LIVIVO - Search results -

Search results

Result 1 - 10 of total 31

Search options

Article ; Online: Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition.

Lee, Jover / Hadfield, James / Black, Allison / Sibley, Thomas R / Neher, Richard A / Bedford, Trevor / Huddleston, John

Frontiers in bioinformatics

2023 Volume 3, Page(s) 1069487

Abstract: Seasonal influenza vaccines must be updated regularly to account for mutations that allow influenza viruses to escape our existing immunity. A successful vaccine should represent the genetic diversity of recently circulating viruses and induce antibodies ...

Abstract	Seasonal influenza vaccines must be updated regularly to account for mutations that allow influenza viruses to escape our existing immunity. A successful vaccine should represent the genetic diversity of recently circulating viruses and induce antibodies that effectively prevent infection by those recent viruses. Thus, linking the genetic composition of circulating viruses and the serological experimental results measuring antibody efficacy is crucial to the vaccine design decision. Historically, genetic and serological data have been presented separately in the form of static visualizations of phylogenetic trees and tabular serological results to identify vaccine candidates. To simplify this decision-making process, we have created an interactive tool for visualizing serological data that has been integrated into Nextstrain's real-time phylogenetic visualization framework, Auspice. We show how the combined interactive visualizations may be used by decision makers to explore the relationships between complex data sets for both prospective vaccine virus selection and retrospectively exploring the performance of vaccine viruses.
Language	English
Publishing date	2023-03-22
Publishing country	Switzerland
Document type	Journal Article
ISSN	2673-7647
ISSN (online)	2673-7647
DOI	10.3389/fbinf.2023.1069487
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Ten recommendations for supporting open pathogen genomic analysis in public health.

Black, Allison / MacCannell, Duncan R / Sibley, Thomas R / Bedford, Trevor

Nature medicine

2020 Volume 26, Issue 6, Page(s) 832–841

Abstract: Increasingly, public-health agencies are using pathogen genomic sequence data to support surveillance and epidemiological investigations. As access to whole-genome sequencing has grown, greater amounts of molecular data have helped improve the ability to ...

Abstract	Increasingly, public-health agencies are using pathogen genomic sequence data to support surveillance and epidemiological investigations. As access to whole-genome sequencing has grown, greater amounts of molecular data have helped improve the ability to detect and track outbreaks of diseases such as COVID-19, investigate transmission chains and explore large-scale population dynamics, such as the spread of antibiotic resistance. However, the wide adoption of whole-genome sequencing also poses new challenges for public-health agencies that must adapt to support a new set of expertise, which means that the capacity to perform genomic data assembly and analysis has not expanded as widely as the adoption of sequencing itself. In this Perspective, we make recommendations for developing an accessible, unified informatic ecosystem to support pathogen genomic analysis in public-health agencies across income settings. We hope that the creation of this ecosystem will allow agencies to effectively and efficiently share data, workflows and analyses and thereby increase the reproducibility, accessibility and auditability of pathogen genomic analysis while also supporting agency autonomy.
MeSH term(s)	Betacoronavirus/genetics ; Betacoronavirus/pathogenicity ; COVID-19 ; Coronavirus Infections/epidemiology ; Coronavirus Infections/genetics ; Coronavirus Infections/transmission ; Coronavirus Infections/virology ; Disease Outbreaks ; Drug Resistance, Microbial/genetics ; Genomics ; Humans ; Pandemics ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/genetics ; Pneumonia, Viral/transmission ; Pneumonia, Viral/virology ; Population Dynamics ; SARS-CoV-2 ; Whole Genome Sequencing
Keywords	covid19
Language	English
Publishing date	2020-06-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	1220066-9
ISSN	1546-170X ; 1078-8956
ISSN (online)	1546-170X
ISSN	1078-8956
DOI	10.1038/s41591-020-0935-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 4212: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 39: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: ISDB: a database toolkit for storing and analyzing viral integration site data.

Sibley, Thomas R / Silberman, Evan J / Mullins, James I

Bioinformatics (Oxford, England)

2018 Volume 35, Issue 6, Page(s) 1073–1075

Abstract: Summary: We introduce ISDB, a set of software tools for the creation and administration of relational databases of viral integration site (IS) data. Using ISDB, investigators can curate a private database from any heterogeneous set of data sources, ... ...

