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Everything Everywhere All at Once? Disentangling the long-lasting riddle of phylogenetic relationships and cryptic hybridization in the amphitropical genus Larrea
M Paula Quiroga and others
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AoB PLANTS
AoB PLANTS, plaf024, https://doi.org/10.1093/aobpla/plaf024
Published: 25 April 2025
...) sequences of the bifoliolate section, Bifolium, including L. tridentata (Lt) from North America, and its South American congeners: L. cuneifolia (Lc) and L. divaricata (Ld), and sequences of the multifoliolate Larrea section: L...
Journal Article
Sequence analysis of the hepatitis D virus across genotypes reveals highly conserved regions amidst evidence of recombination
Shruti Chowdhury and others
Virus Evolution, Volume 11, Issue 1, 2025, veaf012, https://doi.org/10.1093/ve/veaf012
Published: 27 February 2025
... License ( https://creativecommons.org/licenses/by/4.0/ ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Sequence diversity of the hepatitis D virus (HDV) may impact viral clearance, contributing to the development...
Journal Article
Analysis of Ga2 genome structure and activity reveals widespread distribution of functional alleles in modern maize germplasm
Adrienne N Moran Lauter and others
G3 Genes|Genomes|Genetics, Volume 15, Issue 5, May 2025, jkaf035, https://doi.org/10.1093/g3journal/jkaf035
Published: 21 February 2025
... of Ga2P in Zea mays in the apparent absence of a functional female factor remains unclear and may be evidence for an additional role in reproductive tissues. maize cross incompatibility repeated sequences pseudogenes evolution U.S. Department of Agriculture, Agricultural Research Service...
Journal Article
Disentangling the stylonychine ciliates (Ciliophora: Hypotricha): the establishment of two new genera using an integrative taxonomic approach
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Atef Omar and Jae-Ho Jung
Zoological Journal of the Linnean Society, Volume 202, Issue 4, December 2024, zlae144, https://doi.org/10.1093/zoolinnean/zlae144
Published: 02 December 2024
.... nov Apostylonychia gen. nov multigene sequences new combinations new generic characters new species Tetmemena Stylonychine ciliates are one of the most common groups in freshwater habitats, with only a few members found in terrestrial, semiterrestrial, and brackish water...
Journal Article
An efficient deep learning method for amino acid substitution model selection
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Nguyen Huy Tinh and Le Sy Vinh
Journal of Evolutionary Biology, Volume 38, Issue 1, January 2025, Pages 129–139, https://doi.org/10.1093/jeb/voae141
Published: 16 November 2024
... Journals Publication Model ( https://dbpia.nl.go.kr/pages/standard-publication-reuse-rights ) Abstract Amino acid substitution models play an important role in studying the evolutionary relationships among species from protein sequences. The amino acid substitution model consists of a large number...
Journal Article
Evolutionary history written in tandem arrays – satellite repeats in the Lagoseris lineage of Crepis sensu lato (Asteraceae)
Gülru Yücel and others
Botanical Journal of the Linnean Society, boae067, https://doi.org/10.1093/botlinnean/boae067
Published: 05 November 2024
...Gülru Yücel; Natalia Borowska-Zuchowska; Maciej Bisaga; Teresa Nowak; Bozena Kolano The presence of putative satellite sequences in the genomes of Crepis s.s. was analysed using dot blot hybridization to verify if the studied satellite repeats were specific to the Lagoseris group...
Journal Article
Tree Sequences as a General-Purpose Tool for Population Genetic Inference
Logan S Whitehouse and others
Molecular Biology and Evolution, Volume 41, Issue 11, November 2024, msae223, https://doi.org/10.1093/molbev/msae223
Published: 26 October 2024
... unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract As population genetic data increase in size, new methods have been developed to store genetic information in efficient ways, such as tree sequences. These data structures...
Journal Article
Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders
Simone Rancati and others
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae535, https://doi.org/10.1093/bib/bbae535
Published: 24 October 2024
...Simone Rancati; Giovanna Nicora; Mattia Prosperi; Riccardo Bellazzi; Marco Salemi; Simone Marini We converted aa sequences into fixed-length numeric features using k-mers, with k = 3 according to previous works [ 22 , 23 ]. In other words, we represent each Spike protein...
Journal Article
Advancing microbial diagnostics: a universal phylogeny guided computational algorithm to find unique sequences for precise microorganism detection
Gulshan Kumar Sharma and others
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae545, https://doi.org/10.1093/bib/bbae545
Published: 23 October 2024
...Gulshan Kumar Sharma; Rakesh Sharma; Kavita Joshi; Sameer Qureshi; Shubhita Mathur; Sharad Sinha; Samit Chatterjee; Vandana Nunia Table 1 Some of the unique nucleotide MTB (H37Rv) 100-mer sequences predicted by NAUniSeq algorithm S. no. Unique nucleotide sequences 1...
Journal Article
Evolutionary Innovations in Conserved Regulatory Elements Associate With Developmental Genes in Mammals
Severin Uebbing and others
Molecular Biology and Evolution, Volume 41, Issue 10, October 2024, msae199, https://doi.org/10.1093/molbev/msae199
Published: 20 September 2024
...- and time point-specific gene expression programs. Genetic variation within enhancer sequences is an important contributor to phenotypic variation including evolutionary adaptations and human disease. Certain genes and pathways may be more prone to regulatory evolution than others, with different patterns...
