Publication

387. Watanabe D, Okamoto N, Kobayashi Y, Suzuki H, Kato M, Saitoh S, Kanemura Y, Takenouchi T, Yamada M, Nakato D, Sato M, Tsunoda T, Kosaki K, Miya F. Biallelic structural variants in three patients with ERCC8-related Cockayne syndrome and a potential pitfall of copy number variation analysis. Scientific Reports, 14, 19741 (2024).

386. Nakamura Y, Shimada IS, Maroofian R, Falabella M, Zaki MS, Fujimoto M, Sato E, Takase H, Aoki S, Miyauchi A, Koshimizu E, Miyatake S, Arioka Y, Honda M, Higashi T, Miya F, Okubo Y, Ogawa I, Scardamaglia A, Miryounesi M, Alijanpour S, Ahmadabadi F, Herkenrath P, Dafsari HS, Velmans C, Al Balwi M, Vitobello A, Denommé-Pichon AS, Jeanne M, Civit A, Abdel-Hamid MS, Naderi H, Darvish H, Bakhtiari S, Kruer MC, Carroll CJ, Ghayoor Karimiani E, Khailany RA, Abdulqadir TA, Ozaslan M, Bauer P, Zifarelli G, Seifi T, Zamani M, Al Alam C, Alvi JR, Sultan T, Efthymiou S, Pope SAS, Haginoya K, Matsunaga T, Osaka H, Matsumoto N, Ozaki N, Ohkawa Y, Oki S, Tsunoda T, Pitceathly RDS, Taketomi Y, Houlden H, Murakami M, Kato Y, Saitoh S. Biallelic null variants in PNPLA8 cause microcephaly by reducing the number of basal radial glia. Brain, published online 31 July (2024). doi: 10.1093/brain/awae185

385. Sharma A, Lopez Y, Jia S, Lysenko A, Boroevich KA, Tsunoda T. Enhanced analysis of tabular data through Multi-representation DeepInsight. Scientific Reports, 14, 12851 (2024).

384. (Review article) Sharma A, Lysenko A, Jia S, Boroevich KA, Tsunoda T. Advances in AI and machine learning for predictive medicine. Journal of Human Genetics, published online 29 February (2024). doi: 10.1038/s10038-024-01231-y.

383. Chandra A, Sharma A, Dehzangi I, Tsunoda T, Sattar A. PepCNN deep learning tool for predicting peptide binding residues in proteins using sequence, structural, and language model features. Scientific Reports, 13, 20882 (2023).

382. Tanaka Y, Yamagishi M, Motomura Y, Kamatani T, Oguchi Y, Suzuki N, Kiniwa T, Kabata H, Irie M, Tsunoda T, Miya F, Goda K, Ohara O, Funatsu T, Fukunaga K, Moro K, Uemura S, Shirasaki Y. Time-dependent cell-state selection identifies transiently expressed genes regulating ILC2 activation. Communications Biology, 6, 915 (2023).

381. Jia S, Lysenko A, Boroevich KA, Sharma A, Tsunoda T. scDeepInsight: a supervised cell-type identification method for scRNA-seq data with deep learning. Briefings in Bioinformatics, bbad266 (2023).

380. Hamba Y, Kamatani T, Miya F, Boroevich KA, Tsunoda T. Topologically associating domain underlies tissue specific expression of long intergenic noncoding RNAs. iScience, 26, 106640 (2023).

379. Del Conte A, Bouhraoua A, Mehdiabadi M, Clementel D, Monzon AM; CAID predictors (Alex S Holehouse, Daniel Griffith, Ryan J Emenecker, Ashwini Patil, Ronesh Sharma, Tatsuhiko Tsunoda, Alok Sharma, Yi Jun Tang, Bin Liu, Claudio Mirabello, Björn Wallner, Burkhard Rost, Dagmar Ilzhöfer, Maria Littmann, Michael Heinzinger, Lea I M Krautheimer, Michael Bernhofer, Liam J McGuffin, Isabelle Callebaut, Tristan Bitard Feildel, Jian Liu, Jianlin Cheng, Zhiye Guo, Jinbo Xu, Sheng Wang, Nawar Malhis, Jörg Gsponer, Chol-Song Kim, Kun-Sop Han, Myong-Chol Ma, Lukasz Kurgan, Sina Ghadermarzi, Akila Katuwawala, Bi Zhao, Zhenling Peng, Zhonghua Wu, Gang Hu, Kui Wang, Md Tamjidul Hoque, Md Wasi Ul Kabir, Michele Vendruscolo, Pietro Sormanni, Min Li, Fuhao Zhang, Pengzhen Jia, Yida Wang, Michail Yu Lobanov, Oxana V Galzitskaya, Wim Vranken, Adrián Díaz, Thomas Litfin, Yaoqi Zhou, Jack Hanson, Kuldip Paliwal, Zsuzsanna Dosztányi, Gábor Erdős); Tosatto SCE, Piovesan D. CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. Nucleic Acids Research, 51, W62-W69 (2023).

378. Ikeda N, Kubota H, Suzuki R, Morita M, Yoshimura A, Osada Y, Kishida K, Kitamura D, Iwata A, Yotsumoto S, Kurotaki D, Nishimura K, Nishiyama A, Tamura T, Kamatani T, Tsunoda T, Murakawa M, Asahina Y, Hayashi Y, Harada H, Harada Y, Yokota A, Hirai H, Seki T, Kuwahara M, Yamashita M, Shichino S, Tanaka M, Asano K. The early neutrophil-committed progenitors aberrantly differentiate into immunoregulatory monocytes during emergency myelopoiesis. Cell Reports, 42, 112165 (2023).

377. Sharma A, Lysenko A, Boroevich KA, Tsunoda T. DeepInsight-3D architecture for anti-cancer drug response prediction with deep-learning on multi-omics. Scientific Reports, 13, 2483 (2023).

376. Manavi F, Sharma A, Sharma R, Tsunoda T, Shatabda S, Dehzangi I. CNN-Pred: Prediction of single-stranded and doubled-stranded DNA-binding protein using convolution neural networks. Gene, 853, 147045 (2022).

375. Nagata Y, Watanabe R, Eichhorn C, Ohno S, Aiba T, Ishikawa T, Nakano Y, Aizawa Y, Hayashi K, Murakoshi N, Nakajima T, Yagihara N, Mishima H, Sudo T, Higuchi C, Takahashi A, Sekine A, Makiyama T, Tanaka Y, Watanabe A, Tachibana M, Morita H, Yoshiura KI, Tsunoda T, Watanabe H, Kurabayashi M, Nogami A, Kihara Y, Horie M, Shimizu W, Makita N, Tanaka T. Targeted deep sequencing analyses of long QT syndrome in a Japanese population. PLoS One, 17, e0277242 (2022).

374. Yamaguchi K, Ishigaki K, Suzuki A, Tsuchida Y, Tsuchiya H, Sumitomo S, Nagafuchi Y, Miya F, Tsunoda T, Shoda H, Fujio K, Yamamoto K, Kochi Y. Splicing QTL analysis focusing on coding sequences reveals mechanisms for disease susceptibility loci. Nature Communications, 13, 4659 (2022).

373. Kato D, Mitsuhashi S, Miya F, Saitoh S, Okamoto N, Tsunoda T, Kochi Y. Utility of tissue-specific gene expression scores for gene prioritization in Mendelian diseases. Journal of Human Genetics, 2022 Aug 9. doi: 10.1038/s10038-022-01071-8. Online ahead of print.

372. Teshima T, Kobayashi Y, Kawai T, Kushihara Y, Nagaoka K, Miyakawa J, Akiyama Y, Yamada Y, Sato Y, Yamada D, Tanaka N, Tsunoda T, Kume H, Kakimi K. Principal component analysis of early immune cell dynamics during pembrolizumab treatment of advanced urothelial carcinoma. Oncology Letters, 24, 265 (2022).

371. Umehara T, Arita H, Miya F, Achiha T, Shofuda T, Yoshioka E, Kanematsu D, Nakagawa T, Kinoshita M, Kagawa N, Fujimoto Y, Hashimoto N, Kiyokawa H, Morii E, Tsunoda T, Kanemura Y, Kishima H. Revisiting the definition of glioma recurrence based on a phylogenetic investigation of primary and re-emerging tumor samples: a case report. Brain Tumor Pathology, 2022 Jun 6. doi: 10.1007/s10014-022-00438-1. Online ahead of print.

370. Matsuo H, Kamatani T, Hamba Y, Boroevich KA, Tsunoda T. Association between high immune activity and worse prognosis in uveal melanoma and low-grade glioma in TCGA transcriptomic data. BMC Genomics, 23, 351 (2022).

369. Masuda T, Tanaka N, Takamatsu K, Hakozaki K, Takahashi R, Anno T, Kufukihara R, Shojo K, Mikami S, Shinojima T, Kakimi K, Tsunoda T, Aimono E, Nishihara H, Mizuno R, Oya M. Unique characteristics of tertiary lymphoid structures in kidney clear cell carcinoma: prognostic outcome and comparison with bladder cancer. Journal for immunotherapy of cancer, 10, e003883 (2022).

368. Sugawara T, Miya F, Ishikawa T, Lysenko A, Nishino J, Kamatani T, Takemoto A, Boroevich KA, Kakimi K, Kinugasa Y, Tanabe M, Tsunoda T. Immune subtypes and neoantigen-related immune evasion in advanced colorectal cancer. iScience, 25, 103740 (2022).

367. Isobe K, Ieda D, Miya F, Miyachi R, Otsuji S, Asai M, Tsunoda T, Kosaki K, Hattori A, Saitoh S, Mizuno M. Hemorrhagic shock and encephalopathy syndrome in a patient with a de novo heterozygous variant in KIF1A. Brain Development, 2021 Dec 13; S0387-7604(21)00212-6. Online ahead of print.

366. Hakozaki K, Tanaka N, Takamatsu K, Takahashi R, Yasumizu Y, Mikami S, Shinojima T, Kakimi K, Kamatani T, Miya F, Tsunoda T, Aimono E, Nishihara H, Mizuno R, Oya M. Landscape of prognostic signatures and immunogenomics of the AXL/GAS6 axis in renal cell carcinoma. British Journal of Cancer, 125, 1533-1543 (2021).

365. Okamoto N, Miya F, Tsunoda T, Kanemura Y, Saitoh S, Kato M, Yanagi K, Kaname T, Kosaki K. Four pedigrees with aminoacyl-tRNA synthetase abnormalities. Neurological Sciences, 2021 Sep 28. Online ahead of print.

