Article
Microbiology
Mattia Pandolfo, Andrea Telatin, Gioele Lazzari, Evelien M. Adriaenssens, Nicola Vitulo
Summary: Bacteriophages, the most abundant biological entities on earth, play a crucial role in controlling bacterial communities through predation and gene transfer. Choosing the best method and interpreting the results can be challenging for new users. MetaPhage, a comprehensive reads-to-report pipeline, simplifies the use of multiple phage miners and generates an exhaustive report. It offers scalability, reproducibility, and easy expansion for future developments in this field.
Article
Computer Science, Information Systems
Olav Poppe, Johan Ivar Saebo, Jorn Braa
Summary: The study analyzes an initiative from the World Health Organisation to disseminate global standards and guidelines through digital health packages, which has been adopted by 40 countries. The approach combines flexible standards and an integrated approach across health programmes, supported by strong global and regional technical teams.
INTERNATIONAL JOURNAL OF MEDICAL INFORMATICS
(2021)
Article
Biochemical Research Methods
Garrett M. Ginell, Aidan J. Flynn, Alex S. Holehouse
Summary: SHEPHARD is a Python framework that simplifies large-scale integrative protein bioinformatics. It combines an object-oriented hierarchical data structure with database-like features, enabling programmatic annotation, integration, and analysis of complex datatypes. It can be used to examine the relationship between protein sequences and molecular function, uncovering novel biology.
Article
Biochemistry & Molecular Biology
Wei Dai, Jiahui Li, Qi Li, Jiasheng Cai, Jianzhong Su, Christopher Stubenrauch, Jiawei Wang
Summary: Bacteria play a crucial role in various aspects of life, with some engineered to produce commercial quantities of antibiotics and therapeutics. Non-classical secretion systems are at the forefront of these technologies, characterized by diverse pathways for protein transport. Systematically categorizing and investigating non-classically secreted proteins will enhance understanding of their secretion mechanisms.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Analytical
Jongtae Lim, Songhee Park, Dojin Choi, Kyoungsoo Bok, Jaesoo Yoo
Summary: This paper proposes a machine-learning-based road speed prediction scheme that utilizes road environment data analysis. It accurately predicts both average road speed and rapidly changing road speeds by analyzing speed data from the target road and neighboring roads. It considers historical average speed data and events as weights for prediction and uses the LSTM algorithm for sequential data learning.
Article
Biochemical Research Methods
Quentin Lamy-Besnier, Bryan Brancotte, Herve Menager, Laurent Debarbieux
Summary: The study developed a web-based tool to collect and analyze data on different viruses infecting different hosts, which helps to better understand the transmission and host range of viruses.
Article
Computer Science, Software Engineering
Benjamin Lee, Xiaoyun Hu, Maxime Cordeil, Arnaud Prouzeau, Bernhard Jenny, Tim Dwyer
Summary: This study explores how teams use flexible visualization authoring tools for collaborative analysis. The system allows users to freely position visualization tools in the virtual environment, with participants generally using walls to organize 2D visualizations and positioning 3D visualizations in the surrounding space.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2021)
Article
Engineering, Marine
Abdul Razzaq, Syed Agha Hassnain Mohsan, Yanlong Li, Mohammed H. Alsharif
Summary: This study presents an architectural framework and algorithms as a solution for designing and developing an IoUT system. It includes recommendations and forecasts for potential partners in the smart ocean. A case study is implemented to assess the system's usability and agility in exploiting sensor data, executing algorithms, and querying outputs for performance evaluation.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2023)
Article
Biodiversity Conservation
Luguang Jiang, Ye Liu, Si Wu, Cheng Yang
Summary: This study evaluated the changes in China's ecological environment over the past 20 years using long-term NDVI data, revealing that approximately one-third of the country has seen improvements while 10% has experienced deterioration. Provinces such as Ningxia, Shaanxi, Shanxi, Guizhou, and Guangxi have shown the most significant improvements. Forestry projects and oasis agriculture development have effectively promoted the enhancement of the ecological environment in certain areas.
