論文・出版物

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MISC

  1. 井上詞貴. (2023). 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. 実験医学 41 (13): 2160-2163DOI
  2. 井上詞貴. (2020). 大規模並列レポーターアッセイによる神経誘導メカニズムの解読. 実験医学 38(4): 598-601
  3. 井上詞貴. (2019). 視床下部におけるレプチン応答ゲノム・エピゲノム解析. 実験医学 37(14): 2326-2329.

2024

  1. Jiayi Liu, Tal Ashuach, Fumitaka Inoue, Nadav Ahituv, Nir Yosef, Anat Kreimer (2024). Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework. Nucleic Acids Research, 52 (4), 1613-1627DOI
  2. Davide Capauto, Yifan Wang, Feinan Wu, Scott Norton, Jessica Mariani, Fumitaka Inoue, Gregory E Crawford, Nadav Ahituv, Alexej Abyzov, Flora M Vaccarino. (2024). Characterization of enhancer activity in early human neurodevelopment using Massively parallel reporter assay (MPRA) and forebrain organoids. Scientific Reports 14 (1), 3936DOI
  3. Yuanqing Feng, Ning Xie, Fumitaka Inoue, Shaohua Fan, Joshua Saskin, Chao Zhang, Fang Zhang, Matthew EB 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. (2024) Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans. Nature Genetics, 56, 258–272DOI
  4. [as a consortium autor]. (2024) CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biology 25 (1), 1-46DOI

2023

  1. Keough, K. C., Whalen, S., Inoue, F., Przytycki, P. F., Fair, T., Deng, C., Steyert, M., Ryu, H., Lindblad-Toh, K., Karlsson, E., Zoonomia Consortium, Nowakowski, T., Ahituv, N., Pollen, A., Pollard, K. S. (2023). Three-dimensional genome rewiring in loci with human accelerated regions. Science, 380(6643).DOI
  2. Georgakopoulos-Soares, I., Deng, C., Agarwal, V., Chan, C., Zhao, J., Inoue, F., & Ahituv, N. (2023). Transcription factor binding site orientation and order are major drivers of gene regulatory activity. Nature Communications, 14, 2333DOI
  3. Whalen, S.*, Inoue, F.*, Ryu, H.*, Fair, T., Markenscoff-Papadimitriou, E., Keough, K., Kircher, M., Martin, B., Alvarado, B., Elor, O., Laboy Cintron, D., Williams, A., Hassan Samee, M.A., Thomas, S., Krencik, R., Ullian, E.M., Kriegstein, A., Rubenstein, J.L., Shendure, J., Pollen, A.A., Ahituv, N.,^ Pollard, K.S.^ (2023). Machine learning dissection of human accelerated regions in primate neurodevelopment. Neuron, 111(6), 857–873. （*共同筆頭著者）DOI
  4. Koesterich, J., An, J.-Y., Inoue, F., Sohota, A., Ahituv, N., Sanders, S. J. & Kreimer, A. (2023). Characterization of De Novo Promoter Variants in Autism Spectrum Disorder with Massively Parallel Reporter Assays. International Journal of Molecular Sciences, 24(4), 3509DOI

2022

  1. Kreimer, A.*^, Ashuach, T.*, Inoue, F.*, Khodaverdian, A., Deng, C., Yosef, N.^ & Ahituv, N.^ (2022). Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation. Nature Communications, 13(1), 1504. （*共同筆頭著者）DOI
  2. Georgakopoulos-Soares, I., Victorino, J., Parada, G. E., Agarwal, V., Zhao, J., Wong, H. Y., Umar, M. I., Elor, O., Muhwezi, A., An, J.-Y., Sanders, S. J., Kwok, C. K., Inoue, F., Hemberg, M. & Ahituv, N. (2022). High-throughput characterization of the role of non-B DNA motifs on promoter function. Cell Genomics, 100111.DOI

2021

  1. Mathkar, P. P., Chen, X.^, Sulovari, A. & Li, D.^ (2021). Characterization of Hepatitis B Virus Integrations Identified in Hepatocellular Carcinoma Genomes. Viruses, 13(2). DOI
  2. Weiss, C*. V, Harshman, L.*, Inoue, F., Fraser, H. B., Petrov, D. A.^, Ahituv, N.^ & Gokhman, D.^ (2021). The cis-regulatory effects of modern human-specific variants. ELife, 10.DOI

2020

  1. Klein, J. C.*, Agarwal, V.*, Inoue, F.*, Keith, A.*, Martin, B., Kircher, M., Ahituv, N.^ & Shendure, J.^ (2020). A systematic evaluation of the design and context dependencies of massively parallel reporter assays. Nature Methods, 17, 1083-1091.（*共同筆頭著者）DOI
  2. Gordon, M. G.*, Inoue, F.*^, Martin, B.*, Schubach, M.*, Agarwal, V., Whalen, S., Feng, S., Zhao, J., Ashuach, T., Ziffra, R., Kreimer, A., Georgakopoulous-Soares, I., Yosef, N., Ye, C. J., Pollard, K. S., Shendure, J.^, Kircher, M.^ & Ahituv, N.^ (2020). lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nature Protocols, 15(8), 2387–2412.（*共同筆頭著者, ^共同責任著者）DOI

