Publications

• Nikitha Karkera, Nikshita Karkera, Mahanash Kumar, Vishnuvardhan P. Srinivasulu, Samik Ghosh, Sucheendra K. Palaniappan, Large Language Models for Pathway Curation: A Preliminary Investigation, Reference Module in Life Sciences, Elsevier, 2024, https://doi.org/10.1016/B978-0-323-95502-7.00254-2.

• Arata Shirakami, Takeshi Hase, Yuki Yamaguchi, Masanori Shimono; Neural network embedding of functional microconnectome. Network Neuroscience 2024; doi: https://doi.org/10.1162/netn_a_00424

• Anton Kratz, Ayako Yachie, Network Visualization in Systems Biology, Reference Module in Life Sciences, Elsevier, 2024, https://doi.org/10.1016/B978-0-323-95502-7.00051-8

• Akujuobi, U., Kumari, P., Choi, J., Badreddine S., Maruyama K., Palaniappan, SK., Besold, TR. Link prediction for hypothesis generation: an active curriculum learning infused temporal graph-based approach. Artif Intell Rev 57, 244 (2024). https://doi.org/10.1007/s10462-024-10885-1

• Akiyoshi R, Hase T, Sathiyananthavel M, Ghosh S, Kitano H, Yachie A. Noninvasive, label-free image approaches to predict multimodal molecular markers in pluripotency assessment. Sci Rep. 2024 Jul 9;14(1):15760. doi: 10.1038/s41598-024-66591-z. PMID: 38977828.

• Jiang S, Evans-Yamamoto D, Bersenev D, Palaniappan SK, Yachie-Kinoshita A. ProtoCode: Leveraging large language models (LLMs) for automated generation of machine-readable PCR protocols from scientific publications. SLAS Technol. 2024 Apr 24;29(3):100134. doi: 10.1016/j.slast.2024.100134. Epub ahead of print. PMID: 38670311.

• Han X, Bai Z, Mogushi K, Hase T, Takeuchi K, Iida Y, Sumita YI, Wakabayashi N. Machine Learning Prediction of Tongue Pressure in Elderly Patients with Head and Neck Tumor: A Cross-Sectional Study. J Clin Med. 2024 Apr 18;13(8):2363. doi: 10.3390/jcm13082363. PMID: 38673635; PMCID: PMC11051183.

• Nikitha Karkera, Samik Ghosh, Germaine Escames, Sucheendra K. Palaniappan. MelAnalyze: Fact-Checking Melatonin claims using Large Language Models and Natural Language Inference. bioRxiv 2024.03.21.586201; doi: https://doi.org/10.1101/2024.03.21.586201

• Hase T, Ghosh S, Aisaki KI, Kitajima S, Kanno J, Kitano H, Yachie A. DTox: A deep neural network-based in visio lens for large scale toxicogenomics data. J Toxicol Sci. 2024;49(3):105-115. doi: 10.2131/jts.49.105. PMID: 38432953.

• Zolfo M, Silverj A, Blanco-Míguez A, Manghi P, Rota-Stabelli O, Heidrich V, Jensen J, Maharjan S, Franzosa E, Menni C, Visconti A, Pinto F, Ciciani M, Huttenhower C, Cereseto A, Asnicar F, Kitano H, Yamada T, Segata N. Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples. bioRxiv [Preprint]. 2024 Feb 19:2024.02.19.580813. doi: 10.1101/2024.02.19.580813. PMID: 38464031; PMCID: PMC10925137.

