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Harianto Tjong · SciRah

Researcher profile · Semantic Scholar

Harianto Tjong

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Harianto Tjong — researcher profile on SciRah

h-index: 22
Works: 48
Citations: 2,719

Most-cited papers

Solid-phase chromosome conformation capture for structural characterization of genome architectures
R. Kalhor, Harianto Tjong, N. Jayathilaka, F. Alber +1 more
2011Nature Biotechnology563 citations Open access
Semantic Scholar
TopDom: an efficient and deterministic method for identifying topological domains in genomes
Hanjun Shin, Yi Shi, Chao Dai, Harianto Tjong +3 more
2015Nucleic Acids Research318 citations Open access
Semantic Scholar
Oncogenic Extrachromosomal DNA Functions as Mobile Enhancers to Globally Amplify Chromosomal Transcription
Yan-Fen Zhu, Amit D. Gujar, Chee-Hong Wong, Harianto Tjong +15 more
2021Cancer Cell243 citations Open access
Semantic Scholar
Physical tethering and volume exclusion determine higher-order genome organization in budding yeast
Harianto Tjong, Ke Gong, Lin Chen, F. Alber
2012Genome Research208 citations Open access
Semantic Scholar
Population-based 3D genome structure analysis reveals driving forces in spatial genome organization
Harianto Tjong, Wenyuan Li, R. Kalhor, Chao Dai +9 more
2016Proceedings of the National Academy of Sciences of the United States of America174 citations Open access
Semantic Scholar
DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces
Harianto Tjong, Huan-Xiang Zhou
2007Nucleic Acids Research146 citations Open access
Semantic Scholar
Chromatin Interaction Analyses Elucidate PRC2-bound Silencers’ Roles in Mouse Development
C. Ngan, Chee-Hong Wong, Harianto Tjong, Wenbo Wang +13 more
2020Nature Genetics97 citations Open access
Semantic Scholar
Picky Comprehensively Detects High Resolution Structural Variants in Nanopore Long Reads
Liang Gong, Chee-Hong Wong, Wei-Chung Cheng, Harianto Tjong +4 more
2018Nature Methods90 citations Open access
Semantic Scholar
GBr(6): a parameterization-free, accurate, analytical generalized born method.
Harianto Tjong, Huan-Xiang Zhou
2007Journal of Physical Chemistry B89 citations
Semantic Scholar
Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance
J. Bertolini, R. Favaro, Yan-Fen Zhu, Miriam Pagin +19 more
2019Cell Stem Cell85 citations Open access
Semantic Scholar
The three-dimensional genome organization of Drosophila melanogaster through data integration
Qing-Jiao Li, Harianto Tjong, Xiao Li, Ke Gong +3 more
2017Genome Biology81 citations Open access
Semantic Scholar
Producing genome structure populations with the dynamic and automated PGS software
N. Hua, Harianto Tjong, Hanjun Shin, Ke Gong +2 more
2018Nature Protocols64 citations Open access
Semantic Scholar
Prediction of protein solubility from calculation of transfer free energy.
Harianto Tjong, Huan-Xiang Zhou
2008Biophysical Journal56 citations Open access
Semantic Scholar
Spontaneous conformational change and toxin binding in α7 acetylcholine receptor: Insight into channel activation and inhibition
M. Yi, Harianto Tjong, Huan-Xiang Zhou
2008Proceedings of the National Academy of Sciences of the United States of America50 citations Open access
Semantic Scholar
GBr6NL: a generalized Born method for accurately reproducing solvation energy of the nonlinear Poisson-Boltzmann equation.
Harianto Tjong, Huan-Xiang Zhou
2007Journal of Chemical Physics46 citations
Semantic Scholar
ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization
Byoungkoo Lee, Jiahui Wang, Liuyang Cai, Minji Kim +9 more
2020Science Advances41 citations Open access
Semantic Scholar
Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities
Chao Dai, Wenyuan Li, Harianto Tjong, S. Hao +6 more
2016Nature Communications38 citations Open access
Semantic Scholar
Exploring the Spatial and Temporal Organization of a Cell’s Proteome
M. Beck, M. Topf, Zachary Frazier, Harianto Tjong +3 more
2010Journal of Structural Biology37 citations Open access
Semantic Scholar
Global reorganization of budding yeast chromosome conformation in different physiological conditions
E. Dultz, Harianto Tjong, Elodie Weider, Mareike Herzog +6 more
2016Journal of Cell Biology36 citations Open access
Semantic Scholar
PI2PE: protein interface/interior prediction engine
Harianto Tjong, Sanbo Qin, Huan-Xiang Zhou
2007Nucleic Acids Res.32 citations Open access
Semantic Scholar
On the Dielectric Boundary in Poisson-Boltzmann Calculations.
Harianto Tjong, Huan-Xiang Zhou
2008Journal of Chemical Theory and Computation29 citations Open access
Semantic Scholar
ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs
Hao-Xi Chai, Harianto Tjong, Peng Li, W. Liao +6 more
2023Nature Communications23 citations Open access
Semantic Scholar
Comparative 3D Genome Structure Analysis of the Fission and the Budding Yeast
