Filters








492 Hits in 2.2 sec

Next-generation sequencing and large genome assemblies

Joseph Henson, German Tischler, Zemin Ning
<span title="">2012</span> <i title="Future Medicine Ltd"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/gcfq53ko6fekjbl4whca5egjki" style="color: black;">Pharmacogenomics (London)</a> </i> &nbsp;
The next-generation sequencing (NGS) revolution has drastically reduced time and cost requirements for sequencing of large genomes, and also qualitatively changed the problem of assembly. This article reviews the state of the art in de novo genome assembly, paying particular attention to mammalian-sized genomes. The strengths and weaknesses of the main sequencing platforms are highlighted, leading to a discussion of assembly and the new challenges associated with NGS data. Current approaches to
more &raquo; ... assembly are outlined and the various software packages available are introduced and compared. The question of whether quality assemblies can be produced using short-read NGS data alone, or whether it must be combined with more expensive sequencing techniques, is considered. Prospects for future assemblers and tests of assembly performance are also discussed. Keywords de novo assembly; genomics; next-generation sequencing; whole-genome shotgun Genome assembly continues to be one of the central problems of bioinformatics. This is owing, in large part, to the continuing development of the sequencing technology that provides 'reads' of short sequences of DNA, from which the genome is inferred. Larger sets of data, and changes in the properties of reads such as length and errors, bring with them new challenges for assembly. For the earliest sequencing efforts using the whole-genome shotgun (WGS) approach, in which reads are generated from random locations across the entire genome, assembly could be dealt with by arranging print-outs of the reads by hand. Through the next three decades, Sanger capillary sequencing gained substantially in throughput, and WGS became practical for increasingly large and complex genomes, from tens of kilobases in the early 1980s to gigabases by 2001 [1] . In line with this, assembly went on to use not only increasingly powerful computational means, but also increasingly time and memory-efficient assemblers. A further revolution in sequencing began around 2005, when second-generation sequencing (SGS) technologies began to produce massive throughput at far lower costs than Sanger sequencing, enabling a mammalian genome to be sequenced in a matter of days [2] . De novo assemblies of the Panda [3] and Turkey [4] genomes have now been made using SGS data alone, and several human resequencing projects have been completed [5] [6] [7] . The
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2217/pgs.12.72">doi:10.2217/pgs.12.72</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22676195">pmid:22676195</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3960634/">pmcid:PMC3960634</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/b3cz5v6rfrccljnfzkgczmfx2y">fatcat:b3cz5v6rfrccljnfzkgczmfx2y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191121145439/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3960634&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0e/f4/0ef42e183cc28652bdefd93b9ea5bdf136638aec.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2217/pgs.12.72"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3960634" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Oxford Nanopore MinION Sequencing and Genome Assembly

Hengyun Lu, Francesca Giordano, Zemin Ning
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mjqabxhzeveopm6sdbvzz2rmvy" style="color: black;">Genomics, Proteomics &amp; Bioinformatics</a> </i> &nbsp;
The revolution of genome sequencing is continuing after the successful secondgeneration sequencing (SGS) technology. The third-generation sequencing (TGS) technology, led by Pacific Biosciences (PacBio), is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis, or for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes. In 2014, the MinION, the first
more &raquo; ... ercial sequencer using nanopore technology, was released by Oxford Nanopore Technologies (ONT). MinION identifies DNA bases by measuring the changes in electrical conductivity generated as DNA strands pass through a biological pore. Its portability, affordability, and speed in data production makes it suitable for real-time applications, the release of the long read sequencer MinION has thus generated much excitement and interest in the genomics community. While de novo genome assemblies can be cheaply produced from SGS data, assembly continuity is often relatively poor, due to the limited ability of short reads to handle long repeats. Assembly quality can be greatly improved by using TGS long reads, since repetitive regions can be easily expanded into using longer sequencing lengths, despite having higher error rates at the base level. The potential of nanopore sequencing has been demonstrated by various studies in genome surveillance at locations where rapid and reliable sequencing is needed, but where resources are limited.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.gpb.2016.05.004">doi:10.1016/j.gpb.2016.05.004</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27646134">pmid:27646134</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5093776/">pmcid:PMC5093776</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6fim4654yncq3pb67nnqquaj6m">fatcat:6fim4654yncq3pb67nnqquaj6m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171003231338/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/d47/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMTY3MjAyMjkxNjMwMTMwOQ%3D%3D.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/30/e6/30e66baa460edeb7b94505a376d1a1239079db66.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.gpb.2016.05.004"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5093776" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Assessing the gene space in draft genomes

