Hakubi team leader, RIKEN. Resident-in-research, VUMC. Studying immunobiology and endogenous virus elements for clues to improve human health. Views my own.
Joined April 2009
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29 Mar 2022
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/…
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13 May 2023
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.
13 May 2023
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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13 May 2023
We needed to catalog hundreds of MEVs that strongly associate with differential expression of nearby genes to demonstrate this point.
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13 May 2023
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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12 Apr 2023
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!
11 Apr 2023
🆕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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Nick Parrish retweeted
11 Apr 2023
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！
11 Apr 2023
🆕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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29 Mar 2022
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/…
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29 Mar 2022
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…
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29 Mar 2022
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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Nick Parrish retweeted
10 Mar 2021
Our paper is finally out at biorxiv. Hominoid-specific endogenous retrovirus in human primordial germ cell-like cells.
biorxiv.org/content/10.1101/…
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Nick Parrish retweeted
11 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)
11 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/…
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Nick Parrish retweeted
10 Mar 2021
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/…
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Nick Parrish retweeted
20 Jan 2021
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 ✉️!
20 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
15 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)
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Nick Parrish retweeted
7 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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Nick Parrish retweeted
7 Dec 2020
Our latest work, “One hundred million years history of bornavirus infections hidden in vertebrate genomes”, is out in @biorxivpreprint. (1/n)
3 Dec 2020
One hundred million years history of bornavirus infections hidden in vertebrate genomes biorxiv.org/cgi/content/shor… #bioRxiv
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