口頭発表・ハイライト

代謝ネットワーク解析・メタゲノム解析

座長：松本 拡高 (長崎大学情報データ科学部)

1. Saori Uematsu, Satoshi Ohno and Shinya Kuroda
Omics-based label-free metabolic flux inference reveals dysregulation of glucose metabolism in liver associated with obesity
 ﾊｲﾗｲﾄ  https://doi.org/10.1101/2021.06.21.449220

2. Takeyuki Tamura, Ai Muto-Fujita, Yukako Tohsato and Tomoyuki Kosaka
Gene deletion algorithms for minimum reaction network design by mixed-integer linear programming for metabolite production in constraint-based models: gDel_minRN
 口頭発表 

3. 西村陽介、吉澤晋
メタゲノムから構築した5万ゲノムの海洋微生物カタログ
 口頭発表 

4. Shion Hosoda, Tsukasa Fukunaga and Michiaki Hamada
Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model
 ﾊｲﾗｲﾄ  https://doi.org/10.1093/bioinformatics/btab287

バイオインフォマティクス全般1

座長：露崎 弘毅 (理化学研究所)

1. Akihiro Kuno, Yoshihisa Ikeda, Shinya Ayabe and Seiya Mizuno
DAJIN validates the multiallelic genome editing outcomes using machine learning-assisted long-read sequencing
 ﾊｲﾗｲﾄ  https://doi.org/10.1101/2020.12.14.422641

2. Kazuya Ichihara, Akinobu Matsumoto, Hiroshi Nishida, Yuki Kito, Hideyuki Shimizu, Yuichi Shichino, Shintaro Iwasaki, Koshi Imami, Yasushi Ishihama and Keiichi Nakayama
Combinatorial analysis of translation dynamics reveals eIF2 dependence of translation initiation at near-cognate codons
 ﾊｲﾗｲﾄ  https://doi.org/10.1093/nar/gkab549

3. Sho Tsukiyama, Mehedi Md. Hasan and Hiroyuki Kurata
BERTとword2vecを用いたN6-Methyladenineサイトの予測
 口頭発表 

4. Wan Kin Au Yeung, Osamu Maruyama and Hiroyuki Sasaki
A convolutional neural network-based regression model to infer the epigenetic crosstalk responsible for CG methylation patterns
 ﾊｲﾗｲﾄ  https://doi.org/10.1186/s12859-021-04272-8

バイオインフォマティクス全般2

座長：山西 芳裕 (九州工業大学大学院情報工学研究院)

1. Tsukasa Fukunaga and Wataru Iwasaki
The inverse Potts model improves accuracy of phylogenetic profiling
 口頭発表 

2. Xu Yang and Masahiro Kasahara
LPMX: A pure rootless composable container system
 ﾊｲﾗｲﾄ  https://doi.org/10.1101/2021.06.04.445363

3. Y-H. Taguchi and Turki Turki
Mathematical formulation and application of kernel tensor decomposition based unsupervised feature extraction
 ﾊｲﾗｲﾄ  https://doi.org/10.1016/j.knosys.2021.106834

4. Genki Terashi, Xusi Han, Charles Christoffer, Siyang Chen and Daisuke Kihara
VESPER: Global and Local Cryo-EM Map Alignment and Database Search Using Local Density Vectors
 ﾊｲﾗｲﾄ  https://doi.org/10.1038/s41467-021-22401-y

表現学習

座長：水口 賢司 (医薬基盤・健康・栄養研究所、大阪大学蛋白質研究所)

1. Sho Tsukiyama, Md Mehedi Hasan, Satoshi Fujii and Hiroyuki Kurata
LSTM-PHV: prediction of human-virus protein?protein interactions by LSTM with word2vec
 ﾊｲﾗｲﾄ  https://doi.org/10.1093/bib/bbab228

2. 山口秀輝、 齋藤裕
Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins
 ﾊｲﾗｲﾄ  https://doi.org/10.1093/bib/bbab234

