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  • 1
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    Comparing the evolutionary conservation between human essential genes, human orthologs of mouse essential genes and human housekeeping genes (2015)
    Oxford University Press
    Details
    Publication Date: 2015-11-20
    Description: Human housekeeping genes are often confused with essential human genes, and several studies regard both types of genes as having the same level of evolutionary conservation. However, this is not necessarily the case. To clarify this, we compared the differences between human housekeeping genes and essential human genes with respect to four aspects: the evolutionary rate (dN/dS), protein sequence identity, single-nucleotide polymorphism (SNP) density and level of linkage disequilibrium (LD). The results showed that housekeeping genes had lower evolutionary rates, higher sequence identities, lower SNP densities and higher levels of LD compared with essential genes. Together, these findings indicate that housekeeping and essential genes are two distinct types of genes, and that housekeeping genes have a higher level of evolutionary conservation. Therefore, we suggest that researchers should pay careful attention to the distinctions between housekeeping genes and essential genes. Moreover, it is still controversial whether we should substitute human orthologs of mouse essential genes for human essential genes. Therefore, we compared the evolutionary features between human orthologs of mouse essential genes and human housekeeping genes and we got inconsistent results in long-term and short-term evolutionary characteristics implying the irrationality of simply replacing human essential genes with human orthologs of mouse essential genes.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 2
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    MICC: an R package for identifying chromatin interactions from ChIA-PET data (2015)
    Oxford University Press
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    Publication Date: 2015-11-21
    Description: : ChIA-PET is rapidly emerging as an important experimental approach to detect chromatin long-range interactions at high resolution. Here, we present M odel based I nteraction C alling from C hIA-PET data (MICC), an easy-to-use R package to detect chromatin interactions from ChIA-PET sequencing data. By applying a Bayesian mixture model to systematically remove random ligation and random collision noise, MICC could identify chromatin interactions with a significantly higher sensitivity than existing methods at the same false discovery rate. Availability and implementation: http://bioinfo.au.tsinghua.edu.cn/member/xwwang/MICCusage Contact: michael.zhang@utdallas.edu or xwwang@tsinghua.edu.cn 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
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  • 3
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    Preparation of monoPEGylated Cyanovirin-N's derivative and its anti-influenza A virus bioactivity in vitro and in vivo (2015)
    Oxford University Press
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    Publication Date: 2015-05-28
    Description: Influenza A virus (IAV) has been raising public health and safety concerns worldwide. Cyanovirin-N (CVN) is a prominent anti-IAV candidate, but both cytotoxicity and immunogenicity have hindered the development of this protein as a viable therapy. In this article, linker-CVN (LCVN) with a flexible and hydrophilic polypeptide at the N-terminus was efficiently produced from the cytoplasm of Escherichia coli at a 〉15-l scale. PEGylation at the N-terminal α-amine of LCVN was also reformed as 20 kDa PEGylated linkered Cyanovirin-N (PEG 20k –LCVN). The 50% effective concentrations of PEG 20k –LCVN were 0.43 ± 0.11 µM for influenza A/HK/8/68 (H3N2) and 0.04 ± 0.02 µM for A/Swan/Hokkaido/51/96 (H5N3), dramatically lower than that of the positive control, Ribavirin (2.88 ± 0.66 x 10 3 µM and 1.79 ± 0.62 x 10 3 µM, respectively). A total of 12.5 µM PEG 20k –LCVN effectively inactivate the propagation of H3N2 in chicken embryos. About 2.0 mg/kg/day PEG 20k –LCVN increased double the survival rate (66.67%, P = 0.0378) of H3N2 infected mice, prolonged the median survival period, downregulated the mRNA level of viral nuclear protein and decreased (attenuated) the pathology lesion in mice lung. A novel PEGylated CVN derivative, PEG 20k –LCVN, exhibited potent and strain-dependent anti-IAV activity in nanomolar concentrations in vitro, as well as in micromolar concentration in vivo .
