Preprint

  • Géraldine C. Genard, Luca Tirinato, Francesca Pagliari, Jessica Da Silva, Alessandro Giammona, Fatema Alquraish, Marie Bordas, Maria Grazia Marafioti, Simone Di Franco, Jeannette Janssen, Daniel Garcia-Calderón, Rachel Hanley, Clelia Nistico, Yoshinori Fukasawa, Torsten Müller, Jeroen Krijgsveld, Matilde Todaro, Francesco Saverio Costanzo, Giorgio Stassi, Michelle Nessling, Karsten Richter, Kendra K. Maass, Carlo Liberale, Joao Seco: Lipid Droplets Fuel Small Extracellular Vesicle Biogenesis., bioRxiv, 2022

Research papers

  • Géraldine C Genard, Luca Tirinato, Francesca Pagliari, Jessica Da Silva, Alessandro Giammona, Fatema Alquraish, Maria Parra Reyes, Marie Bordas, Maria Grazia Marafioti, Simone Di Franco, Jeannette Janssen, Daniel Garcia-Calderón, Rachel Hanley, Clelia Nistico, Yoshinori Fukasawa, Torsten Müller, Jeroen Krijgsveld, Matilde Todaro, Francesco Saverio Costanzo, Giorgio Stassi, Michelle Nessling, Karsten Richter, Kendra K Maass, Carlo Liberale, Joao Seco: Lipid droplets and small extracellular vesicles: More than two independent entities. Journal of Extracellular Biology, Vol. 3(9), p.e162, 2024
  • Yoshinori Fukasawa, Patrick Driguez, Salim Bougouffa, Karen Carty, Alexander Putra, Ming Sin Cheung, Luca Ermini: Plasticity of repetitive sequences demonstrated by the complete mitochondrial genome of Eucalyptus camaldulensis., Frontiers in Plant Science, Vol. 15, pp. 1339594, 2024.
  • Lama AlAbdi, Hanan E. Shamseldin, Ebtissal Khouj, Rana Helaby, Bayan Aljamal, Mashael Alqahtani, Aisha Almulhim, Halima Hamid, Mais O. Hashem, Firdous Abdulwahab, Omar Abouyousef, Amal Jaafar, Tarfa Alshidi, Mohammed Al-Owain, Amal Alhashem, Saeed Al Tala, Arif O. Khan, Elham Mardawi, Hisham Alkuraya, Eissa Faqeih, Manal Afqi, Salwa Alkhalifi, Zuhair Rahbeeni, Samya T. Hagos, Wijdan Al-Ahmadi, Seba Nadeef, Sateesh Maddirevula, Khalid S A Khabar, Alexander Putra, Angel Angelov, Changsook Park, Ana M. Reyes-Ramos, Husen Umer, Ikram Ullah, Patrick Driguez, Yoshinori Fukasawa, Ming Sin Cheung, Imed Eddine Gallouzi, Fowzan S Alkuraya: Beyond the exome: Utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases., Genome medicine, Vol. 15 (1), pp. 1-16, 2023.
  • Patrick Driguez, Salim Bougouffa, Karen Carty, Alexander Putra, Kamel Jabbari, Muppala Reddy, Richard Soppe, Ming Sin Cheung, Yoshinori Fukasawa, Luca Ermini: LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology., Genome Biology, Vol. 22 (1), pp. 1-18, 2021.
  • Ahmed Alfares, Lamia Alsubaie, Taghrid Aloraini, Aljoharah Alaskar, Azza Althagafi, Ahmed Alahmad, Mamoon Rashid, Abdulrahman Alswaid, Ali Alothaim, Wafaa Eyaid, Faroug Ababneh, Mohammed Albalwi, Raniah Alotaibi, Mashael Almutairi, Nouf Altharawi, Alhanouf Alsamer, Marwa Abdelhakim, Senay Kafkas, Katsuhiko Mineta, Nicole Cheung, Abdallah M. Abdallah, Stine Büchmann-Møller, Yoshinori Fukasawa, Xiang Zhao, Issaac Rajan, Robert Hoehndorf, Fuad Al Mutairi, Takashi Gojobori, Majid Alfadhel: What is the right sequencing approach? Solo VS extended family analysis in consanguineous populations., BMC Medical Genomics, Vol. 13 (1), pp. 1-8, 2020.
