Dr. Tyler A. Elliott

@transposableman.bsky.social

Posts

Transposon obsessed biologist. Research Associate in Adamowicz Lab @ the U of Guelph
Check out the wealth of TE resources on @tehub.bsky.social https://tehub.org
https://www.tyleraelliott.com/research

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Dr. Tyler A. Elliott

Transposable element accumulation drives genome size increase in Hylesia metabus (Lepidoptera: Saturniidae), an urticating moth species from South America https://www.biorxiv.org/content/10.1101/2024.07.11.602864v1 www.biorxiv.org We present the first nuclear genome assembly and a complete mitogenome for Hylesia metabus (Arthropo

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Dr. Tyler A. Elliott

The regulatory potential of transposable elements in maize https://www.biorxiv.org/content/10.1101/2024.07.10.602892v1

The regulatory potential of transposable elements in maize https://www.biorxiv.org/content/10.1101/2024.07.10.602892v1 www.biorxiv.org Since their initial discovery in maize, transposable elements (TEs) have emerged as being integral t

My Philosopher colleague Dr. Stefan Linquist gave a talk about some of the work he's done over the years with myself and others on genome ecology, #transposons and function www.youtube.com/watch?v=dosf...

Stefan Linquist, Genome level ecology, a novel approach to the functional analysis of junk DNAwww.youtube.com YouTube video by Thomas Pradeu

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Dr. Tyler A. Elliott

Quadrupia: Derivation of G-quadruplexes for organismal genomes across the tree of life https://www.biorxiv.org/content/10.1101/2024.07.09.602008v1

Quadrupia: Derivation of G-quadruplexes for organismal genomes across the tree of life https://www.biorxiv.org/content/10.1101/2024.07.09.602008v1 www.biorxiv.org G-quadruplex DNA structures exhibit a profound influence on essential biological processes, includin

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Dr. Tyler A. Elliott

'Cellulose nitrate was used to make dice from the late 1860s until the mid twentieth century, and remains stable for decades. Nitric acid is released in a process called outgassing. The dice cleave, crumble, and then implode.' Deception, Fate & Rotten Luck by Ricky Jay and Rosamond Purcell

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Dr. Tyler A. Elliott

'Birkholz et al. have discovered that a mobile intron containing a homing endonuclease found within a viral RNA polymerase gene in one bacteriophage blocks productive infection by a related and competing coinfecting bacteriophage.' www.science.org/doi/10.1126/...

An intron endonuclease facilitates interference competition between coinfecting viruseswww.science.org Introns containing homing endonucleases are widespread in nature and have long been assumed to be selfish elements that provide no benefit to the host organism. These genetic elements are common in vi...

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Dr. Tyler A. Elliott

Do fungal Starships 🚀 matter for human health? We dive into the pathogen Aspergillus fumigatus and connect the dots between these unusual transposons and strain variability. Spoiler alert: biofilms, secondary metabolites and intra-strain variation, oh my! doi.org/10.1101/2024...

Giant transposons promote strain heterogeneity in a major fungal pathogendoi.org bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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Dr. Tyler A. Elliott

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation https://www.biorxiv.org/content/10.1101/2024.06.27.601086v1

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation https://www.biorxiv.org/content/10.1101/2024.06.27.601086v1 www.biorxiv.org Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their thr

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Dr. Tyler A. Elliott

TEtrimmer: a novel tool to automate the manual curation of transposable elements https://www.biorxiv.org/content/10.1101/2024.06.27.600963v1

TEtrimmer: a novel tool to automate the manual curation of transposable elements https://www.biorxiv.org/content/10.1101/2024.06.27.600963v1 www.biorxiv.org Transposable elements (TEs) are repetitive DNA sequences capable of moving within genomes. Accurate

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Dr. Tyler A. Elliott

The Satellite DNA PcH-Sat, Isolated and Characterized in the Limpet Patella caerulea (Mollusca, Gastropoda), Suggests the Origin from a Nin-SINE Transposable Element http://dlvr.it/T8jvvQ

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Dr. Tyler A. Elliott

We finally put it together! The first ICTV #Virus #Taxonomy Challenge provides a dataset of thousands of contigs from diverse viruses, asking bioinformaticians to classify them in an automated, reproducible way. See: ictv-vbeg.github.io/ICTV-Taxonom... - tell your bioinformaticians and colleagues!

