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1.

CRISPR Activation Reverses Haploinsufficiency and Functional Deficits Caused by TTN Truncation Variants.

Ghahremani, Shahnaz; Kanwal, Aditya; Pettinato, Anthony; Ladha, Feria; Legere, Nicholas; Thakar, Ketan; Zhu, Yanfen; Tjong, Harianto; Wilderman, Andrea; Stump, W Tom; Greenberg, Lina; Greenberg, Michael J; Cotney, Justin; Wei, Chia-Lin; Hinson, J Travis.

Circulation; 149(16): 1285-1297, 2024 Apr 16.

Artículo en Inglés | MEDLINE | ID: mdl-38235591

2.

Picky comprehensively detects high-resolution structural variants in nanopore long reads.

Gong, Liang; Wong, Chee-Hong; Cheng, Wei-Chung; Tjong, Harianto; Menghi, Francesca; Ngan, Chew Yee; Liu, Edison T; Wei, Chia-Lin.

Nat Methods; 15(6): 455-460, 2018 06.

Artículo en Inglés | MEDLINE | ID: mdl-29713081

3.

Population-based 3D genome structure analysis reveals driving forces in spatial genome organization.

Tjong, Harianto; Li, Wenyuan; Kalhor, Reza; Dai, Chao; Hao, Shengli; Gong, Ke; Zhou, Yonggang; Li, Haochen; Zhou, Xianghong Jasmine; Le Gros, Mark A; Larabell, Carolyn A; Chen, Lin; Alber, Frank.

Proc Natl Acad Sci U S A; 113(12): E1663-72, 2016 Mar 22.

Artículo en Inglés | MEDLINE | ID: mdl-26951677

4.

TopDom: an efficient and deterministic method for identifying topological domains in genomes.

Shin, Hanjun; Shi, Yi; Dai, Chao; Tjong, Harianto; Gong, Ke; Alber, Frank; Zhou, Xianghong Jasmine.

Nucleic Acids Res; 44(7): e70, 2016 Apr 20.

Artículo en Inglés | MEDLINE | ID: mdl-26704975

5.

Physical tethering and volume exclusion determine higher-order genome organization in budding yeast.

Tjong, Harianto; Gong, Ke; Chen, Lin; Alber, Frank.

Genome Res; 22(7): 1295-305, 2012 Jul.

Artículo en Inglés | MEDLINE | ID: mdl-22619363

6.

ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs.

Chai, Haoxi; Tjong, Harianto; Li, Peng; Liao, Wei; Wang, Ping; Wong, Chee Hong; Ngan, Chew Yee; Leonard, Warren J; Wei, Chia-Lin; Ruan, Yijun.

Nat Commun; 14(1): 213, 2023 01 13.

Artículo en Inglés | MEDLINE | ID: mdl-36639381

7.

An allelic series of spontaneous Rorb mutant mice exhibit a gait phenotype, changes in retina morphology and behavior, and gene expression signatures associated with the unfolded protein response.

Murray, George C; Bubier, Jason A; Zinder, Oraya J; Harris, Belinda; Clark, James; Christopher, Mia-Cara; Hanley, Courtany; Tjong, Harianto; Li, Meihong; Ngan, Chew Yee; Reinholdt, Laura; Burgess, Robert W; Tadenev, Abigail L D.

G3 (Bethesda); 13(8)2023 08 09.

Artículo en Inglés | MEDLINE | ID: mdl-37300435

8.

Exploring the spatial and temporal organization of a cell's proteome.

Beck, Martin; Topf, Maya; Frazier, Zachary; Tjong, Harianto; Xu, Min; Zhang, Shihua; Alber, Frank.

J Struct Biol; 173(3): 483-96, 2011 Mar.

Artículo en Inglés | MEDLINE | ID: mdl-21094684

9.

Spontaneous conformational change and toxin binding in alpha7 acetylcholine receptor: insight into channel activation and inhibition.

Yi, Myunggi; Tjong, Harianto; Zhou, Huan-Xiang.

Proc Natl Acad Sci U S A; 105(24): 8280-5, 2008 Jun 17.

Artículo en Inglés | MEDLINE | ID: mdl-18541920

10.

Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription.

Zhu, Yanfen; Gujar, Amit D; Wong, Chee-Hong; Tjong, Harianto; Ngan, Chew Yee; Gong, Liang; Chen, Yi-An; Kim, Hoon; Liu, Jihe; Li, Meihong; Mil-Homens, Adam; Maurya, Rahul; Kuhlberg, Chris; Sun, Fanyue; Yi, Eunhee; deCarvalho, Ana C; Ruan, Yijun; Verhaak, Roel G W; Wei, Chia-Lin.

Cancer Cell; 39(5): 694-707.e7, 2021 05 10.

Artículo en Inglés | MEDLINE | ID: mdl-33836152

11.

The folding transition-state ensemble of a four-helix bundle protein: helix propensity as a determinant and macromolecular crowding as a probe.

Tjong, Harianto; Zhou, Huan-Xiang.

Biophys J; 98(10): 2273-80, 2010 May 19.

