| A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity F Inoue, M Kircher, B Martin, GM Cooper, DM Witten, MT McManus, ... Genome research 27 (1), 38-52, 2017 | 299 | 2017 |
| Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model RP Smith, L Taher, RP Patwardhan, MJ Kim, F Inoue, J Shendure, ... Nature genetics 45 (9), 1021-1028, 2013 | 277 | 2013 |
| Decoding enhancers using massively parallel reporter assays F Inoue, N Ahituv Genomics 106 (3), 159-164, 2015 | 262 | 2015 |
| Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution M Kircher, C Xiong, B Martin, M Schubach, F Inoue, RJA Bell, JF Costello, ... Nature communications 10 (1), 3583, 2019 | 184 | 2019 |
| A systematic evaluation of the design and context dependencies of massively parallel reporter assays JC Klein, V Agarwal, F Inoue, A Keith, B Martin, M Kircher, N Ahituv, ... Nature Methods 17 (11), 1083-1091, 2020 | 126 | 2020 |
| Identification and massively parallel characterization of regulatory elements driving neural induction F Inoue, A Kreimer, T Ashuach, N Ahituv, N Yosef Cell stem cell 25 (5), 713-727. e10, 2019 | 88 | 2019 |
| lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements MG Gordon, F Inoue, B Martin, M Schubach, V Agarwal, S Whalen, ... Nature protocols 15 (8), 2387-2412, 2020 | 73 | 2020 |
| The cis-regulatory effects of modern human-specific variants CV Weiss, L Harshman, F Inoue, HB Fraser, DA Petrov, N Ahituv, ... elife 10, e63713, 2021 | 48 | 2021 |
| Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay D Shigaki, O Adato, AN Adhikari, S Dong, A Hawkins‐Hooker, F Inoue, ... Human mutation 40 (9), 1280-1291, 2019 | 44 | 2019 |
| Massively parallel dissection of human accelerated regions in human and chimpanzee neural progenitors H Ryu, F Inoue, S Whalen, A Williams, M Kircher, B Martin, B Alvarado, ... BioRxiv 256313, 2018 | 40 | 2018 |
| Machine learning dissection of human accelerated regions in primate neurodevelopment S Whalen, F Inoue, H Ryu, T Fair, E Markenscoff-Papadimitriou, K Keough, ... Neuron 111 (6), 857-873. e8, 2023 | 37 | 2023 |
| Genomic organization, alternative splicing, and multiple regulatory regions of the zebrafish fgf8 gene F Inoue, S Nagayoshi, S Ota, ME Islam, N Tonou‐Fujimori, Y Odaira, ... Development, growth & differentiation 48 (7), 447-462, 2006 | 33 | 2006 |
| Gbx2 directly restricts Otx2 expression to forebrain and midbrain, competing with class III POU factors F Inoue, D Kurokawa, M Takahashi, S Aizawa Molecular and cellular biology, 2012 | 32 | 2012 |
| The same enhancer regulates the earliest Emx2 expression in caudal forebrain primordium, subsequent expression in dorsal telencephalon and later expression in … Y Suda, K Kokura, J Kimura, E Kajikawa, F Inoue, S Aizawa Development 137 (17), 2939-2949, 2010 | 30 | 2010 |
| Autoregulatory loop and retinoic acid repression regulate pou2/pou5f1 gene expression in the zebrafish embryonic brain MS Parvin, N Okuyama, F Inoue, ME Islam, A Kawakami, H Takeda, ... Developmental Dynamics: An Official Publication of the American Association …, 2008 | 29 | 2008 |
| Three-dimensional genome rewiring in loci with human accelerated regions KC Keough, S Whalen, F Inoue, PF Przytycki, T Fair, C Deng, M Steyert, ... Science 380 (6643), eabm1696, 2023 | 28 | 2023 |
| Transcription of fgf8 is regulated by activating and repressive cis-elements at the midbrain–hindbrain boundary in zebrafish embryos F Inoue, MS Parvin, K Yamasu Developmental biology 316 (2), 471-486, 2008 | 26 | 2008 |
| High-throughput characterization of the role of non-B DNA motifs on promoter function I Georgakopoulos-Soares, J Victorino, GE Parada, V Agarwal, J Zhao, ... Cell genomics 2 (4), 2022 | 23 | 2022 |
| Three enhancer regions regulate gbx2 gene expression in the isthmic region during zebrafish development ME Islam, H Kikuta, F Inoue, M Kanai, A Kawakami, MS Parvin, H Takeda, ... Mechanisms of development 123 (12), 907-924, 2006 | 23 | 2006 |
| Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation A Kreimer, T Ashuach, F Inoue, A Khodaverdian, C Deng, N Yosef, ... Nature communications 13 (1), 1504, 2022 | 22 | 2022 |
