# bib

id: cord-301709-kvyes2lz
author: Baker, Susan C.
title: Developing Bioinformatic Resources for Coronaviruses
date: 2006
extension: .txt
mime: text/plain
words: 1018
sentence: 49
flesch: 41
cache: cache/cord-301709-kvyes2lz.txt
txt: txt/cord-301709-kvyes2lz.txt
summary:
  For example, the Tor2 and Urbani isolates were the first two SARS coronavirus genomes to be sequenced and therefore were named as reference genomes. PATRIC genomes are organized into categories based on phylogenetic relationships.


id: cord-007923-j3jpqd7k
author: O'Brien, Stephen J.
title: Cats
date: 2004-12-14
extension: .txt
mime: text/plain
words: 1213
sentence: 43
flesch: 36
cache: cache/cord-007923-j3jpqd7k.txt
txt: txt/cord-007923-j3jpqd7k.txt
summary:
  Scrutiny by behavioral ecologists has provided a rich literature of distinctive reproductive parameters for several cat species, facilitating advances in assisted reproduction such as artificial insemination, cryopreservation, embryo transfer, in vitro fertilization and the first cloning of a domestic cat in 2002. Domestic cats first gave us feline leukemia virus, which allowed the discovery of scores of 'oncogenes' in the 1970s and 1980s.


id: cord-348059-wa1gjbck
author: Gibbs, Richard A.
title: The Human Genome Project changed everything
date: 2020-08-07
extension: .txt
mime: text/plain
words: 1735
sentence: 69
flesch: 47
cache: cache/cord-348059-wa1gjbck.txt
txt: txt/cord-348059-wa1gjbck.txt
summary:
  The first analyses by two groups, the publicly funded International Human Genome Project (HGP) Consortium and Celera Genomics, were published in Nature 1 and Science 2 , respectively, shortly after. For Huntington disease, a similar time span was needed to go from gene discovery to a new treatment that is only now being tested 7 .


id: cord-268795-tjmx6msm
author: Sardar, Rahila
date: 2020-03-21
extension: .txt
mime: text/plain
words: 2258
sentence: 90
flesch: 40
cache: cache/cord-268795-tjmx6msm.txt
txt: txt/cord-268795-tjmx6msm.txt
title:
  Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis

summary:
  As a host defense mechanism, a repertoire of host miRNAs also target invading viruses. To predict host miRNAs targeting the virus, we collected a list of experimentally verified antiviral miRNAs with their targets from VIRmiRNA database (11) .


id: cord-001340-kqcx7lrq
author: Ladner, Jason T.
title: Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing
date: 2014-06-17
extension: .txt
mime: text/plain
words: 2513
sentence: 93
flesch: 34
cache: cache/cord-001340-kqcx7lrq.txt
txt: txt/cord-001340-kqcx7lrq.txt
summary:
  Despite the small sizes of viral genomes, complications related to limited RNA quantities, host contamination, and secondary structure mean that it is often not time-or cost-effective to finish every genome, and given the intended use, finishing may be unnecessary (5) . One of the most common and important applications for viral genomes is in the study of viral epidemiology, which encompasses our understanding of the patterns, causes, and effects of disease.


id: cord-012473-p66of6kq
author: Celniker, Susan E.
title: Unlocking the secrets of the genome
date: 2009-06-17
extension: .txt
mime: text/plain
words: 2559
sentence: 92
flesch: 30
cache: cache/cord-012473-p66of6kq.txt
txt: txt/cord-012473-p66of6kq.txt
summary:
  Intrinsic signals that define the boundaries of protein-coding genes can only be partly recognized by current algorithms, and signals for other functional elements are even harder to find and interpret. The core of the modENCODE project consists of ten groups who use high-throughput methods to identify functional elements (see Table 1 ).


id: cord-265581-pbv8mjfc
author: Tong, Yaojun
title: An aurora of natural products-based drug discovery is coming
date: 2020-06-06
extension: .txt
mime: text/plain
words: 3079
sentence: 127
flesch: 42
cache: cache/cord-265581-pbv8mjfc.txt
txt: txt/cord-265581-pbv8mjfc.txt
summary:
  Microbes, as the natural products producers, are the start point of the whole journey of microbial natural products discovery, making themselves irreplaceable. We are now more and more confident that a new age of natural products discovery is dawning.


id: cord-267714-ji88tvsl
author: JAKUPCIAK, JOHN P.
title: Biological agent detection technologies
date: 2009-04-21
extension: .txt
mime: text/plain
words: 3528
sentence: 135
flesch: 29
cache: cache/cord-267714-ji88tvsl.txt
txt: txt/cord-267714-ji88tvsl.txt
summary:
  Despite these advances, extension of sequencing technology should include the capacity to distinguish naturally occurring micro-organisms from intentionally distributed pathogens. New opportunities to develop faster and less expensive methods for sequencing DNA are pushing genome sequencing technology to include answers to: • information on the nature and source of a sample • effective data collection for comparison of samples (from known and probable locations)


id: cord-277687-u3q36o3e
author: Shean, Ryan C.
date: 2019-01-23
extension: .txt
mime: text/plain
words: 4073
sentence: 179
flesch: 46
cache: cache/cord-277687-u3q36o3e.txt
txt: txt/cord-277687-u3q36o3e.txt
title:
  VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank

summary:
  handles batch submissions of multiple viruses of different types without prior knowledge of the viral species, correctly annotates RNA editing and ribosomal slippage, performs spellchecking on annotations, handles batch or individual submission of metadata, runs with a simple one-line command, and creates annotated viral sequence files for GenBank submission. Annotation and submission of viral genome sequence is a non-trivial task, especially for groups that do not routinely interact with GenBank for data submissions.