Journal Article
Prevalent Fast Evolution of Genes Involved in Heterochromatin Functions
Leila Lin and others
Molecular Biology and Evolution, Volume 41, Issue 9, September 2024, msae181, https://doi.org/10.1093/molbev/msae181
Published: 27 August 2024
... domain and provides insights into the factors driving the distinctive evolution of heterochromatin. heterochromatin protein evolution transposable elements repetitive sequences arms race positive selection Cancer Research Foundation 10.13039/100002002 NIH 10.13039/501100012264 NIH...
Journal Article
Two sides of the same coin? Transient hybridization in refugia and rapid postglacial ecological divergence ensure the evolutionary persistence of sister Nothofagus
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Andrea C Premoli and others
Journal of Evolutionary Biology, Volume 37, Issue 10, October 2024, Pages 1181–1193, https://doi.org/10.1093/jeb/voae100
Published: 21 August 2024
... used pollen records and genetic information (isozymes, microsatellites, and combined nuclear and chloroplast DNA sequences) of population pairs of Nothofagus antarctica and N. pumilio that belong to the ancient subgenus Nothofagus which can potentially hybridize in nature...
Journal Article
Testing the PEST hypothesis using relevant Rett mutations in MeCP2 E1 and E2 isoforms
Ladan Kalani and others
Human Molecular Genetics, Volume 33, Issue 21, 1 November 2024, Pages 1833–1845, https://doi.org/10.1093/hmg/ddae119
Published: 14 August 2024
... at the differing expression levels of MeCP2 mutants and study their correlation with the corresponding in vivo mouse models. Over the years, our lab has been interested in PEST sequences [ 26 ] that regulate MeCP2 degradation by the proteasome [ 27 ]. As mentioned, degradation by the proteasome has been...
Journal Article
Clinical Presentation of Early Syphilis and Genomic Sequences of Treponema pallidum Strains in Patient Specimens and Isolates Obtained by Rabbit Inoculation
Ligang Yang and others
The Journal of Infectious Diseases, Volume 230, Issue 6, 15 December 2024, Pages e1322–e1333, https://doi.org/10.1093/infdis/jiae322
Published: 17 June 2024
... with secondary syphilis (SS) in Guangzhou, China, for Treponema pallidum subsp pallidum (TPA) quantitative polymerase chain reaction, whole genome sequencing (WGS), and isolation of TPA in rabbits. Results TPA DNA was detected in 15 of 17 ulcer exudates and 3...
Journal Article
COATi: Statistical Pairwise Alignment of Protein-Coding Sequences
Juan José García Mesa and others
Molecular Biology and Evolution, Volume 41, Issue 7, July 2024, msae117, https://doi.org/10.1093/molbev/msae117
Published: 13 June 2024
... and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact [email protected]. Abstract Sequence alignment is an essential method in bioinformatics...
Journal Article
MRI susceptibility artefacts caused by orthodontic wire
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Yuri Iwamoto and others
Dentomaxillofacial Radiology, Volume 53, Issue 6, September 2024, Pages 396–406, https://doi.org/10.1093/dmfr/twae023
Published: 13 June 2024
... , 24 The aim of the present study was to objectively evaluate the magnetic susceptibility artefacts (black and white artefacts) according to ASTM F2119-07 definition which produced by orthodontic wires of various materials and the influence of various MR image sequences on the magnitude of the artefact...
Journal Article
Comparing flow and pulmonary artery growth post-patent ductus arteriosus stenting in patients with ductal-dependent pulmonary flow using 4D magnetic resonance imaging
Faiza A Al Kindi and others
European Heart Journal - Imaging Methods and Practice, Volume 2, Issue 1, January 2024, qyae044, https://doi.org/10.1093/ehjimp/qyae044
Published: 14 May 2024
... included magnetic resonance angiography (MRA) sequences to assess the PAs in addition to the 4D-flow sequences. MRA and 4D-flow data were acquired after the bolus injection of 0.2–0.4 mmol/kg gadolinium-based contrast agent. Abstract Aims The 4D magnetic resonance imaging (4D-flow MRI) provides...
Journal Article
Corallococcus senghenyddensis sp. nov., a myxobacterium with potent antimicrobial activity
Benita S Arakal and others
Journal of Applied Microbiology, Volume 135, Issue 5, May 2024, lxae102, https://doi.org/10.1093/jambio/lxae102
Published: 22 April 2024
... Candida parapsilosis DSM 4237 Candida tropicalis DSM 1346 Clavispora lusitaniae DSM 70102 Meyerozyma guilliermondii DSM 6381 Corallococcus genome sequences antimicrobial peptide predation biofilm Applied Microbiology International Impact Statement...
Journal Article
Fuzzy kernel evidence Random Forest for identifying pseudouridine sites
Mingshuai Chen and others
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae169, https://doi.org/10.1093/bib/bbae169
Published: 15 April 2024
..., there is a growing need for computational techniques that can reliably and quickly identify pseudouridine sites from vast amounts of RNA sequencing data. In this study, we propose fuzzy kernel evidence Random Forest (FKeERF) to identify pseudouridine sites. This method is called PseU-FKeERF, which demonstrates high...
Journal Article
Multigene phylogeny and expanded morphological comparison reveal one new lineage and finer differentiation in the order Peniculida (Alveolata: Ciliophora)
Tian Wang and others
Zoological Journal of the Linnean Society, Volume 203, Issue 1, January 2025, zlae028, https://doi.org/10.1093/zoolinnean/zlae028
Published: 13 March 2024
...; Fig. S1). This test aimed to determine whether alternative hypotheses significantly deviate from our retrieved phylogenetic assumptions, which were based on SSU rDNA and concatenated sequences ( Figs 1 , 2 ) ( Shimodaira 2002 ). In order to reinforce the assumed relationships between the respective...
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