BMC Bioinformatics, Volume 18 - Supplements

Volume 18, Number S-1, January 2017

Selected articles from BGRS\SB-2016: bioinformatics

• 
  Zakhar S. Mustafin, Sergey A. Lashin, Yury G. Matushkin, Konstantin V. Gunbin, Dmitry A. Afonnikov:
  Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles. 28:1-28:9
• 
  Kuang-Lim Chan, Rozana Rosli, Tatiana V. Tatarinova, Michael Hogan, Mohd Firdaus Raih, Eng-Ti Leslie Low:
  Seqping: gene prediction pipeline for plant genomes using self-training gene models and transcriptomic data. 29:1-29:7

Volume 18, Number S-2, February 2017

Proceedings of the Symposium on Biological Data Visualization at VIS 2016

• 
  Paul Murray, Fintan McGee, Angus Graeme Forbes:
  A taxonomy of visualization tasks for the analysis of biological pathway data. 21:1-21:13
• 
  Katarína Furmanová, Miroslava Jaresová, Jan Byska, Adam Jurcík, Július Parulek, Helwig Hauser, Barbora Kozlíková:
  Interactive exploration of ligand transportation through protein tunnels. 22:1-22:16
• 
  Lucia Kocincová, Miroslava Jaresová, Jan Byska, Július Parulek, Helwig Hauser, Barbora Kozlíková:
  Comparative visualization of protein secondary structures. 23:1-23:12
• 
  Chihua Ma, Timothy Luciani, Anna Terebus, Jie Liang, G. Elisabeta Marai:
  PRODIGEN: visualizing the probability landscape of stochastic gene regulatory networks in state and time space. 24:1-24:14
• 
  Marwan Abdellah, Ahmet Bilgili, Stefan Eilemann, Julian C. Shillcock, Henry Markram, Felix Schürmann:
  Bio-physically plausible visualization of highly scattering fluorescent neocortical models for in silico experimentation. 62:1-62:14
• 
  Sophie Engle, Sean Whalen, Alark Joshi, Katherine S. Pollard:
  Unboxing cluster heatmaps. 63:1-63:15
• 
  Rensu P. Theart, Ben Loos, Thomas R. Niesler:
  Virtual reality assisted microscopy data visualization and colocalization analysis. 64:1-64:16
• 
  Viktor Vad, Douglas Cedrim, Wolfgang Busch, Peter Filzmoser, Ivan Viola:
  Generalized box-plot for root growth ensembles. 65:1-65:15

Volume 18, Number S-3, March 2017

Selected articles from the 15th Asia Pacific Bioinformatics Conference (APBC 2017): bioinformatics

• 
  Chuanchao Zhang, Juan Liu, Qianqian Shi, Tao Zeng, Luonan Chen:
  Comparative network stratification analysis for identifying functional interpretable network biomarkers. 1-12
• 
  Weiyun Ma, Dmitriy Smirnov, Ran Libeskind-Hadas:
  DTL reconciliation repair. 13-21
• 
  Yuchao Xia, Yun Liu, Minghua Deng, Ruibin Xi:
  Pysim-sv: a package for simulating structural variation data with GC-biases. 23-30
• 
  Wei-Sheng Tien, Jun-Hong Chen, Kun-Pin Wu:
  SheddomeDB: the ectodomain shedding database for membrane-bound shed markers. 31-48
• 
  Jarno Alanko, Fabio Cunial, Djamal Belazzougui, Veli Mäkinen:
  A framework for space-efficient read clustering in metagenomic samples. 49-60
• 
  Junpeng Zhang, Thuc Duy Le, Lin Liu, Jiuyong Li:
  Identifying miRNA sponge modules using biclustering and regulatory scores. 61-72
• 
  Lei Sun, Jun Wang, Jinmao Wei:
  AVC: Selecting discriminative features on basis of AUC by maximizing variable complementarity. 73-89
• 
  Shifu Chen, Tanxiao Huang, Yanqing Zhou, Yue Han, Mingyan Xu, Jia Gu:
  AfterQC: automatic filtering, trimming, error removing and quality control for fastq data. 91-100
• 
  Chandana Tennakoon, Wing-Kin Sung:
  BATVI: Fast, sensitive and accurate detection of virus integrations. 101-111
• 
  Vikas Bansal:
  A computational method for estimating the PCR duplication rate in DNA and RNA-seq experiments. 113-123
• 
  Shun-Long Weng, Kai-Yao Huang, Fergie Joanda Kaunang, Chien-Hsun Huang, Hui-Ju Kao, Tzu-Hao Chang, Hsin-Yao Wang, Jang-Jih Lu, Tzong-Yi Lee:
  Investigation and identification of protein carbonylation sites based on position-specific amino acid composition and physicochemical features. 125-141
• 
  Mengge Zhang, Lianping Yang, Jie Ren, Nathan A. Ahlgren, Jed A. Fuhrman, Fengzhu Sun:
  Prediction of virus-host infectious association by supervised learning methods. 143-154
• 
  Yinglei Lai:
  A statistical method for the conservative adjustment of false discovery rate (q-value). 155-163
• 
  Hai'e Gong, Haicang Zhang, Jianwei Zhu, Chao Wang, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu:
  Improving prediction of burial state of residues by exploiting correlation among residues. 165-175

