YukinoriOkada @okada_yukinori Twitter profile | Pikagi

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YukinoriOkada

@okada_yukinori

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Professor, Dep. Genome Informatics, The University of Tokyo Professor, Dep. Statistical Genetics, Osaka University Team Leader, Lab. Systems Genetics, RIKEN IMS

Tokyo, Japan

https://t.co/AOg1NklLSZ

Joined September 2019

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@okada_yukinori

YukinoriOkada

@okada_yukinori

4 months

【追加募集】東京大学大学院医学系研究科遺伝情報学では、遺伝統計学やゲノム・オミクス解析による病態解明・創薬・個別化医療に一緒に取り組むIT系技術補佐員を【更にもう一名】募集中です。バイオバンク・ジャパン(BBJ)のデータ解析チームの一員としても活躍して頂きます。

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@okada_yukinori

YukinoriOkada

@okada_yukinori

2 years

東京大学大学院医学系研究科遺伝情報学教室がスタートしました🧬🖥️💊。一緒に研究に取り組んでくれる大学院生を大募集中です!! Just started a new lab (Dep. Genome Informatics) at Univ. Tokyo. Looking for graduate students who work together !!

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@okada_yukinori

YukinoriOkada

@okada_yukinori

1 year

お陰様で三日間の「遺伝統計学・夏の学校」が無事終了しました。御参加頂いた皆様とラボメンバーに感謝です。講義資料と演習データを公開します。 2022年度と類似の内容ですが、情報をアップデートしています。 #Bioinformatics #omics #singlecell #scRNA #LDSC #eQTL #GWAS

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@okada_yukinori

YukinoriOkada

@okada_yukinori

3 years

三日間の「遺伝統計学・夏の学校＠大阪大学」が無事終了しました。御参加頂いた皆様に感謝です。演習データ一式を公開します。・WSL2によるWindowsへのLinux解析環境導入・Anacondaを使ったLDSC (Linkage Disequilibrium SCore regression)解析演習が新規コンテンツです。

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@okada_yukinori

YukinoriOkada

@okada_yukinori

1 year

実験医学増刊「ポストGWAS時代の遺伝統計学」が発刊されました。執筆陣の皆様に感謝です。

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@Yodosha_EM

羊土社実験医学

1 year

【新刊】実験医学増刊『ポストGWAS時代の遺伝統計学』（岡田随象／編集）が発行．公共データベースの情報を疾患研究に活かしたい方，ラボに眠っているオミクスデータがある方は必見！ゲノムの変異と疾患をつなぐ先端研究事例集

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@okada_yukinori

YukinoriOkada

@okada_yukinori

3 years

～今年もやります、遺伝統計学・夏の学校＠大阪大学～ We have "online" summer school of Statistical Genetics in Osaka University (in Japanese). Aug 27th-29th, 2021. Any students who has interests in stat genet is welcome!! #Genetics #gwas #SummerSchool

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@okada_yukinori

YukinoriOkada

@okada_yukinori

3 years

New bioinformatics tool for genomics-driven drug discovery🧬💊🧬. Trans-Phar, Integration of TWAS and pharmacological database, is now at @hmg_journal Given GWAS sumstats, Trans-Phar returns potential therapeutic compounds for drug repositioning.

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@okada_yukinori

YukinoriOkada

@okada_yukinori

1 year

遺伝統計学・夏の学校（8/25-27 web開催）の開催準備を進めています。参加者側PCで解析環境の事前設定が必要ですが、M1/M2チップ搭載macノートでanacondaを使った環境インストールに不具合が生じる例があるようです🙇。対策案検討（=募集）中です。 #gwas #SummerSchool #omics

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@okada_yukinori

YukinoriOkada

@okada_yukinori

4 years

I am delighted to announce that my first textbook on statistical genetics is now on sale (in Japanese). #genetics #genomics #NGS #sequencing #statisticalgenetics #evolution

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@okada_yukinori

YukinoriOkada

@okada_yukinori

3 years

Trans-biobank GWAS on 220 deep phenotypes is now on @NatureGenet !! Deconvolution of phenome-wide GWAS sum stats elucidate disease biology. Get sum stats from . Collabo with @saorisakaue @masakanai @yk_tani @manuelrivascruz @dalygene @FinnGen_FI @uk_biobank