  • Yoshinori Fukasawa, Luca Ermini, Hai Wang, Karen Carty, Ming Sin Cheung: LongQC: a quality control tool for third generation sequencing long read data., G3: Genes, Genomes, Genetics, Vol. 10 (4), pp. 1193-1196, 2020. (表紙に採択)
  • Yoshinori Fukasawa, Kentaro Tomii: Accurate classification of biological and non-biological interfaces in protein crystal structures using subtle covariation signals., Scientific reports, Vol. 9 (1), pp. 1-12, 2019.
  • Tsukasa Nakamura, Toshiyuki Oda, Yoshinori Fukasawa, Kentaro Tomii: Template‐based quaternary structure prediction of proteins using enhanced profile–profile alignments., Proteins: Structure, Function, and Bioinformatics, Vol. 86, pp. 274-282, 2018.
  • Kazunori D. Yamada, Naoki Kunishima, Yoshinori Matsuura, Koshiro Nakai, Hisashi Naitow, Yoshinori Fukasawa, Kentaro Tomii: Designing better diffracting crystals of biotin carboxyl carrier protein from Pyrococcus horikoshii by a mutation based on the crystal-packing propensity of amino acids., Acta Crystallographica Section D: Structural Biology, Vol. 73 (9), pp. 757-766, 2017.
  • Yoshinori Fukasawa, Toshiyuki Oda, Kentaro Tomii, Kenichiro Imai: Origin and evolutionary alteration of the mitochondrial import system in eukaryotic lineages., Molecular Biology and Evolution, Vol, 34 (7), pp. 1574-1586, 2017.
  • Herbert J. Santos, Kenichiro Imai, Yuki Hanadate, Yoshinori Fukasawa, Toshiyuki Oda, Fumika Mi-Ichi, Tomoyoshi Nozaki: Screening and discovery of lineage-specific mitosomal membrane proteins in Entamoeba histolytica., Molecular and Biochemical Parasitology, Vol. 209 (1-2), pp. 10-17, 2016.
  • Takuya Shiota, Kenichiro Imai, Jian Qiu, Victoria L Hewitt, Khershing Tan, Hsin-Hui Shen, Noriyuki Sakiyama, Yoshinori Fukasawa, Sikander Hayat, Megumi Kamiya, Arne Elofsson, Kentaro Tomii, Paul Horton, Nils Wiedemann, Nikolaus Pfanner, Trevor Lithgow, Toshiya Endo: Molecular architecture of the active mitochondrial protein gate., Science, Vol. 349 (6255), pp. 1544-1548, 2015.
  • Yoshinori Fukasawa, Junko Tsuji, Szu-Chin Fu, Kentaro Tomii, Paul Horton, Kenichiro Imai: MitoFates: Improved Prediction of Mitochondrial Targeting Sequences and Their Cleavage Sites., Molecular & Cellular Proteomics, Vol. 14 (4), pp. 1113-1126, 2015.
  • Yoshinori Fukasawa, Ross KK Leung, Stephen KW Tsui, Paul Horton: Plus ça change–evolutionary sequence divergence predicts protein subcellular localization signals., BMC Genomics, Vol. 15 (1), pp. 1-15, 2014.

