Article
Microbiology
Billy Taj, Mobolaji Adeolu, Xuejian Xiong, Jordan Ang, Nirvana Nursimulu, John Parkinson
Summary: Whole microbiome RNASeq (metatranscriptomics) is a powerful technology for functional analysis of microbial communities. MetaPro is a flexible and scalable data analysis pipeline that effectively processes and analyzes metatranscriptomic datasets. It outperforms current state-of-the-art pipelines in terms of performance and functionality.
Article
Microbiology
Daria Shafranskaya, Varsha Kale, Rob Finn, Alla L. Lapidus, Anton Korobeynikov, Andrey D. Prjibelski
Summary: While metagenome sequencing provides insights on microbial communities, metatranscriptome analysis is useful for studying functional activity. However, the complexity, dynamic range, and lack of computational methods for assembling metatranscriptomes pose challenges. This study presents MetaGT, a pipeline that combines metatranscriptomic and metagenomic data to improve assembly coverage and completeness. Results show significant improvement compared to existing methods. The pipeline, implemented in NextFlow, is available athttps://github.com/ablab/metaGT.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biology
Mohammad Mahdi Ershadi, Zeinab Rahimi Rise, Seyed Taghi Akhavan Niaki
Summary: This study proposes a hierarchical model based on FCM clustering, Wrapper feature selection, and twelve classifiers to analyze treatment plans for GBM. The model combines clinical data, biomedical data, and image data to find the best decision, and it demonstrates good performance.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Computer Science, Artificial Intelligence
Jiaqi Ma, Yipeng Zhang, Lefei Zhang
Summary: In this study, a method called DMSMF is proposed to address the drawbacks of existing multiview data clustering methods. By extending linear discriminant analysis and NMF to a multiview version, and incorporating novel regularization terms and optimization algorithms, satisfactory clustering performance is achieved.
PATTERN RECOGNITION
(2021)
Article
Biochemical Research Methods
Renaud Van Damme, Martin Hoelzer, Adrian Viehweger, Bettina Mueller, Erik Bongcam-Rudloff, Christian Brandt
Summary: Metagenomics has revolutionized microbiology, but analyzing metagenome-assembled genomes remains challenging. MUFFIN, a bioinformatics workflow, integrates short and long reads to reconstruct bacterial species and their functions with high reproducibility and efficiency. MUFFIN is a user-friendly tool that automates complex analysis steps and provides valuable insights into microbial communities.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Arianna I. Krinos, Natalie R. Cohen, Michael J. Follows, Harriet Alexander
Summary: This study presents a workflow for eukaryotic metatranscriptome assembly and validates its ability to recapitulate real and manufactured eukaryotic community-level expression data. The authors also reanalyze previously published metatranscriptomic datasets using this approach.
BMC BIOINFORMATICS
(2023)
Article
Virology
Nicolas Bejerman, Ralf G. Dietzgen, Humberto Debat
Summary: The study identified 27 novel rhabdovirus genomes associated with 25 different host plant species and one insect. Through homology searches in the NCBI's SRA data, these viral sequences were discovered, revealing the complexity and diversity of plant rhabdoviruses.
Article
Neurosciences
Shengchao Zhang, Sarah E. Goodale, Benjamin P. Gold, Victoria L. Morgan, Dario J. Englot, Catie Chang
Summary: Patterns in fMRI data can reflect dynamic changes in the brain and are related to individual and group differences in behavior, cognition, and clinical traits. Detecting vigilance states in fMRI data without external measurements is challenging. This study shows that vigilance levels can be detected in the low-dimensional structure of fMRI data, even within individual time frames.
Article
Computer Science, Artificial Intelligence
Xiaodong Wang, Pengtao Wu, Qinghua Xu, Zhiqiang Zeng, Yong Xie
Summary: Traditional K-means struggles with high-dimensional data due to irrelevant features or noise, prompting recent studies to combine it with subspace learning. This study proposes an auto-adjoined subspace clustering approach, enhancing clustering performance through efficient feature selection and clear adjacency exploration.
