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A Novel Approach to Mine for Genetic Markers via Comparing Class Frequency Distributions of Maximal Repeats Extracted from Tagged Whole Genomic Sequences [chapter]

Jing-Doo Wang
2018 Bioinformatics in the Era of Post Genomics and Big Data  
This chapter adopts a scalable approach, developed previously and based on MapReduce programming model, to extract maximal repeats from a huge amount of tagged whole genomic sequences and meanwhile computing  ...  It is expected that this approach may provide a novel direction in the research of biomarker extraction via whole genomic sequence comparison in the era of post genomics.  ...  Acknowledgements This study is supported by Ministry of Science and Technology, Taiwan, under project MOST 106-2632-E-468-002. I thank Prof. Jeffrey J.P. Tsai who provided computational environments  ... 
doi:10.5772/intechopen.75113 fatcat:m4yqga4bhnba5o5enbpwo7dnum

Genome Wide Identification and Analysis of Microsatellite Repeats in the Largest DNA Viruses (Poxviridae Family): An Insilico Approach

Kiran Burranboina, Sunil Abraham, Kumar Murugan, Manjunath Bayyappa, Revanaiah Yogisharadhya, Gajendragad Raghavendra
2018 Annual Research & Review in Biology  
The genome size and GC content is an important factor in affecting the occurrence of repeat motif as well microsatellites, in vertebrate and invertebrate poxviruses.  ...  , and viruses.  ...  INTRODUCTION The poxviruses belong to the family Poxviridae. These pathogenic viruses cause disease which infects both humans and animals (wild and domestic) [1, 2] .  ... 
doi:10.9734/arrb/2018/38367 fatcat:pyk665fnhzbvfojto5glrrra3e

De novo virus inference and host prediction from metagenome using CRISPR spacers [article]

Ryota Sugimoto, Luca Nishimura, Jumpei Ito, Nicholas F Parrish, Hiroshi Mori, Ken Kurokawa, Hirofumi Nakaoka, Ituro Inoue
2020 bioRxiv   pre-print
Viruses are the most numerous biological entity, existing in all environments and infecting all cellular organisms.  ...  Analysing human gut metagenomic data, we extracted 11,391 terminally redundant CRISPR-targeted sequences which are likely complete circular genomes of viruses or plasmids.  ...  co-occurrence of connected protospacers. 383 The weights of edges were observed counts of co-occurrence of the connected protospacers 384 defined in the previous clustering.  ... 
doi:10.1101/2020.09.04.282665 fatcat:run2yefpe5fu3g4kl5odwex5ma

Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: Viruses, plasmids, and more

Ryota Sugimoto, Luca Nishimura, Phuong Thanh Nguyen, Jumpei Ito, Nicholas F. Parrish, Hiroshi Mori, Ken Kurokawa, Hirofumi Nakaoka, Ituro Inoue, Elhanan Borenstein
2021 PLoS Computational Biology  
Viruses are the most numerous biological entity, existing in all environments and infecting all cellular organisms.  ...  Compared with cellular life, the evolution and origin of viruses are poorly understood; viruses are enormously diverse, and most lack sequence similarity to cellular genes.  ...  Acknowledgments The majority of analysis has been done on the supercomputer systems at the National Institute of Genetics (NIG) and Okinawa Institute of Science and Technology Graduate University.  ... 
doi:10.1371/journal.pcbi.1009428 pmid:34673779 pmcid:PMC8530359 fatcat:giyom3etd5hvrfzqnqb7fnt45q

Use of Host-like Peptide Motifs in Viral Proteins Is a Prevalent Strategy in Host-Virus Interactions

Tzachi Hagai, Ariel Azia, M. Madan Babu, Raul Andino
2014 Cell Reports  
We observed that no ELM type had a co-occurrence level significantly higher than expected by chance, suggesting that most of the ELMs that appear in both human and virus could co-occur based on their propensity  ...  The significance of ELM co-occurrence in human and virus homologs was tested by comparing the frequency of each observed ELM co-occurrence with cooccurrence frequencies resulting from a set of 10,000 human-virus  ... 
doi:10.1016/j.celrep.2014.04.052 pmid:24882001 pmcid:PMC4089993 fatcat:66l7bgsgwbe5hksvq4ix5bykdm

Viral categorization and discovery in human circulation by transcriptome sequencing

