| 1. | Hufeng Zhou, Javad Rezaei, Willy Hugo, Shangzhi Gao, Jingjing Jin, Mengyuan Fan, Chern-Han Yong, Michal Wozniak and Limsoon Wong. "Stringent DDI-based Prediction of H. sapiens-M. tuberculosis H37Rv Protein-Protein Interactions". BMC Systems Biology, 7(Suppl 6):S6, December 2013 |
| 5. | Jing-Doo Wang. "Comparing virus classification using genomic materials according to different taxonomic levels". JBCB, 11(6):1343003, December 2013 |
| 8. | Liang Zhao, Steven C. H. Hoi, Zhenhua Li, Limsoon Wong, Hung Nguyen, Jinyan Li. "Coupling graphs, efficient algorithms and B-cell epitope prediction". TCBB, to appear |
| 9. | Slavka Jaromerska, Petr Praus and Young-Rae Cho. "Distance-wise pathway discovery from protein-protein interaction networks weighted by semantic similarity". JBCB, 12(1):1450004, February 2014 |
| 10. | Zhongyuan Tian, Adrien Fauré, Hirotada Mori and Hiroshi Matsuno. "Identification of key regulators in glycogen utilization in E. coli based on the simulations from a hybrid functional Petri net model". BMC Systems Biology, 7(Suppl 6):S1, December 2013 |
| 11. | Yi-Min Chen, Chun-Hui Yu, Chi-Chuan Hwang and Tsunglin Liu. "OMACC: An Optical-Map-Assisted Contig Connector for improving de novo genome assembly". BMC Systems Biology, 7(Suppl 6):S7, December 2013 |
| 13. | Kyung-Ah Sohn, Dokyoon Kim, Jaehyun Lim and Ju Han Kim. "Relative impact of multi-layered genomic data on gene expression phenotypes in serous ovarian tumors". BMC Systems Biology, 7(Suppl 6):S9, December 2013 |
| 14. | Ying Fan, Ruoshui Lu, Lusheng Wang, Massimo Andreatta and Shuai Cheng Li. "Quantifying significance of MHC II residues". TCBB, to appear |
| 18. | Takahiro Mimori, Naoki Nariai, Kaname Kojima, Mamoru Takahashi, Akira Ono, Yukuto Sato, Yumi Yamaguchi-Kabata and Masao Nagasaki. "iSVP: An integrated structural variant calling pipeline from high-throughput sequencing data". BMC Systems Biology, 7(Suppl 6):S8, December 2013 |
| 24. | Yitzhak Friedman and Michal Linial. "Mirror2.0: A platform for assessing the joint action of microRNAs in cell regulation". JBCB, 11(6):1343012, December 2013 |
| 28. | Wan-Shu Cheng and Jung-Hsien Chiang. "CGPredictor: A systematic integrated analytic tool for mining and examining genome-scale cancer independent prognostic epigenetic marker panels". BMC Systems Biology, 7(Suppl 6):S10, December 2013 |
| 29. | Paul D. Yoo, Sami Muhaidat, Kamal Taha, Jamal Bentahar and Abdallah Shami. "Intelligent consensus modeling for proline cis-trans isomerization prediction". TCBB, to appear |
| 30. | Hiroaki Iwata, Sayaka Mizutani, Yasuo Tabei, Masaaki Kotera, Susumu Goto and Yoshihiro Yamanishi. "Inferring protein domains associated with drug side effects based on drug-target interaction network". BMC Systems Biology, 7(Suppl 6):S18, December 2013 |
| 31. | Masaaki Kotera, Yasuo Tabei, Yoshihiro Yamanishi, Yuki Moriya, Toshiaki Tokimatsu, Minoru Kanehisa and Susumu Goto. "KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics". BMC Systems Biology, 7(Suppl 6):S2, December 2013 |
| 32. | Yang Zhao, Morihiro Hayashida, Jira Jindalertudomdee, Hiroshi Nagamochi, Tatsuya Akutsu. "Breadth-first search approach to enumeration of tree-like chemical compounds". JBCB, 11(6):1343007, December 2013 |
| 33. | Ruiqi Liao, Ruichang Zhang, Jihong Guan and Shuigeng Zhou. "A new unsupervised binning approach for metagenomic sequences based on n-grams and automatic feature weighting". TCBB, to appear |
| 38. | Yasuo Tabei and Yoshihiro Yamanishi. "Scalable prediction of compound-protein interactions using minwise hashing". BMC Systems Biology, 7(Suppl 6):S3, December 2013 |
| 39. | Oliver L Tessmer, Yuhua Jiao, Jeffrey A Cruz, David M Kramer and Jin Chen. "Functional approach to high-throughput plant growth analysis". BMC Systems Biology, 7(Suppl 6):S17, December 2013 |
| 41. | Tzu-Hsien Yang and Wei-Sheng Wu. "Inferring functional transcription factor-gene binding pairs by integrating transcription factor binding data with transcription factor knockout data". BMC Systems Biology, 7(Suppl 6):S13, December 2013 |
| 43. | Beibei Ru, Peter A. C. 't Hoen, Fulei Nie, Hao Lin, Feng-Biao Guo and Jian Huang. "PhD7Faster: Predicting clones propagating faster from the Ph.D.-7 phage display peptide library". JBCB, 12(1):1450004, February 2014 |