3. Keisuke Yamada and Michiaki Hamada
Prediction of RNA-protein interactions using a nucleotide language model
 ﾊｲﾗｲﾄ  https://doi.org/10.1101/2021.04.27.441365

4. Natsuki Iwano, Tatsuo Adachi, Kazuteru Aoki, Yoshikazu Nakamura and Michiaki Hamada
RaptGen: A variational autoencoder with profile hidden Markov model for generative aptamer discovery
 ﾊｲﾗｲﾄ  https://doi.org/10.1101/2021.02.17.431338

メディカルインフォマティクス

座長：福永 津嵩 (早稲田大学高等研究所）

1. Qingbo Wang, David Kelley, Jacob Ulirsch, Masahiro Kanai, Shuvom Sadhuka, Ran Cui, Carlos Albors, Nathan Cheng, Yukinori Okada, The Biobank Japan Project, Francois Aguet, Kristin Ardlie, Daniel MacArthur and Hilary Finucane
Leveraging supervised learning for functionally informed fine-mapping of cis-eQTLs identifies an additional 20,913 putative causal eQTLs
 ﾊｲﾗｲﾄ  https://doi.org/10.1038/s41467-021-23134-8

2. Taro Matsutani and Michiaki Hamada
変異アレル頻度を考慮したヒトがんゲノムの変異シグネチャー解析
 ﾊｲﾗｲﾄ  https://doi.org/10.1101/2021.05.08.443215

3. Hiroki Kiyoshima, Kanna Fujita, Toshiyuki Ko, Seitaro Nomura, Momoko Hamano, Issei Komuro and Yoshihiro Yamanishi
心筋細胞の核形態画像を用いた機械学習による心不全の診断モデル
 口頭発表 

4. Mamoru Shimo, Kota Fujisawa, Y-H. Taguchi, Sinya Ikematu and Ryota Miyata
Application of PCA-based unsupervised feature extraction for gene selection associated with COVID-19 severity
 口頭発表 

配列解析

座長：尾崎 遼 (筑波大学医学医療系)

1. Kengo Sato, Manato Akiyama and Yasubumi Sakakibara
RNA secondary structure prediction using deep learning with thermodynamic integration
 ﾊｲﾗｲﾄ  https://doi.org/10.1038/s41467-021-21194-4

2. Saeko Tahara, Takaho Tsuchiya and Haruka Ozaki
k-mer profile analysis clarifies cell-type specific TF binding landscape in human
 口頭発表 

3. Yuka Yoshimura, Akifumi Hamada, Yohann Augey, Manato Akiyama and Yasubumi Sakakibara
Genomic style: a deep-learning approach to characterize bacterial genome sequences
 口頭発表 

4. Atsushi Takeda, Yuta Imazu, Daisuke Nonaka, Tsukasa Fukunaga and Michiaki Hamada
De novo Repeat Detection using Inexact Seed
 口頭発表 

遺伝子発現解析

座長：齋藤 裕 (産業技術総合研究所)

1. Natsu Nakajima, Tomoatsu Hayashi, Katsunori Fujiki, Katsuhiko Shirahige, Tetsu Akiyama, Tatsuya Akutsu and Ryuichiro Nakato
Codependency and mutual exclusivity for gene community detection from sparse single-cell transcriptome data
 ﾊｲﾗｲﾄ  https://doi.org/10.1093/nar/gkab601

2. Michio Iwata, Hiroaki Mutsumine, Yusuke Nakayama, Naomasa Suita and Yoshihiro Yamanishi
テンソル分解による化合物応答シングルセルトランスクリプトームの予測を介したパスウェイ軌道解析
 口頭発表 

3. Hitoshi Iuchi and Michiaki Hamada
Jonckheere-Terpstra-Kendall-based non-parametric analysis of temporal differential gene expression
 ﾊｲﾗｲﾄ  https://doi.org/10.1093/nargab/lqab021

4. Taisuke Hori, Sung-Joon Park and Kenta Nakai
Meta co-expression analysis of genetic heterogeneity in GBM using single-cell RNA-seq data
 口頭発表