Weihua Wang, Xiaoan Zhang, Yanjuan Xu, Adrian M. Di Bisceglie, Xiaofeng Fan
2013 Biochemical and Biophysical Research Communications - BBRC  
In the current study, however, we have documented the use of human serum RNA for viral categorization and discovery through transcriptome sequencing and analysis using well-curated databases and advanced  ...  Serum is the most common and easily accessible patient specimen in a minimally invasive manner.  ...  Page 20 Quinlan (University of Virginia School of Medicine) and John Urban (Brown University) for helpful discussions on data analysis.  ... 
doi:10.1016/j.bbrc.2013.05.139 pmid:23764402 pmcid:PMC3709469 fatcat:e7s3nqvgaffzriwom2h4al3ahq

Investigation of human parvovirus B19 occurrence and genetic variability in different leukaemia entities

A.C. da Costa, I. Bendit, A.C.S. de Oliveira, E.G. Kallas, E.C. Sabino, S.S. Sanabani
2013 Clinical Microbiology and Infection  
The phylogenetic analysis of other regions revealed that 12/40 (30%) of the patients with leukaemia were co-infected with genotypes 1a and 3b.  ...  In this cross-sectional study, we investigated patients in Sao Paulo, Brazil with leukaemia to determine the molecular frequency of B19 variants and characterize the viral genetic variability by partial  ...  Acknowledgements We acknowledge with many thanks the technical assistance of Walter Kleine Neto and critical reading of the manuscript by Dr Shirley Vasconcelos Komninakis.  ... 
doi:10.1111/1469-0691.12058 pmid:23167493 fatcat:spswqchqzjhkjgetzv3qis6iwq

Browsing repeats in genomes: Pygram and an application to non-coding region analysis

Patrick Durand, Frédéric Mahé, Anne-Sophie Valin, Jacques Nicolas
2006 BMC Bioinformatics  
Implementation of the complete configuration is illustrated in an analysis of CRISPR structures in Archaea genomes and the detection of horizontal transfer between Archaea and Viruses.  ...  A large number of studies on genome sequences have revealed the major role played by repeated sequences in the structure, function, dynamics and evolution of genomes.  ...  Acknowledgements This work is supported by a grant from the French Agence Nationale de la Recherche (Modulome project), and uses the bioinformatics platform from Ouest-Genopole.  ... 
doi:10.1186/1471-2105-7-477 pmid:17067389 pmcid:PMC1635066 fatcat:zcndi2jcvrbdxmzrxx7cqkmpru

Presence and role of cytosine methylation in DNA viruses of animals

K. Hoelzer, L. A. Shackelton, C. R. Parrish
2008 Nucleic Acids Research  
One of the most striking discrepancies lies in the frequency of CpG (the dinucleotide CG, linked by a phosphate group), which is underrepresented in most small DNA viruses (those with genomes below 10  ...  kb) but not in larger DNA viruses.  ...  ACKNOWLEDGEMENTS Funding to pay the Open Access publication charges for this article was provided by National Institutes of Health Grant R01 GM080533 to ECH.  ... 
doi:10.1093/nar/gkn121 pmid:18367473 pmcid:PMC2396429 fatcat:klap3c7xvnfzldyo4skxgt3o54

Negative control region at the 5' end of murine leukemia virus long terminal repeats

J R Flanagan, A M Krieg, E E Max, A S Khan
1989 Molecular and Cellular Biology  
Using in vitro protein binding and in vivo functional studies, we have identified novel regulatory sequences near the 5' end of murine leukemia virus (MuLV) long terminal repeats (LTRs).  ...  spleens of five different mouse strains; (ii) in vivo treatment of NFS mice with lipopolysaccharide resulted in the induction of splenic viral transcripts and the concomitant disappearance of UCR-binding  ...  ACKNOWLEDGMENTS We thank Keiko Ozato, Peter Burke, and John Casik for their generous sharing of materials and cell lines, Theodore Theodore for providing the pXenoCAT DNA, and Alfred Steinberg for supplying  ... 
doi:10.1128/mcb.9.2.739 pmid:2540425 pmcid:PMC362651 fatcat:l4sddjgpdfejjc36fzjpvxaoha

The Oncolytic Caprine Herpesvirus 1 (CpHV-1) Induces Apoptosis and Synergizes with Cisplatin in Mesothelioma Cell Lines: A New Potential Virotherapy Approach

