BMC Bioinformatics, Volume 16 - Supplements

Volume 16, Number S-1, January 2015

Selected articles from the Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015): Bioinformatics

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  Van-Nui Nguyen, Kai-Yao Huang, Chien-Hsun Huang, Tzu-Hao Chang, Neil Arvin Bretaña, K. Robert Lai, Julia Weng, Tzong-Yi Lee:
  Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities. S1
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  Yun-Lung Li, Jui-Cheng Weng, Chiung-Chih Hsiao, Min-Te Chou, Chin-Wen Tseng, Jui-Hung Hung:
  PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm. S2
• 
  Hong Sun, Shuang Yang, Liangliang Tun, Yixue Li:
  IAOseq: inferring abundance of overlapping genes using RNA-seq data. S3
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  Takahiro Mimori, Naoki Nariai, Kaname Kojima, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Masao Nagasaki:
  Estimating copy numbers of alleles from population-scale high-throughput sequencing data. S4
• 
  Guan-Mau Huang, Kai-Yao Huang, Tzong-Yi Lee, Julia Weng:
  An interpretable rule-based diagnostic classification of diabetic nephropathy among type 2 diabetes patients. S5
• 
  Wenhui Wang, Xianghong Jasmine Zhou, Zhenqiu Liu, Fengzhu Sun:
  Network tuned multiple rank aggregation and applications to gene ranking. S6
• 
  Jau-Ji Lin, Zih-Lin Lin, Jenn-Kang Hwang, Tsun-Tsao Huang:
  On the packing density of the unbound protein-protein interaction interface and its implications in dynamics. S7
• 
  Tamara Vasylenko, Yi-Fan Liou, Hong-An Chen, Phasit Charoenkwan, Hui-Ling Huang, Shinn-Ying Ho:
  SCMPSP: Prediction and characterization of photosynthetic proteins based on a scoring card method. S8
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  Kai-Yao Huang, Tzong-Yi Lee, Yu-Chuan Teng, Tzu-Hao Chang:
  ViralmiR: a support-vector-machine-based method for predicting viral microRNA precursors. S9
• 
  Dan He, Zhanyong Wang, Laxmi Parida:
  Data-driven encoding for quantitative genetic trait prediction. S10

Volume 16, Number S-2, January 2015

Highlights from the Tenth International Society for Computational Biology (ISCB) Student Council Symposium 2014

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  Farzana Rahman, Katie Wilkins, Annika Jacobsen, Alexander Junge, Esmeralda Vicedo, Dan F. DeBlasio, Anupama Jigisha, Tomás Di Domenico:
  Highlights from the tenth ISCB Student Council Symposium 2014. A1
• 
  Yassine Souilmi, Jae-Yoon Jung, Alex Lancaster, Erik Gafni, Saaid Amzazi, Hassan Ghazal, Dennis P. Wall, Peter J. Tonellato:
  COSMOS: cloud enabled NGS analysis. A2
• 
  Dan F. DeBlasio, John D. Kececioglu:
  Parameter advising for multiple sequence alignment. A3
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  Lin-Yang Cheng, Yansheng Liu, Ching-Yun Chang, Hannes L. Röst, Ruedi Aebersold, Olga Vitek:
  Statistical elimination of spectral features with large between-run variation enhances quantitative protein-level conclusions in experiments with data-independent spectral acquisition. A4
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  Harriet Dashnow, Susan Tan, Debjani Das, Simon Easteal, Alicia Oshlack:
  Genotyping microsatellites in next-generation sequencing data. A5
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  Yi Zhong, Philipp Drewe, Andrew L. Wolfe, Kamini Singh, Hans-Guido Wendel, Gunnar Rätsch:
  Protein translational control and its contribution to oncogenesis revealed by computational methods. A6
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  Benjamin Siranosian, Emma Herold, Edward Williams, Chen Ye, Christopher de Graffenried:
  Tetranucleotide usage in mycobacteriophage genomes: alignment-free methods to cluster phage and infer evolutionary relationships. A7
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  Alex Salazar, Ashlee Earl, Christopher Desjardins, Thomas Abeel:
  Normalizing alternate representations of large sequence variants across multiple bacterial genomes. A8
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  Sarah L. Keasey, Mohan Natesan, Christine Pugh, Teddy Kamata, Stefan Wuchty, Robert G. Ulrich:
  The road to linking genomics and proteomics of pathogenic bacteria: from binary protein complexes to interaction pathways. A9
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  Amin Ardeshirdavani, Erika L. Souche, Luc Dehaspe, Jeroen K. J. Van Houdt, Joris Robert Vermeesch, Yves Moreau:
  NGS-Logistics: data infrastructure for efficient analysis of NGS sequence variants across multiple centers. A10