Genis Parra, Keith Bradnam, Zemin Ning, Thomas Keane, Ian Korf
<span title="2008-11-28">2008</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Genome sequencing projects have been initiated for a wide range of eukaryotes. A few projects have reached completion, but most exist as draft assemblies. As one of the main reasons to sequence a genome is to obtain its catalog of genes, an important question is how complete or completable the catalog is in unfinished genomes. To answer this question, we have identified a set of core eukaryotic genes (CEGs), that are extremely highly conserved and which we believe are present in low copy
more &raquo; ... in higher eukaryotes. From an analysis of a phylogenetically diverse set of eukaryotic genome assemblies, we found that the proportion of CEGs mapped in draft genomes provides a useful metric for describing the gene space, and complements the commonly used N50 length and x-fold coverage values.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkn916">doi:10.1093/nar/gkn916</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19042974">pmid:19042974</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2615622/">pmcid:PMC2615622</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5hpo2wyuxvf6dcvfjvxkigt2r4">fatcat:5hpo2wyuxvf6dcvfjvxkigt2r4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201108023458/https://escholarship.org/content/qt3zg069p3/qt3zg069p3.pdf?t=qajqtb" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fe/2a/fe2afbe8385686f675b4bf2473c74ee02a742e6f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkn916"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2615622" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A numerical model for simulating mechanical behavior of flexible fibers

Zemin Ning, John R. Melrose
<span title="1999-12-15">1999</span> <i title="AIP Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hnc5ddfunnd3taca63uf5ggldm" style="color: black;">Journal of Chemical Physics</a> </i> &nbsp;
A numerical method is developed for simulating the mechanical behavior of flexible fibers. A circular crossed fiber is represented by a number of cylindrical segments linked by spring dash-pot systems. Segments are lined up and bonded to each neighbor. Each bond can be stretched or compressed by changing the bond distance. Bending deflection and twist movement occur, respectively, in the bending and torsion planes. While the bending angle is determined by the positions of two neighboring bonds,
more &raquo; ... a reference twist vector is introduced to record the torsion motion along the segment chain. Fluid drag forces are calculated based on the Stokes' Law, where a free draining assumption is made. The motion of the fiber is determined by solving the translational and rotational equations of individual segments. Computer simulation has been conducted to verify the single fiber model with elastic theory and excellent agreements have been found between the simulation results and the theory in various situations such as beam deflection under static loads, vibrating cantilevers, and dynamics of helical shaped fibers. Examining orientations of rigid fibers in a viscous shear flow, simulation results suggest that the rotational time is sensitive to the fluid drag torque which is related to the shape of the segments. For highly flexible fibers, the effect of bending deformation on the period of rotation and the rotation orbits is also investigated. This numerical model for single flexible fibers linked by discrete segments provides a framework in the future studies on fibrous assemblies.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1063/1.480426">doi:10.1063/1.480426</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vlqiqg2bq5a2pjgdf5i7b6zkom">fatcat:vlqiqg2bq5a2pjgdf5i7b6zkom</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20041211115055/http://homepages.cae.wisc.edu:80/~tozzi/NING_FIBERS.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6b/83/6b83ac4efc2b595c79c879df0cff06ec9a7e09df.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1063/1.480426"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Efficient iterative Hi-C scaffolder based on N-best neighbors

