Article
Biotechnology & Applied Microbiology
Matthew R. Lueder, Regina Z. Cer, Miles Patrick, Logan J. Voegtly, Kyle A. Long, Gregory K. Rice, Kimberly A. Bishop-Lilly
Summary: Manual Annotation Studio (MAS) is a software tool designed to improve the efficiency of manual functional annotation for prokaryotic and viral genomes. It allows users to upload, edit, and track annotations, provides structure to projects, and reduces errors. MAS can interface with HPC clusters, support multiple users, and export data in various formats.
Article
Multidisciplinary Sciences
Thi Thuy Duong Vu, Jaehee Jung
Summary: Protein function prediction is crucial for genome annotation and has seen rapid development, especially with the use of high-throughput sequencing technologies. Gene Ontology (GO) is an important resource that describes protein functional properties, with deep learning showing potential in assigning GO terms to amino acid sequences. Researchers are employing various methods for efficient GO term prediction, and also conducting performance comparisons on selected predictors with a worldwide challenge dataset, while discussing future challenges and directions in the field of protein function prediction with GO.
Article
Microbiology
Songbo Liu, Chengmin Cui, Huipeng Chen, Tong Liu
Summary: This study introduces an ensemble learning-based method for identifying important features in phage protein, aiming to understand its relationship with host bacteria and develop antimicrobial agents. The selected features are found to have significant biological significance based on the analysis conducted.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Chemistry, Analytical
Simon-Martin Schroeder, Rainer Kiko
Summary: The study provides a deeper analysis of the MorphoCluster image annotation tool and finds that labeled training data improve image representations, unsupervised learning outperforms transfer learning, and different clustering algorithms have their own advantages in terms of completeness, efficiency, and runtime.
Article
Biochemical Research Methods
Akshay Khanduja, Manish Kumar, Debasisa Mohanty
Summary: Small open reading frames (smORFs) encoding proteins less than 100 amino acids (aa) are important regulators of cellular processes. Computational identification of smORFs remains challenging. The ProsmORF-pred resource utilizes a machine learning-based method to predict smORFs in prokaryotic genomes, achieving comparable performance to other state-of-the-art approaches. It can also aid in functional annotation of predicted smORFs based on sequence similarity in ProsmORFDB.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Ranjan Kumar Barman, Alok Kumar Chakrabarti, Shanta Dutta
Summary: Antimicrobial resistance is a major problem and alternative products to antibiotics are urgently needed. Phage-driven antibacterial drugs, including phage virion proteins, show great potential in the development of antibacterial drugs for AMR bacteria.
Review
Microbiology
Alban Mathieu, Mickael Leclercq, Melissa Sanabria, Olivier Perin, Arnaud Droit
Summary: Shotgun sequencing of environmental DNA has greatly advanced the field of environmental microbiology, but current alignment methods have limitations. Deep learning models show promise in improving annotation efficiency, but their robustness needs further validation in different environmental samples and genome databases.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Cell Biology
Xiuchun Lin
Summary: Structural variations in the genome are closely related to human health and disease. Detecting and identifying pathogenic synonymous mutations is crucial for studying disease mechanisms and implementing personalized medicine.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Microbiology
Shazeeda Koonjan, Callum J. Cooper, Anders S. Nilsson
Summary: ETEC strains are a significant cause of bacterial diarrheal illness, with potential treatment through bacteriophage therapy. Phage vB_EcoP_SU7, a rare Podoviridae member, exhibits an elongated head C3 morphotype. Despite limited host range and poor infection kinetics, it is unlikely to be used as a standalone therapeutic phage.
Article
Multidisciplinary Sciences
Brieuc Van Nieuwenhuyse, Dimitri Van der Linden, Olga Chatzis, Cedric Lood, Jeroen Wagemans, Rob Lavigne, Kaat Schroven, Jan Paeshuyse, Catherine de Magnee, Etienne Sokal, Xavier Stephenne, Isabelle Scheers, Hector Rodriguez-Villalobos, Sarah Djebara, Maya Merabishvili, Patrick Soentjens, Jean-Paul Pirnay
Summary: In this study, the authors use a combination of bacteriophage and antibiotic therapy to treat extensively drug-resistant Pseudomonas aeruginosa infection in a toddler post liver transplantation. They report on the clinical and microbiological improvement and investigate the reasons why bacterial phage resistance did not lead to therapeutic failure.
