Basic Molecular Biology I (B1)
Place:Room 107, New Building of the Institute of Information Science, Academia Sinica.
Time:Tuesday 09:00-12:00
Chair:Dr. Chuan-Hsiung Chang
Aim: understanding the key concepts in molecular and cell biology and their experimental underpinnings
Textbook: (Required)
1.Molecular Cell Biology, 8th edition, by Harvey Lodish et al. Publisher: W. H. Freeman. International Edition (1 April, 2016). ISBN-13: 978-1464183393.
Local book store:
Reference: (Recommended but not required)
2. Molecular Biology of the Cell, 6th edition, 2014.
3. Molecular Biology : Principles of Genome Function, 2nd edition, 2014.
4. Biochemistry: A Short Course, 2nd edition, by Lubert Stryer et al. Publisher: W. H. Freeman (December 23, 2011). ISBN-10: 1429283602, ISBN-13: 978-1429283601.   

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%.

Week Date Topics/Brief Description Lecturers
1 2019/09/10 Molecules, Cells, and Evolution Dr. Chuan-Hsiung Chang
2 2019/09/17 Chemical Foundations Dr. Chao-Ping Hsu
3 2019/09/24 Protein Structure and Function Dr. Jie-Rong Huang
4 2019/10/01 Transcriptional Control of Gene Expression Dr. Seng-Ling Tang
5 2019/10/08 Basic Molecular Genetic Mechanisms Dr. Ueng-Cheng Yang
6 2019/10/15 Genes, Genomics, and Chromosomes Dr. Chuan-Hsiung Chang
7 2019/10/22 Molecular Genetic Techniques Dr. Ueng-Cheng Yang
8 2019/10/29 Review Week ---
9 2019/11/05 Midterm Exam ---
10 2019/11/12 Post-Transcriptional Gene Control Dr. Ho-Ming Chen
11 2019/11/19 Biomembrane Structure and Transport Dr. Jung-Hsin Lin
12 2019/11/26 Cellular Energetics Dr. Ueng-Cheng Yang
13 2019/12/03 Signal Transduction and G Protein–Coupled Receptors Dr. Wailap Victor Ng
14 2019/12/10 Signaling Pathways That Control Gene Expression Dr. Wailap Victor Ng
15 2019/12/17 The Eukaryotic Cell Cycle Dr. An-Chi Wei
16 2019/12/24 Cancer Dr. Yuh-Shan Jou
17 2019/12/31 Review Week ---
18 2020/01/07 Final Exam ---

Biological Computing (C1)
Place:Room 107, New Building of the Institute of Information Science, Academia Sinica
Time:Friday 14:00-17:00
Chair:Dr. Huai-Kuang Tsai
Aim: The aim of the course is to link issues in computer science to biology and thus capture the interest of students in both areas. It is expected that students will acquire and retain important knowledge about computational biology
Outline:The course provides an introduction to the basic computational concepts and methods used in molecular biology and genetics. It covers classic algorithmic techniques (for examples: divide and conquer algorithm, dynamic programming …), data structures (e.g. queue, tree…), and common computational problems in biology (such as motif finding, sequence alignment …). In addition, Bioinformatics approaches for next generation sequencing and the most up-to-date technology will be addressed as well.
Lecturers:Dr. Wen-Lian Hsu, Dr. Yu-Jung Chang, Dr. Huai-Kuang Tsai, Dr. Hsin-Nan Lin, Dr. Chun-Chieh Shih, Dr. Ting-Yi Sung, Dr. Ching-Tai Chen
Textbook: N/A
TA: Onkar Singh Email:
Office hours: TBD
Grades: Midterm exam 50%. Final exam 50%.
Week Date Topics/Brief Description Lecturers
1 2019/09/13(Holiday)
-->09/16 14:00-17:00
Analysis of Algorithms Dr. Wen-Lian Hsu
2 2019/09/20 Recurrence Dr. Wen-Lian Hsu
3 2019/09/27 Introduction to Data Structure (I) Dr. Yu-Jung Chang
4 2019/10/04 Introduction to Data Structure (II) Dr. Yu-Jung Chang
5 2019/10/11(Holiday)
--> 10/14
Algorithmic Techniques Dr. Wen-Lian Hsu
6 2019/10/18 Motif Finding Dr. Ting-Yi Sung
7 2019/10/25 Graph Algorithms Dr. Ting-Yi Sung
8 2019/11/01 Review Week ---
9 2019/11/08 Midterm Exam ---
10 2019/11/15 Sequence Alignment (I) Dr. Huai-Kuang Tsai
11 2019/11/22 Sequence Alignment (II) Dr. Huai-Kuang Tsai
12 2019/11/29 Combinatorial Pattern Matching Dr. Ching-Tai Chen
13 2019/12/06 Suffix Trees Dr. Ching-Tai Chen
14 2019/12/13 The Analysis of Next Generation Sequencing Data (I) Dr. Hsin-Nan Lin
15 2019/12/20 The Analysis of Next Generation Sequencing Data (II) Dr. Hsin-Nan Lin
16 2019/12/27 Fundamentals of Molecular Evolution and Phylogenetic Tree Construction Dr. Jynn-Jy Lin
17 2020/01/03 Review Week ---
18 2020/01/10 Final Exam ---

