Journal of Bioinformatics and Computational Biology, Volume 16

Volume 16, Number 1, February 2018

Special Issue - Selected Papers from the 9th International Young Scientists School on Systems Biology and Bioinformatics (SBB'2017)

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  Yuriy L. Orlov, Tatiana V. Tatarinova, Maksim V. Zakhartsev, Nikolay A. Kolchanov:
  Introduction to the 9th Young Scientists School on Systems Biology and Bioinformatics (SBB'2017). 1802001:1-1802001:5

Research Papers

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  Olga Kiseleva, Ekaterina Poverennaya, Alexander Shargunov, Andrey Lisitsa:
  Proteomic Cinderella: Customized analysis of bulky MS/MS data in one night. 1740011:1-1740011:13
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  Artem Ryasik, Mikhail A. Orlov, Evgenia Zykova, Timofei Ermak, Anatoly A. Sorokin:
  Bacterial promoter prediction: Selection of dynamic and static physical properties of DNA for reliable sequence classification. 1840003:1-1840003:16
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  George S. Krasnov, Nataliya V. Melnikova, Valentina A. Lakunina, Anastasiya V. Snezhkina, Anna V. Kudryavtseva, Alexey A. Dmitriev:
  MethyMer: Design of combinations of specific primers for bisulfite sequencing of complete CpG islands. 1840004:1-1840004:15
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  Fedor V. Kazantsev, Ilya R. Akberdin, Sergey A. Lashin, Natalia Ree, Vladimir Timonov, Alexander V. Ratushny, Tamara M. Khlebodarova, Vitali A. Likhoshvai:
  MAMMOTh: A new database for curated mathematical models of biomolecular systems. 1740010:1-1740010:16
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  Vladimir Ovchinnikov, Denis V. Antonets, Lyudmila F. Gulyaeva:
  The search of CAR, AhR, ESRs binding sites in promoters of intronic and intergenic microRNAs. 1750029:1-1750029:20
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  Vladislav M. Bezhentsev, Sergey Ivanov, Sandeep Kumar, Rajesh Kumar Goel, Vladimir Poroikov:
  Identification of potential drug targets for treatment of refractory epilepsy using network pharmacology. 1840002:1-1840002:12
• 
  Ivan Antonov, Andrey Marakhonov, Maria Zamkova, Yulia A. Medvedeva:
  ASSA: Fast identification of statistically significant interactions between long RNAs. 1840001:1-1840001:27
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  Oleg V. Vishnevsky, Andrey V. Bocharnikov, Nikolay A. Kolchanov:
  Argo_CUDA: Exhaustive GPU based approach for motif discovery in large DNA datasets. 1740012:1-1740012:23

Regular Papers: Research Papers

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  Dan Luo, Shu-Lin Wang, Jianwen Fang, Wei Zhang:
  MIMPFC: Identifying miRNA-mRNA regulatory modules by combining phase-only correlation and improved rough-fuzzy clustering. 1750028:1-1750028:18
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  Jiang Xie, Dongfang Lu, Jiaxin Li, Jiao Wang, Yong Zhang, Yanhui Li, Qing Nie:
  Kernel differential subgraph reveals dynamic changes in biomolecular networks. 1750027:1-1750027:29

Volume 16, Number 2, April 2018

Special Issue — The 8th International Moscow Conference on Computational Molecular Biology (MCCMB’17)

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  Mikhail S. Gelfand:
  Introduction to Papers Selected from MCCMB'17. 1802002:1-1802002:2