id: cord-298136-mel9fxw8
author: O'Malley, Maureen A.
title: Whole-genome patenting
date: 2005-05-10
extension: .txt
mime: text/plain
words: 4107
sentence: 141
flesch: 36
cache: cache/cord-298136-mel9fxw8.txt
txt: txt/cord-298136-mel9fxw8.txt
summary:
  Patent patents take one step towards answering this question. Genome patents in the second category direct their claims to specified open reading frames (ORFs) or polynucleotides, but do so in the context of a broader specification of the invention that argues for the whole sequenced genome as an integral part of the invention.


id: cord-014461-2ubh9u8r
author: Nelson, Oranmiyan W.
title: Genome sequences published outside of Standards in Genomic Sciences, July - October 2012
date: 2012-10-10
extension: .txt
mime: text/plain
words: 4132
sentence: 196
flesch: 32
cache: cache/cord-014461-2ubh9u8r.txt
txt: txt/cord-014461-2ubh9u8r.txt
summary:
  carotovorum Bacteriophage PP1 Complete Genome Sequences of Two Persicivirga Bacteriophages, P12024S and P12024L Genome sequence of the phage clP1, which infects the beer spoilage bacterium Pediococcus damnosus Complete Genome Sequence of Pseudomonas aeruginosa Siphophage MP1412 Complete Genome Sequences of Two Pseudomonas aeruginosa Temperate Phages, MP29 and MP42, Which Lack the Phage-Host CRISPR Interaction Genome Sequence of the Broad-Host-Range Pseudomonas Phage Φ-S1 Complete Genome Sequence of Pseudomonas aeruginosa Siphophage MP1412 Complete Genome Sequence of Staphylococcus aureus Bacteriophage GH15 Complete Genome Sequence of Vibrio vulnificus Bacteriophage SSP002 Whole genome sequence analyses of three African bovine rotaviruses reveal that they emerged through multiple reassortment events between rotaviruses from different mammalian species Complete Genome Sequence of an Avian Leukosis Virus Isolate Associated with Hemangioma and Myeloid Leukosis in Egg-Type and Meat-Type Chickens Genome Sequence of a Novel Reassortant H3N2 Avian Influenza Virus in Southern China Complete Genome Sequence of an H5N2 Avian Influenza Virus Isolated from a Parrot in Southern China Complete Genome Sequence of an Avian-Like H4N8 Swine Influenza Virus Discovered in Southern China Complete Genome Sequence of a Novel Avian Paramyxovirus Complete Genome Sequence of Avian Tembusu-Related Virus Strain WR Isolated from White Kaiya Ducks in Fujian Complete Genome Sequence of Bluetongue Virus Serotype 9: Implications for Serotyping Complete Genome Sequence of Bluetongue Virus Serotype 16 of Goat Origin from India Genome Sequence of a Bombyx mori Nucleopolyhedrovirus Strain with Cubic Occlusion Bodies Complete Genome Sequence of a Bovine Viral Diarrhea Virus 2 from Commercial Fetal Bovine Serum Complete Genome Sequences of Two Novel European Clade Bovine Foamy Viruses from Germany and Poland Complete Genome Sequences of Novel Canine Noroviruses in Hong Kong Complete Genome Sequence Analysis of a Recent Chicken Anemia Virus Isolate and Comparison with a Chicken Anemia Virus Isolate from Human Fecal Samples in China Complete Genome Sequence of a Chikungunya Virus Isolated in Guangdong Complete Genome Sequences of Two Chinese Virulent Avian Coronavirus Infectious Bronchitis Virus Variants Complete Genome Sequence of a Recombinant Coxsackievirus B4 from a Patient with a Fatal Case of Hand, Foot, and Mouth Disease in Guangxi Complete Genome Sequence of a Novel Human Enterovirus C (HEV-C117) Identified in a Child with Community-Acquired Pneumonia Complete Genome Sequence of the Genotype 4 Hepatitis E Virus Strain Prevalent in Swine in Jiangsu Province, China, Reveals a Close Relationship with That from the Human Population in This Area Complete Genome Sequence of an H10N8 Avian Influenza Virus Isolated from a Live Bird Market in Southern China Complete Genome Sequence of a Novel H9N2 Subtype Influenza Virus FJG9 Strain in China Reveals a Natural Reassortant Event Characterization and Complete Genome Sequence of Human Coronavirus NL63 Isolated in China Whole genome sequence analyses of three African bovine rotaviruses reveal that they emerged through multiple reassortment events between rotaviruses from different mammalian species Complete Genome Sequence of Ikoma Lyssavirus Analysis of the complete genome sequence of two Korean sacbrood viruses in the Honey bee, Apis mellifera The complete mitochondrial genome sequence of the western flower thrips Frankliniella occidentalis (Thysanoptera: Thripidae) contains triplicate putative control regions Genome Sequence of Methylobacterium sp. Complete Genome Sequence of a Street Rabies Virus from Mexico Genome sequence of a waterfowl aviadenovirus, goose adenovirus 4 Jenny)


id: cord-000556-uu1oz2ei
author: Kumar, Ranjit
title: RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen “Histophilus somni 2336”
date: 2012-01-20
extension: .txt
mime: text/plain
words: 4410
sentence: 201
flesch: 43
cache: cache/cord-000556-uu1oz2ei.txt
txt: txt/cord-000556-uu1oz2ei.txt
summary:
  We identified co-expression for 452 pairs (total 730 genes) of H. somni genes ( Table S2 ) that were transcribed together and constituted a minimal operon. Regions where coverage depth was greater than the lower tenth percentile of expressed genes were considered significantly expressed [21] ; in the current study, this corresponded to a coverage depth of 7 reads/bp in pileup format.


