Sakakibara Yasubumi 榊原康文

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SAKAKIBARA Yasubumi 榊原康文

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Researcher Number	10287427
Other IDs
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Affiliation (Current)	2025: 北里大学, 未来工学部, 教授 2025: 慶應義塾大学, 理工学部(矢上), 教授
Affiliation (based on the past Project Information) *help	2025: 北里大学, 未来工学部, 教授 2017 – 2025: 慶應義塾大学, 理工学部(矢上), 教授 2021: 慶應義塾大学, 理工学部, 教授 2017 – 2018: 慶應義塾大学, 理工学部, 教授 2017: 慶応義塾大学, 理工学部, 教授 … More 2011 – 2015: 慶應義塾大学, 理工学部, 教授 2009 – 2010: 慶応大学, 理工学部, 教授 2005 – 2009: 慶應義塾大学, 理工学部, 教授 2006: 慶応義塾大学, 理工学部, 教授 2004: 慶應義塾大学, 電気通信学部, 助教授 2002 – 2004: 慶應義塾大学, 理工学部, 助教授 2001: 東京電機大学, 理工学部, 教授 Less
Review Section/Research Field	Principal Investigator Medium-sized Section 62:Applied informatics and related fields / Transformative Research Areas, Section (II) / Science and Engineering / Bioinformatics/Life informatics / Intelligent informatics / System genome science / Biological Sciences Except Principal Investigator Transformative Research Areas, Section (II) / Basic Section 49020:Human pathology-related / Science and Engineering … More / Experimental pathology / Laboratory animal science / Chemical biology / Environmental and hygienic pharmacy / Neurochemistry/Neuropharmacology / Carcinogenesis / Pediatrics / Neurochemistry/Neuropharmacology / Bioinformatics/Life informatics / Science and Engineering Less
Keywords	Principal Investigator 深層学習 / 非コードRNA / 生成AI / バーチャルスクリーニング / マルチオミックス / バイオインフォマティクス / 次世代シークエンサー / 生理活性 / in vitro/in vivo実験 / タンパク質相互作用 … More / ペプチド配列 / 化合物アレイ / 化合物潜在空間 / 腸内細菌叢 / 遺伝子発見 / アサガオ / マーモセット / 遺伝子発現 / 相互作用 / 化合物フィンガープリント / 人工知能 / ケミカルスペース / EGFR / chromatin immunoprecipitation / promoter sequence / hidden Markov model / transcriptional regulation / transcription biding site / ゲルシフトアッセイ / 転写因子結合部位 / 分子細胞生物学 / レポーターアッセイ / 決定木 / モチーフ変異体 / クラスタリング / 主成分分析 / 血小板由来増殖因子 / クロマチン免疫沈降 / プロモーター / 隠れマルコフモデル / 転写制御 / 転写結合モチーフ / Automaton / Boolean Function / Biotechnology / Massive Parallel / Biomolecule / Machine Learning / Molecular Computing / DNA Computer / 計算理論 / 無細胞タンパク質合成系 / 生体分子 / オートマトン / ブール関数 / バイオテクノロジー / 超並列計算 / 生体高分子 / 学習 / 分子計算 / DNAコンピュータ / マウス / 腫瘍 / 遺伝子発現解析 / 発がん / スコア行列 / 2次構造 / 構造的アライメント / 分子進化距離 / シンテニーブロック / アセンブリ / 機能性RNA / 2次構造予測 / ゲノム再編成 / マルチプルアライメント / 比較ゲノム … More Except Principal Investigator ケミカルバイオロジー / 皮膚発がん / リシーケンシング / 次世代DNAシーケンサー / 細胞移動 / 脳・神経 / 神経科学 / 発生・分化 / 大脳皮質 / 天然物有機化学 / 深層学習 / 生物活性分子 / 化合物潜在空間 / CpGアイランドメチル化形質 / 病理画像 / オミックス解析 / 人工知能 / 病理診断 / ゲノムアノテーション / メタゲノム / ゲノム多型 / ゲノムアッセンブル / スーパーコンピューター / メタゲノム解析 / 1細胞解析 / RNA-Seq / エピゲノム / 新規ゲノム配列決定 / 生物活性リガンド / 天然物化学 / 分子社会学 / 化学コミュニケーション / Chipシーケンシング / p19 / p16 / Hif1α / 扁平上皮がん / TPA / DMBA / SU11274 / ChIP sequencing / 化学発がん / Stk25 / Meis1 / 順遺伝学 / 皮膚発がん抵抗性遺伝子座 / 発がん感受性/抵抗性遺伝子座 / 多段階皮膚発がん / 日本野生由来近交系マウス / 発がん / 日本産野生由来近交系 / DMBA/TPA / 副甲状腺ホルモン / 発がん抵抗性/感受性遺伝子 / 日本産野生マウス系統 / DMBA-TPA多段階皮膚発がん / 糖鎖解析 / Oーグリカン / 糖脂質 / 糖鎖 / グリコサミノグリカン / O-グリカン / 転移性がん細胞 / オリゴ糖 / 腫瘍マーカー / ムコ多糖症 / 糖鎖ライブラリー / iPS細胞 / C型肝炎ウイルス / インフルエンザウイルス / がん細胞 / 質量分析装置 / 糖鎖プライマー / 糖鎖工学 / グライコミクス / NDGA / H. pylori / メトロニダゾール / in silico / 酸化ストレス / 除菌療法 / FecA1 / 鉄 / Helicobacter pylori / 塩基除去修復 / CST複合体 / グアニン4重鎖構造 / 次世代シーケンサー / テロメア / ゲノム不安定性 / 次世代DNAシーケンサ / インフォームドコンセント / GWAS / 個人ゲノム / de novo配列決定 / ChIP-seq / RNA-seq / ルシフェラーゼ / シャペロン / 中枢神経障害 / インシリコ解析 / 低分子化合物 / 治療法開発 / 小児神経学 / 樹状突起形成 / カルシウム / IPA / 辺縁帯 / 神経細胞移動 / プロファイル / 遺伝的アルゴリズム / 隠れマルコフモデル / プロテオーム / コンセンサス配列 / アルゴリズム / HeLa細胞 / ペプチドマスフィンガープリント / 2次元電気泳動 / レプトマイシン / 核外移行シグナル / 分子機械 / 生体機能利用 / 自己組織化 / 情報基礎 / DNAコンピュータ / 階層グラフ書換え / 少数分子系 / 非線形科学 / 自然計算 / バクテリアコンピュータ / 配列設計 / 自律計算 Less

タンパク質相互作用データに基づく生成AIによるペプチド配列の設計と実証Principal Investigator
- Principal Investigator
  
  榊原康文
- Project Period (FY)
  2025 – 2029
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Review Section
  
  Medium-sized Section 62:Applied informatics and related fields
- Research Institution
  Kitasato University
天然物が織り成す化合物潜在空間が拓く生物活性分子デザイン
- Principal Investigator
  
  菊地和也
- Project Period (FY)
  2023 – 2027
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (II)
- Research Institution
  The University of Osaka
Construction of chemical latent space using deep learning and design of artificial molecular structuresPrincipal Investigator
- Principal Investigator
  
  榊原康文
- Project Period (FY)
  2023 – 2027
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (II)
- Research Institution
  Kitasato University
  Keio University
Pathological diagnosis based on integration of morphological images and multi-layer omics data by artificial intelligence
- Principal Investigator
  
  Kanai Yae
- Project Period (FY)
  2021 – 2023
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 49020:Human pathology-related
- Research Institution
  Keio University
Development of a bioinformatics method for genome-wide discovery of non-coding RNA genesPrincipal Investigator
- Principal Investigator
  
  Sakakibara Yasubumi
- Project Period (FY)
  2018 – 2022
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Review Section
  
  Medium-sized Section 62:Applied informatics and related fields
- Research Institution
  Keio University
Deep analysis of chemical communication space using artificial intelligence technologyPrincipal Investigator
- Principal Investigator
  
  Sakakibara Yasubumi
- Project Period (FY)
  2017 – 2021
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Science and Engineering
- Research Institution
  Keio University
Frontiers in Chemical Communications
- Principal Investigator
  
  Kakeya Hideaki
- Project Period (FY)
  2017 – 2021
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Science and Engineering
- Research Institution
  Kyoto University
Platform for Advanced Genome Science
- Principal Investigator
  
  KOHARA Yuji
- Project Period (FY)
  2016 – 2021
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas ― Platforms for Advanced Technologies and Research Resources
- Research Institution
  National Institute of Genetics
Identification of cancer-related gene polymorphisms by genetic integration of mouse and human
- Principal Investigator
  
  Okumura Kazuhiro
- Project Period (FY)
  2015 – 2017
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Laboratory animal science
- Research Institution
  Chiba Cancer Center (Research Institute)
Elucidation of the mechanisms of carcinogenesis regulated by oxidative stress response
- Principal Investigator
  
  WAKABAYASHI Yuichi
- Project Period (FY)
  2015 – 2017
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Experimental pathology
- Research Institution
  Chiba Cancer Center (Research Institute)
Exploitation of pathogenic gastrointestinal bacteria specific molecular tageting therapy
- Principal Investigator
  