KNOWLEDGE-BASED SYSTEMS
(2021)
Article
Computer Science, Information Systems
Guoqiu Wen, Xianxian Li, Yonghua Zhu, Linjun Chen, Qimin Luo, Malong Tan
Summary: This paper proposes a one-step spectral rotation clustering method OSRCIH, which integrates self-paced learning and spectral rotation clustering in a unified framework to simultaneously consider sample selection and dimensionality reduction. Experimental analysis shows that OSRCIH can effectively recognize important samples and features in imbalanced high-dimensional data, improving clustering performance.
INFORMATION PROCESSING & MANAGEMENT
(2021)
Review
Computer Science, Artificial Intelligence
Jui-Hung Chang, Yin-Chung Leung
Summary: This paper proposes a novel framework for dynamic image clustering without prior knowledge of the cluster count. By using deep learning and coordinate learning models to project high dimensional data onto a two-dimensional space, a new clustering algorithm is introduced to evaluate and classify the projected data.
Article
Computer Science, Artificial Intelligence
Chitta Ranjan, Samaneh Ebrahimi, Kamran Paynabar
Summary: Sequence feature embedding is a challenging task and SGT is a feature embedding function that can efficiently extract dependencies from short-term to long-term. Through analysis, SGT's advantages in interpretation and application are proven, and it achieves better results in sequence clustering and classification compared to existing methods.
DATA MINING AND KNOWLEDGE DISCOVERY
(2022)
Article
Health Care Sciences & Services
Jamie D. Feusner, Reza Mohideen, Stephen Smith, Ilyas Patanam, Anil Vaitla, Christopher Lam, Michelle Massi, Alex Leow
Summary: This study analyzed a large dataset of freely reported obsession symptoms to uncover potential OCD subtypes based on semantic relationships in English language using word embeddings. The analysis revealed three major groupings of semantic themes related to relationship and just-right, doubt and checking, and contamination, harm, and sexual harm. The close semantic relationships across clusters suggest that most obsessions share underlying themes related to harm.
JOURNAL OF MEDICAL INTERNET RESEARCH
(2021)
Article
Mathematics
Yilin Yu, Juntao Liu
Summary: Single-cell clustering is important for identifying different cell types, especially rare cells. Preprocessing and dimensionality reduction are crucial steps in single-cell clustering, but different methods have different effects. This study introduces a new algorithm, SCM, that automatically searches for an optimal combination and uses a flexible distance measure for improved clustering results.
Article
Chemistry, Analytical
Mihael Simonic, Matevz Majcen Hrovat, Saso Dzeroski, Ales Ude, Bojan Nemec
Summary: This paper presents an exception strategy learning framework based on statistical learning and context determination to address errors and human intervention in robot assembly tasks. The research proposes a novel approach to generate unified low-dimensional context descriptions from multimodal data and validates its reliability.
Article
Plant Sciences
Nigel Belshaw, Irina Grouneva, Lior Aram, Assaf Gal, Amanda Hopes, Thomas Mock
Summary: CRISPR/Cas technology enables efficient gene targeting by homologous recombination in the diploid photosynthetic organism Thalassiosira pseudonana. Knockout of nitrate reductase and urease genes affected growth on nitrate and urea, respectively, while knockout of the silacidin gene led to a significant increase in cell size.
Article
Mathematics, Applied
Andrew Francis, Katharina T. Huber, Vincent Moulton, Taoyang Wu
Summary: This paper presents a method for encoding X-cactuses in terms of certain collections of partitions of X and introduces a partial order on the set of X-cactuses. The resulting partially ordered set exhibits some structural properties, including the analysis of its least upper and greatest lower bounds. These results not only extend fundamental properties of phylogenetic trees to X-cactuses, but also offer a new approach to solving topical problems in phylogenetic network theory.
