38 Works

Multimolecular characteristics of cell-death related hub genes in human cancers: a comprehensive pan-cancer analysis

Dingtao Hu, Tingyu Zhang, Ziye Yan, Linlin Wang, Yuhua Wang, Nana Meng, Bizhi Tu, Ying Teng, Zhen Li, Xiaoqi Lou, Yu Lei, Xiaoshuang Ren, Yanfeng Zou & Fang Wang
Failure of the normal process of cell death pathways contributes to the defection of immune systems and the occurrence of cancers. The key genes, the multimolecular mechanisms, and the immune functions of these genes in pan-cancers remain unclear. Using online databases of The Cancer Genome Atlas, GEPIA2, TISIDB, HPA, Kaplan-Meier Plotter, PrognoScan, cBioPortal, GSCALite, TIMER, and Sangerbox, we identified the key genes from the six primary cell death-related pathways and performed a comprehensive analysis to...

Genome and annotation of triploid cultivated banana

Xiuxiu Li, Sheng Yu, Zhihao Cheng, Yingzi Yun, Xuequn Chen, Xing Liu, Hua Li, Wenjun Zhu, Shiyao Xu, Yanbing Xu, Chen Zhang, Xianjun Wang, Xingtan Zhang, Zhenguo Lin, Jean-Marc Aury, Yves Van de Peer, Zonghua Wang, Xiaofan Zhou, Peitao Lü & Liangsheng Zhang
Genome assemblies and annotations of Cavendish and Gros Michel bananas

Swimming and schooling data of golden shiners in variable water temperatures

Maria Kuruvilla, Anthony Dell, Ashley R. Olson, Jason Knouft, John Grady, Jacob Forbes & Andrew Berdahl
Temperature is highly influential on the physiology and behaviour of ectotherms. In fish, temperature affects social interactions such as schooling behaviour, a common defence against predation. However, the effect of temperature on the ability of schooling fish to collectively respond to a predator is unknown. Here we used a loom stimulus to simulate an approaching predator that elicited a fleeing response in schooling fish over a range of water temperatures (9-29°C) and group sizes (1-16...

Data From: TERRA-REF, An open reference data set from high resolution genomics, phenomics, and imaging sensors

David LeBauer, Burnette Maxwell, Jeffrey Demieville, Noah Fahlgren, Andrew French, Roman Garnett, Zhenbin Hu, Kimberly Huynh, Rob Kooper, Zongyang Li, Maitiniyazi Maimaitijiang, Jerome Mao, Todd Mockler, Geoffrey Morris, Maria Newcomb, Michael Ottman, Philip Ozersky, Sidike Paheding, Duke Pauli, Robert Pless, Wei Qin, Kristina Riemer, Gareth Rohde, William Rooney, Vasit Sagan … & Charles Zender
The ARPA-E funded TERRA-REF project is generating open-access reference datasets for the study of plant sensing, genomics, and phenomics. Sensor data were generated by a field scanner sensing platform that captures color, thermal, hyperspectral, and active flourescence imagery as well as three dimensional structure and associated environmental measurements. This dataset is provided alongside data collected using traditional field methods in order to support calibration and validation of algorithms used to extract plot level phenotypes from...

Data from: Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls

Allison J. Miller, Naim Matasci, Heidi Schwaninger, Mallikarjuna K. Aradhya, Bernard Prins, Gan-Yuan Zhong, Charles Simon, Edward S. Buckler & Sean Myles
Understanding relationships among species is a fundamental goal of evolutionary biology. Single nucleotide polymorphisms (SNPs) identified through next generation sequencing and related technologies enable phylogeny reconstruction by providing unprecedented numbers of characters for analysis. One approach to SNP-based phylogeny reconstruction is to identify SNPs in a subset of individuals, and then to compile SNPs on an array that can be used to genotype additional samples at hundreds or thousands of sites simultaneously. Although powerful and...

Data from: Evolution of phenotype-environment associations by genetic responses to selection and phenotypic plasticity in a temporally autocorrelated environment

Matt J. Michel, Luis-Miguel Chevin & Jason H. Knouft
Covariation between population-mean phenotypes and environmental variables, sometimes termed a ‘phenotype-environment association’ (PEA), can result from phenotypic plasticity, genetic responses to natural selection, or both. PEAs can potentially provide information on the evolutionary dynamics of a particular set of populations, but this requires a full theoretical characterization of PEAs and their evolution. Here, we derive formulas for the expected PEA in a temporally fluctuating environment for a quantitative trait with a linear reaction norm. We...