  Suzuki Hidekazu
- Project Period (FY)
  2014 – 2015
- Research Category
  
  Grant-in-Aid for Challenging Exploratory Research
- Research Field
  
  Environmental and hygienic pharmacy
- Research Institution
  Keio University
Comprehensive analysis of functional non-coding RNAs in cancer genome on multistage carcinogenesisPrincipal Investigator
- Principal Investigator
  
  SAKAKIBARA Yasubumi
- Project Period (FY)
  2011 – 2014
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Research Field
  
  System genome science
- Research Institution
  Keio University
Analysis and control of cell function based on novel glycomics using saccharide primer method
- Principal Investigator
  
  Sato Toshinori
- Project Period (FY)
  2011 – 2015
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Research Field
  
  Chemical biology
- Research Institution
  Keio University
Platform of large scale and high quality genomics and bioinformatics: Towards the advancement of genome sciences in academia
- Principal Investigator
  
  KOHARA Yuji
- Project Period (FY)
  2010 – 2015
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Research Institution
  National Institute of Genetics
Telomere Functions in Cancer Development
- Principal Investigator
  
  ISHIKAWA Fuyuki
- Project Period (FY)
  2010 – 2015
- Research Category
  
  Grant-in-Aid for Scientific Research (S)
- Research Field
  
  Carcinogenesis
- Research Institution
  Kyoto University
Mechanisms of the development of neuronal cell community in the central nervous system
- Principal Investigator
  
  NAKAJIMA Kazunori
- Project Period (FY)
  2010 – 2013
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Research Field
  
  Neurochemistry/Neuropharmacology
- Research Institution
  Keio University
ケミカルシャペロン療法のための革新的スクリーニング法の開発
- Principal Investigator
  
  難波栄二
- Project Period (FY)
  2009 – 2010
- Research Category
  
  Grant-in-Aid for Challenging Exploratory Research
- Research Field
  
  Pediatrics
- Research Institution
  Tottori University
Mechanisms of the development of neuronal cell community in the central nervous system
- Principal Investigator
  
  NAKAJIMA Kazunori
- Project Period (FY)
  2007 – 2009
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Research Field
  
  Neurochemistry/Neuropharmacology
- Research Institution
  Keio University
Development of computational methods for comparing a large scale multiple genome sequencesPrincipal Investigator
- Principal Investigator
  
  SAKAKIBARA Yasubumi
- Project Period (FY)
  2005 – 2009
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Biological Sciences
- Research Institution
  Keio University
SYS tern Analysis of Transcriptional Regulation ProgramPrincipal Investigator
- Principal Investigator
  
  SAKAKIBARA Yasubumi
- Project Period (FY)
  2004 – 2006
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Research Field
  
  Bioinformatics/Life informatics
- Research Institution
  KEIO UNIVERSITY
計算的プロテオーム解析による核外移行シグナルの同定
- Principal Investigator
  
  IMOTO Masaya
- Project Period (FY)
  2003 – 2004
- Research Category
  
  Grant-in-Aid for Exploratory Research
- Research Field
  
  Bioinformatics/Life informatics
- Research Institution
  Keio University
構造的分子計算理論-自律的計算系の解析と設計のための基礎理論
- Principal Investigator
  
  上田和紀, 横森貴
- Project Period (FY)
  2002 – 2006
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Science and Engineering
- Research Institution
  Waseda University
DNA-based Learning Algorithms and their ApplicationsPrincipal Investigator
- Principal Investigator
  
  SAKAKIBARA Yasubumi
- Project Period (FY)
  2001 – 2003
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Intelligent informatics
- Research Institution
  Keio University
  Tokyo Denki University

[Journal Article] Variational autoencoder-based chemical latent space for large molecular structures with 3D complexity2023
- Author(s)
  Ochiai Toshiki、Inukai Tensei、Akiyama Manato、Furui Kairi、Ohue Masahito、Matsumori Nobuaki、Inuki Shinsuke、Uesugi Motonari、Sunazuka Toshiaki、Kikuchi Kazuya、Kakeya Hideaki、Sakakibara Yasubumi
- Journal Title
  
  Communications Chemistry
  
  Volume: 6 Issue: 1 Pages: 249-249
- DOI
  10.1038/s42004-023-01054-6
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23KK0106, KAKENHI-PROJECT-22K19115, KAKENHI-ORGANIZER-23H04880, KAKENHI-PLANNED-23H04882, KAKENHI-PLANNED-23H04885, KAKENHI-PLANNED-23H04887, KAKENHI-PROJECT-20H00405, KAKENHI-PROJECT-21H04706
[Journal Article] Intraintestinal Analysis of the Functional Activity of Microbiomes and Its Application to the Common Marmoset Intestine2022
- Author(s)
  Uehara Mika、Inoue Takashi、Kominato Minori、Hase Sumitaka、Sasaki Erika、Toyoda Atsushi、Sakakibara Yasubumi
- Journal Title
  
  mSystems
  
  Volume: 7 Issue: 5
- DOI
  10.1128/msystems.00520-22
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18H04127, KAKENHI-PROJECT-20J21477
[Journal Article] Informative RNA base embedding for RNA structural alignment and clustering by deep representation learning2022
- Author(s)
  Akiyama Manato、Sakakibara Yasubumi
- Journal Title
  
  NAR Genomics and Bioinformatics
  
  Volume: 4 Issue: 1
- DOI
  10.1093/nargab/lqac012
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-17H06410, KAKENHI-PROJECT-18H04127, KAKENHI-PROJECT-16H06279
[Journal Article] Deep learning integration of molecular and interactome data for protein-compound interaction prediction2021
- Author(s)
  Watanabe Narumi、Ohnuki Yuuto、Sakakibara Yasubumi
- Journal Title
  
  Journal of Cheminformatics
  
  Volume: 13 Issue: 1
- DOI
  10.1186/s13321-021-00513-3
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-17H06410
[Journal Article] MetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenome assembly2021
- Author(s)
  Liang Kuo-ching、Sakakibara Yasubumi
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 22 Issue: S6 Pages: 427-427
- DOI
  10.1186/s12859-020-03737-6
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-17H06410, KAKENHI-PROJECT-16H06279
[Journal Article] Chromosomal-scale de novo genome assemblies of Cynomolgus Macaque and Common Marmoset2021
- Author(s)
  Jayakumar Vasanthan、Nishimura Osamu、Kadota Mitsutaka、Hirose Naoki、Sano Hiromi、Murakawa Yasuhiro、Yamamoto Yumiko、Nakaya Masataka、Tsukiyama Tomoyuki、Seita Yasunari、Nakamura Shinichiro、Kawai Jun、Sasaki Erika、Ema Masatsugu、Kuraku Shigehiro、Kawaji Hideya、Sakakibara Yasubumi
- Journal Title
  
  Scientific Data
  
  Volume: 8 Issue: 1 Pages: 59-59
- DOI
  10.1038/s41597-021-00935-6
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K21370, KAKENHI-PROJECT-20K21407, KAKENHI-PLANNED-17H06410, KAKENHI-PLANNED-20H05763, KAKENHI-PROJECT-18H04127, KAKENHI-PROJECT-19K16023, KAKENHI-PROJECT-20KK0186
[Journal Article] Genomic style: yet another deep-learning approach to characterize bacterial genome sequences2021
- Author(s)
  Yoshimura Yuka、Hamada Akifumi、Augey Yohann、Akiyama Manato、Sakakibara Yasubumi
- Journal Title
  
  Bioinformatics Advances
  
  Volume: 1 Issue: 1
- DOI
  10.1093/bioadv/vbab039
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-17H06410, KAKENHI-PROJECT-18H04127
[Journal Article] Hamster PIWI proteins bind to piRNAs with stage-specific size variations during oocyte maturation2021
- Author(s)
  Ishino Kyoko、Hasuwa Hidetoshi、Yoshimura Jun、Iwasaki Yuka W、Nishihara Hidenori、Seki Naomi M、Hirano Takamasa、Tsuchiya Marie、Ishizaki Hinako、Masuda Harumi、Kuramoto Tae、Saito Kuniaki、Sakakibara Yasubumi、Toyoda Atsushi、Itoh Takehiko、Siomi Mikiko C、Morishita Shinichi、Siomi Haruhiko
- Journal Title
  
  Nucleic Acids Research
  
  Volume: 49 Issue: 5 Pages: 2700-2720
- DOI
  10.1093/nar/gkab059
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19H05466, KAKENHI-PUBLICLY-19H05268, KAKENHI-PLANNED-19H05753, KAKENHI-PROJECT-18H02421, KAKENHI-PROJECT-18J22025, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-17K19424, KAKENHI-PROJECT-20H03175, KAKENHI-PROJECT-16H06276
[Journal Article] A Max-Margin Model for Predicting Residue-Base Contacts in Protein-RNA Interactions2021
- Author(s)
  Kashiwagi Shunya、Sato Kengo、Sakakibara Yasubumi
- Journal Title
  
