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Search Results: 1 - 10 of 7780 matches for " Zemin Ning "
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Out of the sequencer and into the wiki as we face new challenges in genome informatics
Zemin Ning, Stephen B Montgomery
Genome Biology , 2010, DOI: 10.1186/gb-2010-11-10-308
Abstract: Next generation sequencing (NGS) analysis, open-source software, cloud computing and wiki-style genomics were among the hot topics and discussions at the recent Genome Informatics meeting at the Wellcome Trust Genome Campus, Cambridge, UK. Here we summarize some highlights of the meeting.Comparison of related genomes can generate a wealth of knowledge about genome evolution and function. Recent advances in NGS technologies have greatly increased the scale and scope with which we can interrogate novel genomes and uncover genetic variation. However, for variation detection and statistical analysis, there are false positive errors for various reasons, notably incompleteness of reference genomes, read mapping errors or limitations, and sequencing-induced features. Benjamin Dickins (Penn State University, University Park, USA) discussed an approach to estimate polymorphism accuracy from NGS data by deeply sequencing a small plasmid genome and comparing it with Sanger sequencing.Elliott Margulies (National Human Genome Research Institute, Bethesda, USA) gave an enticing presentation on this topic entitled 'Analysis of identical twins' genomes reveals sources of false-positive variation detection'. With 55× and 50× depth of read coverage from each twin's sample, they initially identified 83,538 discordant genotype calls across 97.6% of the human reference genome. Through inspection of a random set of discordantly genotyped positions, he revealed that a majority occurred in regions with poorly aligned reads. Margulies noted that he would be highly suspicious of genotype calls in regions with high coverage but with low mapping scores. When these events were filtered out, the number dropped to 13,140, a reduction of 84%. By then further introducing other filtering mechanisms, such as incorrect alignments of short reads across indels, Q20 (99% confidence) evidence in the other twin and 10% allele frequency, Margulies' final number of discordant genotype calls was only in the r
Novel Factorization Strategies for Higher Order Tensors: Implications for Compression and Recovery of Multi-linear Data
Zemin Zhang,Gregory Ely,Shuchin Aeron,Ning Hao,Misha Kilmer
Computer Science , 2013,
Abstract: In this paper we propose novel methods for compression and recovery of multilinear data under limited sampling. We exploit the recently proposed tensor- Singular Value Decomposition (t-SVD)[1], which is a group theoretic framework for tensor decomposition. In contrast to popular existing tensor decomposition techniques such as higher-order SVD (HOSVD), t-SVD has optimality properties similar to the truncated SVD for matrices. Based on t-SVD, we first construct novel tensor-rank like measures to characterize informational and structural complexity of multilinear data. Following that we outline a complexity penalized algorithm for tensor completion from missing entries. As an application, 3-D and 4-D (color) video data compression and recovery are considered. We show that videos with linear camera motion can be represented more efficiently using t-SVD compared to traditional approaches based on vectorizing or flattening of the tensors. Application of the proposed tensor completion algorithm for video recovery from missing entries is shown to yield a superior performance over existing methods. In conclusion we point out several research directions and implications to online prediction of multilinear data.
Novel methods for multilinear data completion and de-noising based on tensor-SVD
Zemin Zhang,Gregory Ely,Shuchin Aeron,Ning Hao,Misha Kilmer
Computer Science , 2014,
Abstract: In this paper we propose novel methods for completion (from limited samples) and de-noising of multilinear (tensor) data and as an application consider 3-D and 4- D (color) video data completion and de-noising. We exploit the recently proposed tensor-Singular Value Decomposition (t-SVD)[11]. Based on t-SVD, the notion of multilinear rank and a related tensor nuclear norm was proposed in [11] to characterize informational and structural complexity of multilinear data. We first show that videos with linear camera motion can be represented more efficiently using t-SVD compared to the approaches based on vectorizing or flattening of the tensors. Since efficiency in representation implies efficiency in recovery, we outline a tensor nuclear norm penalized algorithm for video completion from missing entries. Application of the proposed algorithm for video recovery from missing entries is shown to yield a superior performance over existing methods. We also consider the problem of tensor robust Principal Component Analysis (PCA) for de-noising 3-D video data from sparse random corruptions. We show superior performance of our method compared to the matrix robust PCA adapted to this setting as proposed in [4].
