2023

• Kubo, A.; Masugi, Y.; Hase, T.; Nagashima, K.; Kawai, Y.; Takizawa, M.; Hishiki, T.; Shiota, M.; Wakui, M.; Kitagawa, Y.; Kabe, Y.; Sakamoto, M.; Yachie, A.; Hayashida, T.; Suematsu, M. Polysulfide Serves as a Hallmark of Desmoplastic Reaction to Differentially Diagnose Ductal Carcinoma In Situ and Invasive Breast Cancer by SERS Imaging. Antioxidants 2023, 12, 240. https://doi.org/10.3390/antiox12020240

2022

• N. Hird, S. Palaniappan, S. Ghosh, Y. Shimizu, R. Ramanathan, V. Karunanidhi, E. Miura, Y. Tsubono. Co-creating a conceptual AI model to promote personalized communication and engagement for people with dementia. Gerontechnology, 21(s),556-556 https://doi.org/10.4017/gt.2022.21.s.556.opp3
• P. Singh, T. Doktorova, T. Mohoric, B.T. Braak, S.K. Palaniappan, S. Ghosh, B. Hardy, P17-16 EdelweissPredict – A framework and workflow for integrated analysis supporting prediction of drug adverse outcomes demonstrated on a case study for the drug pair troglitazone and rosiglitazone, Toxicology Letters, Volume 368, Supplement,2022, Pages S232-S233
• Syed Ashif Jardary Al Ahmed, Nishad Bapatdhar, Bipin Pradeep Kumar, Samik Ghosh, Ayako Yachie, Sucheendra K. Palaniappan. Large scale text mining for deriving useful insights: (2022). doi: 10.3389/fphys.2022.933069
• Shinada NK, Koyama N, Ikemori M, Nishioka T, Hitaoka S, Hakura A, Asakura S, Matsuoka Y, Palaniappan SK. Optimizing machine-learning models for mutagenicity prediction through better feature selection. Mutagenesis. 2022 May 13:geac010. doi: 10.1093/mutage/geac010. Epub ahead of print. PMID: 35554560.
• Polouliakh N, Hase T, Ghosh S, Kitano H. Toxicity Analysis of Pentachlorophenol Data with a Bioinformatics Tool Set. Methods Mol Biol. 2022;2486:105-125. doi: 10.1007/978-1-0716-2265-0_7. PMID: 35437721.
• Heydari T, A Langley M, Fisher CL, Aguilar-Hidalgo D, Shukla S, Yachie-Kinoshita A, Hughes M, M McNagny K, Zandstra PW. IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data. PLoS Comput Biol. 2022 Feb 25;18(2):e1009907. doi: 10.1371/journal.pcbi.1009907. PMID:35213533; PMCID: PMC8906617.
• Galindo-Martínez CT, Weber M, Avila-Magaña V, Enríquez S, Kitano H, Medina M, Iglesias-Prieto R. The role of the endolithic alga Ostreobium spp. during coral bleaching recovery. Sci Rep. 2022 Feb 22;12(1):2977. doi: 10.1038/s41598-022-07017-6. PMID: 35194106; PMCID: PMC8863988.

2021

• Tsuji S, Hase T, Yachie-Kinoshita A, Nishino T, Ghosh S, Kikuchi M, Shimokawa K, Aburatani H, Kitano H, Tanaka H. Artificial intelligence-based computational framework for drug-target prioritization and inference of novel repositionable drugs for Alzheimer's disease. Alzheimers Res Ther. 2021 May 3;13(1):92. doi: 10.1186/s13195-021-00826-3. PMID: 33941241; PMCID: PMC8091739.
• Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R; COVID-19 Disease Map Community. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol. 2021 Oct;17(10):e10387. doi: 10.15252/msb.202110387. PMID: 34664389.
• Avila-Magaña V, Kamel B, DeSalvo M, Gómez-Campo K, Enríquez S, Kitano H, Rohlfs RV, Iglesias-Prieto R, Medina M. Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress. Nat Commun. 2021 Sep 30;12(1):5731. doi: 10.1038/s41467-021-25950-4. PMID: 34593802.
• Kitano, H. Nobel Turing Challenge: creating the engine for scientific discovery. npj Syst Biol Appl 7, 29 (2021). https://doi.org/10.1038/s41540-021-00189-3
• Nishi, A., Kaifuchi, N., Shimobori, C, Ohbuchi, K., Iizuka, S., Sugiyama, A.,  Ogura, K., Yamamoto, M., Kuroki, H., Nabeshima, S., Yachie, A.,  Matsuoka, Y. & Kitano, H.,Effects of maoto (ma-huang-tang) on host lipid mediator and transcriptome signature in influenza virus infection, Sci Rep 11, 4232 (2021). https://doi.org/10.1038/s41598-021-82707-1
• Nishi, A., Ohbuchi, K., Kaifuchi, N., Shimobori, C ., Kushida,  H., Yamamoto,  M., Kita, Y.,  Tokuoka, S.M., Yachie,  A., Matsuoka, Y., & Kitano,  H., LimeMap: a comprehensive map of lipid mediator metabolic pathways., npj Syst Biol Appl 7, 6 (2021). https://doi.org/10.1038/s41540-020-00163-5