  Life
  
  Volume: 11 Issue: 11 Pages: 1135-1135
- DOI
  10.3390/life11111135
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19K22897, KAKENHI-PLANNED-17H06410, KAKENHI-PROJECT-19H04210
[Journal Article] The complete plastid genome sequence of the enigmatic moss, Takakia lepidozioides (Takakiopsida, Bryophyta): evolutionary perspectives on the largest collection of genes in mosses and the intensive RNA editing2021
- Author(s)
  Sadamitsu Atsushi、Inoue Yuya、Sakakibara Keiko、Tsubota Hiromi、Yamaguchi Tomio、Deguchi Hironori、Nishiyama Tomoaki、Shimamura Masaki
- Journal Title
  
  Plant Molecular Biology
  
  Volume: 107 Issue: 4-5 Pages: 431-449
- DOI
  10.1007/s11103-021-01214-z
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21H04717, KAKENHI-PROJECT-16H06279
[Journal Article] An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data2020
- Author(s)
  Jayakumar Vasanthan、Ishii Hiromi、Seki Misato、Kumita Wakako、Inoue Takashi、Hase Sumitaka、Sato Kengo、Okano Hideyuki、Sasaki Erika、Sakakibara Yasubumi
- Journal Title
  
  BMC Genomics
  
  Volume: 21 Issue: S3 Pages: 243-243
- DOI
  10.1186/s12864-020-6657-2
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K22897, KAKENHI-PROJECT-16K00404, KAKENHI-PROJECT-19K06462, KAKENHI-PROJECT-16H06279, KAKENHI-PLANNED-17H06410, KAKENHI-PROJECT-18H04127, KAKENHI-PROJECT-19H04210
[Journal Article] MetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenomics assembly2020
- Author(s)
  Liang KC, Sakakibara, Y.
- Journal Title
  
  BMC Bioinformatics
  
  Volume: in press
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-17H06410
[Journal Article] Time-Series Analysis of Tumorigenesis in a Murine Skin Carcinogenesis Model2018
- Author(s)
  Aoto Y, Okumura K, Hachiya T, Hase S, Sato K, Wakabayashi Y, Ishikawa F and Sakakibara Y.
- Journal Title
  
  Scientific Reports
  
  Volume: 8 Issue: 1 Pages: 12994-12994
- DOI
  10.1038/s41598-018-31349-x
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18K07080, KAKENHI-PLANNED-17H06410, KAKENHI-PROJECT-16H06276, KAKENHI-PROJECT-16H06279
[Journal Article] Convolutional neural network based on SMILES representation of compounds for detecting chemical motif2018
- Author(s)
  Hirohara Maya、Saito Yutaka、Koda Yuki、Sato Kengo、Sakakibara Yasubumi
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 19 Issue: S19 Pages: 526-526
- DOI
  10.1186/s12859-018-2523-5
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K00404, KAKENHI-PLANNED-17H06410
[Journal Article] Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants2018
- Author(s)
  Higo, A., Kawashima, T., Borg, M., Zhao, M., Lopez-Vidriero, I., Sakayama, H., et al. (他18名)
- Journal Title
  
  Nature Communications
  
  Volume: 9 Issue: 1 Pages: 5283-5283
- DOI
  10.1038/s41467-018-07728-3
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18K06382, KAKENHI-PROJECT-18K19365, KAKENHI-PLANNED-17H06472, KAKENHI-PUBLICLY-18H04836, KAKENHI-PROJECT-15H04391, KAKENHI-PROJECT-15H05237, KAKENHI-PROJECT-16K07398, KAKENHI-PROJECT-16H05764, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-17H07424, KAKENHI-PROJECT-16H04836, KAKENHI-PROJECT-18K06367
[Journal Article] A max-margin training of RNA secondary structure prediction integrated with the thermodynamic model2018
- Author(s)
  Akiyama Manato、Sato Kengo、Sakakibara Yasubumi
- Journal Title
  
  Journal of Bioinformatics and Computational Biology
  
  Volume: 16 Issue: 06 Pages: 1840025-1840025
- DOI
  10.1142/s0219720018400255
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16K00404, KAKENHI-PLANNED-17H06410, KAKENHI-PROJECT-18H04127, KAKENHI-PROJECT-18J21767
[Journal Article] Convolutional neural networks for classification of alignments of non-coding RNA sequences2018
- Author(s)
  Aoki Genta、Sakakibara Yasubumi
- Journal Title
  
  Bioinformatics
  
  Volume: 34 Issue: 13 Pages: i237-i244
- DOI
  10.1093/bioinformatics/bty228
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-17H06410, KAKENHI-PROJECT-18H04127, KAKENHI-PROJECT-16H06279
[Journal Article] Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data2017
- Author(s)
  Vasanthan Jayakumar and Yasubumi Sakakibara
- Journal Title
  
  Briefings in Bioinformatics
  
  Volume: 20 Issue: 3 Pages: 866-876
- DOI
  10.1093/bib/bbx147
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16H06279
[Journal Article] DEclust: A statistical approach for obtaining differential expression profiles of multiple conditions.2017
- Author(s)
  Aoto Y, Hachiya T, Okumura K, Hase S, Sato K, Wakabayashi Y, and Sakakibara Y.
- Journal Title
  
  PLoS One
  
  Volume: 12 (11) Issue: 11 Pages: e0188285-e0188285
- DOI
  10.1371/journal.pone.0188285
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-15K06817, KAKENHI-PROJECT-15K08438, KAKENHI-PROJECT-16H06279, KAKENHI-PLANNED-17H06410
[Journal Article] Inter-species hormonal control of host root morphology by parasitic plants.2017
- Author(s)
  Spallek, T., Melnyk, C.W., Wakatake, T., Zhang, J., Sakamoto, Y., Kiba, T., Yoshida, S., Matsunaga, S., Sakakibara, H., *Shirasu, K.
- Journal Title
  
  Proc. Natl. Acad. Sci. USA.
  
  Volume: 印刷中 Issue: 20 Pages: 5283-5288
- DOI
  10.1073/pnas.1619078114
- Peer Reviewed / Acknowledgement Compliant / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-15H05959, KAKENHI-PROJECT-24228008, KAKENHI-PROJECT-17K07705, KAKENHI-INTERNATIONAL-15K21750, KAKENHI-PROJECT-25711019, KAKENHI-PLANNED-15H05962, KAKENHI-PUBLICLY-16H01477, KAKENHI-PROJECT-16H06279
[Journal Article] Genome sequence and analysis of the Japanese morning glory Ipomoea nil.2016
- Author(s)
  Hoshino A, Jayakumar V, Nitasaka E, Toyoda A, Noguchi H, Itoh T, Shin T, Minakuchi Y, Koda Y, Nagano AJ, Yasugi M, Honjo MN, Kudoh H, et al.
- Journal Title
  
  Nature Communications
  
  Volume: 7 Issue: 1 Pages: 132395-132395
- DOI
  10.1038/ncomms13295
- NAID
  120005997914
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26221106, KAKENHI-PROJECT-16H04719, KAKENHI-PROJECT-15K07118, KAKENHI-PROJECT-16H06279
[Journal Article] An algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing.2016
- Author(s)
  Tsuchiya M, Amano K, Abe M, Seki M, Hase S, Sato K, Sakakibara Y.
- Journal Title
  
  Bioinformatics
  
  Volume: 32 Issue: 12 Pages: i369-i377
- DOI
  10.1093/bioinformatics/btw273
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16H06279
[Journal Article] A machine learning based approach to de novo sequencing of glycans from tandem mass spectrometry spectrum2015
- Author(s)
  Kumozaki, S., Sato, K., Sakakibara, Y.
- Journal Title
  
  IEEE/ACM Trans Comput Biol Bioinform
  
  Volume: 印刷中
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-23241066
[Journal Article] Nordihydroguaiaretic acid disrupts the antioxidant ability of Helicobacter pylori through the repression of SodB activity in vitro.2015
- Author(s)
  Tsugawa, H., Mori, H., Matsuzaki, J., Masaoka, T., Hirayama, T., Nagasawa, H., Sakakibara, Y., Suematsu, M., Suzuki, H.
- Journal Title
  
  Biomed. Res. Int.
  
