@nickparrish

Hakubi team leader, RIKEN. Resident-in-research, VUMC. Studying immunobiology and endogenous virus elements for clues to improve human health. Views my own.

 Yokohama, Japan; Nashville, TN
ims.riken.jp/labo/76/index.html
Joined April 2009
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  • Following273
  • Followers341
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Happy to share our preprint showing how transposons/mobile elements (MEs) make us who we are. Highlights: 🧬A LINE-1 insertion causes increased keloid risk 🧬ME variants coherently regulate gene expression 🧬Population-specific patterns of Alu insertion biorxiv.org/content/10.1101/…

Mobile elements in human population-specific genome and phenotype divergence

Mobile genetic elements (MEs) are heritable mutagens that contribute to divergence between lineages by recursively generating structural variants. ME variants (MEVs) are difficult to genotype,...

biorxiv.org
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Thanks for reading the paper! Calculating the false positive rate involves comparing MEGAnE MEV calls to gold-standard calls generated using multiple technologies. No need to wonder if the rate is higher than 3% based on these other analyses. It’s a calculation, not rhetoric.
Geoff Faulkner@Faulkner_Lab13 May 2023
Replying to @Faulkner_Lab
There are many other people with more expertise in this area than me, and I certainly could be wrong, but I look at the de novo rate of 1/2.4 and this PCR validation experiment and wonder if the false-positive rate is a higher than 3%? 8/n
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We needed to catalog hundreds of MEVs that strongly associate with differential expression of nearby genes to demonstrate this point.
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I hope I’ll have time to make a thread about the merits of this work soon. But for now, @Faulkner_Lab's criticism highlights that there is much work to be done to bring the field of mobile DNA into the bright light of rigorous statistical genetics.
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Incredible #scicomm by super-postdoc @ShoheiKojima and colleagues in collaboration with @mextjapan. Huge honor for him to represent @RIKEN_JP and @RIKEN_IMS and the SPDR program (riken.jp/en/careers/programs…), not to mention my team, in this way!
文部科学省　MEXT
@mextjapan11 Apr 2023
Replying to @mextjapan
🆕お知らせ📢 本日(4月11日)、学習資料「一家に１枚　ウイルス」特設サイト、PR動画、解説動画を公開しました。それぞれ、下記リンクよりご覧ください！ 🖥️特設サイト ims.riken.jp/poster_virus/ 🎦PR動画 youtube.com/shorts/tYQAoOKko… 🎦解説動画 youtu.be/TDEs1dOkBso #一家に１枚 #文部科学省
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本日4月11日（火）理化学研究所が企画した文部科学省の学習資料「一家に一枚　ウイルス」の特設サイト、PR動画、解説動画が公開！
文部科学省　MEXT
@mextjapan11 Apr 2023
Replying to @mextjapan
🆕お知らせ📢 本日(4月11日)、学習資料「一家に１枚　ウイルス」特設サイト、PR動画、解説動画を公開しました。それぞれ、下記リンクよりご覧ください！ 🖥️特設サイト ims.riken.jp/poster_virus/ 🎦PR動画 youtube.com/shorts/tYQAoOKko… 🎦解説動画 youtu.be/TDEs1dOkBso #一家に１枚 #文部科学省
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These findings were enabled by a new tool for accurate ME discovery/genotyping using short-read data. Before now, statistical genetics approaches have been limited to common variants already sequence-resolved by long-reads. Get MEGAnE (👓) here: github.com/shohei-kojima/MEG…

GitHub - shohei-kojima/MEGAnE: MEGAnE

MEGAnE. Contribute to shohei-kojima/MEGAnE development by creating an account on GitHub.

github.com
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This is the result of collaboration between many groups at @RIKEN_JP @riken_en @RIKEN_IMS @RIKEN_CPR. I would sincerely appreciate critical feedback on this work; please DM or email me if you have any!
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Our paper is finally out at biorxiv. Hominoid-specific endogenous retrovirus in human primordial germ cell-like cells. biorxiv.org/content/10.1101/…

Endogenous retrovirus rewired the gene regulatory network shared between primordial germ cells and...

Although the gene regulatory network controlling germ cell development is critical for gamete integrity, this network has been substantially diversified during mammalian evolution. Here, we show that...

biorxiv.org
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Nick Parrish retweeted
Jumpei Ito
@jampei211 Mar 2021
研究成果をbioRxivに公開しました. ゲノム中には古代のウイルス感染によって生じた内在性レトロウイルス(ERV)が多数存在します. 本研究では, 類人猿に特異的に挿入されたERVがエンハンサーとして働き, 生殖細胞の遺伝子発現制御において重要な役割を果たすことを明らかにしました(1/n)
The Sato Lab (Kei Sato)@SystemsVirology11 Mar 2021
【拡散希望】当ラボの新しい研究成果を @biorxivpreprint に掲載しました。 #内在性レトロウイルス というウイルスの化石が、ヒトを含む #霊長類の進化 と、生命誕生において最重要な細胞のひとつである #始原生殖細胞 で重要な役割を果たしていることを示唆した論文です。1/4 biorxiv.org/content/10.1101/…

Endogenous retrovirus rewired the gene regulatory network shared between primordial germ cells and...

Although the gene regulatory network controlling germ cell development is critical for gamete integrity, this network has been substantially diversified during mammalian evolution. Here, we show that...

biorxiv.org
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Our new study "A hominoid-specific endogenous retrovirus has rewired the gene regulatory network shared between primordial germ cells and naïve pluripotent cells" is out @biorxivpreprint ! Great work by an awesome postdoc Jumpei @jampei2 . Please RT!! 1/2 biorxiv.org/content/10.1101/…

Endogenous retrovirus rewired the gene regulatory network shared between primordial germ cells and...

Although the gene regulatory network controlling germ cell development is critical for gamete integrity, this network has been substantially diversified during mammalian evolution. Here, we show that...

biorxiv.org
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Thank you for sharing your exciting research at the EVE study club! This study club is cohosted by @Masayuki_Horie and @nickparrish, who are experts on endogenous viral elements 🧬🦠. Anyone interested in joining this study club can contact me via Twitter DM ✉️!
Arnon Plianchaisuk (Chain)
@chainorato20 Jan 2021
Got a lot of helpful comments and suggestions from the EVE study club today, Thank you everyone 🥰
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Nick Parrish retweeted
SalehLab@SalehLabParis15 Dec 2020
Happy to finish 2020 with the publication of our discovery of transgenerational antiviral immunity in drosophila and mosquito! cell.com/cell-reports/fullte… It took more than 6 years to cook this beauty! Congratulations to @LabMefistofeles and everybody involved! In a nutshell…(1/8)

Evidence For Long-Lasting Transgenerational Antiviral Immunity in Insects

Mondotte et al. determine that antiviral transgenerational immune priming in Drosophila and mosquitoes occurs after parental priming with different single-stranded RNA viruses. The progeny are...

cell.com
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Nick Parrish retweeted
Craig Wilen@WilenLab7 Dec 2020
We havent forgotten our other favorite virus: #norovirus. We asked what cell types were murine norovirus infected. We deleted the CD300lf receptor from ~8 cell types. Tuft cells were essential for CR6 virus. @WilenLab @Yale_LabMed @YaleIBIO @VinnieViruses jvi.asm.org/content/early/20…
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Our latest work, “One hundred million years history of bornavirus infections hidden in vertebrate genomes”, is out in @biorxivpreprint. (1/n)
bioRxiv@biorxivpreprint3 Dec 2020
One hundred million years history of bornavirus infections hidden in vertebrate genomes biorxiv.org/cgi/content/shor… #bioRxiv
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