Conference proceedings

  • Yoshinori Fukasawa, Ross KK Leung, Stephen KW Tsui, Paul Horton: Evolutionary sequence divergence predicts protein sub-cellular localization signals. IEEE International Conference on Systems Biology, pp. 307-312, 2011 
  • Yoshinori Fukasawa, Raymond Wan, Szu-Chin Fu, Junko Tsuji, Noriyuki Sakiyama, Kenichiro Imai, Paul Horton: Mitochondrial protein cleavage site predictor. IEEE International Conference on Bioinformatics and Biomedicine Workshops, pp. 870-871, 2010

Conference talks and presentations

  • 正木 亜嘉理, 細井 昂人, 深沢 嘉紀, 太治 輝昭, 篠村 知子, 児玉 豊: 群体性緑藻クンショウモの細胞数制御に及ぼす温度の影響, 日本植物学会第88回大会、2024.9 (ポスター発表)
  • 深沢 嘉紀: 植物ゲノムに対する変異解析手法ベンチマークと新たな課題, 日本植物学会第88回大会、2024.9 (ポスター発表)
  • 鈴木 智大、浅川 倫宏、前川 文彦、木村 栄輝、佐藤 匠、高田 翔子、鈴木 雅一、道羅 英夫、深沢 嘉紀、河岸 洋和: スギヒラタケ摂取による急性脳症の分子機構解明, 第66回天然有機化合物討論会, 2024.9 (口頭発表)
  • 深沢 嘉紀: 高精度ロングリード時代の変異検出 – 植物ゲノムが突きつける課題と展望, 第7回植物インフォマティクス研究会, 2024.9 (口頭発表)
  • 佐藤匠、中村瑠奈、茅谷佳祐、小野晶子、田中裕基、崔宰熏、道羅英夫、平井浩文、深沢嘉紀、河岸洋和、鈴木智大: スギヒラタケが引き起こす急性脳症に関与する毒性タンパク質の生化学的研究, 日本農芸化学会 2024年度東京大会, 2024.3 (一般講演)
  • Yoshinori Fukasawa, Patrick Driguez, Salim Bougouffa, Karen Carty, Alexander Putra, Luca Ermini: Plasticity of repetitive sequences demonstrated by the complete mitochondrial genome of Eucalyptus camaldulensis, International Plant & Animal Genome/PAG31, 2024.1 (ポスター発表)
  • 深沢嘉紀: ヒトゲノムに最適化された正確なロングリードの配列解析法の植物や他の種のゲノムへの適用性, 第46回日本分子生物学会年会, 2023.12. (ポスター発表)
  • 川渕真優、深沢嘉紀 、瀬戸義哉、謝肖男、野村崇人: 根寄生植物ヤセウツボのストリゴラクトン生合成酵素の解析, 第58回植物化学調節学会, 2023.11. (口頭発表)
  • Yoshinori Fukasawa: Solutions and new challenges of bioinformatics in long-accurate read era, GIW/ISCB-Asia 2022, 2022.12. (招待公演)
  • Patrick Driguez, Salim Bougouffa, Karen Carty, Alexander Putra, Kamel Jabbari, Muppala Reddy, Richard Soppe, Ming Sin Cheung, Yoshinori Fukasawa, Luca Ermini: LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology., Plant & Animal Genome Conference XXIX, 2022.1. (招待公演)
  • Yoshinori Fukasawa: Reference-free data quality control using LongQC, Nanopore Community Meeting 2020, 2020.12. (口頭発表)
  • Toshiyuki Oda, Tsukasa Nakamura, Yoshinori Fukasawa, Kentaro Tomii.: Improved Profile Construction Methods and their Applications to 3D Structure Prediction of Proteins, CASP12 Final meeting, 2016.12. (招待公演)
  • 深沢嘉紀、小田俊之、富井健太郎、今井賢一郎: ミトコンドリアタンパク質膜透装置TOM複合体の祖先モデルの推定と進化解析, 第39回日本分子生物学会年会, 2016.12.
