• Toju H, Peay KG, Yamamichi M, Narisawa K, Hiruma K, Naito K, Fukuda S, Ushio M, Nakaoka S, Onoda Y, Yoshida K, Schlaeppi K, Bai Y, Sugiura R, Ichihashi Y, Minamisawa K, Kiers ET, Core microbiomes for sustainable agroecosystems. Nature Plants 4: 247-257. 2018
  • Ostria-Gallardo E, Ranjan A, Ichihashi Y, Corcuera L, Sinha N, Decoding the gene co-expression network underlying the ability of Gevuina avellana to live in diverse light conditions. New Phytologist 220(1): 278-287. 2018
  • Sato K, Kadota Y, Gan P, Bino T, Uehara T, Yamaguchi K, Ichihashi Y, Maki N, Iwahori H, Suzuki T, Shigenobu S, Shirasu K, High-Quality Genome Sequence of the Root-Knot Nematode Meloidogyne arenaria Genotype A2-O. Genome Announc. 6(26): e00519-18. 2018
  • Nakayama H, Sakamoto T, Okegawa Y, Kaminoyama K, Fujie M, Ichihashi Y, Kurata T, Motohashi K, Al-Shehbaz I, Sinha N, Kimura S. Comparative transcriptomics with self-organizing map reveals cryptic photosynthetic differences between two accessions of North American Lake cress. Scientific Reports 8: 3302. 2018
  • Ichihashi Y, Fukushima A, Shibata A, Shirasu K. High Impact Gene Discovery: Simple Strand Specific mRNA Library Construction and Differential Regulatory Analysis Based on Gene Co-expression Network. Methods in Molecular Biology 1830: 163-189. 2018
  • Ichihashi Y, Kusano M, Kobayashi M, Suetsugu K, Yoshida S, Wakatake T, Kumaishi K, Shibata A, Saito K, Shirasu K. Transcriptomic and Metabolomic Reprogramming from Roots to Haustoria in the Parasitic Plant, Thesium chinense. Plant Cell Physiol. 59(4): 729-738. 2018
  • Uemura A, Yamaguchi N, Xu Y, Wee W, Ichihashi Y, Suzuki T, Shibata A, Shirasu K, Ito T. Regulation of floral meristem activity through the interaction of AGAMOUS, SUPERMAN, and CLAVATA3 in Arabidopsis. Plant Reproduction 31(1): 89-105. 2018
  • An CI†, Ichihashi Y†, Peng J, Sinha NR, and Hagiwara N. Transcriptome Dynamics and Potential Roles of Sox6 in the Postnatal Heart. PLOS ONE 11(11): e0166574. 2016 †equal contribution.
  • Fulop D, Ranjan A, Ofner I, Covington MF, Chitwood DH, West D, Ichihashi Y, Headland L, Zamir D, Maloof JN, and Sinha N. A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification. G3 6(10): 3169-3184. 2016
  • Ranjan A, Budke J, Rowland SD, Chitwood DH, Kumar R, Carriedo LG, Ichihashi Y, Zumstein K, Maloof JN, and Sinha N. eQTL regulating Transcript Levels Associated with Diverse Biological Processes in Tomato. Plant Physiol. 172(1): 328-340. 2016
  • Kondo Y, Nurani AM, Saito C, Ichihashi Y, Saito M, Yamazaki K, Mitsuda N, Ohme-Takagi M, and Fukuda H. Vascular Cell Induction Culture System Using Arabidopsis Leaves (VISUAL) Reveals the Sequential Differentiation of Sieve Element-like Cells. Plant Cell 28(6): 1250-1262. 2016
  • Ostria-Gallardo E, Ranjan A, Chitwood DH, Kumar R, Townsley BT, Ichihashi Y, Corcuera LJ, and Sinha NR. Transcriptomic analysis suggests a key role for SQUAMOSA PROMOTER BINDING PROTEIN LIKE, NAC and YUCCA genes in the heteroblastic development of the temperate rainforest tree Gevuina avellana (Proteaceae). New Phytologist. 210(2): 694-708. 2016
  • Chitwood DH, Kumar R,Ranjan A, Pelletier JM, Townsley B, Ichihashi Y, Martinez CC, Zumstein K, Harada JJ, Maloof JN, and Sinha N. Light-induced indeterminacy alters shade avoiding tomato leaf morphology. Plant Physiol. 169(3): 2030-2047. 2015
  • Townsley BT, Covington MF, Ichihashi Y, Zumstein K, Sinha NR. BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction. Front Plant Sci. 6: 366. 2015
  • Mutuku JM, Yoshida S, Shimizu T, Ichihashi Y, Wakatake T, Seo M, Takahashi A, Shirasu K. The WRKY45-dependent signaling pathway is required for resistance against Striga parasitism. Plant Physiol. 168(3): 1152-1163. 2015
  • Nozue K, Tat A, Devisetty UK, Robinson M, Ichihashi Y, Lekkala S, Maloof J. Shade avoidance components and pathways in adult plants revealed by phenotypic profiling. PLOS Genet. 11(4): e1004953. 2015
  • Ranjan A, Townsley, BT, Ichihashi Y, Sinha NR and Chitwood DH. An Intracellular Transcriptomic Atlas of the Giant Coenocyte Caulerpa taxifolia. PLOS Genet. 11(1): e1004900. 2015
  • Ichihashi Y, Aguilar-Martínez JA, Farhi M, Chitwood DH, Kumar R, Millon LV, Peng J, Maloof JN, and Sinha NR. Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape. PNAS 111(25): E2616-E2621. 2014
  • Ranjan A, Ichihashi Y, Farhi M, Zumstein K, Townsley B, David-Schwartz R, Sinha NR. De novo assembly and characterization of the transcriptome of the parasitic weed Cuscuta pentagona identifies genes associated with plant parasitism. Plant Physiol. 166(3): 1186-1199. 2014
  • Chitwood DH, Ranjan A, Kumar R, Ichihashi Y, Zumstein K, Headland L, Gallardo E, Aguilar-Martinez JA, Bush S, Carriedo L, Fulop D, Martinez C, Peng J, Maloof J, and Sinha NR. Resolving distinct genetic regulators of tomato leaf shape within a heteroblastic and ontogenetic context. Plant Cell 26(9): 3616-3629. 2014
  • Chitwood DH, Kumar R, Headland LR, Ranjan A, Covington MF, Ichihashi Y, Fulop D, Jiménez-Gómez JM, Peng J, Maloof JN, Sinha NR. A quantitative genetic basis for leaf morphology in a set of precisely defined tomato introgression lines. Plant Cell 25(7): 2465-248. 2013
  • Kumar R†, Ichihashi Y†, Kimura S, Chitwood DH, Headland LR, Peng J, Maloof JN, Sinha NR. A High-Throughput Method for Illumina RNA-Seq Library Preparation. Front Plant Sci. 3: 202. 2012. † equal contribution.
  • Ichihashi Y, Kawade K, Usami T, Horiguchi G, Takahashi T, Tsukaya H. Key proliferative activity in the junction between the leaf blade and leaf petiole of Arabidopsis. Plant Physiol. 157(3): 1151-1162. 2011
  • Ichihashi Y, Horiguchi G, Gleissberg S, Tsukaya H. The bHLH transcription factor SPATULA controls final leaf size in Arabidopsis thaliana. Plant Cell Physiol. 51: 252-261. 2010
  • Kazama T, Ichihashi Y, Murata S, Tsukaya H. The mechanism of cell cycle arrest front progression explained by a KLUH/CYP78A5-dependent mobile growth factor in developing leaves of Arabidopsis thaliana. Plant Cell Physiol. 51: 1046-1054. 2010
  • Ichihashi Y, Minami M. Phylogenetic positions of Tokai hilly land element, Drosera tokaiensis (Droseraceae) and its parental species, D. rotundifolia and D. spatulata. J Phytogeo Tax. 57: 7-16. 2009