Abstract	Summary: We introduce ISDB, a set of software tools for the creation and administration of relational databases of viral integration site (IS) data. Using ISDB, investigators can curate a private database from any heterogeneous set of data sources, including previously-published datasets and internal, work-in-progress data. To make data visible and accessible to collaborators with varying degrees of computational expertise, ISDB automatically generates web sites describing database contents and data exports in several common formats. Compared to a public depository database, the ability to build local, private databases makes ISDB suitable for use in testing hypotheses and developing analyses in the long pre-publication phase of most research. Availability and implementation: Installation and usage documentation for ISDB are provided on our website https://mullinslab.microbiol.washington.edu/isdb/. Source code is available under the open source MIT license from https://github.com/MullinsLab/ISDB. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Databases, Factual ; Genome ; Software ; Virus Integration
Language	English
Publishing date	2018-08-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/bty712
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2374: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: ISDB: a database toolkit for storing and analyzing viral integration site data

Sibley, Thomas R. / Silberman, Evan J. / Mullins, James I.

Bioinformatics. 2019 Mar. 15, v. 35, no. 6, p. 1073-1075

2019 , Page(s) 1073–1075

Abstract: We introduce ISDB, a set of software tools for the creation and administration of relational databases of viral integration site (IS) data. Using ISDB, investigators can curate a private database from any heterogeneous set of data sources, including ... ...

Abstract	We introduce ISDB, a set of software tools for the creation and administration of relational databases of viral integration site (IS) data. Using ISDB, investigators can curate a private database from any heterogeneous set of data sources, including previously-published datasets and internal, work-in-progress data. To make data visible and accessible to collaborators with varying degrees of computational expertise, ISDB automatically generates web sites describing database contents and data exports in several common formats. Compared to a public depository database, the ability to build local, private databases makes ISDB suitable for use in testing hypotheses and developing analyses in the long pre-publication phase of most research. Installation and usage documentation for ISDB are provided on our website https://mullinslab.microbiol.washington.edu/isdb/. Source code is available under the open source MIT license from https://github.com/MullinsLab/ISDB. Supplementary data are available at Bioinformatics online.
Keywords	Internet ; bioinformatics ; computer software ; data collection ; databases
Language	English
Dates of publication	2019-0315
Size	p. 1073-1075
Publishing place	Oxford University Press
Document type	Article ; Online
Note	NAL-AP-2-clean ; Use and reproduction
ZDB-ID	1468345-3
ISSN	1367-4811 ; 1460-2059
ISSN	1367-4811 ; 1460-2059
DOI	10.1093/bioinformatics/bty712
Database	NAL-Catalogue (AGRICOLA)

Order via subito

Article: Ten recommendations for supporting open pathogen genomic analysis in public health

Black, Allison / MacCannell, Duncan R / Sibley, Thomas R / Bedford, Trevor

Nat Med

Abstract	Increasingly, public-health agencies are using pathogen genomic sequence data to support surveillance and epidemiological investigations. As access to whole-genome sequencing has grown, greater amounts of molecular data have helped improve the ability to detect and track outbreaks of diseases such as COVID-19, investigate transmission chains and explore large-scale population dynamics, such as the spread of antibiotic resistance. However, the wide adoption of whole-genome sequencing also poses new challenges for public-health agencies that must adapt to support a new set of expertise, which means that the capacity to perform genomic data assembly and analysis has not expanded as widely as the adoption of sequencing itself. In this Perspective, we make recommendations for developing an accessible, unified informatic ecosystem to support pathogen genomic analysis in public-health agencies across income settings. We hope that the creation of this ecosystem will allow agencies to effectively and efficiently share data, workflows and analyses and thereby increase the reproducibility, accessibility and auditability of pathogen genomic analysis while also supporting agency autonomy.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #594839
Database	COVID19

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

Article: Streptococcus pneumoniae

Frontiers in pediatrics

2023 Volume 11, Page(s) 1198278

Abstract: Background: Respiratory viruses might influence : Methods: From November 2019-June 2021, we enrolled participants in a remote household surveillance study of respiratory pathogens. Participants submitted weekly reports of acute respiratory illness ( ... ...

Abstract	Background: Respiratory viruses might influence Methods: From November 2019-June 2021, we enrolled participants in a remote household surveillance study of respiratory pathogens. Participants submitted weekly reports of acute respiratory illness (ARI) symptoms. Mid-turbinate or anterior nasal swabs were self-collected at enrollment, when ARI occurred, and, in the second year of the study only, from household contacts after SARS-CoV-2 was detected in a household member. Specimens were tested using multiplex reverse-transcription PCR for respiratory pathogens, including Results: We collected 346 swabs from 239 individuals in 151 households that tested positive for Conclusion: Detection of common respiratory viruses was associated with greater concurrent
Language	English
Publishing date	2023-07-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2711999-3
ISSN	2296-2360
ISSN	2296-2360
DOI	10.3389/fped.2023.1198278
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens.

Huddleston, John / Hadfield, James / Sibley, Thomas R / Lee, Jover / Fay, Kairsten / Ilcisin, Misja / Harkins, Elias / Bedford, Trevor / Neher, Richard A / Hodcroft, Emma B

Journal of open source software

2021 Volume 6, Issue 57

Abstract: The analysis of human pathogens requires a diverse collection of bioinformatics tools. These tools include standard genomic and phylogenetic software and custom software developed to handle the relatively numerous and short genomes of viruses and ... ...