Volume 18, Number S-4, March 2017

• 
  Byung-Jun Yoon, Xiaoning Qian, Tamer Kahveci:
  Selected research articles from the 2016 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). 1-3
• 
  Osama A. Arshad, Aniruddha Datta:
  Towards targeted combinatorial therapy design for the treatment of castration-resistant prostate cancer. 5-15
• 
  Kevin Matlock, Noah Berlow, Charles Keller, Ranadip Pal:
  Combination therapy design for maximizing sensitivity and minimizing toxicity. 17-29
• 
  Hamed Hassani-Saadi, Reza Sameni, Amin Zollanvari:
  Interpretive time-frequency analysis of genomic sequences. 31-39
• 
  Arzu Burcak Sonmez, Tolga Can:
  Comparison of tissue/disease specific integrated networks using directed graphlet signatures. 41-50
• 
  Haijing Jin, Ying-Wooi Wan, Zhandong Liu:
  Comprehensive evaluation of RNA-seq quantification methods for linearity. 51-59

Volume 18, Number S-5, March 2017

• 
  Paolo Romano, Ralf Hofestädt, Matthias Lange, Domenica D'Elia:
  The joint NETTAB/Integrative Bioinformatics 2015 Meeting: aims, topics and outcomes. 1-5
• 
  Raquel Dias, Bryan Kolaczkowski:
  Improving the accuracy of high-throughput protein-protein affinity prediction may require better training data. 7-18
• 
  Ashwini Jeggari, Andrey Alexeyenko:
  NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis. 19-28
• 
  Umberto Perron, Paolo Provero, Ivan Molineris:
  In silico prediction of lncRNA function using tissue specific and evolutionary conserved expression. 29-39
• 
  Francesca Mulas, Amy Li, David H. Sherr, Stefano Monti:
  Network-based analysis of transcriptional profiles from chemical perturbations experiments. 41-55
• 
  Simona De Summa, Giovanni Malerba, Rosamaria Pinto, Antonio Mori, Vladan Mijatovic, Stefania Tommasi:
  GATK hard filtering: tunable parameters to improve variant calling for next generation sequencing targeted gene panel data. 57-65

Volume 18, Number 6, June 2017

• 
  Guohao Zhang, Peter V. Kochunov, L. Elliot Hong, Sinead Kelly, Christopher D. Whelan, Neda Jahanshad, Paul M. Thompson, Jian Chen:
  ENIGMA-Viewer: interactive visualization strategies for conveying effect sizes in meta-analysis. 17-29
• 
  Marianna Milano, Pietro Hiram Guzzi, Olga Tymofiyeva, Duan Xu, Christopher Paul Hess, Pierangelo Veltri, Mario Cannataro:
  An extensive assessment of network alignment algorithms for comparison of brain connectomes. 31-45
• 
  Sugeerth Murugesan, Kristofer E. Bouchard, Edward F. Chang, Max Dougherty, Bernd Hamann, Gunther H. Weber:
  Multi-scale visual analysis of time-varying electrocorticography data via clustering of brain regions. 236:1-236:15

Volume 18, Number 7, May 2017

Proceedings of the Tenth International Workshop on Data and Text Mining in Biomedical Informatics