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@NatureGenet

Nature Genetics

3 years

🔥 ONLINE @NatureGenet by @okada_yukinori @saorisakaue @masakanai and colleagues: 🌐A cross-population atlas of genetic associations for 220 human phenotypes 🔗 @uk_biobank and @FinnGen_FI

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@okada_yukinori

YukinoriOkada

@okada_yukinori

5 years

Human genetics widely contributes to individuals' dietary habits in Japanese, including ALDH2 rs671 pleiotropic effects on alcohol, coffee, green tea, milk, yoghurt, natto, tofu, fish, and meat !! See our work in @NatureHumBehav

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@okada_yukinori

YukinoriOkada

@okada_yukinori

2 years

New bioinfo tool🖥️🛠️!! OMARU (Omnibus Metagenome-wide Association study with RobUstness): end-to-end workflow on metagenome-wide association study (MWAS) of microbe shotgun sequencing. Kishikawa T. NAR Genom Bioinform #microbiome #metagenomics #bacteria

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@okada_yukinori

YukinoriOkada

@okada_yukinori

10 months

Half or X chromosomes in females are inactivated (XCI), but some escape. scLinax: tool to quantify XCI escape using millions of single cells by @YoshiTomofuji as Asian Immune Diverstiy (AIDA) Nework projects of @humancellatlas with @shyam_lab & colleagues.

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@okada_yukinori

YukinoriOkada

@okada_yukinori

10 months

Multimodal omics deconvoluted molecular & clinical heterogeneity in patient subtypes of atopic dermatitis (AD): blood & skin RNA-seq & EMR with longitudinal follow-up. Now in @NatureComms by Sekita A & @RIKEN_IMS team. #dermatology #Bioinformatics #RNAseq

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@okada_yukinori

YukinoriOkada

@okada_yukinori

2 years

Multi-trait & cross-pop GWAS identified shared & distinct genetics of autoimmune (rheumatoid arthritis, Graves' disease, type 1 diabetes, SLE, psoriasis) & allergic diseases (asthma, pollinosis, atopic dermatitis). Now at Ann Rheum Dis @ARD_BMJ !! #GWAS

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@okada_yukinori

YukinoriOkada

@okada_yukinori

1 year

📣COVID-19 single-cell RNA-seq & host genetics of Japanese led by @RyuyaEdahiro is finally online at @NatureGenet 🎉. Innate immune cells have critical roles in COVID-19 severity. Thank for the great team !!

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@NatureGenet

Nature Genetics

1 year

🚨 ONLINE @NatureGenet 📰 Single-cell analyses and host genetics highlight the role of innate immune cells in COVID-19 severity 🧑‍🤝‍🧑 @okada_yukinori Atsushi Kumanogoh and team 👇🏿

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@okada_yukinori

YukinoriOkada

@okada_yukinori

1 year

Non-human genome🦠🧬in human🧑‍🤝‍🧑is interesting, & human genome🧑‍🤝‍🧑🧬in non-human🦠is too !! Quantitative assessment how we can reconstruct personal genome from gut metagenome shotgun-seq is @NatureMicrobiol . Nice work by @YTomofuji_1107 & teams!! #microbiome

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@NatureMicrobiol

Nature Microbiology

@NatureMicrobiol

1 year

OUT NOW💩Fecal metagenomic sequencing data can be mined for personal information such as genetic sex, ancestry and clinically relevant genetic variants

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@okada_yukinori

YukinoriOkada

@okada_yukinori

3 years

Glad to launch a new lab at @RIKEN_IMS in Yokohama: Laboratory for Systems Genetics. Looking for post-doc researchers, technical staff, graduate students who work together on human genomics for disease system biology, drug discovery, personalized medicine.

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@okada_yukinori

YukinoriOkada

@okada_yukinori

3 years

Our primer on genome-wide association study (GWAS) is out today at @MethodsPrimers !! #GWAS

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@MethodsPrimers

Nature Reviews Methods Primers

@MethodsPrimers

3 years

Check out our Primer (out today!) for how to carry out genome wide association studies, including best practices, ethical considerations and future directions in the field. @euffelmann @hilsomartin @DPosthu @sangerinstitute @hilsomartin @qinqin_huang

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@okada_yukinori

YukinoriOkada

@okada_yukinori

5 years

Eating is surviving!! Biobank-scale and phenome-wide natural selection scans identified dietary habits as population-specific targets of human evolution – alcohol in Japanese but bread intake in Europeans. See our work in @MolBioEvol