  Volume: 2015 Pages: 734548-734548
- DOI
  10.1155/2015/734548
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-26670065, KAKENHI-PROJECT-25460173, KAKENHI-PROJECT-25460301, KAKENHI-PROJECT-25293178, KAKENHI-PROJECT-25702050
[Journal Article] A machine learning based approach to de novo sequencing of glycans from tandem mass spectrometry spectrum.2015
- Author(s)
  Kumozaki, S., Sato, K., and Sakakibara, Y.
- Journal Title
  
  IEEE/ACM Trans Comput Biol Bioinform,
  
  Volume: in press
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-221S0002
[Journal Article] MetaVelvet-SL: An extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning2015
- Author(s)
  Afiahayati, Sato, K., and Sakakibara, Y.
- Journal Title
  
  DNA Research
  
  Volume: 22 Issue: 1 Pages: 69-77
- DOI
  10.1093/dnares/dsu041
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-23241066, KAKENHI-PROJECT-25330348, KAKENHI-PROJECT-221S0002
[Journal Article] Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis2015
- Author(s)
  Sato, K., Kuroki, Y., Kumita, W., Fujiyama, A., Toyoda, A., Kawai, J., Iriki, A., Sasaki, E., Okano, H., Sakakibara, Y.
- Journal Title
  
  Scientific Reports
  
  Volume: 5 Issue: 1 Pages: 16894-16894
- DOI
  10.1038/srep16894
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-25330348, KAKENHI-PROJECT-221S0002
[Journal Article] Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads2014
- Author(s)
  Kamada, M., Hase, S., Sato, K., Toyoda, A., Fujiyama, A., Sakakibara, Y.
- Journal Title
  
  PLOS ONE
  
  Volume: 9 Issue: 10 Pages: e109999-e109999
- DOI
  10.1371/journal.pone.0109999
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PROJECT-23241066, KAKENHI-PROJECT-25330348, KAKENHI-PROJECT-221S0002
[Journal Article] Meis1 regulates epidermal stem cells and is required for skin tumorigenesis2014
- Author(s)
  Okumura K, Saito M, Isogai E, Aoto Y, Hachiya T, Sakakibara Y, Katsuragi Y, Hirose S, Kominami R, Goitsuka R, Nakamura T and Wakabayashi Y.
- Journal Title
  
  PLOS ONE
  
  Volume: 9 Issue: 7 Pages: e102111-e102111
- DOI
  10.1371/journal.pone.0102111
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23241066, KAKENHI-ORGANIZER-24111001, KAKENHI-PUBLICLY-25111513, KAKENHI-PROJECT-25292194, KAKENHI-PROJECT-26250029, KAKENHI-PROJECT-26640085
[Journal Article] An extended genovo metagenomic assembler by incorporating paired-end information2013
- Author(s)
  Afiahayati, Sato K., Sakakibara Y.
- Journal Title
  
  PeerJ
  
  Volume: 1 Pages: e196-e196
- DOI
  10.7717/peerj.196
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23241066, KAKENHI-PROJECT-221S0002
[Journal Article] Screening for candidate genes involved in the production of mouse subventricular zone proliferative cells and an estimation of their changes in evolutionary pressure during primate evolution2013
- Author(s)
  Tabata H, Hachiya T, Nagata K, Sakakibara Y, Nakajima K
- Journal Title
  
  Front Neuroanat
  
  Volume: 7 Pages: 24-24
- DOI
  10.3389/fnana.2013.00024
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-ORGANIZER-22111001, KAKENHI-PLANNED-22111004, KAKENHI-PROJECT-22240041, KAKENHI-PUBLICLY-25123727, KAKENHI-PROJECT-25430046, KAKENHI-PROJECT-221S0002
[Journal Article] TAG-1-assisted progenitor elongation streamlines nuclear migration to optimize subapical crowding.2013
- Author(s)
  Okamoto M, Namba T, Shinoda T, Kondo T, Watanabe T, Inoue Y, Takeuchi K, Enomoto Y, Ota K, Oda K, Wada Y, Sagou K, Saito K, Sakakibara A, Kawaguchi A, Nakajima K, Adachi T, Fujimori T, Ueda M, Hayashi S, Kaibuchi K, Miyata T
- Journal Title
  
  Nature Neuroscience
  
  Volume: 16 Issue: 11 Pages: 1556-66
- DOI
  10.1038/nn.3525
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21116005, KAKENHI-ORGANIZER-22111001, KAKENHI-PLANNED-22111002, KAKENHI-PLANNED-22111004, KAKENHI-PLANNED-22111006, KAKENHI-PLANNED-22111007, KAKENHI-PROJECT-22240041, KAKENHI-PROJECT-23500410, KAKENHI-PROJECT-23700463, KAKENHI-PROJECT-25830033
[Journal Article] Development of a rifampicin-resistant Bacillus subtilis strain for natto-fermentation showing enhanced exoenzyme production.2013
- Author(s)
  Yuji Kubo
- Journal Title
  
  Journal of Bioscience and Bioengineering
  
  Volume: 115 Issue: 6 Pages: 654-657
- DOI
  10.1016/j.jbiosc.2012.12.012
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22780078, KAKENHI-PROJECT-221S0002
[Journal Article] SAMSCOPE: An OpenGL based real-time interactive scale-free SAM viewer2012
- Author(s)
  Popendorf, K. and Sakakibara, Y.
- Journal Title
  
  Bioinformatics
  
  Volume: 28 Issue: 9 Pages: 1276-1277
- DOI
  10.1093/bioinformatics/bts122
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23241066, KAKENHI-PROJECT-221S0002
[Journal Article] COPICAT : A software system for predicting interactions between proteins and chemical compounds2012
- Author(s)
  Sakakibara, Y., Hachiya, T., Uchida, M., Nagamine, N., Sugawara, Y., Yokota, M., Nakamura, M., Popendorf, K., Komori, T., Sato, K.
- Journal Title
  
  Bioinformatics
  
  Volume: 28 Issue: 5 Pages: 745-746
- DOI
  10.1093/bioinformatics/bts031
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-221S0002
[Journal Article] An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds2012
- Author(s)
  Nakamura, M., Hachiya, T., Saito, Y., Sato, K., and Sakakibara, Y.
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 13 Issue: S17
- DOI
  10.1186/1471-2105-13-s17-s8
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23241066, KAKENHI-PROJECT-221S0002
[Journal Article] MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads2012
- Author(s)
  Namiki, T., Hachiya, T., Tanaka, H., and Sakakibara, Y.
- Journal Title
  
  Nucleic Acids Research
  
  Volume: 40 Issue: 20 Pages: e155-e155
- DOI
  10.1093/nar/gks678
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23241066, KAKENHI-PROJECT-221S0002
[Journal Article] DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition2012
- Author(s)
  Kengo Sato, Yuki Kato, Tatsuya Akutsu, Kiyoshi Asai, Yasubumi Sakakibara
- Journal Title
  
  Bioinformatics
  
  Volume: 28 Issue: 24 Pages: 3218-3224
- DOI
  10.1093/bioinformatics/bts612
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22240009, KAKENHI-PROJECT-22240031, KAKENHI-PROJECT-23241066, KAKENHI-PROJECT-23650153, KAKENHI-PROJECT-24700296, KAKENHI-PROJECT-221S0002
[Journal Article] Improved measurements of RNA structure conservation with generalized centroid estimators2011
- Author(s)
  Okada, Y., Saito, Y., Sato, K., Sakakibara, Y.
- Journal Title
  
  Frontiers in Genetics
  
  Volume: 2 Pages: 54-54
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-221S0002
[Journal Article] Improved measurements of RNA structure conservation with generalized centroid estimators2011
- Author(s)
  Yohei Okada
- Journal Title
  
  Frontiers in Genetics
  
  Volume: 2 Pages: 54-54
- DOI
  10.3389/fgene.2011.00054
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22700305, KAKENHI-PROJECT-23241066
[Journal Article] Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures2011
- Author(s)
  Saito, Y., Sato, K., Sakakibara, Y.
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 12
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-221S0002
[Journal Article] Genome-wide searching with base-pairing kernel functions for non-coding RNAs : computational and expression analysis of snoRNA families in Caenorhabditis elegans2009
- Author(s)
  Morita, M., Saito, Y., Sato, K., Oka, K., Hotta, K., Sakakibara, Y.
- Journal Title
  
  Nucleic Acids Research 37(3)
  
  Pages: 999-1009
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Genome-wide searching with base-pairing kernel functions for non-coding RNAs2009
- Author(s)
  M. Morita, Y. Saito, K Sato, K Oka, K Hotta, and Y. Sakakibara
- Journal Title
  
  Nucleic Acids Research 37
  
  Pages: 999-1009
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Integrating statistical predictions and experimental Verifications for enhancing protein-chemical interaction predictions in virtual screening2009
- Author(s)
  Nagamine, N., Shirakawa, T., Minato, Y., Torii, K., Kobayashi, H., Imoto, M., Sakakibara, Y.
- Journal Title
  
  PLoS Computational Biology 5(6)
  
  Pages: 1000397-1000397
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Whole-genome tiling array analysis of Mycobacterium leprae RNA reveals high expression of pseudogenes and noncoding regions2009
- Author(s)
  Akama, T., Suzuki, K., Tanigawa, T., Kawashima, A., Wu, H., Nakata, N., Osana, Y., Sakakibara, Y., Ishii, N.
- Journal Title
  
  Journal of Bacteriology 191
  
  Pages: 3321-3327
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Genome-wide searching with base-pairing kernel functions for non-coding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans2009
- Author(s)
  Morita, M., Saito, Y., Sato, K., Oka, K., Hotta, K., Sakakibara, Y.
- Journal Title
  
  Nucleic Acids Research 37(3)
  
  Pages: 999-1009
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Accurate identification of orthologous segments among multiple genomes2009
- Author(s)
  Hachiya, T., Osana, Y., Popendorf, K., Sakakibara, Y.
- Journal Title
  
  Bioinformatics 25(7)
  
  Pages: 853-860
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Whole-genome tiling array analysis of Mycobacterium leprae RNA reveals high expression of pseudogenes and noncoding regions2009
- Author(s)
  Akama, T., Suzuki, K., Tanigawa, T., Kawashima, A., Wu, H., Nakata, N., Osana. Y.. Sakakibara, Y.. Ishii, N.
- Journal Title
  
  Journal of Bacteriology 191
  
  Pages: 3321-3327
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Sensitive detection of conserved gene clusters unravels the evolutionary forces behind the correlation between protein sequence homology and geneorder conservation.2009
- Author(s)
  Hachiya, T., Sakakibara, Y.
- Journal Title
  
