Article
Gastroenterology & Hepatology
Jinlong Ru, Mohammadali Khan Mirzaei, Jinling Xue, Xue Peng, Li Deng
Summary: ViroProfiler is a computer analysis tool for analyzing shotgun viral metagenomic data. It can be run on a local or cloud computing environment. It uses containerization technology to ensure computational reproducibility and facilitate collaborative research.
Article
Biochemical Research Methods
Kijin Kim, Kyungmin Park, Seonghyeon Lee, Seung-Hwan Baek, Tae-Hun Lim, Jongwoo Kim, Balachandran Manavalan, Jin-Won Song, Won-Keun Kim
Summary: VirPipe is a new pipeline for detecting viral genomes from Nanopore or Illumina sequencing, with streamlined installation and customization.
Article
Biology
Chen Yang, Theodora Lo, Ka Ming Nip, Saber Hafezqorani, Rene L. Warren, Inanc Birol
Summary: Meta-NanoSim is a fast and versatile utility that characterizes and simulates nanopore metagenomic reads, improving microbial abundance estimation. It can simulate complex microbial communities and shows high congruence with experimental data, facilitating the development of metagenomic algorithms and experimental design.
Article
Biochemical Research Methods
Xu Zhu, Lili Zhao, Lihong Huang, Wenxian Yang, Liansheng Wang, Rongshan Yu
Summary: We developed the cgMSI tool for nanopore metagenomic pathogen detection within species. The tool utilizes a two-stage maximum a posteriori probability estimation method to accurately detect strains and estimate relative abundance at low computational cost.
BMC BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Leon Bichmann, Shubham Gupta, George Rosenberger, Leon Kuchenbecker, Timo Sachsenberg, Phil Ewels, Oliver Alka, Julianus Pfeuffer, Oliver Kohlbacher, Hannes Rost
Summary: DIA is a leading analysis method in biomedical mass spectrometry with advantages such as reproducibility and sensitivity, but its data analysis complexity requires expert knowledge. DIAproteomics is a multifunctional, automated pipeline that allows easy processing of DIA datasets.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Guowei Chen, Xubo Tang, Mang Shi, Yanni Sun
Summary: In this study, we developed VirBot, a simple yet effective RNA virus identification tool based on protein families and adaptive score cutoffs. Compared to seven popular tools for virus identification, VirBot demonstrated high specificity in metagenomic datasets and superior sensitivity in detecting novel RNA viruses on both simulated and real sequencing data.
Article
Biochemical Research Methods
Zoe Yandle, Gabriel Gonzalez, Michael Carr, Jelle Matthijnssens, Cillian De Gascun
Summary: This study developed an unbiased methodology using Oxford Nanopore Technology (ONT) sequencing to obtain whole-genome sequences (WGS) of Rotavirus A (RVA) from clinical samples. The developed protocol generated 146 near-complete RVA WGS out of the 157 RVA-positive clinical samples, with high quality and accuracy. The protocol can be extended to other viral agents in other sample types.
JOURNAL OF VIROLOGICAL METHODS
(2023)
Article
Biology
Guilhem Sempere, Adrien Petel, Magsen Abbe, Pierre Lefeuvre, Philippe Roumagnac, Frederic Mahe, Gael Baurens, Denis Filloux
Summary: metaXplor is a scalable, distributable, fully web-interfaced application for managing, sharing, and exploring metagenomic data. It offers a flexible data model, supports incremental data feeding, allows for exhaustive content browsing, rapid narrowing to find specific records, and features various interactive data visualization tools.
Article
Computer Science, Artificial Intelligence
Huan Min Gan, Senaka Fernando, Miguel Molina-Solana
Summary: This study applies the YOLOv3 object detection algorithm to analyze traffic camera feeds in London, creating Docker pipelines for data extraction and visualization. Different confidence thresholds were found to significantly impact object detections, leading to the successful creation of a large-scale dataset.