Volume 16, Number S-3, February 2015

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  Margherita Francescatto, Susanne M. A. Hermans, Sepideh Babaei, Esmeralda Vicedo, Alexandre Borrel, Pieter Meysman:
  Highlights from the Third European International Society for Computational Biology (ISCB) Student Council Symposium 2014. A1
• 
  Darius Kazlauskas, Ceslovas Venclovas:
  Viral DNA replication: new insights and discoveries from large scale computational analysis. A2
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  Aya Narunsky, Haim Ashkenazy, Rachel Kolodny, Nir Ben-Tal:
  Using ConTemplate and the PDB to explore conformational space: on the detection of rare protein conformations. A3
• 
  Isidro Cortes-Ciriano, Gerard J. P. van Westen, Daniel S. Murrell, Eelke B. Lenselink, Andreas Bender, Therese E. Malliavin:
  Applications of proteochemometrics - from species extrapolation to cell line sensitivity modelling. A4
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  Mélaine A. Kuenemann, Laura M. L. Bourbon, Céline M. Labbé, Bruno O. Villoutreix, Olivier Sperandio:
  An exploration of the 3D chemical space has highlighted a specific shape profile for the compounds intended to inhibit protein-protein interactions. A5
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  Stefan Naulaerts, Pieter Meysman, Wim Vanden Berghe, Kris Laukens:
  Mining the human proteome for conserved mechanisms. A6
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  Matthias Döring, Gilles Gasparoni, Jasmin Gries, Karl Nordström, Pavlo Lutsik, Jörn Walter, Nico Pfeifer:
  Identification and analysis of methylation call differences between bisulfite microarray and bisulfite sequencing data with statistical learning techniques. A7
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  Dagoberto Armenta-Medina, Ernesto Pérez-Rueda:
  Hybrid approaches for the detection of networks of critical residues involved in functional motions in protein families. A8
• 
  Amélie Peres, Hugues Roest Crollius:
  Improving duplicated nodes position in vertebrate gene trees. A9

Volume 16, Number S-4, February 2015

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  Abdollah Dehzangi, Sohrab Sohrabi, Rhys Heffernan, Alok Sharma, James G. Lyons, Kuldip K. Paliwal, Abdul Sattar:
  Gram-positive and gram-negative subcellular localization using rotation forest and physicochemical-based features. S1
• 
  Dusan Popovic, Alejandro Sifrim, Jesse Davis, Yves Moreau, Bart De Moor:
  Problems with the nested granularity of feature domains in bioinformatics: the eXtasy case. S2
• 
  Zina M. Ibrahim, Alioune Ngom:
  The relative vertex clustering value - a new criterion for the fast discovery of functional modules in protein interaction networks. S3
• 
  Erdogan Taskesen, Frank J. T. Staal, Marcel J. T. Reinders:
  An integrated approach of gene expression and DNA-methylation profiles of WNT signaling genes uncovers novel prognostic markers in Acute Myeloid Leukemia. S4
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  Erdogan Taskesen, Sepideh Babaei, Marcel J. T. Reinders, Jeroen de Ridder:
  Integration of gene expression and DNA-methylation profiles improves molecular subtype classification in acute myeloid leukemia. S5
• 
  Jose Nunes, Martín Piquerez, Leonardo Pujadas, Eileen Armstrong, Alicia Fernández, Federico Lecumberry:
  Beef quality parameters estimation using ultrasound and color images. S6
• 
  Antonino Fiannaca, Massimo La Rosa, Laura La Paglia, Riccardo Rizzo, Alfonso Urso:
  Analysis of miRNA expression profiles in breast cancer using biclustering. S7
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  Hossam M. Ashtawy, Nihar R. Mahapatra:
  BgN-Score and BsN-Score: Bagging and boosting based ensemble neural networks scoring functions for accurate binding affinity prediction of protein-ligand complexes. S8

Volume 16, Number S-5, March 2015

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  Jingchun Sun, Kevin W. Zhu, W. Jim Zheng, Hua Xu:
  A comparative study of disease genes and drug targets in the human protein interactome. S1
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  Ruichang Zhang, Zhanzhan Cheng, Jihong Guan, Shuigeng Zhou:
  Exploiting topic modeling to boost metagenomic reads binning. S2
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  Hao Wu, Lin Gao, Feng Li, Fei Song, Xiaofei Yang, Nikola K. Kasabov:
  Identifying overlapping mutated driver pathways by constructing gene networks in cancer. S3
• 
  Qing Zhan, Yongtao Ye, Tak Wah Lam, Siu-Ming Yiu, Yadong Wang, Hing-Fung Ting:
  Improving multiple sequence alignment by using better guide trees. S4
• 
  Andrew Quitadamo, Lu Tian, Benika Hall, Xinghua Shi:
  An integrated network of microRNA and gene expression in ovarian cancer. S5
• 
  Rong Xu, QuanQiu Wang:
  Comparing a knowledge-driven approach to a supervised machine learning approach in large-scale extraction of drug-side effect relationships from free-text biomedical literature. S6
• 
  Haitao Jiang, Guohui Lin, Weitian Tong, Daming Zhu, Binhai Zhu:
  Isomorphism and similarity for 2-generation pedigrees. S7
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  Xiaoqing Peng, Jianxin Wang, Zhen Zhang, Qianghua Xiao, Min Li, Yi Pan:
  Re-alignment of the unmapped reads with base quality score. S8
• 
  Danny S. Park, Yael Baran, Farhad Hormozdiari, Celeste Eng, Dara G. Torgerson, Esteban Gonzàlez Burchard, Noah Zaitlen:
  PIGS: improved estimates of identity-by-descent probabilities by probabilistic IBD graph sampling. S9
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  Jeffery Li, Travers Ching, Sijia Huang, Lana X. Garmire:
  Using epigenomics data to predict gene expression in lung cancer. S10
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  Mai A. Hamdalla, Reda A. Ammar, Sanguthevar Rajasekaran:
  A molecular structure matching approach to efficient identification of endogenous mammalian biochemical structures. S11