2020

• N. W. Hird, J. Kato, S. Ghosh, K. Maeda, Digital technology for personalized multisensory stimulation to promote communication and engagement in dementia care, Gerontechnology, 19(0), 1-1 https://doi.org/10.4017/gt.2020.19.s.70022
• Gregory J. Baker, Jeremy L. Muhlich, Sucheendra K. Palaniappan, Jodene K. Moore, Stephanie H. Davis, Sandro Santagata, Peter K. Sorger, SYLARAS: A Platform for the Statistical Analysis and Visual Display of Systemic Immunoprofiling Data and Its Application to Glioblastoma , Cell Systems, 2020,doi:10.1016/j.cels.2020.08.001
• U. Akujuobi, M. Spranger, S. Palanniappan and X. Zhang, "T-PAIR: Temporal Node-pair Embedding for Automatic Biomedical Hypothesis Generation" in IEEE Transactions on Knowledge & Data Engineering, vol. , no. 01, pp. 1-1, 5555. doi: 10.1109/TKDE.2020.3017687, url: https://doi.ieeecomputersociety.org/10.1109/TKDE.2020.3017687
• Nock R, Polouliakh N, Nielsen F, Oka K, Connell CR, Heimhofer C, Shibanai K, Ghosh S, Aisaki K, Kitajima S, Kanno J, Akama K, Kitano H., A Geometric Clustering Tool (AGCT) to robustly unravel the inner cluster structures of time-series gene expressions. PLOS ONE 15(7): e0233755. 2020, https://doi.org/10.1371/journal.pone.0233755
• Nishimura, T., Nakamura, H., Yachie, A. et al. Disease-related cellular protein networks differentially affected under different EGFR mutations in lung adenocarcinoma. Sci Rep 10, 10881 (2020). https://doi.org/10.1038/s41598-020-67894-7
• Ostaszewski, M., Mazein, A., Gillespie, M.E. et al. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Sci Data 7, 136 (2020). https://doi.org/10.1038/s41597-020-0477-8

2019

• Uchida, Shinichi, Yoshiyuki Asai, Yoshiaki Kariya, Kunichika Tsumoto, Hiroshi Hibino, Masashi Honma, Takeshi Abe, Fumiaki Nin, Yasutaka Kurata, Kazuharu Furutani, Hiroshi Suzuki, Hiroaki Kitano, Ryuji Inoue, Yoshihisa Kurachi. Integrative and theoretical research on the architecture of a biological system and its disorder. The Journal of Physiological Sciences (2019): 1-19.
• Masahito Ohue, Anastasiia Gryniukova, Petro Borysko, Sergey Zozulya, Nobuaki Yasuo, Ryunosuke Yoshino, Kazuyoshi Ikeda, Woong-Hee Shin, Daisuke Kihara, Mitsuo Iwadate, Hideaki Umeyama, Takaaki Ichikawa, Reiji Teramoto, Kun-Yi Hsin, Vipul Gupta, Hiroaki Kitano, Mika Sakamoto, Akiko Higuchi, Nobuaki Miura, Kei Yura, Masahiro Mochizuki, Chandrasekaran Ramakrishnan, A. Mary Thangakani, D. Velmurugan, M. Michael Gromiha, Itsuo Nakane, Nanako Uchida, Hayase Hakariya, Modong Tan, Hironori K. Nakamura, Shogo D. Suzuki, Tomoki Ito, Masahiro Kawatani, Kentaroh Kudoh, Sakurako Takashina, Kazuki Z. Yamamoto, Yoshitaka Moriwaki, Keita Oda, Daisuke Kobayashi, Tatsuya Okuno, Shintaro Minami, George Chikenji, Philip Prathipati, Chioko Nagao, Attayeb Mohsen, Mari Ito, Kenji Mizuguchi, Teruki Honma, Takashi Ishida, Takatsugu Hirokawa, Yutaka Akiyama & Masakazu Sekijima, A prospective compound screening contest identified broader inhibitors for Sirtuin 1. Sci Rep 9, 19585 (2019). https://doi.org/10.1038/s41598-019-55069-y
• Gupta, V., Crudu, A., Matsuoka, Y., Ghosh, S., Rozot, R., Marat, X., … Breton, L. (2019). Multi-dimensional computational pipeline for large-scale deep screening of compound effect assessment: an in silico case study on ageing-related compounds. Npj Systems Biology and Applications, 5(1), 42.

• Nakamura, H., Fujii, K., Gupta, V., Hata, H., Koizumu, H., Hoshikawa, M., … Nishimura, T. (2019). Identification of key modules and hub genes for small-cell lung carcinoma and large-cell neuroendocrine lung carcinoma by weighted gene co-expression network analysis of clinical tissue-proteomes. PLOS ONE, 14(6), e0217105.

