Basic Information

Professional Memberships

• American society of human genetics
• 日本発生生物学会
• 日本分子生物学会

Academic Degree

• 修士（理学）(埼玉大学)
• 博士（理学）(埼玉大学)

Research History

• From Jul. 2020, To Present

  Kyoto University, Institute for the Advanced Study of Human Biology (ASHBi), Associate Professor, Co-PI
• From Aug. 2018, To Jun. 2020

  University of California, San Francisco, Department of Bioengineering and Therapeutic Sciences, Assistant Researcher
• From Aug. 2017, To Jul. 2018

  University of California, San Francisco, Department of Bioengineering and Therapeutic Sciences, Associate Specialist
• From Aug. 2012, To Jul. 2017

  University of California, San Francisco, Department of Bioengineering and Therapeutic Sciences, Postdoctoral Fellow
• From Apr. 2008, To Jul. 2012

  RIKEN, Center for Developmental Biology, Researcher

Language of Instruction

• Japanese
• English

ID,URL

• ORCID ID

  0000-0003-0657-434X

• J-Global ID

  202001021459982977

• External link

  https://sites.google.com/view/inouelabwebsite

researchmap URL

• https://researchmap.jp/fumitakainoue

Research

Research Topics, Overview of the research

• Research Topics

  Understanding human regulome that underlies cell differentiation, development and evolution

Research Interests

• ゲノム進化
• 神経分化
• Massively Parallel Reporter Assay
• エンハンサー

Research Areas

• Life sciences, Developmental biology
• Life sciences, Molecular biology
• Life sciences, Genomics

Papers

• Author Correction: Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery

  Boyan Bonev; Gonçalo Castelo-Branco; Fei Chen; Simone Codeluppi; M. Ryan Corces; Jean Fan; Myriam Heiman; Kenneth Harris; Fumitaka Inoue; Manolis Kellis; Ariel Levine; Mo Lotfollahi; Chongyuan Luo; Kristen R. Maynard; Mor Nitzan; Vijay Ramani; Rahul Satijia; Lucas Schirmer; Yin Shen; Na Sun; Gilad S. Green; Fabian Theis; Xiao Wang; Joshua D. Welch; Ozgun Gokce; Genevieve Konopka; Shane Liddelow; Evan Macosko; Omer Ali Bayraktar; Naomi Habib; Tomasz J. Nowakowski

  Nature Neuroscience, Jan. 2025, Peer-reviewed

  
• Statistically and functionally fine-mapped blood eQTLs and pQTLs from 1,405 humans reveal distinct regulation patterns and disease relevance

  Qingbo Wang; Takanori Hasegawa; Ho Namkoong; Ryunosuke Saiki; Ryuya Edahiro; Kyuto Sonehara; Hiromu Tanaka; Shuhei Azekawa; Shotaro Chubachi; Yugo Takahashi; Saori Sakaue; Shinichi Namba; Kenichi Yamamoto; Yuichi Shiraishi; Kenichi Chiba; Hiroko Tanaka; HIDEKI MAKISHIMA; Yasuhito Nannya; Zicong Zhang; Rika Tsujikawa; Ryuji Koike; Tomomi Takano; Makoto Ishii; Akinori Kimura; Fumitaka Inoue; Takanori Kanai; Koichi Fukunaga; Seishi Ogawa; Seiya Imoto; Satoru Miyano; Yukinori Okada; Japan COVID-19 Task Force

  Nature Genetics, 24 Sep. 2024, Peer-reviewed

  
• Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation

  William DeGroat; Fumitaka Inoue; Tal Ashuach; Nir Yosef; Nadav Ahituv; Anat Kreimer

  Genome Biology, 14 Aug. 2024, Peer-reviewed

  
• Massively parallel characterization of regulatory elements in the developing human cortex.

  Chengyu Deng; Sean Whalen; Marilyn Steyert; Ryan Ziffra; Pawel F Przytycki; Fumitaka Inoue; Daniela A Pereira; Davide Capauto; Scott Norton; Flora M Vaccarino; Alex A Pollen; Tomasz J Nowakowski; Nadav Ahituv; Katherine S Pollard

  Science (New York, N.Y.), 24 May 2024, Peer-reviewed

  
• Cryptic endogenous retrovirus subfamilies in the primate lineage

  Xun Chen; Zicong Zhang; Yizhi Yan; Clement Goubert; Guillaume Bourque; Fumitaka Inoue

  08 Dec. 2023

  
• Best practices for perturbation MPRA—a computational evaluation framework of sequence design strategies