EXPERT SYSTEMS WITH APPLICATIONS
(2021)
Article
Biology
Johan Rollin, Wei Rong, Sebastien Massart
Summary: This article introduces a bioinformatics tool called Cont-ID, which can detect cross-contamination by analyzing the relative abundance and duplication of virus sequencing reads in sequence metagenomic datasets. By using 273 real datasets, including 68 virus species from different hosts and several library preparation protocols, the study demonstrates that Cont-ID can accurately classify viral species detection into true infection or contamination, with an accuracy rate of 91%. This classification increases confidence in the detection results and facilitates the downstream interpretation and confirmation by prioritizing the virus detections that should be confirmed.
Article
Computer Science, Hardware & Architecture
Junfeng Li, Dan Li, Huiyou Jiang, Du Lin, Jinkun Geng, Yukai Huang, K. K. Ramakrishnan, Kai Zheng
Summary: With the increase in CPU cores and Ethernet NICs on server machines, the network stack in the kernel has become a bottleneck for high throughput and low latency applications. Moving the network stack out of the kernel poses challenges due to the lack of POSIX API compatibility and the complexity of application transplantation. This work proposes LIGHT, a user-level network stack that achieves both high scalability and compatibility with legacy applications. LIGHT adopts efficient blocking APIs, intercepts network-related APIs, and utilizes FD space separation technique for API redirection. It also utilizes lock-free shared queue based inter-process communication and full connection affinity for high performance. Experiments show that legacy applications can run on LIGHT without modifying source code, and Nginx on LIGHT outperforms the latest kernel stack with significantly higher throughput and lower tail latency.
Article
Ecology
Phil Wilkes, Mathias Disney, John Armston, Harm Bartholomeus, Lisa Bentley, Benjamin Brede, Andrew Burt, Kim Calders, Cecilia Chavana-Bryant, Daniel Clewley, Laura Duncanson, Brieanne Forbes, Sean Krisanski, Yadvinder Malhi, David Moffat, Niall Origo, Alexander Shenkin, Wanxin Yang
Summary: Above-ground biomass (AGB) is an important metric for quantifying carbon storage in terrestrial ecosystems. Terrestrial laser scanning (TLS) has emerged as a disruptive technology that can provide a more accurate assessment of tree and plot scale AGB. This study presents TLS2trees, an automated processing pipeline and set of Python command line tools designed to overcome the challenges in segmenting individual trees from plot-level point clouds. Results show that TLS2trees performs well for larger trees, but segmentation performance decreases for smaller trees. The researchers suggest that an automated processing pipeline like TLS2trees is required to fully utilize the increasing volume and scale of TLS data captured in forest plots.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Biochemical Research Methods
Akshatha Prasanna, Vidya Niranjan
Summary: The study introduces a robust automated pipeline for the analysis of clinical metagenomic data for pathogen identification and classification. By comparing results from different tools and versions, the reliability and accuracy of the data are ensured. The pipeline includes multiple steps from quality check to pathogen identification.
CURRENT BIOINFORMATICS
(2021)
Article
Biology
Gayathri Mahalingam, Russel Torres, Daniel Kapner, Eric T. Trautman, Tim Fliss, Shamishtaa Seshamani, Eric Perlman, Rob Young, Samuel Kinn, JoAnn Buchanan, Marc M. Takeno, Wenjing Yin, Daniel J. Bumbarger, Ryder P. Gwinn, Julie Nyhus, Ed Lein, Steven J. Smith, R. Clay Reid, Khaled A. Khairy, Stephan Saalfeld, Forrest Collman, Nuno Macarico da Costa
Summary: Serial-section electron microscopy is a high-resolution method for studying biological samples, with applications in reconstructing neural wiring diagrams. We present ASAP, a software pipeline that can handle large datasets in a distributed computational environment, offering high throughput and modular design.
Article
Computer Science, Information Systems
Xin Wang, Pei Guo, Xingyan Li, Aryya Gangopadhyay, Carl E. Busart, Jade Freeman, Jianwu Wang
Summary: This article introduces the use of serverless computing and containerization techniques to address the challenges of reproducing batch based Big Data analytics in the cloud. It also presents the development of an open-source toolkit for automated execution and reproducibility. Experiments on AWS and Azure demonstrate that the toolkit achieves good performance, scalability, and efficient reproducibility for cloud-based Big Data analytics.