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@okada_yukinori

YukinoriOkada

@okada_yukinori

2 years

Genetic footprints of assortative mating (AM) in Japanese for metabolic traits and dietary habits. @NatureHumBehav Collabo with @go_kenbo , @LoicYengo , and colleagues!! #GWAS #PGS #PRS

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@okada_yukinori

YukinoriOkada

@okada_yukinori

2 years

GWAS of 5.4 millions discovered a saturated map of common variants on height. Now at turning point of GWAS era. Wonderful teams with @LoicYengo Sailaja Vedantam @MarouliEirini Eric Bartell @saorisakaue @GLettre @drarwood Peter Visscher @joelhirschhorn

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@okada_yukinori

YukinoriOkada

@okada_yukinori

2 years

The first version of the GWAS-SSF format; a recommendation format when depositing GWAS summary statistics to public database such as @GWASCatalog . "A community driven GWAS summary statistics standard" in @biorxivpreprint #GWAS

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@biorxivpreprint

bioRxiv

@biorxivpreprint

2 years

A community driven GWAS summary statistics standard #bioRxiv

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@okada_yukinori

YukinoriOkada

@okada_yukinori

4 years

Combination of linear and non-linear machine learning (PCA-UMAP) can deconvolute high resolution genetic structure of worldwide populations including Japanese, UK, Malaysian, and Arab!! See our work with @saorisakaue in @NatureComms .

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@okada_yukinori

YukinoriOkada

@okada_yukinori

2 years

Our platform talk at ASHG2022🧬. PrgNbr 202 (2:15pm, 26th Wed, Petree C/West). Namba S @NambaShinichi , Saito T et al. "The impact of common germline risk on somatic alterations and clinical features across cancers." #ASHG22 #PolygenicRiskScore #PRS #Cancer

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@okada_yukinori

YukinoriOkada

@okada_yukinori

5 years

Our metagenome-wide association study (MWAS) in Japanese identified microbiome features of rheumatoid arthritis (RA) and population-specific pathway link with RA GWAS (MWAS-GWAS interaction). Kishikawa T. Ann Rheum Dis 2019. #microboime #GWAS #metagenome

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@okada_yukinori

YukinoriOkada

@okada_yukinori

3 years

CookHLA: New HLA imputation method. (1) An upgraded hidden Markov model. (2) Local embedding of markers on exons and consensus calling. (3) Adaptive learning of genetic map. Nice work, Buhm!!

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Accurate imputation of human leukocyte antigens with CookHLA

Nature Communications - Human leukocyte antigen (HLA) genes influence many immune phenotypes, however methods to impute HLA type have been limited in accuracy. Here, the authors present an HLA...

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@okada_yukinori

YukinoriOkada

@okada_yukinori

10 months

👇Please check out platform talks from our group at #ASHG2023 in D.C. 1. Pan-cancer GWAS & shared genomics between prostate & breast cancers by Dr. Go Sato. Session 010. Thr Nov 2. 2. Cross-population Gene x Environmental (GxE) catlogue by @NambaShinichi . Session 020, Thr Nov 2.

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@okada_yukinori

YukinoriOkada

@okada_yukinori

2 years

Interaction of common germline risk (polygenic risk score; PRS) and somatic alterations across cancers. Wonderful works with @NambaShinichi @yukisaito_1990 @kataoka_lab , now published at Cancer Research. #cancer #PRS #PGS

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@NambaShinichi

Shinichi Namba

2 years

Common germline variants can predict the risk of cancer development📈, but can they affect somatic alterations🧬? Yes! they have universal effects on mutations and SCNAs across cancer types. ➡️See published in @CR_AACR today!

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@okada_yukinori

YukinoriOkada

@okada_yukinori

5 years

Our recent publication for NGS-based HLA sequencing of 1,150 Japanese. We expanded HLA imputation into both classical and non-classical HLA genes with upto 6-digit alleles, followed by a phenome-wide association study (PheWAS) of ~100 clinical phenotypes of ~170,000 indivdiduals.

@NatureGenet

Nature Genetics

6 years

Genetic and phenotypic landscape of the major histocompatibilty complex region in the Japanese population (Hirata et al.)

