Article
Biology
Martin J. Sergeant, Jim R. Hughes, Lance Hentges, Gerton Lunter, Damien J. Downes, Stephen Taylor
Summary: The web-based tool Multi Locus View allows researchers to interact with genomics datasets at multiple scales. Users can browse, annotate, combine or analyze raw data on this platform. User-generated datasets can also be made public, increasing access to genomic data for the academic community.
COMMUNICATIONS BIOLOGY
(2021)
Article
Engineering, Electrical & Electronic
Zhikai Xing, Yigang He
Summary: A novel multi-modal information analysis method is proposed to evaluate power transformer fault effectively and quickly. The method utilizes a Selective Kernel Network, a bidirectional gated recurrent unit, and a cross attention mechanism, resulting in higher diagnostic accuracy and shorter diagnostic time compared to other approaches.
INTERNATIONAL JOURNAL OF ELECTRICAL POWER & ENERGY SYSTEMS
(2023)
Article
Computer Science, Artificial Intelligence
Parisa Niloofar, Sanja Lazarova-Molnar
Summary: Fault tree analysis is a probability-based technique to estimate the risk of an undesired top event, with the integration of IoT devices allowing for the extraction of fault trees that reflect the true fault-related behavior of systems. The DDFTAnb algorithm is proposed for learning fault trees using time series data, enhancing the estimation of future fault-related behavior using Naive Bayes classifiers and estimating system reliability through proxel-based simulation.
EXPERT SYSTEMS WITH APPLICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Muhammad Saqib Sohail, Raymond H. Y. Louie, Zhenchen Hong, John P. Barton, Matthew R. McKay
Summary: This article introduces a method for inferring epistasis and the fitness effects of individual mutations from observed evolutionary histories. Simulations show that this method can accurately infer pairwise epistatic interactions when there is sufficient genetic diversity in the data.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Cell Biology
Stephen Lindsly, Can Chen, Sijia Liu, Scott Ronquist, Samuel Dilworth, Michael Perlman, Indika Rajapakse
Summary: Researchers have developed the '4DNvestigator', a network-based toolbox for analyzing time series genome-wide genome structure and gene expression data, as well as methods for quantifying significant changes in time series Hi-C data at different genomic scales.
Article
Chemistry, Multidisciplinary
Jingzhou Wang, Huachao Xie, Yuanqing Wang, Runhai Ouyang
Summary: In this study, a method of sign-constrained multi-task learning was used to distill accurate descriptors from multi-source experimental data for accelerated catalyst discovery. A new 2D descriptor (dB, nB) based on 13 experimental data sets was obtained, showing great universality, predictive accuracy, and bulk-surface correspondence. Hundreds of unreported candidate perovskites with activity greater than the benchmark catalyst Ba0.5Sr0.5Co0.8Fe0.2O3 were identified, and experimental validations confirmed the high activity of three perovskite catalysts. This work provides an important new approach for dealing with inconsistent multi-source data in data-driven catalysis and beyond.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Computer Science, Artificial Intelligence
Alperen Karan, Atabey Kaygun
Summary: This paper introduces topological data analysis methods for classification tasks on univariate time series, enhancing accuracy and reducing noise through stable topological features and subwindow processing.
EXPERT SYSTEMS WITH APPLICATIONS
(2021)
Article
Computer Science, Information Systems
Ashton T. Williams, Ryan E. Sperl, Soon M. Chung
Summary: This paper proposes a new multi-seasonal forecasting model for anomaly detection in time series data. The model is able to accurately capture multiple seasonal patterns in the data.
Article
Engineering, Mechanical
Huimei Ma, Xiaofan Lu, Linan Zhang
Summary: In this paper, a data-driven regression approach is proposed to identify parametric governing equations from time-series data. Iterative computations are performed for each time stamp to determine if the governing equations to be recovered are time dependent. The results are then used to extract the parametric equations. The proposed method outperforms other sparse-promoting algorithms in identifying parametric differential equations in the low-noise regime in terms of accuracy and computation time.
NONLINEAR DYNAMICS
(2023)
Article
Environmental Sciences
Liujun Zhu, Shanshui Yuan, Yi Liu, Cheng Chen, Jeffrey P. Walker
Summary: Time series algorithms for soil moisture retrieval from SAR data have gained popularity due to their feasibility and the availability of dense time series SAR data. However, how to constrain a time series retrieval for global soil moisture mapping is still unresolved. In this study, three kinds of time series constraints were developed and evaluated, providing suggestions for improving soil moisture retrieval.