  Genes, Genomes and Genomics 3(1)
  
  Pages: 31-45
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] PSSMTS: position specific scoring matrices on tree structures2008
- Author(s)
  Sato, K., Morita, K., and Sakakibara, Y.
- Journal Title
  
  Journal of Mathematical Biology y 56
  
  Pages: 201-214
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Software. ncrna. org: web servers for analyses of RNA sequences2008
- Author(s)
  Asai, K, Kiryu, H, Hamada, M, Tabei, Y, Sato, K, Matsui, H, Sakakibara, Y, Terai, G,, Mituyama, T.
- Journal Title
  
  Nucleic Acids Res. 36
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Directed acyclic graph kernels for structural RNA analysis2008
- Author(s)
  K Sato, T. Mituyama, K Asai, and Y. Sakakibara
- Journal Title
  
  BMC Bioinformatics 9
  
  Pages: 318-318
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] PSSMTS: position specific scoring matrices on tree structures2008
- Author(s)
  Sato, K., Morita, K., Sakakibara, Y.
- Journal Title
  
  Journal of Mathematical Biology 56
  
  Pages: 201-214
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Software.ncrna.org : web servers for analyses of RNA sequences2008
- Author(s)
  Asai, K, Kiryu, H, Hamada., M., Tabei, Y., Sato, K, Matsui, H., Sakakibara, Y., Terai, G., and Mituyama. T.
- Journal Title
  
  Nucleic Acids Research 36
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Directed acyclic graph kernels for structural RNA analysis2008
- Author(s)
  Sato, K., Mituyama, T., Asai, K., Sakakibara, Y.
- Journal Title
  
  BMC Bioinformatics 9
  
  Pages: 318-318
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Stem kernels for KNA sequence analyses2007
- Author(s)
  Sakakibara, Y., Ogawa, N・, Popendorf, K., Asai, K., and K. Sato
- Journal Title
  
  Journal of Bioinformatics and Computational Biology 5・6
  
  Pages: 1103-1122
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Stem Kernels for RNA Sequence Analyses2007
- Author(s)
  Sakakibara, Y., Asai, K., Sato, K.
- Journal Title
  
  Proc. 1st International Conference on Bioinformatics Research and Development
  
  Pages: 278-291
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300095
[Journal Article] Stem kernels for RNA sequence analyses2007
- Author(s)
  Sakakibara, Y., Ogawa, N., Popendorf, K., Asai, K., K. Sato
- Journal Title
  
  Journal of Bioinformatics and Computational Biology 5(6)
  
  Pages: 1103-1122
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Statistical prediction of protein-chemical interactions based on chemical structure and mass spectrometry data2007
- Author(s)
  Nagamine, N., Sakakibara, Y.
- Journal Title
  
  Bioinformatics 23(15)
  
  Pages: 2004-2012
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Stem Kernels for RNA Sequence Analyze2007
- Author(s)
  Sakakibara, Y., Asai, K., Sato, K.
- Journal Title
  
  Proc. 1st International Conference on Bioinformatics Research And Development
  
  Pages: 278-291
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300095
[Journal Article] Statistical prediction of protein-chemical interactions based on chemical structure and mass spectrometry data2007
- Author(s)
  Nagamine, N. and Sakakibara, Y.
- Journal Title
  
  Bioinformatics 23・15
  
  Pages: 2004-2012
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Stem Kernels for RNA Sequence Analyses2007
- Author(s)
  Sakakibara, Y., Asai, K., Sato, K.
- Journal Title
  
  Proc. 1st International Conference on Bioinformatics Research and Development
  
  Pages: 278-291
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Detection of Cis-Acting Regulatory Variation from Location Data2006
- Author(s)
  Kawada, Y., Sakakibara, Y.
- Journal Title
  
  Proceedings of the 4th Asia-Pacific Bioinformatics Conference (APBC 2006)
  
  Pages: 89-98
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Probabilistic Inference in Test Tube and Its Application to Gene Expression Profiles2006
- Author(s)
  Y.Sakakibara, T.Yokomori, S.Kobayashi, A.Suyama
- Journal Title
  
  Formal Models, Languages And Applications (edited by Subramanian et al.) (World Scientific Pub.)
  
  Pages: 304-319
- Data Source
  KAKENHI-PROJECT-14085205
[Journal Article] Detection of Cis-Acting Regulatory Variation from Location Data2006
- Author(s)
  Kawada, Y., Sakakibara, Y.
- Journal Title
  
  Proceedings of the 4th Asia-Pacific Bioinformatics Conference (APBC 2006)
  
  Pages: 89-98
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300095
[Journal Article] Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures2005
- Author(s)
  atsui, H., Sato, K., Sakakibara, Y.
- Journal Title
  
  Bioinformatics 21(11)
  
  Pages: 2611-2617
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] バイオインフォマティクス概説2005
- Author(s)
  榊原康文
- Journal Title
  
  情報処理学会雑誌 46・3
  
  Pages: 230-238
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300095
[Journal Article] Identifying cooperative transcriptional regulations using protein-protein interactions2005
- Author(s)
  Nagamine, N., Kawada, Y., Sakakibara, Y.
- Journal Title
  
  Nucleic Acids Research 33・15
  
  Pages: 4828-4837
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300095
[Journal Article] バイオインフォマティクス概説2005
- Author(s)
  榊原康文
- Journal Title
  
  情報処理学会雑誌 Vol.46,No.3
  
  Pages: 230-238
- Data Source
  KAKENHI-PROJECT-16300095
[Journal Article] Identifying cooperative transcriptional regulations using protein-protein interactions2005
- Author(s)
  Nagamine, N., Kawada, Y., Sakakibara, Y.
- Journal Title
  
  Nucleic Acids Research 33・15
  
  Pages: 4828-4837
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Grammatical Inference in Bioinformatics2005
- Author(s)
  Sakakibara, Y.
- Journal Title
  
  IEEE Transactions on Pattern Analysis and Machine Intelligence 27(7)
  
  Pages: 1051-1062
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Intensive in vitro experiments of implementing and executing finite automata in test tube2005
- Author(s)
  J.Kuramochi, Y.Sakakibara
- Journal Title
  
  Proceedings of 11th International Meeting on DNA Based Computers
  
  Pages: 59-67
- Data Source
  KAKENHI-PROJECT-14085205
[Journal Article] RNA secondary structural alignment with conditional random fields2005
- Author(s)
  Sato, K., Sakakibara, Y.
- Journal Title
  
  Bioinformatics 21・2
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Grammatical Inference in Bioinformatics2005
- Author(s)
  Sakakibara, Y.
- Journal Title
  
  IEEE Transactions on Pattern Analysis and Machine Intelligence 27(7)
  
  Pages: 1051-1062
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300095
[Journal Article] Development of an in vivo computer based on Escherichia coli2005
- Author(s)
  H, Nakagawa, K.Sakamoto, Y.Sakakibara
- Journal Title
  
  Proceedings of 11th International Meeting on DNA Based Computers
  
  Pages: 68-77
- Data Source
  KAKENHI-PROJECT-14085205
[Journal Article] RNA secondary structural alignment with conditional random fields2005
- Author(s)
  Sato, K., Sakakibara, Y.
- Journal Title
  
  Bioinformatics 21(2)
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300095
[Journal Article] Identifying cooperative transcriptional regulations using protein-protein interactions2005
- Author(s)
  Nagamine, N., Kawada, Y., Sakakibara, Y.
- Journal Title
  
  Nucleic Acids Research 33(15)
  
  Pages: 4828-4837
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Searching biologically plausible synteny blocks among multiple genomes2005
- Author(s)
  Sakakibara, Y.
- Journal Title
  
  BIOINFO 2005 (proceedings of 2005 International Joint Conference of InCoB, AASBi and KSBI)
  
  Pages: 113-117
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Grammatical Inference in Bioinformatics2005
- Author(s)
  Sakakibara, Y.
- Journal Title
  
  IEEE Transactions on Pattern Analysis and Machine Intelligence 27・7
  
  Pages: 1051-1062
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300095
[Journal Article] RNA secondary structural alignment with conditional random fields2005
- Author(s)
  Sato, K., Sakakibara, Y.
- Journal Title
  
  Bioinformatics 21(Suppl.2)
  
  Pages: 237-242
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] Identifying cooperative transcriptional regulations using protein-protein interactions2005
- Author(s)
  Nagamine, N., Kawada, Y., Sakakibara, Y.
- Journal Title
  
  Nucleic Acids Research 33(15)
  
  Pages: 4828-4837
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300095
[Journal Article] Grammatical Inference in Bioinformatics2005
- Author(s)
  Sakakibara, Y.
- Journal Title
  
  IEEE Transactions on Pattern Analysis and Machine Intelligence 27・7
  
  Pages: 1051-1062
- Data Source
  KAKENHI-PROJECT-17018029
[Journal Article] RNA secondary structural alignment with conditional random fields2005
- Author(s)
  Sato, K., Sakakibara, Y.
- Journal Title
  
  Bioinformatics 21・2
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300095
[Journal Article] 分子計算の理論モデル2004
- Author(s)
  小林聡, 榊原康文, 横森貴
- Journal Title
  