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@okada_yukinori

YukinoriOkada

@okada_yukinori

2 years

Public release of Japanese gut metagenome and virus databases (JMAG & JVD) at @CellGenomics . Population-specific microbiome features like Natto & Nori. Autoimmune disease risk of crAss-like phage sub-families. Nice work by @YTomofuji_1107 !! #microbiome

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@CellGenomics

Cell Genomics

2 years

Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases

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@okada_yukinori

YukinoriOkada

@okada_yukinori

3 years

※再度アナウンスです。奮っての応募お待ちしています※ 理研IMSシステム遺伝学チームは、研究員・RA・技術補佐員を募集中です。大規模ゲノミクス解析による病態解明・創薬・個別化医療に取り組んでくれる人、応募ください。多様な人材（数理・情報・統計・バイオインフォ・基礎生物学）大歓迎です。

@RIKEN_IMS

RIKEN-IMS

3 years

研究員、特別研究員またはリサーチアソシエイト募集（IMS208-2101）生命医科学研究センター ( @RIKEN_IMS ) システム遺伝学チーム（チームリーダー: 岡田随象）

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@okada_yukinori

YukinoriOkada

@okada_yukinori

5 years

It is a great honor to have talk at the ICDA meeting. Thank you for all the collaborators. @ICDAbio #icdabio #icdabio2019

@ceclindgren

Cecilia Lindgren

5 years

Prof. Yuki Okada outlining the wonderful work from Biobank Japan and outlining his vision for 5 key areas for human genetics research ⁦ @ICDAbio ⁩ #icdabio2019

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@okada_yukinori

YukinoriOkada

@okada_yukinori

1 year

東京大学大学院医学系研究科遺伝情報学教室では、遺伝統計学やゲノム・オミクス解析を通じた病態解明・創薬・個別化医療に一緒に取り組んでくれるIT系技術補佐員を募集中です。バイオバンク・ジャパン（BBJ）のデータ解析チームの一員としても活躍してもらう予定です。

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@okada_yukinori

YukinoriOkada

@okada_yukinori

3 years

Metagenome-wide association study (MWAS) of gut microbiome of systemic lupus erythematosus (SLE) in Japanese is now at @ARD_BMJ ! Dysbiosis, increased Streptococcus, dosage correlation with serum acylcarnitine , GWAS-MWAS pathway interaction.🧬

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@ARD_BMJ

Annals of the Rheumatic Diseases

3 years

Additional evidence for changes in the gut #microbiome in patients with #lupus and overlap between biological pathways activated in the #SLE microbiome and by SLE genetic risk factors 👇!

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@okada_yukinori

YukinoriOkada

@okada_yukinori

5 years

Trans-ethnic collaborations by the ROHGen consortium finally unlocked relationships between human phenotypes and genetic autozygosity. #GWAS #PheWAS

@NatureComms

Nature Communications

5 years

A study on more than 1.4 million individuals reveals groups of human phenotypes sensitive to inbreeding depression: @mrc_hgu

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@okada_yukinori

YukinoriOkada

@okada_yukinori

5 years

Our platform talks at ASHG2019. (2) PgmNr 171 (Thu). Hirata J, Sakaue S. “ML-based deconvolution of biobank-driven GWAS data with 170k individuals enlightens the finest-scale genetic, evolutional, and PRS divergence within Japanese.” #ASHG2019 #PolygenicRiskScore #machinelearning

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@okada_yukinori

YukinoriOkada

@okada_yukinori

5 years

Our platform talks at ASHG2019. (1) PgmNr 63 (Wed). Sakaue S, Kanai M. “Trans-ethnic mega-biobank PRS analysis involving 676,000 individuals identified blood pressure and obesity as causal drivers affecting human longevity.” #ASHG2019 #PolygenicRiskScore #PrecisionMedicine

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@okada_yukinori

YukinoriOkada

@okada_yukinori

5 years

[Recent work from our group] Using BioBank Japan data, we found that functional missense SNPs of ADH1B rs1229984 and ALDH2 rs671, under positive selection in Japanese for past ~3,000 years, still affects all cause mortality of modern Japanese (Sakaue S. Eur J Hum Genet 2019 ).

