Publications

• González-Pech RA, Li VY, Garcia V, Boville E, Mammone M, Kitano H, Ritchie KB, Medina M. The Evolution, Assembly, and Dynamics of Marine Holobionts. Ann Rev Mar Sci. 2023 Aug 8. doi: 10.1146/annurev-marine-022123-104345. Epub ahead of print. PMID: 37552896.

• Sano, H., Kratz, A., Nishino, T. et al. Nicotinamide mononucleotide (NMN) alleviates the poly(I:C)-induced inflammatory response in human primary cell cultures. Sci Rep 13, 11765 (2023). https://doi.org/10.1038/s41598-023-38762-x

• Karkera, N., Acharya, S. & Palaniappan, S.K. Leveraging pre-trained language models for mining microbiome-disease relationships. BMC Bioinformatics 24, 290 (2023). https://doi.org/10.1186/s12859-023-05411-z

• 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

• 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.

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• 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

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• 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

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