Research Papers

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  Dmitry A. Suplatov, Yana A. Sharapova, Daria Timonina, Kirill E. Kopylov, Vytas K. Svedas:
  The visualCMAT: A web-server to select and interpret correlated mutations/co-evolving residues in protein families. 1840005:1-1840005:15
• 
  Ekaterina N. Grafskaia, Nadezhda F. Polina, Vladislav V. Babenko, Daria D. Kharlampieva, Pavel A. Bobrovsky, Valentin A. Manuvera, Tatyana E. Farafonova, Nikolay A. Anikanov, Vassili N. Lazarev:
  Discovery of novel antimicrobial peptides: A transcriptomic study of the sea anemone Cnidopus japonicus. 1840006:1-1840006:17
• 
  Alexander M. Andrianov, Ivan A. Kashyn, Alexander V. Tuzikov:
  Potential HIV-1 fusion inhibitors mimicking gp41-specific broadly neutralizing antibody 10E8: In silico discovery and prediction of antiviral potency. 1840007:1-1840007:21
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  Ekaterina M. Myasnikova, Alexander V. Spirov:
  Relative sensitivity analysis of the predictive properties of sloppy models. 1840008:1-1840008:18
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  Evgeny E. Akkuratov, Mikhail S. Gelfand, Ekaterina Khrameeva:
  Neanderthal and Denisovan ancestry in Papuans: A functional study. 1840011:1-1840011:12
• 
  Oxana A. Volkova, Yury V. Kondrakhin, Timur A. Kashapov, Ruslan N. Sharipov:
  Comparative analysis of protein-coding and long non-coding transcripts based on RNA sequence features. 1840013:1-1840013:14

Regular Papers: Research Papers

• 
  Hossam M. Ashtawy, Nihar R. Mahapatra:
  Boosted neural networks scoring functions for accurate ligand docking and ranking. 1850004:1-1850004:18
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  Óscar Álvarez, Juan Luis Fernández Martínez, Celia Fernández-Brillet, Ana Cernea, Zulima Fernández-Muñiz, Andrzej Kloczkowski:
  Principal component analysis in protein tertiary structure prediction. 1850005:1-1850005:34
• 
  Myungjin Moon, Kenta Nakai:
  Integrative analysis of gene expression and DNA methylation using unsupervised feature extraction for detecting candidate cancer biomarkers. 1850006:1-1850006:20

Volume 16, Number 3, June 2018

Special Issue: Selected Papers from GIW 2017

• 
  Lee Sael:
  Introduction to Selected Papers from GIW2017. 1802003:1-1802003:2

Research Papers

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  Amr Alhossary, Yaw Awuni, Chee Keong Kwoh, Yuguang Mu:
  Proposing drug fragments for dengue virus NS5 protein. 1840017:1-1840017:20
• 
  Naoki Arai, Shunsuke Yoshikawa, Nobuaki Yasuo, Ryunosuke Yoshino, Masakazu Sekijima:
  Compound property enhancement by virtual compound synthesis. 1840016:1-1840016:13
• 
  Bingxin Lu, Hon Wai Leong:
  GI-Cluster: Detecting genomic islands via consensus clustering on multiple features. 1840010:1-1840010:19
• 
  Xin Ma, Jing Guo, Xiao Sun:
  Prediction of microRNA-binding residues in protein using a Laplacian support vector machine based on sequence information. 1840009:1-1840009:13
• 
  Maria Satti, Yasuhiro Tanizawa, Akihito Endo, Masanori Arita:
  Comparative analysis of probiotic bacteria based on a new definition of core genome. 1840012:1-1840012:17
• 
  Turki Turki, Zhi Wei, Jason T. L. Wang:
  A transfer learning approach via procrustes analysis and mean shift for cancer drug sensitivity prediction. 1840014:1-1840014:31
• 
  Amir Zeb, Chanin Park, Minky Son, Shailima Rampogu, Syed Ibrar Alam, Seok Ju Park, Keun Woo Lee:
  Investigation of non-hydroxamate scaffolds against HDAC6 inhibition: A pharmacophore modeling, molecular docking, and molecular dynamics simulation approach. 1840015:1-1840015:23