  Jiayi Liu; Tal Ashuach; Fumitaka Inoue; Nadav Ahituv; Nir Yosef; Anat Kreimer

  29 Sep. 2023

  
• Massively parallel characterization of transcriptional regulatory elements

  Vikram Agarwal; Fumitaka Inoue; Max Schubach; Dmitry Penzar; Beth K. Martin; Pyaree Mohan Dash; Pia Keukeleire; Zicong Zhang; Ajuni Sohota; Jingjing Zhao; Ilias Georgakopoulos-Soares; William S. Noble; Galip Gürkan Yardımcı; Ivan V. Kulakovskiy; Martin Kircher; Jay Shendure; Nadav Ahituv

  Nature, 13 Mar. 2025, Peer-reviewed, Lead author

  
• Characterization of De Novo Promoter Variants in Autism Spectrum Disorder with Massively Parallel Reporter Assays

  Justin Koesterich; Joon-Yong An; Fumitaka Inoue; Ajuni Sohota; Nadav Ahituv; Stephan J. Sanders; Anat Kreimer

  International Journal of Molecular Sciences, 09 Feb. 2023

  
• Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids.

  Davide Capauto; Yifan Wang; Feinan Wu; Scott Norton; Jessica Mariani; Fumitaka Inoue; Gregory E Crawford; Nadav Ahituv; Alexej Abyzov; Flora M Vaccarino

  Scientific reports, 16 Feb. 2024, Peer-reviewed

  
• Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans.

  Yuanqing Feng; Ning Xie; Fumitaka Inoue; Shaohua Fan; Joshua Saskin; Chao Zhang; Fang Zhang; Matthew E B Hansen; Thomas Nyambo; Sununguko Wata Mpoloka; Gaonyadiwe George Mokone; Charles Fokunang; Gurja Belay; Alfred K Njamnshi; Michael S Marks; Elena Oancea; Nadav Ahituv; Sarah A Tishkoff

  Nature genetics, Feb. 2024, Peer-reviewed

  
• Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework.

  Jiayi Liu; Tal Ashuach; Fumitaka Inoue; Nadav Ahituv; Nir Yosef; Anat Kreimer

  Nucleic acids research, 31 Jan. 2024, Peer-reviewed

  
• Molecular mechanism of transcriptional regulation of Otx2 gene in the forebrain and midbrain

  Fumitaka Inoue; Daisuke Kurokawa; Nobuyoshi Takasaki; Tomomi Ohmura; Kyo Yamasu; Shinichi Aizawa

  MECHANISMS OF DEVELOPMENT, Aug. 2009

  
• Three-dimensional genome rewiring in loci with human accelerated regions

  Kathleen C. Keough; Sean Whalen; Fumitaka Inoue; Pawel F. Przytycki; Tyler Fair; Chengyu Deng; Marilyn Steyer; Hane Ryu; Kerstin Lindblad-Toh; Elinor Karlsson; Zoonomia Consortium; Tomasz Nowakowski; Nadav Ahituv; Alex Pollen; Katherine S. Pollard

  Science, 28 Apr. 2023, Peer-reviewed

  
• Transcription factor binding site orientation and order are major drivers of gene regulatory activity

  Ilias Georgakopoulos-Soares; Chengyu Deng; Vikram Agarwal; Candace S. Y. Chan; Jingjing Zhao; Fumitaka Inoue; Nadav Ahituv

  Nature Communications, 22 Apr. 2023, Peer-reviewed

  
• Machine learning dissection of human accelerated regions in primate neurodevelopment

  Sean Whalen; Fumitaka Inoue; Hane Ryu; Tyler Fair; Eirene Markenscoff-Papadimitriou; Kathleen Keough; Martin Kircher; Beth Martin; Beatriz Alvarado; Orry Elor; Dianne Laboy Cintron; Alex Williams; Md. Abul Hassan Samee; Sean Thomas; Robert Krencik; Erik M. Ullian; Arnold Kriegstein; John L. Rubenstein; Jay Shendure; Alex A. Pollen; Nadav Ahituv; Katherine S. Pollard

  Neuron, Jan. 2023, Peer-reviewed, Lead author

  
• High-throughput characterization of the role of non-B DNA motifs on promoter function

  Ilias Georgakopoulos-Soares; Jesus Victorino; Guillermo Parada; Vikram Agarwal; Jingjing Zhao; Hei Yuen Wong; Mubarak Ishaq Umar; Orry Elor; Allan Muhwezi; Joon-Yong An; Stephan J. Sanders; Chun Kit Kwok; Fumitaka Inoue; Martin Hemberg; Nadav Ahituv

  Cell Genomics, Apr. 2022, Peer-reviewed

  
• The cis-regulatory effects of modern human-specific variants.