Expansion of CORE-SINEs in the genome of the Tasmanian devil
Maria A Nilsson Janke, Axel Janke, Elizabeth P Murchison, Zemin Ning, Bj?rn M Hallstr?m
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-172
Abstract: The temporal history of Tasmanian devil SINEs, elucidated using a transposition in transposition analysis, indicates that WSINE1, a CORE-SINE present in around 200,000 copies, is the most recently active element. Moreover, we discovered a new subtype of WSINE1 (WSINE1b) that comprises at least 90% of all Tasmanian devil WSINE1s. The frequencies of WSINE1 subtypes differ in the genomes of two of the other Australian marsupial orders. A co-segregation analysis indicated that at least 66 subfamilies of WSINE1 evolved during the evolution of Dasyuromorphia. Using a substitution rate derived from WSINE1 insertions, the ages of the subfamilies were estimated and correlated with a newly established phylogeny of Dasyuromorphia. Phylogenetic analyses and divergence time estimates of mitochondrial genome data indicate a rapid radiation of the Tasmanian devil and the closest relative the quolls (Dasyurus) around 14 million years ago.The radiation and abundance of CORE-SINEs in marsupial genomes indicates that they may be a major player in the evolution of marsupials. It is evident that the early phases of evolution of the carnivorous marsupial order Dasyuromorphia was characterized by a burst of SINE activity. A correlation between a speciation event and a major burst of retroposon activity is for the first time shown in a marsupial genome.
PoolHap: Inferring Haplotype Frequencies from Pooled Samples by Next Generation Sequencing
Quan Long,Daniel C. Jeffares,Qingrun Zhang,Kai Ye,Viktoria Nizhynska,Zemin Ning,Chris Tyler-Smith,Magnus Nordborg
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0015292
Abstract: With the advance of next-generation sequencing (NGS) technologies, increasingly ambitious applications are becoming feasible. A particularly powerful one is the sequencing of polymorphic, pooled samples. The pool can be naturally occurring, as in the case of multiple pathogen strains in a blood sample, multiple types of cells in a cancerous tissue sample, or multiple isoforms of mRNA in a cell. In these cases, it's difficult or impossible to partition the subtypes experimentally before sequencing, and those subtype frequencies must hence be inferred. In addition, investigators may occasionally want to artificially pool the sample of a large number of individuals for reasons of cost-efficiency, e.g., when carrying out genetic mapping using bulked segregant analysis. Here we describe PoolHap, a computational tool for inferring haplotype frequencies from pooled samples when haplotypes are known. The key insight into why PoolHap works is that the large number of SNPs that come with genome-wide coverage can compensate for the uneven coverage across the genome. The performance of PoolHap is illustrated and discussed using simulated and real data. We show that PoolHap is able to accurately estimate the proportions of haplotypes with less than 2% error for 34-strain mixtures with 2X total coverage Arabidopsis thaliana whole genome polymorphism data. This method should facilitate greater biological insight into heterogeneous samples that are difficult or impossible to isolate experimentally. Software and users manual are freely available at http://arabidopsis.gmi.oeaw.ac.at/quan/p?oolhap/.
Identification of Novel and Conserved MicroRNAs Related to Drought Stress in Potato by Deep Sequencing
Ning Zhang, Jiangwei Yang, Zemin Wang, Yikai Wen, Jie Wang, Wenhui He, Bailin Liu, Huaijun Si, Di Wang
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0095489
Abstract: MicroRNAs (miRNAs) are a group of small, non-coding RNAs that play important roles in plant growth, development and stress response. There have been an increasing number of investigations aimed at discovering miRNAs and analyzing their functions in model plants (such as Arabidopsis thaliana and rice). In this research, we constructed small RNA libraries from both polyethylene glycol (PEG 6,000) treated and control potato samples, and a large number of known and novel miRNAs were identified. Differential expression analysis showed that 100 of the known miRNAs were down-regulated and 99 were up-regulated as a result of PEG stress, while 119 of the novel miRNAs were up-regulated and 151 were down-regulated. Based on target prediction, annotation and expression analysis of the miRNAs and their putative target genes, 4 miRNAs were identified as regulating drought-related genes (miR811, miR814, miR835, miR4398). Their target genes were MYB transcription factor (CV431094), hydroxyproline-rich glycoprotein (TC225721), quaporin (TC223412) and WRKY transcription factor (TC199112), respectively. Relative expression trends of those miRNAs were the same as that predicted by Solexa sequencing and they showed a negative correlation with the expression of the target genes. The results provide molecular evidence for the possible involvement of miRNAs in the process of drought response and/or tolerance in the potato plant.