IEEE TRANSACTIONS ON CLOUD COMPUTING
(2023)
Article
Infectious Diseases
L. M. Vos, R. Bruyndonckx, N. P. A. Zuithoff, P. Little, J. J. Oosterheert, B. D. L. Broekhuizen, C. Lammens, K. Loens, M. Viveen, C. C. Butler, D. Crook, K. Zlateva, H. Goossens, E. C. J. Claas, M. Ieven, A. M. Van Loon, T. J. M. Verheij, F. E. J. Coenjaerts
Summary: This study found that respiratory virus infections lead to more severe symptoms and longer duration, and are positively correlated with viral load.
CLINICAL MICROBIOLOGY AND INFECTION
(2021)
Article
Immunology
Lennard Y. W. Lee, Stefan Rozmanowski, Matthew Pang, Andre Charlett, Charlotte Anderson, Gareth J. Hughes, Matthew Barnard, Leon Peto, Richard Vipond, Alex Sienkiewicz, Susan Hopkins, John Bell, Derrick W. Crook, Nick Gent, A. Sarah Walker, Tim E. A. Peto, David W. Eyre
Summary: The study found that the infectivity of SARS-CoV-2 varies with case viral load, contact event type, and age. Those with high viral loads are the most infectious. The B.1.1.7 variant increases transmission by 50%. The best performing LFDs can detect most infectious cases.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Microbiology
Leon Peto, Gillian Rodger, Daniel P. Carter, Karen L. Osman, Mehmet Yavuz, Katie Johnson, Mohammad Raza, Matthew D. Parker, Matthew D. Wyles, Monique Andersson, Anita Justice, Alison Vaughan, Sarah Hoosdally, Nicole Stoesser, Philippa C. Matthews, David W. Eyre, Timothy E. A. Peto, Miles W. Carroll, Thushan de Silva, Derrick W. Crook, Cariad M. Evans, Steven T. Pullan
Summary: LamPORE is a novel diagnostic platform for detecting SARS-CoV-2 RNA with high sensitivity and specificity, making it suitable for high-throughput testing.
JOURNAL OF CLINICAL MICROBIOLOGY
(2021)
Article
Medicine, General & Internal
Peter W. Horby, Martin J. Landray
Summary: Convalescent plasma therapy did not improve survival or other clinical outcomes in hospitalized COVID-19 patients.
Article
Multidisciplinary Sciences
Erik Volz, Swapnil Mishra, Meera Chand, Jeffrey C. Barrett, Robert Johnson, Lily Geidelberg, Wes R. Hinsley, Daniel J. Laydon, Gavin Dabrera, Aine O. Toole, Robert Amato, Manon Ragonnet-Cronin, Ian Harrison, Ben Jackson, Cristina Ariani, Olivia Boyd, Nicholas J. Loman, John T. McCrone, Sonia Goncalves, David Jorgensen, Richard Myers, Verity Hill, David K. Jackson, Katy Gaythorpe, Natalie Groves, John Sillitoe, Dominic P. Kwiatkowski, Seth Flaxman, Oliver Ratmann, Samir Bhatt, Susan Hopkins, Axel Gandy, Andrew Rambaut, Neil M. Ferguson
Summary: Genetic and testing data from England indicate that the SARS-CoV-2 variant B.1.1.7 has a transmission advantage over other lineages, showing a rapid expansion during autumn 2020. Analysis of S gene target failures (SGTF) in community-based diagnostic PCR testing suggests that B.1.1.7 is more transmissible than non-variant of concern lineages and has a significant transmission advantage, with a reproduction number 50% to 100% higher. Additionally, cases of B.1.1.7 appear to include a larger share of under 20-year-olds compared to non-variant cases.