Artículo en Inglés | MEDLINE | ID: mdl-20483336

12.

ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization.

Lee, Byoungkoo; Wang, Jiahui; Cai, Liuyang; Kim, Minji; Namburi, Sandeep; Tjong, Harianto; Feng, Yuliang; Wang, Ping; Tang, Zhonghui; Abbas, Ahmed; Wei, Chia-Lin; Ruan, Yijun; Li, Sheng.

Sci Adv; 6(28): eaay2078, 2020 07.

Artículo en Inglés | MEDLINE | ID: mdl-32832596

13.

Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development.

Ngan, Chew Yee; Wong, Chee Hong; Tjong, Harianto; Wang, Wenbo; Goldfeder, Rachel L; Choi, Cindy; He, Hao; Gong, Liang; Lin, Junyan; Urban, Barbara; Chow, Julianna; Li, Meihong; Lim, Joanne; Philip, Vivek; Murray, Stephen A; Wang, Haoyi; Wei, Chia-Lin.

Nat Genet; 52(3): 264-272, 2020 03.

Artículo en Inglés | MEDLINE | ID: mdl-32094912

14.

DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces.

Tjong, Harianto; Zhou, Huan-Xiang.

Nucleic Acids Res; 35(5): 1465-77, 2007.

Artículo en Inglés | MEDLINE | ID: mdl-17284455

15.

PI2PE: protein interface/interior prediction engine.

Tjong, Harianto; Qin, Sanbo; Zhou, Huan-Xiang.

Nucleic Acids Res; 35(Web Server issue): W357-62, 2007 Jul.

Artículo en Inglés | MEDLINE | ID: mdl-17526530

16.

Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance.

Bertolini, Jessica A; Favaro, Rebecca; Zhu, Yanfen; Pagin, Miriam; Ngan, Chew Yee; Wong, Chee Hong; Tjong, Harianto; Vermunt, Marit W; Martynoga, Ben; Barone, Cristiana; Mariani, Jessica; Cardozo, Marcos Julián; Tabanera, Noemi; Zambelli, Federico; Mercurio, Sara; Ottolenghi, Sergio; Robson, Paul; Creyghton, Menno P; Bovolenta, Paola; Pavesi, Giulio; Guillemot, Francois; Nicolis, Silvia K; Wei, Chia-Lin.

Cell Stem Cell; 24(3): 462-476.e6, 2019 03 07.

Artículo en Inglés | MEDLINE | ID: mdl-30849367

17.

Prediction of protein solubility from calculation of transfer free energy.

Tjong, Harianto; Zhou, Huan-Xiang.

Biophys J; 95(6): 2601-9, 2008 Sep 15.

Artículo en Inglés | MEDLINE | ID: mdl-18515380

18.

Producing genome structure populations with the dynamic and automated PGS software.

Hua, Nan; Tjong, Harianto; Shin, Hanjun; Gong, Ke; Zhou, Xianghong Jasmine; Alber, Frank.

Nat Protoc; 13(5): 915-926, 2018 05.

Artículo en Inglés | MEDLINE | ID: mdl-29622804

19.

Quantitative Methods to Investigate the 4D Dynamics of Heterochromatic Repair Sites in Drosophila Cells.

Caridi, Christopher P; Delabaere, Laetitia; Tjong, Harianto; Hopp, Hannah; Das, Devika; Alber, Frank; Chiolo, Irene.

Methods Enzymol; 601: 359-389, 2018.

Artículo en Inglés | MEDLINE | ID: mdl-29523239

20.

GBr(6): a parameterization-free, accurate, analytical generalized born method.

Tjong, Harianto; Zhou, Huan-Xiang.

J Phys Chem B; 111(11): 3055-61, 2007 Mar 22.

Artículo en Inglés | MEDLINE | ID: mdl-17309289

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CRISPR Activation Reverses Haploinsufficiency and Functional Deficits Caused by TTN Truncation Variants.

Picky comprehensively detects high-resolution structural variants in nanopore long reads.

Population-based 3D genome structure analysis reveals driving forces in spatial genome organization.

TopDom: an efficient and deterministic method for identifying topological domains in genomes.

Physical tethering and volume exclusion determine higher-order genome organization in budding yeast.

ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs.

An allelic series of spontaneous Rorb mutant mice exhibit a gait phenotype, changes in retina morphology and behavior, and gene expression signatures associated with the unfolded protein response.

Exploring the spatial and temporal organization of a cell's proteome.

Spontaneous conformational change and toxin binding in alpha7 acetylcholine receptor: insight into channel activation and inhibition.

Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription.

The folding transition-state ensemble of a four-helix bundle protein: helix propensity as a determinant and macromolecular crowding as a probe.

ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization.

Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development.

DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces.

PI2PE: protein interface/interior prediction engine.

Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance.

Prediction of protein solubility from calculation of transfer free energy.

Producing genome structure populations with the dynamic and automated PGS software.

Quantitative Methods to Investigate the 4D Dynamics of Heterochromatic Repair Sites in Drosophila Cells.

GBr(6): a parameterization-free, accurate, analytical generalized born method.