Regular Papers: Research Papers

• 
  Haixia Dou, Yun Fang, Xiaoqi Zheng:
  Universal informative CpG sites for inferring tumor purity from DNA methylation microarray data. 1750030:1-1750030:12
• 
  A. Ranjitha Dhanasekaran, Katheleen J. Gardiner:
  RPPAware: A software suite to preprocess, analyze and visualize reverse phase protein array data. 1850001:1-1850001:17
• 
  Suman Jyoti Deka, Ashalata Roy, Debasis Manna, Vishal Trivedi:
  Integrating virtual screening and biochemical experimental approach to identify potential anti-cancer agents from drug databank. 1850002:1-1850002:20
• 
  Cong Liu, Wuping Zhou, Tao Zhang, Keming Jiang, Haiwen Li, Wenfei Dong:
  An automated approach to classification of duplex assay for digital droplet PCR. 1850003:1-1850003:14

Volume 16, Number 4, August 2018

Research Papers

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  Hasan Fehmi Danaci, Rengül Çetin-Atalay, Volkan Atalay:
  EClerize: A customized force-directed graph drawing algorithm for biological graphs with EC attributes. 1850007:1-1850007:12
• 
  Indrani Ray, Abhijit Dasgupta, Rajat K. De:
  Succinate aggravates NAFLD progression to liver cancer on the onset of obesity: An in silico model. 1850008:1-1850008:15
• 
  Chi-Kan Chen:
  Inference of gene networks from gene expression time series using recurrent neural networks and sparse MAP estimation. 1850009:1-1850009:30
• 
  Jiyun Choi, Kipoong Kim, Hokeun Sun:
  New variable selection strategy for analysis of high-dimensional DNA methylation data. 1850010:1-1850010:18
• 
  Bangli Lu, Chen Li, Qingfeng Chen, Jiangning Song:
  ProBAPred: Inferring protein-protein binding affinity by incorporating protein sequence and structural features. 1850011:1-1850011:18
• 
  Seyed Amir Malekpour, Parsa Pakzad, Mohammad-Hadi Foroughmand-Araabi, Sama Goliaei, Ruzbeh Tusserkani, Bahram Goliaei, Mehdi Sadeghi:
  Modeling the probability distribution of the bacterial burst size via a game-theoretic approach. 1850012:1-1850012:22
• 
  Mohammad Mohebbi, Liang Ding, Russell L. Malmberg, Cory Momany, Khaled Rasheed, Liming Cai:
  Accurate prediction of human miRNA targets via graph modeling of the miRNA-target duplex. 1850013:1-1850013:18
• 
  Abdul Hannan Basit, Wajid Arshad Abbasi, Amina Asif, Sadaf Gull, Fayyaz ul Amir Afsar Minhas:
  Training host-pathogen protein-protein interaction predictors. 1850014:1-1850014:18
• 
  Lamiche Chaabane:
  A hybrid solver for protein multiple sequence alignment problem. 1850015:1-1850015:20
• 
  Maryam Mousavizadegan, Hassan Mohabatkar:
  Computational prediction of antifungal peptides via Chou's PseAAC and SVM. 1850016:1-1850016:16

Volume 16, Number 5, October 2018

• 
  Hisham Al-Mubaid, Qin Ding, Oliver Eulenstein:
  Introduction to JBCB Special Issue on BICOB-2018. 1802004:1-1802004:3

Research Papers

• 
  Yuanfang Ren, Ahmet Ay, Travis A. Gerke, Tamer Kahveci:
  Identification of jointly correlated gene sets. 1840019:1-1840019:23
• 
  Ronald J. Nowling, Scott J. Emrich:
  Adjusted likelihood-ratio test for variants with unknown genotypes. 1840020:1-1840020:15
• 
  Dawid Dabkowski, Pawel Tabaszewski, Pawel Górecki:
  Minimizing the deep coalescence cost. 1840021:1-1840021:18
• 
  Richard Olney, Aaron Tuor, Filip Jagodzinski, Brian Hutchinson:
  A systematic exploration of ΔΔG cutoff ranges in machine learning models for protein mutation stability prediction. 1840022:1-1840022:19