S1 course Material
Fundamental Statistical Methods in Bioinformatics (S1)
Place:Room 108, Old Building of the Institute of Information Science, Academia Sinica
Time:Thursday, 09:00 am-12:00 pm
Chair:Dr. Hsin-Chou Yang
Outline:This course covers the fundamentals of statistics and basic tools for bioinformatics analysis. In the first part students will learn basic statistical concepts and methods, including probability, random variables and distributions, parameter estimation, hypothesis testing, regression analysis, and categorical data analysis. In the second part several commonly used methods in bioinformatics will be introduced, including statistical meta analysis, survival analysis, clustering, classification, and nonparametric statistics.
Textbook: Fundamentals of Biostatistics (author: Bernard Rosner), Cengage Learning.
Reference book: Pattern Recognition (author: Richard O. Duda, Peter E. Hart, and David G. Stork), Wiley.
Lecturers: Chen-Hsiang Yeang, Hsin-Chou Yang, Shinsheng Yuan, Grace Shieh, Hsuan-Yu Chen, and Wei-Chung Liu
TA: Jen-Hung Wang 王人弘 Email:
Office hours: TBD
Grades: Midterm exam 50%. Final exam 50%.
Week Date Topics/Brief Description Sub-topics/Detailed Description Lecturers
1 2019/09/12 Descriptive Statistics, Genomic Data Analysis (1) Introduction to statistics
(2) Descriptive statistics
(3) Fundamental of molecular biology
(4) Genomic data analysis
Dr. Chen-Hsiang Yeang
2 2019/09/19 Probability (1) Applications in statistical genetics
(2) Combinatorial analysis
(3) Axioms of probabilities
(4) Conditional probability and independence
(5) Random variable and distribution function
Dr. Hsin-Chou Yang
3 2019/09/26 Discrete Distributions and Contingency Tables (1) An application inpharmacogenetic study
(2) Discrete/continuous/mixed distributions
(3) Joint/marginal/conditional distributions
(4) Special discrete distributions
(5) Introduction to contingency table
Dr. Hsin-Chou Yang
4 2019/10/03 Continuous Distributions, Expectations and Basic Statistics (1) Continuous random variable
(2) Expectation
(3) Basic statistics
(4) Limit theorems (optional)
Dr. Hsin-Chou Yang
5 2019/10/10
-->10/16 14:00-17:00
Parameter Estimation and Confidence Interval (1) Unbiasedness
(2) Point estimation (substitution principles, least square estimate, maximum likelihood estimate)
(3) Interval estimation
Dr. Shinsheng Yuan
6 2019/10/17 Hypothesis Testing, P-value and False Discovery Rate (1) Hypothesis testing
(2) Type I error and type II error
(3) P-value
(4) One-sample and two-sample z-tests
(5) One-sample, two-sample, and paired t-tests
(6) Bonferroni adjustment, false discovery rate, and q value
Dr. Grace Shieh
7 2019/10/24 Analysis of Categorical Data, Chisq and Multinomial (1) Incidence proportion and odds ratio
(2) Two-sample test for binomial proportions
(3) Contingency-table approach
(4) Fisher’s exact test (5) McNemar’s test
(6) Kappa statistic
Dr. Hsuan-Yu Chen
8 2019/10/31 Review Week
9 2019/11/07 Midterm Exam
10 2019/11/14 Correlation, Regression Analysis and ANOVA (1) Linear regression with one independent variable
(2) Inference in regression analysis
(3) Diagnostic and remedial measures (4) Simultaneous inferences and other topics
(5) Matrix approach to simple linear regression (6) Multiple linear regression
(7) Building the regression model
(8) Qualitative predictor variables(9) Analysis of variance
Dr. Grace Shieh
11 2019/11/21 Logistic Regression and Statistical Meta Analysis (1) Logistic regression
(2) Meta analysis
(effect size, precision, study weights, summary effect, heterogeneity, fixed-effect model, random-effect model, software)
Dr. Shinsheng Yuan
12 2019/11/28 Survival Data Analysis (1) Mantel-Haenszel test
(2) Survival and hazard functions
(3) Kaplan Meier estimate
(4) Log-rank test
(5) Proportional-hazards model
(6) Lung cancer study
Dr. Hsuan-Yu Chen
13 2019/12/05 Clustering (1) Clustering by geometry (K-means, EM algorithm, hierarchical clustering, self- organizing map, principal component analysis, independent component analysis) (2)
Clustering on graphs (Basic concepts, max flow – min cut, normal cuts, spectral clustering, and community detection)
(3) Advanced topics (Chinese restaurant process and affinity propagation)
Dr. Chen-Hsiang Yeang
14 2019/12/12 Classification (1) Binary classifications (Bayesian detection theory, naïve Bayes and other generative models, non-parametric methods, Fisher linear discriminant, support vector machines and kernel techniques, artificial neural networks, and boosting)
(2) Advanced topics in supervised learning (multi-class classification, feature selection, semi-supervised learning, active learning)
Dr. Chen-Hsiang Yeang
15 2019/12/19 Nonparametric Statistics (I) (1) Bootstrap
(2) One-sample sign test
(3) One-sample Wilcoxon signed-rank test
(4) Wilcoxon rank-sum test (Mann-Whitney U test)
(5) Sign test for paired data
(6) Wilcoxon signed-rank test for paired data
Dr. Wei-Chung Liu
16 2019/12/26 Nonparametric Statistics (II) (1) Kruskal-Wallis test
(2) Randomization/permutation test for two-way ANOVA
(3) The product-moment correlation coefficient
(4) Spearman rank correlation
(5) Kendall’s coefficient of rank correlation
Dr. Wei-Chung Liu
17 2020/01/02 Review Week
18 2020/01/09 Final Exam