2019

  1. Inoue, F.*, Kreimer, A.*, Ashuach, T., Ahituv, N.^ & Yosef, N.^ (2019). Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction. Cell Stem Cell, 25(5), 713-727.e10. （*共同筆頭著者）DOI
  2. Kircher, M.*^, Xiong, C.*, Martin, B.*, Schubach, M.*, Inoue, F., Bell, R. J. A., Costello, J. F., Shendure, J.^ & Ahituv, N.^ (2019). Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution. Nature Communications, 10(1), 1–15. DOI
  3. Shigaki, D., Adato, O., Adhikari, A. N., Dong, S., Hawkins‐Hooker, A., Inoue, F., Juven‐Gershon, T., Kenlay, H., Martin, B., Patra, A., Penzar, D. D., Schubach, M., Xiong, C., Yan, Z., Boyle, A. P., Kreimer, A., Kulakovskiy, I. V., Reid, J., Unger, R., … Beer, M. A.^ (2019). Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay. Human Mutation, humu.23797. DOI
  4. Inoue, F.*, Eckalbar, W. L.*, Wang, Y., Murphy, K. K., Matharu, N., Vaisse, C.^ & Ahituv, N.^ (2019). Genomic and epigenomic mapping of leptin-responsive neuronal populations involved in body weight regulation. Nature Metabolism, 1, 475-484.（*共同筆頭著者）DOI

2018

  1. Inoue, F., Kircher, M., Martin, B., Cooper, G. M., Witten, D. M., McManus, M. T., Ahituv, N. & Shendure, J. (2018). Corrigendum: A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity. Genome Research. DOI

2017

  1. Inoue, F.*, Kircher, M.*, Martin, B., Cooper, G. M., Witten, D. M., McManus, M. T., Ahituv, N.^ & Shendure, J.^ (2017). A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity. Genome Research, 27(1), 38–52.（*共同筆頭著者）DOI

2015

  1. Inoue, F. & Ahituv, N. (2015). Decoding enhancers using massively parallel reporter assays. Genomics, 106(3), 159–164. DOI

2013

  1. Smith, R. P.*, Taher, L.*, Patwardhan, R. P., Kim, M. J., Inoue, F., Shendure, J.^, Ovcharenko, I.^ & Ahituv, N.^ (2013). Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. Nat Genet, 45(9), 1021–1028.DOI

2012

  1. Inoue, F., Kurokawa, D., Takahashi, M. & Aizawa, S. (2012). Gbx2 directly restricts Otx2 expression to forebrain and midbrain, competing with class III POU factors. Molecular and Cellular Biology, 32(13), 2618–2627. DOI

2010

  1. Suda, Y., Kokura, K., Kimura, J., Kajikawa, E., Inoue, F. & Aizawa, S. (2010). 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. Development (Cambridge, England), 137(17), 2939–2949DOI
  2. Kurokawa, D., Ohmura, T., Ogino, H., Takeuchi, M., Inoue, A., Inoue, F., Suda, Y. & Aizawa, S. (2010). Evolutionary origin of the Otx2 enhancer for its expression in visceral endoderm. Developmental Biology, 342(1), 110–120.

2008

  1. Parvin, M. S., Okuyama, N., Inoue, F., Islam, M. E., Kawakami, A., Takeda, H. & Yamasu, K. (2008). Autoregulatory loop and retinoic acid repression regulate pou2/pou5f1 gene expression in the zebrafish embryonic brain. Dev Dyn, 237(5), 1373–1388.DOI
  2. Inoue, F, Parvin, M. S. & Yamasu, K. (2008). Transcription of fgf8 is regulated by activating and repressive cis-elements at the midbrain-hindbrain boundary in zebrafish embryos. Dev Biol, 316(2), 471–486.DOI

2006

  1. Islam, M. E., Kikuta, H., Inoue, F., Kanai, M., Kawakami, A., Parvin, M. S., Takeda, H. & Yamasu, K. (2006). Three enhancer regions regulate gbx2 gene expression in the isthmic region during zebrafish development. Mechanisms of Development, 123(12), 907–924.
  2. Inoue, F.*, Nagayoshi, S.*, Ota, S., Islam, M. E., Tonou-Fujimori, N., Odaira, Y., Kawakami, K. & Yamasu, K. (2006). Genomic organization, alternative splicing, and multiple regulatory regions of the zebrafish fgf8 gene. Dev Growth Differ, 48(7), 447–462.（*共同筆頭著者）DOI