progenitor cell fate (2019)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2019
    Description: 〈p〉Hypercholesterolemia, the driving force of atherosclerosis, accelerates the expansion and mobilization of hematopoietic stem and progenitor cells (HSPCs). The molecular determinants connecting hypercholesterolemia with hematopoiesis are unclear. Here, we report that a somite-derived prohematopoietic cue, AIBP, orchestrates HSPC emergence from the hemogenic endothelium, a type of specialized endothelium manifesting hematopoietic potential. Mechanistically, AIBP-mediated cholesterol efflux activates endothelial Srebp2, the master transcription factor for cholesterol biosynthesis, which in turn transactivates Notch and promotes HSPC emergence. Srebp2 inhibition impairs hypercholesterolemia-induced HSPC expansion. Srebp2 activation and Notch up-regulation are associated with HSPC expansion in hypercholesterolemic human subjects. Genome-wide chromatin immunoprecipitation followed by sequencing (ChIP-seq), RNA sequencing (RNA-seq), and assay for transposase-accessible chromatin using sequencing (ATAC-seq) indicate that Srebp2 transregulates Notch pathway genes required for hematopoiesis. Our studies outline an AIBP-regulated Srebp2-dependent paradigm for HSPC emergence in development and HPSC expansion in atherosclerotic cardiovascular disease.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 9
    facet.materialart.
    Unknown
    Travelling wave solutions in periodic monostable equations on a two-dimensional spatial lattice (2015)
    Oxford University Press
    Details
    Publication Date: 2015-07-16
    Description: This paper is concerned with travelling wave solutions of periodic monostable differential equations on a two-dimensional lattice. The existence, stability and uniqueness of supercritical travelling wave solutions are obtained by comparison principle.
    Print ISSN: 0272-4960
    Electronic ISSN: 1464-3634
    Topics: Mathematics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 10
    facet.materialart.
    Unknown
    SRAMP: prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-03
    Description: N 6 -methyladenosine (m 6 A) is a prevalent RNA methylation modification involved in the regulation of degradation, subcellular localization, splicing and local conformation changes of RNA transcripts. High-throughput experiments have demonstrated that only a small fraction of the m 6 A consensus motifs in mammalian transcriptomes are modified. Therefore, accurate identification of RNA m 6 A sites becomes emergently important. For the above purpose, here a computational predictor of mammalian m 6 A site named SRAMP is established. To depict the sequence context around m 6 A sites, SRAMP combines three random forest classifiers that exploit the positional nucleotide sequence pattern, the K-nearest neighbor information and the position-independent nucleotide pair spectrum features, respectively. SRAMP uses either genomic sequences or cDNA sequences as its input. With either kind of input sequence, SRAMP achieves competitive performance in both cross-validation tests and rigorous independent benchmarking tests. Analyses of the informative features and overrepresented rules extracted from the random forest classifiers demonstrate that nucleotide usage preferences at the distal positions, in addition to those at the proximal positions, contribute to the classification. As a public prediction server, SRAMP is freely available at http://www.cuilab.cn/sramp/ .
    Keywords: RNA characterisation and manipulation
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...