id: cord-265857-fs6dj3dp
author: Liu, Yu-Tsueng
title: Infectious Disease Genomics
date: 2010-12-24
extension: .txt
mime: text/plain
words: 4346
sentence: 139
flesch: 33
cache: cache/cord-265857-fs6dj3dp.txt
txt: txt/cord-265857-fs6dj3dp.txt
summary:
  S-OIV emerged in the spring of 2009 in Mexico and was also discovered in specimens from two unrelated children in the San Diego area in April 2009 (CDC, 2009; Dawood et al., 2009) . S-OIV has three genome segments (HA, NP, NS) from the classic North American swine (H1N1) lineage, two segments (PB2, PA) from the North American avian lineage, one segment (PB1) from the seasonal H3N2, and most notably, two segments (NA, M) from the Eurasian swine (H1N1) lineage (Dawood et al., 2009) .


id: cord-320005-i30t7cvr
author: Pardo, A.
title: The Human Genome and Advances in Medicine: Limits and Future Prospects
date: 2004-03-31
extension: .txt
mime: text/plain
words: 4923
sentence: 177
flesch: 45
cache: cache/cord-320005-i30t7cvr.txt
txt: txt/cord-320005-i30t7cvr.txt
summary:
  A blueprint for the genomic era Human genome sequencing Available at The genome sequence of Drosophila melanogaster Genome sequence of the rematode C. elegans: a platform for investigating biology. The identification of the different groups of genes involved in the pathogenic processes of human disease will also facilitate the discovery of new molecular targets that can eventually be used in the treatment of such diseases.


id: cord-265329-bsypo08l
author: van Dorp, Lucy
title: Emergence of genomic diversity and recurrent mutations in SARS-CoV-2
date: 2020-05-05
extension: .txt
mime: text/plain
words: 4923
sentence: 181
flesch: 40
cache: cache/cord-265329-bsypo08l.txt
txt: txt/cord-265329-bsypo08l.txt
summary:
  However, this lineage shares 96% identity with SARS-CoV-2, which is not sufficiently high to implicate it as the immediate ancestor of SARS-CoV-2 (2) . Betacoronaviridae comprise a large number of lineages that are found in a wide range of mammals and birds (2) , including the other human zoonotic pathogens SARS-CoV-1 and MERS-COV.


id: cord-324811-yjwavea5
author: Kidgell, Claire
title: Elucidating genetic diversity with oligonucleotide arrays
date: 2005
extension: .txt
mime: text/plain
words: 5580
sentence: 199
flesch: 30
cache: cache/cord-324811-yjwavea5.txt
txt: txt/cord-324811-yjwavea5.txt
summary:
  With regard to genetic diversity analyses, an important practical limitation is the number of specific probe features that can be synthesized on a single array platform, which restricts the extent of variability that can be discovered. Both the spotted DNA microarray and oligonucleotide array platforms can be successfully applied to genetically characterize a strain or species.


id: cord-000902-ew8orn0z
author: Zhao, Xiangyan
title: Coevolution between simple sequence repeats (SSRs) and virus genome size
date: 2012-08-30
extension: .txt
mime: text/plain
words: 5836
sentence: 226
flesch: 46
cache: cache/cord-000902-ew8orn0z.txt
txt: txt/cord-000902-ew8orn0z.txt
summary:
  An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction Microsatellite is an important component of complete Hepatitis C virus genomes The contribution of slippage-like processes to genome evolution Simple sequences in a 'minimal' genome Simple sequences and the expanding genome DNA repeat arrays in chicken and human genomes and the adaptive evolution of avian genome size The repetitive landscape of the chicken genome DNA sequence organization in avian genomes Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias Initial sequencing and comparative analysis of the mouse genome MGSC genome assembly release 3 Analysis of the largest tandemly repeated DNA families in the human genome Comparative analyses of human single-and multilocus tandem repeats Simple sequence repeats in Escherichia coli: abundance, distribution, composition, and polymorphism The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA Bacteria-phage antagonistic coevolution in soil Coevolution with viruses drives the evolution of bacterial mutation rates Nature and Intensity of Selection Pressure on CRISPR-Associated Genes A bird's-eye view of the C-value enigma: Genome size, cell size, and metabolic rate in the class Aves Cell size and nuclear DNA content in vertebrates Similar distribution of simple sequence repeats in diverse completed Human Immunodeficiency Virus Type 1 genomes Microsatellites in different Potyvirus genomes: Survey and analysis Compound microsatellites in complete Escherichia coli genomes Survey of simple sequence repeats in completed fungal genomes Genomic Distribution of Simple Sequence Repeats in Brassica rapa The genome-wide determinants of human and chimpanzee microsatellite evolution Genome-wide analysis of tandem repeats in Daphnia pulex-a comparative approach Coevolution between simple sequence repeats (SSRs) and virus genome size We would like to thank Chuansheng He for the language editing and 3 anonymous reviewers for constructive comments on the earlier version of the manuscript. key: cord-000902-ew8orn0z authors: Zhao, Xiangyan; Tian, Yonglei; Yang, Ronghua; Feng, Haiping; Ouyang, Qingjian; Tian, You; Tan, Zhongyang; Li, Mingfu; Niu, Yile; Jiang, Jianhui; Shen, Guoli; Yu, Ruqin title: Coevolution between simple sequence repeats (SSRs) and virus genome size date: 2012-08-30 journal: BMC Genomics DOI: 10.1186/1471-2164-13-435 sha: doc_id: 902 cord_uid: ew8orn0z BACKGROUND: Relationship between the level of repetitiveness in genomic sequence and genome size has been investigated by making use of complete prokaryotic and eukaryotic genomes, but relevant studies have been rarely made in virus genomes.