NATURE COMMUNICATIONS
(2022)
Article
Engineering, Chemical
Javier Merrill-Cifuentes, Matthew J. Cracknell, Angela Escolme
Summary: The balance between the valuable metal content and the cost of obtaining a commercial product from an ore body is crucial for its exploitation. Rock texture, although difficult to model and quantify, plays an important role in various stages of the business. This study applied the Mineral Co-Occurrence Probability Fields method to a large dataset of hyperspectral imaging to incorporate textural features into the predictive modeling of rock hardness and copper recovery. The results showed a significant improvement in precision and accuracy of the predictions, suggesting that acquiring hyperspectral imagery from drill cores can enhance the forecasting of metallurgical parameters reliant on rock textures.
MINERALS ENGINEERING
(2023)
Article
Genetics & Heredity
Mitra Vajjala, Brady Johnson, Lauren Kasparek, Michael Leuze, Qiuming Yao
Summary: With the advancement of omics technology and bioinformatics, small proteins encoded by small open reading frames are gaining attention. They have been found to play important roles in various biological functions, such as cellular metabolism, protein regulation, cell cycle control, and disease physiology. However, the study of small proteins in prokaryotes, especially bacteria, is still lacking. In this study, a toolkit called metaBP has been developed to explore the small protein universe from metagenomic samples. It uses protein-level meta-assembly and clustering tools, as well as a small protein-specific machine learning module, to construct a landscape of bacterial peptides. This toolkit demonstrates innovation in its approach, providing a comprehensive analysis of small proteins and revealing their functional characteristics from a microbial community perspective.
FRONTIERS IN GENETICS
(2022)
Review
Computer Science, Artificial Intelligence
Weiwei Jiang
Summary: Cellular networks are vital for the success of modern communication systems, and with the advancement of artificial intelligence, they are becoming smarter. This survey reviews the relevant studies on cellular traffic prediction, categorizing the prediction problems and models. It also summarizes various applications based on cellular traffic prediction and points out future research directions.
EXPERT SYSTEMS WITH APPLICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Max Highsmith, Jianlin Cheng
Summary: 4DMax is a novel method that predicts dynamic chromosome conformation using time-series Hi-C data, effectively interpolating chromatin position, recovering higher order features, and predicting contact maps even at time points where Hi-C data is unavailable.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Economics
Ana Pegado-Bardayo, Antonio Lorenzo-Espejo, Jesus Munuzuri, Pablo Aparicio-Ruiz
Summary: The increasing demand for last mile services has led to couriers being overloaded and unable to complete all their assigned tasks within their working day. Uncompleted services are a major source of dissatisfaction for customers, and predicting which services will remain uncompleted provides an effective decision-making tool to improve service levels without increasing resources. This study combines machine learning and clustering techniques to estimate the number of uncompleted services on a given route and predict the routes to be followed by couriers, demonstrating promising results in a case study in Spain.
TRANSPORTATION RESEARCH PART A-POLICY AND PRACTICE
(2023)
Article
Ecology
Lais F. O. Lima, Amanda T. Alker, Bhavya Papudeshi, Megan M. Morris, Robert A. Edwards, Samantha J. de Putron, Elizabeth A. Dinsdale
Summary: The microbial community structure in the coral surface mucus layer (SML) varies between different local reef environments, which affects coral health and ecosystem functioning. The fluctuating environment in the inner patch reefs of Bermuda promotes a more beneficial coral SML microbiome, potentially enhancing holobiont resilience to environmental changes and disease.
Letter
Gastroenterology & Hepatology
Alyce M. Martin, Michael Roach, Lauren A. Jones, Daniel Thorpe, Rosemary A. Coleman, Caitlin Allman, Robert Edwards, Damien J. Keating
Article
Virology
Dann Turner, Andrey N. Shkoporov, Cedric Lood, Andrew D. Millard, Bas E. Dutilh, Poliane Alfenas-Zerbini, Leonardo J. van Zyl, Ramy K. Aziz, Hanna M. Oksanen, Minna M. Poranen, Andrew M. Kropinski, Jakub Barylski, J. Rodney Brister, Nina Chanisvili, Rob A. Edwards, Francois Enault, Annika Gillis, Petar Knezevic, Mart Krupovic, Ipek Kurtboke, Alla Kushkina, Rob Lavigne, Susan Lehman, Malgorzata Lobocka, Cristina Moraru, Andrea Moreno Switt, Vera Morozova, Jesca Nakavuma, Alejandro Reyes Munoz, Janis Rumnieks, B. L. Sarkar, Matthew B. Sullivan, Jumpei Uchiyama, Johannes Wittmann, Tong Yigang, Evelien M. Adriaenssens
Summary: This article summarizes the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses from March 2021 to March 2022. It provides an overview of the new classifications proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. The taxonomy of bacterial viruses underwent significant changes, including the abolition of the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae, as well as the order Caudovirales, and the establishment of a binomial nomenclature system for species. Additionally, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.