• 
  Yoon Hyeok Lee, Hojae Choi, Seongyong Park, Boah Lee, Gwan-Su Yi:
  Drug repositioning for enzyme modulator based on human metabolite-likeness. 15-24
• 
  Eunyoung Kim, Hojung Nam:
  Prediction models for drug-induced hepatotoxicity by using weighted molecular fingerprints. 25-34
• 
  Baeksoo Kim, Jihoon Jo, Jonghyun Han, Chungoo Park, Hyunju Lee:
  In silico re-identification of properties of drug target proteins. 35-44
• 
  Go Eun Heo, Keun Young Kang, Min Song, Jeong-Hoon Lee:
  Analyzing the field of bioinformatics with the multi-faceted topic modeling technique. 45-57
• 
  Judita Preiss, Mark Stevenson:
  Quantifying and filtering knowledge generated by literature based discovery. 59-67
• 
  Hai J. Tran, Gil Speyer, Jeff Kiefer, Seungchan Kim:
  Contextualization of drug-mediator relations using evidence networks. 69-78
• 
  Kiseong Kim, Sangyeon Lee, Doheon Lee, Kwang Hyung Lee:
  Coupling effects on turning points of infectious diseases epidemics in scale-free networks. 79-88
• 
  Namshik Han, Harry Noyes, Andy Brass:
  TIGERi: modeling and visualizing the responses to perturbation of a transcription factor network. 260:1-260:13

Volume 18, Number 8, June 2017

Selected articles from the Fifth IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2015): Bioinformatics

• 
  Sharma V. Thankachan, Sriram P. Chockalingam, Yongchao Liu, Ambujam Krishnan, Srinivas Aluru:
  A greedy alignment-free distance estimator for phylogenetic inference. 238:1-238:8
• 
  Trevor Cickovski, Eli Peake, Vanessa Aguiar-Pulido, Giri Narasimhan:
  ATria: a novel centrality algorithm applied to biological networks. 239:1-239:10
• 
  Ekaterina Gerasimov, Alex Zelikovsky, Ion I. Mandoiu, Yurij Ionov:
  Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire. 244:1-244:6
• 
  Sunny Raj, Faraz Hussain, Zubir Husein, Neslisah Torosdagli, Damla Turgut, Narsingh Deo, Sumanta N. Pattanaik, Chung-Che Jeff Chang, Sumit Kumar Jha:
  A theorem proving approach for automatically synthesizing visualizations of flow cytometry data. 245:1-245:11
• 
  Thomas Olson, Rahul Singh:
  Predicting anatomic therapeutic chemical classification codes using tiered learning. 266:1-266:13

Volume 18, Number S-9, September 2017

• 
  Eric C. Rouchka, Julia H. Chariker, David Tieri, Juw Won Park, Shreedharkumar D. Rajurkar, Vikas Singh, Nishchal K. Verma, Yan Cui, Mark L. Farman, Bradford Condon, Neil Moore, Jerzy W. Jaromczyk, Jolanta Jaromczyk, Daniel R. Harris, Patrick Calie, Eun Kyong Shin, Robert L. Davis, Arash Shaban-Nejad, Joshua M. Mitchell, Robert M. Flight, Qing Jun Wang, Richard M. Higashi, Teresa W.-M. Fan, Andrew N. Lane, Hunter N. B. Moseley, Liangqun Lu, Bernie J. Daigle, Xi Chen, Andrey Smelter, Li Chen, Bailey K. Phan, Nathaniel J. Serpico, Ethan G. Toney, Caroline E. Melton, Jennifer R. Mandel, Bernie J. Daigle Jr., Hao Chen, Kazi I. Zaman, Ramin Homayouni, Patrick J. Trainor, Samantha M. Carlisle, Andrew P. DeFilippis, Shesh N. Rai:
  Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: bioinformatics: Burns, TN, USA. April 21-23, 2017.

