Journal of Bioinformatics and Computational Biology, Volume 15

Volume 15, Number 1, February 2017

Regular Papers: Research Papers

• 
  Byungmin Kim, Saud Alguwaizani, Xiang Zhou, De-Shuang Huang, Byunkyu Park, Kyungsook Han:
  An improved method for predicting interactions between virus and human proteins. 1650024:1-1650024:17
• 
  Liqi Li, Qifa Luo, Weidong Xiao, Jinhui Li, Shiwen Zhou, Yongsheng Li, Xiaoqi Zheng, Hua Yang:
  A machine-learning approach for predicting palmitoylation sites from integrated sequence-based features. 1650025:1-1650025:18
• 
  Tianci Song, Yan Wang, Wei Du, Sha Cao, Yuan Tian, Yanchun Liang:
  The method for breast cancer grade prediction and pathway analysis based on improved multiple kernel learning. 1650037:1-1650037:21
• 
  Steven M. Graff, William E. Bentley:
  Mathematical model of LsrR-binding and derepression in Escherichia coli K12. 1650039:1-1650039:26
• 
  Shun-Tsung Chen, Chien-Hung Huang, Victor C. Kok, Chi-Ying F. Huang, Jin-Shuei Ciou, Jeffrey J. P. Tsai, Nilubon Kurubanjerdjit, Ka-Lok Ng:
  Drug repurposing and therapeutic anti-microRNA predictions for inhibition of oxidized low-density lipoprotein-induced vascular smooth muscle cell-associated diseases. 1650043:1-1650043:23
• 
  Cong Pian, Yuan-yuan Chen, Jin Zhang, Zhi Chen, Guang-Le Zhang, Qiang Li, Tao Yang, Liang-Yun Zhang:
  V-ELMpiRNAPred: Identification of human piRNAs by the voting-based extreme learning machine (V-ELM) with a new hybrid feature. 1650046:1-1650046:16
• 
  Bo Liao, Xiangjun Wang, Wen Zhu, Xiong Li, Lijun Cai, Haowen Chen:
  New multilocus linkage disequilibrium measure for tag SNP selection. 1750001:1-1750001:16
• 
  Carla Negri Lintzmayer, Guillaume Fertin, Zanoni Dias:
  Sorting permutations by prefix and suffix rearrangements. 1750002:1-1750002:46
• 
  Yue Hou, Huan Huang, Wenqiao Hu, Hongde Liu, Xiao Sun:
  Histone modifications influence skipped exons inclusion. 1750003:1-1750003:17

Volume 15, Number 2, April 2017

Special Issue - Selected Papers from BGRS\SB-2016

• 
  Yuriy L. Orlov, Nikolay A. Kolchanov, Ralf Hofestädt, Limsoon Wong:
  Editorial - Bioinformatics development at the BGRS\SB conference series: 10th anniversary. 1702001:1-1702001:5
• 
  Milos Nikolic, Tamara Stankovic, Marko Djordjevic:
  Contribution of bacterial promoter elements to transcription start site detection accuracy. 1650038:1-1650038:22
• 
  Olga A. Tarasova, Dmitry Filimonov, Vladimir Poroikov:
  PASS-based approach to predict HIV-1 reverse transcriptase resistance. 1650040:1-1650040:15
• 
  Irina V. Medvedeva, Pavel S. Demenkov, Vladimir A. Ivanisenko:
  SITEX 2.0: Projections of protein functional sites on eukaryotic genes. Extension with orthologous genes. 1650044:1-1650044:14
• 
  Kirill E. Medvedev, Nikolay A. Kolchanov, Dmitry A. Afonnikov:
  Identification of residues of the archaeal RNA-binding Nip7 proteins specific to environmental conditions. 1650036:1-1650036:18
• 
  M. Sh. Barkovskaya, Anton G. Bogomolov, N. Yu. Knauer, N. B. Rubtsov, V. A. Kozlov:
  Development of software and modification of Q-FISH protocol for estimation of individual telomere length in immunopathology. 1650041:1-1650041:18
• 
  Konstantin Kozlov, Vera Kosheverova, Rimma Kamentseva, Marianna Kharchenko, Alena Sokolkova, Elena Kornilova, Maria Samsonova:
  Quantitative analysis of the heterogeneous population of endocytic vesicles. 1750008:1-1750008:19
• 
  Olga V. Petrovskaya, Evgeny D. Petrovskiy, Inna N. Lavrik, Vladimir A. Ivanisenko:
  A study of structural properties of gene network graphs for mathematical modeling of integrated mosaic gene networks. 1650045:1-1650045:14
• 
  Tamara M. Khlebodarova, Vladislav V. Kogai, Stanislav I. Fadeev, Vitali A. Likhoshvai:
  Chaos and hyperchaos in simple gene network with negative feedback and time delays. 1650042:1-1650042:19