  • 山田和範, 松浦祥悟, Nakai Koshiro, 深沢嘉紀, 内藤久志, 国島直樹, 富井健太郎: Improving protein crystallization based on the results of statistical analysis of crystal contacts, 第5回生命医薬情報学連合大会 (IIBMP 2016), 2016.9. (ポスター発表)
  • 深沢嘉紀、小田 俊之、富井 健太郎、今井 賢一郎: ミトコンドリアタンパク質膜透装置TOM複合体の独立した進化, 第16回日本蛋白質科学会年会, 2016.6. (ポスター発表)
  • 塩田拓也，今井賢一郎，深沢嘉紀，富井健太郎，Horton Paul，遠藤斗志也: ミトコンドリアタンパク質搬入口，TOM 複合体の分子形態，および機能, 第16回日本蛋白質科学会年会 若手奨励賞シンポジウム, 2016.6. (ポスター発表)
  • 富井健太郎, 今井賢一郎, 清水佳奈, 深沢嘉紀, Lim Kyungtaek, 小田俊之: 創薬等支援に向けたタンパク質インフォマティクス技術の開発, LS-BT 合同研究発表会, 2016.2. (ポスター発表)
  • 今井賢一郎, 深沢嘉紀, 富井健太郎, Horton Paul: ミトコンドリア内膜局在プロテアーゼ PARL の基質予測による新規ストレス応答因子の探索, 第 15 回 LS-BT 合同研究発表会, 2016.2. (ポスター発表)
  • 深沢嘉紀、小田 俊之、富井 健太郎、今井 賢一郎: 真核生物におけるミトコンドリアタンパク質輸送機構の動的な進化, BMB2015(第38回日本分子生物学会年会、第88回日本生化学会大会 合同大会), 2015.12. (ポスター発表)
  • 今井賢一郎, 深沢嘉紀, 富井健太郎, Horton Paul: ミトコンドリア内膜局在 Rhomboid プロテアーゼ PARL の基質予測, BMB2015(第38回日本分子生物学会年会、第88回日本生化学会大会 合同大会), 2015.12. (口頭発表)
  • 深沢嘉紀, 今井賢一郎, 富井健太郎, Horton Paul: Mitochondrial proteome analysis of human and other eukaryotes by novel mitochondrial targeting signal prediction, 第14回 LS-BT 合同研究発表会, 2015.2. (ポスター発表)
  • Yoshinori Fukasawa, Toshiyuki Oda, Kentaro Tomii, Kenichiro Imai: Dynamic evolution of mitochondrial protein importing system in eukaryotes, 2nd International symposium & 4th annual research meeting on Matryoshka-type evolution of Eukaryotic cells, 2015.10. (ポスター発表)
  • 今井賢一郎、深沢嘉紀、富井健太郎、Paul Horton: 新規ミトコンドリア局在化シグナル予測手法を用いたヒトのミトコンドリアプロテオーム解析, 第14回日本ミトコンドリア学会年会, 2014.12. (ポスター発表)
  • Kenichiro Imai, Yoshinori Fukasawa, Kentaro Tomii, Paul Horton: Human mitochondrial proteome analysis by novel mitochondrial targeting signal prediction, GIW/ISCB-ASIA 2014, 2014.12. (ポスター発表)
  • Paul Horton, Kenichiro Imai, Kentaro Tomii, Yoshinori Fukasawa: Computational Prediction of Mitochondrial Targeting Signals and Their Cleavage Sites, The Twelfth Mini-symposium and Workshop on Bioinformatics and Systems Biology in Taiwan (BIT2014), 2014.11. (ポスター発表)
  • Kenichiro Imai, Yoshinori Fukasawa, Kentaro Tomii, Paul Horton: Human mitochondrial proteome analysis by novel mitochondrial targeting signal prediction, 第37回日本分子生物学会年会, 2014.11. (ポスター発表)
  • Kenichiro Imai, Yoshinori Fukasawa, Kentaro Tomii, Paul Horton: Improved prediction of mitochondrial presequence for detecting undiscovered mitochondrial proteins, 第52回日本生物物理学会年会, 2014.9. (ポスター発表)
  • Yoshinori Fukasawa, Kenichiro Imai, Szu-chin Fu, Junko Tsuji, Kentaro Tomii, Paul Horton: Accurate prediction of mitochondrial presequences and their cleavage sites with MitoFates identifies hundreds of novel human mitochondrial protein candidates, ISMB 2014, LBR13 (PT), 2014.7. (口頭発表)