Regular Papers: Research Papers

• 
  Aman Sharma, Rinkle Rani:
  An integrated framework for identification of effective and synergistic anti-cancer drug combinations. 1850017:1-1850017:23
• 
  Sanjeev Kumar, Suneeta Agarwal, Ranvijay:
  WBFQC: A new approach for compressing next-generation sequencing data splitting into homogeneous streams. 1850018:1-1850018:16
• 
  Ioannis A. Tamposis, Margarita C. Theodoropoulou, Konstantinos D. Tsirigos, Pantelis G. Bagos:
  Extending hidden Markov models to allow conditioning on previous observations. 1850019:1-1850019:21
• 
  Zafer Aydin, Oguz Kaynar, Yasin Gormez:
  Dimensionality reduction for protein secondary structure and solvent accesibility prediction. 1850020:1-1850020:16
• 
  Yanbu Guo, Bingyi Wang, Weihua Li, Bei Yang:
  Protein secondary structure prediction improved by recurrent neural networks integrated with two-dimensional convolutional neural networks. 1850021:1-1850021:19
• 
  Keerthi S. Shetty, Annappa B.:
  Transcriptional processes: Models and inference. 1850023:1-1850023:17

Volume 16, Number 6, December 2018

• 
  Jinyan Li, Kenta Nakai, Yun Zheng, Kengo Sato, Limsoon Wong:
  Introduction to Selected Papers from GIW2018. 1802005:1-1802005:2

Research Papers

• 
  Rui Yin, Xinrui Zhou, Jie Zheng, Chee Keong Kwoh:
  Computational identification of physicochemical signatures for host tropism of influenza A virus. 1840023:1-1840023:21
• 
  Aotian Yang, David Miller, Qing Pan:
  Constrained maximum entropy models to select genotype interactions associated with censored failure times. 1840024:1-1840024:23
• 
  Manato Akiyama, Kengo Sato, Yasubumi Sakakibara:
  A max-margin training of RNA secondary structure prediction integrated with the thermodynamic model. 1840025:1-1840025:15
• 
  Sungkyoung Choi, Sungyoung Lee, Yongkang Kim, Heungsun Hwang, Taesung Park:
  HisCoM-GGI: Hierarchical structural component analysis of gene-gene interactions. 1840026:1-1840026:25
• 
  Wen-Juan Hou, Bamfa Ceesay:
  Extraction of drug-drug interaction using neural embedding. 1840027:1-1840027:22
• 
  Joungmin Choi, Yoonjae Park, Sun Kim, Heejoon Chae:
  Cloud-BS: A MapReduce-based bisulfite sequencing aligner on cloud. 1840028:1-1840028:10
• 
  Haitao Jiang, Letu Qingge, Daming Zhu, Binhai Zhu:
  A 2-approximation algorithm for the contig-based genomic scaffold filling problem. 1850022:1-1850022:15
• 
  Sabyasachi Patra, Anjali Mohapatra:
  Motif discovery in biological network using expansion tree. 1850024:1-1850024:24
• 
  Sovan Saha, Abhimanyu Prasad, Piyali Chatterjee, Subhadip Basu, Mita Nasipuri:
  Protein function prediction from protein-protein interaction network using gene ontology based neighborhood analysis and physico-chemical features. 1850025:1-1850025:15
• 
  Qiangrong Jiang, Jiajia Ma:
  A novel graph kernel on chemical compound classification. 1850026:1-1850026:8
• 
  Quanfeng Liu, Liping Li, Fei Xu:
  Systematic analysis and integrative discovery of active-site subpocket-specific dehydroquinate synthase inhibitors combating antibiotic-resistant Staphylococcus aureus infection. 1850027:1-1850027:20