Abstract	The analysis of human pathogens requires a diverse collection of bioinformatics tools. These tools include standard genomic and phylogenetic software and custom software developed to handle the relatively numerous and short genomes of viruses and bacteria. Researchers increasingly depend on the outputs of these tools to infer transmission dynamics of human diseases and make actionable recommendations to public health officials (Black et al., 2020; Gardy et al., 2015). In order to enable real-time analyses of pathogen evolution, bioinformatics tools must scale rapidly with the number of samples and be flexible enough to adapt to a variety of questions and organisms. To meet these needs, we developed Augur, a bioinformatics toolkit designed for phylogenetic analyses of human pathogens.
Language	English
Publishing date	2021-01-07
Publishing country	United States
Document type	Journal Article
ISSN	2475-9066
ISSN	2475-9066
DOI	10.21105/joss.02906
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Effects of weather-related social distancing on city-scale transmission of respiratory viruses: a retrospective cohort study.

Jackson, Michael L / Hart, Gregory R / McCulloch, Denise J / Adler, Amanda / Brandstetter, Elisabeth / Fay, Kairsten / Han, Peter / Lacombe, Kirsten / Lee, Jover / Sibley, Thomas R / Nickerson, Deborah A / Rieder, Mark J / Starita, Lea / Englund, Janet A / Bedford, Trevor / Chu, Helen / Famulare, Michael

BMC infectious diseases

2021 Volume 21, Issue 1, Page(s) 335

Abstract: Background: Unusually high snowfall in western Washington State in February 2019 led to widespread school and workplace closures. We assessed the impact of social distancing caused by this extreme weather event on the transmission of respiratory viruses. ...

Abstract	Background: Unusually high snowfall in western Washington State in February 2019 led to widespread school and workplace closures. We assessed the impact of social distancing caused by this extreme weather event on the transmission of respiratory viruses. Methods: Residual specimens from patients evaluated for acute respiratory illness at hospitals in the Seattle metropolitan area were screened for a panel of respiratory viruses. Transmission models were fit to each virus to estimate the magnitude reduction in transmission due to weather-related disruptions. Changes in contact rates and care-seeking were informed by data on local traffic volumes and hospital visits. Results: Disruption in contact patterns reduced effective contact rates during the intervention period by 16 to 95%, and cumulative disease incidence through the remainder of the season by 3 to 9%. Incidence reductions were greatest for viruses that were peaking when the disruption occurred and least for viruses in an early epidemic phase. Conclusion: High-intensity, short-duration social distancing measures may substantially reduce total incidence in a respiratory virus epidemic if implemented near the epidemic peak. For SARS-CoV-2, this suggests that, even when SARS-CoV-2 spread is out of control, implementing short-term disruptions can prevent COVID-19 deaths.
MeSH term(s)	COVID-19 ; Cities ; Epidemics/prevention & control ; Humans ; Incidence ; Models, Theoretical ; Physical Distancing ; Respiratory Tract Infections/transmission ; Respiratory Tract Infections/virology ; Retrospective Studies ; Washington ; Weather
Language	English
Publishing date	2021-04-09
Publishing country	England
Document type	Journal Article
ISSN	1471-2334
ISSN (online)	1471-2334
DOI	10.1186/s12879-021-06028-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Minority and majority pretreatment HIV-1 drug resistance associated with failure of first-line nonnucleoside reverse-transcriptase inhibitor antiretroviral therapy in Kenyan women.

Milne, Ross S / Silverman, Rachel A / Beck, Ingrid A / Mckernan-Mullin, Jennifer / Deng, Wenjie / Sibley, Thomas R / Dross, Sandra / Kiarie, James N / Sakr, Samah R / Coombs, Robert W / Chung, Michael H / Frenkel, Lisa M

AIDS (London, England)

2019 Volume 33, Issue 6, Page(s) 941–951

Abstract: Objectives: Among women initiating first-line nonnucleoside reverse-transcriptase inhibitor (NNRTI)-based-ART with and without a history of single-dose nevirapine (sdNVP) with or without zidovudine with or without lamivudine (ZDV with and without 3TC) ... ...

