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Ashley I. Teufel, Jing Zhao, Malgorzata O'Reilly, Liang Liu and David A. Liberles
Characterizing the mechanisms of duplicate gene retention using phylogenetic methods requires models that are consistent with different biological processes. The interplay between complex biological processes and necessarily simpler statistical models le...
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Nadia El-Mabrouk
Syntenies are genomic segments of consecutive genes identified by a certain conservation in gene content and order. The notion of conservation may vary from one definition to another, the more constrained requiring identical gene contents and gene orders...
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Brona Brejová and Rastislav Královic
In the reconciliation problem, we are given two phylogenetic trees. A species tree represents the evolutionary history of a group of species, and a gene tree represents the history of a family of related genes within these species. A reconciliation maps ...
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Sultan Noman Qasem, Saeed Samadianfard, Hamed Sadri Nahand, Amir Mosavi, Shahaboddin Shamshirband and Kwok-wing Chau
In the current study, the ability of three data-driven methods of Gene Expression Programming (GEP), M5 model tree (M5), and Support Vector Regression (SVR) were investigated in order to model and estimate the dew point temperature (DPT) at Tabriz statio...
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Joaquim Carreras, Yara Yukie Kikuti, Masashi Miyaoka, Shinichiro Hiraiwa, Sakura Tomita, Haruka Ikoma, Yusuke Kondo, Atsushi Ito, Naoya Nakamura and Rifat Hamoudi
The prognosis of diffuse large B-cell lymphoma (DLBCL) is heterogeneous. Therefore, we aimed to highlight predictive biomarkers. First, artificial intelligence was applied into a discovery series of gene expression of 414 patients (GSE10846). A dimension...
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Ruriko Yoshida, Lillian Paul and Peter Nesbitt
Unweighted Pair Group Method with Arithmetic Mean (UPGMA) is one of the most popular distance-based methods to reconstruct an equidistant phylogenetic tree from a distance matrix computed from an alignment of sequences. Since we use equidistant trees as ...
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Qiaoji Xu, Lingling Jin, James H. Leebens-Mack and David Sankoff
The RACCROCHE pipeline reconstructs ancestral gene orders and chromosomal contents of the ancestral genomes at all internal vertices of a phylogenetic tree. The strategy is to accumulate a very large number of generalized adjacencies, phylogenetically ju...
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Shaymaa H. Ali, Jaladet M. S. Jubrael, Caroline Bowsher
Pág. 1 - 10
Introduction: DNA sequencing-based methods and nucleotide sequence analysis have become the most common molecular approaches currently used for molecular typing purposes and phylogenetic diversity analysis. Methods: In this study, the nucleotide sequence...
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Jeonghoon Han, Han-Jun Kim, Kyun-Woo Lee and Young-Ung Choi
In this study, we document the first recorded range extension of the genus Synaphobranchus from the East Mariana Basin in the Western Pacific Ocean. We sequenced the complete mitochondrial (mt) genome of two deep-sea eels (Synaphobranchus brevidorsalis a...
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Elad Nehoray Rachmilovitz, Omri Shabbat, Maayan Yerushalmy and Baruch Rinkevich
Accurate identification of scleractinian coral species is fundamental for proper biodiversity estimates, for aiding in efforts of reef monitoring, conservation, restoration, and for the management of coral reefs. Here, we provide the first DNA barcoding ...
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Bo Liu, Yali Yan, Nan Zhang, Huayang Guo, Baosuo Liu, Jingwen Yang, Kecheng Zhu and Dianchang Zhang
Species markers can be quickly and accurately assessed using DNA barcoding. We investigated samples from the parrotfish family Scaridae using DNA barcoding in Hainan. A total of 401 DNA barcodes were analyzed, including 51 new barcodes generated from fre...
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Minhyuk Park, Paul Zaharias and Tandy Warnow
The estimation of phylogenetic trees for individual genes or multi-locus datasets is a basic part of considerable biological research. In order to enable large trees to be computed, Disjoint Tree Mergers (DTMs) have been developed; these methods operate ...
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Angelo Ciaramella and Antonino Staiano
As of today, bioinformatics is one of the most exciting fields of scientific research. There is a wide-ranging list of challenging problems to face, i.e., pairwise and multiple alignments, motif detection/discrimination/classification, phylogenetic tree ...
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Soroush Rashidi, Prakash Ranjitkar, Orosz Csaba, Andy Hooper
Pág. 1444 - 1456
Bunching is recognized as one of the deteriorating factors affecting the performance of public transport networks. In this study, for the first time, Gene Expression Programming (GEP) and Decision Tree (DT) methods are utilized to estimate and model bus ...
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Enrique Hernández-Tecles,Jorge de las Heras,Zaida Lorenzo,Miguel Navascués,Ricardo Alia
Pág. e05S
Aim of study: To contribute to the characterization of the origin of material used in afforestation, restoration or conservation activities by using Cp-SSR markers.Area of study: We used information from the natural range of Iberian pines, from Spain.Mat...
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Yanchao Yuan, Ningning Zhou, Shuaishuai Bai, Feng Zeng, Chunying Liu, Yuxi Zhang, Shupeng Gai and Weiling Gai
The brief longevity of tree peony blossoms constrains its ornamental value and economic worth. Gibberellins (GAs) are crucial in the modulation of flower senescence, and GA 20-oxidase (GA20ox), GA 3-oxidase (GA3ox), and GA 2-oxidase (GA2ox) catalyze the ...
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Hang Ye, Hengzhao Liu, Mian Han, Naiyu Zhang, Xiaolong Feng, Ting Gao, Dingfan Lei, Haochen Li, Zhimei Gao, Yu Su, Min Chai, Huijuan Zhou and Yiling Wang
Plant NAPDH oxidase (NOX) gene family members are critical producers of ROS and play crucial roles in plant signaling, development, and stress responses. Opisthopappus taihangensis is a pivotal wild genetic resource in Asteraceae. To date, little knowled...
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Giusy D?Attoma, Angelantonio Minafra, Pasquale Saldarelli and Massimiliano Morelli
Wisteria vein mosaic virus (WVMV) is a member of the genus Potyvirus, found to be associated with the Wisteria mosaic disease (WMD). In 2022, severe symptoms resembling WMD were observed on the foliage of a Chinese wisteria (Wisteria sinensis) tree growi...
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Tao Zhang, Ju Cai, Sisi Wang, Litang Lv, Dandan Yuan, Xiaofang Zeng, Jianrong Li and Yan Li
The ERF gene family is widely present in plants and has crucial regulatory importance in plant seed development, organ morphogenesis, the synthesis of secondary metabolites, and coping with abiotic stresses such as cold and drought. In this study, 90 mem...
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Aijun Cui, Yongjiang Xu, Kiyoshi Kikuchi, Yan Jiang, Bin Wang, Takashi Koyama and Xuezhou Liu
To clarify the population genetic structure, intrapopulation diversity, and interpopulation differentiation of yellowtail kingfish (Seriola aureovittata), we sampled 143 individuals from five collections of yellowtail kingfish: farmed (n = 30) and wild (...
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