Iris Maria Forte, Paola Indovina, Serena Montagnaro, Aurora Costa, Carmelina Antonella Iannuzzi, Francesca Capone, Rosa Camerlingo, Anna Maria Malfitano, Francesca Pentimalli, Gianmarco Ferrara, Massimiliamo Quintiliani, Giuseppe Portella (+2 others)
2021 Viruses  
Some non-human OVs offer advantages over human OVs, including the non-pathogenicity in humans and the absence of pre-existing immunity.  ...  Oncolytic virotherapy is a promising therapeutic approach, for which MM is an ideal candidate; indeed, the pleural location provides direct access for the intra-tumoral injection of oncolytic viruses (  ...  Pascale" of Naples, Italy, for bibliographic assistance.  ... 
doi:10.3390/v13122458 pmid:34960727 pmcid:PMC8703924 fatcat:vimy2iwfzzajnelvgp6nkzmmpq

Viral spillover risk in High Arctic increases with melting glaciers [article]

Audree Lemieux, Graham A. Colby, Alexandre J. Poulain, Stephane Aris-Brosou
2021 bioRxiv   pre-print
We used DNA and RNA sequencing to reconstruct the lake's virosphere and its range of eukaryotic hosts, and show that spillover risk is higher in lake sediments than in soil and increased with runoff from  ...  Influenza A, Ebola, or the SARS-CoV-2 viruses.  ...  This study was financially supported by the Natural Sciences Research Council of Canada (A.J.P., S.A.B.) and by the University of Ottawa (A.L., G.A.C.).  ... 
doi:10.1101/2021.08.23.457348 fatcat:3g6torpt65fjvpn4boilpibv6i

ViR: a tool to account for intrasample variability in the detection of viral integrations [article]

Elisa Pischedda, Cristina Crava, Martina Carlassara, Leila Gasmi, Mariangela Bonizzoni
2020 bioRxiv   pre-print
We benchmarked ViR to work with sequencing data from both single and pooled DNA samples and show its applicability using WGS data of a non-model organism, the arboviral vector Aedes albopictus.  ...  Modern genomic sequencing analyses showed that eukaryotic genomes may harbor hundreds of EVEs, which derive not only from DNA viruses and retroviruses, but also from nonretroviral RNA viruses and are mostly  ...  Additionally, integrated viral sequences in both plants and animals derive not only from DNA viruses and retroviruses but also from non-retroviral RNA viruses and are enriched in repetitive regions of  ... 
doi:10.1101/2020.06.16.155119 fatcat:2fjrc2yifjdrfc7uukc4cgze3m

Coinfection with Two Closely Related Alphaherpesviruses Results in a Highly Diversified Recombination Mosaic Displaying Negative Genetic Interference

B. Muylkens, F. Farnir, F. Meurens, F. Schynts, A. Vanderplasschen, M. Georges, E. Thiry
2009 Journal of Virology  
ACKNOWLEDGMENTS We are grateful to Wojtek Socha, Dominique Ziant, and Lorène Dams for their enthusiastic technical assistance and to Corinne Fasquelle and Bernard Grisart for their support in the sequencing  ...  and the TaqMan genotyping processes.  ...  I values ranging from 0 to 1 indicate that the occurrence of one crossing over (CO) decreases the probability of a second CO occurring nearby.  ... 
doi:10.1128/jvi.02474-08 pmid:19153224 pmcid:PMC2655596 fatcat:w4vfsepkrfddhcc6jvxdicxrpy

Tat-independent replication of human immunodeficiency viruses

L Luznik, G Kraus, J Guatelli, D Richman, F Wong-Staal
1995 Journal of Clinical Investigation  
The replication of human immunodeficiency retroviruses involves a complex series of events that is regulated at both transcriptional and posttranscriptional levels.  ...  In this study, we report that tat-defective HIV-1 and HIV-2 viral DNA transfected into U937 cells can direct efficient viral replication in the presence of transcriptional stimulators such as TNF-a and  ...  Looney and E. Poeschla for critical comments and N. Riggs Tat-independent Replication of Human Immunodeficiency Viruses 331  ... 
doi:10.1172/jci117660 pmid:7814633 pmcid:PMC295435 fatcat:3hyv6kynhfd2xawvohne4nb6y4
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