Harianto Tjong, Ph.D.

Computational Scientist

My primary research field is three-dimensional genome organization which includes development of computational analysis methods from data generated using genome technologies such as ChIA-PET, ChIA-Drop, and HiC-based sequencing techniques.

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Bioinformatics
Computational Biology
Genetics and Genomics

As computational scientist under the Dept. of Genome Technologies, my main role include supporting scientific research in the group and R&D team for GT production.

Develop and maintain computational tools or pipelines for NGS data QC & analysis.
Design & implement methods and problem-solving strategies for scientific research.
Perform QC, kit testing, and troubleshooting in support for JGM scientific service.

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Selected Publications

53 Zhu Y, Gujar AD, Wong CH, Tjong H, Ngan CY, Gong L, Chen YA, Kim H, Liu J, Li M, Mil-Homens A, Maurya R, Kuhlberg C, Sun F, Yi E, deCarvalho AC, Ruan Y, Verhaak RGW, Wei CL. Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. Cancer Cell. 2021 May 10; 39(5):694-707.e7
32 Lee B, Wang J, Cai L, Kim M, Namburi S, Tjong H, Feng Y, Wang P, Tang Z, Abbas A, Wei CL, Ruan Y, Li S. ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization. Sci Adv. 2020 Jul; 6(28):eaay2078
73 Ngan CY, Wong CH, Tjong H, Wang W, Goldfeder RL, Choi C, He H, Gong L, Lin J, Urban B, Chow J, Li M, Lim J, Philip V, Murray SA, Wang H, Wei CL. Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development. Nat Genet. 2020 Mar; 52(3):264-272
52 Bertolini JA, Favaro R, Zhu Y, Pagin M, Ngan CY, Wong CH, Tjong H, Vermunt MW, Martynoga B, Barone C, Mariani J, Cardozo MJ, Tabanera N, Zambelli F, Mercurio S, Ottolenghi S, Robson P, Creyghton MP, Bovolenta P, Pavesi G, Guillemot F, Nicolis SK, Wei CL. Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance. Cell Stem Cell. 2019 Mar 7; 24(3):462-476.e6
36 Gong L, Wong CH, Cheng WC, Tjong H, Menghi F, Ngan CY, Liu ET, Wei CL. Picky comprehensively detects high-resolution structural variants in nanopore long reads. Nat Methods. 2018 Jun; 15(6):455-460
45 Hua N, Tjong H, Shin H, Gong K, Zhou XJ, Alber F. Producing genome structure populations with the dynamic and automated PGS software. Nat Protoc. 2018 May; 13(5):915-926
83 Caridi CP, Delabaere L, Tjong H, Hopp H, Das D, Alber F, Chiolo I. Quantitative Methods to Investigate the 4D Dynamics of Heterochromatic Repair Sites in Drosophila Cells. Methods Enzymol. 2018; 601:359-389
83 Li Q, Tjong H, Li X, Gong K, Zhou XJ, Chiolo I, Alber F. The three-dimensional genome organization of Drosophila melanogaster through data integration. Genome Biol. 2017 Jul 31; 18(1):145
80 Batra J, Tjong H, Zhou HX. Electrostatic effects on the folding stability of FKBP12. Protein Eng Des Sel. 2016 Aug; 29(8):301-308
54 Dai C, Li W, Tjong H, Hao S, Zhou Y, Li Q, Chen L, Zhu B, Alber F, Jasmine Zhou X. Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities. Nat Commun. 2016 May 31; 7:11549
28 Shin H, Shi Y, Dai C, Tjong H, Gong K, Alber F, Zhou XJ. TopDom: an efficient and deterministic method for identifying topological domains in genomes. Nucleic Acids Res. 2016 Apr 20; 44(7):e70
57 Tjong H, Li W, Kalhor R, Dai C, Hao S, Gong K, Zhou Y, Li H, Zhou XJ, Le Gros MA, Larabell CA, Chen L, Alber F. Population-based 3D genome structure analysis reveals driving forces in spatial genome organization. Proc Natl Acad Sci U S A. 2016 Mar 22; 113(12):E1663-72

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Harianto Tjong, Ph.D.

Computational Scientist

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Selected Publications