Article
Immunology
Sheila F. Lumley, Gillian Rodger, Bede Constantinides, Nicholas Sanderson, Kevin K. Chau, Teresa L. Street, Denise O'Donnell, Alison Howarth, Stephanie B. Hatch, Brian D. Marsden, Stuart Cox, Tim James, Fiona Warren, Liam J. Peck, Thomas G. Ritter, Zoe de Toledo, Laura Warren, David Axten, Richard J. Cornall, E. Yvonne Jones, David Stuart, Gavin Screaton, Daniel Ebner, Sarah Hoosdally, Meera Chand, Derrick W. Crook, Anne-Marie O'donnell, Christopher P. Conlon, Koen B. Pouwels, A. Sarah Walker, Tim E. A. Peto, Susan Hopkins, Timothy M. Walker, Nicole E. Stoesser, Philippa C. Matthews, Katie Jeffery, David W. Eyre
Summary: Natural infection with detectable anti-spike antibodies and two doses of vaccine provide robust protection against SARS-CoV-2 infection, including the B.1.1.7 variant in healthcare workers. Single dose vaccination significantly reduces the risk of symptomatic infection.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Microbiology
Jia Wei, Nicole Stoesser, Philippa C. Matthews, Daniel Ayoubkhani, Ruth Studley, Iain Bell, John I. Bell, John N. Newton, Jeremy Farrar, Ian Diamond, Emma Rourke, Alison Howarth, Brian D. Marsden, Sarah Hoosdally, E. Yvonne Jones, David I. Stuart, Derrick W. Crook, Tim E. A. Peto, Koen B. Pouwels, David W. Eyre, A. Sarah Walker
Summary: A longitudinal study on 45,965 adults in the UK revealed that older individuals, especially those aged >60 years, had lower antibody levels after a single dose of ChAdOx1 or BNT162b2 COVID-19 vaccines. Prioritizing vaccine allocation for those not previously infected and older individuals for the second dose is recommended based on the findings. Further data is needed to fully understand the relationship between quantitative antibody responses and vaccine-mediated protection.
NATURE MICROBIOLOGY
(2021)
Article
Infectious Diseases
Samuel Lipworth, Natasha Hough, Natasha Weston, Berit Muller-Pebody, Nick Phin, Richard Myers, Stephen Chapman, William Flight, Eliza Alexander, E. Grace Smith, Esther Robinson, Tim E. A. Peto, Derrick W. Crook, A. Sarah Walker, Susan Hopkins, David W. Eyre, Timothy M. Walker, Lancet Microbe, S. Chapman, W. Flight, D. W. Eyre, T. M. Walker, N. Phin, R. Myers
Summary: This study investigated the transmission of Mycobacterium abscessus in healthcare settings in England by analyzing whole-genome sequencing data and healthcare usage information. The findings showed that there were similar levels of genomic clusters in patients with and without cystic fibrosis, and that person-to-person transmission was not the main mechanism for M abscessus dissemination at a national level in England. The study provides reassurance that the risk of acquisition from other patients in healthcare settings is relatively low and suggests future research should focus on identifying acquisition routes outside of the cystic fibrosis healthcare-associated niche.
Article
Biology
Wei Wang, Peter Balfe, David W. Eyre, Sheila F. Lumley, Denise O'Donnell, Fiona Warren, Derrick W. Crook, Katie Jeffery, Philippa C. Matthews, Elizabeth B. Klerman, Jane A. McKeating
Summary: The COVID-19 pandemic presents unprecedented challenges to global public health, with vaccinations playing a crucial role in slowing down the spread of the virus and reducing disease severity. Factors such as vaccination timing, type, participant demographics, and days post-vaccination influence the antibody response, offering insights for optimizing vaccine efficacy against SARS-CoV-2.
JOURNAL OF BIOLOGICAL RHYTHMS
(2022)
Article
Infectious Diseases
Sheila F. Lumley, Nicholas Richens, Emily Lees, Jack Cregan, Elizabeth Kalimeris, Sarah Oakley, Marcus Morgan, Shelley Segal, Moya Dawson, A. Sarah Walker, David W. Eyre, Derrick W. Crook, Sally Beer, Alex Novak, Nicole E. Stoesser, Philippa C. Matthews
Summary: The SARS-CoV-2 pandemic had a significant impact on the incidence of paediatric viral respiratory tract infection in Oxfordshire, UK. The findings have implications for clinical service demand, testing strategies, timing of palivizumab RSV prophylaxis, and the effectiveness of public health interventions in preventing respiratory virus infections.
