Lecturers: Dr. Chuan-Hsiung Chang, Dr. Ueng-Cheng Yang, Dr.
Ho-Ming Chen, Dr. Jung-Hsin Lin, Dr. Wailap Victor Ng, Dr. Yuh-Shan Jou, Dr.
Jie-Rong Huang, Dr. Seng-Ling Tang, Dr. An-Chi Wei
TA: N/A (Please refers to the lectures respectively
shall you have any questions of each class)
Office hours: N/A
Grades: Midterm exam 50%. Final exam 50%.
Place:Room 101, New Building of the Institute of Information
Science, Academia Sinica
Time:Thursday, 3:30 Pm-5:00 pm
Chair:Dr. Chuan-Hsiung Chang
*Effective from 2014 Fall semester, all TIGP-BP students are required to present
once a semester in seminar.
*Students are required to submit the topics by 09/12/2019 (First Year Students: The
paper will be assigned by your lab professor)
*The following schedule is confirmed and will not be changed. Please contact Dr.
Chuan-Hsiung Change if you do have a difficulty on the assigned date.
*The presenter shall introduce the host and attended professors in the beginning of
*Seminar presentation guidelines for PhD program students_20190909
Novel insights on green sulfur bacteria in coral skeletons
Student / Teacher
Shan-Hua Yang, Kshitij Tandon, Chih-Ying Lu, Naohisa Wada, Chao-Jen Shih, Silver Sung-Yun Hsiao, Wann-Neng Jane, Tzan-Chain Lee, Chi-Ming Yang, Chi-Te Liu, Vianney Denis, Yu-Ting Wu, Li-Ting Wang, Lina Huang, Der-Chuen Lee, Yu-Wei Wu, Hideyuki Yamashiro and Sen-Lin Tang
"Metagenomic, phylogenetic, and functional characterization of predominant endolithic green sulfur bacteria in the coral Isopora palifera", Microbiome, 7:3, 4 January2019.
Journal details: https://doi.org/10.1186/s40168-018-0616-z
Ching-Ching Yeh, Jun-Liang Luo, Nam Nhut Phan, Yi-Chun Cheng, Lu-Ping Chow, Mong-Hsun Tsai, Eric Y. Chuang and Liang-Chuan Lai, "Different effects of long noncoding RNA NDRG1-OT1 fragments on NDRG1 transcription in breast cancer cells under hypoxia", RNA Biology, 04 December 2018.Available from: https://www.tandfonline.com/doi/full/10.1080/15476286.2018.1553480?scroll=top&needAccess=true
Salawu, E. O.* In Silico Study Reveals How E64 Approaches, Binds to, and Inhibits Falcipain-2 of Plasmodium falciparum that Causes Malaria in Humans. Sci. Rep. 2018, 8, 34622. Available from https://doi.org/10.1038/s41598-018-34622-1. (2017 IF: 4.1; 5-yr IF 4.6)
Neha Warikoo, Yung-Chun Chang, Wen-Lian Hsu; "LPTK: a linguistic pattern-aware dependency tree kernel approach for the BioCreative VI CHEMPROT task," Database, Volume 2018, 1 January 2018, bay108,https://doi.org/10.1093/database/bay108
Neha Warikoo, Yung-Chun Chang, Hong-Jie Dai, and Wen-Lian Hsu, "An Ensemble Neural Network Model for Benefiting Pregnancy Health Stats from Mining Social Media," to appear in The Asia Information Retrieval Societies Conference 2018.
Joanito, I., Chu J.-W., Wu S.H. and Hsu C.-P., An incoherent feed-forward loop switches the Arabidopsis clock rapidly between two hysteretic states. Scientific Reports, 2018. 8(1): p. 13944. doi: 10.1038/s41598-018-32030-z
Chang, K.-C.#,*; Salawu, E. O.#; Chang, Y.-Y.; Wen, J.-D.; Yang, L.-W.* Resolution-Exchanged Structural Modeling and Simulations Jointly Unravel That Subunit Rolling Underlies the Mechanism of Programmed Ribosomal Frameshifting. Bioinformatics 2018, bty762. Available from: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty762/5086394?guestAccessKey=3484e180-0783-4552-aa80-2bcea3e406e8. (2017 IF: 5.5; 5-yr IF: 8.6)
Salawu, E. O.*. The Impairment of TorsinA’s Binding to and Interactions with Its Activator: An Atomistic Molecular Dynamics Study of Primary Dystonia. Front. Mol. Biosci. 2018, 5. Available from: https://doi.org/10.3389/fmolb.2018.00064.
