Search Results - "Fleming, James F."

nRCFV: a new, dataset-size-independent metric to quantify compositional heterogeneity in nucleotide and amino acid datasets by Fleming, James F, Struck, Torsten H

“…Compositional heterogeneity-when the proportions of nucleotides and amino acids are not broadly similar across the dataset-is a cause of a great number of…”
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The Evolution of Temperature and Desiccation-Related Protein Families in Tardigrada Reveals a Complex Acquisition of Extremotolerance by Fleming, James F, Pisani, Davide, Arakawa, Kazuharu

“…Tardigrada is an ecdysozoan lineage famed for its resilience. Tardigrades can tolerate high doses of radiation, low-oxygen environments, desiccation, and both…”
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Identifying and addressing methodological incongruence in phylogenomics: A review by Fleming, James F., Valero‐Gracia, Alberto, Struck, Torsten H.

“…The availability of phylogenetic data has greatly expanded in recent years. As a result, a new era in phylogenetic analysis is dawning—one in which the methods…”
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A Novel Approach to Investigate the Effect of Tree Reconstruction Artifacts in Single-Gene Analysis Clarifies Opsin Evolution in Nonbilaterian Metazoans by Fleming, James F, Feuda, Roberto, Roberts, Nicholas W, Pisani, Davide

“…Abstract Our ability to correctly reconstruct a phylogenetic tree is strongly affected by both systematic errors and the amount of phylogenetic signal in the…”
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Eye-Transcriptome and Genome-Wide Sequencing for Scolecophidia: Implications for Inferring the Visual System of the Ancestral Snake by Gower, David J, Fleming, James F, Pisani, Davide, Vonk, Freek J, Kerkkamp, Harald M I, Peichl, Leo, Meimann, Sonja, Casewell, Nicholas R, Henkel, Christiaan V, Richardson, Michael K, Sanders, Kate L, Simões, Bruno F

“…Abstract Molecular genetic data have recently been incorporated in attempts to reconstruct the ecology of the ancestral snake, though this has been limited by…”
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The wealth of shared resources: Improving molecular taxonomy using eDNA and public databases by Fleming, James F.

“…Public databases such as the NCBI's GenBank have been used as repositories for genomic studies for more than 30 years. In this time, our understanding of the…”
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Systematics of tardigrada: A reanalysis of tardigrade taxonomy with specific reference to Guil et al. (2019) by Fleming, James F., Arakawa, Kazuharu

“…The Tardigrada are a clade with a disputed and complex taxonomy. The three traditional tardigrade classes are the Heterotardigrada, Eutardigrada and the…”
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Comprehensive Transcriptome Sequencing of Tanaidacea with Proteomic Evidences for Their Silk by Kakui, Keiichi, Fleming, James F, Mori, Masaru, Fujiwara, Yoshihiro, Arakawa, Kazuharu

“…Abstract Tanaidaceans are small benthic crustaceans that mainly inhabit diverse marine environments, and they comprise one of the most diverse and abundant…”
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Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data by Puttick, Mark N., O'Reilly, Joseph E., Tanner, Alastair R., Fleming, James F., Clark, James, Holloway, Lucy, Lozano-Fernandez, Jesus, Parry, Luke A., Tarver, James E., Pisani, Davide, Donoghue, Philip C. J.

“…Morphological data provide the only means of classifying the majority of life's history, but the choice between competing phylogenetic methods for the analysis…”
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Pancrustacean Evolution Illuminated by Taxon-Rich Genomic-Scale Data Sets with an Expanded Remipede Sampling by Lozano-Fernandez, Jesus, Giacomelli, Mattia, Fleming, James F, Chen, Albert, Vinther, Jakob, Thomsen, Philip Francis, Glenner, Henrik, Palero, Ferran, Legg, David A, Iliffe, Thomas M, Pisani, Davide, Olesen, Jørgen

“…Abstract The relationships of crustaceans and hexapods (Pancrustacea) have been much discussed and partially elucidated following the emergence of phylogenomic…”
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New Tardigrade Opsins and Differential Expression Analyses Show Ontogenic Variation in Light Perception by Fleming, James F, Pisani, Davide, Arakawa, Kazuharu

“…Abstract Opsins are light-sensitive proteins involved in many photoreceptive processes, including, but not limited to, vision and regulation of circadian…”
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The Ediacaran origin of Ecdysozoa; integrating fossil and phylogenomic data by Howard, Richard J, Giacomelli, Mattia, Lozano-Fernandez, Jesus, Edgecombe, Gregory D, Fleming, James F, Kristensen, Reinhardt M, Ma, Xiaoya, Olesen, Jorgen, Sorensen, Martin V, Thomsen, Philip F, Wills, Matthew A, Donoghue, Philip C. J, Pisani, Davide

