James Frederick Fleming

Postdoktor - Komparativ og evolusjonær genomikk

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E-post j.f.fleming@nhm.uio.no

Brukernavn

Besøksadresse Sars gate 1 Colletts hus 0318 Oslo

Postadresse Postboks 1172 0316 Oslo

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Samarbeid

Yu, Daqi; Ren, Yandong; Uesaka, Masahiro; Beavan, Alan; Muffato, Matthieu & Shen, Jieyu [Vis alle 44 forfattere av denne artikkelen] (2024). Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences. Nature Ecology and Evolution. ISSN 2397-334X. doi: 10.1038/s41559-023-02299-z.
Fleming, James Frederick; Pisani, Davide & Arakawa, Kazuharu (2023). The evolution of temperature and desiccation-related protein families in Tardigrada reveals the complex acquisition of extremotolerance. Genome Biology and Evolution (GBE). ISSN 1759-6653. 16(1). doi: 10.1093/gbe/evad217.
Fleming, James Frederick; Eriksen, Pia Merete & Struck, Torsten H (2023). Scoutknife: A naïve, whole genome informed phylogenetic robusticity metric [version 1; peer review: awaiting peer review]. F1000 Research. ISSN 2046-1402. 12(945). doi: 10.12688/f1000research.139356.1. Fulltekst i vitenarkiv
Fleming, James Frederick & Struck, Torsten H (2023). nRCFV: a new, dataset-size-independent metric to quantify compositional heterogeneity in nucleotide and amino acid datasets. BMC Bioinformatics. ISSN 1471-2105. 24. doi: 10.1186/s12859-023-05270-8. Fulltekst i vitenarkiv
Fleming, James Frederick; Valero Gracia, Alberto & Struck, Torsten H (2023). Identifying and addressing methodological incongruence in phylogenomics: A review. Evolutionary Applications. ISSN 1752-4571. 16(6), s. 1087–1104. doi: 10.1111/eva.13565. Fulltekst i vitenarkiv
Fleming, James Frederick (2023). The wealth of shared resources: Improving molecular taxonomy using eDNA and public databases. Zoologica Scripta. ISSN 0300-3256. doi: 10.1111/zsc.12591.
Fleming, James Frederick & Struck, Torsten H (2022). nRCFV: A new, dataset-size-independent metric to quantify compositional heterogeneity in nucleotide and amino acid datasets. Research Square. ISSN 2693-5015. doi: 10.21203/rs.3.rs-2354937/v1.
Howard, Richard J.; Giacomelli, Mattia; Lozano-Fernandez, Jesus; Edgecombe, Gregory D.; Fleming, James Frederick & Kristensen, Reinhardt M. [Vis alle 13 forfattere av denne artikkelen] (2022). The Ediacaran origin of Ecdysozoa: integrating fossil and phylogenomic data. Journal of the Geological Society. ISSN 0016-7649. 179(4). doi: 10.1144/jgs2021-107. Fulltekst i vitenarkiv
Fleming, James Frederick; Pisani, Davide & Arakawa, Kazuharu (2021). New Tardigrade Opsins and Differential Expression Analyses Show Ontogenic Variation in Light Perception. Genome Biology and Evolution (GBE). ISSN 1759-6653. doi: 10.1093/gbe/evab164. Fulltekst i vitenarkiv
Kakui, Keiichi; Fleming, James Frederick; MORI, MASARU; Fujiwara, Yoshihiro & Arakawa, Kazuharu (2021). Comprehensive Transcriptome Sequencing of Tanaidacea with Proteomic Evidences for Their Silk. Genome Biology and Evolution (GBE). ISSN 1759-6653. doi: 10.1093/gbe/evab281.
Gower, David J.; Fleming, James Frederick; Pisani, Davide; Vonk, Freek J.; KERKKAMP, HARALD M I & PEICHL, LEO [Vis alle 12 forfattere av denne artikkelen] (2021). Eye-Transcriptome and Genome-Wide Sequencing for Scolecophidia: Implications for Inferring the Visual System of the Ancestral Snake. Genome Biology and Evolution (GBE). ISSN 1759-6653. doi: 10.1093/gbe/evab253.
Fleming, James Frederick & Arakawa, Kazuharu (2021). Systematics of tardigrada: A reanalysis of tardigrade taxonomy with specific reference to Guil et al. (2019). Zoologica Scripta. ISSN 0300-3256. 50(3), s. 376–382. doi: 10.1111/zsc.12476.

