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
    Historic distribution and driving factors of human-caused fires in the Chinese boreal forest between 1972 and 2005 (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-17
    Description: Aims The pattern and driving factors of forest fires are of interest for fire occurrence prediction and forest fire management. The aims of the study were: (i) to describe the history of human-caused fires by season and size of burned area over time; (ii) to identify the spatial patterns of human-caused fires and test for the existence of ‘hotspots’ to determine their exact locations in the Daxing’an Mountains; (iii) to determine the driving factors that determine the spatial distribution and the possibility of human-caused fire occurrence. Methods In this study, K -function and Kernel density estimation were used to analyze the spatial pattern of human-caused fires. The analysis was conducted in S-plus and ArcGIS environments, respectively. The analysis of driving factors was performed in SPSS 19.0 based on a logistic regression model. The variables used to identify factors that influence fire occurrence included vegetation types, meteorological conditions, socioeconomic factors, topography and infrastructure factors, which were extracted and collected through the spatial analysis mode of ArcGIS and from official statistics, respectively. Important Findings The annual number of human-caused fires and the area burnt have declined since 1987 due to the implementation of a forest fire protection act. There were significant spatial heterogeneity and seasonal variations in the distribution of human-caused fires in the Daxing’an Mountains. The heterogeneity was caused by elevation, distance to the nearest railway, forest type and temperature. A logistic regression model was developed to predict the likelihood of human-caused fire occurrence in the Daxing’an Mountains; its global accuracy attained 64.8%. The model was thus comparable to other relevant studies.
    Print ISSN: 1752-993X
    Electronic ISSN: 1752-9921
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 2
    facet.materialart.
    Unknown
    Phylogenomic Distance Method for Analyzing Transcriptome Evolution Based on RNA-seq Data (2013)
    Oxford University Press
    Details
    Publication Date: 2013-10-01
    Description: Thanks to the microarray technology, our understanding of transcriptome evolution at the genome level has been considerably advanced in the past decade. Yet, further investigation was challenged by several technical limitations of this technology. Recent innovation of next-generation sequencing, particularly the invention of RNA-seq technology, has shed insightful lights on resolving this problem. Though a number of statistical and computational methods have been developed to analyze RNA-seq data, the analytical framework specifically designed for evolutionary genomics remains an open question. In this article we develop a new method for estimating the genome expression distance from the RNA-seq data, which has explicit interpretations under the model of gene expression evolution. Moreover, this distance measure takes the data overdispersion, gene length variation, and sequencing depth variation into account so that it can be applied to multiple genomes from different species. Using mammalian RNA-seq data as example, we demonstrated that this expression distance is useful in phylogenomic analysis.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 3
    facet.materialart.
    Unknown
    Identification of cell types from single-cell transcriptomes using a novel clustering method (2015)
    Oxford University Press
    Details
    Publication Date: 2015-06-14
    Description: Motivation: The recent advance of single-cell technologies has brought new insights into complex biological phenomena. In particular, genome-wide single-cell measurements such as transcriptome sequencing enable the characterization of cellular composition as well as functional variation in homogenic cell populations. An important step in the single-cell transcriptome analysis is to group cells that belong to the same cell types based on gene expression patterns. The corresponding computational problem is to cluster a noisy high dimensional dataset with substantially fewer objects (cells) than the number of variables (genes). Results: In this article, we describe a novel algorithm named shared nearest neighbor (SNN)-Cliq that clusters single-cell transcriptomes. SNN-Cliq utilizes the concept of shared nearest neighbor that shows advantages in handling high-dimensional data. When evaluated on a variety of synthetic and real experimental datasets, SNN-Cliq outperformed the state-of-the-art methods tested. More importantly, the clustering results of SNN-Cliq reflect the cell types or origins with high accuracy. Availability and implementation: The algorithm is implemented in MATLAB and Python. The source code can be downloaded at http://bioinfo.uncc.edu/SNNCliq . Contact: zcsu@uncc.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
  • 4
    facet.materialart.