| 44. | Claudiu Mihaila and Sophia Ananiadou. "Recognising discourse causality triggers in the biomedical domain". JBCB, 11(6):1343008, December 2013 |
| 46. | Hsiuying Wang, Chia-Chun Chiu, Yi-Ching Wu and Wei-Sheng Wu. "Shrinkage regression-based methods for microarray missing value imputation". BMC Systems Biology, 7(Suppl 6):S11, December 2013 |
| 47. | Jianmin Ma, Frank Eisenhaber and Sebastian Maurer-Stroh. "Automatic phylogenetic classification of bacterial beta-lactamase sequences including structural and antibiotic substrate reference information". JBCB, 11(6):1343011, December 2013 |
| 48. | Sebastian Maurer-Stroh, Vithiagaran Gunalan, Wing Cheong Wong and Frank Eisenhaber. "A simple shortcut to unsupervised alignment-free phylogenetic genome groupings, even from unassembled sequence reads". JBCB, 11(6):1343005, December 2013 |
| 51. | Meiyappan Lakshmanan, Bevan Kai-Sheng Chung, Chengcheng Liu, Seon-Won Kim, Dong-Yup Lee. "Cofactor modification analysis: A computational framework to identify cofactor specificity engineering targets for strain improvement". JBCB, 11(6):1343006, December 2013 |
| 52. | Jiin Choi and Taesung Park. "Multivariate generalized multifactor dimensionality reduction to detect gene-gene interactions". BMC Systems Biology, 7(Suppl 6):S15, December 2013 |
| 53. | Yanglan Gan, Jihong Guan, Shuigeng Zhou and Weixiong Zhang. "Identifying cis-regulatory elements and modules using conditional random fields". TCBB, to appear |
| 54. | Jui-Chen Hsiao, Chih-Hsuan Wei and Hung-Yu Kao. "Gene name disambiguation using multi-scope species detection". TCBB, to appear |
| 55. | Yu-Lun Chen, Chien-Ming Chen, Tun-Wen Pai, Hon-Wai Leong and Ket-Fah Chong. "Homologous synteny block detection based on suffix tree algorithms". JBCB, 11(6):1343004, December 2013 |
| 56. | Chasanah Kusumastuti Widita and Osamu Maruyama. "PPSampler2: Predicting protein complexes more accurately and efficiently by sampling". BMC Systems Biology, 7(Suppl 6):S14, December 2013 |
| 60./61. | Chia-Chun Chiu, Shih-Yao Chan, Chung-Ching Wang and Wei-Sheng Wu. "Missing value imputation for microarray data: A comprehensive comparison study and a web tool". BMC Systems Biology, 7(Suppl 6):S12, December 2013 |
| 65. | Masahiko Nakatsui, Michihiro Araki and Akihiko Kondo. "An approach for dynamical network reconstruction of simple network motifs". BMC Systems Biology, 7(Suppl 6):S4, December 2013 |
| 68. | Laleh Soltan Ghoraie, Forbes Burkowski, Shuai Cheng Li and Mu Zhu. "Residue-specific side-chain polymorphisms via particle belief propagation". TCBB, to appear |
| 69. | Jing Guo, Ritika Jain, Peng Yang, Rui Fan, Chee Keong Kwoh and Jie Zheng. "Reliable and fast estimation of recombination rates by convergence diagnosis and parallel Markov chain Monte Carlo". TCBB, to appear |
| 71. | Agnieszka Podsiadlo, Mariusz Wrzesien, Wieslaw Paja, Witold Rudnicki and Bartek Wilczynski. "Active enhancer positions can be accurately predicted from chromatin marks and collective sequence motif data". BMC Systems Biology, 7(Suppl 6):S16, December 2013 |
| 73. | Florian Goebels and Dmitrij Frishman. "Prediction of protein interaction types based on sequence and network features". BMC Systems Biology, 7(Suppl 6):S5, December 2013 |
| 76. | Yuta Taniguchi, Yasuhiro Yamada, Osamu Maruyama, Satoru Kuhara and Daisuke Ikeda. "The purity measure for genomic regions leads to horizontally transferred genes". JBCB, 11(6):1343002, December 2013 |
| 84. | Sriganesh Srihari, Venkatesh Raman, Hon Wai Leong and Mark A. Ragan. "Evolution and controllability of cancer networks: A Boolean perspective". TCBB, to appear |
| 89. | Venkata Rajesh Yella and Manju Bansal. "DNA structural features and architecture of promoter regions play a role in gene responsiveness of S. cerevisiae". JBCB, 11(6):1343001, December 2013 |
| 91. | Igor I. Titov and Pavel S. Vorozheykin. "Ab initio human miRNA and pre-miRNA prediction". JBCB, 11(6):1343009, December 2013 |
| 94. | M. P. Grover, S. Ballouz, K. A. Mohanasundaram, R. A. George, C. D. H. Sherman, T. M. Crowley and M. A. Wouters. "Identification of novel therapeutics for complex diseases from genome-wide association data". JBCB, under revision |
| 98. | Henry Han, Xiao-Li Li, See-Kiong Ng and Zhou Ji. "Multi-resolution test for consistent phenotype discrimination and biomarker discovery in translational bioinformatics". JBCB, 11(6):1343010, December 2013 |