Dengfeng Guan, Shane A. McCarthy, Zemin Ning, Guohua Wang, Yadong Wang, Richard Durbin
<span title="2021-11-27">2021</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Background Efficient and effective genome scaffolding tools are still in high demand for generating reference-quality assemblies. While long read data itself is unlikely to create a chromosome-scale assembly for most eukaryotic species, the inexpensive Hi-C sequencing technology, capable of capturing the chromosomal profile of a genome, is now widely used to complete the task. However, the existing Hi-C based scaffolding tools either require a priori chromosome number as input, or lack the
more &raquo; ... ty to build highly continuous scaffolds. Results We design and develop a novel Hi-C based scaffolding tool, pin_hic, which takes advantage of contact information from Hi-C reads to construct a scaffolding graph iteratively based on N-best neighbors of contigs. Subsequent to scaffolding, it identifies potential misjoins and breaks them to keep the scaffolding accuracy. Through our tests on three long read based de novo assemblies from three different species, we demonstrate that pin_hic is more efficient than current standard state-of-art tools, and it can generate much more continuous scaffolds, while achieving a higher or comparable accuracy. Conclusions Pin_hic is an efficient Hi-C based scaffolding tool, which can be useful for building chromosome-scale assemblies. As many sequencing projects have been launched in the recent years, we believe pin_hic has potential to be applied in these projects and makes a meaningful contribution.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-021-04453-5">doi:10.1186/s12859-021-04453-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34837944">pmid:34837944</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8627104/">pmcid:PMC8627104</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hqiv2xzbqzhaviyrmwus6rypoe">fatcat:hqiv2xzbqzhaviyrmwus6rypoe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220119045344/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04453-5.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c3/d7/c3d7a47379ada96c72d3fdfa0467e5cd2197c82d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-021-04453-5"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8627104" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The opium poppy genome and morphinan production

Li Guo, Thilo Winzer, Xiaofei Yang, Yi Li, Zemin Ning, Zhesi He, Roxana Teodor, Ying Lu, Tim A. Bowser, Ian A. Graham, Kai Ye
<span title="2018-08-30">2018</span> <i title="American Association for the Advancement of Science (AAAS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qirzh7firjdsjhg4tutxtir6ey" style="color: black;">Science</a> </i> &nbsp;
Ning, Zhesi He, Roxana Teodor, Ying Lu, Tim A.  ...  protein-coding genes 51,213 Average length of protein- coding genes 3,454bp Supported by RNA-seq or homologs 100% Supported by Protein families 68.8% Guo, Thilo Winzer, Xiaofei Yang, Yi Li, Zemin  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1126/science.aat4096">doi:10.1126/science.aat4096</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30166436">pmid:30166436</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lqv4hpvicfgujb34ueqwsnm35m">fatcat:lqv4hpvicfgujb34ueqwsnm35m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430062412/http://eprints.whiterose.ac.uk/135262/1/aat4096_ArticleContent_plus_figures.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/28/f0/28f0390ba6ce4beffa8eb63e163877ba5b763176.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1126/science.aat4096"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> sciencemag.org </button> </a>

Stability Analysis for Nonlinear Impulsive Control System with Uncertainty Factors

Zemin Ren, Shiping Wen, Qingyu Li, Yuming Feng, Ning Tang, Michele Migliore
<span title="2020-11-21">2020</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3wwzxqpotbc73bzpemzybzg7ee" style="color: black;">Computational Intelligence and Neuroscience</a> </i> &nbsp;
Considering the limitation of machine and technology, we study the stability for nonlinear impulsive control system with some uncertainty factors, such as the bounded gain error and the parameter uncertainty. A new sufficient condition for this system is established based on the generalized Cauchy–Schwarz inequality in this paper. Compared with some existing results, the proposed method is more practically applicable. The effectiveness of the proposed method is shown by a numerical example.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2020/8818794">doi:10.1155/2020/8818794</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33273901">pmid:33273901</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7700033/">pmcid:PMC7700033</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yaegvnjz2zfjzhomw2vn42pmye">fatcat:yaegvnjz2zfjzhomw2vn42pmye</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210714234521/https://opus.lib.uts.edu.au/bitstream/10453/146994/2/Stability%20Analysis%20for%20Nonlinear%20Impulsive%20Control%20System%20with%20Uncertainty%20Factors.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b5/49/b5499ec5eb0cd416a8ac29ee577594ec15e9b320.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2020/8818794"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> hindawi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7700033" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Expansion of CORE-SINEs in the genome of the Tasmanian devil