Volume 18, Number S-10, September 2017

• 
  Divya Tej Sowpati, Surabhi Srivastava, Jyotsna Dhawan, Rakesh K. Mishra:
  C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search. 13-24
• 
  Henry Heberle, Marcelo Falsarella Carazzolle, Guilherme P. Telles, Gabriela Meirelles, Rosane Minghim:
  CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components. 25-37
• 
  Marwan Abdellah, Juan Hernando, Nicolas Antille, Stefan Eilemann, Henry Markram, Felix Schürmann:
  Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies. 39-50
• 
  Alexandre V. Fassio, Pedro M. Martins, Samuel da S. Guimarães, Sócrates S. A. Junior, Vagner S. Ribeiro, Raquel Cardoso de Melo Minardi, Sabrina de Azevedo Silveira:
  Vermont: a multi-perspective visual interactive platform for mutational analysis. 51-63
• 
  Lan H. Nguyen, Susan P. Holmes:
  Bayesian Unidimensional Scaling for visualizing uncertainty in high dimensional datasets with latent ordering of observations. 65-79
• 
  Chen He, Luana Micallef, ZiaurRehman Tanoli, Samuel Kaski, Tero Aittokallio, Giulio Jacucci:
  MediSyn: uncertainty-aware visualization of multiple biomedical datasets to support drug treatment selection. 393:1-393:12

Volume 18, Number S-11, October 2017

Selected articles from the International Conference on Intelligent Biology and Medicine (ICIBM) 2016: bioinformatics

• 
  Jonathan D. Young, Chunhui Cai, Xinghua Lu:
  Unsupervised deep learning reveals prognostically relevant subtypes of glioblastoma. 5-17
• 
  Santosh Philips, Heng-Yi Wu, Lang Li:
  Using machine learning algorithms to identify genes essential for cell survival. 19-29
• 
  Haixu Tang, Etienne Nzabarushimana:
  STRScan: targeted profiling of short tandem repeats in whole-genome sequencing data. 31-36
• 
  Yongsheng Bai, Jeff Kinne, Lizhong Ding, Ethan Rath, Aaron Cox, Siva Dharman Naidu:
  Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly. 37-48
• 
  Leandro de Araújo Lima, Kai Wang:
  PennCNV in whole-genome sequencing data. 49-56
• 
  Yuanhang Liu, Ping Wu, Jingqi Zhou, Teresa L. Johnson-Pais, Zhao Lai, Wasim H. Chowdhury, Ronald Rodriguez, Yidong Chen:
  XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylation. 57-65
• 
  Yuan-De Tan, Xiang H. F. Zhang, Qianxing Mo:
  New statistical methods for estimation of recombination fractions in F2 population. 67-78
• 
  Haodi Li, Qingcai Chen, Buzhou Tang, Xiaolong Wang, Hua Xu, Baohua Wang, Dong Huang:
  CNN-based ranking for biomedical entity normalization. 79-86
• 
  Xiaomei Han, Jenny Wang, Jie Wang, Sheng Liu, Jianfei Hu, Heng Zhu, Jiang Qian:
  ScaPD: a database for human scaffold proteins. 87-91
• 
  Zhandong Liu, W. Jim Zheng, Genevera I. Allen, Yin Liu, Jianhua Ruan, Zhongming Zhao:
  The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools. 405:1-405:3

Volume 18, Number S-12, October 2017

Selected articles from the 12th International Symposium on Bioinformatics Research and Applications (ISBRA 2016): bioinformatics

• 
  Xiaoxiong Zheng, Yang Wang, Kai Tian, Jiaogen Zhou, Jihong Guan, Libo Luo, Shuigeng Zhou:
  Fusing multiple protein-protein similarity networks to effectively predict lncRNA-protein interactions. 11-18
• 
  Bin Xu, Yang Wang, Zewei Wang, Jiaogen Zhou, Shuigeng Zhou, Jihong Guan:
  An effective approach to detecting both small and large complexes from protein-protein interaction networks. 19-28
• 
  Colleen M. Bosworth, Sneha Grandhi, Meetha P. Gould, Thomas LaFramboise:
  Detection and quantification of mitochondrial DNA deletions from next-generation sequence data. 29-36
• 
  Wooyoung Kim, Lynnette Haukap:
  NemoProfile as an efficient approach to network motif analysis with instance collection. 37-45
• 
  Felix Kühnl, Peter F. Stadler, Sebastian Will:
  Tractable RNA-ligand interaction kinetics. 47-55
• 
  Michal Startek, Jakub Nogly, Agnieszka Gromadka, Dariusz Grzebelus, Anna Gambin:
  Inferring transposons activity chronology by TRANScendence - TEs database and de-novo mining tool. 57-66
• 
  Dinghua Li, Yukun Huang, Henry C. M. Leung, Ruibang Luo, Hing-Fung Ting, Tak Wah Lam:
  MegaGTA: a sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs. 67-75
• 
  Prapaporn Techa-angkoon, Yanni Sun, Jikai Lei:
  A sensitive short read homology search tool for paired-end read sequencing data. 77-89
• 
  Min Li, Ping Huang, Xiaodong Yan, Jianxin Wang, Yi Pan, Fang-Xiang Wu:
  VAliBS: a visual aligner for bisulfite sequences. 91-98
• 
  Hongda Bu, Yanglan Gan, Yang Wang, Shuigeng Zhou, Jihong Guan:
  A new method for enhancer prediction based on deep belief network. 99-105
• 
  Matthew Hayes, Jeremy S. Pearson:
  Detecting large deletions at base pair level by combining split read and paired read data. 107-113
• 
  Ghada Hany Badr, Haifa A. Al-aqel:
  DCJ-RNA - double cut and join for RNA secondary structures. 115-131
• 
  Jian-Yu Shi, Jia-Xin Li, Ke Gao, Peng Lei, Siu-Ming Yiu:
  Predicting combinative drug pairs towards realistic screening via integrating heterogeneous features. 409:1-409:9