  分子コンピュータの現状と展望(萩谷編),サイエンス社
  
  Pages: 32-40
- Data Source
  KAKENHI-PROJECT-14085205
[Journal Article] A DNA-based Computational Model using a Specific Type of Restriction Enzymes2004
- Author(s)
  Y.Sakakibara, H.Imai
- Journal Title
  
  Journal of Automata, Languages and Combinatorics 9・1
  
  Pages: 111-119
- Data Source
  KAKENHI-PROJECT-14085205
[Journal Article] 分子コンピューティングの新しいモデル2004
- Author(s)
  榊原康文
- Journal Title
  
  分子コンピュータの現状と展望(萩谷編),サイエンス社
  
  Pages: 84-90
- Data Source
  KAKENHI-PROJECT-14085205
[Journal Article] Genome-Wide Analyses of Cooperative Transcriptional Regulations with Context-Dependent Probabilistic Models2004
- Author(s)
  Y.Kawada, Y.Sakakibara
- Journal Title
  
  12th Inter. Conf. on Intelligent Systems for Molecular Biology and 3rd European Conf. on Computational Biology
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300095
[Journal Article] Genome-Wide Analyses of Cooperative Transcriptional Regulations with Context-Dependent Probabilistic Models2004
- Author(s)
  Y.Kawada, Y.Sakakibara
- Journal Title
  
  12th Inter.Conf.on Intelligent Systems for Molecular Biology and
  
  Pages: 106-106
- Data Source
  KAKENHI-PROJECT-15650054
[Journal Article] Pair Stochastic Tree Adjoining Grammars for Aligning and Predicting Pseudoknot RNA Structures2004
- Author(s)
  H.Matsui, K.Sato, Y.Sakakibara
- Journal Title
  
  Proceedings of 3rd Computational Systems Bioinformatics Conference (CSB2004)
  
  Pages: 290-299
- Description
  「研究成果報告書概要(和文)」より
- Data Source
  KAKENHI-PROJECT-16300095
[Journal Article] Pair Stochastic Tree Adjoining Grammars for Aligning and Predicting Pseudoknot RNA Structures2004
- Author(s)
  H.Matsui, K.Sato, Y.Sakakibara
- Journal Title
  
  Proceedings of 3rd Computational Systems Bioinformatics Conference
  
  Pages: 290-299
- Data Source
  KAKENHI-PROJECT-15650054
[Journal Article] Genome-Wide Analyses of Cooperative Transcriptional Regulations with Context-Dependent Probabilistic Models2004
- Author(s)
  Y.Kawada, Y.Sakakibara
- Journal Title
  
  12th Inter. Conf. on Intelligent Systems for Molecular Biology and 3rd European Conf. on Computational Biology D-32
  