ARCHIVES OF VIROLOGY
(2023)
Article
Medicine, Legal
Nicole R. Foster, Belinda Martin, Jurian Hoogewerff, Michael G. Aberle, Patrice de Caritat, Paul Roffey, Robert Edwards, Arif Malik, Priscilla Thwaites, Michelle Waycott, Jennifer Young
Summary: Environmental DNA and elemental and mineralogical analysis of soil can be used in forensic intelligence work by analyzing the airborne fraction of soil (dust). Massive parallel sequencing technologies enable the identification of genetic fingerprints in dust particles. Combining this with elemental and mineralogical compositions offers multiple lines of evidence for tracing the origin of dust samples.
FORENSIC SCIENCE INTERNATIONAL
(2023)
Article
Microbiology
Bhavya Papudeshi, Douglas B. Rusch, David VanInsberghe, Curtis M. Lively, Robert A. Edwards, Farrah Bashey
Summary: In this study, the authors investigated the host specificity and geographic structure of the insect pathogen and nematode mutualist Xenorhabdus bovienii to understand the extent to which generalist species are cohesive evolutionary units. The results showed that X. bovienii forms associations with multiple nematode species, but the bacterial and nematode phylogenies were not entirely congruent. Additionally, genetic similarity and gene flow decreased with increasing geographic distance across nematode species, suggesting the presence of differentiation and constraints on gene flow.
Letter
Microbiology
Peter Speck, Jason Mackenzie, Rowena A. Bull, Barry Slobedman, Heidi Drummer, Johanna Fraser, Lara Herrero, Karla Helbig, Sarah Londrigan, Gregory Moseley, Natalie Prow, Grant Hansman, Robert Edwards, Chantelle Ahlenstiel, Allison Abendroth, David Tscharke, Jody Hobson-Peters, Robson Kriiger-Loterio, Rhys Parry, Glenn Marsh, Emma Harding, David A. Jacques, Matthew J. Gartner, Wen Shi Lee, Julie McAuley, Paola Vaz, Frank Sainsbury, Michelle D. Tate, Jane Sinclair, Allison Imrie, Stephen Rawlinson, Andrew Harman, Jillian M. Carr, Ebony A. Monson, Merilyn Hibma, Timothy J. Mahony, Thomas Tu, Robert J. Center, Lok Bahadur Shrestha, Robyn Hall, Morgyn Warner, Vernon Ward, Danielle E. Anderson, Nicholas S. Eyre, Natalie E. Netzler, Alison J. Peel, Peter Revill, Michael Beard, Alistair R. Legione, Alexandra J. Spencer, Adi Idris, Jade Forwood, Subir Sarker, Damian F. J. Purcell, Nathan Bartlett, Joshua M. Deerain, Bruce J. Brew, Sassan Asgari, Helen Farrell, Alexander Khromykh, Daniel Enosi Tuipulotu, David Anderson, Sevim Mese, Yaman Tayyar, Kathryn Edenborough, Jasim Muhammad Uddin, Abrar Hussain, Connor J. Daymond, Jacinta Agius, Karyn N. Johnson, Paniz Shirmast, Mahdi Abedinzadeshahri, Robin MacDiarmid, Caroline L. Ashley, Jay Laws, Lucy L. Furfaro, Thomas D. Burton, Stephen M. R. Johnson, Zahra Telikani, Mary Petrone, Justin A. Roby, Carolyn Samer, Andreas Suhrbier, April van der Kamp, Anthony Cunningham, Celeste Donato, Jackie Mahar, Wesley D. Black, Subhash Vasudevan, Roman Lenchine, Kirsten Spann, Daniel J. Rawle, Penny Rudd, Jessica Neil, Richard Kingston, Timothy P. Newsome, Ki Wook Kim, Johnson Mak, Kym Lowry, Nathan Bryant, Joanne Meers, Jason A. Roberts, Nigel McMillan, Larisa I. Labzin, Andrii Slonchak, Leon E. Hugo, Bennett Henzeler, Natalee D. Newton, Cassandra T. David, Patrick C. Reading, Camille Esneau, Tatiana Briody, Najla Nasr, Donna McNeale, Brian McSharry, Omid Fakhri, Bethany A. Horsburgh, Grant Logan, Paul Howley, Paul Young
Review
Microbiology
Evan Pargin, Michael J. J. Roach, Amber Skye, Bhavya Papudeshi, Laura K. K. Inglis, Vijini Mallawaarachchi, Susanna R. R. Grigson, Clarice Harker, Robert A. A. Edwards, Sarah K. K. Giles
Summary: The gut virome, which consists of complex gut ecosystem, plays a role in disease states, yet its impact on human health remains unknown. New approaches are needed to address this knowledge gap. The gut virome is established at birth, remains stable in adulthood, and is influenced by factors such as age, diet, disease state, and antibiotic use. Bacteriophages, particularly order Crassvirales and other Caudoviricetes, make up the gut virome primarily. Disease disrupts the stability of the regular virome constituents, but transferring the fecal microbiome from a healthy individual can restore gut functionality and alleviate symptoms of chronic diseases. There are significant challenges in understanding the gut virome due to a large amount of unknown sequences, known as 'viral dark matter'. Strategies to overcome this challenge include mining viral datasets, untargeted metagenomic approaches, and using advanced bioinformatic tools for viral species quantification and classification. This article reviews the literature on the gut virome, its establishment, its impact on human health, the methods used to investigate it, and the challenges posed by the viral dark matter.