Why do we need a computational taxonomy?ictv-vbeg.github.io A community challenge to evaluate and compare viral genome taxonomy classifiers

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Dr. Tyler A. Elliott

github.com/piosierra/pa...

GitHub - piosierra/pantera: Identification of transposable element families from pangenome polymorphismsgithub.com Identification of transposable element families from pangenome polymorphisms - piosierra/pantera

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Dr. Tyler A. Elliott

mobilednajournal.biomedcentral.com/articles/10....

Identification of transposable element families from pangenome polymorphisms - Mobile DNAmobilednajournal.biomedcentral.com Background Transposable Elements (TEs) are segments of DNA, typically a few hundred base pairs up to several tens of thousands bases long, that have the ability to generate new copies of themselves in...

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Dr. Tyler A. Elliott

First paper from my student Daria Frolova's PhD now on biorxiv: www.biorxiv.org/content/10.1... The key question: plasmids change structurally ~as fast as they mutate, so how can we decide whether 2 plasmids are "the same plasmid" for epi purposes? 1/n

www.biorxiv.org

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Dr. Tyler A. Elliott

Important paper on the horrible H5N1 outbreak in seals:

Massive outbreak of Influenza A H5N1 in elephant seals at Peninsula Valdes, Argentina: increased evidence for mammal-to-mammal transmission https://www.biorxiv.org/content/10.1101/2024.05.31.596774v1

Massive outbreak of Influenza A H5N1 in elephant seals at Peninsula Valdes, Argentina: increased evidence for mammal-to-mammal transmission https://www.biorxiv.org/content/10.1101/2024.05.31.596774v1 www.biorxiv.org H5N1 high pathogenicity avian influenza (HPAI) viruses of the clade 2.3.4.4b have killed thousands o

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Dr. Tyler A. Elliott

Hi 🧪 community, #eDNA #environmentalDNA #ecology communities etc. We are engaged in a research study on ethics and eDNA. We value your perspective. Help us by completing our survey forms.office.com/r/P6R57BAbZq Please pass it along to other users. Post, like repost. Help us reach a wider community.

Microsoft Formsforms.office.com

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Dr. Tyler A. Elliott

Early male and female footprints of modern humans across Eurasia and Australasia https://www.biorxiv.org/content/10.1101/2024.05.27.596017v1

Early male and female footprints of modern humans across Eurasia and Australasia https://www.biorxiv.org/content/10.1101/2024.05.27.596017v1 www.biorxiv.org As an alternative to a recent coastal southern route followed by modern humans to colonize Eurasia a

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Dr. Tyler A. Elliott

In our new paper, we use 20 years of #remotesensing data for over 9500 fires to document the "Biogeographic patterns of daily wildfire spread and extremes across North America." Congrats to postdoctoral scholar Jared Balik for leading this effort! 🧪🌏🔥

You know what's cool? >20 years of #remotesensing data that allows one to produce #wildfire progression, or day-of-burning, maps. Such maps have enabled some cool studies. The pub below describes a process to produce such maps. I distribute code, with no strings attached, to anyone who asks.🧪

Mapping day-of-burning with coarse-resolution satellite fire-detection data | US Forest Service Research and Developmentwww.fs.usda.gov

Biogeographic patterns of daily wildfire spread and extremes across North Americawww.frontiersin.org Climate change is predicted to increase the frequency of extreme single-day wildfire events. Spatio-temporal patterns of wildfire causes and seasonality are well documented at the resolution of final ...

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Dr. Tyler A. Elliott

For abomination crustacean #InsertAnInvert2024, the featured parasitic species all look weird but it turns out they cover the entire diversity of crustaceans with a common ancestor over 500 million years ago 🧪🦑 Modified from my paper with @jimmybernot.bsky.social academic.oup.com/mbe/article/...