  Pages: 106-106
- Description
  「研究成果報告書概要(欧文)」より
- Data Source
  KAKENHI-PROJECT-16300095
[Patent] 宿主異物排除応答依存的除菌剤2015
- Inventor(s)
  鈴木秀和、津川仁、榊原康文
- Industrial Property Rights Holder
  鈴木秀和、津川仁、榊原康文
- Industrial Property Rights Type
  特許
- Filing Date
  2015-05-22
- Data Source
  KAKENHI-PROJECT-26670065
[Patent] 宿主異物排除応答依存的除菌剤2014
- Inventor(s)
  鈴木秀和、津川仁、榊原康文
- Industrial Property Rights Holder
  鈴木秀和、津川仁、榊原康文
- Industrial Property Rights Type
  特許
- Filing Date
  2014-05-22
- Data Source
  KAKENHI-PROJECT-26670065
[Presentation] Deep Generative Model for Constructing Chemical Latent Space to Design and Discover Novel Drug Structures2024
- Author(s)
  Yasubumi Sakakibara
- Organizer
  12th International Conference on Bioinformatics and Computational Biology (ICBCB 2024)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-23H04885
[Presentation] 化合物潜在空間の構築によるバーチャル化合物構造の探索と設計2023
- Author(s)
  榊原康文
- Organizer
  「AIと有機合成化学」第１１回勉強会「数理・情報解析が拓く新物質創製」
- Invited
- Data Source
  KAKENHI-PLANNED-23H04885
[Presentation] 化合物潜在空間の構築によるバーチャル化合物構造の探索と設計2023
- Author(s)
  榊原康文
- Organizer
  CBI学会2023年大会シンポジウム
- Invited
- Data Source
  KAKENHI-ORGANIZER-23H04880
[Presentation] 生物配列情報解析と創薬支援における先進的なバイオインフォマティクス研究2023
- Author(s)
  榊原康文
- Organizer
  2023年日本バイオインフォマティクス学会年会・第12回生命医薬情報学連合大会（IIBMP2023）
- Invited
- Data Source
  KAKENHI-PLANNED-23H04885
[Presentation] 化合物潜在空間の構築によるバーチャル化合物構造の探索と設計2023
- Author(s)
  榊原康文
- Organizer
  CBI学会2023年大会シンポジウム、CBI学会
- Data Source
  KAKENHI-PLANNED-23H04885
[Presentation] Genomic style: a deep-learning approach to characterize bacterial genome sequences2021
- Author(s)
  Yuka Yoshimura, Akifumi Hamada, Yohann Augey, Manato Akiyama and Yasubumi Sakakibara
- Organizer
  2021年日本バイオインフォマティクス学会年会・第10回生命医薬情報学連合大会（IIBMP2021）
- Data Source
  KAKENHI-PROJECT-18H04127
[Presentation] Comprehensive detection of RNA targets that bind to chemical compounds using next-generation sequencing and data-driven method2020
- Author(s)
  H. Fujimoto, Y. Kondoh, T. Kawamura, S. Hase, M. Imoto, H. Osada, Y. Sakakibara
- Organizer
  The 25th Annual Meeting of the RNA Society (RNA2020)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H06279
[Presentation] 慶應大学における医療へのＡＩ活用の現状と動向について2019
- Author(s)
  榊原康文
- Organizer
  公益社団法人日本技術士会神奈川県支部第80回CPD講座
- Invited
- Data Source
  KAKENHI-PLANNED-17H06410
[Presentation] Development of meta-transcriptome analysis method and its application to meta-transcriptome map of common marmoset2019
- Author(s)
  Uehara M, Kominato M, Hase S, Inoue T, Sasaki E, Toyoda A, Sakakibara Y
- Organizer
  Intelligent Systems for Molecular Biology (ISMB) / International Society for Computational Biology (ISCB) 2019
- Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-17H06410
[Presentation] Long-read sequence data improves the contiguity of Marmoset genome2019
- Author(s)
  Vasanthan Jayakumar，Yasubumi Sakakibara
- Organizer
  第8回日本マーモセット研究会大会
- Data Source
  KAKENHI-PROJECT-18H04127
[Presentation] MetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenomics assembly2019
- Author(s)
  Liang KC, Sakakibara Y
- Organizer
  International Conference on Bioinformatics (InCoB) 2019
- Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-17H06410
[Presentation] Development of meta-transcriptome analysis method and its application to meta-transcriptome map of common marmoset2019
- Author(s)
  Uehara M, Kominato M, Hase S, Inoue T, Sasaki E, Toyoda A, Sakakibara Y
- Organizer
  Intelligent Systems for Molecular Biology (ISMB) / International Society for Computational Biology (ISCB) 2019
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04127
[Presentation] 慶應大学における医療へのＡＩ活用の現状と動向について2019
- Author(s)
  榊原康文
- Organizer
  公益社団法人日本技術士会神奈川県支部第80回CPD講座
- Invited
- Data Source
  KAKENHI-PROJECT-18H04127
[Presentation] 人工知能を用いた化学コミュニケーション空間の多様性の解明に向けて2018
- Author(s)
  榊原康文
- Organizer
  日本農芸化学会2018年度大会シンポジウム
- Data Source
  KAKENHI-PLANNED-17H06410
[Presentation] Enhancer of Flavonoid Productionによるカルコン合成酵素の生成物特異性制御2018
- Author(s)
  和氣駿之，大豆田亮，中野拓也，山田彩友美，寺下美穂，宇野海地，森田裕将，榊原圭子，星野敦，高橋征司，中山亨
- Organizer
  日本農芸化学会2018年度北海道支部・東北支部合同支部大会
- Data Source
  KAKENHI-PROJECT-18H04127
[Presentation] Development of meta-transcriptome analysis method and its application to meta-transcriptome map of common marmoset2018
- Author(s)
  Mika Uehara, Minori Kominato, Sumitaka Hase, Takashi Inoue, Erika Sasaki, Yasubumi Sakakibara
- Organizer
  6th World Congress on Targeting Microbiota
- Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-17H06410
[Presentation] Convolutional neural networks for classification of alignments of non-coding RNA sequences2018
- Author(s)
  Genta Aoki and Yasubumi Sakakibara
- Organizer
  The 26th International conference on Intelligent Systems for Molecular Biology (ISMB2018)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H04127
[Presentation] Convolutional neural networks for classification of alignments of non-coding RNA sequences2018
- Author(s)
  Genta Aoki and Yasubumi Sakakibara
- Organizer
  The 26th International conference on Intelligent Systems for Molecular Biology (ISMB2018)
- Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-17H06410
[Presentation] Development of meta-transcriptome analysis method and its application to meta-transcriptome map of common marmoset2018
- Author(s)
  榊原康文
- Organizer
  第77回日本癌学会学術総会
- Data Source
  KAKENHI-PLANNED-17H06410
[Presentation] Convolutional neural network based on SMILES representation of compounds for detecting chemical motif2018
- Author(s)
  Maya Hirohara, Yutaka Saito, Yuki Koda, Kengo Sato, Yasubumi Sakakibara
- Organizer
  The 29th International Conference on Genome Informatics (GIW 2018)
- Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-17H06410
[Presentation] 化学発がんにより誘発した皮膚腫瘍におけるMeis1の転写制御2017
- Author(s)
  吉澤康博、奥村和弘、斎藤慈、宗形春花、青戸良賢、磯貝恵理子、榊原康文、若林雄一
- Organizer
  第30回モロシヌス研究会
- Data Source
  KAKENHI-PROJECT-15K08438
[Presentation] 化学発がんにより誘発した皮膚腫瘍におけるMeis1の転写制御2017
- Author(s)
  吉澤康博、奥村和弘、斎藤慈、宗形春花、青戸良賢、磯貝恵理子、榊原康文、若林雄一
- Organizer
  第30回モロシヌス研究会
- Data Source
  KAKENHI-PROJECT-15K06817
[Presentation] ChIP sequencingをもちいた皮膚腫瘍におけるMeis1の機能解析2016
- Author(s)
  吉澤康博、奥村和弘、斎藤慈、宗形春花、青戸良賢、磯貝恵理子、榊原康文、若林雄一
- Organizer
  第63回日本実験動物学会総会
- Place of Presentation
  ミューザ川崎シンフォニーホール
- Year and Date
  2016-05-18
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15K08438
[Presentation] ChIP sequencingにより示唆されたMeis1の皮膚腫瘍におけるグルコース代謝の制御2016
- Author(s)
  吉澤康博、奥村和弘、斎藤慈、宗形春花、青戸良賢、磯貝恵理子、榊原康文、若林雄一
- Organizer
  第75回日本癌学会学術総会
- Place of Presentation
  パシフィコ横浜
- Year and Date
  2016-10-06
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15K08438
[Presentation] 皮膚悪性腫瘍においてMeis1が制御する下流因子の探索2016
- Author(s)
  吉澤康博、奥村和弘、斎藤慈、宗形春花、青戸良賢、磯貝恵理子、榊原康文、若林雄一
- Organizer
  第39回日本分子生物学会年会
- Place of Presentation
  パシフィコ横浜
- Year and Date
  2016-11-30
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15K08438
[Presentation] 発がん過程の継時的ゲノム解析2015
- Author(s)
  青戸良賢, 奥村和弘, 石川冬木, 若林雄一, 榊原康文
- Organizer
  第74回日本癌学会学術総会
- Place of Presentation
  愛知県名古屋市
- Year and Date
  2015-10-08
- Data Source
  KAKENHI-PROJECT-15K06817
[Presentation] 納豆菌ゲノムのPacBioシークエンシングと高精度配列の再決定．2015
- Author(s)
  鎌田真由美，長谷純崇，木村啓太郎，佐藤健吾，豊田敦，藤山秋佐夫，榊原康文
- Organizer
  第８回日本ゲノム微生物学会年会
- Place of Presentation
  東京農業大学
- Year and Date
  2015-03-07
- Data Source
  KAKENHI-PROJECT-221S0002
[Presentation] 機械学習を用いたタンパク質とRNAのコンタクト予測2014
- Author(s)
  佐藤健吾，柏木駿也，榊原康文
- Organizer
  第3回生命医薬情報学連合大会，日本バイオインフォマティクス学会2014年年会
- Place of Presentation
  仙台国際センター（宮城県・仙台市）
- Year and Date
  2014-10-03
- Data Source
  KAKENHI-PROJECT-23241066
[Presentation] RNA-Seqを用いた肺腺がん悪性化過程のマルチオミックス解析2014
- Author(s)
  白木澤沙衣，飯笹俊彦，横井左奈，榊原康文
- Organizer
  第73回日本癌学会学術総会
- Place of Presentation
  パシフィコ横浜（神奈川県・横浜市）
- Year and Date
  2014-09-25
- Data Source
  KAKENHI-PROJECT-23241066
[Presentation] デジタルクラスタリングを用いた発がん過程の経時的トランスクリプトーム解析2013
- Author(s)
  青戸良賢，若林雄一，榊原康文
- Organizer
  第72回日本癌学会学術総会
- Place of Presentation
  パシフィコ横浜
- Data Source
  KAKENHI-PROJECT-221S0002
[Presentation] Interkinetic nuclear migration through TAG-1-assisted progenitor elongation prevents neuroepithelial overcrowding and ensures neocortical histogenesis2013
- Author(s)
  Mayumi Okamoto, Takashi Namba, Tomoyasu Shinoda, Ken Sagou, Kanako Saito, Akira Sakakibara, Ayako Kawaguchi, Kazunori Nakajima, Masahiro Ueda, Shigeo Hayashi, Toshihiko Fujimori, Kozo Kaibuchi, and Takaki Miyata
- Organizer
  第46回日本発生生物学会年会
- Place of Presentation
  くにびきメッセ（島根県）
- Data Source
  KAKENHI-PROJECT-22240041
[Presentation] Functional screening of the genes involved in the production of progenitor cells in the subventricular zone in mice2013
- Author(s)
  Hidenori Tabata, Yasubumi Sakakibara, Koh-ichi Nagata, and Kazunori Nakajima
- Organizer
  Society for Neuroscience, Neuroscience 2013 Meeting
- Place of Presentation
  San Diego (U.S.A.)
- Data Source
  KAKENHI-PROJECT-22240041
[Presentation] 発がんゲノムにおける非コードRNA の網羅的発現解析2013
- Author(s)
  天野浩司郎，青戸良賢，若林雄一，榊原康文
- Organizer
  第72回日本癌学会学術総会
- Place of Presentation
  パシフィコ横浜
- Data Source
  KAKENHI-PROJECT-23241066
[Presentation] デジタルクラスタリングを用いた発がん過程の経時的トランスクリプトーム解析2013
- Author(s)
  ６）青戸良賢，八谷剛史，奥村和弘，長谷純崇，佐藤健吾，若林雄一，榊原康文
- Organizer
  情報処理学会第33回バイオ情報学研究発表会
- Place of Presentation
  仙台
- Data Source
  KAKENHI-PROJECT-23241066
