(* co-first, ^co-corresponding authors)

2025

1. Chen, X.^, Zhang, Z., Yan, Y., Goubert, C., Bourque, G.^, and Inoue, F.^ (2025).
   A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage.
   Science Advances 11. https://doi.org/10.1126/sciadv.ads9164.
   
   

2. Agarwal, V.*, Inoue, F.*, Schubach, M., Penzar, D., Martin, B.K., Dash, P.M., Keukeleire, P., Zhang, Z., Sohota, A., Zhao, J., Georgakopoulos-Soares, I., Noble, W.S., Yardımcı, G.G., Kulakovskiy, I. V., Kircher, M., Shendure, J., and Ahituv, N. (2025).
   Massively parallel characterization of transcriptional regulatory elements.
   Nature 639, 411–420. https://doi.org/10.1038/s41586-024-08430-9.
   
   

3. Takahashi, Y., Wang, Q.S., Hasegawa, T., Namkoong, H., Inoue, F., Fukunaga, K., Imoto, S., Miyano, S., and Okada, Y. (2025).
   JOB: Japan Omics Browser provides integrative visualization of multi-omics data.
   BMC Genomics 26, 451. https://doi.org/10.1186/s12864-025-11639-1.
   
   

2024

4. (Review article)
   Bonev, B., Gonçalo, C.-B., Chen, F., Codeluppi, S., Corces, M.R., Fan, J., Heiman, M., Harris, K., Inoue, F., Kellis, M., Levine, A., Lotfollahi, M., Luo, C., Maynard, K.R., Nitzan, M., Ramani, V., Satijia, R., Schirmer, L., Shen, Y., Sun, N., Green, G.S., Theis, F., Wang, X., Welch, J.D., Gokce, O., Konopka, G., Liddelow, S., Macosko, E., Bayraktar, O., Habib, N., and Nowakowski, T.J. (2024).
   Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.
   Nature Neuroscience 27, 2292–2309. https://doi.org/10.1038/s41593-024-01806-0.

5. Wang, Q.S., Hasegawa, T., Namkoong, H., Saiki, R., Edahiro, R., Sonehara, K., Tanaka, H., Azekawa, S., Chubachi, S., Takahashi, Y., Sakaue, S., Namba, S., Yamamoto, K., Shiraishi, Y., Chiba, K., Tanaka, H., Makishima, H., Nannya, Y., Zhang, Z., Tsujikawa, R., Koike, R., Takano, T., Ishii, M., Kimura, A., Inoue, F., Kanai, T., Fukunaga, K., Ogawa, S., Imoto, S., Miyano, S., and Okada, Y; Japan COVID-19 Task Force. (2024).  
   Statistically and functionally fine-mapped blood eQTLs and pQTLs from 1,405 humans reveal distinct regulation patterns and disease relevance.
   Nature Genetics 56, 2054-2067. https://doi.org/10.1038/s41588-024-01896-3.
   
   

6. Deng, C., Whalen, S., Steyert, M., Ziffra, R., Przytycki, P.F., Inoue, F., Pereira, D.A., Capauto, D., Norton, S., Vaccarino, F.M., Pollen, A.A., Nowakowski, T.J., Ahituv, N., Pollard, K.S. (2024)
   Massively parallel characterization of regulatory elements in the developing human cortex.
   Science 384. https://doi.org/10.1126/science.adh0559.

7. (as a consortium author)
   Emani, P.S., Liu, J.J., Clarke, D., Jensen, M., Warrell, J., Gupta, C., Meng, R., Lee, C.Y., Xu, S., Dursun, C., Lou, S., Chen, Y., Chu, Z., Galeev, T., Hwang, A., Li, Y., Ni, P., Zhou, X., Bakken, T.E., Bendl, J., Bicks, L., Chatterjee, T., Cheng, L., Cheng, Y., Dai, Y., Duan, Z., Flaherty, M., Fullard, J.F., Gancz, M., Garrido-Martín, D., Gaynor-Gillett, S., Grundman, J., Hawken, N., Henry, E., Hoffman, G.E., Huang, A., Jiang, Y., Jin, T., Jorstad, N.L., Kawaguchi, R., Khullar, S., Liu, J., Liu, J., Liu, S., Ma, S., Margolis, M., Mazariegos, S., Moore, J., Moran, J.R., Nguyen, E., Phalke, N., Pjanic, M., Pratt, H., Quintero, D., Rajagopalan, A.S., Riesenmy, T.R., Shedd, N., Shi, M., Spector, M., Terwilliger, R., Travaglini, K.J., Wamsley, B., Wang, G., Xia, Y., Xiao, S., Yang, A.C., Zheng, S., Gandal, M.J., Lee, D., Lein, E.S., Roussos, P., Sestan, N., Weng, Z., White, K.P., Won, H., Girgenti, M.J., Zhang, J., Wang, D., Geschwind, D., Gerstein, M. (2024)
   Single-cell genomics and regulatory networks for 388 human brains.
   Science 384. https://doi.org/10.1126/science.adi5199.