    Unknown
    Inner envelopes: efficient estimation in multivariate linear regression (2012)
    Oxford University Press
    Details
    Publication Date: 2012-08-22
    Description: In this article we propose a new model, called the inner envelope model, which leads to efficient estimation in the context of multivariate normal linear regression. The asymptotic distribution and the consistency of its maximum likelihood estimators are established. Theoretical results, simulation studies and examples all show that the efficiency gains can be substantial relative to standard methods and to the maximum likelihood estimators from the envelope model introduced recently by Cook et al. (2010). Compared to the envelope model, the inner envelope model is based on a different construction and it can produce substantial efficiency gains in situations where the envelope model offers no gains. In effect, inner envelopes open a new frontier to the way in which reducing subspaces can be used to improve efficiency in multivariate problems.
    Print ISSN: 0006-3444
    Electronic ISSN: 1464-3510
    Topics: Biology , Mathematics , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 5
    facet.materialart.
    Unknown
    The Genome of a Mongolian Individual Reveals the Genetic Imprints of Mongolians on Modern Human Populations (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-11
    Description: Mongolians have played a significant role in modern human evolution, especially after the rise of Genghis Khan (1162[?]–1227). Although the social cultural impacts of Genghis Khan and the Mongolian population have been well documented, explorations of their genome structure and genetic imprints on other human populations have been lacking. We here present the genome of a Mongolian male individual. The genome was de novo assembled using a total of 130.8-fold genomic data produced from massively parallel whole-genome sequencing. We identified high-confidence variation sets, including 3.7 million single nucleotide polymorphisms (SNPs) and 756,234 short insertions and deletions. Functional SNP analysis predicted that the individual has a pathogenic risk for carnitine deficiency. We located the patrilineal inheritance of the Mongolian genome to the lineage D3a through Y haplogroup analysis and inferred that the individual has a common patrilineal ancestor with Tibeto-Burman populations and is likely to be the progeny of the earliest settlers in East Asia. We finally investigated the genetic imprints of Mongolians on other human populations using different approaches. We found varying degrees of gene flows between Mongolians and populations living in Europe, South/Central Asia, and the Indian subcontinent. The analyses demonstrate that the genetic impacts of Mongolians likely resulted from the expansion of the Mongolian Empire in the 13th century. The genome will be of great help in further explorations of modern human evolution and genetic causes of diseases/traits specific to Mongolians.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 6
    facet.materialart.
    Unknown
    PNRD: a plant non-coding RNA database (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-16
    Description: The first ncRNA found was an alanine tRNA in baker's yeast, and the first detected microRNAs (miRNAs) promoted ncRNA research to a whole new level. Research on ncRNAs in animals has focused on the medical field, while in plant scientists are more concerned with improving agronomic traits. In 2010, we constructed a plant miRNA database named PMRD to meet the demand for miRNA research in plants. To provide a way to do fundamental research on plant ncRNAs and take full advantage of tremendous public resources, we designed an updated platform called plant ncRNA database (PNRD) based on its predecessor PMRD, which is accessible at http://structuralbiology.cau.edu.cn/PNRD . We collected a total of 25739 entries of 11 different types of ncRNAs from 150 plant species. Targets of miRNAs were extended to 178138 pairs in 46 species, while the number of miRNA expression profiles reached 35. Improvements in PNRD are not only the larger amounts of data, but also better service, such as a more user-friendly interface, more multifunctional and browsing options and more background data for users to download. We also integrated currently prevalent technologies and toolkits to strengthen the capability of the database and provide a one-stop service for scientific users.
    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
  • 7
    facet.materialart.
    Unknown
    Asymmetric Evolution of Human Transcription Factor Regulatory Networks (2014)
    Oxford University Press
    Details
    Publication Date: 2014-07-19
    Description: Changes in cis or trans regulatory regions are the major driving forces that underlie the evolution of gene expression. Transcription factors (TFs) are the main trans factors involved in transcriptional regulation. Here, we studied the divergence of upstream and downstream regulatory networks between duplicate TFs in light of the Encyclopedia of DNA Elements project. We found that the divergence of upstream regulatory networks was generally smaller than the divergence of downstream regulatory networks. Further analysis showed that the downstream regulatory circuits of duplicate TFs evolve faster in the early stage than the late stage after gene duplication. Upstream regulatory circuits are generally more conserved than downstream regulatory circuits in the early stage and in small TF families. Our results indicate the asymmetric evolution of upstream and downstream regulatory circuits between duplicate TFs, which suggest that after gene duplication, human TF families tend to evolve asymmetrically between coding regions and promoter regions.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 8
    facet.materialart.