• Pichené, Matthieu, Sucheendra K. Palanniappan, Eric Fabre, and Blaise Genest. Modeling Variability in Populations of Cells using Approximated Multivariate Distributions. IEEE/ACM transactions on computational biology and bioinformatics (2019).
• Kato, Yu, Kimiyo Tabata, Takayuki Kimura, Ayako Yachie-Kinoshita, Yoichi Ozawa, Kazuhiko Yamada, Junichi Ito, Sho Tachino, Yusaku Hori, Masahiro Matsuki, Yukiko Matsuoka, Samik Ghosh, Hiroaki Kitano, Kenichi Nomoto, Junji Matsui , Yasuhiro Funahashi Lenvatinib plus anti-PD-1 antibody combination treatment activates CD8+ T cells through reduction of tumor-associated macrophage and activation of the interferon pathway. PloS one 14, no. 2 (2019): e0212513.
• Sucheendra K. Palaniappan, Ayako Yachie-Kinoshita , Samik Ghosh. Computational Systems Biology. in Encyclopedia of Bioinformatics and Computational Biology 789–795 (Elsevier, 2019). doi:10.1016/b978-0-12-809633-8.20287-2
• S. Muko, L. Legendre, R. Steneck, M. J. H. van Oppen, R. Albright, P. Ang Jr., R. C. Carpenter, A. P. Y. Chui, T.-Y. Fan, R. D. Gates, S. Harii, H. Kitano, H. Kurihara, S. Mitarai, J. L. Padilla-Gamiño, K. Sakai, G. Suzuki, P. J. Edmunds, Global Biogeography of Coral Recruitment: Tropical Decline and Subtropical Increase, Marine Ecology Progress Series 621, 1-17
• Ackerman, E., Alcorn, J., Hase, T. et al. A dual controllability analysis of influenza virus-host protein-protein interaction networks for antiviral drug target discovery. 
• Ayako Yachie-Kinoshita, Sucheendra K. Palaniappan , Samik Ghosh Computational Systems Biology Applications . in Encyclopedia of Bioinformatics and Computational Biology 66–73 (Elsevier, 2019). doi:10.1016/b978-0-12-809633-8.20079-4

2018

• Natalia Polouliakh, Paul Horton, Kazuhiro Shibanai, Kodai Takata, Vanessa Ludwig, Samik Ghosh and Hiroaki Kitano Sequence homology in eukaryotes (SHOE): interactive visual tool for promoter analysis; BMC Genomics September 2018 19:715;
• Gregory J. Baker, Sucheendra K. Palaniappan, Stephanie H. Davis, Jodene K. Moore and Peter K. Sorger. Systemic lymphoid architecture response assessment (SYLARAS): Application to system-wide immunophenotyping of glioblastoma; Cancer Res July 2018 (78) (13 Supplement) 5670; DOI: 10.1158/1538-7445.AM2018-5670
• Ayako Yachie‐Kinoshita, Kento Onishi, Joel Ostblom, Matthew A. Langley, Eszter Posfai, Janet Rossant, and Peter W. Zandstra. "Modeling signaling‐dependent pluripotency with Boolean logic to predict cell fate transitions." Molecular systems biology 14, no. 1 (2018): e7952.

2017

• Archana Bajpai, Takashi Ishii, Kosuke Miyauchi, Vipul Gupta, Yuka Nishio-Masaike, Yuki Shimizu-Yoshida, Masato Kubo and Hiroaki Kitano. Insights into gene expression profiles induced by Socs3 depletion in keratinocytes Scientific Reports 7, Article number: 15830 (2017), doi:10.1038/s41598-017-16155-1.
• Akinori Nishi, Katsuya Ohbuchi, Hirotaka Kushida, Takashi Matsumoto, Keiko Lee, Haruo Kuroki, Shigeki Nabeshima, Chika Shimobori, Nagisa Komokata, Hitomi Kanno, Naoko Tsuchiya, Makoto Zushi, Tomohisa Hattori, Masahiro Yamamoto, Yoshio Kase, Yukiko Matsuoka and Hiroaki Kitano. Deconstructing the traditional Japanese medicine “Kampo”: compounds, metabolites and pharmacological profile of maoto, a remedy for flu-like symptoms. npj Systems Biology and Applications 3, Article number: 32 (2017), doi:10.1038/s41540-017-0032-1.
• Matthieu Pichené, Sucheendra K. Palaniappan, Eric Fabre and Blaise Genest. Non-Disjoint Clustered Representation for Distributions over a Population of Cells. 15th International Conference on Computational Methods in Systems Biology, CMSB 2017, Darmstadt, Germany. Springer, LNCS/LNBI (10545), pp.324-326, 2017.
• Nozomu Yachie; Robotic Biology Consortium; Tohru Natsume. Robotic crowd biology with Maholo LabDroids. Nature Biotechnology. 35, 4, 310-312, April 2017.
• Gregory J. Baker, P.S. Thiagarajan, Sucheendra K. Palaniappan, Stephanie H. Davis, Jodene K. Moore and Peter K. Sorger. A flow-based immunoprofiling strategy for interrogating system-wide leukocyte composition in response to glioblastoma; Cancer Res July 1 2017 (77) (13 Supplement) 1678; DOI: 10.1158/1538-7445.AM2017-1678
• Caron, E., Roncagalli, R., Hase, T., Wolski, W.E., Choi, M., Menoita,M.G., Durand, S., García-Blesa, A., Fierro-Monti, I., Sajic, T., Heusel, M., Weiss, T., Malissen, M.,Schlapbach, R., Collins, B.C., Ghosh, S., Kitano, H., Aebersold, R., Malissen, B., Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry. Cell Reports 18, 3219–3226 (2017).
• Takeshi Hase, Samik Ghosh, Sucheendra K. Palaniappan, and Hiroaki Kitano (Chapter 13. Cancer Network Medicine), Network Medicine - Complex Systems in Human Disease and Therapeutics (Joseph Loscalzo, Albert-László Barabási, and Edwin K. Silverman (Eds.)), Harvard University Press 2017 ISBN 9780674436534
• Sucheendra K. Palaniappan, Francois Bertaux, Matthieu Pichené, Gregory Batt, Eric Fabre and Blaise Genest. Abstracting Biological Pathways using Information theory measures: A case study of Apoptosis Pathway. February 2017, Oxford Bioinformatics 
• Kitano, H. Biological Complexity and the need for Computational Approaches. Philosophy of Systems Biology: Perspectives from Scientists and Philosophers (Sara Green ed., Springer), 169-180, Mar. 21, 2017. (book chapter)