id: cord-004123-1s8kuno2
author: Jaiswal, Arun Kumar
date: 2020-01-10
extension: .txt
mime: text/plain
words: 5943
sentence: 309
flesch: 48
cache: cache/cord-004123-1s8kuno2.txt
txt: txt/cord-004123-1s8kuno2.txt
title:
  The pan-genome of Treponema pallidum reveals differences in genome plasticity between subspecies related to venereal and non-venereal syphilis

summary:
  pallidum might be responsible for different molecular modes of infection as T. pallidum genome contains two operons for the Che response regulators endemicum (TEN) causes endemic syphilis (bejel); T. pallidum subsp.


id: cord-000012-p56v8wi1
author: Bigot, Yves
title: Molecular evidence for the evolution of ichnoviruses from ascoviruses by symbiogenesis
date: 2008-09-18
extension: .txt
mime: text/plain
words: 6431
sentence: 252
flesch: 40
cache: cache/cord-000012-p56v8wi1.txt
txt: txt/cord-000012-p56v8wi1.txt
summary:
  Since parasitoid wasps are able to vector different viruses [44, 45] , this second scenario opens the exciting possibility that virus genes involved in the ichnovirus biology might correspond to a gene patchwork resulting from transfers from viruses belonging to different NCLDV and non-NCLVD families. Indeed, they match an evolutionary scenario of endosymbiogenesis during which, from a single integration event of symbiotic virus genome, viral genes were lost and/or translocated from the provirus to other chromosomal regions (Fig. 5 ).


id: cord-005281-wy0zk9p8
author: Blinov, V. M.
title: Viral component of the human genome
date: 2017-05-09
extension: .txt
mime: text/plain
words: 6592
sentence: 235
flesch: 37
cache: cache/cord-005281-wy0zk9p8.txt
txt: txt/cord-005281-wy0zk9p8.txt
summary:
  The reverse process, i.e., the acquisition of host genes or shorter sequences by viruses, is also possible, although viral genomes obviously have a lower abso-lute capacity for storing the acquired material. However, these relations are in fact two-sided and involve modifications of both the virus and host genomes.


id: cord-348515-bqqyly23
author: Zhao, Suhui
date: 2014-12-08
extension: .txt
mime: text/plain
words: 6584
sentence: 219
flesch: 34
cache: cache/cord-348515-bqqyly23.txt
txt: txt/cord-348515-bqqyly23.txt
title:
  Re-emergent Human Adenovirus Genome Type 7d Caused an Acute Respiratory Disease Outbreak in Southern China After a Twenty-one Year Absence

summary:
  As an example, a higher mortality rate was reported for children infected by HAdV-7 in China during and also in Korea (Seoul) during 1990-2000, with mortality rates of 18%, caused by HAdV-7 genome types 7d and 7l, as compared with 3.6% noted for HAdV-3 infections 15 . Although seemingly antiquated in comparison to genome sequencing, REA profiles are still useful for comparisons with unsequenced but previously reported genome types and strains, and also as rapid and less-expensive alternatives for large-scale characterizations of viruses given a correct reference strain.


id: cord-281959-g4sjyytr
author: Phillippy, Adam M
title: Efficient oligonucleotide probe selection for pan-genomic tiling arrays
date: 2009-09-16
extension: .txt
mime: text/plain
words: 7401
sentence: 309
flesch: 51
cache: cache/cord-281959-g4sjyytr.txt
txt: txt/cord-281959-g4sjyytr.txt
summary:
  For example, probe coverage can be redefined as the number of genomes a probe targets, rather than the number of windows, and probes targeting multiple windows in the same genome can be appropriately downweighted. This bacterial species is particularly well suited for pan-genome array design because there are a remarkable number of strains that have been sequenced.


id: cord-304607-td0776wj
author: Paszkiewicz, Konrad H.
title: Omics, Bioinformatics, and Infectious Disease Research
date: 2010-12-24
extension: .txt
mime: text/plain
words: 7023
sentence: 274
flesch: 39
cache: cache/cord-304607-td0776wj.txt
txt: txt/cord-304607-td0776wj.txt
summary:
  In addition, 21 nonannotated regions had clear levels of transcription and should therefore be considered as genes (Passalacqua et al., 2009) . Indeed, the first bacterial genomes sequenced were those from pathogens Fraser et al., 1995; Tomb et al., 1997) , and these were preceded by many bacteriophage genomes such as bacteriophage MS2 (Fiers et al., 1976) and ϕX174 (Sanger et al., 1977) and viral genomes (Fiers et al., 1978) .


id: cord-016798-tv2ntug6
author: Gautam, Ablesh
title: Bioinformatics Applications in Advancing Animal Virus Research
date: 2019-06-06
extension: .txt
mime: text/plain
words: 6983
sentence: 270
flesch: 35
cache: cache/cord-016798-tv2ntug6.txt
txt: txt/cord-016798-tv2ntug6.txt
summary:
  VIDA retrieves virus sequences from GenBank and the files are parsed into subfields. VIDA also provides functional classification of virus proteins into broad functional classes based on typical virus processes such as DNA and RNA replication, virus structural proteins, nucleotide and nucleic acid metabolism, transcription, glycoproteins and others.


id: cord-003316-r5te5xob
author: Balloux, Francois
title: From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic
date: 2018-12-17
extension: .txt
mime: text/plain
words: 7342
sentence: 270
flesch: 29
cache: cache/cord-003316-r5te5xob.txt
txt: txt/cord-003316-r5te5xob.txt
summary:
  However, a micro-costing analysis covering laboratory and personnel costs estimated the cost of clinical WGS to £481 per M. tuberculosis isolate versus £518 applying standard methods, representing relatively marginal cost savings but with significant time savings [63] . Somewhat ironically, the extremely rich information of WGS data, with every genome being unique, generates problems of its own.