“…Ecdysozoans (Phyla Arthropoda, Kinorhyncha, Loricifera, Nematoda, Nematomorpha, Onychophora, Priapulida, Tardigrada) are invertebrates bearing a tough,…”
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Molecular palaeontology illuminates the evolution of ecdysozoan vision by Fleming, James F., Kristensen, Reinhardt Møbjerg, Sørensen, Martin Vinther, Park, Tae-Yoon S., Arakawa, Kazuharu, Blaxter, Mark, Rebecchi, Lorena, Guidetti, Roberto, Williams, Tom A., Roberts, Nicholas W., Vinther, Jakob, Pisani, Davide

“…Colour vision is known to have arisen only twice—once in Vertebrata and once within the Ecdysozoa, in Arthropoda. However, the evolutionary history of…”
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Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown et al by Puttick, Mark N., O'Reilly, Joseph E., Oakley, Derek, Tanner, Alistair R., Fleming, James F., Clark, James, Holloway, Lucy, Lozano-Fernandez, Jesus, Parry, Luke A., Tarver, James E., Pisani, Davide, Donoghue, Philip C. J.

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Translocation-arrested Apolipoprotein B Evades Proteasome Degradation via a Sterol-sensitive Block in Ubiquitin Conjugation by Du, E Z, Fleming, J F, Wang, S L, Spitsen, G M, Davis, R A

“…In this study, we explored how sterol metabolism altered by the expression of cholesterol-7α-hydroxylase NADPH:oxygen oxidoreductase (7α-hydroxylase) affects…”
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Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown et al by Puttick, Mark N., O'Reilly, Joseph E., Oakley, Derek, Tanner, Alistair R., Fleming, James F., Clark, James, Holloway, Lucy, Lozano-Fernandez, Jesus, Parry, Luke A., Tarver, James E., Pisani, Davide, Donoghue, Philip C. J.

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Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences by Yu, Daqi, Ren, Yandong, Uesaka, Masahiro, Beavan, Alan J. S., Muffato, Matthieu, Shen, Jieyu, Li, Yongxin, Sato, Iori, Wan, Wenting, Clark, James W., Keating, Joseph N., Carlisle, Emily M., Dearden, Richard P., Giles, Sam, Randle, Emma, Sansom, Robert S., Feuda, Roberto, Fleming, James F., Sugahara, Fumiaki, Cummins, Carla, Patricio, Mateus, Akanni, Wasiu, D’Aniello, Salvatore, Bertolucci, Cristiano, Irie, Naoki, Alev, Cantas, Sheng, Guojun, de Mendoza, Alex, Maeso, Ignacio, Irimia, Manuel, Fromm, Bastian, Peterson, Kevin J., Das, Sabyasachi, Hirano, Masayuki, Rast, Jonathan P., Cooper, Max D., Paps, Jordi, Pisani, Davide, Kuratani, Shigeru, Martin, Fergal J., Wang, Wen, Donoghue, Philip C. J., Zhang, Yong E., Pascual-Anaya, Juan

“…Polyploidy or whole-genome duplication (WGD) is a major event that drastically reshapes genome architecture and is often assumed to be causally associated with…”
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Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data by Puttick, Mark N., O'Reilly, Joseph E., Tanner, Alastair R., Fleming, James F., Clark, James, Holloway, Lucy, Lozano-Fernandez, Jesus, Parry, Luke A., Tarver, James E., Pisani, Davide, Donoghue, Philip C. J.

“…Morphological data provide the only means of classifying the majority of life's history, but the choice between competing phylogenetic methods for the analysis…”
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Chinese Hamster Ovary Cells Require the Coexpression of Microsomal Triglyceride Transfer Protein and Cholesterol 7α-Hydroxylase for the Assembly and Secretion of Apolipoprotein B-containing Lipoproteins by Fleming, James F., Spitsen, Gary M., Hui, To Y., Olivier, Lisa, Du, Emma Z., Raabe, Martin, Davis, Roger A.

“…Due to the absence of microsomal triglyceride transfer protein (MTP), Chinese hamster ovary (CHO) cells lack the ability to translocate apoB into the lumen of…”
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Chinese Hamster Ovary Cells Require the Coexpression of Microsomal Triglyceride Transfer Protein and Cholesterol 7α-Hydroxylase for the Assembly and Secretion of Apolipoprotein B-containing Lipoproteins by James F. Fleming, Gary M. Spitsen, To Y. Hui, Lisa Olivier, Emma Z. Du, Martin Raabe, Roger A. Davis

“…Due to the absence of microsomal triglyceride transfer protein (MTP), Chinese hamster ovary (CHO) cells lack the ability to translocate apoB into the lumen of…”
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