About Us

Human Genome Center, The Institute of Medical Science,
The University of Tokyo

Sung-Joon Park

Kenta Nakai

HGC Supercomputer



Genome Modality: Understanding physical properties of the genome

Genome Modality WebSite

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BlueSky



References

Soya Shinkai, Masaki Nakagawa, Takeshi Sugawara, Yuichi Togashi, Hiroshi Ochiai, Ryuichiro Nakato, Yuichi Taniguchi, and Shuichi Onami.
PHi-C: deciphering Hi-C data into polymer dynamics.
NAR Genomics and Bioinformatics 2(2):lqaa020, 2020. PMID: 33575580

van Heeringen SJ, Veenstra GJ.
GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments.
Bioinformatics 27(2):270-1, 2011. PMID: 21081511

Hongyoon Choi, Jeongbin Park, Sumin Kim, Jiwon Kim, Dongjoo Lee, Sungwoo Bae, Haenara Shin, Daeseung Lee.
CELLama: Foundation Model for Single Cell and Spatial Transcriptomics by Cell Embedding Leveraging Language Model Abilities.
bioRxiv doi: https://doi.org/10.1101/2024.05.08.593094

Robinson JT, Turner D, Durand NC, Thorvaldsdóttir H, Mesirov JP, Aiden EL.
Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data.
Cell Syst. 6(2):256-258.e1, 2018. PMID: 29428417

Sehnal D, Bittrich S, Deshpande M, Svobodová R, Berka K, Bazgier V, et al.
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures.
Nucleic Acids Res. 49(W1):W431–7, 2021. PMID: 33956157

Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G, Goodstein DM, Elsik CG, Lewis SE, Stein L, Holmes IH.
JBrowse: a dynamic web platform for genome visualization and analysis.
Genome Biol. 17:66, 2016. PMID: 27072794

Diesh C, Stevens GJ, Xie P, De Jesus Martinez T, Hershberg EA, Leung A, Guo E, Dider S, Zhang J, Bridge C, Hogue G, Duncan A, Morgan M, Flores T, Bimber BN, Haw R, Cain S, Buels RM, Stein LD, Holmes IH.
JBrowse 2: a modular genome browser with views of synteny and structural variation.
Genome Biol. 17;24(1):74, 2023. PMID:37069644

Speir ML, Bhaduri A, Markov NS, Moreno P, Nowakowski TJ, Papatheodorou I, Pollen AA, Raney BJ, Seninge L, Kent WJ, Haeussler M.
UCSC Cell Browser: visualize your single-cell data.
Bioinformatics. 2021. PMID: 34244710