364. Takamatsu K, Tanaka N, Hakozaki K, Takahashi R, Teranishi Y, Murakami T, Kufukihara R, Niwa N, Mikami S, Shinojima T, Sasaki T, Sato Y, Kume H, Ogawa S, Kakimi K, Kamatani T, Miya F, Tsunoda T, Aimono E, Nishihara H, Sawada K, Imamura T, Mizuno R, Oya M. Profiling the inhibitory receptors LAG-3, TIM-3, and TIGIT in renal cell carcinoma reveals malignancy. Nature Communications, 12, 5547 (2021).

363. Sharma A, Lysenko A, Boroevich KA, Vans E, Tsunoda T. DeepFeature: feature selection in nonimage data using convolutional neural network. Briefings in Bioinformatics. 2021 Aug 6:bbab297. doi: 10.1093/bib/bbab297. Online ahead of print.

362. Murakami T, Tanaka N, Takamatsu K, Hakozaki K, Fukumoto K, Masuda T, Mikami S, Shinojima T, Kakimi K, Tsunoda T, Sawada K, Imamura T, Mizuno R, Oya M. Multiplexed single-cell pathology reveals the association of CD8 T-cell heterogeneity with prognostic outcomes in renal cell carcinoma. Cancer Immunology, Immunotherapy. 2021 Jul 14. doi: 10.1007/s00262-021-03006-2. Online ahead of print.

361. Hosoe J, Suzuki K, Miya F, Kato T, Tsunoda T, Okada Y, Horikoshi M, Shojima N, Yamauchi T, Kadowaki T. Human Genome Variation, 8, 25 (2021).

360. Kumar S, Sharma R, Tsunoda T, Kumarevel T, Sharma A. Forecasting the spread of COVID-19 using LSTM network. BMC Bioinformatics, 22(Suppl 6), 316 (2021).

359. Kumar S, Tsunoda T#, Sharma A# (#: co-last). SPECTRA: a tool for enhanced brain wave signal recognition. BMC Bioinformatics, 22(Suppl 6), 195 (2021).

358. Hosoe J, Kawashima Sonoyama Y, Miya F, Kadowaki H, Suzuki K, Kato T, Matsuzawa F, Aikawa SI, Okada Y, Tsunoda T, Hanaki K, Kanzaki S, Shojima N, Yamauchi T, Kadowaki T. Genotype-Structure-Phenotype Correlations in Disease-Associated IGF1R Variants and Similarities to Those in INSR Variants. Diabetes, 2021 Jun 1;db201145. doi: 10.2337/db20-1145. Online ahead of print.

357. Miyatake S, Kato M, Kumamoto T, Hirose T, Koshimizu E, Matsui T, Takeuchi H, Doi H, Hamada K, Nakashima M, Sasaki K, Yamashita A, Takata A, Hamanaka K, Satoh M, Miyama T, Sonoda Y, Sasazuki M, Torisu H, Hara T, Sakai Y, Noguchi Y, Miura M, Nishimura Y, Nakamura K, Asai H, Hinokuma N, Miya F, Tsunoda T, Togawa M, Ikeda Y, Kimura N, Amemiya K, Horino A, Fukuoka M, Ikeda H, Merhav G, Ekhilevitch N, Miura M, Mizuguchi T, Miyake N, Suzuki A, Ohga S, Saitsu H, Takahashi H, Tanaka F, Ogata K, Ohtaka-Maruyama C, Matsumoto N. De novo ATP1A3 variants cause polymicrogyria. Science Advances, 7, eabd2368 (2021).

356. Okamoto N, Miya F, Kitai Y, Tsunoda T, Kato M, Saitoh S, Kanemura Y, Kosaki K. Homozygous ADCY5 mutation causes early-onset movement disorder with severe intellectual disability. Neurological Sciences, 2021 Mar 11. doi: 10.1007/s10072-021-05152-y. Online ahead of print.

355. DU R, Xie S, Fang Y, Igarashi-Yokoi T, Moriyama M, Ogata S, Tsunoda T, Kamatani T, Yamamoto S, Cheng CY, Saw SM, Ting D, Wong TY, Ohno-Matsui K. Deep Learning Approach for Automated Detection of Myopic Maculopathy and Pathologic Myopia in Fundus Images. Ophthalmology Retina, 2021 Feb 18:S2468-6530(21)00056-7. doi: 10.1016/j.oret.2021.02.006. Online ahead of print.

354. Nishiguchi KM, Miya F, Mori Y, Fujita K, Akiyama M, Kamatani T, Koyanagi Y, Sato K, Takigawa T, Ueno S, Tsugita M, Kunikata H, Cisarova K, Nishino J, Murakami A, Abe T, Momozawa Y, Terasaki H, Wada Y, Sonoda KH, Rivolta C, Tsunoda T, Tsujikawa M, Ikeda Y, Nakazawa T. A hypomorphic variant in EYS detected by genome-wide association study contributes toward retinitis pigmentosa. Communications Biology, 4, 140 (2021).

353. Takaoka A, Ishikawa T, Okazaki S, Watanabe S, Miya F, Tsunoda T, Kikuchi A, Yamauchi S, Matsuyama T, Tokunaga M, Uetake H, Kinugasa Y. ELF3 Overexpression as Prognostic Biomarker for Recurrence of Stage II Colorectal Cancer. In Vivo, 35, 191-201 (2021).

352. Chandra AA, Sharma A, Dehzangi A, Tsunoda T. RAM-PGK: Prediction of Lysine Phosphoglycerylation Based on Residue Adjacency Matrix. Genes, 11, 1524 (2020).

351. Singh V, Sharma A, Dehzangi A, Tsunoda T. PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids. Genes, 11, E1431 (2020).

350. Shigemizu D, Akiyama S, Higaki S, Sugimoto T, Sakurai T, Boroevich KA, Sharma A, Tsunoda T, Ochiya T, Niida S, Ozaki K. Prognosis prediction model for conversion from mild cognitive impairment to Alzheimer's disease created by integrative analysis of multi-omics data. Alzheimer's Research & Therapy, 12, 145 (2020).

349. Johnson TA, Mashimo Y, Wu JY, Yoon D, Hata A, Kubo M, Takahashi A, Tsunoda T, Ozaki K, Tanaka T, Ito K, Suzuki H, Hamada H, Kobayashi T, Hara T, Chen CH, Lee YC, Liu YM, Chang LC, Chang CP, Hong YM, Jang GY, Yun SW, Yu JJ, Lee KY, Kim JJ, Park T; Korean Kawasaki Disease Genetics Consortium, Taiwan Kawasaki Disease Genetics Consortium, Taiwan Pediatric ID Alliance, Japan Kawasaki Disease Genome Consortium, Lee JK, Chen YT, Onouchi Y. Association of an IGHV3-66 gene variant with Kawasaki disease. Journal of Human Genetics. 2020 Oct 26. doi: 10.1038/s10038-020-00864-z. Online ahead of print.

348. Sato Y, Wada I, Odaira K, Hosoi A, Kobayashi Y, Nagaoka K, Karasaki T, Matsushita H, Yagi K, Yamashita H, Fujita M, Watanabe S, Kamatani T, Miya F, Mineno J, Nakagawa H, Tsunoda T, Takahashi S, Seto Y, Kakimi K. Integrative immunogenomic analysis of gastric cancer dictates novel immunological classification and the functional status of tumor-infiltrating cells. Clinical & Translational Immunology, 9, e1194 (2020).

347. Hosoe J, Miya F, Kadowaki H, Fujiwara T, Suzuki K, Kato T, Waki H, Sasako T, Aizu K, Yamamura N, Sasaki F, Kurano M, Hara K, Tanaka M, Ishiura H, Tsuji S, Honda K, Yoshimura J, Morishita S, Matsuzawa F, Aikawa SI, Boroevich KA, Nangaku M, Okada Y, Tsunoda T, Shojima N, Yamauchi T, Kadowaki T. Clinical usefulness of multigene screening with phenotype-driven bioinformatics analysis for the diagnosis of patients with monogenic diabetes or severe insulin resistance. Diabetes Research and Clinical Practice, 169, 108461 (2020).

346. Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Kelso S; MC3 Working Group; PCAWG novel somatic mutation calling methods working group, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L; PCAWG Consortium (including Tsunoda T). Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications, 11, 4748 (2020).

345. Sharma R, Kumar S, Tsunoda T, Kumarevel T, Sharma A. Single-stranded and double-stranded DNA-binding protein prediction using HMM profiles. Analytical Biochemistry, 612, 113954 (2020).

344. Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N; PCAWG Tumour Subtypes and Clinical Translation, Boutros PC; PCAWG Consortium (including Tsunoda T). Sex differences in oncogenic mutational processes. Nature Communications, 11, 4330 (2020).

343. Wardah W, Dehzangi A, Taherzadeh G, Rashid MA, Khan MGM, Tsunoda T, Sharma A. Predicting protein-peptide binding sites with a Deep Convolutional Neural Network. Journal of Theoretical Biology, 496, 110278 (2020).

342. Mutai H, Wasano K, Momozawa Y, Kamatani Y, Miya F, Masuda S, Morimoto N, Nara K, Takahashi S, Tsunoda T, Homma K, Kubo M, Matsunaga T. Variants encoding a restricted carboxy-terminal domain of SLC12A2 cause hereditary hearing loss in humans. PLoS Genetics, 16, e1008643 (2020).

341. Onodera K, Shimojo D, Ishihara Y, Yano M, Miya F, Banno H, Kuzumaki N, Ito T, Okada R, de Araújo Herculano B, Ohyama M, Yoshida M, Tsunoda T, Katsuno M, Doyu M, Sobue G, Okano H, Okada Y. Unveiling synapse pathology in spinal bulbar muscular atrophy by genome-wide transcriptome analysis of purified motor neurons derived from disease specific iPSCs. Molecular Brain, 13, 18 (2020).

340. Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N; PCAWG Drivers and Functional Interpretation Working Group; PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G; PCAWG Consortium. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature, 578, 102-111 (2020).

339. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (including Tsunoda T). Pan-cancer analysis of whole genomes. Nature, 578, 82-93 (2020).

338. Carlevaro-Fita J, Lanzós A, Feuerbach L, Hong C, Mas-Ponte D, Pedersen JS; PCAWG Drivers and Functional Interpretation Group (including Tsunoda T), Johnson R; PCAWG Consortium. Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Communications Biology, 3, 56 (2020).

337. Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A; PCAWG Drivers and Functional Interpretation Working Group (including Tsunoda T), Reimand J, Stuart JM, Raphael BJ; PCAWG Consortium. Pathway and network analysis of more than 2500 whole cancer genomes. Nature Communications, 11, 729 (2020).

336. Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC; PCAWG Drivers and Functional Interpretation Working Group (including Tsunoda T), Reimand J; PCAWG Consortium. Integrative pathway enrichment analysis of multivariate omics data. Nature Communications, 11, 735 (2020).

335. Shuai S; PCAWG Drivers and Functional Interpretation Working Group (including Tsunoda T), Gallinger S, Stein L; PCAWG Consortium. Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nature Communications, 11, 734 (2020).

334. PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H; PCAWG Transcriptome Working Group, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z; PCAWG Consortium (including Tsunoda T). Genomic basis for RNA alterations in cancer. Nature, 578, 129-136 (2020).

333. Alexandrov LB, Kim J, Haradhvala NJ, Huang MN, Tian Ng AW, Wu Y, Boot A, Covington KR, Gordenin DA, Bergstrom EN, Islam SMA, Lopez-Bigas N, Klimczak LJ, McPherson JR, Morganella S, Sabarinathan R, Wheeler DA, Mustonen V; PCAWG Mutational Signatures Working Group, Getz G, Rozen SG, Stratton MR; PCAWG Consortium (including Tsunoda T). The repertoire of mutational signatures in human cancer. Nature, 578, 94-101 (2020).

332. Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD; PCAWG Evolution & Heterogeneity Working Group, Spellman PT, Wedge DC, Van Loo P; PCAWG Consortium (including Tsunoda T). The evolutionary history of 2,658 cancers. Nature, 578, 122-128 (2020).

331. Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M; PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Campbell PJ; PCAWG Consortium (including Tsunoda T). Patterns of somatic structural variation in human cancer genomes. Nature, 578, 112-121 (2020).

330. Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS; PCAWG Structural Variation Working Group, Park PJ; PCAWG Consortium (including Tsunoda T). Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nature Genetics, 52, 331-341 (2020).

329. Zapatka M, Borozan I, Brewer DS, Iskar M, Grundhoff A, Alawi M, Desai N, Sültmann H, Moch H; PCAWG Pathogens, Cooper CS, Eils R, Ferretti V, Lichter P; PCAWG Consortium (including Tsunoda T). The landscape of viral associations in human cancers. Nature Genetics, 52, 320-330 (2020).

328. Akdemir KC, Le VT, Chandran S, Li Y, Verhaak RG, Beroukhim R, Campbell PJ, Chin L, Dixon JR, Futreal PA; PCAWG Structural Variation Working Group; PCAWG Consortium (including Tsunoda T). Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nature Genetics, 52, 294-305 (2020).

327. Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PAW, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine K, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH; PCAWG Structural Variation Working Group, Campbell PJ, Tubio JMC; PCAWG Consortium (including Tsunoda T). Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nature Genetics, 52, 306-319 (2020).

326. Yuan Y, Ju YS, Kim Y, Li J, Wang Y, Yoon CJ, Yang Y, Martincorena I, Creighton CJ, Weinstein JN, Xu Y, Han L, Kim HL, Nakagawa H, Park K, Campbell PJ, Liang H; PCAWG Consortium (including Tsunoda T). Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nature Genetics, 52, 342-352 (2020).

325. Yakneen S, Waszak SM; PCAWG Technical Working Group, Gertz M, Korbel JO; PCAWG Consortium (including Tsunoda T). Butler enables rapid cloud-based analysis of thousands of human genomes. Nature Biotechnology, 38, 288-292 (2020).

324. Jiao W, Atwal G, Polak P, Karlic R, Cuppen E; PCAWG Tumor Subtypes and Clinical Translation Working Group, Danyi A, de Ridder J, van Herpen C, Lolkema MP, Steeghs N, Getz G, Morris Q, Stein LD; PCAWG Consortium (including Tsunoda T). A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns. Nature Communications, 11, 728 (2020).

323. Cmero M, Yuan K, Ong CS, Schröder J; PCAWG Evolution and Heterogeneity Working Group, Corcoran NM, Papenfuss T, Hovens CM, Markowetz F, Macintyre G; PCAWG Consortium (including Tsunoda T). Inferring structural variant cancer cell fraction. Nature Communications, 11, 730 (2020).

322. Rubanova Y, Shi R, Harrigan CF, Li R, Wintersinger J, Sahin N, Deshwar A; PCAWG Evolution and Heterogeneity Working Group, Morris Q; PCAWG Consortium (including Tsunoda T). Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. Nature Communications, 11, 731 (2020).

321. Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A; PCAWG Transcriptome Working Group; PCAWG Structural Variation Working Group, Creighton CJ; PCAWG Consortium (including Tsunoda T). High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nature Communications, 11, 736 (2020).

320. Bhandari V, Li CH, Bristow RG, Boutros PC; PCAWG Consortium (including Tsunoda T). Divergent mutational processes distinguish hypoxic and normoxic tumours. Nature Communications, 11, 737 (2020).

319. Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M; PCAWG-Structural Variation Working Group, Brors B, Rippe K, Jones DTW, Feuerbach L; PCAWG Consortium (including Tsunoda T). Genomic footprints of activated telomere maintenance mechanisms in cancer. Nature Communications, 11, 733 (2020).

318. Nishino J, Watanabe S, Miya F, Kamatani T, Sugawara T, Boroevich KA, Tsunoda T. Quantification of multicellular colonization in tumor metastasis using exome sequencing data. International Journal of Cancer, 146, 2488-2497 (2020).

317. Chandra A, Sharma A, Dehzangi A, Shigemizu D, Tsunoda T. Bigram-PGK: phosphoglycerylation prediction using the technique of bigram probabilities of position specific scoring matrix. BMC Molecular and Cell Biology, 20(Suppl 2), 57 (2019).

316. Shigemizu D, Akiyama S, Asanomi Y, Boroevich KA, Sharma A, Tsunoda T, Sakurai T, Ozaki K, Ochiya T, Niida S. A comparison of machine learning classifiers for dementia with Lewy bodies using miRNA expression data. BMC Med Genomics, 12, 150 (2019).

315. Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R; DREAM Module Identification Challenge Consortium (including Keith A. Boroevich, , Piotr J. Kamola, Artem Lysenko, Tatsuhiko Tsunoda), Subramanian A, Zhang JD, Stolovitzky G, Kutalik Z, Lage K, Slonim DK, Saez-Rodriguez J, Cowen LJ, Bergmann S, Marbach D. Assessment of network module identification across complex diseases. Nature Methods, 16, 843-852 (2019).

314. Sharma A, Vans E, Shigemizu D, Boroevich KA, Tsunoda T. DeepInsight: A methodology to transform a non-image data to an image for convolution neural network architecture. Scientific Reports, 9, 11399 (2019).

313. Kumar S, Sharma A, Tsunoda T. Brain wave classification using long short-term memory network based OPTICAL predictor. Scientific Reports, 9, 9153 (2019).

312. Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M, Astra-Zeneca-Sanger Drug Combination DREAM Consortium (including Boroevich KA, Lysenko A, Tsunoda T) , Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications, 10, 2674 (2019).

311. Sharma A, Lysenko A, López Y, Dehzangi A, Sharma R, Reddy H, Sattar A, Tsunoda T. HseSUMO: Sumoylation site prediction using half-sphere exposures of amino acids residues. BMC Genomics, 19(Suppl 9), 982 (2019).

310. Chandra AA, Sharma A, Dehzangi A, Tsunoda T. EvolStruct-Phogly: incorporating structural properties and evolutionary information from profile bigrams for the phosphoglycerylation prediction. BMC Genomics, 19(Suppl 9), 984 (2019).

309. Shigemizu D, Akiyama S, Asanomi Y, Boroevich KA, Sharma A, Tsunoda T, Matsukuma K, Ichikawa M, Sudo H, Takizawa S, Sakurai T, Ozaki K, Ochiya T, Niida S. Risk prediction models for dementia constructed by supervised principal component analysis using miRNA expression data. Communications Biology, 2, 77 (2019).

308. Sharma R, Sharma A, Patil A, Tsunoda T. Discovering MoRFs by trisecting intrinsically disordered protein sequence into terminals and middle regions. BMC Bioinformatics, 19(Suppl 13), 378 (2019).

307. Reddy HM, Sharma A, Dehzangi A, Shigemizu D, Chandra AA, Tsunoda T. GlyStruct: glycation prediction using structural properties of amino acid residues. BMC Bioinformatics, 19(Suppl 13), 547 (2019).

306. Kato K, Miya F, Hamada N, Negishi Y, Narumi-Kishimoto Y, Ozawa H, Ito H, Hori I, Hattori A, Okamoto N, Kato M, Tsunoda T, Kanemura Y, Kosaki K, Takahashi Y, Nagata KI, Saitoh S. MYCN de novo gain-of-function mutation in a patient with a novel megalencephaly syndrome. Journal of Medical Genetics, 56, 388-395 (2019).

305. Chandra A, Sharma A, Dehzangi A, Ranganathan S, Jokhan A, Chou KC, Tsunoda T. PhoglyStruct: Prediction of phosphoglycerylated lysine residues using structural properties of amino acids. Scientific Reports, 8, 17923 (2018).

304. Dehzangi A, López Y, Taherzadeh G, Sharma A, Tsunoda T. SumSec: Accurate Prediction of Sumoylation Sites Using Predicted Secondary Structure. Molecules, 23, 3260 (2018).

303. Lysenko A, Sharma A, Boroevich KA, Tsunoda T. An integrative machine learning approach for prediction of toxicity-related drug safety. Life Science Alliance, 1, e201800098 (2018).

302. Nguyen DT, Nguyen HH, Nguyen TD, Nguyen TTH, Nakano K, Maejima K, Sasaki-Oku A, Nguyen VB, Nguyen DB, Le BQ, Wong JH, Tsunoda T, Nakagawa H, Fujimoto A, Nong VH. Whole Genome Sequencing of a Vietnamese Family from a Dioxin Contamination Hotspot Reveals Novel Variants in the Son with Undiagnosed Intellectual Disability. International Journal of Environmental Research and Public Health, 15, 2629 (2018).

301. Mutai H, Miya F, Shibata H, Yasutomi Y, Tsunoda T, Matsunaga T. Gene expression dataset for whole cochlea of Macaca fascicularis. Scientific Reports, 8, 15554 (2018).