Data from: Influence of introgression and geological processes on phylogenetic relationships of western North American mountain suckers (Pantosteus, Catostomidae)

Peter J. Unmack, Thomas E. Dowling, Nina J. Laitinen, Carol L. Secor, Richard L. Mayden, Dennis K. Shiozawa & Gerald R. Smith
Intense geological activity caused major topographic changes in Western North America over the past 15 million years. Major rivers here are composites of different ancient rivers, resulting in isolation and mixing episodes between river basins over time. This history influenced the diversification of most of the aquatic fauna. The genus Pantosteus is one of several clades centered in this tectonically active region. The eight recognized Pantosteus species are widespread and common across southwestern Canada, western...

Data from: Local population density and group composition influence signal-preference relationships in Enchenopa treehoppers (Hemiptera: Membracidae)

Kasey D. Fowler-Finn, Daniel C. Cruz & Rafael L. Rodriguez
Many animals exhibit social plasticity—changes in phenotype or behavior in response to experience with conspecifics—that change how evolutionary processes like sexual selection play out. Here, we asked whether social plasticity arising from variation in local population density in male advertisement signals and female mate preferences influences the form of sexual selection. We manipulated local density and determined whether this changed how the distribution of male signals overlapped with female preferences—i.e., the signal-mate preference relationship. We...

Data from: Prior information and social experience influence male reproductive decisions

Jesse Balaban-Feld & Thomas J. Valone
Increasing attention has focused on understanding how past experiences can influence and explain variation in mating preferences among individuals. We examined how previous social experiences affected courtship preferences in Drosophila melanogaster by exposing individual males to different frequency distributions of high- and low-quality (HQ and LQ) females and by allowing them to copulate with either a HQ or LQ mate. For a male, a large female represents a high-quality mate while a small female is...

Data from: Multispecies conservation of freshwater fish assemblages in response to climate change in the southeastern United States

Michelle VanCompernolle, Jason H. Knouft & Darren L. Ficklin
Aim: Streamflow and water temperature are primary variables influencing the distribution of freshwater taxa. Climate-induced changes in these variables are already causing shifts in species distributions, with continued changes projected in the coming decades. The Mobile River Basin (MRB), located in the southeastern United States, contains some of the highest levels of temperate freshwater biodiversity in North America. We integrated species distribution data with contemporary and future streamflow and water temperature data as well as...

RAD-seq reveals patterns of diversification, hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees

Alexander Linan, , Allison Miller, George Schatz, Jean Claude Sevathian & Christine Edwards
A common pattern observed in temperate tree clades is that species are often morphologically distinct and partially interfertile but maintain species cohesion despite ongoing hybridization where ranges overlap. Although closely related species commonly occur in sympatry in tropical ecosystems, little is known about patterns of hybridization within a clade over time, and the implications of this hybridization for the maintenance of species boundaries. In this study, we focused on a clade of sympatric trees in...

Dataset for: Water, environment, and socioeconomic justice in California: A multi-benefit cropland repurposing framework

Angel Santiago Fernandez-Bou, José Manuel Rodríguez-Flores, Alexander Guzman, J. Pablo Ortiz-Partida, Leticia Margarita Classen-Rodriguez, Humberto Florez-Landeros, Jorge Valero-Fandiño, Chantelise Pells, Thomas Harmon & Josué Medellín-Azuara
Low-income, rural frontline communities of California’s Central Valley experience environmental and socioeconomic injustice, water insecurity, extremely poor air quality, and lack of fundamental infrastructure (sewage, green areas, health services), which makes them less resilient. Many communities depend financially on agriculture, while water scarcity and associated policy may trigger farmland retirement, further hindering socioeconomic opportunities. Here we propose a multi-benefit framework to repurpose cropland in buffers inside and around (400-m and 1600-m buffers) 154 rural disadvantaged...

Genome and annotation of triploid cultivated banana

Xiuxiu Li, Sheng Yu, Zhihao Cheng, Yingzi Yun, Xuequn Chen, Xing Liu, Hua Li, Wenjun Zhu, Shiyao Xu, Yanbing Xu, Chen Zhang, Xianjun Wang, Xingtan Zhang, Zhenguo Lin, Jean-Marc Aury, Yves Van de Peer, Zonghua Wang, Xiaofan Zhou, Peitao Lü & Liangsheng Zhang
Genome assemblies and annotations of Cavendish and Gros Michel bananas

Registration Year

  • 2022
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Resource Types

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Affiliations

  • Saint Louis University
    38
  • Chinese Academy of Medical Sciences & Peking Union Medical College
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  • Central South University
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  • Huazhong University of Science and Technology
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  • Shanxi Medical University
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  • Washington University in St. Louis
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  • Shanghai Jiao Tong University
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