2016

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• Hu Y., Hase T., Li H.P., Prabhakar S., Kitano H., Ng S.K., Ghosh S., Wee L.J.K., A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic data, BMC Genomics 17, 1025 (2016). DOI: 10.1186/s12864-016-3317-7
• Koeda, Michihiko; Hase, Takeshi; Hama, Tomoko; Ikeda, Yumiko; Yahata, Noriaki; Tateno, Amane; Takahashi, Hidehiko; Matsuura, Masato; Suzuki, Hidenori; Okubo, Yoshiro, Effect of placebo and lorazepam on functional connectivity in fearful vocal processing: an fMRI study. INTERNATIONAL JOURNAL OF NEUROPSYCHOPHARMACOLOGY   19(Suppl_1) 54-5
• Hsin K.Y., Matsuoka Y, Asai Y, Kamiyoshi K, Watanabe T, Kawaoka Y, Kitano K., systemsDock: a web server for network pharmacology-based prediction and analysis. 2016 Nucleic Acids Res. gkw335. doi:10.1093/nar/gkw335
• Kitano, H. (2016) Artificial Intelligence to Win the Nobel Prize and Beyond: Creating the Engine for Scientific Discovery. AI Magazine37(1)
• Kitano, H. (2016), 人工知能がノーベル賞を獲る日、 - 究極のグランドチャレンジが工もたらすもの-,人工知能 31,2
• Kitano, H. グランドチャレンジの彼方へ. 人工知能  31, 1, 111-124, Jan. 1, 2016 
• Hird, N., Ghosh, S., & Kitano, H. (2016). Digital health revolution: perfect storm or perfect opportunity for pharmaceutical R&D? Drug Discovery Today. http://doi.org/10.1016/j.drudis.2016.01.010
• Kawakami, E., Singh, V.K., Matsubara, K., Ishii, T., Matsuoka,Y., Hase, T., Kulkarni, P., Siddiqui, K., Kodilkar, J., Danve, N., Subramanian, I., Katoh, M., Shimizu-Yoshida, Y., Ghosh, S., Jere A., & Kitano, H. (2016). Network analyses based on comprehensive molecular interaction maps reveal robust control structures in yeast stress response pathways, Npj Systems Biology and Applications,2, 15018. http://doi.org/10.1038/npjsba.2015.18
• Michael Spranger, Sucheendra K. Palaniappan, Samik Ghosh. Measuring the State of the Art of Automated Pathway Curation Using Graph Algorithms - A Case Study of the mTOR Pathway. BioNLP 2016, Berlin, Germany.
• Carlos Prada; Bishoy Hanna; Ann F. Budd; Cheryl M. Woodley; Jeremy Schmutz; Jane Grimwood; Roberto Iglesias-Prieto; John M. Pandolfi; Don Levitan; Kenneth G. Johnson; Nancy Knowlton; Hiroaki Kitano; Michael DeGiorgio; and Mónica Medina. Empty Niches after Extinctions Increase Population Sizes of Modern Corals. Current Biology. 26, 1–5, Dec. 5, 2016.
• Eiryo Kawakami; Shinji Nakaoka; Tazro Ohta and Hiroaki Kitano. Weighted enrichment method for prediction of transcription regulators from transcriptome and global chromatin immunoprecipitation data. Nucleic Acids Research. 44, 11, 5010-5021, June 20, 2016, doi: 10.1093/nar/gkw355, published online, Apr. 30, 2016.