REMOTE SENSING OF ENVIRONMENT
(2023)
Article
Physics, Multidisciplinary
Anass B. El-Yaagoubi, Moo K. Chung, Hernando Ombao
Summary: This article introduces the concepts and applications of topological data analysis (TDA), as well as a method for analyzing multivariate time series data. The focus is on the application to multivariate brain signals and brain connectivity networks, and the article explores some open problems and potential applications in modeling brain network directionality and capturing variations in topological properties of data collected from multiple subjects.
Article
Physics, Multidisciplinary
Sreekanth K. Manikandan, Subhrokoli Ghosh, Avijit Kundu, Biswajit Das, Vipin Agrawal, Dhrubaditya Mitra, Ayan Banerjee, Supriya Krishnamurthy
Summary: The paper proposes a minimal strategy using the short-time Thermodynamic Uncertainty Relation (TUR) to infer the thermodynamic force field and entropy production rate from experimental short-time trajectory data. The authors successfully benchmarked this scheme in experimental particle systems and hydrodynamic flow fields, demonstrating its effectiveness in estimating entropy production rate.
COMMUNICATIONS PHYSICS
(2021)
Article
Energy & Fuels
Sambeet Mishra, Chiara Bordin, Kota Taharaguchi, Adri Purkayastha
Summary: This study proposes an event-based prediction method for data-driven decision-making, which effectively reduces computational time and data volume while maintaining high prediction accuracy. The method is applied to a wind power dataset, and the experimental results show its superiority over traditional time series prediction methods.
Article
Biochemical Research Methods
Margaret R. Woodhouse, Shatabdi Sen, David Schott, John L. Portwood, Michael Freeling, Justin W. Walley, Carson M. Andorf, James C. Schnable
Summary: RNA-Seq whole-genome sequencing has become a widely used method for measuring and understanding transcriptome-level changes in gene expression. The comparative gene expression tool qTeller has been revamped to take advantage of the growing number of public RNA-Seq datasets, enabling users to evaluate gene expression data in a defined genomic interval and perform two-gene comparisons across multiple user-chosen tissues. The updated qTeller now supports multiple genomes for intergenomic comparisons, and includes capabilities for both mRNA and protein abundance datasets, along with support for additional data formats and a modernized interface.
Article
Computer Science, Information Systems
Xinyu Zou, Xiangnan Liu, Meiling Liu, Lingwen Tian, Lihong Zhu, Qian Zhang
Summary: Earth observation technology has enhanced the detection of land cover changes, but existing pixel-based methods are insufficient for describing the spatial-temporal association of geographic objects. Thus, a method based on spatiotemporal graphs was developed to analyze land cover evolution. This approach generated a graph from a time series of land cover maps, capturing the spatial and temporal relationships between land cover objects. The method was applied to analyze land cover evolution in Fujian Province, China, providing valuable insights for long-term land cover dynamics and geospatial applications.
INTERNATIONAL JOURNAL OF GEOGRAPHICAL INFORMATION SCIENCE
(2023)
Article
Evolutionary Biology
Neda Barghi, Christian Schloetterer
GENOME BIOLOGY AND EVOLUTION
(2020)
Article
Evolutionary Biology
Claire Burny, Viola Nolte, Pierre Nouhaud, Marlies Dolezal, Christian Schloetterer
GENOME BIOLOGY AND EVOLUTION
(2020)
Article
Biochemistry & Molecular Biology
Ana Marija Jaksic, Julia Karner, Viola Nolte, Sheng-Kai Hsu, Neda Barghi, Francois Mallard, Kathrin Anna Otte, Lidija Svecnjak, Kirsten-Andre Senti, Christian Schloetterer
MOLECULAR BIOLOGY AND EVOLUTION
(2020)
Article
Biochemistry & Molecular Biology
Sheng-Kai Hsu, Chaimae Belmouaden, Viola Nolte, Christian Schloetterer
Summary: The study compared expression profiles of replicated Drosophila melanogaster populations exposed to two different temperature regimes in the laboratory for more than 80 generations. It identified genes and gene modules that evolved in the same direction in both temperature regimes, reflecting adaptation to common selection pressures. Additionally, temperature-specific expression changes were observed, with overlap between adaptive genes in experimental evolution and natural Drosophila populations along different temperature clines.