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Dr. Tyler A. Elliott

EEfinder, a tool for identification of bacterial and viral endogenized elements in eukaryotic genomes https://www.biorxiv.org/content/10.1101/2024.05.24.595709v1

EEfinder, a tool for identification of bacterial and viral endogenized elements in eukaryotic genomes https://www.biorxiv.org/content/10.1101/2024.05.24.595709v1 www.biorxiv.org Horizontal transfer is a phenomenon of genetic material transmission between species with no parenta

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Dr. Tyler A. Elliott

Pipolins are bimodular platforms that maintain a reservoir of defense systems exchangeable with various bacterial genetic mobile elements https://www.biorxiv.org/content/10.1101/2024.05.22.595293v1

Pipolins are bimodular platforms that maintain a reservoir of defense systems exchangeable with various bacterial genetic mobile elements https://www.biorxiv.org/content/10.1101/2024.05.22.595293v1 www.biorxiv.org Defense genes gather in diverse types of genomic islands in bacteria and provide immunity against vi

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Dr. Tyler A. Elliott

Hot off the press! Check out the latest version of our deep dive into Y chromosome degeneration and TE invasion in Rumex hastatulus! @stepheniwright.bsky.social @zoehumphries.bsky.social

New preprint led by Zoë Humphries & I! We characterized rapid genome evolution and extensive degeneration in young Y chromosomes that arose in a repetitive region of low recombination. Taking a deep-dive into this phased assembly with Zoë and Stephen (not on this site yet) was super fun!

Phased assembly of neo-sex chromosomes reveals extensive Y degeneration and rapid genome evolution i...www.biorxiv.org bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Phased assembly of neo-sex chromosomes reveals extensive Y degeneration and rapid genome evolution in Rumex hastatulusacademic.oup.com Abstract. Y chromosomes are thought to undergo progressive degeneration due to stepwise loss of recombination and subsequent reduction in selection efficie

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Dr. Tyler A. Elliott

A complete and dynamic tree of birds https://www.biorxiv.org/content/10.1101/2024.05.20.595017v1

A complete and dynamic tree of birds https://www.biorxiv.org/content/10.1101/2024.05.20.595017v1 www.biorxiv.org We present a complete, time-scaled, evolutionary tree of the world's bird species. This tree unites

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Dr. Tyler A. Elliott

Landscape of Evolutionary Arms Races between Transposable Elements and KRAB-ZFP Family https://www.biorxiv.org/content/10.1101/2024.05.20.595046v1

Landscape of Evolutionary Arms Races between Transposable Elements and KRAB-ZFP Family https://www.biorxiv.org/content/10.1101/2024.05.20.595046v1 www.biorxiv.org Transposable elements (TEs) are mobile parasitic sequences that have expanded within the host genome

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Dr. Tyler A. Elliott

Small but mitey: long-read assembly of a streamlined mite genome from contaminated host plant sequencing data https://www.biorxiv.org/content/10.1101/2024.05.17.594625v1

Small but mitey: long-read assembly of a streamlined mite genome from contaminated host plant sequencing data https://www.biorxiv.org/content/10.1101/2024.05.17.594625v1 www.biorxiv.org Technological advances have propelled DNA sequencing of non-model organisms, making sequencing more

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Dr. Tyler A. Elliott

New report from Pew finds 38% of webpages that existed in 2013 are no longer accessible a decade later. This research underscores how critical web archiving efforts are. www.pewresearch.org/data-labs/20...

When Online Content Disappearswww.pewresearch.org A quarter of all webpages that existed at one point between 2013 and 2023 are no longer accessible.

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Dr. Tyler A. Elliott

I read papers on TE evolution that say "TEs do X" And every time I think it's not too dissimilar from saying "vertebrates in the forest do X". Sure there are a few things you could say like "are less active in Winter" which would be mostly right. But frogs and vultures and bears are different. 1/

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Dr. Tyler A. Elliott

TEENA: an integrated web server for transposable element enrichment analysis in various model and non-model organisms academic.oup.com/nar/article/...

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Dr. Tyler A. Elliott

Former CBC producer documents consistent pattern of anti-Palestinian bias in coverage, including being told she was “crossing the line” in pitching an interview with two genocide scholars debating whether Israel’s actions fit the legal definition. breachmedia.ca/cbc-whitewas...

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Dr. Tyler A. Elliott

Our new preprint is online. Ribozymes with translation initiation (IRES) activity in the 5' UTRs of viruses!

Self-cleaving ribozymes conserved in RNA viruses unveil a new role in protein translation https://www.biorxiv.org/content/10.1101/2024.05.16.594327v1

Self-cleaving ribozymes conserved in RNA viruses unveil a new role in protein translation https://www.biorxiv.org/content/10.1101/2024.05.16.594327v1 www.biorxiv.org Small self-cleaving ribozymes are catalytic RNAs originally discovered in viroid-like agents, which