FRONTIERS IN MICROBIOLOGY
(2023)
Letter
Microbiology
Peter Speck, Jason Mackenzie, Rowena A. Bull, Barry Slobedman, Heidi Drummer, Johanna Fraser, Lara Herrero, Karla Helbig, Sarah Londrigan, Gregory Moseley, Natalie Prow, Grant Hansman, Robert Edwards, Chantelle Ahlenstiel, Allison Abendroth, David Tscharke, Jody Hobson-Peters, Robson Kriiger-Loterio, Rhys Parry, Glenn Marsh, Emma Harding, David A. Jacques, Matthew J. Gartner, Wen Shi Lee, Julie McAuley, Paola Vaz, Frank Sainsbury, Michelle D. Tate, Jane Sinclair, Allison Imrie, Stephen Rawlinson, Andrew Harman, Jillian M. Carr, Ebony A. Monson, Merilyn Hibma, Timothy J. Mahony, Thomas Tu, Robert J. Center, Lok Bahadur Shrestha, Robyn Hall, Morgy Warner, Vernon Ward, Danielle E. Anderson, Nicholas S. Eyre, Natalie E. Netzler, Alison J. Peel, Peter Revill, Michael Beard, Alistair R. Legione, Alexandra J. Spencer, Adi Idris, Jade Forwood, Subir Sarker, Damian F. J. Purcell, Nathan Bartlett, Joshua M. Deerain, Bruce J. Brew, Sassan Asgari, Helen Farrell, Alexander Khromykh, Daniel Enosi Tuipulotu, David Anderson, Sevim Mese, Yaman Tayyar, Kathryn Edenborough, Jasim Muhammad Uddin, Abrar Hussain, Connor J. I. Daymond, Jacinta Agius, Karyn N. Johnson, Paniz Shirmast, Mahdi Abedinzadeshahri, Robin MacDiarmid, Caroline L. Ashley, Jay Laws, Lucy L. Furfaro, Thomas D. Burton, Stephen M. R. Johnson, Zahra Telikani, Mary Petrone, Justin A. Roby, Carolyn Samer, Andreas Suhrbier, April van der Kamp, Anthony Cunningham, Celeste Donato, Jackie Mahar, Wesley D. Black, Subhash Vasudevan, Roman Lenchine, Kirsten Spann, Daniel J. Rawle, Penny Rudd, Jessica Neil, Richard Kingston, Timothy P. Newsome, Ki Wook Kim, Johnson Mak, Kym Lowry, Nathan Bryant, Joanne Meers, Jason A. Roberts, Nigel McMillan, Larisa I. Labzin, Andrii Slonchak, Leon E. Hugo, Bennett Henzeler, Natalee D. Newton, Cassandra T. David, Patrick C. Reading, Camille Esneau, Tatiana Briody, Najla Nasr, Donna McNeale, Brian McSharry, Omid Fakhri, Bethany A. Horsburgh, Grant Logan, Paul Howley, Paul Young
Article
Genetics & Heredity
Nicole R. Foster, Duncan Taylor, Jurian Hoogewerff, Michael G. Aberle, Patrice de Caritat, Paul Roffey, Robert Edwards, Arif Malik, Michelle Waycott, Jennifer M. Young
Summary: The airborne fraction of soil (dust) can be used as a potential medium for forensic intelligence by analyzing its unique biological and chemical signatures. This study investigates the changes in bacterial and fungal communities in dust over time and their comparability to soil samples from the same site. The results demonstrate that both metabarcoding and geochemical/mineralogical analyses can be conducted on a single swabbed sample, providing important information for tracing the origin of dust samples.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2023)
Letter
Biotechnology & Applied Microbiology
Evelien M. M. Adriaenssens, Simon Roux, J. Rodney Brister, Ilene Karsch-Mizrachi, Jens H. H. Kuhn, Arvind Varsani, Tong Yigang, Alejandro Reyes, Cedric Lood, Elliot J. J. Lefkowitz, Matthew B. B. Sullivan, Robert A. A. Edwards, Peter Simmonds, Luisa Rubino, Sead Sabanadzovic, Mart Krupovic, Bas E. E. Dutilh
NATURE BIOTECHNOLOGY
(2023)
Correction
Biotechnology & Applied Microbiology