ECOLOGICAL INDICATORS
(2021)
Article
Biochemical Research Methods
Joseph Bloom, Aaron Triantafyllidis, Anna Quaglieri, Paula Burton Ngov, Giuseppe Infusini, Andrew Webb
Summary: Mass Dynamics 1.0 (MD 1.0) is a web-based tool for analyzing and visualizing LFQ data, with a cloud-based architecture for data storage and automatic processing, as well as generating quality control reports. It facilitates standardized analysis and collaboration among researchers in proteomics research.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Patrick Willems, Jingjing Huang, Joris Messens, Frank Van Breusegem
Summary: Deep learning algorithms, such as AlphaFold2, accurately predict the three-dimensional structure of proteins, providing an unparalleled resource for annotating protein function. This study analyzed the function and evolution of cysteine residues in plants using AlphaFold2 predicted structures. The analysis identified metal ligands coordinated by cysteine residues and systematically analyzed cysteine disulfides. The results showed that most of the predicted disulfides were reliable, with high agreement with known protein structures and characteristic features.
FREE RADICAL BIOLOGY AND MEDICINE
(2023)
Article
Engineering, Multidisciplinary
Mostafa Telima, Mohamed El Esawey, Karim El-Basyouny, Ahmed Osama
Summary: This study investigates the potential of using crowdsourced data to identify hotspot locations for pedestrian safety. The results showed that incidents in the study area are generally dispersed, but some locations were identified as hotspots. This approach can help transportation authorities in developing countries prioritize sites that require more safety attention.
AIN SHAMS ENGINEERING JOURNAL
(2023)
Article
Construction & Building Technology
Keyvan Ezimand, Mohsen Azadbakht, Hossein Aghighi
Summary: The study investigated the effects of 2D and 3D urban structures on LST changes in Tartu, Estonia using LiDAR point clouds and Landsat-8 imagery. The results showed a high overall accuracy of 97.33% in land cover classification using RF, with NDBI having a higher correlation with LST than FVC. Height was found to play a significant role in impervious surfaces and vegetation in influencing LST.
SUSTAINABLE CITIES AND SOCIETY
(2021)
Article
Construction & Building Technology
Xingyu Tao, Moumita Das, Yuhan Liu, Jack C. P. Cheng
Summary: The DCDE framework utilizes blockchain and IPFS to create a distributed common data environment for BIM-based design, ensuring irreversible design changes storage and secure design file storage. Performance testing shows that DCDE latency, TPS, and storage costs are within acceptable ranges, demonstrating its feasibility as a secure design collaboration solution.
AUTOMATION IN CONSTRUCTION
(2021)
Article
Computer Science, Information Systems
Mengjun Hu
Summary: This study investigates three-way decision making and its application in data analytics, categorizing existing topics into three aspects and proposing potential new topics, offering a new perspective for further research in the field of data analytics.
INFORMATION SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Monica Rosas-Lemus, George Minasov, Ludmilla Shuvalova, Zdzislaw Wawrzak, Olga Kiryukhina, Nathan Mih, Lukasz Jaroszewski, Bernhard Palsson, Adam Godzik, Karla J. F. Satchell
Article
Biochemical Research Methods
Mayya Sedova, Lukasz Jaroszewski, Arghavan Alisoltani, Adam Godzik
Review
Biochemistry & Molecular Biology
Eduard Porta-Pardo, Alfonso Valencia, Adam Godzik
Article
Biochemistry & Molecular Biology
Zhanwen Li, Lukasz Jaroszewski, Mallika Iyer, Mayya Sedova, Adam Godzik
NUCLEIC ACIDS RESEARCH
(2020)
Article
Multidisciplinary Sciences
Mallika Iyer, Zhanwen Li, Lukasz Jaroszewski, Mayya Sedova, Adam Godzik
Article
Multidisciplinary Sciences
Kamaldeep Kaur, Indu Khatri, Akil Akhtar, Srikrishna Subramanian, T. N. C. Ramya
Article
Biochemistry & Molecular Biology
George Minasov, Matthew R. Lam, Monica Rosas-Lemus, Joanna Slawek, Magdalena Woinska, Ivan G. Shabalin, Ludmilla Shuvalova, Bernhard O. Palsson, Adam Godzik, Wladek Minor, Karla J. F. Satchell
Article
Biochemistry & Molecular Biology
Youngchang Kim, Robert Jedrzejczak, Natalia I. Maltseva, Mateusz Wilamowski, Michael Endres, Adam Godzik, Karolina Michalska, Andrzej Joachimiak