2015

• Kitano, H. (2015). Accelerating systems biology research and its real world deployment. Npj Systems Biology and Applications, 1, 15009. http://doi.org/10.1038/npjsba.2015.9
• Amemiya, T., Honma, M., Kariya, Y., Ghosh, S., Kitano, H., Kurachi, Y., et al. (2015). Elucidation of the molecular mechanisms underlying adverse reactions associated with a kinase inhibitor using systems toxicology. Npj Systems Biology and Applications, 1, 15005. http://doi.org/10.1038/npjsba.2015.5
• Matsuoka, Y., Fujita, K., Ghosh, S., & Kitano, H. (2015). Weaving Knowledge into Biological Pathways in a Collaborative Manner. In Computational Systems Toxicology (pp. 181–208). Springer New York. http://doi.org/10.1007/978-1-4939-2778-4_8
• Kamide, T., Okumura, S., Ghosh, S., Shinoda, Y., Mototani, Y., Ohnuki, Y., et al. (2015). Oscillation of cAMP and Ca2+ in cardiac myocytes: a systems biology approach. The Journal of Physiological Sciences, 65(2), 195–200. http://doi.org/10.1007/s12576-014-0354-3
• Shoemaker, J. E., Fukuyama, S., Eisfeld, A. J., Zhao, D., Kawakami, E., Sakabe, S., et al. An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation. PLOS Pathogens, 2015, 11(6), e1004856. doi:10.1371/journal.ppat.1004856
• Nim HT, Furtado MB, Costa MW, Rosenthal NA, Kitano H, Boyd SE, VISIONET: intuitive visualisation of overlapping transcription factor networks, with applications in cardiogenic gene discovery, BMC Bioinformatics 2015, 16 :141
• Book in Japanese 北野宏明, Dr.北野のゼロから始めるシステムバイオロジー, ISBN-10: 4758120544
• Edmunds, P. J., Steneck R., Albright, R., Carpenter, R.C., Chui, A. P. Y., Fan, T.-Y., Harii, S., Kitano, H., Kurihara, H., Legendre, L., Mitarai, S., Muko, S., Nozawa, Y., Padilla-Gamino, J., Price, N. N., Sakai, K., Suzuki, G., van Oppen, M. J. H. Yarid, A. and GatesR. D., Geographic variation in long-term trajectories of change in coral recruitment: a global-to-local perspective. Marine and Freshwater Research (2015). doi:10.1071/MF14139
• Michael Spranger, Sucheendra K. Palaniappan, Samik Ghosh. Extracting Biological Pathway Models From NLP Event Representations  Proceedings of the ACL 2015 Workshop on Biomedical Natural Language Processing (BioNLP’15)
• Asai Y, Abe T, Li L, Oka, H, Nomura T, Kitano H. Databases for multilevel biophysiology research available at Physiome.jp. Frontiers in Physiology. 6:251 (2015) doi:10.3389/fphys.2015.00251, Sep. 9, 2015.
• Tiago J. S. Lopes, Jason E. Shoemaker, Yukiko Matsuoka, Yoshihiro Kawaoka, Hiroaki Kitano. Identifying problematic drugs based on the characteristics of their targets. frontiers in Pharmacology. 6, 186, doi: 10.3389/fphar.2015.00186, Sep. 1, 2015.

2014

• Watanabe, T, Kawakami W, Shoemaker JE, Lopes TJS, Matsuoka Y, Tomita Y, Kozuka-Hata H, Gorai T, Kuwahara T, Takeda E, Nagata A, Takano R, Kiso M, Yamashita M, Sakai-Tagawa Y, Katsura H, Nonaka N, Fujii H, Fujii K, Sugita Y, Noda T, Goto H, Fukuyama S, Watanabe S, Neumann G, Oyama M, Kitano H, Kawaoka Y. (2014) Influenza Virus-Host Interactome Screen as a Platform for Antiviral Drug Development. Cell Host & Microbe. doi:10.1016/j.chom.2014.11.002
• Asai Y, Abe T, Oka H, Okita M, Hagihara K, Ghosh S, Matsuoka Y, Kurachi Y, Nomurak T, Kitano H. (2014) A Versatile Platform for Multilevel Modeling of Physiological Systems: SBML-PHML Hybrid Modeling and Simulation. Advanced Biomedical Engineering, 3(0), pp. 50-8. doi: 10.14326/abe.3.50
• Matsuoka, Y., Funahashi, A., Ghosh, S. & Kitano, H. Modeling and Simulation Using CellDesigner. Methods Mol Biol. (2014) 1164:121-45. doi: 10.1007/978-1-4939-0805-9_11
• Muramoto, Y, Shoemaker JE, Mai LTQ, Itoh Y, Tamura D, Sakai-Tagawa Y, Imai H, Uraki R, Takano R, Kawakami E, Ito M, Okamoto, K, Ishigaki H, Mimuro H, Sasakawa C, Matsuoka Y, Noda T, Fukuyama S, Ogasawara K, Kitano H, Kawaoka Y. Disease severity is associated with differential gene expression at the early and late phases of infection in non-human primates infected with different H5N1 highly pathogenic avian influenza viruses. Journal of Virology (2014). doi:10.1128/JVI.00907-14
• Marti-Solano M, Birney E, Bril A, Della Pasqua O, Kitano H, Mons B, Xenarios I, Sanz F., Integrative knowledge management to enhance pharmaceutical R&D. Nature Reivew Drug Discovery 13, 239 (2014) doi:10.1038/nrd4290