ADVANCES IN APPLIED MATHEMATICS
(2023)
Article
Mathematics, Applied
Katharina T. Huber, Vincent Moulton, Megan Owen, Andreas Spillner, Katherine St. John
Summary: In this paper, the equidistant X-cactus, a type of directed acyclic graph used in biology to represent the evolutionary history of a set of species, is introduced and investigated. It is shown that the space of equidistant X-cactuses, which includes the space of ultrametric trees, is a CAT(0)-metric space, implying unique geodesic paths between points. A combinatorial result concerning ranked rooted X-cactuses is presented, encoding such graphs in terms of a pairwise compatibility condition. This result also provides an alternative proof of the CAT(0) property for the space of ultrametric trees. These findings are expected to have implications for statistical analyses and understanding of arc-weighted phylogenetic networks.
ANNALS OF COMBINATORICS
(2023)
Article
Computer Science, Theory & Methods
David Bryant, Katharina T. Huber, Vincent Moulton, Paul F. Tupper
Summary: The generalized circumradius of a set of points A with respect to a convex body K is the minimum value of ?. = 0 such that a translate of ?K contains A. We characterize the functions on bounded subsets of R-d that arise from different choices of K, drawing on the theory of diversities. We also study functions obtained by restricting the generalized circumradius to a finite subset of R-d, obtaining elegant characterizations in the case of a simplex or parallelotope.
DISCRETE & COMPUTATIONAL GEOMETRY
(2023)
Article
Mathematics
M. Hellmuth, K. T. Huber, V. Moulton, G. E. Scholz, P. F. Stadler
Summary: This paper studies the properties of split systems, with a focus on injective split systems that can be used to represent symbolic tree maps. The authors prove the existence of an injective split system on any set X and provide a characterization for when a split system is injective. They also introduce related concepts such as injective dimension and provide upper and lower bounds for these dimensions. An important motivation for studying injective split systems is their application in representing three-way symbolic maps.
GRAPHS AND COMBINATORICS
(2023)
Article
Biochemical Research Methods
Vincent Moulton, Taoyang Wu
Summary: We investigated planar rooted phylogenetic networks and found three natural subclasses that form a hierarchy. We also studied the special planarity properties of different level networks and discovered that level-1,-2,-3 networks are always outer, terminal, and upward planar, respectively. Furthermore, we revealed that a regular network is terminal planar only if it is pyramidal. We believe that the relationship between phylogenetic networks and planar graphs can lead to the development of new approaches for constructing and visualizing phylogenetic networks.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Editorial Material
Plant Sciences
Thomas Mock
JOURNAL OF PHYCOLOGY
(2023)
Article
Plant Sciences
Antonia Otte, Johanna C. Winder, Longji Deng, Jeremy Schmutz, Jerry Jenkins, Igor V. Grigoriev, Amanda Hopes, Thomas Mock
Summary: Diatoms are important primary producers in cold, turbulent, and nutrient-rich surface oceans, particularly in polar regions. The cold-adapted pennate diatom Fragilariopsis cylindrus is considered a key species in polar oceans and sea ice due to its ability to thrive in different environmental conditions if temperatures are low. This perspective paper provides insights into recent molecular research on F. cylindrus and discusses its role as a model alga for understanding cold-adapted life.
JOURNAL OF PHYCOLOGY
(2023)
Article
Biology
Suzanne Bennett-Keki, Emily K. Fowler, Leighton Folkes, Simon Moxon, Tracey Chapman
Summary: Differences in lifespan between males and females are influenced by differential responses to diet, with females showing higher dietary sensitivity. This is mediated by higher and more dynamic expression in nutrient-sensing pathways in females. These findings highlight the importance of sex-specific dietary responses on health and lifespan.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Multidisciplinary Sciences
Anthony Duncan, Kerrie Barry, Chris Daum, Emiley Eloe-Fadrosh, Simon Roux, Katrin Schmidt, Susannah G. Tringe, Klaus U. Valentin, Neha Varghese, Asaf Salamov, Igor Grigoriev, Richard M. Leggett, Vincent Moulton, Thomas Mock
Summary: This article presents metagenome-assembled genomes (MAGs) for both eukaryotic and prokaryotic organisms from the Arctic and Atlantic oceans, along with gene prediction and functional annotation for MAGs from both domains. These data provide draft genomes for uncultured marine microbes, including some of the first MAGs for polar eukaryotes, and can be used for genomic comparisons between environments.