Evelien M. M. Adriaenssens, Simon Roux, J. Rodney Brister, Ilene Karsch-Mizrachi, Jens H. Kuhn, Arvind Varsani, Tong Yigang, Alejandro Reyes, Cedric Lood, Elliot J. Lefkowitz, Matthew B. B. Sullivan, Robert A. A. Edwards, Peter Simmonds, Luisa Rubino, Sead Sabanadzovic, Mart Krupovic, Bas E. E. Dutilh
NATURE BIOTECHNOLOGY
(2023)
Article
Virology
Ana Georgina Cobian Guemes, Tram Le, Maria Isabel Rojas, Nicole E. Jacobson, Helena Villela, Katelyn Mcnair, Shr-Hau Hung, Lili Han, Lance Boling, Jessica Claire Octavio, Lorena Dominguez, Vito Adrian Cantu, Sinead Archdeacon, Alejandro A. Vega, Michelle A. An, Hamza Hajama, Gregory Burkeen, Robert A. Edwards, Douglas J. Conrad, Forest Rohwer, Anca M. Segall, Mao Ye
Summary: This study reports the detection of antibiotic-resistant bacteria Achromobacter species in the airways of patients with Cystic Fibrosis, as well as the discovery of lytic phages with potential therapeutic value. The results of the study showed that most Achromobacter strains were susceptible to the phages isolated in the study, and the method of phage production met the safety standards for human administration. This study provides a comprehensive framework for the treatment of Achromobacter infections in Cystic Fibrosis.
Article
Multidisciplinary Sciences
Michael P. P. Doane, Michael B. B. Reed, Jody McKerral, Lais Farias Oliveira Lima, Megan Morris, Asha Z. Z. Goodman, Shaili Johri, Bhavya Papudeshi, Taylor Dillon, Abigail C. C. Turnlund, Meredith Peterson, Maria Mora, Rafael de la Parra Venegas, Richard Pillans, Christoph A. A. Rohner, Simon J. J. Pierce, Christine G. G. Legaspi, Gonzalo Araujo, Deni Ramirez-Macias, Robert A. A. Edwards, Elizabeth A. A. Dinsdale
Summary: This study analyzed the diversity and architectural complexity of the epidermal microbiome of 74 individual whale sharks across five global aggregations, finding that network properties may be more indicative of the microbiome-host relationship. The results showed that whale shark aggregation was the most important factor in discriminating taxonomic diversity patterns, and the microbiome network architecture was similar across all aggregations but displayed modularity. Additionally, the whale sharks hosted 35 high-quality metagenome assembled genomes, with 25 present at all sample locations, suggesting the presence of an abundant "core".
SCIENTIFIC REPORTS
(2023)
Article
Computer Science, Artificial Intelligence
Peter Salamon, David Salamon, V. Adrian Cantu, Michelle An, Tyler Perry, Robert A. Edwards, Anca M. Segall
Summary: This paper investigates the post-hoc calibration of confidence for exploratory machine learning classification problems. The authors argue for the use of one-versus-all approach and introduce four new algorithms for category-specific confidence estimation. The use of kernel density ratios for confidence calibration is highlighted. The experiments on bioinformatics application and MNIST benchmark confirm the importance of post-hoc calibration, which can be performed using only the test dataset and visually checked for sanity.
MACHINE LEARNING AND KNOWLEDGE EXTRACTION
(2023)
Meeting Abstract
Biophysics
Peter Salamon, David Salamon, V. Adrian Cantu, Michelle An, Tyler Perry, Robert A. Edwards, Anca M. Segall
BIOPHYSICAL JOURNAL
(2023)