• Niarakis A, Ostaszewski M, Mazein A, Kuperstein I, Kutmon M, Gillespie ME, Funahashi A, Acencio ML, Hemedan A, Aichem M, Klein K, Czauderna T, Burtscher F, Yamada TG, Hiki Y, Hiroi NF, Hu F, Pham N, Ehrhart F, Willighagen EL, Valdeolivas A, Dugourd A, Messina F, Esteban-Medina M, Peña-Chilet M, Rian K, Soliman S, Aghamiri SS, Puniya BL, Naldi A, Helikar T, Singh V, Fernández MF, Bermudez V, Tsirvouli E, Montagud A, Noël V, Ponce-de-Leon M, Maier D, Bauch A, Gyori BM, Bachman JA, Luna A, Piñero J, Furlong LI, Balaur I, Rougny A, Jarosz Y, Overall RW, Phair R, Perfetto L, Matthews L, Rex DAB, Orlic-Milacic M, Gomez LCM, De Meulder B, Ravel JM, Jassal B, Satagopam V, Wu G, Golebiewski M, Gawron P, Calzone L, Beckmann JS, Evelo CT, D'Eustachio P, Schreiber F, Saez-Rodriguez J, Dopazo J, Kuiper M, Valencia A, Wolkenhauer O, Kitano H, Barillot E, Auffray C, Balling R, Schneider R; COVID-19 Disease Map Community. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Front Immunol. 2024 Feb 13;14:1282859. doi: 10.3389/fimmu.2023.1282859. PMID: 38414974; PMCID: PMC10897000.

• 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. 2024 Jan 17;16:443-466. doi: 10.1146/annurev-marine-022123-104345. Epub 2023 Aug 8. PMID: 37552896.

• Hird N, Osaki T, Ghosh S, Palaniappan SK, Maeda K. Enabling Personalization for Digital Cognitive Stimulation to Support Communication With People With Dementia: Pilot Intervention Study as a Prelude to AI Development. JMIR Form Res. 2024 Jan 16;8:e51732. doi: 10.2196/51732. PMID: 38227357.

• Sathwik Acharya, Nicolas K. Shinada, Naoki Koyama, Megumi Ikemori, Tomoki Nishioka, Seiji Hitaoka, Atsushi Hakura, Shoji Asakura, Yukiko Matsuoka, and Sucheendra K. Palaniappan, Asking the right questions for mutagenicity prediction from BioMedical text. npj Syst Biol Appl 9, 63 (2023). https://doi.org/10.1038/s41540-023-00324-2 

• Maruoka H, Hattori T, Hase T, Takahashi K, Ohara M, Orimo S, Yokota T. Aberrant morphometric networks in Alzheimer's disease have hemispheric asymmetry and age dependence. Eur J Neurosci. 2023 Dec 17. doi: 10.1111/ejn.16225. Epub ahead of print. PMID: 38105486.

• Yachie Ayako, Yumiko Imai, Taiko Nishino, Sucheendra Kumar Palaniappan. COVID-19 severity prediction orchestrated in medical MLOps. The 97th Annual Meeting of the Japanese Pharmacological Society. https://doi.org/10.1254/jpssuppl.97.0_2-B-S31-1

• S Jiang, D Evans-Yamamoto, D Bersenev, SK Palaniappan, A Yachie-Kinoshita, ProtoCode: Leveraging Large Language Models for Automated Generation of Machine-Readable Protocols from Scientific Publications. arXiv preprint arXiv:2312.06241, 2023.

• 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, Imamura H, Yoshida Y, Shimizu N, Kitano H, Yachie A. 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

• Mori T, Takase T, Lan KC, Yamane J, Alev C, Kimura A, Osafune K, Yamashita JK, Akutsu T, Kitano H, Fujibuchi W. eSPRESSO: topological clustering of single-cell transcriptomics data to reveal informative genes for spatio-temporal architectures of cells. BMC Bioinformatics. 2023 Jun 15;24(1):252. doi: 10.1186/s12859-023-05355-4. PMID: 37322439; PMCID: PMC10268514.

• 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.

• Katsuda T, Sato N, Mogushi K, Hase T, Muramatsu M. Sub-GOFA: A tool for Sub-Gene Ontology function analysis in clonal mosaicism using semantic (logical) similarity. Bioinformation. 2022 Jan 31;18(1):53-60. doi: 10.6026/97320630018053. PMID: 35815201; PMCID: PMC9200605.

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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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