P1 Course Material
Programming (Python) (P1)
Place:Room 108, Old Building of the Institute of Information Science, Academia Sinica
Time:Friday, 10:00am-12:00pm
Chair:Dr. Wang, John
Outline:This course introduces basic aspects f programming language and its application in bioinformatics. First, fundamental programming techniques in Python are introduced. After that, this course focuses on the practical implementation of programs to analyze various biological data. The use of existing available resources from the Internet is also incorporated. Finally, the students implement bioinformatics projects (i.e., motif finding, pattern matching, sequence alignment, biomedical database analysis, etc.)
Lecturers: BP- Dr. Wang, John; Dr. Huang, Jia Hsin SHNCC-Dr. Wang, Chih-Yu; Dr. Li, Su
Textbook: Python for Biologists: A complete programming course for beginners Advanced Python for Biologists (Reference) Python for Everybody - Exploring Data In Python 3
TA: Erickson Erigio Fajiculary 艾瑞克 Email:
Office hours: TBD
Grades: Midterm exam 25%. Final exam 30%. Homework 35%. Class performance (10%).
Week Date Topics/Brief Description Lecturers

-->09/18 09:00-11:00

Introduction to Python Dr. Li Su
2 2019/09/20 Basic Elements of Python I Dr. Su Li
3 2019/09/27 Basic Elements of Python II Dr. Su Li
4 2019/10/04 Basic statements I: branching programs and inputs Dr. John Wang
5 2019/10/11
(Holiday) -
10/5 10:00-12:00
Basic statements II: iterative programs Dr. John Wang
6 2019/10/18 Functions: scope rules and passing arguments Dr. John Wang
7 2019/10/25 Modules, Files, and Structured Types Dr. Te-Chuan Chiu
8 2019/11/01 Exception handling Dr. Te-Chuan Chiu
9 2019/11/08 Review week
10 2019/11/15 Midterm exam
11 2019/11/22 Introduction to Biopython Dr. Ching-Fen Chang
12 2019/11/29 Regular expressions Dr. Ching-Fen Chang
13 2019/12/06 Object-oriented programming: classes Dr. John Wang (Chih-Ming Chen)
14 2019/12/13 Data analysis toolbox : NumPy, Pandas, Matplotlib Dr. Jia Hsin Huang
15 2019/12/20 Machine learning I: scikit-learn Dr. Jia Hsin Huang
16 2019/12/27 Machine learning II: scikit-learn & keras Dr. Jia Hsin Huang
17 2019/01/03 Review week
18 2019/01/10 Final exam

Student Presentation

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 each seminar.