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 4
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    De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles (2016)
    Oxford University Press
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    Publication Date: 2016-06-21
    Description: Defining chromatin interaction frequencies and topological domains is a great challenge for the annotations of genome structures. Although the chromosome conformation capture (3C) and its derivative methods have been developed for exploring the global interactome, they are limited by high experimental complexity and costs. Here we describe a novel computational method, called CITD, for de novo prediction of the chromatin interaction map by integrating histone modification data. We used the public epigenomic data from human fibroblast IMR90 cell and embryonic stem cell (H1) to develop and test CITD, which can not only successfully reconstruct the chromatin interaction frequencies discovered by the Hi-C technology, but also provide additional novel details of chromosomal organizations. We predicted the chromatin interaction frequencies, topological domains and their states (e.g. active or repressive) for 98 additional cell types from Roadmap Epigenomics and ENCODE projects. A total of 131 protein-coding genes located near 78 preserved boundaries among 100 cell types are found to be significantly enriched in functional categories of the nucleosome organization and chromatin assembly. CITD and its predicted results can be used for complementing the topological domains derived from limited Hi-C data and facilitating the understanding of spatial principles underlying the chromosomal organization.
    Keywords: Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Token-Leakage Tolerant and Vector Obfuscated IPE and Application in Privacy-Preserving Two-Party Point/Polynomial Evaluations (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-29
    Description: In mobile environments, data stored in nodes are subject to side-channel attacks such as power analysis, emitted signal, detected radiation, etc. In this work, we propose a leakage-resilient inner-product encryption that the decryption will succeed if and only if the decryption attribute vector (generate the token) meets the orthogonal encryption attribute vector (obfuscated encryption policy), that is, the match holds that the inner product of two vectors is zero. Propose scheme supports the security of attribute-hiding and leakage-resilient in the standard model. The adversary cannot only issue any token reveal query on non-match vector, but also can request at most $\ell $ -bit information on the token-leakage query even if the queried vector matches the challenge vector. We prove the security by the technique of dual system encryption in the orthogonal subgroups, to be strongly leakage-resilient and adaptively attribute-hiding. We also deploy our scheme as a building block to devise a secure two-party point/polynomial evaluation protocol in mobility environments, in which two parties cooperate to evaluate a polynomial in the sense that their sensitive inputs of both point and polynomial are fully preserved. Finally, we assess the performance of leakage resilience including the leakage bound and the leakage fraction (LF). Analysis shows that the leakage bound is approximate $(n-1)\log {\pi _2}$ and the LF is about ${1}/{2(1+\omega _1+\omega _3)}$ , where $n$ is the length of vector, $\pi _2$ is the order of subgroup $\mathbb {G}_{\pi _2}$ and $\omega _1,\omega _3$ are the constants. We can obtain optimized LF $1/2-o(1)$ by varying the sizes of subgroups.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 6
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    NONCODE 2016: an informative and valuable data source of long non-coding RNAs (2016)
    Oxford University Press
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    Publication Date: 2016-01-07
    Description: NONCODE ( http://www.bioinfo.org/noncode/ ) is an interactive database that aims to present the most complete collection and annotation of non-coding RNAs, especially long non-coding RNAs (lncRNAs). The recently reduced cost of RNA sequencing has produced an explosion of newly identified data. Revolutionary third-generation sequencing methods have also contributed to more accurate annotations. Accumulative experimental data also provides more comprehensive knowledge of lncRNA functions. In this update, NONCODE has added six new species, bringing the total to 16 species altogether. The lncRNAs in NONCODE have increased from 210 831 to 527,336. For human and mouse, the lncRNA numbers are 167,150 and 130,558, respectively. NONCODE 2016 has also introduced three important new features: (i) conservation annotation; (ii) the relationships between lncRNAs and diseases; and (iii) an interface to choose high-quality datasets through predicted scores, literature support and long-read sequencing method support. NONCODE is also accessible through http://www.noncode.org/ .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Design and bioinformatics analysis of genome-wide CLIP experiments (2015)
    Oxford University Press
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    Publication Date: 2015-06-24