2013

• Kitano H. (2013) The Grand Challenge of Systems Medicine. World Health Summit Yearbook 2013.
• Hsin KY, Ghosh S, Kitano H (2013) Combining machine learning systems and multiple docking simulation packages to improve docking prediction reliability for network pharmacology. PLoS One 8 (12):e83922. doi:10.1371/journal.pone.0083922
• Ghosh S, Matsuoka Y, Asai Y, Hsin KY, Kitano H (2013) Toward an integrated software platform for systems pharmacology. Biopharmaceutics & drug disposition 34 (9):508-526. doi:10.1002/bdd.1875
• Hase T,  Ghosh S,  Yamanaka R,  Kitano H  (2013) Harnessing Diversity towards the Reconstructing of Large Scale Gene Regulatory Networks. PLoS Comput Biol 9(11): e1003361.  
• Matsuoka Y, Matsumae H, Katoh M, Eisfeld AJ, Neumann G, Hase T, Ghosh S, Shoemaker JE, Lopes TJ, Watanabe T, Watanabe S, Fukuyama S, Kitano H, Kawaoka Y. A comprehensive map of the influenza A virus replication cycle. BMC Syst Biol. 2013 Oct 2;7(1):97.
• Yamashita F, Sasa Y, Yoshida S, Hisaka A, Asai Y, Kitano H, Hashida M, Suzuki H., Modeling of Rifampicin-Induced CYP3A4 Activation Dynamics for the Prediction of Clinical Drug-Drug Interactions from In Vitro Data. PLoS One. 2013 Sep 24;8(9):e70330. doi:10.1371/journal.pone.0070330
• Fujita KA, Ostaszewski M, Matsuoka Y, Ghosh S, Glaab E, Trefois C,Crespo I, Peruma TMl, Jurkowski W, Antony PMA, Diederich N, Buttini M, Kodama A, Satagopam VP, Eifes S, del Sol A, Schneider R, Kitano H, Balling R, Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map., Molecular Neurobiology 2013 doi:10.1007/s12035-013-8489-4
• Makanae K, Kintaka R, Makino T, Kitano H, Moriya H., Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method., Genome Res. 2013 Feb;23(2):300-11. doi: 10.1101/gr.146662.112. Epub 2012 Dec 28.
• Adams R, Clark A, Yamaguchi A, Hanlon N, Tsorman N, Ali S, Lebedeva G, Goltsov A, Sorokin A, Akman OE, Troein C, Millar AJ, Goryanin I, Gilmore S., SBSI: An extensible distributed software infrastructure for parameter estimation in systems biology. Bioinformatics, 2013 doi: 10.1093/bioinformatics/btt023
• Schaefer MH, Lopes TJ, Nancy Mah, Shoemaker JE, Matsuoka Y, Fontaine JF, Louis-Jeune C, Eisfeld AJ, Neumann G, Perez-Iratxeta C, Kawaoka Y, Kitano H, Andrade-Navarro M., Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions., PLoS Comput Biol. 01/2013; 9(1):e1002860.
• (Book chapter) Ghosh S, Matsuoka Y, Asa Y, Kitano H, Bhardwaj A, Scaria V, Vashisht R, Shah A, Mondal AK, Vishnoi P, Sonal K, Jain A, Priyadarshini P, Bhattacharyya K, Kumar V, Passi A, Sharma P, Brahmachari S., Software Platform for Metabolic Network Reconstruction of Mycobacterium tuberculosis., Systems Biology of Tuberculosis, 2013, pp 21-35 ed. McFadden J, Beste DJB, Kierzek AM, 01/2013; Springer., ISBN: 978-1-4614-4965-2 (Print) 978-1-4614-4966-9 (Online)

2012

• Shoemaker JE, Lopes TJ, Ghosh S, Matsuoka Y, Kawaoka Y, Kitano H., CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data., BMC Genomics. 2012 Sep 6;13(1):460. [Epub ahead of print] PMID: 22953731
  
• Shoemaker JE, Fukuyama S, Eisfeld AJ, Muramoto Y, Watanabe S, Watanabe T, Matsuoka Y, Kitano H, Kawaoka Y., Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs., BMC Syst Biol. 2012 Aug 31;6(1):117. [Epub ahead of print] PMID: 22937776
• Mizuno S, Iijima R, Ogishima S, Kikuchi M, Matsuoka Y, Ghosh S, Miyamoto T, Miyashita A, Kuwano R, Tanaka H., AlzPathway: a comprehensive map of signaling pathways of Alzheimer's disease. BMC Syst Biol. 2012 May 30;6(1):52.
• van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le Novère N, Schreiber F., Software support for SBGN maps: SBGN-ML and LibSBGN, Bioinformatics (2012)
• Tiger CF, Krause F, Cedersund G, Palmér R, Klipp E, Hohmann S, Kitano H, Krantz M., A framework for mapping, visualisation and automatic model creation of signal-transduction networks, Mol Syst Biol. 2012 Apr 24;8:578. doi: 10.1038/msb.2012.12.
  