Se alle arbeider i Cristin

Fleming, James Frederick & Melteig, Elina (2024). Blekkspruten er i slekt med snegler, men ingen vet nøyaktig hvordan. [Internett]. https://www.titan.uio.no/naturvitenskap/2023/blekkspruten-er.
Fleming, James Frederick (2024). Stories from Slime Eels: How the Hagfish Helps Us Understand Humans. [Internett]. https://blog.annelida.de/2024/01/15/stories-from-slime-eels-.
Nhu Dinh, Le Yen & Fleming, James Frederick (2023). Day 20: Defending Against Rising Ocean Acidification.
Struck, Torsten H & Fleming, James Frederick (2023). RCFV Reader.
Struck, Torsten H; Fleming, James Frederick & Huelsenbeck, John (2023). Wammel.
Fleming, James Frederick; Struck, Torsten H & Eriksen, Pia Merete (2023). Scoutknife.
Fleming, James Frederick (2023). Scoutknife: Understanding Likelihood in an Era of Perfect Data.
Fleming, James Frederick (2023). Wammel: Directly Evaluating Phylogenetic Hypotheses.
Fleming, James Frederick (2023). Scoutknife: Understanding Likelihood in an Era of Perfect Data.
Fleming, James Frederick (2023). Whole Genome Data and Non-Model Organisms: Challenges and Pathways to the Future. Vis sammendrag
The genomics revolution completely altered our understanding of phylogeny - the study of the relationships between animals. The identification of new cryptic species through phylogenetic methods that combine molecular and morphological data has led to an appreciation of phylogenetic relatedness as a biodiversity concept. Currently, however, phylogenetics has adopted a conservative stance towards this deluge of “big data”, selecting genes that fit well within our models of evolution - this has the benefit of evading artifactual topologies that violate these models, but may well be presenting us with hypotheses of evolution that are preselected according to our own biases, or incorrectly causing us to adopt great confidence in hypotheses that are not as well supported by the data as it first appears. This can have a powerful impact on our understanding of the relationships between taxa, which in turn could erroneously inform future sampling or conservation efforts. From this perspective, new phylogenetic methods that are optimized to make the most of “big data” may be of critical importance to advancing the field. As part of the University of Oslo’s Invertomics project, a small part of the broader European effort to sequence every Eukaryotic genome on the continent, we have developed new methods to assess phylogenetic data and new software to reconstruct phylogenetics optimized for whole genome data. We are additionally in the process of applying that to real genomic challenges across the second largest invertebrate superphylum, Lophotrochozoa. This talk will cover three new software packages, one of which has already been released, that hope to advance our understanding of organismal relationships in this new era of data. It will also explore the challenges of applying big data approaches to organismal phylogenetics.
Fleming, James Frederick (2023). Day 15: What’s coming next year! [Internett]. https://blog.annelida.de/2023/12/15/day-15-whats-coming-next.
Fleming, James Frederick (2023). Day 14: When is a Larva like a Birthday Present? [Internett]. https://blog.annelida.de/2023/12/14/day-14-when-is-a-larva-l.
Fleming, James Frederick (2023). Day 8: Working in Phylogenetic Methods. [Internett]. https://blog.annelida.de/2023/12/08/day-8-working-in-phyloge.
Fleming, James Frederick (2023). On Pre-Prints, Publishing and Peer Review. [Internett]. https://blog.annelida.de/2023/08/08/on-pre-prints-publishing.
Fleming, James Frederick (2023). Group of the Month: Placozoa. [Internett]. https://blog.annelida.de/2023/07/01/group-of-the-month-placo.
Fleming, James Frederick (2023). Writing a Review: Introducing Your Field. [Internett]. https://blog.annelida.de/2023/06/28/writing-a-review-introdu.
Fleming, James Frederick (2023). The measure of our reach: understanding evolution when our models break down. [Internett]. https://blog.annelida.de/2023/04/19/the-measure-of-our-reach.
Fleming, James Frederick (2023). Tardigrades, Public Databases and Science From Your Settee. [Internett]. https://blog.annelida.de/2023/03/07/tardigrades-public-datab.
Melteig, Elina & Fleming, James Frederick (2023). Dyret som gjenoppstår fra de døde – helt naturlig. [Internett]. https://www.titan.uio.no/naturvitenskap/2023/dyret-som-gjeno.
Fleming, James Frederick (2022). Fez Advent Calendar 2022: Day 6, a stocking-filler of a phylogenetic review.
Fleming, James Frederick (2022). FEZ Advent Calendar Day 10: Ten Tardis Tunning.
Fleming, James Frederick (2022). Advent Calendar Day 16: The March To Land.
Fleming, James Frederick (2022). RCFV_Reader.
Fleming, James Frederick & Struck, Torsten H (2022). nRCFV: a sequence, taxon and character state-normalised metric for the pre-reconstruction evaluation of compositional heterogeneity.
Fleming, James Frederick (2022). Group of the month: Tardigrades.
Fleming, James Frederick (2022). Crustacean Silk from under the Sea. [Internett]. FEZ group blog.
Fleming, James Frederick (2021). What’s in a Postdoc? Life inside the gears of the academic machine. [Internett]. FEZ group blog.
Fleming, James Frederick (2021). Maths and Models: The Mechanics of Invertomics. [Internett]. FEZ group blog.
Fleming, James Frederick (2021). Science From Lockdown: Advent Calendar December 4th 2021. [Internett]. FEZ group blog.
Fleming, James Frederick (2021). A Story of Snakes and Sight (don’t we research invertebrates)? [Internett]. FEZ group blog.
Fleming, James Frederick (2021). A new paper on tardigrades! What’s in a (scientific) name? [Internett]. FEZ group blog.
Fleming, James Frederick & Weisberger, Mindy (2021). Tardigrades probably see in black and white. [Internett]. Live Science.
Marshall, Michael & Fleming, James Frederick (2021). Tardigrades: nature's great survivors. [Avis]. The Observer Newspaper.