8. (as a consortium author)
   Ruzicka, W.B., Mohammadi, S., Fullard, J.F., Davila-Velderrain, J., Subburaju, S., Tso, D.R., Hourihan, M., Jiang, S., Lee, H.-C., Bendl, J., Voloudakis, G., Haroutunian, V., Hoffman, G.E., Roussos, P., Kellis, M. (2024)
   Single-cell multi-cohort dissection of the schizophrenia transcriptome.
   Science 384. https://doi.org/10.1126/science.adg5136.
   
   

9. DeGroat, W., Inoue, F., Ashuach, T., Yosef, N., Ahituv, N., and Kreimer, A. (2024).
   Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation.
   Genome Biology 25, 221. https://doi.org/10.1186/s13059-024-03365-w. 

10. Capauto, D., Wang, Y., Wu, F., Norton, S., Mariani, J., Inoue, F., Crawford, G.E., Ahituv, N., Abyzov, A., and Vaccarino, F.M. (2024).
    Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids.
    Sci. Rep. 14, 3936. https://doi.org/10.1038/s41598-024-54302-7.

11. Feng, Y., Xie, N., Inoue, F., Fan, S., Saskin, J., Zhang, C., Zhang, F., Hansen, M.E.B., Nyambo, T., Mpoloka, S.W., Mokone, G.G., Fokunang, C., Belay, G., Njamnshi, A.K., Marks, M.S., Oancea, E., Ahituv, N., and Tishkoff, S.A. (2024).
    Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans.
    Nature Genetics 56, 258–272. https://doi.org/10.1038/s41588-023-01626-1.

12. Liu, J., Ashuach, T., Inoue, F., Ahituv, N., Yosef, N., and Kreimer, A. (2024).
    Optimizing sequence design strategies for perturbation MPRAs: a computational evaluation framework.
    Nucleic Acids Res. 52, 1613–1627. https://doi.org/10.1093/nar/gkae012.

13. (as a consortium author)
    The Critical Assessment of Genome Interpretation Consortium (2024).
    CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods.
    Genome Biology 25, 53. https://doi.org/10.1186/s13059-023-03113-6.

2023

14. 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, Md.A., Thomas, S., Krencik, R., Ullian, E.M., Kriegstein, A., Rubenstein, J.L., Shendure, J., Pollen, A.A., Ahituv, N., and Pollard, K.S. (2023).
    Machine learning dissection of human accelerated regions in primate neurodevelopment.
    Neuron 111, 857-873.e8. https://doi.org/10.1016/j.neuron.2022.12.026.

15. Keough, K.C., Whalen, S., Inoue, F., Przytycki, P.F., Fair, T., Deng, C., Steyert, M., Ryu, H., Lindblad-Toh, K., Karlsson, E., Nowakowski, T., Ahituv, N., Pollen, A., Pollard, K.S. (2023).
    Three-dimensional genome rewiring in loci with human accelerated regions.
    Science 380. https://doi.org/10.1126/science.abm1696.

16. Georgakopoulos-Soares, I., Deng, C., Agarwal, V., Chan, C.S.Y., Zhao, J., Inoue, F., and Ahituv, N. (2023).
    Transcription factor binding site orientation and order are major drivers of gene regulatory activity.
    Nature Commun. 14, 2333. https://doi.org/10.1038/s41467-023-37960-5.

17. Koesterich, J., An, J.-Y., Inoue, F., Sohota, A., Ahituv, N., Sanders, S.J., and Kreimer, A. (2023).
    Characterization of De Novo Promoter Variants in Autism Spectrum Disorder with Massively Parallel Reporter Assays.
    Int. J. Mol. Sci. 24, 3509. https://doi.org/10.3390/ijms24043509.

2022

18. Kreimer, A.*, Ashuach, T.*, Inoue, F.*, Khodaverdian, A., Deng, C., Yosef, N., and Ahituv, N. (2022).
    Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation.
    Nature Commun. 13, 1504. https://doi.org/10.1038/s41467-022-28659-0.

19. 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., and Ahituv, N. (2022).
    High-throughput characterization of the role of non-B DNA motifs on promoter function.
    Cell Genomics, 100111. https://doi.org/10.1016/j.xgen.2022.100111.

2021

20. Weiss, C. V*, Harshman, L.*, Inoue, F., Fraser, H.B., Petrov, D.A., Ahituv, N., and Gokhman, D. (2021).
    The cis-regulatory effects of modern human-specific variants.
    Elife 10. https://doi.org/10.7554/eLife.63713.

2020

21. Klein, J.C.*, Agarwal, V.*, Inoue, F.*, Keith, A., Martin, B., Kircher, M., Ahituv, N., and Shendure, J. (2020).
    A systematic evaluation of the design and context dependencies of massively parallel reporter assays.
    Nature Methods 17, 1083–1091. https://doi.org/10.1038/s41592-020-0965-y. 

22. 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.^, and Ahituv, N.^ (2020).
    lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.
    Nature Protocols 15, 2387–2412. https://doi.org/10.1038/s41596-020-0333-5.