Volume 18, Number S-13, November 2017

Selected articles from the IEEE BIBM International Conference on Bioinformatics & Biomedicine (BIBM) 2016: bioinformatics

• 
  Ye-tian Fan, Xiwei Tang, Xiaohua Hu, Wei Wu, Qing Ping:
  Prediction of essential proteins based on subcellular localization and gene expression correlation. 13-21
• 
  Le Ou-Yang, Hong Yan, Xiao-Fei Zhang:
  A multi-network clustering method for detecting protein complexes from multiple heterogeneous networks. 23-34
• 
  Xu Min, Wanwen Zeng, Shengquan Chen, Ning Chen, Ting Chen, Rui Jiang:
  Predicting enhancers with deep convolutional neural networks. 35-46
• 
  Yongjun Tang, Diwei Liu, Zixiang Wang, Ting Wen, Lei Deng:
  A boosting approach for prediction of protein-RNA binding residues. 47-58
• 
  Wen Zhang, Xiaopeng Zhu, Yu Fu, Junko Tsuji, Zhiping Weng:
  Predicting human splicing branchpoints by combining sequence-derived features and multi-label learning methods. 464:1-464:11

Volume 18, Number 14, December 2017

Proceedings of the 14th Annual MCBIOS Conference

• 
  Cory B. Giles, Chase A. Brown, Michael Ripperger, Zane Dennis, Xiavan Roopnarinesingh, Hunter Porter, Aleksandra Perz, Jonathan D. Wren:
  ALE: automated label extraction from GEO metadata. 7-16
• 
  Zongliang Yue, Itika Arora, Eric Y. Zhang, Vincent Laufer, S. Louis Bridges, Jake Y. Chen:
  Repositioning drugs by targeting network modules: a Parkinson's disease case study. 17-30
• 
  Dan Li, Mary Qu Yang:
  Identification and characterization of conserved lncRNAs in human and rat brain. 31-38
• 
  Keqin Liu, Li He, Zhichao Liu, Junmei Xu, Yuan Liu, Qifan Kuang, Zhining Wen, Menglong Li:
  Mutation status coupled with RNA-sequencing data can efficiently identify important non-significantly mutated genes serving as diagnostic biomarkers of endometrial cancer. 39-49
• 
  Recep Erol, Mustafa Bayraktar, Sinan Kockara, Sertan Kaya, Tansel Halic:
  Texture based skin lesion abruptness quantification to detect malignancy. 51-60
• 
  Shahin Boluki, Mohammad Shahrokh Esfahani, Xiaoning Qian, Edward R. Dougherty:
  Incorporating biological prior knowledge for Bayesian learning via maximal knowledge-driven information priors. 61-80
• 
  Se-Ran Jun, Trudy M. Wassenaar, Visanu Wanchai, Preecha Patumcharoenpol, Intawat Nookaew, David Wayne Ussery:
  Suggested mechanisms for Zika virus causing microcephaly: what do the genomes tell us? 81-92
• 
  Mohsen Sharifi, Dan A. Buzatu, Stephen Harris, Jon G. Wilkes:
  Development of models for predicting Torsade de Pointes cardiac arrhythmias using perceptron neural networks. 93-102
• 
  Chun-Chi Chen, Xiaoning Qian, Byung-Jun Yoon:
  Effective computational detection of piRNAs using n-gram models and support vector machine. 103-109
• 
  Ethan Rath, Stephanie Pitman, Kyu Hong Cho, Yongsheng Bai:
  Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data. 111-120
• 
  Andrew S. Maxwell, Runzhi Li, Bei Yang, Heng Weng, Aihua Ou, Huixiao Hong, Zhaoxian Zhou, Ping Gong, Chaoyang Zhang:
  Deep learning architectures for multi-label classification of intelligent health risk prediction. 121-131
• 
  Hyundoo Jeong, Xiaoning Qian, Byung-Jun Yoon:
  CUFID-query: accurate network querying through random walk based network flow estimation. 133-146
• 
  Visanu Wanchai, Preecha Patumcharoenpol, Intawat Nookaew, David Wayne Ussery:
  dBBQs: dataBase of Bacterial Quality scores. 147-153
• 
  Quang Tran, Diem-Trang Pham, Vinhthuy Phan:
  Using 16S rRNA gene as marker to detect unknown bacteria in microbial communities. 155-161
• 
  Mike Mikailov, Fu-Jyh Luo, Stuart Barkley, Lohit Valleru, Stephen Whitney, Zhichao Liu, Shraddha Thakkar, Weida Tong, Nicholas Petrick:
  Scaling bioinformatics applications on HPC. 163-169
• 
  Jonathan D. Wren, Mikhail G. Dozmorov, Inimary T. Toby, Bindu Nanduri, Ramin Homayouni, Prashanti Manda, Shraddha Thakkar:
  Proceedings of the 2017 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. 498:1-498:5