300.Sharma R, Sharma A, Raicar G, Tsunoda T, Patil A. OPAL+: Length-Specific MoRF Prediction in Intrinsically Disordered Protein Sequences. Proteomics, 19, e1800058 (2019).

299. Otani T, Noma H, Sugasawa S, Kuchiba A, Goto A, Yamaji T, Kochi Y, Iwasaki M, Matsui S, Tsunoda T. Exploring predictive biomarkers from clinical genome-wide association studies via multidimensional hierarchical mixture models. European Journal of Human Genetics, 27, 140-149 (2019).

298. Akiyama M, Takahashi A, Momozawa Y, Arakawa S, Miya F, Tsunoda T, Ashikawa K, Oshima Y, Yasuda M, Yoshida S, Enaida H, Tan X, Yanagi Y, Yasukawa T, Ogura Y, Nagai Y, Takahashi K, Fujisawa K, Inoue M, Arakawa A, Tanaka K, Yuzawa M, Kadonosono K, Sonoda KH, Ishibashi T, Kubo M. Genome-wide association study suggests four variants influencing outcomes with ranibizumab therapy in exudative age-related macular degeneration. Journal of Human Genetics, 63, 1083-1091 (2018).

297. Yamaguchi-Kabata Y, Morihara T, Ohara T, Ninomiya T, Takahashi A, Akatsu H, Hashizume Y, Hayashi N, Shigemizu D, Boroevich KA, Ikeda M, Kubo M, Takeda M, Tsunoda T. Integrated analysis of human genetic association study and mouse transcriptome suggests LBH and SHF genes as novel susceptible genes for amyloid-β accumulation in Alzheimer's disease. Human Genetics, 137, 521-533 (2018).

296. Nishino J, Ochi H, Kochi Y, Tsunoda T, Matsui S. Sample Size for Successful Genome-Wide Association Study of Major Depressive Disorder. Frontiers in Genetics, 9, 227 (2018).

295. Ton ND, Nakagawa H, Ha NH, Duong NT, Nhung VP, Hien LTT, Hue HTT, Hoang NH, Wong JH, Nakano K, Maejima K, Sasaki-Oku A, Tsunoda T, Fujimoto A, Van Hai N. Whole genome sequencing and mutation rate analysis of trios with paternal dioxin exposure. Human Mutation, 39(10):1384-1392 (2018).

294. Hori I, Miya F, Negishi Y, Hattori A, Ando N, Boroevich KA, Okamoto N, Kato M, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Saitoh S. A novel homozygous missense mutation in the SH3-binding motif of STAMBP causing microcephaly-capillary malformation syndrome. Journal of Human Genetics, 63, 957-963 (2018).

293. Suzuki N, Mutai H, Miya F, Tsunoda T, Terashima H, Morimoto N, Matsunaga T. A case report of reversible generalized seizures in a patient with Waardenburg syndrome associated with a novel nonsense mutation in the penultimate exon of SOX10. BMC Pediatrics, 18, 171 (2018).

292. Nishino J, Kochi Y, Shigemizu D, Kato M, Ikari K, Ochi H, Noma H, Matsui K, Morizono T, Boroevich KA, Tsunoda T, Matsui S. Empirical Bayes Estimation of Semi-parametric Hierarchical Mixture Models for Unbiased Characterization of Polygenic Disease Architectures. Frontiers in Genetics, 9, 115 (2018).

291. Saqi M, Lysenko A, Guo YK, Tsunoda T, Auffray C. Navigating the disease landscape: knowledge representations for contextualizing molecular signatures. Briefings in Bioinformatics, 20, 609-623 (2019).

290. Shigemizu D, Miya F, Akiyama S, Okuda S, Boroevich KA, Fujimoto A, Nakagawa H, Ozaki K, Niida S, Kanemura Y, Okamoto N, Saitoh S, Kato M, Yamasaki M, Matsunaga T, Mutai H, Kosaki K, Tsunoda T. IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis. Scientific Reports, 8, 5608 (2018).

289. Dehzangi A, López Y, Lal SP, Taherzadeh G, Sattar A, Tsunoda T, Sharma A. Improving succinylation prediction accuracy by incorporating the secondary structure via helix, strand and coil, and evolutionary information from profile bigrams. PLoS One, 13, e0191900 (2018).

288. Ikeda Y, Nishiguchi KM, Miya F, Shimozawa N, Funatsu J, Nakatake S, Fujiwara K, Tachibana T, Murakami Y, Hisatomi T, Yoshida S, Yasutomi Y, Tsunoda T, Nakazawa T, Ishibashi T, Sonoda KH. Discovery of a Cynomolgus Monkey Family With Retinitis Pigmentosa. Investigative Ophthalmology & Visual Science, 59, 826-830 (2018).

287. López Y, Sharma A, Dehzangi A, Lal SP, Taherzadeh G, Sattar A, Tsunoda T. Success: evolutionary and structural properties of amino acids prove effective for succinylation site prediction. BMC Genomics, 19(Suppl 1), 923 (2018).

286. Sharma R, Raicar G, Tsunoda T, Patil A, Sharma A. OPAL: Prediction of MoRF regions in intrinsically disordered protein sequences. Bioinformatics, 34(11):1850-1858 (2018).

285. Demenais F, Margaritte-Jeannin P, Barnes KC, Cookson WOC, Altmüller J, Ang W, Barr RG, Beaty TH, Becker AB, Beilby J, Bisgaard H, Bjornsdottir US, Bleecker E, Bønnelykke K, Boomsma DI, Bouzigon E, Brightling CE, Brossard M, Brusselle GG, Burchard E, Burkart KM, Bush A, Chan-Yeung M, Chung KF, Couto Alves A, Curtin JA, Custovic A, Daley D, de Jongste JC, Del-Rio-Navarro BE, Donohue KM, Duijts L, Eng C, Eriksson JG, Farrall M, Fedorova Y, Feenstra B, Ferreira MA; Australian Asthma Genetics Consortium (AAGC) collaborators, Freidin MB, Gajdos Z, Gauderman J, Gehring U, Geller F, Genuneit J, Gharib SA, Gilliland F, Granell R, Graves PE, Gudbjartsson DF, Haahtela T, Heckbert SR, Heederik D, Heinrich J, Heliövaara M, Henderson J, Himes BE, Hirose H, Hirschhorn JN, Hofman A, Holt P, Hottenga J, Hudson TJ, Hui J, Imboden M, Ivanov V, Jaddoe VWV, James A, Janson C, Jarvelin MR, Jarvis D, Jones G, Jonsdottir I, Jousilahti P, Kabesch M, Kähönen M, Kantor DB, Karunas AS, Khusnutdinova E, Koppelman GH, Kozyrskyj AL, Kreiner E, Kubo M, Kumar R, Kumar A, Kuokkanen M, Lahousse L, Laitinen T, Laprise C, Lathrop M, Lau S, Lee YA, Lehtimäki T, Letort S, Levin AM, Li G, Liang L, Loehr LR, London SJ, Loth DW, Manichaikul A, Marenholz I, Martinez FJ, Matheson MC, Mathias RA, Matsumoto K, Mbarek H, McArdle WL, Melbye M, Melén E, Meyers D, Michel S, Mohamdi H, Musk AW, Myers RA, Nieuwenhuis MAE, Noguchi E, O'Connor GT, Ogorodova LM, Palmer CD, Palotie A, Park JE, Pennell CE, Pershagen G, Polonikov A, Postma DS, Probst-Hensch N, Puzyrev VP, Raby BA, Raitakari OT, Ramasamy A, Rich SS, Robertson CF, Romieu I, Salam MT, Salomaa V, Schlünssen V, Scott R, Selivanova PA, Sigsgaard T, Simpson A, Siroux V, Smith LJ, Solodilova M, Standl M, Stefansson K, Strachan DP, Stricker BH, Takahashi A, Thompson PJ, Thorleifsson G, Thorsteinsdottir U, Tiesler CMT, Torgerson DG, Tsunoda T, Uitterlinden AG, van der Valk RJP, Vaysse A, Vedantam S, von Berg A, von Mutius E, Vonk JM, Waage J, Wareham NJ, Weiss ST, White WB, Wickman M, Widén E, Willemsen G, Williams LK, Wouters IM, Yang JJ, Zhao JH, Moffatt MF, Ober C, Nicolae DL. Multiancestry association study identifies new asthma risk loci that colocalize with immune-cell enhancer marks. Nature Genetics, 50, 42-53 (2018).

284. Sobrin L, Chong YH, Fan Q, Gan A, Stanwyck LK, Kaidonis G, Craig JE, Kim J, Liao WL, Huang YC, Lee WJ, Hung YJ, Guo X, Hai Y, Ipp E, Pollack S, Hancock H, Price A, Penman A, Mitchell P, Liew G, Smith AV, Gudnason V, Tan G, Klein BEK, Kuo J, Li X, Christiansen MW, Psaty BM, Sandow K; Asian Genetic Epidemiology Network Consortium (Tsunoda T et al), Jensen RA, Klein R, Cotch MF, Wang JJ, Jia Y, Chen CJ, Chen YI, Rotter JI, Tsai FJ, Hanis CL, Burdon KP, Wong TY, Cheng CY. Genetically Determined Plasma Lipid Levels and Risk of Diabetic Retinopathy: A Mendelian Randomization Study. Diabetes, 66, 3130-3141 (2017).

283. Kumar S, Sharma A, Tsunoda T. An improved discriminative filter bank selection approach for motor imagery EEG signal classification using mutual information. BMC Bioinformatics, 18(Suppl 16), 545 (2017).

282. Sharma A, Kamola PJ, Tsunoda T. 2D-EM clustering approach for high-dimensional data through folding feature vectors. BMC Bioinformatics, 18(Suppl 16), 547 (2017).

281.Sharma A, López Y, Tsunoda T. Divisive hierarchical maximum likelihood clustering. BMC Bioinformatics, 18(Suppl 16), 546 (2017).

280.Ueki M, Maeda M, Sugiyama T, Kohmoto R, Kojima S, Ikeda T, Harada A, Kanemura Y, Miya F, Tsunoda T, Yamasaki M. A Case of Dandy-Walker Malformation Complicated by Axenfeld-Rieger Syndrome. International Journal of Opthalmology & Eye Science, S1:02:001, 1-3 (2017).

279.Sharma R, Bayarjargal M, Tsunoda T, Patil A, Sharma A. MoRFPred-plus: Computational Identification of MoRFs in Protein Sequences using Physicochemical Properties and HMM profiles. Journal of Theoretical Biology, 437, 9-16 (2018).