2011

• Ghosh S, Matsuoka Y, Asai Y, Hsin KY, Kitano H., Software for systems biology: from tools to integrated platforms. Nature Reviews Genetics (2011) doi: 10.1038/nrg3096
• Mi H, Muruganujan A, Demir E, Matsuoka Y, Funahashi A, Kitano H, Thomas PD, BioPAX Support in CellDesigner. Bioinformatics (2011)
• Kitano H, Ghosh S, Matsuoka Y, Social engineering for virtual big science in systems biology, Nat Chem Biol. (2011) 7, 323-6. doi:10.1038/nchembio.574
• Oyama M, Nagashima T, Suzuki T, Kozuka-Hata H, Yumoto N, Shiraishi Y, Ikeda K, Kuroki Y, Gotoh N, Ishida T, Inoue S, Kitano H, Okada-Hatakeyama M., Integrated quantitative analysis of the phosphoproteome and transcriptome in tamoxifen-resistant breast cancer, Biol. Chem. (2011) 286: 818-829. PMID: 21044952

2010

• Etienne Caron, Samik Ghosh, Yukiko Matsuoka, Dariel Ashton-Beaucage, Marc Therrien, Sébastien Lemieux, Claude Perreault, Philippe P Roux & Hiroaki Kitano, A comprehensive map of the mTOR signaling network, Mol Syst Biol (2010) doi:10.1038/msb.2010.108
• Ghosh, S., Matsuoka, Y., Kitano, H., Connecting the dots: role of standardization and technology sharing in biological simulation, Drug Discov Today (2010) Oct 8. [Epub ahead of print] PMID: 20934535
• Kaizu K., Ghosh, S., Matsuoka, Y., Moriya, H., Shimizu-Yoshida, Y., Kitano, H., A comprehensive molecular interaction map of the budding yeast cell cycle. Mol Syst Biol (2010) vol. 6 (1) pp.
• Shiraishi, T., Matsuyama, S., Kitano, H.. Large-scale analysis of network bistability for human cancers. PLoS Comput Biol (2010) vol. 6 (7) pp. e1000851
• Kitano, H. Violations of robustness trade-offs, Mol Syst Biol (2010) vol. 6: 384
• Kitano, H. Grand challenges in systems physiology. Frontiers in Physiology, published: 07 May 2010
  [doi: 10.3389/fphys.2010.00003]
• Kaizu K, Moriya H, Kitano H, Fragilities Caused by Dosage Imbalance in Regulation of the Budding Yeast Cell Cycle. PLoS Genet 2010, 6(4): e1000919. [doi:10.1371/journal.pgen.1000919]
• Matsuoka, Y., Ghosh, S., Kikuchi, N., Kitano, H., Payao: A Community Platform for SBML Pathway Model Curation. Bioinformatics, 2010 [doi:10.1093/bioinformatics/btq143]
• Gehlenborg N, O'Donoghue S, Baliga N, Goesmann A, Hibbs M, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D & Gavin A, Visualization of omics data for systems biology. Nat Meth (2010) vol. 7 pp. S56 [doi:10.1038/nmeth.1436]

2009

• Hase T, Tanaka H, Suzuki Y, Nakagawa S, Kitano H, 2009 Structure of Protein Interaction Networks and Their Implications on Drug Design. PLoS Comput Biol 5(10): e1000550. [doi:10.1371/journal.pcbi.1000550]
• Nicolas Le Novère, Michael Hucka, Huaiyu Mi, Stuart Moodie, Falk Schreiber, Anatoly Sorokin, Emek Demir, Katja Wegner, Mirit I Aladjem, Sarala M Wimalaratne, Frank T Bergman, Ralph Gauges, Peter Ghazal, Hideya Kawaji, Lu Li, Yukiko Matsuoka, Alice Villéger, Sarah E Boyd, Laurence Calzone, Melanie Courtot, Ugur Dogrusoz, Tom C Freeman, Akira Funahashi, Samik Ghosh, Akiya Jouraku, Sohyoung Kim, Fedor Kolpakov, Augustin Luna, Sven Sahle, Esther Schmidt, Steven Watterson, Guanming Wu, Igor Goryanin, Douglas B Kell, Chris Sander, Herbert Sauro, Jacky L Snoep, Kurt Kohn & Hiroaki Kitano, The Systems Biology Graphical Notation, Nature Biotechnol. 2009 Aug;27(7) 735 - 741 [doi:10.1038/nbt1558]
• Krantz M, Ahmadpour D, Ottosson LG, Warringer J, Waltermann C, Nordlander B, Klipp E, Blomberg A, Hohmann S, Kitano H., Robustness and fragility in the yeast high osmolarity glycerol (HOG) signal-transduction pathway. Mol Syst Biol. 2009;5:281. Epub 2009 Jun 16 [doi:10.1038/msb.2009.36]
• Matsuoka Y.; Ghosh S.; Kitano H. ; Consistent design schematics for biological systems: standardization of representation in biological engineering. J. R. Soc. Interface. 2009 [doi:10.1098/rsif.2009.0046.focus]
• Book chapter in Japanese: Sakurada, K., Polouliakh, N., Kitano, H., 第一編 "細胞分化の多能性•全能性とレプログラミング" in 幹細胞の分化誘導と応用, NTS, 2009. ISBN978-4-86043-160-0
• Polouliakh N, Nock R, Nielsen F, Kitano H 2009 G-Protein Coupled Receptor Signaling Architecture of Mammalian Immune Cells. PLoS ONE 4(1): e4189 doi:10.1371/journal.pone.0004189

2008

• Funahashi, A.; Matsuoka, Y.; Jouraku, A.; Morohashi, M.; Kikuchi, N.; Kitano, H.; ."CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks", Proceedings of the IEEE Volume 96, Issue 8, Aug. 2008 Page(s):1254 - 1265 [doi 10.1109/JPROC.2008.925458] Abstract  | Full Text: PDF (1379 KB)

*Please also check publication list (symbio.jst.go.jp) for extensive list of the publications up to 2007.