2019

23. Inoue, F.*, Kreimer, A.*, Ashuach, T., Ahituv, N., and Yosef, N. (2019).
    Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction.
    Cell Stem Cell 25, 713-727.e10. https://doi.org/10.1016/J.STEM.2019.09.010.

24. Kircher, M., Xiong, C., Martin, B., Schubach, M., Inoue, F., Bell, R.J.A., Costello, J.F., Shendure, J., and Ahituv, N. (2019).
    Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution.
    Nature Commun 10, 3583. https://doi.org/10.1038/s41467-019-11526-w. 

25. Shigaki, D., Adato, O., Adhikari, A.N., Dong, S., Hawkins‐Hooker, A., Inoue, F., Juven‐Gershon, T., Kenlay, H., Martin, B., Patra, A., et al. (2019).
    Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.
    Hum. Mutat., humu.23797. https://doi.org/10.1002/humu.23797.

26. Inoue, F.*, Eckalbar, W.L.*, Wang, Y., Murphy, K.K., Matharu, N., Vaisse, C., and Ahituv, N. (2019).
    Genomic and epigenomic mapping of leptin-responsive neuronal populations involved in body weight regulation.
    Nature Metabolism 1, 475–484. https://doi.org/10.1038/s42255-019-0051-x. 

〜2018

27. Inoue, F.*, Kircher, M.*, Martin, B., Cooper, G.M., Witten, D.M., McManus, M.T., Ahituv, N., and Shendure, J. (2017).
    A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity.
    Genome Research 27, 38–52. https://doi.org/10.1101/gr.212092.116. 

28. (Review article)
    Inoue, F., and Ahituv, N. (2015).
    Decoding enhancers using massively parallel reporter assays.
    Genomics 106, 159–164. https://doi.org/10.1016/j.ygeno.2015.06.005.

29. Smith, R.P., Taher, L., Patwardhan, R.P., Kim, M.J., Inoue, F., Shendure, J., Ovcharenko, I., and Ahituv, N. (2013).
    Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model.
    Nature Genet 45, 1021–1028. https://doi.org/10.1038/ng.2713.

30. Inoue, F., Kurokawa, D., Takahashi, M., and Aizawa, S. (2012).
    Gbx2 directly restricts Otx2 expression to forebrain and midbrain, competing with class III POU factors.
    Mol. Cell. Biol. 32, 2618–2627. https://doi.org/10.1128/MCB.00083-12.

31. Suda, Y., Kokura, K., Kimura, J., Kajikawa, E., Inoue, F., and 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 137, 2939–2949. https://doi.org/10.1242/dev.048843.

32. Kurokawa, D., Ohmura, T., Ogino, H., Takeuchi, M., Inoue, A., Inoue, F., Suda, Y., and Aizawa, S. (2010).
    Evolutionary origin of the Otx2 enhancer for its expression in visceral endoderm.
    Dev. Biol. 342, 110–120.

33. Parvin, M.S., Okuyama, N., Inoue, F., Islam, M.E., Kawakami, A., Takeda, H., and Yamasu, K. (2008).
    Autoregulatory loop and retinoic acid repression regulate pou2/pou5f1 gene expression in the zebrafish embryonic brain.
    Dev Dyn 237, 1373–1388. https://doi.org/10.1002/dvdy.21539.

34. Inoue, F., Parvin, M.S., and 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, 471–486. https://doi.org/10.1016/j.ydbio.2008.01.013.

35. Inoue, F.*, Nagayoshi, S.*, Ota, S., Islam, M.E., Tonou-Fujimori, N., Odaira, Y., Kawakami, K., and Yamasu, K. (2006).
    Genomic organization, alternative splicing, and multiple regulatory regions of the zebrafish fgf8 gene.
    Dev Growth Differ 48, 447–462. https://doi.org/10.1111/j.1440-169X.2006.00882.x.

36. Islam, M.E., Kikuta, H., Inoue, F., Kanai, M., Kawakami, A., Parvin, M.S., Takeda, H., and Yamasu, K. (2006).
    Three enhancer regions regulate gbx2 gene expression in the isthmic region during zebrafish development.
    Mech. Dev. 123, 907–924.

1. Zicong Zhang, Ilias Georgakopoulos-Soares, Guillaume Bourque, Nadav Ahituv, Fumitaka Inoue
   Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA
   BioRxiv, June 30, 2025.
   https://doi.org/10.1101/2025.06.26.661849
   
   

2. Coline Arnould,  Pia Keukeleire,  Fumitaka Inoue, Xiekui Cui, Kelly An, Elizabeth Murray, Xuhuiqun Zhang, Radoje Drmanac, Brock A. Peters, Jay Shendure, Yin Shen, Martin Kircher, Nadav Ahituv
   Capture-C MPRA: A high-throughput method to simultaneously characterize promoter interactions and regulatory activity
   BioRxiv, June 14, 2025.
   https://doi.org/10.1101/2025.06.11.658967
   
   

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): 2160-2163
   https://doi.org/10.18958/7309-00003-0000548-00

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
   https://doi.org/10.18958/6543-00003-0000891-00

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.