278. Kim JJ, Yun SW, Yu JJ, Yoon KL, Lee KY, Kil HR, Kim GB, Han MK, Song MS, Lee HD, Ha KS, Sohn S, Johnson TA, Takahashi A, Kubo M, Tsunoda T, Ito K, Onouchi Y, Hong YM, Jang GY, Lee JK; Korean Kawasaki Disease Genetics Consortium. A genome-wide association analysis identifies NMNAT2 and HCP5 as susceptibility loci for Kawasaki disease. Journal of Human Genetics, 62, 1023-1029 (2017).

277. Okamoto N, Tsuchiya Y, Miya F, Tsunoda T, Yamashita K, Boroevich KA, Kato M, Saitoh S, Yamasaki M, Kanemura Y, Kosaki K, Kitagawa D. A novel genetic syndrome with STARD9 mutation and abnormal spindle morphology. Am Journal of Medical Genetics A, 173, 2690-2696 (2017).

276. Hosoe J, Kadowaki H, Miya F, Aizu K, Kawamura T, Miyata I, Satomura K, Ito T, Hara K, Tanaka M, Ishiura H, Tsuji S, Suzuki K, Takakura M, Boroevich KA, Tsunoda T, Yamauchi T, Shojima N, Kadowaki T. Structural Basis and Genotype-Phenotype Correlations of INSR Mutations Causing Severe Insulin Resistance. Diabetes, 66, 2713-2723 (2017).

275. Lysenko A, Boroevich KA, Tsunoda T. Arete - candidate gene prioritization using biological network topology with additional evidence types. BioData Mining, 10, 22 (2017).

274. Okamoto N, Miya F, Hatsukawa Y, Suzuki Y, Kawato K, Yamamoto Y, Tsunoda T, Kato M, Saitoh S, Yamasaki M, Kanemura Y, Kosaki K. Siblings with optic neuropathy and RTN4IP1 mutation. Journal of Human Genetics, 173, 2690-2696 (2017).

273. Hori I, Otomo T, Nakashima M, Miya F, Negishi Y, Shiraishi H, Nonoda Y, Magara S, Tohyama J, Okamoto N, Kumagai T, Shimoda K, Yukitake Y, Kajikawa D, Morio T, Hattori A, Nakagawa M, Ando N, Nishino I, Kato M, Tsunoda T, Saitsu H, Kanemura Y, Yamasaki M, Kosaki K, Matsumoto N, Yoshimori T, Saitoh S. Defects in autophagosome-lysosome fusion underlie Vici syndrome, a neurodevelopmental disorder with multisystem involvement. Scientific Reports, 7, 3552 (2017).

272. Ishigaki K, Kochi Y, Suzuki A, Tsuchida Y, Tsuchiya H, Sumitomo S, Yamaguchi K, Nagafuchi Y, Nakachi S, Kato R, Sakurai K, Shoda H, Ikari K, Taniguchi A, Yamanaka H, Miya F, Tsunoda T, Okada Y, Momozawa Y, Kamatani Y, Yamada R, Kubo M, Fujio K, Yamamoto K. Polygenic burdens on cell-specific pathways underlie the risk of rheumatoid arthritis. Nature Genetics, 49, 1120-1125 (2017).

271. Shigemizu D, Iwase T, Yoshimoto M, Suzuki Y, Miya F, Boroevich KA, Katagiri T, Zembutsu H, Tatsuhiko Tsunoda. The prediction models for postoperative overall survival and disease-free survival in patients with breast cancer. Cancer Medicine, 6, 1627-1638 (2017).

270. Kato K+, Miya F+(+: co-first), Hori I, Ieda D, Ohashi K, Negishi Y, Hattori A, Okamoto N, Kato M, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Saitoh S. A novel missense mutation in the HECT domain of NEDD4L identified in a girl with periventricular nodular heterotopia, polymicrogyria and cleft palate. Journal of Human Genetics, 62, 861-863 (2017).

269. Kawamura S, Onai N, Miya F, Sato T, Tsunoda T, Kurabayashi K, Yotsumoto S, Kuroda S, Takenaka K, Akashi K, Ohteki T. Identification of a Human Clonogenic Progenitor with Strict Monocyte Differentiation Potential: A Counterpart of Mouse cMoPs. Immunity, 46, 835-848 (2017).

268. Dehzangi A, López Y, Lal SP, Taherzadeh G, Michaelson J, Sattar A, Tsunoda T (co-last), Sharma A (co-last). PSSM-Suc: Accurately predicting succinylation using position specific scoring matrix into bigram for feature extraction. Journal of Theoretical Biology, 425, 97-102 (2017).

267.Okamoto N, Miya F, Tsunoda T, Kato M, Saitoh S, Yamasaki M, Kanemura Y, Kosaki K. Novel MCA/ID syndrome with ASH1L mutation. American Journal of Medical Genetics Part A, 173, 1644-1648 (2017).

266. López Y, Dehzangi A, Lal SP, Taherzadeh G, Michaelson J, Sattar A, Tsunoda T*, Sharma A*. SucStruct: Prediction of succinylated lysine residues by using structural properties of amino acids. Analytical Biochemistry, 527, 24-32 (2017).

265. Spracklen CN, Chen P, Kim YJ, Wang X, Cai H, Li S, Long J, Wu Y, Wang YX, Takeuchi F, Wu JY, Jung KJ, Hu C, Akiyama K, Zhang Y, Moon S, Johnson TA, Li H, Dorajoo R, He M, Cannon ME, Roman TS, Salfati E, Lin KH, Guo X, Sheu WH, Absher D, Adair LS, Assimes TL, Aung T, Cai Q, Chang LC, Chen CH, Chien LH, Chuang LM, Chuang SC, Du S, Fan Q, Fann CS, Feranil AB, Friedlander Y, Gordon-Larsen P, Gu D, Gui L, Guo Z, Heng CK, Hixson J, Hou X, Hsiung CA, Hu Y, Hwang MY, Hwu CM, Isono M, Juang JJ, Khor CC, Kim YK, Koh WP, Kubo M, Lee IT, Lee SJ, Lee WJ, Liang KW, Lim B, Lim SH, Liu J, Nabika T, Pan WH, Peng H, Quertermous T, Sabanayagam C, Sandow K, Shi J, Sun L, Tan PC, Tan SP, Taylor KD, Teo YY, Toh SA, Tsunoda T, van Dam RM, Wang A, Wang F, Wang J, Wei WB, Xiang YB, Yao J, Yuan JM, Zhang R, Zhao W, Chen YI, Rich SS, Rotter JI, Wang TD, Wu T, Lin X, Han BG, Tanaka T, Cho YS, Katsuya T, Jia W, Jee SH, Chen YT, Kato N, Jonas JB, Cheng CY, Shu XO, He J, Zheng W, Wong TY, Huang W, Kim BJ, Tai ES, Mohlke KL, Sim X. Association analyses of East Asian individuals and trans-ancestry analyses with European individuals reveal new loci associated with cholesterol and triglyceride levels. Human Molecular Genetics, 26, 1770-1784 (2017).

264. Sharma R, Kumar S, Tsunoda T, Patil A, Sharma A. Predicting MoRFs in protein sequences using HMM profiles. BMC Bioinformatics, 17(Suppl 19), 504 (2016).

263. Saini H*, Lal SP, Naidu VV, Pickering VW, Singh G, Tsunoda T*, Sharma A. Gene masking - a technique to improve accuracy for cancer classification with high dimensionality in microarray data. BMC Medical Genomics, 9(Suppl 3), 74 (2016).

262. Negishi Y, Miya F, Hattori A, Johmura Y, Nakagawa M, Ando N, Hori I, Togawa T, Aoyama K, Ohashi K, Fukumura S, Mizuno S, Umemura A, Kishimoto Y, Okamoto N, Kato M, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Nakanishi M, Saitoh S. A combination of genetic and biochemical analyses for the diagnosis of PI3K-AKT-mTOR pathway-associated megalencephaly. BMC Medical Genetics, 18, 4 (2017).

261. Shimizu C, Eleftherohorinou H, Wright VJ, Kim J, Alphonse MP, Perry JC, Cimaz R, Burgner D, Dahdah N, Hoang LT, Khor CC, Salgado A, Tremoulet AH, Davila S, Kuijpers TW, Hibberd ML, Johnson TA, Takahashi A, Tsunoda T, Kubo M, Tanaka T, Onouchi Y, Yeung RS, Coin LJ, Levin M, Burns JC. Genetic Variation in the SLC8A1 Calcium Signaling Pathway Is Associated with Susceptibility to Kawasaki Disease and Coronary Artery Abnormalities. Circulation: Cardiovascular Genetics, 9, 559-568 (2016).

260. Hamada N, Negishi Y, Mizuno M, Miya F, Hattori A, Okamoto N, Kato M, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Tabata H, Saitoh S, Nagata KI. Role of a heterotrimeric G-protein, Gi2, in the corticogenesis: Possible involvement in periventricular nodular heterotopia and intellectual disability. Journal of Neurochemistry, 140, 82-95 (2017).

259. Ichikawa M, Aiba T, Ohno S, Shigemizu D, Ozawa J, Sonoda K, Fukuyama M, Itoh H, Miyamoto Y, Tsunoda T, Makiyama T, Tanaka T, Shimizu W, Horie M. Phenotypic Variability of ANK2 Mutations in Patients With Inherited Primary Arrhythmia Syndromes. Circulation Journal, 80, 2435-2442 (2016).

258. Furuta M, Ueno M, Fujimoto A, Hayami S, Yasukawa S, Kojima F, Arihiro K, Kawakami Y, Wardell CP, Shiraishi Y, Tanaka H, Nakano K, Maejima K, Sasaki-Oku A, Tokunaga N, Boroevich KA, Abe T, Aikata H, Ohdan H, Goto K, Kubo M, Tsunoda T, Miyano S, Chayama K, Yamaue H, Nakagawa H. Whole genome sequencing discriminates hepatocellular carcinoma with intrahepatic metastasis from multicentric tumors. Journal of Hepatology, 66, 363-373 (2017).

257.Chang SW, McDonough CW, Gong Y, Johnson TA, Tsunoda T, Gamazon ER, Perera MA, Takahashi A, Tanaka T, Kubo M, Pepine CJ, Johnson JA, Cooper-DeHoff RM. Genome-wide association study identifies pharmacogenomic loci linked with specific antihypertensive drug treatment and new-onset diabetes. Pharmacogenomics Journal, 18, 106-112 (2018).