  • Ichihashi Y, Ishigaki Y, Shirasu K.「植物と根圏微生物叢の相互作用」 アグリバイオ 9月号, 67-84, 2017
  • Ichihashi Y. Evolutionary developmental studies of leaf shape. BSJ-Review. 7. 288. 2016
  • Sinha NR, Rowland SD, and Ichihashi Y. Using gene networks in EvoDevo analyses. Curr. Opin. Plant Biol. 33: 133-139. 2016 30.Ichihashi Y and Fukushima A. Frontiers of Transcriptomics in Plant Science. BSJ-Review. 7. 110. 2016
  • Yoshida S, Cui S, Ichihashi Y, and Shirasu K. The Haustorium, a Specialized Invasive Organ in Parasitic Plants. Annual Review of Plant Biology 67: 643-667. 2016
  • Ichihashi Y, Tsukaya H. Behavior of Leaf Meristems and Their Modification. Front Plant Sci. 6: 1060. 2015
  • Ichihashi Y. Developmental mechanism underpinning leaf shape evolution. Plant Morphology 26: 43-50. 2015
  • Ichihashi Y, Mutuku JM, Yoshida S, Shirasu K. Transcriptomics exposes the uniqueness of parasitic plants. Briefings in Functional Genomics 14(4): 275-282. 2015
  • Ichihashi Y and Sinha NR. From genome to phenome and back in tomato. Curr. Opin. Plant Biol. 18: 9-15. 2014
  • Ranjan A, Ichihashi Y, Sinha NR. 2012. The tomato genome: implications for plant breeding, genomics and evolution. Genome Biol. 13(8): 167. 2012
  • Aichi M, Ichihashi Y, Minami M.「<第4章>食虫植物トウカイコモウセンゴケとその両親種の話」アリーナ,中部大学,7,pp389-396,2009
  • Ajioka Y, Ichihashi Y, Kyuushima H, Kogaya K, Horikawa D, Minami M.「DNA多型を用いた遺伝的多様性解析と鑑定法」中部大学生物機能開発研究所紀要, 中部大学, 7, 49-74, 2007
  • Ichihashi Y, Hattori K, Minami M.「総説 東海丘陵要素植物群落の保全生態学的研究 保全•修復とその管理に関する研究 (4) モウセンゴケ属(Drosera)の種多様性と分子系統学的研究について」 中部大学生物機能開発研究所紀要, 中部大学, 6, 67-84, 2006


  • Ichihashi Y, Kawade K, Tsukaya H. Arabidopsis thaliana leaf blade and leaf petiole. Noguchi T, Kawano S, Tsukaya H, Matsunaga S, Sakai A, Karahara I, Hayashi Y (Eds.). Atlas of Plant Cell Structure. Springer. 2014


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