Search Results - "Xing SHEN"

ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference by Steenwyk, Jacob L, Buida, 3rd, Thomas J, Li, Yuanning, Shen, Xing-Xing, Rokas, Antonis

“…Highly divergent sites in multiple sequence alignments (MSAs), which can stem from erroneous inference of homology and saturation of substitutions, are thought…”
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Contentious relationships in phylogenomic studies can be driven by a handful of genes by Shen, Xing-Xing, Hittinger, Chris Todd, Rokas, Antonis

“…Phylogenomic studies have resolved countless branches of the tree of life, but remain strongly contradictory on certain, contentious relationships. Here, we…”
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Rooting the Animal Tree of Life by Li, Yuanning, Shen, Xing-Xing, Evans, Benjamin, Dunn, Casey W, Rokas, Antonis

“…Abstract Identifying our most distant animal relatives has emerged as one of the most challenging problems in phylogenetics. This debate has major implications…”
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PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data by Steenwyk, Jacob L, Buida, Thomas J, Labella, Abigail L, Li, Yuanning, Shen, Xing-Xing, Rokas, Antonis

“…Abstract Motivation Diverse disciplines in biology process and analyze multiple sequence alignments (MSAs) and phylogenetic trees to evaluate their information…”
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Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets by Zhou, Xiaofan, Shen, Xing-Xing, Hittinger, Chris Todd, Rokas, Antonis

“…The sizes of the data matrices assembled to resolve branches of the tree of life have increased dramatically, motivating the development of programs for fast,…”
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A General Approach to Design Dual Ratiometric Fluorescent and Photoacoustic Probes for Quantitatively Visualizing Tumor Hypoxia Levels In Vivo by Zhang, Shuping, Chen, Hua, Wang, Liping, Qin, Xue, Jiang, Bang‐Ping, Ji, Shi‐Chen, Shen, Xing‐Can, Liang, Hong

“…Herein, we describe an energy balance strategy between fluorescence and photoacoustic effects by sulfur substitution to transform existing hemicyanine dyes…”
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Recent Advances in Carbon Nanomaterials for Cancer Phototherapy by Jiang, Bang‐Ping, Zhou, Bo, Lin, Zhaoxing, Liang, Hong, Shen, Xing‐Can

“…Carbon nanomaterials have received great attention from the scientific community over the past few decades because of their unique physical and chemical…”
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Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts by Steenwyk, Jacob L, Opulente, Dana A, Kominek, Jacek, Shen, Xing-Xing, Zhou, Xiaofan, Labella, Abigail L, Bradley, Noah P, Eichman, Brandt F, Čadež, Neža, Libkind, Diego, DeVirgilio, Jeremy, Hulfachor, Amanda Beth, Kurtzman, Cletus P, Hittinger, Chris Todd, Rokas, Antonis

“…Cell-cycle checkpoints and DNA repair processes protect organisms from potentially lethal mutational damage. Compared to other budding yeasts in the subphylum…”
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The development of three long universal nuclear protein-coding locus markers and their application to osteichthyan phylogenetics with nested PCR by Shen, Xing-Xing, Liang, Dan, Zhang, Peng

“…Universal nuclear protein-coding locus (NPCL) markers that are applicable across diverse taxa and show good phylogenetic discrimination have broad applications…”
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An investigation of irreproducibility in maximum likelihood phylogenetic inference by Shen, Xing-Xing, Li, Yuanning, Hittinger, Chris Todd, Chen, Xue-xin, Rokas, Antonis

“…Phylogenetic trees are essential for studying biology, but their reproducibility under identical parameter settings remains unexplored. Here, we find that 3515…”
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OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees by Steenwyk, Jacob L, Goltz, Dayna C, Buida, Thomas J, Li, Yuanning, Shen, Xing-Xing, Rokas, Antonis

“…Molecular evolution studies, such as phylogenomic studies and genome-wide surveys of selection, often rely on gene families of single-copy orthologs (SC-OGs)…”
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Exosomes Derived from Mesenchymal Stem Cells Rescue Myocardial Ischaemia/Reperfusion Injury by Inducing Cardiomyocyte Autophagy Via AMPK and Akt Pathways by Liu, Liang, Jin, Xian, Hu, Cui-Fen, Li, Rong, Zhou, Zhong’e, Shen, Cheng-Xing