*Seminar presentation guidelines for PhD program students_20190909

Week Date TIGP Bioinformatics
1 2019/09/12 N/A
2 2019/09/19 N/A
3 2019/09/26 倪崇恩 (YMU)Topic:
4 2019/10/03 呂俊良(YMU)Topic:
5 2019/10/10(Holiday) N/A
6 2019/10/17 段惟芳(YMU)Topic:
7 2019/10/24 Erickson Erigio Fajiculary
8 2019/10/31 葉奕成(YMU)Topic: Clinical-grade computational pathology using weakly supervised deep learning on whole slide images
9 2019/11/07 Midterm Exam
10 2019/11/14 Yu-Hsin Chen
11 2019/11/21 Chayanika Goswami
12 2019/11/28 Adeshina Oyedele Bello
13 2019/12/05 Jen-Hung Wang
14 2019/12/12 Yu-Hsiang Chen
15 2019/12/19 Yueh-Hua Tu
16 2019/12/26 Samarth Gupta
17 2020/01/02 Review Week
18 2020/01/09 Final Exam

Place: Room 101, New Building of the Institute of Information Science, Academia Sinica
Time:Thursday 14:00-15:20
Chair: Academia Sinica: Dr. Chun-Yen Lin (Informatics), Dr. Chien-Ling Lin (Biology), Dr. Wei-Chung Liu (Statistic)
Attend any 2 none-BP Seminars (either on campus or off campus is fine) and submit a report for each seminar to advisor/lab professor (Format: 1 page A4, 12pts font, single space). Please download the report form from BP web-page Grades: attendance 100%
Week Date Topics/Brief Description Speaker / Host
1 2019/09/12 N/A
Refers to Remarks 1
2 2019/09/19 N/A
Refers to Remarks 1
3 2019/09/26

Novel insights on green sulfur bacteria in coral skeletons

Dr. Shan-Hua Yang
Institute of fisheries science,National Taiwan UniversityHost: Yu-Hsiang Chen
4 2019/10/03-2019/10/02
AI Democratization in Taiwan Dr. Sheng-Wei (Kuan-Ta) Chen
5 2019/10/10
6 2019/10/17 TBD Dr. Trees-Juen Chuang
Host: Dr. Chien-Ling Lin
7 2019/10/24 TBD Prof. Cho-Yi Chen
8 2019/10/31 Review Week
9 2019/11/07 Midterm Week
10 2019/11/14 TBD Prof. Chen-Ching Lin
11 2019/11/21 TBD Dr. Hsueh-Fen Juan
12 2019/11/28 TBD Dr. Chao-Yuan Yeh
13 2019/12/05 TBD Dr. Ming-Jing Hwang
14 2019/12/12 TBD Prof. Chun-Yu lin
15 2019/12/19 TBD Dr. Ching-Tai Chen
16 2019/12/26 TBD Dr. Hsin-Nan Lin
17 2019/01/02 Review Week
18 2019/01/09 Final Exam

Lab Rotation
All 1st year students: Please inform BP office for the laboratory you are rotating

(Deadline for 2019 Fall Semester: 09/30/2019)
Student Advisor
Student Name Lab
Yueh-Hua Tu 杜岳華 (2019)
Samarth Gupta 山瑪斯 (2019)

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, January2019.                                     

Journal details:


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:

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 (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,

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 Reports2018. 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: (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:

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,

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 Reportsvolume 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 precisionBMC Bioinformatics BMC series – open, inclusive and trusted201718(Suppl 16):571© The Author(s) 2017
Published: 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: (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 |