Maria A Nilsson, Axel Janke, Elizabeth P Murchison, Zemin Ning, Björn M Hallström
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
The genome of the carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia), was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious devil facial tumor disease that is threatening the species' survival. To better understand the Tasmanian devil genome, we screened it for transposable elements and investigated the dynamics of short interspersed element (SINE) retroposons. Results: The temporal history of Tasmanian devil
more &raquo; ... NEs, 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. Conclusions: 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.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-13-172">doi:10.1186/1471-2164-13-172</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22559330">pmid:22559330</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3403934/">pmcid:PMC3403934</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tohbxbq65ndz7eh6i2jhuowujm">fatcat:tohbxbq65ndz7eh6i2jhuowujm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830020055/https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-13-172?site=http://bmcgenomics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/4d/9c/4d9ce05646e8e0a43ea7791e8438b9dcc5245806.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-13-172"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3403934" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Out of the sequencer and into the wiki as we face new challenges in genome informatics

Zemin Ning, Stephen B Montgomery
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
. © 2010 BioMed Central LtdOut of the sequencer and into the wiki as we face new challenges in genome informaticsZemin Ning 1 * and Stephen B Montgomery 2 © 2010 BioMed Central Ltd  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2010-11-10-308">doi:10.1186/gb-2010-11-10-308</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21067526">pmid:21067526</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3218654/">pmcid:PMC3218654</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qc7xatmbgfdmjikp6lxq3ftdiq">fatcat:qc7xatmbgfdmjikp6lxq3ftdiq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170814025224/https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2010-11-10-308?site=genomebiology.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/30/6e/306e5ef942a72f529e47afed9b7f7aa08012bb78.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2010-11-10-308"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218654" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Novel Lipid-Free Nanoformulation for Improving Oral Bioavailability of Coenzyme Q10

Huafeng Zhou, Guoqing Liu, Jing Zhang, Ning Sun, Mingxing Duan, Zemin Yan, Qiang Xia
<span title="">2014</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/icbhosh775h7bgzgot6avm3cua" style="color: black;">BioMed Research International</a> </i> &nbsp;
To improve the bioavailability of orally administered lipophilic coenzyme Q10 (CoQ10), we formulated a novel lipid-free nano-CoQ10 system stabilized by various surfactants. Nano-CoQ10s, composed of 2.5% (w/w) CoQ10, 1.67% (w/w) surfactant, and 41.67% (w/w) glycerol, were prepared by hot high-pressure homogenization. The resulting formulations were characterized by particle size, zeta potential, differential scanning calorimetry, and cryogenic transmission electron microscopy. We found that the
more &raquo; ... ean particle size of all nano-CoQ10s ranged from66.3±1.5 nm to92.7±1.5 nm and the zeta potential ranged from-12.8±1.4 mV to-41.6±1.4 mV. The CoQ10 in nano-CoQ10s likely existed in a supercooled state, and nano-CoQ10s stored in a brown sealed bottle were stable for 180 days at 25°C. The bioavailability of CoQ10 was evaluated following oral administration of CoQ10 formulations in Sprague-Dawley rats. Compared to the values observed following administration of CoQ10-Suspension, nano-CoQ10 modified with various surfactants significantly increased the maximum plasma concentration and the area under the plasma concentration-time curve. Thus, the lipid-free system of a nano-CoQ10 stabilized with a surfactant may be an effective vehicle for improving oral bioavailability of CoQ10.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2014/793879">doi:10.1155/2014/793879</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24995328">pmid:24995328</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4068099/">pmcid:PMC4068099</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/joknr3uvijfpniepxoqeqipad4">fatcat:joknr3uvijfpniepxoqeqipad4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190223041029/http://pdfs.semanticscholar.org/3f50/cd388013002825f53752b99f1cb2a19f9739.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3f/50/3f50cd388013002825f53752b99f1cb2a19f9739.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2014/793879"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> hindawi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4068099" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

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, Thomas Mailund
<span title="2011-01-05">2011</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
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
more &raquo; ... g, 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
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0015292">doi:10.1371/journal.pone.0015292</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21264334">pmid:21264334</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3016441/">pmcid:PMC3016441</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/whe6qfevobflhhkmh6ad4nu5pu">fatcat:whe6qfevobflhhkmh6ad4nu5pu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170927044639/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0015292&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/9f/73/9f73e6bf4865757a853c3eb30b4efa03392c53c2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0015292"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3016441" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Finishing the finished human chromosome 22 sequence