Article
Computer Science, Information Systems
Leo van Iersel, Vincent Moulton, Yukihiro Murakami
Summary: Graph invariants are useful in distinguishing non-isomorphic graphs, and there has been interest in defining such invariants for phylogenetic networks. However, the current polynomial invariants for phylogenetic networks require vertex labels or have complex forms. This paper presents polynomial invariants for rooted cactuses that address these challenges and can also be extended to leaf-labelled rooted cactuses and cactuses.
INFORMATION PROCESSING LETTERS
(2023)
Article
Ecology
Taylor Priest, Wilken-Jon von Appen, Ellen Oldenburg, Ovidiu Popa, Sinhue Torres-Valdes, Christina Bienhold, Katja Metfies, William Boulton, Thomas Mock, Bernhard M. Fuchs, Rudolf Amann, Antje Boetius, Matthias Wietz
Summary: The Arctic Ocean is undergoing unprecedented changes due to climate warming, and it is important to analyze the ecology and dynamics of biological communities to understand ecosystem shifts. Through extensive data collection, we assessed the impact of Atlantic water influx and sea-ice cover on bacterial communities in the Arctic Ocean, identified bacterial signature populations, and revealed metabolic distinctions between Arctic and Atlantic conditions. Our findings provide novel insights into Arctic ecology and indicate a progressing Biological Atlantification of the warming Arctic Ocean.
Article
Computer Science, Hardware & Architecture
Katharina T. Huber, Leo van Iersel, Remie Janssen, Mark Jones, Vincent Moulton, Yukihiro Murakami, Charles Semple
Summary: This paper investigates the relationship between undirected and directed phylogenetic networks, and provides corresponding algorithms. The study reveals that the directed phylogenetic network is unique under specific conditions. Additionally, an algorithm for directing undirected binary networks is described, applicable to certain classes of directed phylogenetic networks.
JOURNAL OF COMPUTER AND SYSTEM SCIENCES
(2024)
Review
Environmental Sciences
Madison M. Smith, Helene Angot, Emelia J. Chamberlain, Elise S. Droste, Salar Karam, Morven Muilwijk, Alison L. Webb, Stephen D. Archer, Ivo Beck, Byron W. Blomquist, Jeff Bowman, Matthew Boyer, Deborah Bozzato, Melissa Chierici, Jessie Creamean, Alessandra 'Angelo, Bruno Delille, Ilker Fer, Allison A. Fong, Agneta Fransson, Niels Fuchs, Jessie Gardner, Mats A. Granskog, Clara J. M. Hoppe, Mario Hoppema, Mario Hoppmann, Thomas Mock, Sofia Muller, Oliver Muller, Marcel Nicolaus, Daiki Nomura, Tuukka Petaja, Evgenii Salganik, Julia Schmale, Katrin Schmidt, Kirstin M. Schulz, Matthew D. Shupe, Jacqueline Stefels, Linda Thielke, Sandra Tippenhauer, Adam Ulfsbo, Maria van Leeuwe, Melinda Webster, Masaki Yoshimura, Liyang Zhan
Summary: The rapid melt of snow and sea ice during the Arctic summer contributes to the formation of thin meltwater layers on sea ice, which play a crucial role in the Arctic system by reducing ice melt, facilitating new ice formation, and impacting exchanges between the atmosphere and ocean.
ELEMENTA-SCIENCE OF THE ANTHROPOCENE
(2023)