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


Wu J.-F., Tsai H.-L., Joanito I., Wu Y.-C., Chang C.-W., Li Y.-H., Wang Y., Hong J. C., Chu J.-W., Hsu C.-P., and Wu S.-H. LWD-TCP complex activates the morning gene CCA1 in Arabidopsis. Nature Communications2016. 7: p. 13181. doi: 10.1038/ncomms13181
Huang, M.-C., Chuang, T.-P., Chen, C.-H., Wu, J.-Y., Chen, Y.-T., Li, L.-H.CA and Yang, H.-C. "An integrated analysis tool for hybridization intensities and genotypes using new-generation population-optimized human arrays."  BMC Genomics 17:266 .31 March 2016 DOI: 10.1186/s12864-016-2478-8
Sheng-Yao Su, Shu-Hwa Chen, I-Hsuan Lu, Yih-Shien Chiang, Yu-Bian Wang, Pao-Yang Chen and Chung-Yen Lin. "TEA: the epigenome platform for Arabidopsis methylome study." BMC Genomics 2016, 17:3326 DOI:10.1186/s12864-016-3326-6
Kevin J. Tsai, Mei-Yeh Jade Lu, Kai-Jung Yang, Mengyun Li, Yuchuan Teng, Shihmay Chen, Maurice S. B. Ku & Wen-Hsiung Li. "Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance." Scientific Reports 6, no. 35076(2016) doi:10.1038/srep35076
Jian, Jhih-Wei, Pavadai Elumalai, Thejkiran Pitti, Chih Yuan Wu, Keng-Chang Tsai, Jeng-Yih Chang, Hung-Pin Peng, and An-Suei Yang. "Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms." PloS one 11, no. 8 (2016): e0160315.
Divya Sahu, Chia-Lang Hsu, Chen-Ching Lin, Tz-Wen Yang, Wen-Ming Hsu, Shinn-Ying Ho1, Hsueh-Fen Juan, Hsuan-Cheng Huang, "Co-expression analysis identifies long noncoding RNA SNHG1 as a novel predictor for event-free survival in neuroblastomaOncotarget, DOI: 10.18632/oncotarget.11158
Chen, W.-T.; Huang, W.-Y.; Chen, T.; Salawu, E. O.; Wang, D.; Lee, Y.-Z.; Chang, Y.-Y.; Yang, L.-W.; Sue, S.-C.; Wang, X.; Yin H-S*. Structure and Function of Chicken Interleukin-1 Beta Mutants: Uncoupling of Receptor Binding and in Vivo Biological Activity. Sci. Rep. 20166, 27729. Available from: (2017 IF: 4.1; 5-yr IF 4.6)
Salawu, E. O.* RaFoSA: Random Forests Secondary Structure Assignment for Coarse-Grained and All-Atom Protein Systems. Cogent Biol. 20162 (1), 1214061. Available from: 
Priori, D.*; de Sousa, G.; Roisenberg, M.; Stopford, C.; Hesse, E.; Salawu, E. O.; Davey, N.; Sun, Y. Using Machine Learning Techniques to Recover Prismatic Cirrus Ice Crystal Size from 2-Dimensional Light Scattering Patterns. In International Conference on Artificial Neural Networks2016; pp 372–379. Available from:
Maloyjo Joyraj Bhattacharjee, Chun-Ping Yu, Jinn-Jy Lin, Cheng Siang Ng, Tzi-Yuan Wang, Hsin-Hung Lin, and Wen-Hsiung Li, "Regulatory Divergence among Beta-Keratin Genes during Bird Evolution." Molecular Biology and Evolution (2016): msw165.
Hui-Yin Chang, Ching-Tai Chen, T. Mamie Lih, Ke-Shiuan Lynn, Chiun-Gung Juo, Wen-Lian Hsu, Ting-Yi Sung, "iMet-Q: a user-friendly tool for metabolomics quantitation using dynamic peak-width determination,"   PLoS ONE, volume 11, number 1, pages e0146112, January 2016.
Chun-Ping Yu, Jinn-Jy Lin and Wen-Hsiung Li. (2016). "Positional distribution of transcription factor binding sites in Arabidopsis thaliana." Scientific Reports, doi:10.1038/srep25164
Lih, T. M., Choong, W. K., Chen, C. C., Cheng, C. W., Lin, H. N., Chen, C. T., ... & Sung, T. Y. (2016). "MAGIC-web: a platform for untargeted and targeted N-linked glycoprotein identification." Nucleic acids research.
Yang, H. C., Chu, S. K., Huang, C. L., Kuo, H. W., Wang, S. C., Liu, S. W., ... & Liu, Y. L. (2016). "Genome-wide pharmacogenomic study on Methadone Maintenance Treatment identifies SNP rs17180299 and multiple haplotypes on CYP2B6, SPON1, and GSG1L associated with plasma concentrations of methadone R-and S-enantiomers in heroin-dependent patients.PLOS Genet,12(3), e1005910.
Chia-Hsin Hsu, Austin W. T. Chiang, Ming-Jing Hwang and Ben-Yang Liao, "Proteins with highly evolvable domain architectures are non-essential but highly retained." Molecular Biology and Evolution (2016): msw006.