Article
Biochemistry & Molecular Biology
Kathrin A. Otte, Christian Schloetterer
Summary: Shifting from SNP analysis to haplotype reconstruction improves the interpretation of E&R experiments, with haplovalidate allowing for detection of selected haplotypes in Pool-seq data.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Evolutionary Biology
Anna Maria Langmueller, Marlies Dolezal, Christian Schloetterer
Summary: Evolve and Resequence (E&R) studies explore the genomic selection response of populations in Experimental Evolution setups. Secondary E&R, as a promising experimental follow-up procedure, can enhance mapping resolution by allowing for additional recombination events. The crossing scheme and population size are crucial factors determining the power and resolution of secondary E&R, with a minimum population size of 4,800 individuals needed to achieve at least 75% power.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
Claire Burny, Viola Nolte, Marlies Dolezal, Christian Schloetterer
Summary: This study used a modified evolve and resequence (E&R) design to investigate polygenic adaptation in fruit flies, by exposing them to a high-temperature environment. The findings suggest that the X chromosome shows a stronger selection response than autosomes, possibly due to dominance effects, and that adaptive responses were more pronounced in a two-genotype experiment compared to classic E&R studies.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Wei-Yun Lai, Christian Schloetterer
Summary: The study found that after 100 generations of adaptation to a new laboratory environment, the variance of gene expression in Drosophila simulans males was significantly reduced in 125 and 97 genes, suggesting that the drastic loss in environmental complexity may have triggered selection for reduced variance. This observation could have important implications for studies of adaptation processes in natural and experimental populations.
Article
Biology
Rupert Mazzucco, Christian Schloetterer
Summary: The influence of the microbiome on its host is well-documented, but the interplay among members of the microbiome is not yet well-understood. Longitudinal studies provide a promising approach to studying such interactions, and a recent study found that the composition of microbiome changes systematically across different temperature regimes, indicating functional interdependence among different microbiome components.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Genetics & Heredity
Manolis Lirakis, Viola Nolte, Christian Schloetterer
Summary: The genetic basis of adaptation to different environments has long been of interest to evolutionary biologists. This study performed a genome-wide scan on the sibling species of D. melanogaster, D. simulans, to characterize the genetic basis of dormancy. The results suggest that dormancy is a polygenic trait with many loci of small effect.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Robert Kofler, Viola Nolte, Christian Schlotterer
Summary: The dynamics of transposable element invasions are influenced by multiple factors, and the transposition rate is only one of them. By studying the temperature-dependent activity of the P-element, researchers found that despite differences in transposition rates, the copy numbers of the P-element were very similar at different temperatures. The decrease in insertion rate as the copy number approached a plateau was accompanied by the production of piRNAs. However, fewer P-element insertions were observed in piRNA clusters than expected, indicating that factors other than the trap model influenced the dynamics of TE invasions.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Claire Burny, Viola Nolte, Marlies Dolezal, Christian Schloetterer
Summary: Experimental evolution combined with whole-genome sequencing is a powerful method to study the adaptive architecture of selected traits. This study shows that the presence of a second stressor affects the genomic selection response, and the combination of temperature and laboratory adaptation results in widespread synergistic effects.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Review
Biology
Christian Schloetterer
Summary: Experimental evolution is a useful tool for testing the predictability of evolution without the confounding effects of inaccurate forecasts. Parallel evolution has been studied in both asexual microorganisms and sexual species, but the predictability varies between different aspects. The predictability of genomic selection response for polygenic traits depends on the founder population and the adaptive architecture in the ancestral populations.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Eirini Christodoulaki, Viola Nolte, Wei-Yun Lai, Christian Schloetterer
Summary: This study proposes a new measurement of pleiotropy by integrating information from multiple phenotypes and generations. The results suggest that multiple loci of weak effect contribute to pleiotropy at the genome-wide level. The study also suggests that the modular architecture of gene expression can reduce the costs of pleiotropy.
Article
Biotechnology & Applied Microbiology
Kathrin A. Otte, Viola Nolte, Francois Mallard, Christian Schloetterer
Summary: Understanding the genetic architecture of temperature adaptation is crucial for predicting the impact of climate change on natural populations. Research showed that the adaptive architecture is more dependent on the ancestry of the founder population rather than the specific selection regime, as replicate populations from different environments demonstrated similar responses to cold temperature adaptation.