“…Background/Aims: Reperfusion after an ischaemic insult might cause infarct extension. Mesenchymal stem cell (MSC)-derived exosomes could attenuate myocardial…”
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Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum by Shen, Xing-Xing, Opulente, Dana A., Kominek, Jacek, Zhou, Xiaofan, Steenwyk, Jacob L., Buh, Kelly V., Haase, Max A.B., Wisecaver, Jennifer H., Wang, Mingshuang, Doering, Drew T., Boudouris, James T., Schneider, Rachel M., Langdon, Quinn K., Ohkuma, Moriya, Endoh, Rikiya, Takashima, Masako, Manabe, Ri-ichiroh, Čadež, Neža, Libkind, Diego, Rosa, Carlos A., DeVirgilio, Jeremy, Hulfachor, Amanda Beth, Groenewald, Marizeth, Kurtzman, Cletus P., Hittinger, Chris Todd, Rokas, Antonis

“…Budding yeasts (subphylum Saccharomycotina) are found in every biome and are as genetically diverse as plants or animals. To understand budding…”
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PhyloFisher: A phylogenomic package for resolving eukaryotic relationships by Tice, Alexander K, Zihala, David, Pánek, Tomás, Jones, Robert E, Salomaki, Eric D, Nenarokov, Serafim, Burki, Fabien, Eliás, Marek, Eme, Laura, Roger, Andrew J, Rokas, Antonis, Shen, Xing-Xing, Strassert, Jürgen F. H, Kolísko, Martin, Brown, Matthew W

“…Phylogenomic analyses of hundreds of protein-coding genes aimed at resolving phylogenetic relationships is now a common practice. However, no software…”
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HGT is widespread in insects and contributes to male courtship in lepidopterans by Li, Yang, Liu, Zhiguo, Liu, Chao, Shi, Zheyi, Pang, Lan, Chen, Chuzhen, Chen, Yun, Pan, Ronghui, Zhou, Wenwu, Chen, Xue-xin, Rokas, Antonis, Huang, Jianhua, Shen, Xing-Xing

“…Horizontal gene transfer (HGT) is an important evolutionary force shaping prokaryotic and eukaryotic genomes. HGT-acquired genes have been sporadically…”
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Evolutionary instability of CUG-Leu in the genetic code of budding yeasts by Krassowski, Tadeusz, Coughlan, Aisling Y., Shen, Xing-Xing, Zhou, Xiaofan, Kominek, Jacek, Opulente, Dana A., Riley, Robert, Grigoriev, Igor V., Maheshwari, Nikunj, Shields, Denis C., Kurtzman, Cletus P., Hittinger, Chris Todd, Rokas, Antonis, Wolfe, Kenneth H.

“…The genetic code used in nuclear genes is almost universal, but here we report that it changed three times in parallel during the evolution of budding yeasts…”
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Surface‐Enhanced Raman Probes Based on Gold Nanomaterials for in vivo Diagnosis and Imaging by Wen, Changchun, Wang, Liping, Liu, Li, Shen, Xing‐Can, Chen, Hua

“…Surface‐enhanced Raman scattering (SERS) has received considerable attention from researchers due to its high molecular specificity, high sensitivity,…”
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Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data by Shen, Xing-Xing, Zhou, Xiaofan, Kominek, Jacek, Kurtzman, Cletus P, Hittinger, Chris Todd, Rokas, Antonis

“…Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their…”
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Recent progress in metal complexes functionalized nanomaterials for photodynamic therapy by Wei, Fangmian, Chen, Zhuoli, Shen, Xing-Can, Ji, Liangnian, Chao, Hui

“…Metal complexes have shown promise as photosensitizers for cancer diagnosis and therapeutics. However, the vast majority of metal photosensitizers are not…”
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Near-infrared-II-activatable sulfur-deficient plasmonic Bi2S3-x-Au heterostructures for photoacoustic imaging-guided ultrasound enhanced high performance phototherapy by Meng, Nianqi, Xu, Peijing, Wen, Changchun, Liu, Huihui, Gao, Cunji, Shen, Xing-Can, Liang, Hong

“…An “all-in-one” phototheranostic nanoplatform based on a single NIR-II light-responsive Schottky-type Bi2S3-x-Au heterostructure for photoacoustic…”
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