Chi-Fa Huang, Yao-Ming Chang, Jinn-Jy Lin, Chun-Ping Yu, Hsin-Hung Lin, Wen-Yu Liu, Suying Yeh, Shih-Long Tu, Shu-Hsing Wu, Maurice SB Ku, Wen-Hsiung Li, "Insights into the regulation of C4 leaf development from comparative transcriptomic analysis.", Current Opinion in Plant Biology 30 (2016): 1-10.
Bernhard Schaefke, Tzi-Yuan Wang, Chuen-Yi Wang, Wen-Hsiung Li. "Gains and losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and S. paradoxus" Accepted for publication by : Genome Biology and Evolution
Ke-Shiuan Lynn*, Chen-Chun Chen*, T. Mamie Lih*, Cheng-Wei Cheng, Wan-Chih Su, Chun-Hao Chang, Chia-Ying Cheng, Wen-Lian Hsu, Yu-Ju Chen, and Ting-Yi Sung, "MAGIC: an automated N-linked glycoprotein identification tool Using a Y1-ion pattern matching algorithm and in silico MS2 approach,"   Analytical Chemistry, volume 87, number 4, pages 2466-2473, February 2015. (*: co-first authors)
Ke-Shiuan Lynn, Mei-Ling Cheng, Yet-Ran Chen, Chin Hsu, Ann Chen, T. Mamie Lih, Hui-Yin Chang, Ching-jang Huang, Ming-Shi Shiao, Wen-Harn Pan, Ting-Yi Sung, and Wen-Lian Hsu, "Metabolite identification for mass spectrometry-based metabolomics using multiple types of correlated ion information,"   Analytical Chemistry, volume 87, number 4, pages 2143–2151, February 2015.
Chun-Ping Yu, Sean Chun-Chang Chen, Yao-Ming Chang, Wen-Yu Liu, Hsin-Hung Lin, Jinn-Jy Lin, Hsiang June Chen, Yu-Ju Lu, Yi-Hsuan Wu, Mei-Yeh Jade Lu, Chen-Hua Lu, Arthur Chun-Chieh Shih, Maurice Sun-Ben Ku, Shin-Han Shiu, Shu-Hsing Wu and Wen-Hsiung Li. "Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors", Proceedings of the National Academy of Sciences, April, 2015 doi:10.1073/pnas.1500605112.
Ching-Hung Tseng, Pei-Wen Chiang, Hung-Chung Lai, Fuh-Kwo Shiah, Ting-Chang Hsu, Yi-Lung Cheng, Liang-Saw Wen, Chun-Mao Tseng, Wung-Yang Shieh, Isaam saeed, Saman Halgamuge and Sen-Lin Tang. "Prokaryotic assemblages and metagenomes in pelagic zones of the South China Sea,"BMC  Genomics 2015, 16:219  doi:10.1186/s12864-015-1434-3
Barh, D.; Chaitankar, V.; Yiannakopoulou, E. C.; Salawu, E. O.; Chowbina, S.; Ghosh, P.; Azevedo, V. In Silico Models: From Simple Networks to Complex Diseases. In Animal Biotechnology; Elsevier, 2014; pp 385–404. Available from:
Shu-Mei Lai, Wei-Chung Liu and Ferenc Jordán, "A trophic overlap-based measure for species uniqueness in ecological networks" Ecol. M. Dec. 18, 2014
Che-Lun Hung andChi-Chun Chen.   "Computational Approaches for Drug Discovery"   Drug Development Research,   Volume 75, Issue 6, pages 412–418, Sep 04, 2014
Ching-Hung Tseng and Sen-Li Tang. "Marine Microbial Metagenomics: From Individual to the Environment" Int. J. Mol. Sci. 2014, 15(5), 8878-8892; doi:10.3390/ijms15058878
Kevin J. Tsai, Chuan-Hsiung Chang. "Diagnostics for Stochastic Genome-Scale Modeling via Model Slicing and Debugging" Plos ONE, DOI:10.1371/journal.pone.0100380, November 04, 2014
Jinn-Jy Lin, Chun-Ping Yu, Yao-Ming Chang, Sean Chun-Chang Chen and Wen-Hsiung Li, "Maize and millet transcription factors annotated using comparative genomic and transcriptomic data." BMC Genomics, volume 15, page 818, September 2014
Peng, H.-P., K. H. Lee, J.-W. Jian and A.-S. Yang. "Origins of specificity and affinity in antibodyprotein interactions."Proceedings of the National Academy of Sciences, doi:10.1073/pnas.1401131111, June, 2014.
  • Khong-Loon Tiong, Kuo-Ching Chang, Kun-Tu Yeh, Ting-Yuan Liu, Jia-Hong Wu, Ping-Heng Hsieh, Shu-Hui Lin, Wei-Yun Lai, Yu-Chin Hsu, Jeou-Yuan Chen, Jan-Gowth Chang, Grace S. Shieh.   "CSNK1E/CTNNB1 Are Synthetic Lethal To TP53 in Colorectal Cancer and Are Markers for Prognosis."  Neoplasia, doi:10.1016/j.neo.2014.04.007.  Volume 16, Issue 5, May 2014
Tsai, Z.T.Y., Chu, W.Y., Cheng, J.H., and Tsai, H.K.*, "Associations between intronic non-B DNA structures and exon skipping," Nucleic Acids Research, volume 42, number 2, pages 739-747, January 2014.
Tien WS, Chen YT, Wu KP. "SecretePipe: a screening pipeline for secreted proteins with competence to identify potential membrane-bound shed markers." J Proteome Res. 2013 Mar 1;12(3):1235-44. doi: 10.1021/pr3009012.
Schaefke, B., J. J. Emerson, T. Y. Wang, M. Y. Lu, L. C. Hsieh and W. H. Li (2013).