id: cord-018804-wj35q88f
author: Lázaro, Ester
date: 2007
extension: .txt
mime: text/plain
words: 8515
sentence: 379
flesch: 43
cache: cache/cord-018804-wj35q88f.txt
txt: txt/cord-018804-wj35q88f.txt
title:
  Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity

summary:
  Finally, the heterogeneity of RNA virus populations makes it also difficult to eradicate diseases with antiviral drugs, due to the emergence of drug-resistant mutants [10] , a problem that will be treated in more detail in the next sections. Analysis of RNA virus populations, either at the phenotypic or genotypic level showed that these populations have a structure similar to the molecular quasi-species described theoretically


id: cord-017932-vmtjc8ct
author: Georgiev, Vassil St.
title: Genomic and Postgenomic Research
date: 2009
extension: .txt
mime: text/plain
words: 8483
sentence: 292
flesch: 30
cache: cache/cord-017932-vmtjc8ct.txt
txt: txt/cord-017932-vmtjc8ct.txt
summary:
  Next, these gene predictions can be further refined by searching for nearby regulatory sites such as the ribosome-binding sites, as well as by aligning protein sequences to other species. Large-scale prepublication information on genome sequences is a unique research resource for the scientific community, and rapid and unrestricted sharing of microbial genome sequence data is essential for advancing research on infectious agents responsible for human disease.


id: cord-016588-f8uvhstb
author: Sintchenko, Vitali
title: Informatics for Infectious Disease Research and Control
date: 2009-10-03
extension: .txt
mime: text/plain
words: 8187
sentence: 261
flesch: 25
cache: cache/cord-016588-f8uvhstb.txt
txt: txt/cord-016588-f8uvhstb.txt
summary:
  These tools use either a statistical approach, in which the inferred model and prediction are 1 Informatics for Infectious Disease Research and Control treated as regression problems, or machine learning algorithms, in which the model is addressed as a classification problem (Sintchenko et al. 2008a) . ualberta.ca/basys/cgi/submit.pl) also support comparative analysis and the automated annotation of bacterial genomic (chromosomal and plasmid) sequences (Van Domselaar et al. 2005) .


id: cord-018437-yjvwa1ot
author: Mitchell, Michael
title: Taxonomy
date: 2013-08-26
extension: .txt
mime: text/plain
words: 9285
sentence: 420
flesch: 42
cache: cache/cord-018437-yjvwa1ot.txt
txt: txt/cord-018437-yjvwa1ot.txt
summary:
  Structure-function relations The DNA sequence of human herpesvirus-6: structure, coding content, and genome evolution Processing of genome 5′ termini as a strategy of negative-strand RNA viruses to avoid RIG-Idependent interferon induction Respiratory syncytial virus and parainfl uenza virus Infl uenza virus, Chap 42 Global and regional distribution of HIV-1 genetic subtypes and recombinants in Parainfl uenza viruses Gene mapping of the putative structural region of the hepatitis C virus genome by in vitro processing analysis Evolutionary history and phylogeography of human viruses What does virus evolution tell us about virus origins? Nucleotide sequence and genome organization of human parvovirus B19 isolated from the serum of a child during aplastic crisis CXCR4 as a functional coreceptor for human immunodeficiency virus type 1 infection of primary macrophages The genome length of human parainfl uenza virus type 2 follows the rule of six, and recombinant viruses recovered from non-poly-hexameric-length antigenomic cDNAs contain a biased distribution of correcting mutations Respiratory syncytial virus nonstructural proteins decrease levels of multiple members of the cellular interferon pathways Infl uenza virus evolution, host adaptation, and pandemic formation Mechanisms and enzymes involved in SARS coronavirus genome expression


id: cord-310406-5pvln91x
author: Asbury, Thomas M
date: 2010-09-02
extension: .txt
mime: text/plain
words: 3016
sentence: 142
flesch: 39
cache: cache/cord-310406-5pvln91x.txt
txt: txt/cord-310406-5pvln91x.txt
title:
  Genome3D: A viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome

summary:
  Background A significant portion of genomic data that is currently being generated extends beyond traditional primary sequence information. To meet these challenges, Genome3D manipulates and displays genomic data at multiple resolutions.


id: cord-264746-gfn312aa
author: Muse, Spencer
title: GENOMICS AND BIOINFORMATICS
date: 2012-03-29
extension: .txt
mime: text/plain
words: 10983
sentence: 501
flesch: 54
cache: cache/cord-264746-gfn312aa.txt
txt: txt/cord-264746-gfn312aa.txt
summary:
  In addition to providing storage and retrieval of gene sequences, several of these databases also offer advanced sequence analysis methods and powerful visualization tools. However, if two or more such distantly related organisms have gene sequences that are nearly identical, a strong argument can be made that the gene is critical in both organisms and that the same function has been maintained throughout evolutionary history.


id: cord-318392-r9bbomvk
author: Woo, Patrick CY
date: 2017-06-21
extension: .txt
mime: text/plain
words: 3781
sentence: 130
flesch: 45
cache: cache/cord-318392-r9bbomvk.txt
txt: txt/cord-318392-r9bbomvk.txt
title:
  Coronavirus HKU15 in respiratory tract of pigs and first discovery of coronavirus quasispecies in 5′-untranslated region

summary:
  The presence of the virus in respiratory samples provides an alternative clinical sample to confirm the diagnosis of Coronavirus HKU15 infection. Third, the presence of the virus in respiratory samples provides an alternative clinical sample to confirm the diagnosis of Coronavirus HKU15 infection.