Regular Papers:

• 
  Samira Fotoohifiroozabadi, Mohd Saberi Mohamad, Safaai Deris:
  Samira-VP: A simple protein alignment method with rechecking the alphabet vector positions. 1750004:1-1750004:24
• 
  Masih Sherafatian, Seyed Javad Mowla:
  The origins and evolutionary history of human non-coding RNA regulatory networks. 1750005:1-1750005:14
• 
  Dong-Chul Kim, Mingon Kang, Ashis Kumer Biswas, Chin-Rang Yang, Xiaoyu Wang, Jean X. Gao:
  Effects of low dose ionizing radiation on DNA damage-caused pathways by reverse-phase protein array and Bayesian networks. 1750006:1-1750006:18

Volume 15, Number 3, June 2017

Special Issue - Selected Papers from the 8th International Conference on BICOB 2016

• 
  Nurit Haspel, Thomas R. Ioerger, Hisham Al-Mubaid:
  Introduction to selected papers from the 8th International Conference on Bioinformatics and Computational Biology (BICOB 2016). 1702002:1-1702002:2

Research Papers

• 
  Diem-Trang Pham, Shanshan Gao, Vinhthuy Phan:
  An accurate and fast alignment-free method for profiling microbial communities. 1740001:1-1740001:12
• 
  Jucheol Moon, Oliver Eulenstein:
  Synthesizing large-scale species trees using the strict consensus approach. 1740002:1-1740002:17
• 
  Arghya Kusum Das, Praveen Kumar Koppa, Sayan Goswami, Richard Platania, Seung-Jong Park:
  Large-scale parallel genome assembler over cloud computing environment. 1740003:1-1740003:21

Regular Papers: Research Papers

• 
  Ehsan Faghih-Mirzaee, Maryam Dehestani, Leila Zeidabadinejad:
  Computational study on transfer of L-ascorbic acid by UlaA through Escherichia coli membrane. 1750007:1-1750007:15
• 
  Bruno Grisci, Márcio Dorn:
  NEAT-FLEX: Predicting the conformational flexibility of amino acids using neuroevolution of augmenting topologies. 1750009:1-1750009:22
• 
  Ze Liu, Hongqiang Lv, Jiuqiang Han, Ruiling Liu:
  A computational model for predicting transmembrane regions of retroviruses. 1750010:1-1750010:13
• 
  Vijay Dave, Rohit Manchanda:
  A computational model of the Ca2+ transients and influence of buffering in guinea pig urinary bladder smooth muscle cells. 1750011:1-1750011:16
• 
  Weifu Li, Hao Deng, Qiang Rao, Qiwei Xie, Xi Chen, Hua Han:
  An automated pipeline for mitochondrial segmentation on ATUM-SEM stacks. 1750015:1-1750015:26

Volume 15, Number 4, August 2017

Research Papers

• 
  Abdulrakeeb M. Al-Ssulami, Aqil M. Azmi, Hassan Mathkour:
  An efficient method for significant motifs discovery from multiple DNA sequences. 1750014:1-1750014:20
• 
  Longlong Liu, Mingjiao Ma, Jing Cui:
  A novel model-based on FCM-LM algorithm for prediction of protein folding rate. 1750012:1-1750012:19
• 
  Hanaa Torkey, Lenwood S. Heath, Mahmoud ElHefnawi:
  MicroTarget: MicroRNA target gene prediction approach with application to breast cancer. 1750013:1-1750013:17
• 
  Sudip Mandal, Goutam Saha, Rajat Kumar Pal:
  Recurrent neural network-based modeling of gene regulatory network using elephant swarm water search algorithm. 1750016:1-1750016:23
• 
  Wentian Li, Jane E. Cerise, Yaning Yang, Henry Han:
  Application of t-SNE to human genetic data. 1750017:1-1750017:14