  Carly V Weiss; Lana Harshman; Fumitaka Inoue; Hunter B Fraser; Dmitri A Petrov; Nadav Ahituv; David Gokhman

  eLife, 22 Apr. 2021, Peer-reviewed

  
• A systematic evaluation of the design and context dependencies of massively parallel reporter assays

  Jason C. Klein; Vikram Agarwal; Fumitaka Inoue; Aidan Keith; Beth Martin; Martin Kircher; Nadav Ahituv; Jay Shendure

  Nature Methods, 12 Nov. 2020, Peer-reviewed, Lead author

  
• lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements

  M. Grace Gordon; Fumitaka Inoue; Beth Martin; Max Schubach; Vikram Agarwal; Sean Whalen; Shiyun Feng; Jingjing Zhao; Tal Ashuach; Ryan Ziffra; Anat Kreimer; Ilias Georgakopoulous-Soares; Nir Yosef; Chun Jimmie Ye; Katherine S. Pollard; Jay Shendure; Martin Kircher; Nadav Ahituv

  Nature Protocols, 08 Jul. 2020, Peer-reviewed, Lead author, Corresponding author

  
• Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction

  Fumitaka Inoue; Anat Kreimer; Tal Ashuach; Nadav Ahituv; Nir Yosef

  Cell Stem Cell, 07 Nov. 2019, Peer-reviewed, Lead author

  
• Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution

  Martin Kircher; Chenling Xiong; Beth Martin; Max Schubach; Fumitaka Inoue; Robert J.A. Bell; Joseph F. Costello; Jay Shendure; Nadav Ahituv

  Nature Communications, 08 Aug. 2019, Peer-reviewed

  
• Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay

  Dustin Shigaki; Orit Adato; Aashish N. Adhikari; Shengcheng Dong; Alex Hawkins-Hooker; Fumitaka Inoue; Tamar Juven-Gershon; Henry Kenlay; Beth Martin; Ayoti Patra; Dmitry D. Penzar; Max Schubach; Chenling Xiong; Zhongxia Yan; Alan P. Boyle; Anat Kreimer; Ivan V. Kulakovskiy; John Reid; Ron Unger; Nir Yosef; Jay Shendure; Nadav Ahituv; Martin Kircher; Michael A. Beer

  Human Mutation, 20 May 2019, Peer-reviewed

  
• Genomic and epigenomic mapping of leptin-responsive neuronal populations involved in body weight regulation

  Fumitaka Inoue; Walter L. Eckalbar; Yi Wang; Karl K. Murphy; Navneet Matharu; Christian Vaisse; Nadav Ahituv

  Nature Metabolism, 08 Apr. 2019, Peer-reviewed, Lead author

  
• Corrigendum: A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

  Fumitaka Inoue; Martin Kircher; Beth Martin; Gregory M. Cooper; Daniela M. Witten; Michael T. McManus; Nadav Ahituv; Jay Shendure

  Genome research, May 2018, Peer-reviewed

  
• A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

  Fumitaka Inoue; Martin Kircher; Beth Martin; Gregory M. Cooper; Daniela M. Witten; Michael T. McManus; Nadav Ahituv; Jay Shendure

  Genome Research, Jan. 2017, Peer-reviewed, Lead author

  
• Decoding enhancers using massively parallel reporter assays

  Fumitaka Inoue; Nadav Ahituv

  Genomics, Sep. 2015, Peer-reviewed, Lead author

  
• Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model

  Robin P. Smith; Leila Taher; Rupali P. Patwardhan; Mee J. Kim; Fumitaka Inoue; Jay Shendure; Ivan Ovcharenko; Nadav Ahituv

  Nature Genetics, 28 Jul. 2013, Peer-reviewed

  
• Gbx2 Directly Restricts Otx2 Expression to Forebrain and Midbrain, Competing with Class III POU Factors

  Fumitaka Inoue; Daisuke Kurokawa; Maiko Takahashi; Shinichi Aizawa

  Molecular and Cellular Biology, Jul. 2012, Peer-reviewed, Lead author

  
• The same enhancer regulates the earliest Emx2 expression in caudal forebrain primordium, subsequent expression in dorsal telencephalon and later expression in the cortical ventricular zone

  Yoko Suda; Kenji Kokura; Jun Kimura; Eriko Kajikawa; Fumitaka Inoue; Shinichi Aizawa