2007

• Book in Japanese 北野宏明・竹内薫, したたかな生命, ダイヤモンド社, ISBN-13: 978-4478810033
• Hiroaki Kitano, Towards a theory of biological robustness
  Molecular Systems Biology 3 Article number: 137 doi:10.1038/msb4100179
  Published online: 18 September 2007, Citation: Molecular Systems Biology 3:137
• Funahashi, A, Jouraku, A, Matsuoka, Y, Kitano, H., Integration of CellDesigner and SABIO-RK, In Silico Biology 7 S1, 10 (2007)
• Kitano, H, A robustness-based approach to systems-oriented drug design, Nature Reviews Drug Discovery 6 , 202-210 (March 2007) | doi :10.1038/nrd2195
• Murray, DB, Beckmann, M, Kitano, H., Regulation of yeast oscillatory dynamics, PNAS published February 6, 2007, 10.1073/pnas.0606677104 ( Cell Biology )

2006

• Onami S, Kitano H, "Genome-wide prediction of genetic interactions in a metazoan", BioEssays 28:1087-1090; 2006
• Moriya H, Shimizu-Yoshida Y, Kitano H (2006); In vivo Robustness Analysis of Cell Division Cycle Genes in S. cerevisiae PLoS Genet. DOI: 10.1371/journal.pgen.0020111. (2006/6/15)
• Kitano,H.; Oda, K.; Self-Extending Symbiosis: A Mechanism for Increasing Robustness Through Evolution, Biological Theory Winter 2006, Vol. 1, No. 1: 61-66. (2006/05/22)
• Oda, K., Kitano, H.;"A comprehensive map of the toll-like receptor signaling network", Mol Syst Biol : msb4100057. Apr. 18, 2006 (2006/04/18)
  
• Hiroi, N.; Funahashi, A.; Kitano, H.;" Comparative studies of suppression of malignant cancer cell phenotype by antisense oligo DNA and small interfering RNA ", Cancer Gene Therapy August 2005
• Kitano, H.and Oda, K.;"Robustness trade-offs and host–microbial symbiosis in the immune system", Mol Syst Biol 2(1): msb4100039-E1. Jan. 17, 2006

2005

• Hiroi, N.; Funahashi, A.; Kitano, H.; Comparative studies of suppression of malignant cancer cell phenotype by antisense oligo DNA and small interfering RNA Cancer Gene Therapy advance online publication 05 August 2005
• Kitano, H.; Funahashi, A.; Matsuoka, Y.; Oda, K.; Using process diagrams for the graphical representation of biological networks Nature Biotechnology 23(8), 961 - 966 (2005)
• Oda, K.; Matsuoka, Y.; Funahashi, A.; Kitano, H.; A comprehensive pathway map of epidermal growth factor receptor signaling, Molecular Systems Biology
  *Download the structured data (supplementary SBML file) to view the PubMed reference using the new function of CellDesigner 2.2 - Database connection.
• Huaiyu Mi, Betty Lazareva-Ulitsky, Rozina Loo, Anish Kejariwal, Jody Vandergriff, Steven Rabkin, Nan Guo, Anushya Muruganujan, Olivier Doremieux, Michael J. Campbell, Hiroaki Kitano and Paul D. Thomas. 2005.
  The PANTHER database of protein families, subfamilies, functions and pathways.
  Nucl. Acids. Res., 31:334-341.

2004

• Kitano, H., Oda, K., Kimura, T., Matsuoka, Y., Csete, M., Doyle, J., Muramatsu, M.. Metabolic Syndrome and Robustness Tradeoffs, Diabetes 53, S6-S15, 2004 PFD file
• Kitano, H.. Biological Robustness. Nature Review Genetics. 5, 826-837, 2004 PDF file
• Oda, K.; Kimura, T, Matsuoka, Y.; Funahashi, A.; Muramatsu, M.; Kitano, H. Molecular Interaction Map of Macrophage. AfCS Report. 2004. PDF file
• M. Hucka; A. Finney; B.J. Bornstein; S.M. Keating; B.E. Shapiro; J. Matthews; B.L. Kovitz; M.J. Schilstra; A. Funahashi; J.C. Doyle; and H. Kitano Evolving a lingua franca and associated software infrastructure for computational systems biology: theSystemsBiologyMarkupLanguage(SBML) project. IEE Systems Biology. 1:41-53, 2004
• Kitano, H. Cancer as a robust system: implications for anticancer therapy. Nature Reviews Cancer 4:227-235, 2004. Abstract..

2003

• Kitano, H. Cancer as a robust system: implications for anticancer therapy. Nature Reviews Cancer 4:227-235, 2004. Abstract..
• Hucka, M.; Finney, A.; Sauro, H.M.; Bolouri, H.; Doyle, J.C.; Kitano, H. et al. The Systems Biology Markup Language(SBML): A Medium for Representation and Exchange of Biochemical Network Models. Bioinformatics. 19. 524-531. 2003.