Article
Biochemistry & Molecular Biology
Mayya Sedova, Lukasz Jaroszewski, Mallika Iyer, Zhanwen Li, Adam Godzik
Summary: There is a significant gap between the number of proteins characterized only by their amino acid sequence and those with structurally characterized by direct experiment. To bridge this gap, homology-based inference and modeling are used to predict the structures of uncharacterized proteins. The use of different templates with distinct structural flexibility can provide more informative results depending on the research questions.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Houriiyah Tegally, Eduan Wilkinson, Marta Giovanetti, Arash Iranzadeh, Vagner Fonseca, Jennifer Giandhari, Deelan Doolabh, Sureshnee Pillay, Emmanuel James San, Nokukhanya Msomi, Koleka Mlisana, Anne von Gottberg, Sibongile Walaza, Mushal Allam, Arshad Ismail, Thabo Mohale, Allison J. Glass, Susan Engelbrecht, Gert Van Zyl, Wolfgang Preiser, Francesco Petruccione, Alex Sigal, Diana Hardie, Gert Marais, Nei-Yuan Hsiao, Stephen Korsman, Mary-Ann Davies, Lynn Tyers, Innocent Mudau, Denis York, Caroline Maslo, Dominique Goedhals, Shareef Abrahams, Oluwakemi Laguda-Akingba, Arghavan Alisoltani-Dehkordi, Adam Godzik, Constantinos Kurt Wibmer, Bryan Trevor Sewell, Jose Lourenco, Luiz Carlos Junior Alcantara, Sergei L. Kosakovsky Pond, Steven Weaver, Darren Martin, Richard J. Lessells, Jinal N. Bhiman, Carolyn Williamson, Tulio de Oliveira
Summary: The article describes a newly emerged lineage of SARS-CoV-2, 501Y.V2, characterized by eight mutations in the spike protein, which may result in increased transmissibility or immune escape. This lineage originated in South Africa and quickly became dominant in Eastern Cape, Western Cape, and KwaZuluNatal provinces within weeks.
Article
Biochemistry & Molecular Biology
Isuru Karunatillaka, Lukasz Jaroszewski, Adam Godzik
Summary: A study investigated a PETase enzyme from environmental samples and its distribution in other bacterial communities, identifying similar homologs in JGI metagenomic datasets through BLAST searches. By verifying the protein sequences and conducting phylogenetic analyses, it confirmed that these proteins are putative PETases, and docking analysis further confirmed their functional assignment.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Lukasz Jaroszewski, Mallika Iyer, Arghavan Alisoltani, Mayya Sedova, Adam Godzik
Summary: The mutation patterns in the SARS-CoV-2 virus genomes are closely linked to the structure and function of the proteins they encode, with highly mutated regions corresponding to more easily adaptable structural regions. Understanding these patterns is important for developing tools like antibodies, vaccines, and drugs to target conserved genomic regions due to natural selection.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Cell Biology
Xinru Qiu, Jiang Li, Jeff Bonenfant, Lukasz Jaroszewski, Aarti Mittal, Walter Klein, Adam Godzik, Meera G. Nair
Summary: This study uses single-cell analysis to examine short-term temporal changes in immune cell populations in sepsis patients, finding that platelet and erythroid precursor responses are drivers of fatal sepsis. It also identifies dynamic effects in individual cell subsets, showing that hypoxic stress plays a key role in immune and metabolic dysfunction. Additionally, the study supports CD52 as a prognostic biomarker and therapeutic target for sepsis.
JOURNAL OF LEUKOCYTE BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Abraham Takkouche, Xinru Qiu, Mayya Sedova, Lukasz Jaroszewski, Adam Godzik
Summary: Leucine Rich Repeat (LRR) domains, present in various proteins, play important roles in protein-protein interactions and ligand recognition. The least characterized class of LRR proteins, TpLRR-like LRRs, have unique structural features and sequence patterns. These proteins are involved in interactions between human pathogens and the host immune system. This study analyzed the relation of conserved residues, specific structural features, and functions of these proteins using experimental structures and AlphaFold models.
JOURNAL OF STRUCTURAL BIOLOGY
(2023)
Meeting Abstract
Biochemical Research Methods
Urmi Shah, Srikrishna Subramanian
BMC BIOINFORMATICS
(2020)