Divya Sahu, Shinn-Ying Ho, Hsueh-Fen Juan, Hsuan-Cheng Huang. "High-risk, Expression-Based Prognostic Long Noncoding RNA Signature in Neuroblastoma" JNCI Cancer Spectrum, Volume 2, Issue 2, 1 February 2018, pky015, https://doi.org/10.1093/jncics/pky015
Kshitij Tandon, Shan-Hua Yang, Min-Tao Wan, Chia-Chin Yang, Bayanmunkh Baatar, Chih-Yu Chiu, Jeng-Wei Tsai, Wen-Cheng Liu, Sen-Lin Tang. "Bacterial Community in Water and Air of Two Sub-Alpine Lakes in Taiwan" Microbes Environ. Vol.00, No.0, 000-000, 2018.
Kshitij Tandona,b,c, Pei-Wen Chianga, Wen-Ming Chend, Sen-Lin Tanga "Draft Genome Sequence of Endozoicomonas acroporae Strain Acr-14T, Isolated from Acropora Coral" Genome Announc 6:e01576-17. Published 8 February 2018.
Jinn-Jy Lin, Feng-Yu Wang, Wen-Hsiung Li & Tzi-Yuan Wang "The rises and falls of opsin genes in 59 ray-finned fish genomes and their implications for environmental adaptation" Scientific Reports, volume 7, Article number: 15568 (2017)
Sen-Lin Tang, Kshitij Tandon, David Ackland and Saman Kumara Halgamuge, "CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision" BMC Bioinformatics BMC series – open, inclusive and trusted201718(Suppl 16):571https://doi.org/10.1186/s12859-017-1967-3© The Author(s) 2017Published: 28 December 2017
Chu SK, Yang HC. "Interethnic DNA methylation difference and its implications in pharmacoepigenetics."Epigenomics. 2017 Nov;9(11):1437-1454.doi: 10.2217/epi-2017-0046. Epub 2017 Sep 8.
Hsiang-Wei Kuo, Chia-Lung Shih, Jieh-Hen Tsung, Sheng-Wen Liu, Shih-Kai Chu, Hsin-Chou Yang, Hsiao-Hui Tsou, Zih-Hsiang Wang, Andrew C. H. Chen, Yu-Li Liu "Pharmacogenomics study on cadherin 2 network with regard to HIV infection and methadone treatment outcome" PLOS ONE, March 30, 2017.
Lai E-Y, Chen Y-H, Wu K-P (2017) "A knowledge-based T2-statistic to perform pathway analysis for quantitative proteomic data." PLoS Computational Biology June 16, 2017.
Salawu, E. O.; Hesse, E.*; Stopford, C.; Davey, N.; Sun, Y.* Applying Machine Learning Methods for Characterization of Hexagonal Prisms from Their 2D Scattering Patterns--an Investigation Using Modelled Scattering Data. J. Quant. Spectrosc. Radiat. Transf. 2017, 201, 115–127. Available from: https://doi.org/10.1016/j.jqsrt.2017.07.001. (2017 IF: 2.6; 5-yr IF 2.7)
Shan-Hua Yang1†, Ching-Hung Tseng2†, Chang-Rung Huang1‡, Chung-Pin Chen3, Kshitij Tandon1,4,5, Sonny T. M. Lee6, Pei-Wen Chiang1 , Jia-Ho Shiu1,7,8 , Chaolun A. Chen1 and Sen-Lin Tang. "Long-Term Survey Is Necessary to Reveal Various Shifts of Microbial Composition in Corals" frontiers in Microbiology, 13 June 2017 | doi.org/10.3389/fmicb.2017.01094
Wei-Sheng Tien, Jun-Hong Chen and Kun-Pin Wu. "SheddomeDB: the ectodomain shedding database for membrane-bound shed markers." BMC Bioinformatics BMC series – open, inclusive and trusted201718(Suppl 3):42 DOI: 10.1186/s12859-017-1465-7
Sean Chun-Chang Chen, Trees-Juen Chuang and Wen-Hsiung Li. "The Relationships Among MicroRNA Regulation, Intrinsically Disordered Regions, and Other Indicators of Protein Evolutionary Rate." Mol Biol Evol (2011) 28 (9): 2513-2520.doi: 10.1093/molbev/msr068 First published online: March 11, 2011
Bioinformatics Program, TIGP, Academia Sinica, Taiwan©2019