Volume 18, Number 15, December 2017

Selected articles from the 6th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS): bioinformatics

• 
  Chunchun Zhao, Sartaj Sahni:
  Cache and energy efficient algorithms for Nussinov's RNA Folding. 15-30
• 
  Nurit Haspel, Dong Luo, Eduardo Gonzalez:
  Detecting intermediate protein conformations using algebraic topology. 31-39
• 
  Sergey Aganezov Jr., Max A. Alekseyev:
  CAMSA: a tool for comparative analysis and merging of scaffold assemblies. 41-50
• 
  Osamu Maruyama, Yuki Kuwahara:
  RocSampler: regularizing overlapping protein complexes in protein-protein interaction networks. 51-62
• 
  Jan Jelínek, Petr Skoda, David Hoksza:
  Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites. 63-72
• 
  Ning Yu, Zeng Yu, Yi Pan:
  A deep learning method for lincRNA detection using auto-encoder algorithm. 73-81

Volume 18, Number 16, December 2017

16th International Conference on Bioinformatics (InCoB 2017): Bioinformatics

• 
  Ari Hardianto, Muhammad Yusuf, Fei Liu, Shoba Ranganathan:
  Exploration of charge states of balanol analogues acting as ATP-competitive inhibitors in kinases. 19-30
• 
  Ching-Yu Yen, Jian-Cheng Lin, Kun-Tze Chen, Chin Lung Lu:
  R3D-BLAST2: an improved search tool for similar RNA 3D substructures. 31-38
• 
  Nikhil Pathak, Mei-Ling Lai, Wen-Yu Chen, Betty-Wu Hsieh, Guann-Yi Yu, Jinn-Moon Yang:
  Pharmacophore anchor models of flaviviral NS3 proteases lead to drug repurposing for DENV infection. 39-51
• 
  Yahui Sun, Chenkai Ma, Saman K. Halgamuge:
  The node-weighted Steiner tree approach to identify elements of cancer-related signaling pathways. 53-65
• 
  Jiajie Peng, Honggang Wang, Junya Lu, Weiwei Hui, Yadong Wang, Xuequn Shang:
  Identifying term relations cross different gene ontology categories. 67-74
• 
  Kyoungyeul Lee, Minho Lee, Dongsup Kim:
  Utilizing random Forest QSAR models with optimized parameters for target identification and its application to target-fishing server. 75-86
• 
  Marzio Pennisi, Giulia Russo, Silvia Ravalli, Francesco Pappalardo:
  Combining agent based-models and virtual screening techniques to predict the best citrus-derived vaccine adjuvants against human papilloma virus. 87-97
• 
  Wei Wang, Xi Yang, Canqun Yang, Xiaowei Guo, Xiang Zhang, Chengkun Wu:
  Dependency-based long short term memory network for drug-drug interaction extraction. 99-109
• 
  Herty Liany, Jagath C. Rajapakse, R. Krishna Murthy Karuturi:
  MultiDCoX: Multi-factor analysis of differential co-expression. 111-124
• 
  Shiu Kumar, Alok Sharma, Tatsuhiko Tsunoda:
  An improved discriminative filter bank selection approach for motor imagery EEG signal classification using mutual information. 125-137
• 
  Alok Sharma, Yosvany López, Tatsuhiko Tsunoda:
  Divisive hierarchical maximum likelihood clustering. 139-147
• 
  Matloob Khushi, Imraan M. Dean, Erdahl T. Teber, Megan Chircop, Jonathan W. Arthur, Neftali Flores-Rodriguez:
  Automated classification and characterization of the mitotic spindle following knockdown of a mitosis-related protein. 149-159
• 
  Damayanthi Herath, Sen-Lin Tang, Kshitij Tandon, David C. Ackland, Saman Kumara Halgamuge:
  CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision. 161-172
• 
  Wenzheng Bao, Zhichao Jiang, De-Shuang Huang:
  Novel human microbe-disease association prediction using network consistency projection. 173-181
• 
  Zhen Tian, Maozu Guo, Chunyu Wang, Xiaoyan Liu, Shiming Wang:
  Refine gene functional similarity network based on interaction networks. 183-193
• 
  Alok Sharma, Piotr J. Kamola, Tatsuhiko Tsunoda:
  2D-EM clustering approach for high-dimensional data through folding feature vectors. 195-209
• 
  Lei Deng, Chao Fan, Zhiwen Zeng:
  A sparse autoencoder-based deep neural network for protein solvent accessibility and contact number prediction. 211-220
• 
  Clarence White, Hamid D. Ismail, Hiroto Saigo, K. C. Dukka B.:
  CNN-BLPred: a Convolutional neural network based predictor for β-Lactamases (BL) and their classes. 221-232
• 
  Yuting Xing, Gen Li, Zhenguo Wang, Bolun Feng, Zhuo Song, Chengkun Wu:
  GTZ: a fast compression and cloud transmission tool optimized for FASTQ files. 233-242
• 
  Joel Z. B. Low, Tsung Fei Khang, Martti T. Tammi:
  CORNAS: coverage-dependent RNA-Seq analysis of gene expression data without biological replicates. 243-253
• 
  Jiaojiao Miao, Na Han, Yujun Qiang, Tingting Zhang, Xiuwen Li, Wen Zhang:
  16SPIP: a comprehensive analysis pipeline for rapid pathogen detection in clinical samples based on 16S metagenomic sequencing. 255-259
• 
  Haiyong Zheng, Ruchen Wang, Zhibin Yu, Nan Wang, Zhaorui Gu, Bing Zheng:
  Automatic plankton image classification combining multiple view features via multiple kernel learning. 570:1-570:18

Volume 18, Number S-17, December 2017

Selected articles from the first International Workshop on Cells in ExperimentaL Life Sciences (CELLS-2017) at the 2017 International Conference on Biomedical Ontology (ICBO-2017)

• 
  Trygve E. Bakken, Lindsay G. Cowell, Brian D. Aevermann, Mark Novotny, Rebecca D. Hodge, Jeremy A. Miller, Alexandra Lee, Ivan Chang, Jamison M. McCorrison, Bali Pulendran, Yu Qian, Nicholas J. Schork, Roger S. Lasken, Ed S. Lein, Richard H. Scheuermann:
  Cell type discovery and representation in the era of high-content single cell phenotyping. 7-16
• 
  Senay Kafkas, Sirarat Sarntivijai, Robert Hoehndorf:
  Usage of cell nomenclature in biomedical literature. 17-24
• 
  Edison Ong, Sirarat Sarntivijai, Simon Jupp, Helen E. Parkinson, Yongqun He:
  Comparison, alignment, and synchronization of cell line information between CLO and EFO. 25-33
• 
  David Osumi-Sutherland:
  Cell ontology in an age of data-driven cell classification. 35-42
• 
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