  Development, Sep. 2010, Peer-reviewed

  
• Evolutionary origin of the Otx2 enhancer for its expression in visceral endoderm

  Daisuke Kurokawa; Tomomi Ohmura; Hajime Ogino; Masaki Takeuchi; Ai Inoue; Fumitaka Inoue; Yoko Suda; Shinichi Aizawa

  Developmental Biology, Jun. 2010, Peer-reviewed

  
• Autoregulatory loop and retinoic acid repression regulate pou2/pou5f1 gene expression in the zebrafish embryonic brain

  Mst Shahnaj Parvin; Noriko Okuyama; Fumitaka Inoue; Md Ekramul Islam; Atsushi Kawakami; Hiroyuki Takeda; Kyo Yamasu

  Developmental Dynamics, May 2008, Peer-reviewed

  
• Transcription of fgf8 is regulated by activating and repressive cis-elements at the midbrain-hindbrain boundary in zebrafish embryos

  Fumitaka Inoue; Mst Shahnaj Parvin; Kyo Yamasu

  Developmental Biology, Apr. 2008, Peer-reviewed, Lead author

  
• Three enhancer regions regulate gbx2 gene expression in the isthmic region during zebrafish development

  Md Ekramul Islam; Hiroshi Kikuta; Fumitaka Inoue; Maiko Kanai; Atsushi Kawakami; Mst Shahnaj Parvin; Hiroyuki Takeda; Kyo Yamasu

  Mechanisms of Development, Dec. 2006, Peer-reviewed

  
• Genomic organization, alternative splicing, and multiple regulatory regions of the zebrafish fgf8 gene

  Fumitaka Inoue; Saori Nagayoshi; Satoshi Ota; Md Ekramul Islam; Noriko Tonou-Fujimori; Yuko Odaira; Koichi Kawakami; Kyo Yamasu

  Development Growth and Differentiation, Sep. 2006, Peer-reviewed, Lead author

  
• Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation.

  Anat Kreimer; Tal Ashuach; Fumitaka Inoue; Alex Khodaverdian; Chengyu Deng; Nir Yosef; Nadav Ahituv

  Nature communications, 21 Mar. 2022, Peer-reviewed, Lead author

  Access this paper :

  

Misc.

• ヒト加速領域（HAR）の機能と進化を機械学習により検証する

  井上詞貴

  実験医学, Aug. 2023, Lead author

  
• Decoding neural induction using massively parallel reporter assays

  Fumitaka Inoue

  Jikken Igaku, Mar. 2020, Lead author

  
• Genomic and epigenomic mapping of leptin-responsive neurons in the hypothalamus

  Fumitaka Inoue

  Jikken Igaku, Sep. 2019, Lead author

  

Presentations

• Deciphering human functional genome using Massively Parallel Reporter Assays

  Fumitaka Inoue

  The 47th Molecular Biology Society of Japan, 27 Nov. 2024, Invited

  
• Deciphering human functional genome using Massively Parallel Reporter Assays

  Fumitaka Inoue

  HIGOプログラム最先端研究セミナー, 02 Oct. 2024, Invited

  
• 大規模並列レポーターアッセイ（MPRA）による転移因子エンハンサーの機能解析

  井上詞貴

  第６回転移因子研究会（2023年度遺伝研研究会）, 24 Aug. 2023, Invited

  
• Massively parallel dissection of regulatory code underlying neural differentiation

  Fumitaka Inoue

  The 56th Annual Meeting of the Japanese Society of Developmental Biologists, 25 Jul. 2023, Invited

  
• Massively parallel functional dissection of transposable element enhancer variants

  Fumitaka Inoue

  The 45th Molecular Biology Society of Japan, 30 Nov. 2022, Invited

  
• Decoding non-coding genome using massively parallel reporter assays

  Fumitaka Inoue

  NGS EXPO 2022, 19 Oct. 2022, Invited

  
• 大規模並列レポーターアッセイが紐解く細胞分化、進化、疾患

  井上詞貴

  第10回 都医学研シンポジウム ゲノム機能解析の進展とその医科学への応用, 27 Nov. 2020, Invited

  
• Functional Dissection of Neural Enhancers Using Massively Parallel Reporter Assays

  Fumitaka Inoue

  The 7th Annual Molecular Psychiatry Meeting, 17 Oct. 2019, Invited

  
• Decoding the mechanism of neural differentiation by massively parallel reporter assays

  Fumitaka Inoue; Anat Kreimer; Nir Yosef; Nadav Ahituv

  Consortium of Biological Sciences 2017 (ConBio2017), Dec. 2017

  
• Gbx2 directly restricts Otx2 expression to forebrain and midbrain, competing with Class III POU factors