256. Tsutsumi M, Yokoi S, Miya F, Miyata M, Kato M, Okamoto N, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Saitoh S, Kurahashi H. Novel compound heterozygous variants in PLK4 identified in a patient with autosomal recessive microcephaly and chorioretinopathy. European Journal of Human Genetics, 24, 1702-1706 (2016).

255. Yagihara N, Watanabe H, Barnett P, Duboscq-Bidot L, Thomas AC, Yang P, Ohno S, Hasegawa K, Kuwano R, Chatel S, Redon R, Schott JJ, Probst V, Koopmann TT, Bezzina CR, Wilde AA, Nakano Y, Aiba T, Miyamoto Y, Kamakura S, Darbar D, Donahue BS, Shigemizu D, Tanaka T, Tsunoda T, Suda M, Sato A, Minamino T, Endo N, Shimizu W, Horie M, Roden DM, Makita N. Variants in the SCN5A Promoter Associated With Various Arrhythmia Phenotypes. Journal of American Heart Association, 5, pii: e003644 (2016).

254. Sharma A, Shigemizu D, Boroevich KA, López Y, Kamatani Y, Kubo M, Tsunoda T. Stepwise iterative maximum likelihood clustering approach. BMC Bioinformatics, 17, 319 (2016).

253. Fujimoto A, Okada Y, Boroevich KA, Tsunoda T, Taniguchi H, Nakagawa H. Systematic analysis of mutation distribution in three dimensional protein structures identifies cancer driver genes. Scientific Reports, 6, 26483 (2016).

252. Hori I+, Miya F+(+: co-first), Ohashi K, Negishi Y, Hattori A, Ando N, Okamoto N, Kato M, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Saitoh S. Novel splicing mutation in the ASXL3 gene causing Bainbridge-Ropers syndrome. American Journal of Medical Genetics Part A, 170, 1863-1867 (2016).

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249. Morishita M, Muramatsu T, Suto Y, Hirai M, Konishi T, Hayashi S, Shigemizu D, Tsunoda T, Moriyama K, Inazawa J. Chromothripsis-like chromosomal rearrangements induced by ionizing radiation using proton microbeam irradiation system. Oncotarget, 7, 10182-10192 (2016).

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247. Nozaki F, Kusunoki T, Okamoto N, Yamamoto Y, Miya F, Tsunoda T, Kosaki K, Kumada T, Shibata M, Fujii T. ALDH18A1-related cutis laxa syndrome with cyclic vomiting. Brain Development, 38, 678-684 (2016).

246. Lyons J, Paliwal KK, Dehzangi A, Heffernan R, Tsunoda T, Sharma A. Protein fold recognition using HMM-HMM alignment and Dynamic Programming. Journal of Theoretical Biology, 393, 67-74 (2016).

245. Konta A, Ozaki K, Sakata Y, Takahashi A, Morizono T, Suna S, Onouchi Y, Tsunoda T, Kubo M, Komuro I, Eishi Y, Tanaka T. A functional SNP in FLT1 increases risk of coronary artery disease in a Japanese population. Journal of Human Genetics, 61, 435-441 (2016).

244. Carbone M, Flores EG, Emi M, Johnson TA, Tsunoda T, Behner D, Hoffman H, Hesdorffer M, Nasu M, Napolitano A, Powers A, Minaai M, Baumann F, Bryant-Greenwood P, Lauk O, Kirschner MB, Weder W, Opitz I, Pass HI, Gaudino G, Pastorino S, Yang H. Combined Genetic and Genealogic Studies Uncover a Large BAP1 Cancer Syndrome Kindred Tracing Back Nine Generations to a Common Ancestor from the 1700s. PLoS Genetics, 11, e1005633 (2015).

243. Ito A, Shimazu T, Maeda S, Shah AA, Tsunoda T, Iemura S, Natsume T, Suzuki T, Motohashi H, Yamamoto M, Yoshida M. The subcellular localization and activity of cortactin is regulated by acetylation and interaction with Keap1. Science Signaling, 8, ra120 (2015).

242. Sharma R, Dehzangi A, Lyons J, Paliwal K, Tsunoda T, Sharma A. Predict Gram-Positive and Gram-Negative Subcellular Localization via Incorporating Evolutionary Information and Physicochemical Features Into Chou's General PseAAC. IEEE Transactions on NanoBioscience, 14, 915-926 (2015).

241. Yokoi S, Ishihara N, Miya F, Tsutsumi M, Yanagihara I, Fujita N, Yamamoto H, Kato M, Okamoto N, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Kojima S, Saitoh S, Kurahashi H, Natsume J. TUBA1A mutation can cause a hydranencephaly-like severe form of cortical dysgenesis. Scientific Reports, 5, 15165 (2015).

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239. Miya F, Mutai H, Fujii M, Boroevich KA, Matsunaga T, Tsunoda T. Gene expression profiling of DBA/2J mice cochleae treated with L-methionine and valproic acid. Genomics Data, 5, 323-325 (2015).

238. Parra EJ, Botton MR, Perini JA, Krithika S, Bourgeois S, Johnson TA, Tsunoda T, Pirmohamed M, Wadelius M, Limdi NA, Cavallari LH, Burmester JK, Rettie AE, Klein TE, Johnson JA, Hutz MH, Suarez-Kurtz G. Genome-wide association study of warfarin maintenance dose in a Brazilian sample. Pharmacogenomics, 16, 1253-1263 (2015).

237. Shigemizu D, Momozawa Y, Abe T, Morizono T, Boroevich KA, Takata S, Ashikawa K, Kubo M, Tsunoda T. Performance comparison of four commercial human whole-exome capture platforms. Scientific Reports, 5, 12742 (2015).

236. Shigemizu D, Aiba T, Nakagawa H, Ozaki K, Miya F, Satake W, Toda T, Miyamoto Y, Fujimoto A, Suzuki Y, Kubo M, Tsunoda T, Shimizu W, Tanaka T. Exome analyses of long QT syndrome reveal candidate pathogenic mutations in calmodulin-interacting genes. PLoS One, 10, e0130329 (2015).

235. Ono A, Fujimoto A, Yamamoto Y, Akamatsu S, Hiraga N, Imamura M, Kawaoka T, Tsuge M, Abe H, Hayes CN, Miki D, Furuta M, Tsunoda T, Miyano S, Kubo M, Aikata H, Ochi H, Kawakami YI, Arihiro K, Ohdan H, Nakagawa H, Chayama K. Circulating Tumor DNA Analysis for Liver Cancers and Its Usefulness as a Liquid Biopsy. Cellular and Molecular Gastroenterology and Hepatology, 1, 516-534 (2015).

234. Imai Y, Morita H, Takeda N, Miya F, Hyodo H, Fujita D, Tajima T, Tsunoda T, Nagai R, Kubo M, Komuro I. A deletion mutation in myosin heavy chain 11 causing familial thoracic aortic dissection in two Japanese pedigrees. International Journal of Cardiology, 195, 290-292 (2015).

233. Mutai H, Miya F, Fujii M, Tsunoda T, Matsunaga T. Attenuation of Progressive Hearing Loss in DBA/2J Mice by Reagents That Affect Epigenetic Modifications Is Associated with Up-Regulation of the Zinc Importer Zip4. PLoS One, 10, e0124301 (2015).

232. Miya F, Kato M, Shiohama T, Okamoto N, Saitoh S, Yamasaki M, Shigemizu D, Abe T, Morizono T, Boroevich KA, Kosaki K, Kanemura Y, Tsunoda T. A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations, Scientific Reports, 5, 9331 (2015).

231. Nakamura K, Inui T, Miya F, Kanemura Y, Okamoto N, Saitoh S, Yamasaki M, Tsunoda T, Kosaki K, Tanaka S, Kato M. Primary microcephaly with anterior predominant pachygyria caused by novel compound heterozygous mutations in ASPM. Pediatric Neurology, 52, e7-8 (2015).

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225. Saloura V, Cho HS, Kiyotani K, Alachkar H, Zuo Z, Nakakido M, Tsunoda T, Seiwert T, Lingen M, Licht J, Nakamura Y, Hamamoto R. WHSC1 Promotes Oncogenesis through Regulation of NIMA-related-kinase-7 in Squamous Cell Carcinoma of the Head and Neck. Molecular Cancer Research, 13, 293-304 (2015).

224. Okamoto N, Miya F, Tsunoda T, Yanagihara K, Kato M, Saitoh S, Yamasaki M, Kanemura Y, Kosaki K. KIF1A mutation in a patient with progressive neurodegeneration. Journal of Human Genetics, 59, 639-641 (2014).

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219. Hirokawa M, Morita H, Tajima T, Takahashi A, Ashikawa K, Miya F, Shigemizu D, Ozaki K, Sakata Y, Nakatani D, Suna S, Imai Y, Tanaka T, Tsunoda T, Matsuda K, Kadowaki T, Nakamura Y, Nagai R, Komuro I, Kubo M. A genome-wide association study identifies PLCL2 and AP3D1-DOT1L-SF3A2 as new susceptibility loci for myocardial infarction in Japanese. European Journal of Human Genetics, 23, 374-380 (2015).

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217. Wen W, Zheng W, Okada Y, Takeuchi F, Tabara Y, Hwang JY, Dorajoo R, Li H, Tsai FJ, Yang X, He J, Wu Y, He M, Zhang Y, Liang J, Guo X, Sheu WH, Delahanty R, Guo X, Kubo M, Yamamoto K, Ohkubo T, Go MJ, Liu JJ, Gan W, Chen CC, Gao Y, Li S, Lee NR, Wu C, Zhou X, Song H, Yao J, Lee IT, Long J, Tsunoda T, Akiyama K, Takashima N, Cho YS, Ong RT, Lu L, Chen CH, Tan A, Rice TK, Adair LS, Gui L, Allison M, Lee WJ, Cai Q, Isomura M, Umemura S, Kim YJ, Seielstad M, Hixson J, Xiang YB, Isono M, Kim BJ, Sim X, Lu W, Nabika T, Lee J, Lim WY, Gao YT, Takayanagi R, Kang DH, Wong TY, Hsiung CA, Wu IC, Juang JM, Shi J, Choi BY, Aung T, Hu F, Kim MK, Lim WY, Wang TD, Shin MH, Lee J, Ji BT, Lee YH, Young TL, Shin DH, Chun BY, Cho MC, Han BG, Hwu CM, Assimes TL, Absher D, Yan X, Kim E, Kuo JZ, Kwon S, Taylor KD, Chen YD, Rotter JI, Qi L, Zhu D, Wu T, Mohlke KL, Gu D, Mo Z, Wu JY, Lin X, Miki T, Tai ES, Lee JY, Kato N, Shu XO, Tanaka T. Meta-analysis of genome-wide association studies in East Asian-ancestry populations identifies four new loci for body mass index. Human Molecular Genetics, 23, 5492-5504 (2014).