id: cord-297669-22fctxk4
author: Proudfoot, Chris
title: Genome editing for disease resistance in pigs and chickens
date: 2019-06-25
extension: .txt
mime: text/plain
words: 4555
sentence: 185
flesch: 38
cache: cache/cord-297669-22fctxk4.txt
txt: txt/cord-297669-22fctxk4.txt
summary:
  CD163 consists of nine globular domains, organized like beads on a string, with domain 5 determined to mediate the key-lock interaction allowing viral entry into pig cells (Van Gorp et al., 2010) . Technical improvements in the generation of genome editing animals will undoubtedly reduce the cost implications of this technology.


id: cord-269124-oreg7rnj
author: Spyrou, Maria A.
title: Ancient pathogen genomics as an emerging tool for infectious disease research
date: 2019-04-05
extension: .txt
mime: text/plain
words: 11937
sentence: 362
flesch: 32
cache: cache/cord-269124-oreg7rnj.txt
txt: txt/cord-269124-oreg7rnj.txt
summary:
  In this Review, we discuss methodological advancements, persistent challenges and novel revelations gained through the study of ancient pathogen genomes. In the absence of ancient pathogen genomes, the tim ings of infectious disease emergence and early spread are inferred mainly through comparative genomics of modern pathogen diversity 92, 93 , palaeopathological eval uation of ancient skeletal remains 94 or analysis of his torical records 95, 96 .


id: cord-330312-1pjolkql
author: Liu, Y.-T.
title: Infectious Disease Genomics
date: 2017-01-20
extension: .txt
mime: text/plain
words: 5181
sentence: 208
flesch: 36
cache: cache/cord-330312-1pjolkql.txt
txt: txt/cord-330312-1pjolkql.txt
summary:
  16, 17 The genomes of human malaria parasite Plasmodium falciparum and its major mosquito vector Anopheles gambiae were published in 2002. In order to understand potential functions of human genes through comparative sequence analyses, they also advised that the HGP must not be restricted to the human genome and should include model organisms including mouse, bacteria, yeast, fruit fly, and worm.


id: cord-346335-el45v0a5
author: Tan, H.S.
title: Fourier spectral density of the coronavirus genome
date: 2020-08-11
extension: .txt
mime: text/plain
words: 4647
sentence: 161
flesch: 47
cache: cache/cord-346335-el45v0a5.txt
txt: txt/cord-346335-el45v0a5.txt
summary:
  Beyond the specific linear form of the correlation function postulated in (6), it is also representative of a large class of correlation functions of the form where τ ≡ l − j,κ is a small constant andτ =κ |τ | M . Thus, (6) could approximate correlation functions of the general form F κ |τ | M whereκ is a small dimensionless parameter, and For example, if the correlation function turns out to be an exponentially decaying function of the form e − B|τ | M with B 1, then to a good approximation we can identify κ ∼ B. The power-law decay in (A) parametrizes the decay of the envelope whereas the model in (6) could account for non-vanishing local minima in the low-frequency domain.


id: cord-350747-5t5xthk6
author: Gmyl, A. P.
title: Diverse Mechanisms of RNA Recombination
date: 2005
extension: .txt
mime: text/plain
words: 8188
sentence: 358
flesch: 36
cache: cache/cord-350747-5t5xthk6.txt
txt: txt/cord-350747-5t5xthk6.txt
summary:
  Studies of crosses between a normal horse serum-resistant mutant and several guanidine-resistant mutants of the same strain Evidence of genetic recombination in foot-and-mouth disease virus A genetic map of poliovirus temperature-sensitive mutants Biochemical evidence for intertypic genetic recombination of polioviruses Intertypic recombination in poliovirus: Genetic and biochemical studies Multiple sites of recombination within the RNA genome of foot-and-mouth disease virus Analysis of oligonucleotide maps as a method for identifying intertypic recombination in poliovirus The primary structure of crossover region in the genome of two intertypic polyovirus recombinants The primary structure of crossover regions of intertypic poliovirus recombinants: A model of recombination between RNA genomes The mechanism of RNA recombination in poliovirus Genetics of picornaviruses Recombination between RNA genomes RNA recombination in animal and plant viruses Recombination and other genomic rearrangements in picornaviruses Evolutionary aspects of recombination in RNA viruses Phylogenetic analysis reveals a low rate of homologous recombination in negative-sense RNA virus New insights into the mechanisms of RNA recombination How RNA viruses exchange their genetic material Heterologous recombination in the doublestranded RNA bacteriophage phi 6 Recombination in bacteriophage Qβ its satellite RNAs: It was believed until recently that the only possible mechanism of RNA recombination is replicative template switching, with synthesis of a complementary strand starting on one viral RNA molecule and being completed on another.


id: cord-275683-1qj9ri18
author: Roux, Simon
title: Metagenomics in Virology
date: 2019-06-12
extension: .txt
mime: text/plain
words: 5893
sentence: 189
flesch: 32
cache: cache/cord-275683-1qj9ri18.txt
txt: txt/cord-275683-1qj9ri18.txt
summary:
  Viromes provide a deeper description of the virus community, since most of the sequencing data will be obtained from virus genomes. While the analyses outlined above were foundational for our current understanding of virus diversity, they were limited by the short length of next-generation sequencing reads which fragmented the view of viral genomes.


id: cord-352619-s2x53grh
author: Payne, Natalie
title: Novel Circoviruses Detected in Feces of Sonoran Felids
date: 2020-09-15
extension: .txt
mime: text/plain
words: 3266
sentence: 124
flesch: 37
cache: cache/cord-352619-s2x53grh.txt
txt: txt/cord-352619-s2x53grh.txt
summary:
  Phylogenetic analyses reveal that one circovirus species is more closely related to rodent associated circoviruses and the other to bat associated circoviruses, sharing highest genome-wide pairwise identity of approximately 70% and 63%, respectively. [12] and antibodies to CDV, feline panleukopenia virus, feline calicivirus, and feline enteric coronavirus have been detected in pumas from southern Arizona [13] , other viruses circulating in populations of Sonoran felids are largely unknown.