    Description: The past decades have witnessed a surge of discoveries revealing RNA regulation as a central player in cellular processes. RNAs are regulated by RNA-binding proteins (RBPs) at all post-transcriptional stages, including splicing, transportation, stabilization and translation. Defects in the functions of these RBPs underlie a broad spectrum of human pathologies. Systematic identification of RBP functional targets is among the key biomedical research questions and provides a new direction for drug discovery. The advent of cross-linking immunoprecipitation coupled with high-throughput sequencing (genome-wide CLIP) technology has recently enabled the investigation of genome-wide RBP–RNA binding at single base-pair resolution. This technology has evolved through the development of three distinct versions: HITS-CLIP, PAR-CLIP and iCLIP. Meanwhile, numerous bioinformatics pipelines for handling the genome-wide CLIP data have also been developed. In this review, we discuss the genome-wide CLIP technology and focus on bioinformatics analysis. Specifically, we compare the strengths and weaknesses, as well as the scopes, of various bioinformatics tools. To assist readers in choosing optimal procedures for their analysis, we also review experimental design and procedures that affect bioinformatics analyses.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    The perplexing population genetic structure of Bellamya purificata (Gastropoda: Viviparidae): low genetic differentiation despite low dispersal ability (2015)
    Oxford University Press
    Details
    Publication Date: 2015-10-24
    Description: Bellamya purificata is a widely distributed Chinese freshwater snail. It plays a significant role in ecosystem services. However, its natural habitats are under severe threat due to fragmentation and loss. In order to estimate the genetic diversity and population structure of B. purificata , 182 individuals from eight locations throughout its distribution across China were sampled. Seven microsatellite loci and the mitochondrial COI gene were genotyped. Our results showed that (1) the genetic diversity of B. purificata was high in all studied populations; (2) a low level of genetic differentiation existed among the eight populations with little restriction to gene flow; (3) no clear geographic structure was revealed by either Bayesian clustering, haplotype networks or AMOVA; (4) effective population size ( N e ) was moderate to high for all studied populations. The results of Bayesian Skyline plot analysis detected unstable population sizes through time for most populations. Passive dispersal during flooding events, zoochoric dispersal, possibly anthropogenic translocations and the large population sizes might be the major reasons for the lack of differentiation among Chinese B. purificata populations.
    Print ISSN: 0260-1230
    Electronic ISSN: 1464-3766
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Functional Encryption Resilient to Hard-to-Invert Leakage (2015)
    Oxford University Press
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    Publication Date: 2015-03-27
    Description: Functional encryption (FE) systems provide a flexible and expressive encryption mechanism that private keys and ciphertexts are associated with attributes and predicate formulae and decryption are possible whenever keys and ciphertexts are related, i.e. . In this work, we put forward a leakage-resilient FE scheme against the amount of leakage output over a hard-to-invert function family. In our scheme, the encryption policy is specified as an arbitrary monotonic formula, and the adversary can learn the arbitrary length output of the master key and the private key from any computationally irreversible function with the input (master) keys. To improve the efficiency, we employ the set of minimal sets to describe the predicate formula or access structure, and initiate the formal model of leakage-resilient FE, which is a generic extension of identity-based encryption and attribute-based encryption in the presence of key leakage with auxiliary inputs. We provide the concrete construction in bilinear groups of composite order, and prove the adaptively leakage-resilient security in the standard model based on static assumptions. Our hard-to-invert leakage resilience employs the Goldreich–Levin theorem and its extension as a hard-core value over large fields. We also give an extensional construction in the case of obtaining the hard-to-invert randomness leakage of the encryption, which uses a strong extractor to prevent leakage of randomness and a hard-to-invert encryption to prevent the leakage of the key. Finally, we analyze and discuss the stepped-up security on master leakage and continual leakage, and the lower bound of the irreversible leakage function.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 10
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    Public Key Encryption with Delegated Equality Test in a Multi-User Setting (2015)
    Oxford University Press
    Details
    Publication Date: 2015-03-27
    Description: Probabilistic public key encryption with equality test (PKEET), introduced by Yang et al. in CT-RSA 2010, is able to check whether two ciphertexts are encryptions of the same message under different public keys without leaking anything else about the message encrypted under either public key. PKEET schemes have many applications, for example, in constructing searchable encryption and partitioning encrypted data. Previous PKEET schemes lack a delegation mechanism for users to specify who can perform the equality test between their ciphertexts. In this paper, we propose the notion of public key encryption with delegated equality test (PKE-DET), which requires only the delegated party to deal with the work in a practical multi-user setting, and present a concrete construction in Type 2 pairing, which is provably secure under the newly introduced security notions.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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