    Unknown
    Scaled envelopes: scale-invariant and efficient estimation in multivariate linear regression (2013)
    Oxford University Press
    Details
    Publication Date: 2013-11-27
    Description: Efficient estimation of the regression coefficients is a fundamental problem in multivariate linear regression. The envelope model proposed by Cook et al. (2010) was shown to have the potential to achieve substantial efficiency gains by accounting for linear combinations of the response vector that are essentially immaterial to coefficient estimation. This requires in part that the distribution of those linear combinations be invariant to changes in the nonstochastic predictor vector. However, inference based on an envelope is not invariant or equivariant under rescaling of the responses, tending to limit application to responses that are measured in the same or similar units. The efficiency gains promised by envelopes often cannot be realized when the responses are measured in different scales. To overcome this limitation and broaden the scope of envelope methods, we propose a scaled version of the envelope model, which preserves the potential of the original envelope methods to increase efficiency and is invariant to scale changes. Likelihood-based estimators are derived and theoretical properties of the estimators are studied in various circumstances. It is shown that estimating appropriate scales for the responses can produce substantial efficiency gains when the original envelope model offers none. Simulations and an example are given to support the theoretical claims.
    Print ISSN: 0006-3444
    Electronic ISSN: 1464-3510
    Topics: Biology , Mathematics , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 9
    facet.materialart.
    Unknown
    Sparse envelope model: efficient estimation and response variable selection in multivariate linear regression (2016)
    Oxford University Press
    Details
    Publication Date: 2016-09-04
    Description: The envelope model allows efficient estimation in multivariate linear regression. In this paper, we propose the sparse envelope model, which is motivated by applications where some response variables are invariant with respect to changes of the predictors and have zero regression coefficients. The envelope estimator is consistent but not sparse, and in many situations it is important to identify the response variables for which the regression coefficients are zero. The sparse envelope model performs variable selection on the responses and preserves the efficiency gains offered by the envelope model. Response variable selection arises naturally in many applications, but has not been studied as thoroughly as predictor variable selection. In this paper, we discuss response variable selection in both the standard multivariate linear regression and the envelope contexts. In response variable selection, even if a response has zero coefficients, it should still be retained to improve the estimation efficiency of the nonzero coefficients. This is different from the practice in predictor variable selection. We establish consistency and the oracle property and obtain the asymptotic distribution of the sparse envelope estimator.
    Print ISSN: 0006-3444
    Electronic ISSN: 1464-3510
    Topics: Biology , Mathematics , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 10
    facet.materialart.
    Unknown
    An Update of DIVERGE Software for Functional Divergence Analysis of Protein Family (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-19
    Description: DIVERGE is a software system for phylogeny-based analyses of protein family evolution and functional divergence. It provides a suite of statistical tools for selection and prioritization of the amino acid sites that are responsible for the functional divergence of a gene family. The synergistic efforts of DIVERGE and other methods have convincingly demonstrated that the pattern of rate change at a particular amino acid site may contain insightful information about the underlying functional divergence following gene duplication. These predicted sites may be used as candidates for further experiments. We are now releasing an updated version of DIVERGE with the following improvements: 1) a feasible approach to examining functional divergence in nearly complete sequences by including deletions and insertions (indels); 2) the calculation of the false discovery rate of functionally diverging sites; 3) estimation of the effective number of functional divergence-related sites that is reliable and insensitive to cutoffs; 4) a statistical test for asymmetric functional divergence; and 5) a new method to infer functional divergence specific to a given duplicate cluster. In addition, we have made efforts to improve software design and produce a well-written software manual for the general user.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    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...