 "Inheritance of gene expression level and selective constraints on trans- and cis-regulatory changes in yeast." Mol Biol Evol.(2013) doi: 10.1093/molbev/mst114 First published online: June 22, 2013
Ching-Hung Tseng1,2,3,Pei-Wen Chiang3, Fuh-Kwo Shiah4, Yi-Lung Chen4, Jia-Rong Liou4, Ting-Chang Hsu4, Suhinthan Maheswararajah5, Isaam Saeed5, Saman Halgamuge5 and Sen-Lin Tang1,3 "Microbial and viral metagenomes of a subtropical freshwater reservoir subject to climatic disturbances,"The ISME Journal (2013) 7, 2374–2386; doi:10.1038/ismej.2013.118; published online 11 July 2013
Chen, Y.C., Cheng, J.H., Tsai, Z.T.Y., Tsai, H.K.*, and Chuang T.J.*, "The Impact of Trans-Regulation on the Evolutionary Rates of Metazoan Proteins," Nucleic Acids Research, volume 41, number 13, pages 6371-80, May 2013.
Tien WS, Chen YT, Wu KP. "SecretePipe: a screening pipeline for secreted proteins with competence to identify potential membrane-bound shed markers." J Proteome Res. 2013 Mar 1;12(3):1235-44. doi: 10.1021/pr3009012.
C.-H. Hsu, Chien-Kuo Chen, and Ming-Jing Hwang "The architectural design of networks of protein domain architectures" Biol. Lett.. 2013; doi:10.1098/rsbl.2013.0268
Lai EY, Wang WB, Jiang T, Wu KP. "A linear-time algorithm for reconstructing zero-recombinant haplotype configuration on a pedigree." BMC Bioinformatics. 2012;13 Suppl 17:S19. doi: 10.1186/1471-2105-13-S17-S19.
Tsai, Z.T.Y., Tsai, H.K.*, Cheng, J.H., Lin, C.H., Tsai, Y.F. and Wang, D.*, "Evolution of cis-regulatory elements in yeast de novo and duplicated new genes," BMC Genomics, volume 13, pages 717, December 2012.
Chiang, S., Swamy, B.S. K., Hsu, T.W., Tsai, Z. T.Y., Lu, H.S., Wang, D., and Tsai, H.K.*, "Analysis of the association between transcription factor binding site variants and distinct accompanying regulatory motifs in yeast," Gene, volume 491, pages 237-245, January 2012.
Lu C-H, Lin Y-F, Lin J-J, Yu C-S (2012) "Prediction of Metal Ion–Binding Sites in Proteins Using the Fragment Transformation Method." PLoS ONE 7(6): e39252.doi:10.1371/journal.pone.0039252
Lin KT, Wang YW, Chen CT, Ho CM, Su WH, Jou YS. "HDAC inhibitors augmented cell migration and metastasis through induction of PKCs leading to identification of low toxicity modalities for combination cancer therapy." Clinical Cancer Res. 2012 Sep 1;18(17):4691-701. (SCI: Impact factor: 7.837, 12/196 ONCOLOGY)
Chang CY, Lin SC, Su WH, Ho CM, Jou YS. "Somatic LMCD1 mutations promoted cell migration and tumor metastasis in hepatocellular carcinoma." Oncogene 2012, May 24; 31(21):2640-52. (SCI: Impact factor: 7.357, 19/196 ONCOLOGY)
Kao S, Shiau CK, Gu DL, Ho CM, Su WH, Chen CF, Lin CH, Jou YS. IGDB.NSCLC: Integrated Genomic Database of Non-Small Cell Lung CancerNucleic Acids Res. 2012 Jan; 40:D972-D977 (SCI: Impact factor: 8.278, 27/290 BIOCHEMISTRY & MOLECULAR BIOLOGY)
Lin YC, Hsiao CL, Hsieh AR, Lian IeB, Fann CS. "Using maximal segmental score in genome-wide association studies." Genet Epidemiol. 2012 Sep;36(6):594-601.
Yu, C.-M., H.-P. Peng, I.-C. Chen, Y.-C. Lee, J.-B. Chen, K.-C. Tsai, C.-T. Chen, J.-Y. Chang, E.-W. Yang, P.-C. Hsu, J.-W. Jian, H.-J. Hsu, H.-J. Chang, W.-L. Hsu, K.-F. Huang, A. C. Ma and A.-S. Yang."Rationalization and Design of the Complementarity Determining Region Sequences in an Antibody-Antigen Recognition Interface." PLoS ONE7(3): e33340, March, 2012.
Shu-Mei Lai, Wei-Chung Liu and Ferenc Jordán, "On the centrality and uniqueness of species from the network perspective" Biol. Lett. Feb. 22, 2012
Tsai, Z. T.Y., Huang, G. T.W., and Tsai, H.K.*, "Simultaneous identification for synergistic transcription factors and their transcription factor binding sites," The Fourth International Workshop on Intelligent Informatics in Biology and Medicine (IIBM 2011), June 2011.
Swamy, B.S. K., Chu, W.Y., Wang, C.Y., Tsai, H.K.*, and Wang, D., "Evidence of association between Nucleosome Occupancy and the Evolution of Transcription Factor Binding Sites in Yeast," BMC Evolutionary Biology, volume 11:150, May 2011.