  • 今井賢一郎, 深沢嘉紀, 富井健太郎, Horton Paul: Three classes of mitochondrial presequences in yeast, 第36回日本分子生物学会年会, 2013.12. (ポスター発表)
  • 深沢嘉紀: Evolutionary analysis of translocase of mitochondrial outer membrane Tom40, 第36回日本分子生物学会年会, 2013.12. (ポスター発表)
  • 今井賢一郎, 深沢嘉紀, 富井健太郎, Horton Paul: Improved prediction of mitochondrial presequence and cleavage site throws light on novel presequence clusters, The 4th International Symposium on Dynamics of Mitochondria, 2013.10. (ポスター発表)
  • Yoshinori Fukasawa, Ross KK Leung, Stephen KW Tsui, Paul Horton: Plus ça change – evolutionary sequence divergence predicts protein subcellular localization signals, 7th AYRCOB, 2013.9. (ポスター発表)
  • Yoshinori Fukasawa, Szu-chin Fu, Junko Tsuji, Noriyuki Sakiyama, Kenichiro Imai, Paul Horton: MoiraiSP: a novel mitochondrial localization signal predictor, 6th AYRCOB, 2012.12. (ポスター発表)
  • Paul Horton, Yoshinori Fukasawa: Improvement of mitochondrial cleavage prediction, ISMB 2012, 2012.7. (ポスター発表)
  • Yoshinori Fukasawa, Szu-chin Fu, Junko Tsuji, Noriyuki Sakiyama, Kenichiro Imai, Paul Horton: MoiraiSP: a novel mitochondrial cleavage site predictor, BIOINFORMATICS 2012, 2012.6. (口頭発表)
  • 深沢嘉紀, 今井賢一郎, 富井健太郎, Horton Paul: 大規模プロテオミクス解析に基づいたミトコンドリアプレ配列の情報学的解析, 第12回日本蛋白質科学会年会, 2012.6. (ポスター発表)
  • Yoshinori Fukasawa, Raymond Wan, Szu-chin Fu, Junko Tsuji, Noriyuki Sakiyama, Kenichiro Imai, Paul Horton: Computational analysis of mitochondrial cleaved proteins based on proteomic analyses, 第34回日本分子生物学会 2011年会, 2011.12. (口頭発表)
  • Yoshinori Fukasawa, Raymond Wan, Szu-chin Fu, Junko Tsuji, Noriyuki Sakiyama, Kenichiro Imai, Paul Horton: MoiraiSP: a novel mitochondrial cleavage site predictor, 2011年JSBi年会(CBI学会 ・JSBi 合同大会), 2011.11. (口頭発表)
  • Yoshinori Fukasawa, Raymond Wan, Szu-chin Fu, Junko Tsuji, Noriyuki Sakiyama, Kenichiro Imai, Paul Horton: Mitochondrial Cleavage Site Predictor, IEEE International Conference on Bioinformatics & Biomedicine, 2010.12. (ポスター発表)
  • Yoshinori Fukasawa, Raymond Wan, Szu-chin Fu, Junko Tsuji, Noriyuki Sakiyama, Kenichiro Imai, Paul Horton: Informatic analysis of mitochondrial cleavage sites and predictor development based on large-scale proteomics datasets, 第33回日本分子生物学会年会・第83回日本生化学会大会合同大会, 2010.12. (ポスター発表)
  • Choungyoun Park, Yoshinori Fukasawa, Naohisa Ohta N: Developing Digital Cue System for Networked Performance, The 7th IEEE Tokyo Young Researchers Workshop, 2010.11. (ポスター発表)