JOURNAL OF INFECTION
(2022)
Article
Infectious Diseases
Sheila F. Lumley, Bede Constantinides, Nicholas Sanderson, Gillian Rodger, Teresa L. Street, Jeremy Swann, Kevin K. Chau, Denise O'Donnell, Fiona Warren, Sarah Hoosdally, Anne-Marie O'Donnell, Timothy M. Walker, Nicole E. Stoesser, Lisa Butcher, Tim E. A. Peto, Derrick W. Crook, Katie Jeffery, Philippa C. Matthews, David W. Eyre
Summary: This study investigated the epidemiological characteristics of healthcare-associated SARS-CoV-2 acquisition. The findings suggest that current surveillance definitions underestimate nosocomial acquisition, with most nosocomial transmission occurring from a relatively limited number of highly infectious individuals.
JOURNAL OF INFECTION
(2021)
Article
Infectious Diseases
Dongxin Liu, Fei Huang, Guoliang Zhang, Wencong He, Xichao Ou, Ping He, Bing Zhao, Baoli Zhu, Fei Liu, Zhiyuan Li, Chunfa Liu, Hui Xia, Shengfen Wang, Yang Zhou, Timothy M. Walker, Lei Liu, Derrick W. Crook, Yanlin Zhao
Summary: The study evaluated the accuracy of whole-genome sequencing (WGS) in predicting drug resistance in tuberculosis (TB) and its potential use in drug-resistance surveillance. The results showed that WGS can accurately predict susceptibility to isoniazid, rifampin, ethambutol, and six second-line drugs. Specific mutations were found to confer high or low-level resistance.
CLINICAL MICROBIOLOGY AND INFECTION
(2022)
Article
Genetics & Heredity
Denis Volk, Fan Yang-Turner, Xavier Didelot, Derrick W. Crook, David Wyllie
Summary: Researchers have developed a software tool called Catwalk that can quickly detect highly similar sequences in large collections of microbial genomes. The tool performs well and can rapidly identify close relatives of SARS-CoV-2 and Mycobacterium tuberculosis genomes among millions of samples.
MICROBIAL GENOMICS
(2022)
Article
Microbiology
Yifei Xu, Ti Liu, Yan Li, Xuemin Wei, Zhaoguo Wang, Ming Fang, Yuwei Zhang, Huaning Zhang, Lifang Zhang, Jinbo Zhang, Jin Xu, Yunlong Tian, Nianzheng He, Yuhan Zhang, Yao Wang, Mingxiao Yao, Bo Pang, Shuang Wang, Hongling Wen, Zengqiang Kou
Summary: In spring 2022, SARS-CoV-2 Omicron caused a large wave of COVID-19 cases in China. Shandong was highly affected but effectively contained the transmission. This study investigated the origin, genetic diversity, and transmission patterns of the Omicron epidemic in Shandong using a dynamic clearance strategy. Multiple introductions of Omicron sublineages from foreign countries and other regions in China were observed, with a small number leading to the majority of local cases. Superspreading events and cryptic transmissions contributed to rapid spread.
MICROBIOLOGY SPECTRUM
(2023)
Article
Health Care Sciences & Services
Timothy M. Walker, Marc Choisy, Martin Dedicoat, Philip G. Drennan, David Wyllie, Fan Yang-Turner, Derrick W. Crook, Esther R. Robinson, A. Sarah Walker, E. Grace Smith, Timothy E. A. Peto
Summary: This study utilized over 10 years of whole-genome sequencing (WGS) data of Mycobacterium tuberculosis in Birmingham to investigate epidemiological trends and risk factors for transmission. The research found that there was seasonal variation in diagnoses, specifically among clustered cases. Risk factors for future clustered cases included UK birth, infectious forms of tuberculosis, and infection with lineage 3 or 4. There was also significant heterogeneity in transmission patterns between postcode districts.
LANCET REGIONAL HEALTH-EUROPE
(2022)