Volume 15, Number 5, October 2017

Special Issue: Selected Papers from the 16th International Conference on Bioinformatics (InCoB 2017)

• 
  Tatsuya Akutsu:
  Selected Papers from the 16th International Conference on Bioinformatics (InCoB 2017). 1702003:1-1702003:2

Research Papers

• 
  Dongdong Sun, Minghui Wang, Ao Li:
  MPTM: A tool for mining protein post-translational modifications from literature. 1740005:1-1740005:21
• 
  Hironori Shigeta, Tomohiro Mashita, Junichi Kikuta, Shigeto Seno, Haruo Takemura, Masaru Ishii, Hideo Matsuda:
  Bone marrow cavity segmentation using graph-cuts with wavelet-based texture feature. 1740004:1-1740004:16

Regular Papers: Research Papers

• 
  Guoli Ji, Qianmin Lin, Yuqi Long, Congting Ye, Wenbin Ye, Xiaohui Wu:
  PAcluster: Clustering polyadenylation site data using canonical correlation analysis. 1750018:1-1750018:19
• 
  Christophe Guyeux, Stéphane Chrétien, Nathalie M.-L. Côté, Jacques M. Bahi:
  Systematic investigations of gene effects on both topologies and supports: An Echinococcus illustration. 1750019:1-1750019:27
• 
  Na You, Xueqin Wang:
  An empirical Bayes method for robust variance estimation in detecting DEGs using microarray data. 1750020:1-1750020:14
• 
  Yan-Shuo Chu, Zhenxing Wang, Rongjie Wang, Ningyi Zhang, Jie Li, Yang Hu, Mingxiang Teng, Yadong Wang:
  WDNfinder: A method for minimum driver node set detection and analysis in directed and weighted biological network. 1750021:1-1750021:18

Volume 15, Number 6, December 2017

Special Issue: Selected Papers from the 9th International Conference on Bioinformatics and Computational Biology (BICOB 2017)

• 
  Oliver Eulenstein, Qin Ding, Hisham Al-Mubaid:
  Foreword. 1702004:1-1702004:2

Research Papers

• 
  Mohammad Arifur Rahman, Nathan Lapierre, Huzefa Rangwala, Daniel Barbará:
  Metagenome sequence clustering with hash-based canopies. 1740006:1-1740006:18
• 
  Abdullah N. Arslan, Jithendar Anandan, Eric Fry, Keith Monschke, Nitin Ganneboina, Jason Bowerman:
  Efficient RNA structure comparison algorithms. 1740009:1-1740009:27
• 
  Lu Liu, Jianhua Ruan:
  Utilizing networks for differential analysis of chromatin interactions. 1740008:1-1740008:16
• 
  Esaie Kuitche, Manuel Lafond, Aïda Ouangraoua:
  Reconstructing protein and gene phylogenies using reconciliation and soft-clustering. 1740007:1-1740007:25

Regular Papers: Research Papers

• 
  A. Sreeja, K. P. Vinayan:
  Multidimensional knowledge-based framework is an essential step in the categorization of gene sets in complex disorders. 1750022:1-1750022:23
• 
  Soheila Montaseri, Fatemeh Zare-Mirakabad, Mohammad Ganjtabesh:
  Evaluating the quality of SHAPE data simulated by k-mers for RNA structure prediction. 1750023:1-1750023:17
• 
  Debika Choudhury, Amit Agarwal, Supreet Saini:
  Robustness versus evolvability analysis for regulatory feed-forward loops. 1750024:1-1750024:16
• 
  Abolfazl Rezvan, Changiz Eslahchi:
  Comparison of different approaches for identifying subnetworks in metabolic networks. 1750025:1-1750025:26
• 
  S. Subasri, Santosh Kumar Chaudhary, Kanagaraj Sekar, Manish Kesherwani, Devadasan Velmurugan:
  Molecular docking and molecular dynamics simulations of fumarate hydratase and its mutant H235N complexed with pyromellitic acid and citrate. 1750026:1-1750026:22