  Fumitaka Inoue; Daisuke Kurokawa; Maiko Takahashi; Shinichi Aizawa

  第34回日本分子生物学会年会, Dec. 2011

  
• Molecular evolution of the vertebrate Fgf8 subfamily of fibroblast growth factors and their enhancers for the midbrain-hindbrain boundary

  Fumitaka Inoue; Daisuke Kobayashi; Hiroyuki Takeda; Kyo Yamasu

  第30回日本分子生物学会年会, Dec. 2007

  
• ゼブラフィッシュ胚の中脳後脳境界におけるfgf8遺伝子の転写制御

  井上詞貴; 弥益恭

  第12回小型魚類研究会, Sep. 2006

  
• Regulatory mechanism of the transcription of fgf8 during zebrafish brain formation

  Fumitaka Inoue; Saori Nagayoshi; Yuko Odaira; Koichi Kawakami; Kyo Yamasu

  10th Japanese Medaka and Zebrafish Meeting, Nov. 2004

  

Awards

• 07 Feb. 2018

  ENCODE Consortium Meeting, Best Poster Award

External funds: Kakenhi

• 大規模並列レポーターアッセイ法による転移因子進化メカニズムの解明

  Grant-in-Aid for Scientific Research (C)

  Basic Section 43050:Genome biology-related

  Kyoto University

  井上 詞貴

  From 01 Apr. 2021, To 31 Mar. 2024, Granted

  エンハンサー;転移因子;MPRA;ゲノム進化;エピゲノム;iPS細胞;神経前駆細胞

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-21K06119/
• Evaluating the role of cis-regulatory tandem DNA repeats in human disease and evolution

  Grant-in-Aid for Scientific Research (B)

  Basic Section 43050:Genome biology-related

  Kyoto University

  ウォルツェン クヌート

  From 01 Apr. 2021, To 31 Mar. 2024, Granted

  DNAリピート;ゲノム編集;CRISPR-Cas9;iPS細胞;レポーターアッセイ;ゲノム解析;ヒトiPS細胞

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-21H02460/
• ヒト特性に関わるノンコーディング変異の網羅的同定

  Grant-in-Aid for Scientific Research (B)

  Basic Section 43050:Genome biology-related

  Kyoto University

  井上 詞貴

  From 01 Apr. 2024, To 31 Mar. 2027, Granted

  エンハンサー;遺伝子発現制御;MPRA;ゲノム進化;ヒト進化

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-24K02004/

External funds: others

• 大規模集団ゲノムデータを利用した遺伝子発現制御文法の学習による、非コードVUS病原性の網羅的評価と実験検証

  遺伝性疾患のゲノム解析で得られたVUSへの機能的ｱﾉﾃｰｼｮﾝに資する基盤研究

  国立研究開発法人日本医療研究開発機構, ゲノム創薬基盤推進研究事業・ゲノム情報研究の医療への実利用を促進する研究

  From 01 Apr. 2022, To 31 Mar. 2025

  王 青波

  井上 詞貴

  研究分担者
• ヒト特性を担う遺伝子制御領域の大規模機能アノテーション

  公益財団法人三菱財団, 自然科学研究助成

  From 01 Oct. 2022, To 30 Sep. 2023

  井上詞貴

  研究代表者
• 大規模並列レポーターアッセイによるヒト特性と非コードゲノム進化の解明

  公益財団法人武田科学振興財団, 生命科学研究助成

  From 01 Oct. 2022, To 31 Mar. 2027

  井上詞貴

  研究代表者
• Massively parallel functional analysis of gene regulatory elements

  上原記念生命科学財団

  From 01 Jan. 2013, To 31 Dec. 2013

  井上詞貴

Education

Teaching subject(s)

• From 01 Apr. 2024, To 31 Mar. 2025

  ILAS Seminar

  Z001, Spring, Institute for Liberal Arts and Sciences, 2

Academic, Social Contribution

Academic Contribution

• 45th Molecular Biology Society of Japan (Makuhari Messe), Wrokshop "Genome autonomy, woven by various functional elements: its frontline and technology development"

  Planning, management, etc., Panel moderator

  Fumitaka Inoue, Taro Tsujimura, From 30 Nov. 2022, To 30 Nov. 2022

  

Social Contribution

• ゲノムに隠された「ヒトを特徴づける暗号」とは? ノンコーディングDNAの機能解析で謎にせまる

  Lecturer

  Kyoto Research Park, Researchers’ Co-Learning Community, From 28 Jul. 2022