id: cord-015850-ef6svn8f
author: Saitou, Naruya
title: Eukaryote Genomes
date: 2013-08-22
extension: .txt
mime: text/plain
words: 7442
sentence: 359
flesch: 48
cache: cache/cord-015850-ef6svn8f.txt
txt: txt/cord-015850-ef6svn8f.txt
summary:
  The complete nucleotide sequence of the tobacco mitochondrial genome: Comparative analysis of mitochondrial genomes in higher plants and multipartite organization Widespread horizontal transfer of mitochondrial genes in fl owering plants Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin Small, repetitive DNAs contribute signifi cantly to the expanded mitochondrial genome of cucumber The complete nucleotide sequence of the tobacco chloroplast genome: Its gene organization and expression Changes in the structure of DNA molecules and the amount of DNA per plastid during chloroplast development in maize Pattern of organization of human mitochondrial pseudogenes in the nuclear genome Why genes in pieces? Introns. As for plants, Kaplinsky [ 62 ] ) compared genome sequences of Arabidopsis, grape rice, and Brachypodium and found >100 times more abundant CNSs from monocots than dicots.


id: cord-304498-ty41xob0
author: Denison, Mark R
title: Coronaviruses: An RNA proofreading machine regulates replication fidelity and diversity
date: 2011-03-01
extension: .txt
mime: text/plain
words: 7361
sentence: 219
flesch: 26
cache: cache/cord-304498-ty41xob0.txt
txt: txt/cord-304498-ty41xob0.txt
summary:
  This review will discuss the role of RNA replication fidelity in RNA virus replication and pathogenesis, and will focus on a novel exoribonuclease universally encoded within CoV genomes that likely mediates RNA-dependent RNA proofreading during virus replication. key: cord-304498-ty41xob0 authors: Denison, Mark R; Graham, Rachel L; Donaldson, Eric F; Eckerle, Lance D; Baric, Ralph S title: Coronaviruses: An RNA proofreading machine regulates replication fidelity and diversity date: 2011-03-01 journal: RNA Biology DOI: 10.4161/rna.8.2.15013 sha: doc_id: 304498 cord_uid: ty41xob0 In order to survive and propagate, RNA viruses must achieve a balance between the capacity for adaptation to new environmental conditions or host cells with the need to maintain an intact and replication competent genome.


id: cord-340423-f8ab7413
author: Barr, J.N.
title: Genetic Instability of RNA Viruses
date: 2016-09-09
extension: .txt
mime: text/plain
words: 9780
sentence: 380
flesch: 40
cache: cache/cord-340423-f8ab7413.txt
txt: txt/cord-340423-f8ab7413.txt
summary:
  Sequence analysis of RNA virus genomes has revealed that they preferentially accumulate A-to-G transitions, which are characteristic hallmarks of ADAR activity. Because the majority of nucleotide changes in RNA virus genomes are either strongly deleterious or lethal, the population is perpetually refined as deleterious genomes become purged through selection, leaving only mutations with phenotypically neutral or advantageous consequences to persist [69, 70] .


id: cord-302047-vv5gpldi
author: Willemsen, Anouk
title: On the stability of sequences inserted into viral genomes
date: 2019-11-14
extension: .txt
mime: text/plain
words: 12562
sentence: 416
flesch: 34
cache: cache/cord-302047-vv5gpldi.txt
txt: txt/cord-302047-vv5gpldi.txt
summary:
  However, genomic deletions that disrupt the inserted sequence will be subject to less constraints, as for example they can disrupt the reading frame of the insert without affecting the expression of virus genes. A large number of virus genomes have been engineered to carry additional sequences for a variety of purposes.


id: cord-334394-qgyzk7th
author: Edgar, Robert C.
title: Petabase-scale sequence alignment catalyses viral discovery
date: 2020-08-10
extension: .txt
mime: text/plain
words: 8139
sentence: 369
flesch: 49
cache: cache/cord-334394-qgyzk7th.txt
txt: txt/cord-334394-qgyzk7th.txt
summary:
  Innovative fields such as high-throughput functional viromics [39] leverage these broad and rapidly growing collections of viral sequences, and can inform evidence-based policies responding to emerging pandemics [40, 41] . Accurate annotation of CoV genomes is challenging due to ribosomal frameshifts and polyproteins which are cleaved into maturation proteins [56] , and thus previously-annotated viral genomes offer a guide to accurate gene-calls and protein functional predictions.


id: cord-314594-xvc8hvpq
author: Singh, Roshan Kumar
title: Breeding and biotechnological interventions for trait improvement: status and prospects
date: 2020-09-18
extension: .txt
mime: text/plain
words: 9532
sentence: 286
flesch: 26
cache: cache/cord-314594-xvc8hvpq.txt
txt: txt/cord-314594-xvc8hvpq.txt
summary:
  Various modern NGS-driven QTL mapping strategies like bulk population resequencing: QTL-seq, individual population resequencing, and MutMap utilizing bi-parental mapping and mutant populations are found expedient for identification of major QTLs modulating agronomic traits in crop plants. These markers enabled the development of high-density genetic maps useful for mapping of target genes and utilize them in crop breeding.


id: cord-316033-xg8eb2nm
author: Easton, Alice
date: 2020-11-06
extension: .txt
mime: text/plain
words: 10463
sentence: 353
flesch: 35
cache: cache/cord-316033-xg8eb2nm.txt
txt: txt/cord-316033-xg8eb2nm.txt
title:
  Molecular evidence of hybridization between pig and human Ascaris indicates an interbred species complex infecting humans

summary:
  Previous studies using Ascaris mitochondrial genomes or genes suggest there are A. lumbricoides-type (human-associated) and A. suum-type (pig-associated) clades (Anderson and Jaenike, 1997; Cavallero et al., 2013; Zhou et al., 2011) . Draft A. suum genomes have previously been constructed from worms obtained from pigs in Australia (Jex et al., 2011) and in the United States Wang et al., 2012) .