Abstract	Objectives: Among women initiating first-line nonnucleoside reverse-transcriptase inhibitor (NNRTI)-based-ART with and without a history of single-dose nevirapine (sdNVP) with or without zidovudine with or without lamivudine (ZDV with and without 3TC) for prevention of mother-to-child HIV transmission (PMTCT), we hypothesized that pre-ART HIV-drug resistance would be associated with virologic failure DESIGN/METHODS:: In a prospectively enrolled study, three genotypic drug-resistance assays [oligonucleotide-ligation-assay (OLA), consensus sequencing, and next-generation sequencing by Illumina] were retrospectively performed to detect pre-ART drug resistance. Minority or majority drug-resistant variants identified in pre-ART RNA and/or DNA, a history of antiretrovirals for PMTCT, and other risk factors were assessed for association with virologic failure. Results: Failure occurred in 38/169 (22.5%) women, and was associated with pre-ART drug resistance detected by any assay (OLA of plasma or PBMC, consensus sequencing of PBMC and/or plasma, and next-generation sequencing of PBMC at frequencies of at least 10% and as minority variants; all P < 0.0001). Failure was also associated with PMTCT using sdNVP and ZDV with or without 3TC, but not sdNVP only; however, the longer time-interval between PMTCT and ART initiation observed for sdNVP-only women showed no interaction with failure. Viral loads and OLA of PBMC in longitudinal specimens demonstrated rapid failure and emergence of drug resistance, particularly among sdNVP and ZDV with or without 3TC-experienced women with pre-ART drug-resistant minority variants by next-generation sequencing but without drug resistance by OLA or consensus sequencing. Conclusion: Pre-ART drug resistance was detected similarly by OLA of PBMC or plasma and by consensus sequencing, and was associated with virologic failure soon after initiation of first-line NVP-based ART. A history of sdNVP and ZDV with or without 3TC for PMTCT or minority variants detected by next-generation sequencing identified additional women with failure. These findings emphasize the value of assessing individual antiretroviral history, particularly nonsuppressive antiretrovirals with at least two drug classes, and testing for pre-ART drug resistance, including minority variants.
MeSH term(s)	Adolescent ; Adult ; Anti-Retroviral Agents/pharmacology ; Drug Resistance, Viral ; Female ; Genotype ; Genotyping Techniques ; HIV Infections/drug therapy ; HIV Infections/virology ; HIV-1/drug effects ; HIV-1/genetics ; HIV-1/isolation & purification ; Humans ; Kenya ; Mutation ; Retrospective Studies ; Young Adult
Chemical Substances	Anti-Retroviral Agents
Language	English
Publishing date	2019-04-04
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	639076-6
ISSN	1473-5571 ; 0269-9370 ; 1350-2840
ISSN (online)	1473-5571
ISSN	0269-9370 ; 1350-2840
DOI	10.1097/QAD.0000000000002134
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2228: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article: Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data.

Burstein, Roy / Althouse, Benjamin M / Adler, Amanda / Akullian, Adam / Brandstetter, Elizabeth / Cho, Shari / Emanuels, Anne / Fay, Kairsten / Gamboa, Luis / Han, Peter / Huden, Kristen / Ilcisin, Misja / Izzo, Mandy / Jackson, Michael L / Kim, Ashley E / Kimball, Louise / Lacombe, Kirsten / Lee, Jover / Logue, Jennifer K /

Rogers, Julia / Chung, Erin / Sibley, Thomas R / Van Raay, Katrina / Wenger, Edward / Wolf, Caitlin R / Boeckh, Michael / Chu, Helen / Duchin, Jeff / Rieder, Mark / Shendure, Jay / Starita, Lea M / Viboud, Cecile / Bedford, Trevor / Englund, Janet A / Famulare, Michael

medRxiv : the preprint server for health sciences

2022

Abstract: Background: Co-circulating respiratory pathogens can interfere with or promote each other, leading to important effects on disease epidemiology. Estimating the magnitude of pathogen-pathogen interactions from clinical specimens is challenging because ... ...

Abstract	Background: Co-circulating respiratory pathogens can interfere with or promote each other, leading to important effects on disease epidemiology. Estimating the magnitude of pathogen-pathogen interactions from clinical specimens is challenging because sampling from symptomatic individuals can create biased estimates. Methods: We conducted an observational, cross-sectional study using samples collected by the Seattle Flu Study between 11 November 2018 and 20 August 2021. Samples that tested positive via RT-qPCR for at least one of 17 potential respiratory pathogens were included in this study. Semi-quantitative cycle threshold (Ct) values were used to measure pathogen load. Differences in pathogen load between monoinfected and coinfected samples were assessed using linear regression adjusting for age, season, and recruitment channel. Results: 21,686 samples were positive for at least one potential pathogen. Most prevalent were rhinovirus (33·5%), Conclusions: Viral load data can be used to overcome sampling bias in studies of pathogen-pathogen interactions. When applied to respiratory pathogens, we found evidence of viral-
Language	English
Publishing date	2022-02-06
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.02.04.22270474
Database	MEDical Literature Analysis and Retrieval System OnLINE

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾

To top

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Inter-library loan at ZB MED