216. Londono D+, Kou I+, Johnson TA+ (+: co-first), Sharma S, Ogura Y, Tsunoda T, Takahashi A, Matsumoto M, Herring JA, Lam TP, Wang X, Tam EM, Song YQ, Fan YH, Chan D, Cheah KS, Qiu X, Jiang H, Huang D; Japanese Scoliosis Clinical Research Group, TSRHC IS Clinical Group, International Consortium for Scoliosis Genetics, Su P, Sham P, Cheung KM, Luk KD, Gordon D, Qiu Y, Cheng J, Tang N, Ikegawa S, Wise CA. A meta-analysis identifies adolescent idiopathic scoliosis association with LBX1 locus in multiple ethnic groups. Journal of Medical Genetics, 51, 401-406 (2014).

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212. Miki D, Ochi H, Takahashi A, Hayes CN, Urabe Y, Abe H, Kawaoka T, Tsuge M, Hiraga N, Imamura M, Kawakami Y, Aikata H, Takahashi S, Akuta N, Suzuki F, Ikeda K, Kumada H, Karino Y, Toyota J, Tsunoda T, Kubo M, Kamatani N, Nakamura Y, Chayama K. HLA-DQB1*03 Confers Susceptibility to Chronic Hepatitis C in Japanese: A Genome-Wide Association Study. PLoS One, 8, e84226 (2013).

211. Kogure M, Takawa M, Saloura V, Sone K, Piao L, Ueda K, Ibrahim R, Tsunoda T, Sugiyama M, Atomi Y, Nakamura Y, Hamamoto R. The Oncogenic Polycomb Histone Methyltransferase EZH2 Methylates Lysine 120 on Histone H2B and Competes Ubiquitination. Neoplasia, 15, 1251-1261 (2013).

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209. Miyake A, Kou I, Takahashi Y, Johnson TA, Ogura Y, Dai J, Qiu X, Takahashi A, Jiang H, Yan H, Kono K, Kawakami N, Uno K, Ito M, Minami S, Yanagida H, Taneichi H, Hosono N, Tsuji T, Suzuki T, Sudo H, Kotani T, Yonezawa I, Kubo M, Tsunoda T, Watanabe K, Chiba K, Toyama Y, Qiu Y, Matsumoto M, Ikegawa S. Identification of a Susceptibility Locus for Severe Adolescent Idiopathic Scoliosis on Chromosome 17q24.3. PLoS One, 8, e72802 (2013).

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71. S.Ashida, H.Nakagawa, T.Katagiri, M.Fumihata, M.IIzumi, Y.Anazawa, T.Tsunoda, R.Takata, K.Kasahara, T.Miki, T.Fujioka, T.Shuin, and Y.Nakamura. Molecular Features of the Transition from Prostatic Intraepithelial Neoplasia (PIN) to Prostate Cancer: Genome-wide Gene-expression Profiles of Prostate Cancers and PINs. Cancer Research, 64, 5963-5972 (2004).

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69. Y.Harima, A.Togashi, K.Horikoshi, M.Imamura, M.Sougawa, S.Sawada, T.Tsunoda, Y.Nakamura, and T.Katagiri. Prediction of outcome of advanced cervical cancer to thermoradiotherapy according to expression profiles of 35 genes selected by cDNA microarray analysis. International Journal of Radiation Oncology Biology Physics, 60, 237-248 (2004).

68. N.Jinawath, Y.Furukawa, S.Hasegawa, M.Li, T.Tsunoda, S.Satoh, T.Yamaguchi, H.Imamura, M.Inoue, H.Shiozaki, and Y.Nakamura. Comparison of gene-expression profiles between diffuse- and intestinal-type gastric cancers using a genome-wide cDNA microarray. Oncogene, 23, 6830-6844 (2004).

67. M.Onda, M.Emi, H.Nagai, T.Nagahata, K.Tsumagari, T.Fujimoto, F.Akiyama, G.Sakamoto, M.Makita, F.Kasumi, Y.Miki, T.Tanaka, T.Tsunoda, and Y.Nakamura. Gene expression patterns as marker for 5-year postoperative prognosis of primary breast cancers. Journal of Cancer Research and Clinical Oncology, 130, 537-545 (2004).

66. T.Nakamura, Y.Furukawa, H.Nakagawa, T.Tsunoda, H.Ohigashi, K.Murata, O.Ishikawa, K.Ohgaki, N.Kashimura, M.Miyamoto, S.Hirano, S.Kondo, H.Katoh, Y.Nakamura, and T.Katagiri. Genome-wide cDNA microarray analysis of gene expression profiles in pancreatic cancers using populations of tumor cells and normal ductal epithelial cells selected for purity by laser microdissection. Oncogene, 23, 2385-2400 (2004).

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64. Y.Kochi, R.Yamada, K.Kobayashi, A.Takahashi, A.Suzuki, A.Sekine, A.Mabuchi, F.Akiyama, T.Tsunoda, Y.Nakamura, and K.Yamamoto. Analysis of single-nucleotide polymorphisms in Japanese rheumatoid arthritis patients shows additional susceptibility markers besides the classic shared epitope susceptibility sequences. Arthritis & Rheumatism, 50, 63-71 (2004).

63. M.Li, Y-M.Lin, S.Hasegawa, T.Shimokawa, K.Murata, M.Kameyama, O.Ishikawa, T.Katagiri, T.Tsunoda, Y.Nakamura, and Y.Furukawa. Genes associated with liver metastasis of colon cancer, identified by genome-wide cDNA microarray. International Journal of Oncology, 24, 305-312 (2004).

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57. Y.Kaneta, Y.Kagami, T.Tsunoda, R.Ohno, Y.Nakamura, and T.Katagiri. Genome-wide analysis of gene-expression profiles in chronic myeloid leukemia cells using a cDNA microarray. International Journal of Oncology, 23, 681-691 (2003).

56. K.Ochi, Y.Daigo, T.Katagiri, A.Saito-Hisaminato, T.Tsunoda, Y.Toyama, H.Matsumoto, and Y.Nakamura. Expression profiles of two types of human knee-joint cartilage. Journal of Human Genetics, 48, 177-182 (2003).

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43. F.Akiyama, T.Tanaka, R.Yamada, Y.Ohnishi, T.Tsunoda, S.Maeda, T.Takei, W.Obara, K.Ito, K.Honda, K.Uchida, K.Tsuchiya, K.Nitta, W.Yumura, H.Nihei, T.Ujiie, Y.Nagane, S.Miyano, Y.Suzuki, T.Fujioka, I.Narita, F.Gejyo, and Y.Nakamura. Single-nucleotide polymorphisms in the class II region of the major histocompatibility complex in Japanese patients with immunoglobulin A nephropathy. Journal of Human Genetics, 47, 532-538 (2002).

42. H.Ishiguro, T.Shimokawa, T.Tsunoda, T.Tanaka, Y.Fujii, Y.Nakamura, and Y.Furukawa. Isolation of HELAD1, a novel human helicase gene up-regulated in colorectal carcinomas. Oncogene, 21, 6387-6394 (2002).

41. Y.Kaneta, Y.Kagami, T.Katagiri, T.Tsunoda, I.Jin-nai, H.Taguchi, H.Hirai, K.Ohnishi, T.Ueda, N.Emi, A.Tomida, T.Tsuruo, Y.Nakamura, and R.Ohno. Prediction of Sensitivity to STI571 among Chronic Myeloid Leukemia Patients by Genome-wide cDNA Microarray Analysis. Cancer Science, 93, 849-856 (2002).

40. M.Nishiu, R.Yanagawa, S.Nakatsuka, M.Yao, T.Tsunoda, Y.Nakamura, and K.Aozasa. Microarray Analysis of Gene-expression Profiles in Diffuse Large B-cell Lymphoma: Identification of Genes Related to Disease Progression. Cancer Science, 93, 894-901 (2002).　

39. M.Takahashi, T.Tsunoda, M.Seiki, Y.Nakamura, and Y.Furukawa. Identification of membrane-type matrix metalloproteinase-1 as a target of the beta-catenin/Tcf4 complex in human colorectal cancers. Oncogene, 21, 5861-5867 (2002).

38. O.Kitahara, T.Katagiri, T.Tsunoda, Y.Harima, and Y.Nakamura. Classification of Sensitivity or Resistance of Cervical Cancers to Ionizing Radiation According to Expression Profiles of 62 Genes Selected by cDNA Microarray Analysis. Neoplasia, 4, 295-303 (2002).

37. Y-M.Lin, Y.Furukawa, T.Tsunoda, C-T.Yue, K-C.Yang, and Y.Nakamura. Molecular Diagnosis of Colorectal Tumors by Expression Profiles of 50 Genes Expressed Differentially in Adenomas and Carcinomas. Oncogene, 21, 4120-4128 (2002).

36. M.Iizaka, Y.Furukawa, T.Tsunoda, H.Akashi, M.Ogawa, and Y.Nakamura. Expression Profile Analysis of Colon Cancer Cells in Response to Sulindac or Aspirin. Biochemical and Biophysical Research Communications, 292, 498-512 (2002).

35. A.Saito-Hisaminato, T.Katagiri, S.Kakiuchi, T.Nakamura, T.Tsunoda, and Y.Nakamura. Genome-Wide Profiling of Gene Expression in 29 Normal Human Tissues with a cDNA Microarray. DNA Research, 9, 35-45 (2002).

34. M.Nakamura, T.Tsunoda, and J.Obokata. Photosynthesis nuclear genes generally lack TATA-boxes: a tobacco photosystem I gene responses light through an initiator. The Plant Journal, 29, 1-10 (2002).

33. C.Kihara+, T.Tsunoda+, T.Tanaka, H.Yamana, Y.Furukawa, K.Ono, O.Kitahara, H.Zenbutsu, R.Yanagawa, K.Hirata, T.Takagi, and Y.Nakamura. Prediction of Sensitivity of Esophageal Tumors to Adjuvant Chemotherapy by cDNA Microarray Analysis of Gene-Expression Profiles. Cancer Research, 61, 6474-6479 (2001). (+ equally contributed).