@saorisakaue

Saori Sakaue

5 years

Why did we East Asians evolve to be intolerant to alcohol? We are glad to provide some hints to this question!🍷

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@okada_yukinori

YukinoriOkada

@okada_yukinori

2 years

Please visit/join/enjoy the Human Cell Atlas (HCA) Asia Meeting 2022. Nov 3-4th, 2022, in Bangkok, Thailand. Now open for registration!! #HCA2022Asia @humancellatlas #singlecell #Genomics #hybrid

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@humancellatlas

Human Cell Atlas

@humancellatlas

2 years

Registration for the HCA Asia Meeting November 3-4th, 2022 is now open! The #HCA2022Asia meeting in Bangkok, Thailand will be hybrid, both in-person and online. Register your interest for an in-person space or register for virtual attendance at

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@okada_yukinori

YukinoriOkada

@okada_yukinori

5 years

The second day of #ICDAbio2019 #ICDAbio @ICDAbio started! The live stream is available at;

@ceclindgren

Cecilia Lindgren

5 years

Our awsome executive director ⁦ @RachelGLiao ⁩ outlining the M2M2M challenge ⁦ @ICDAbio ⁩ is tackling and highlighting the virtual attendees (>300 people joined remotely) #icdabio #icdabio2019

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@okada_yukinori

YukinoriOkada

@okada_yukinori

5 years

Hi, just started up my Twitter. @okada_yukinori

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@okada_yukinori

YukinoriOkada

@okada_yukinori

2 years

Really wonderful to see my mentor @soumya_boston in person, after several years of quarantine!! #ACR2022

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@okada_yukinori

YukinoriOkada

@okada_yukinori

2 years

If you are in ACR 2022 @ Philadelphia, please join the joint JCR/ACR session (Sun 4:30pm) for trans-omics approaches of rheuamatic diseases. 13S168: Trans-Omics Dissection of Gene Regulation in Immune-mediated Diseases: A Joint JCR/ACR Session #ACR22

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@okada_yukinori

YukinoriOkada

@okada_yukinori

5 years

Presentations and discussions from the ICDA meeting is now available online! #ICDAbio #ICDAbio2019 @ICDAbio

@ICDAbio

International Common Disease Alliance

5 years

Videos from the ICDA Scientific Plenary & Launch are now available online. Even if you couldn't join us live, we hope you enjoy the fantastic science and discussion! #ICDAbio2019

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@okada_yukinori

YukinoriOkada

@okada_yukinori

3 years

Congrats! Qingbo Wang! @qbw_128

@qbw_128

Qingbo Seiha Wang

3 years

The Expression Modifier Score (EMS) paper, describing results of functionally-informed fine-mapping for GTEx v8 in 49 tissues (+ co-localization with 95 phenotypes in UKBB) is now online in @NatureComms ! 1/3

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@okada_yukinori

YukinoriOkada

@okada_yukinori

10 months

Immuno-phenotypes dissected AIRD patients into several clusters. RA- or SLE-like clusters were exclusively dominant, showing their immunological polalization. Clusters showed clinical heterogeneity such as treatment resistance in RA patients with SLE-like immuno-phenotypes.

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@okada_yukinori

YukinoriOkada

@okada_yukinori

3 years

理研IMSシステム遺伝学チームは、研究員・リサーチアソシエイトを募集中です。大規模ゲノミクス情報の遺伝統計解析による病態解明・ゲノム創薬・個別化医療に一緒に取り組んでくれる人、是非とも応募ください。多様なバックグランド（数理・情報・統計・バイオインフォ・基礎生物学）を歓迎します。

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@RIKEN_IMS

RIKEN-IMS

3 years

研究員、特別研究員またはリサーチアソシエイト募集（IMS208-2101）生命医科学研究センター ( @RIKEN_IMS ) システム遺伝学チーム（チームリーダー: 岡田随象）

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@okada_yukinori

YukinoriOkada

@okada_yukinori

5 years

2. Introduction of statistical genetics software from my lab; MIGWAS; miRNA-target gene networks enrichment on GWAS. This software integrates GWAS summary statistics and cell type-specific microRNA expression profiels to point biomarker microRNA.

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@okada_yukinori

YukinoriOkada

@okada_yukinori

5 years

1. Introduction of statistical genetics software from my lab; Grimon; Graphical interface to visualize multi-layer omics networks. This software deconvolutes high-dimensional omics data and provides 3D visualization of multi-layer omics networks.

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@okada_yukinori

YukinoriOkada

@okada_yukinori

4 years

@carninci @NatureMedicine @saorisakaue @masakanai @dalygene @APalotie @FinnGen_FI @uk_biobank Thanks, Piero. Yes, it was a long way for publish, but now we are happy to announce our collaboration.

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