The Leukocyte Receptor Complex in Chicken Is Characterized by Massive Expansion and Diversification of Immunoglobulin-Like Loci
Katja Laun,Penny Coggill,Sophie Palmer,Sarah Sims,Zemin Ning,Jiannis Ragoussis,Emanuela Volpi,Natalie Wilson,Stephan Beck,Andreas Ziegler ,Armin Volz
PLOS Genetics , 2006, DOI: 10.1371/journal.pgen.0020073
Abstract: The innate and adaptive immune systems of vertebrates possess complementary, but intertwined functions within immune responses. Receptors of the mammalian innate immune system play an essential role in the detection of infected or transformed cells and are vital for the initiation and regulation of a full adaptive immune response. The genes for several of these receptors are clustered within the leukocyte receptor complex (LRC). The purpose of this study was to carry out a detailed analysis of the chicken (Gallus gallus domesticus) LRC. Bacterial artificial chromosomes containing genes related to mammalian leukocyte immunoglobulin-like receptors were identified in a chicken genomic library and shown to map to a single microchromosome. Sequencing revealed 103 chicken immunoglobulin-like receptor (CHIR) loci (22 inhibitory, 25 activating, 15 bifunctional, and 41 pseudogenes). A very complex splicing pattern was found using transcript analyses and seven hypervariable regions were detected in the external CHIR domains. Phylogenetic and genomic analysis showed that CHIR genes evolved mainly by block duplications from an ancestral inhibitory receptor locus, with transformation into activating receptors occurring more than once. Evolutionary selection pressure has led not only to an exceptional expansion of the CHIR cluster but also to a dramatic diversification of CHIR loci and haplotypes. This indicates that CHIRs have the potential to complement the adaptive immune system in fighting pathogens.
Recent progress in understanding protein and lipid factors affecting hepatic VLDL assembly and secretion
Meenakshi Sundaram, Zemin Yao
Nutrition & Metabolism , 2010, DOI: 10.1186/1743-7075-7-35
Abstract: Lipids of dietary origin as well as those stored in the adipose tissues act as energy sources for mammalian cells. Since lipids are hydrophobic in nature, mammals have evolved a mechanism such that the insoluble lipids are made soluble in the form of lipoproteins for transportation and delivery to various organs and tissues by the circulatory system. Formation and secretion of lipoprotein particles is primarily achieved in the liver (as VLDL) and in the intestine (as chylomicrons). The process involved in the assembly and secretion of hepatic VLDL or intestinal chylomicrons is complex and has been studied extensively for the past 2-3 decades. Lipid and protein factors that affect various steps during the assembly and secretion of VLDL and chylomicrons have been identified. The assembly process of hepatic VLDL is initiated in the endoplasmic reticulum (ER) as soon as apoB-100 is translated and translocated into the lumenal side where the elongating apoB-100 polypeptide chain recruits various lipids co-translationally. Each VLDL is composed of one molecule of apoB-100, multiple copies of other apolipoproteins, together with varied amounts of triacylglycerol (TAG) and cholesteryl esters, depending upon the size of resulting particles. Cellular and molecular mechanisms by which different lipid and protein components are brought together for VLDL assembly are not fully understood and remain to be defined. A protein factor other than apoB that is absolutely required for VLDL assembly is the microsomal triglyceride-transfer protein (MTP). The obligatory role of MTP in VLDL assembly/secretion is exemplified by human familial abetalipoproteinemia, characterized by nearly a complete absence of apoB-containing lipoproteins including VLDL (and chylomicrons as well). Available evidence indicates that among different lipid and protein constituents of VLDL, the availability of functional apoB-100 and TAG are by far the most critical for the assembly of secretion-competent VLDL wit
Quasisymmetric boundary correspondence and Gr tzsch problem
Wu Zemin,Lai Wancai
Chinese Science Bulletin , 1998, DOI: 10.1007/BF02884631
Abstract: Two necessary and sufficient conditions for the validity of the conjectureK 0(h) =K 1(h) are given, which are independent of the complex dilatations of extremal quasiconformal mappings, where K0(h) is the maximal conformal modulus dilatation of the boundary homeomorphismh, K 1(h) is the maximal dilatation of extremal quasiconformal mappings that agree withh on the boundary. In addition, when the complex dilatation of an extremal quasiconformal mapping is known, the proof of the result simplifies Reich and Chen Jixiu-Chen Zhiguo’s result.
Partitioning complete graphs by heterochromatic trees
Zemin Jin,Xueliang Li
Mathematics , 2007,
Abstract: A {\it heterochromatic tree} is an edge-colored tree in which any two edges have different colors. The {\it heterochromatic tree partition number} of an $r$-edge-colored graph $G$, denoted by $t_r(G)$, is the minimum positive integer $p$ such that whenever the edges of the graph $G$ are colored with $r$ colors, the vertices of $G$ can be covered by at most $p$ vertex-disjoint heterochromatic trees. In this paper we determine the heterochromatic tree partition number of an $r$-edge-colored complete graph.
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