id: cord-016293-pyb00pt5
author: Newell-McGloughlin, Martina
title: The flowering of the age of Biotechnology 1990–2000
date: 2006
extension: .txt
mime: text/plain
words: 22413
sentence: 857
flesch: 45
cache: cache/cord-016293-pyb00pt5.txt
txt: txt/cord-016293-pyb00pt5.txt
summary:
  These DNA chips have broad commercial applications and are now used in many areas of basic and clinical research including the detection of drug resistance mutations in infectious organisms, direct DNA sequence comparison of large segments of the human genome, the monitoring of multiple human genes for disease associated mutations, the quantitative and parallel measurement of mRNA expression for thousands of human genes, and the physical and genetic mapping of genomes. Of course for such a radical approach certain basal level criteria needed to be established for selecting disease candidates for human gene therapy.


id: cord-022128-r8el8nqm
author: Domingo, Esteban
title: Molecular basis of genetic variation of viruses: error-prone replication
date: 2019-11-08
extension: .txt
mime: text/plain
words: 17674
sentence: 576
flesch: 30
cache: cache/cord-022128-r8el8nqm.txt
txt: txt/cord-022128-r8el8nqm.txt
summary:
  Mechanisms and Consequences Structure-function relationships underlying the replication fidelity of viral RNAdependent RNA polymerases Phage as agents of lateral gene transfer Incorporation fidelity of the viral RNA-dependent RNA polymerase: a kinetic, thermodynamic and structural perspective Mutations and A/I hypermutations in measles virus persistent infections Evolution of sex in RNA viruses Viral RNAdirected RNA polymerases use diverse mechanisms to promote recombination between RNA molecules Insertion/deletion frequencies match those of point mutations in the hypervariable regions of the simian immunodeficiency virus surface envelope gene Arbovirus high fidelity variant loses fitness in mosquitoes and mice Genetic variation in retroviruses Variation in RNA virus mutation rates across host cells Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection The vaccinia virus DNA polymerase and its processivity factor Silent mutations in sight: co-variations in tRNA abundance as a key to unravel consequences of silent mutations Improvement of phi29 DNA polymerase amplification performance by fusion of DNA binding motifs Linking RNA sequence, structure, and function on massively parallel highthroughput sequences Defective interfering influenza virus RNAs: time to reevaluate their clinical potential as broad-spectrum antivirals? Virus entry into error catastrophe as a new antiviral strategy Viral Quasispecies Nucleotide sequence heterogeneity of an RNA phage population Genetic variability and antigenic diversity of foot-and-mouth disease virus Quasispecies: the concept and the word Quasispecies and RNA Virus Evolution: Principles and Consequences Evolution of footand-mouth disease virus Viral quasispecies: dynamics, interactions and pathogenesis A constant rate of spontaneous mutation in DNA-based microbes Mutation rates among RNA viruses Detenction of truncated virus particles in a persistent RNA virus infection in vivo Evolvability is a selectable trait High fidelity of murine hepatitis virus replication is decreased in nsp14 exoribonuclease mutants Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing Error catastrophe and antiviral strategy Sequence space and quasispecies distribution Adaptive value of high mutation rates of RNA viruses: separating causes from consequences Multiple molecular pathways for fitness recovery of an RNA virus debilitated by operation of Muller's ratchet RT-PCR amplification and cloning of large viral sequences Adaptation of mRNA structure to control protein folding A comparison of viral RNA-dependent RNA polymerases Structural insights into replication initiation and elongation processes by the FMDV RNA-dependent RNA polymerase Random mutagenesis using error-prone DNA polymerases Specialized DNA polymerases, cellular survival, and the genesis of mutations DNA Repair and Mutagenesis Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection Extremely high mutation rate of a hammerhead viroid RNA recombination in vivo in the absence of viral replication Comparative analysis of the molecular mechanisms of recombination in hepatitis C virus DNA replication-a matter of fidelity Evolutionary transition toward defective RNAs that are infectious by complementation Information dynamics in carcinogenesis and tumor growth Evolution of circulating wild poliovirus and of vaccine-derived poliovirus in an immunodeficient patient: a unifying model In-depth, longitudinal analysis of viral quasispecies from an individual triply infected with late-stage human immunodeficiency virus type 1, using a multiple PCR primer approach Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution Molecular Basis of Virus Evolution Functional and genetic plasticities of the poliovirus genome: quasi-infectious RNAs modified in the 5'-untranslated region yield a variety of pseudorevertants Nonreplicative homologous RNA recombination: promiscuous joining of RNA pieces? Mutation frequencies measured by subjecting virus to a specific selective agent (e.g., mutants that escape the neutralizing activity of a monoclonal antibody or mutants that escape inhibition by a drug) span a broad range of values (10 À 3 to 10 À 8 ) for DNA and RNA viruses (Smith and Inglis, 1987; Sarisky et al., 2000; Domingo et al., 2001) (Table 2 .1).


id: cord-022262-ck2lhojz
author: Gromeier, Matthias
title: Genetics, Pathogenesis and Evolution of Picornaviruses
date: 2007-09-02
extension: .txt
mime: text/plain
words: 28053
sentence: 1027
flesch: 39
cache: cache/cord-022262-ck2lhojz.txt
txt: txt/cord-022262-ck2lhojz.txt
summary:
  With this experiment, reverse genetics of RNA viruses was born as the RNA genome was now amenable to manipulations developed for DNA. As is discussed in Chapter 7, this phenomenon has profound biological consequences for RNA viruses.


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