Charlotte G Cole, Owen T McCann, John E Collins, Karen Oliver, David Willey, Susan M Gribble, Fengtang Yang, Karen McLaren, Jane Rogers, Zemin Ning, David M Beare, Ian Dunham
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
Finishing chromosome 22 A combination of approaches was used to close 8 of the 11 gaps in the original sequence of human chromosome 22, and to generate a total 1.018 Mb of new sequence. Abstract Background: Although the human genome sequence was declared complete in 2004, the sequence was interrupted by 341 gaps of which 308 lay in an estimated approximately 28 Mb of euchromatin. While these gaps constitute only approximately 1% of the sequence, knowledge of the full complement of human genes
more &raquo; ... d regulatory elements is incomplete without their sequences.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2008-9-5-r78">doi:10.1186/gb-2008-9-5-r78</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18477386">pmid:18477386</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2441464/">pmcid:PMC2441464</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/f7677r3pk5hmzdz553675uxy7u">fatcat:f7677r3pk5hmzdz553675uxy7u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170706075801/http://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2008-9-5-r78?site=genomebiology.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/17/0b/170b4d65b409dd4107a73222e45be86a4c259aac.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2008-9-5-r78"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2441464" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Novel Methods for Multilinear Data Completion and De-noising Based on Tensor-SVD

Zemin Zhang, Gregory Ely, Shuchin Aeron, Ning Hao, Misha Kilmer
<span title="">2014</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ilwxppn4d5hizekyd3ndvy2mii" style="color: black;">2014 IEEE Conference on Computer Vision and Pattern Recognition</a> </i> &nbsp;
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
more &raquo; ... ith 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] .
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/cvpr.2014.485">doi:10.1109/cvpr.2014.485</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/cvpr/ZhangEAHK14.html">dblp:conf/cvpr/ZhangEAHK14</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/axfdkv3y4bdwbjrfi2pikropwa">fatcat:axfdkv3y4bdwbjrfi2pikropwa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20161118111936/http://www.cv-foundation.org/openaccess/content_cvpr_2014/papers/Zhang_Novel_Methods_for_2014_CVPR_paper.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5c/32/5c32e6850159ac722f7a63aece616b55a68bf289.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/cvpr.2014.485"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Novel methods for multilinear data completion and de-noising based on tensor-SVD [article]

Zemin Zhang, Gregory Ely, Shuchin Aeron, Ning Hao, Misha Kilmer
<span title="2014-10-30">2014</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
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
more &raquo; ... th 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].
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1407.1785v2">arXiv:1407.1785v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yanfp5mpwfciphyavdmcffhb2q">fatcat:yanfp5mpwfciphyavdmcffhb2q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200902135802/https://arxiv.org/pdf/1407.1785v2.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8d/68/8d68bc943a63172cf2f94c9ab120407ce4674d6c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1407.1785v2" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Mobilization of giant piggyBac transposons in the mouse genome

Meng Amy Li, Daniel J. Turner, Zemin Ning, Kosuke Yusa, Qi Liang, Sabine Eckert, Lena Rad, Tomas W. Fitzgerald, Nancy L. Craig, Allan Bradley
<span title="2011-09-24">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The development of technologies that allow the stable delivery of large genomic DNA fragments in mammalian systems is important for genetic studies as well as for applications in gene therapy. DNA transposons have emerged as flexible and efficient molecular vehicles to mediate stable cargo transfer. However, the ability to carry DNA fragments >10 kb is limited in most DNA transposons. Here, we show that the DNA transposon piggyBac can mobilize 100-kb DNA fragments in mouse embryonic stem (ES)
more &raquo; ... lls, making it the only known transposon with such a large cargo capacity. The integrity of the cargo is maintained during transposition, the copy number can be controlled and the inserted giant transposons express the genomic cargo. Furthermore, these 100-kb transposons can also be excised from the genome without leaving a footprint. The development of piggyBac as a large cargo vector will facilitate a wider range of genetic and genomic applications.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr764">doi:10.1093/nar/gkr764</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21948799">pmid:21948799</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3239208/">pmcid:PMC3239208</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/26sk53yzgvhn7p22jmj3bt64fu">fatcat:26sk53yzgvhn7p22jmj3bt64fu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808152330/http://www.bs.jhmi.edu/mbg/craiglab/pdf/articles/Mobilization_giant_piggyBac_transposons_mouse_genome.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a5/d9/a5d9a4fb32eef886ad621709237c35b1a1c4c4f6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr764"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3239208" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
&laquo; Previous Showing results 1 &mdash; 15 out of 492 results