32. O.Kitahara, Y.Furukawa, T.Tanaka, C.Kihara, K.Ono, R.Yanagawa, M.E.Nita, T.Takagi, Y.Nakamura, and T.Tsunoda. Alterations of Gene Expression During Colorectal Carcinogenesis Revealed by cDNA Microarrays after Laser-Capture Microdissection of Tumor Tissues and Normal Epithelia. Cancer Research, 61, 3544-3549 (2001).

31. R.Yamada, T.Tanaka, M.Unoki, T.Nagai, T.Sawada, Y.Ohnishi, T.Tsunoda, M.Yukioka, A.Maeda, K.Suzuki, H.Tateishi, T.Ochi, Y.Nakamura, and K.Yamamoto. Association between a Single-Nucleotide Polymorphism in the Promoter of the Human Interleukin-3 Gene and Rheumatoid Arthritis in Japanese Patients, and Maximum-likelihood Estimation of Combinatorial Effect That Two Genetic Loci Have on Susceptibility to the Disease. American Journal of Human Genetics, 68, 674-685 (2001).

30. M.Fujita, Y.Furukawa, T.Tsunoda, T.Tanaka, M.Ogawa, and Y.Nakamura. Up-Regulation of the Ectodermal-Neural Cortex (ENC1) Gene, a Downstream Target of the Beta-Catenin/T-Cell Factor Complex, in Colorectal Carcinomas. Cancer Research, 61, 7722-7726 (2001).

29. Y-M.Lin, K.Ono, S.Satoh, H.Ishiguro, M.Fujita, N.Miwa, T.Tanaka, T.Tsunoda, K-C.Yang, Y.Nakamura, and Y.Furukawa. Identification of AF17 as a downstream gene of the beta-catenin/Tcf pathway, and its involvement in colorecatal carcinogenesis. Cancer Research, 61, 6345-6349 (2001).

28. M.Matsushima-Nishiu, M.Unoki, K.Ono, T.Tsunoda, T.Minaguchi, H.Kuramoto, M.Nishida, T.Satoh, T.Tanaka, and Y.Nakamura. Growth and Gene-Expression Profile Analysis of Endometrial Cancer Cells Expressing Exogenous PTEN. Cancer Research, 61, 3741-3749 (2001).

27. H.Okabe, S.Satoh, T.Kato, O.Kitahara, R.Yanagawa, Y.Yamaoka, T.Tsunoda, Y.Furukawa, and Y.Nakamura. Genome-Wide Analysis of Gene Expression in Human Hepatocellular Carcinomas Using cDNA Microarray: Identification of Genes Involved in Viral Carcinogenesis and Tumor Progression. Cancer Research, 61, 2129-2137 (2001).

26. R.Yanagawa, Y.Furukawa, T.Tsunoda, O.Kitahara, K.Murata, O.Ishikawa, and Y.Nakamura. Genome-wide Screening of Genes Showing Altered Expression in Liver Metastasis of Human Colorectal Cancers by cDNA Microarray. Neoplasia, 3, 395-401 (2001).

25. H.Ishiguro, Y.Furukawa, T.Tsunoda, T.Tanaka, Y.Fujii, and Y.Nakamura. Identification of AXUD1, a novel human gene induced by AXIN1 and involved in human carcinogenesis of the lung, liver, colon, and kidney. Oncogene, 20, 5062-5066 (2001).
24. Y.Suzuki, T.Tsunoda, J.Sese, H.Taira, J. Mizushima-Sugano, H.Hata, T.Ota, T.Isogai, T.Tanaka, Y.Nakamura, A.Suyama, Y.Sakaki, S.Morishita, K.Okubo, and S.Sugano. Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes. Genome Research, 11, 677-684 (2001).

23. Y.Suzuki, H.Taira, T.Tsunoda, J. Mizushima-Sugano, J.Sese, H.Hata, T.Ota, T.Isogai, T.Tanaka, S.Morishita, K.Okubo, Y.Sakaki, Y.Nakamura, A.Suyama, and S.Sugano. Diverse Transcriptional Initiation Revealed by Fine, Large-Scale Mapping of the mRNA Start Sites. EMBO reports, 2, 388-393 (2001).

22. T.Kato, S.Satoh, H.Okabe, O.Kitahara, K.Ono, C.Kihara, T.Tanaka, T.Tsunoda, Y.Yamaoka, Y.Nakamura, and Y.Furukawa. Isolation of a novel human gene, MARKL1, homologous to MARK3 and its involvement in hepatocellular carcinogenesis. Neoplasia, 3, 4-9 (2001).

21. T.Tsunoda, R.Yamada, T.Tanaka, Y.Ohnishi, and N.Kamatani. Environmental Factor Dependent Maximum Likelihood Method for Association Study Targeted to Personalized Medicine. Genome Informatics, 11, 96-105 (2000).

20. M.Kato, T.Tsunoda, and T.Takagi. Inferring Genetic Networks from DNA Microarray Data by Multiple Regression Analysis. Genome Informatics, 11, 118-128 (2000).

19. K.Ono, T.Tanaka, T.Tsunoda, O.Kitahara, C.Kihara, A.Okamoto, K.Ochiai, T.Takagi, and Y.Nakamura. Identification by cDNA Microarray of Genes Involved in Ovarian Carcinogenesis. Cancer Research, 60, 5007-5011 (2000).

18. Y.Ajima, K.Anraku, T.Haga, Y.Higashi, H.Honda, M.Imori, S.Inaba, N.Kimura, M.Kobayashi, Y.Makida, N.Matsui, H.Matsumoto, H.Matsunaga, M.Motoki, M.Nozaki, Y.Nishihara, J.Nishimura, S.Orito, M.Otoba, T.Saeki, T.Sanuki, M.Sasaki, K.Shimamura, J.Suzuki, K.Suzuki, N.Takimi, K.Tanaka, T.Tsunoda, I.Ueda, T.Yajima, T.Yamagami, A.Yamamoto, H.Yamaoka, T.Yoshida, and K.Yoshimura. A Superconducting Solenoidal Spectrometer for a Balloon-borne Experiment. Nuclear Instruments & Methods in Physics Research Section A - Accelerators Spectrometers Detectors and Associated Equipment, 443, 71-100 (2000).

17. T.Tsunoda, and T.Takagi. Estimating Transcription Factor Bindability on DNA. Bioinformatics, 15, 622-630 (1999).

16. T.Tsunoda, M.Fukagawa, and T.Takagi. Time and Memory Efficient Algorithm for Extracting Palindromic and Repetitive Subsequences in Nucleic Acid Sequences. Pacific Symposium on Biocomputing, 202-213 (1999).

15. T.Tsunoda, and T.Takagi. Automatic Extraction of Position Specific Cooccurrence of Transcription Factor Bindings on Promoters. Pacific Symposium on Biocomputing, 252-263 (1998).

14. K.Fukuda, T.Tsunoda, A.Tamura, and T.Takagi. Toward Information Extraction: Identifying protein names from biological papers. Pacific Symposium on Biocomputing, 705-716 (1998).

13. K.Fukuda, T.Tsunoda, A.Tamura, T.Takagi. Extracting Technical Terms from Medical and Biological Articles. Transactions of Information Processing Society of Japan, 39, 2421-2430 (1998).

12. T.Tsunoda, T.Oishi, Y.Watanabe and M.Nagao. Automatic Alignment between TV News and Newspaper Articles by Maximum Length String Matching between Captions and Article Texts. Transactions of Information Processing Society of Japan, 38, 1149-1162 (1997).

11. T.Tsunoda and M.Hashiba. Disambiguation of Noun Sense by Scene Knowledge Based on Pictorial Dictionary and LDOCE Subject-Codes. Transactions of Information Processing Society of Japan, 38, 235-244 (1997).

10. M.Matsumoto, T.Tsunoda and Y.Matsumoto. A Coding Scheme which Enables Fast Direct Search in Compressed Files. The Transactions of the Institute of Electronics, Information and Communication Engineers A, J80-A, 969-976 (1997).

9. K.Araya, T.Tsunoda, T.Oishi and M.Nagao. Retrieval Method of Relevant Newspaper Articles Using Words' Cooccurrence Frequency and their Position. Transactions of Information Processing Society of Japan, 38, 855-862 (1997).

8. Y.Watanabe, Y.Okada, T.Tsunoda and M.Nagao. Aligning Articles in TV Newscasts and Newspapers. Journal of Japanese Society for Artificial Intelligence, 12, 921-927 (1997).

7. T.Tsunoda and H.Tanaka. Evaluation of Scene Information as Context for English Noun Disambiguation. Journal of Natural Language Processing, 3, 3-27 (1996).

6. T.Tsunoda, S.Nakamura, S.Orito and M.Minowa. A Search for Back-to-Back e+e- Pairs in the Spontaneous-Fission Disintegration of 252Cf. Europhys. Lett, 30, 273-276 (1995).

5. T.Tsunoda and H.Tanaka. Analysis of Scene Identification Ability of Associative Memory with Pictorial Dictionary. The 15th International Conference on Computational Linguistics (COLING 1994), 310-316 (1994).

4. K.Anraku, T.Haga, M.Imori, M.Nozaki, S.Orito, K.Shimamura, T.Tsunoda, T.Yoshida, K.Yoshimura, Y.Ajima, H.Ikeda, S.Inaba, T.Haruyama, Y.Higashi, Y.Makida, J.Suzuki, A.Yamamoto, J.Nishimura, T.Yamaguchi, R.Golden, and B.Kimbell. Search for Antiparticlees of Cosmic Origin with a Superconducting Sepectrometer. Advances in Space Research, 13, 169-172 (1993).

3. M.Imori, K.Anraku, S.Inaba, I.Ueda, T.Saeki, T.Haga, T.Tsunoda, M.Nozaki, T.Yamagami, T.Yoshida and K.Yoshimura. Real-Time Data Processes in a Balloon-borne Apparatus. IEEE Transactions on Nuclear Science, 39, 1389-1393 (1992).

2. K.Anraku, M.Imori, T.Saeki, I.Ueda, S.Inaba, K.Shimamura, M.Nozaki, T.Tsunoda and T.Yoshida. A Flash ADC System with Fast Data Compression for a Balloon-borne Experiment. IEEE Transactions on Nuclear Science, 39, 987-992 (1992).

1. T.Asanuma, M.Minowa, T.Tsukamoto, S.Orito and T.Tsunoda. A Search for Correlated e+e- Pairs in the Decay of 241Am. Physics Letters B, 237, 588-591 (1990).