Ke Gong, Harianto Tjong, X. Zhou, F. Alber
2015PLoS ONE22 citations Open access
Semantic Scholar
The folding transition-state ensemble of a four-helix bundle protein: helix propensity as a determinant and macromolecular crowding as a probe.
Harianto Tjong, Huan-Xiang Zhou
2010Biophysical Journal20 citations Open access
Semantic Scholar
Inverse tuning of metal binding affinity and protein stability by altering charged coordination residues in designed calcium binding proteins
A. Maniccia, Wei Yang, Julian A. Johnson, Shun-yi Li +4 more
2009PMC Biophysics18 citations Open access
Semantic Scholar
Rational design of a conformation switchable Ca2+ and Tb3+ binding protein without using multiple coupled metal binding sites
Shun-yi Li, Wei Yang, A. Maniccia, D. Barrow +3 more
2008The FEBS Journal18 citations Open access
Semantic Scholar
Quantitative methods to investigate the 4D dynamics of heterochromatic repair sites in Drosophila cells
Christopher P. Caridi, Laetitia Delabaere, Harianto Tjong, Hannah Hopp +3 more
2017bioRxiv17 citations Open access
Semantic Scholar
Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription
Aziz Taghbalout, Chia-Hao Tung, Patricia A. Clow, Harianto Tjong +8 more
2025Cancer Cell16 citations Open access
Semantic Scholar
The dependence of electrostatic solvation energy on dielectric constants in Poisson-Boltzmann calculations.
Harianto Tjong, Huan-Xiang Zhou
2006Journal of Chemical Physics16 citations
Semantic Scholar
Accurate Calculations of Binding, Folding, and Transfer Free Energies by a Scaled Generalized Born Method
Harianto Tjong, Huan-Xiang Zhou
2008Journal of Chemical Theory and Computation10 citations Open access
Semantic Scholar
Solid-phase chromosome conformation capture for structural characterization of genome architectures
R. Kalhor, Harianto Tjong, N. Jayathilaka, F. Alber +2 more
20138 citations
Semantic Scholar
Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription
Aziz Taghbalout, Chia-Hao Tung, Patricia A. Clow, Ping Wang +8 more
2024bioRxiv7 citations
Semantic Scholar
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
G. Murray, J. Bubier, O. Zinder, B. Harris +9 more
2023G35 citations Open access
Semantic Scholar
Electrostatic effects on the folding stability of FKBP12.
J. Batra, Harianto Tjong, Huan-Xiang Zhou
2016Protein engineering, design & selection : PEDS5 citations Open access
Semantic Scholar
ChIA-PIPE: A fully automated pipeline for ChIA-PET data analysis and visualization
D. Capurso, Jiahui Wang, S. Tian, Liuyang Cai +8 more
2018bioRxiv4 citations Open access
Semantic Scholar
Nanopore Sequencing Reveals High-Resolution Structural Variation in the Cancer Genome
Liang Gong, Chee-Hong Wong, Wei-Chung Cheng, Harianto Tjong +4 more
2017bioRxiv4 citations Open access
Semantic Scholar
Modeling Protein–Protein and Protein–Nucleic Acid Interactions: Structure, Thermodynamics, and Kinetics
Huan-Xiang Zhou, Sanbo Qin, Harianto Tjong
20084 citations
Semantic Scholar
PGS: a dynamic and automated population-based genome structure software
N. Hua, Harianto Tjong, Hanjun Shin, Ke Gong +2 more
2017bioRxiv2 citations Open access
Semantic Scholar
An allelic series of spontaneous mutations in Rorb cause a gait phenotype, retinal abnormalities, and transcriptomic changes relevant to human neurodevelopmental conditions
G. Murray, J. Bubier, O. Zinder, B. Harris +9 more
2021bioRxiv1 citations Open access
Semantic Scholar
Additional file 2: of The three-dimensional genome organization of Drosophila melanogaster through data integration
Qing-Jiao Li, Harianto Tjong, Xiao Li, Ke Gong +3 more
20171 citations
Semantic Scholar
The 3D genome organization of Drosophila melanogaster through data integration
Qing-Jiao Li, Harianto Tjong, Xiao Li, Ke Gong +3 more
2017bioRxiv1 citations Open access
Semantic Scholar
Modeling Protein Solubility in Implicit Solvent
Harianto Tjong, Huan-Xiang Zhou
20101 citations
Semantic Scholar
GBr$^{6}$: a Parameterization-Free, Accurate, Analytical Generalized Born Model
Harianto Tjong, Huan-Xiang Zhou
20061 citations
Semantic Scholar
genome organization in budding yeast Physical tethering and volume exclusion determine higher-order Material
Harianto Tjong, Ke Gong, Lin Chen, F. Alber
20120 citations
Semantic Scholar
3D genome universe of the budding yeast
Harianto Tjong, Ke Gong, Lin Chen, F. Alber
20120 citations
Semantic Scholar
Computational Model to Predict Folding Stability of FKBP
Harianto Tjong, J. Batra, Huan-Xiang Zhou
20090 citations Open access
Semantic Scholar
Modeling Electrostatic Contributions to Protein Folding and Binding
Harianto Tjong
20080 citations
Semantic Scholar
Mechanism of folding/unfolding of Rd-apocyt $b_{562}$: a molecular dynamics simulation study
Harianto Tjong, Huan-Xiang Zhou
20050 citations
Semantic Scholar

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