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

Chung-Pin Chen, Ching-Hung Tseng, Chaolun A. Chen, Sen-Lin Tang. (2010)The dynamics of microbial parternships in the coral Isopora palifera. ISME Journal, doi:10.1038/ismej.2010.151
Sean Chun-Chang Chen, Feng-Chi Chen and Wen-Hsiung Li. "Phosphorylated and Nonphosphorylated Serine and Threonine Residues Evolve at Different Rates in Mammals." Mol Biol Evol (2010) 27 (11): 2548-2554.2548-2554. doi: 10.1093/molbev/msq142 First published online: June 9, 2010
Yang, H.-C., Lin, H.-C., Huang, M.-C., Li, L.-H., Pan, W.-H., Wu, J.-Y. and Chen, Y.-T.  "A new analysis tool for individual-level allele frequency for genomic studies." BMC Genomics  2010 Jul 5. doi: 10.1186/1471-2164-11-415
Swamy, B. S. K., Cho, C.Y., Chiang, S., Tsai, Z. T.Y., and Tsai, H.K. *, "Impact of DNA binding position variants on yeast gene expression," Nucleic Acids Research, volume 37, number 21, pages 6991-7001, December 2009.
 Lin, C.-H., Huang, M.-C., Li, L.-H., Wu, J.-Y., Chen, Y.-T. and Fann, C. S. J., "Genome-wide copy number analysis using copy number inferring tool (CNIT) and DNA pooling."  Human Mutation 9 May 2008, DOI: 10.1002/humu.20760
 Yang, H.-C., Huang, M.-C., Li, L.-H., Lin, C.-H., Yu, L. T., Diccianni, M. B., Wu, J.-Y., Chen, Y.-T. and Fann, C. S. J. "MPDA: microarray-based pooled DNA analyzer." BMC Bioinformatics