[Presentation] ヒト膵臓がんにおける臓器内真正細菌のゲノム解析2013
- Author(s)
  榊原康文，鈴木秀和
- Organizer
  第72回日本癌学会学術総会
- Place of Presentation
  パシフィコ横浜
- Data Source
  KAKENHI-PROJECT-23241066
[Presentation] 脳室下帯分裂細胞の産生調節に関わる分子の探索（Screening of the genes involving in the production of progenitor cells in the subventricular zone）2013
- Author(s)
  田畑秀典、榊原康文、永田浩一、仲嶋一範
- Organizer
  第36回日本神経科学大会・第56回日本神経化学会大会・第23回日本神経回路学会大会合同大会（Neuro2013）
- Place of Presentation
  国立京都国際会館（京都府）
- Data Source
  KAKENHI-PROJECT-22240041
[Presentation] 形態依存的な神経前駆細胞の核移動は神経上皮の混雑を防ぎ、大脳組織形成を確実にする(Interkinetic nuclear migration through TAG-1 assisted progenitor elongation prevents neuroepithelial overcrowding and ensures neocortical histogenesis)2013
- Author(s)
  岡本麻友美、難波隆志、篠田友靖、佐合健、斉藤加奈子、榊原明、川口綾乃、仲嶋一範、上田昌宏、林茂生、藤森俊彦、貝淵弘三、宮田卓樹
- Organizer
  第36回日本神経科学大会・第56回日本神経化学会大会・第23回日本神経回路学会大会合同大会（Neuro2013）
- Place of Presentation
  国立京都国際会館（京都府）
- Data Source
  KAKENHI-PROJECT-22240041
[Presentation] 発がんゲノムにおける非コードRNA の網羅的発現解析2013
- Author(s)
  天野浩司郎，青戸良賢，若林雄一，榊原康文
- Organizer
  第72回日本癌学会学術総会
- Place of Presentation
  パシフィコ横浜
- Data Source
  KAKENHI-PROJECT-221S0002
[Presentation] デジタルクラスタリングを用いた発がん過程の経時的トランスクリプトーム解析2013
- Author(s)
  青戸良賢，若林雄一，榊原康文
- Organizer
  第72回日本癌学会学術総会
- Place of Presentation
  パシフィコ横浜
- Data Source
  KAKENHI-PROJECT-23241066
[Presentation] Interkinetic nuclear migration based on neuroepithelial-cell elongation ensures brain histogenesis through ‘crowd control’2013
- Author(s)
  M.Okamoto, T.Namba, T.Shinoda, K.Sagou, K.Saito, A.Sakakibara, A.Kawaguchi, K.Nakajima, M.Ueda, S.Hayashi, T.Fujimori, K.Kaibuchi, and T.Miyata
- Organizer
  第118回日本解剖学会総会・全国学術集会
- Place of Presentation
  サンポートホール高松・かがわ国際会議場（香川県）
- Data Source
  KAKENHI-PROJECT-22240041
[Presentation] ヒト膵臓がんにおける臓器内真正細菌のゲノム解析2013
- Author(s)
  榊原康文，鈴木秀和
- Organizer
  第72回日本癌学会学術総会
- Place of Presentation
  パシフィコ横浜
- Data Source
  KAKENHI-PROJECT-221S0002
[Presentation] マウス大脳皮質発生過程における脳室下帯分裂細胞の産生と維持の調節 (Regulation of the production and maintenance of the progenitors in the subventricular zone during the mouse cortical development)2012
- Author(s)
  田畑秀典、八谷剛史、榊原康文、仲嶋一範
- Organizer
  第35回日本神経科学大会
- Place of Presentation
  名古屋国際会議場（愛知県）
- Data Source
  KAKENHI-PROJECT-22240041
[Presentation] Comprehensive analysis of small non-coding RNAs in medaka transcriptome by deep RNA-seq approach2011
- Author(s)
  ９） Abe, M., Hase, S., Ogawa, M., Okada, Y., Sato, K., Saito, Y., and Sakakibara, Y.
- Organizer
  RNA 2011 Sixteenth Annual Meeting of the RNA Society,
- Place of Presentation
  Kyoto, Japan
- Data Source
  KAKENHI-PROJECT-23241066
[Presentation] 霊長類進化過程で大脳皮質発達に寄与した遺伝子の機能的、生物情報科学的探索(Functional and bioinformatic screening for the genes involved in the expansion of cerebral cortex during the primate evolution)2011
- Author(s)
  田畑秀典、八谷剛史、榊原康文、仲嶋一範
- Organizer
  34回日本神経科学大会
- Place of Presentation
  パシフィコ横浜(神奈川県)
- Data Source
  KAKENHI-PROJECT-22240041
[Presentation] MetaVelvet : An extension of Velvet assembler to de novo metagenome assembly from short sequence reads2011
- Author(s)
  Namiki, T., Hachiya, T., Tanaka, H., Sakakibara, Y.
- Organizer
  ACM Conference on Bioinformatics, Computational Biology and Biomedicine 2011
- Place of Presentation
  Chicago, USA
- Data Source
  KAKENHI-PROJECT-221S0002
[Presentation] Comprehensive analysis of small non-coding RNAs in medaka transcriptome by deep RNA-seq approach2011
- Author(s)
  Abe, M., Hase, S., Ogawa, M., Okada, Y., Sato, K., Saito, Y., Sakakibara, Y.
- Organizer
  RNA 2011 Sixteenth Annual Meeting of the RNA Society
- Place of Presentation
  Kyoto, Japan
- Data Source
  KAKENHI-PROJECT-221S0002
[Presentation] Gradient-based optimization of hyperparamers for base-pairing profile local alignment kernels2009
- Author(s)
  Sato, K., Saito, Y., Sakakibara, Y.
- Organizer
  Genome Informatics
- Place of Presentation
  Yokohama, Japan
- Year and Date
  2009-12-14
- Data Source
  KAKENHI-PROJECT-17018029
[Presentation] Gradient-based optimization of hyperparamers for base-pairing profile localalignment kernels2009
- Author(s)
  Sato, K., Saito, Y., Sakakibara, Y.
- Organizer
  Genome Informatics
- Place of Presentation
  横浜
- Year and Date
  2009-12-14
- Data Source
  KAKENHI-PROJECT-17018029
[Presentation] A non-parametric Bayesian approach for predicting RNA secondary structures2009
- Author(s)
  Sato, K., Hamada, M., Mituyama, T., Asai, K., Sakakibara, Y.
- Organizer
  Proceedings of 9th Workshop on Algorithms in Bioinformatics (WABI 2009)
- Place of Presentation
  Philadelphia, USA
- Year and Date
  2009-09-12
- Data Source
  KAKENHI-PROJECT-17018029
[Presentation] A non-parametric Bayesian approach for predicting RNA secondarystructures2009
- Author(s)
  Sato, K., Hamada, M., Mituyama, T., Asai, K., Sakakibara, Y.
- Organizer
  Proceedings of 9th Workshop on Algorithms in Bioinformatics (WABI 2009)
- Place of Presentation
  フィラデルフィア,米国
- Year and Date
  2009-09-12
- Data Source
  KAKENHI-PROJECT-17018029
[Presentation] Detection of Secondary-Structure Conserved Regions by Genome Comparison2008
- Author(s)
  Saito, Y., Sato, K., Sakakibara, Y.
- Organizer
  The 2008 Annual Conference of Japanese Society for Bioinformatics (JSBi 2008)
- Place of Presentation
  Osaka, Japan(口頭発表)
- Year and Date
  2008-12-16
- Data Source
  KAKENHI-PROJECT-17018029
[Presentation] Detection of secondary-structure conserved regions by genome comparison2008
- Author(s)
  Y. Saito, K Sato, and Y. Sakakibara
- Organizer
  The 2008 Annual Conference of Japanese Soci etv for Bioinformatics (JSBi 2008)
- Place of Presentation
  Osaka, Japan
- Year and Date
  2008-12-15
- Data Source
  KAKENHI-PROJECT-17018029
[Presentation] OSfinder: an accurate orthology mapping program and its application to placental mammalian genomes2007
- Author(s)
  Hachiya, T., Osana, Y., Popendorf, K., Sakakibara, Y.
- Organizer
  Proc. 2007 Annual Conference of Japanese Society for Bioinformatics (JSBi 2007)
- Place of Presentation
  Tokyo, Japan
- Year and Date
  2007-12-18
- Data Source
  KAKENHI-PROJECT-17018029
[Presentation] Osfinder: an accurate orthology mapping program and its application to placental mammalian genomes2007
- Author(s)
  Hachiya, T., Osana, Y., Popendorf, K., and Sakakibara, Y.
- Organizer
  2007 Annual Conference of Japanese Society for Bioinformatics (JSBi 2007)
- Place of Presentation
  Tokyo, Japan
- Year and Date
  2007-12-18
- Data Source
  KAKENHI-PROJECT-17018029
[Presentation] Stem Kernels for RNA Sequence Analyses2007
- Author(s)
  Sakakibara, Y., Asai, K., Sato, K.
- Organizer
  Proc. 1st International Conference on Bioinformatics Research and Development
- Place of Presentation
  Berlin, Germany
- Year and Date
  2007-03-13
- Data Source
  KAKENHI-PROJECT-17018029
[Presentation] Detection of Cis-Acting Regulatory Variation from Location Data2006
- Author(s)
  Kawada, Y., Sakakibara, Y.
- Organizer
  Proceedings of the 4th Asia-Pacific Bioinformatics Conference (APBC 2006)
- Place of Presentation
  Taiwan, China
- Year and Date
  2006-02-14
- Data Source
  KAKENHI-PROJECT-17018029
[Presentation] Searching biologically plausible synteny blocks among multiple genomes2005
- Author(s)
  Hachiya, T., Sakakibara, Y.
- Organizer
  BIOINFO 2005 (proceedings of 2005 International Joint Conference of InCoB, AASBi and KSBI)
- Place of Presentation
  Busan, Korea
- Year and Date
  2005-09-22
- Data Source
  KAKENHI-PROJECT-17018029
[Presentation] Histological organization of mouse and primate subventricular zone in the developing cerebral neocortex
- Author(s)
  Hidenori Tabata, Satoshi Yoshinaga, Yasubumi Sakakibara, Koh-ichi Nagata, Kazunori Nakajima
- Organizer
  Neuro2013 Satellite Symposium “Molecular & Cellular Mechanisms of Brain Development & Evolution”
- Place of Presentation
  京都府立医科大学（京都府）
- Data Source
  KAKENHI-PROJECT-22240041
[Presentation] Screening for candidate genes involved in the production of mouse subventricular zone proliferative cells and an estimation of their changes in evolutionary pressure during primate evolution.
- Author(s)
  田畑秀典、八谷剛史、永田浩一、榊原康文、仲嶋一範
- Organizer
  日本バイオインフォマティクス学会2013年年会
- Place of Presentation
  タワーホール船堀（東京都）
- Data Source
  KAKENHI-PROJECT-22240041

1. WAKABAYASHI Yuichi (40303119)

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Sakakibara Yasubumi 榊原 康文

SAKAKIBARA Yasubumi 榊原 康文

Research Projects

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Co-Researchers

タンパク質相互作用データに基づく生成AIによるペプチド配列の設計と実証Principal Investigator

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Construction of chemical latent space using deep learning and design of artificial molecular structuresPrincipal Investigator

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Development of a bioinformatics method for genome-wide discovery of non-coding RNA genesPrincipal Investigator

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Deep analysis of chemical communication space using artificial intelligence technologyPrincipal Investigator

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Comprehensive analysis of functional non-coding RNAs in cancer genome on multistage carcinogenesisPrincipal Investigator

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Sakakibara Yasubumi 榊原康文

SAKAKIBARA Yasubumi 榊原康文