Volume 16, Number S-6, April 2015

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  Marta Avalos, Hélène Pouyes, Yves Grandvalet, Ludivine Orriols, Emmanuel Lagarde:
  Sparse conditional logistic regression for analyzing large-scale matched data from epidemiological studies: a simple algorithm. S1
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  Massimo La Rosa, Antonino Fiannaca, Riccardo Rizzo, Alfonso Urso:
  Probabilistic topic modeling for the analysis and classification of genomic sequences. S2
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  Hossam M. Ashtawy, Nihar R. Mahapatra:
  Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteins. S3
• 
  Pietro Pinoli, Davide Chicco, Marco Masseroli:
  Computational algorithms to predict Gene Ontology annotations. S4
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  Ernst C. Wit, Antonino Abbruzzo:
  Inferring slowly-changing dynamic gene-regulatory networks. S5

Volume 16, Number S-7, April 2015

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  Robert Smith, John T. Prince, Dan Ventura:
  A coherent mathematical characterization of isotope trace extraction, isotopic envelope extraction, and LC-MS correspondence. S1
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  Robert Smith, Ryan M. Taylor, John T. Prince:
  Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal. S2
• 
  Gaurav Kaushik, Michael A. Thomas, Ken A. Aho:
  Psychoactive pharmaceuticals as environmental contaminants may disrupt highly inter-connected nodes in an Autism-associated protein-protein interaction network. S3
• 
  Azusa Ito, Takenao Ohkawa:
  A method of searching for related literature on protein structure analysis by considering a user's intention. S4
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  Paul M. Bodily, M. Stanley Fujimoto, Cameron Ortega, Nozomu Okuda, Jared C. Price, Mark J. Clement, Quinn Snell:
  Heterozygous genome assembly via binary classification of homologous sequence. S5
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  Tsendsuren Munkhdalai, Oyun-Erdene Namsrai, Keun Ho Ryu:
  Self-training in significance space of support vectors for imbalanced biomedical event data. S6
• 
  Haijun Gong, Jakob Klinger, Kevin Damazyn, Xiangrui Li, Shiyang Huang:
  A novel procedure for statistical inference and verification of gene regulatory subnetwork. S7
• 
  Saman Sargolzaei, Arman Sargolzaei, Mercedes Cabrerizo, Gang Chen, Mohammed Goryawala, Shirin Noei, Qi Zhou, Ranjan Duara, Warren Barker, Malek Adjouadi:
  A practical guideline for intracranial volume estimation in patients with Alzheimer's disease. S8
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  Saman Sargolzaei, Mercedes Cabrerizo, Arman Sargolzaei, Shirin Noei, Anas Salah Eddin, Hoda Rajaei, Alberto Pinzon-Ardila, Sergio M. Gonzalez-Arias, Prasanna Jayakar, Malek Adjouadi:
  A probabilistic approach for pediatric epilepsy diagnosis using brain functional connectivity networks. S9
• 
  Ruibang Luo, Jeanno Cheung, Edward Wu, Heng Wang, Sze-Hang Chan, Wai-Chun Law, Guangzhu He, Chang Yu, Chi-Man Liu, Dazong Zhou, Yingrui Li, Ruiqiang Li, Jun Wang, Xiaoqian Zhu, Shaoliang Peng, Tak Wah Lam:
  MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC). S10

Volume 16, Number S-8, April 2015

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  R. Parra, Franco L. Simonetti, Marcia A. Hasenahuer, Gabriel J. Olguin-Orellana, Avinash Kumar Shanmugam:
  Highlights from the 1st ISCB Latin American Student Council Symposium 2014. A1
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  Raony Guimarães Corrêa Do Carmo Lisboa Cardenas, Natália Duarte Linhares, Sérgio D. Junho Pena:
  Mendel, MD: a user-friendly online program for clinical exome analysis. A2
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  Julliane D. Medeiros, Laura R. Leite, Sara Cuadros-Orellana, Guilherme C. Oliveira:
  Taxonomic and functional diversity of microbial community from a mining environment. A3
• 
  Danillo C. Almeida-E.-Silva, Ricardo Z. N. Vêncio:
  Sifter-T: A scalable framework for phylogenomic probabilistic protein domain functional annotation. A4
• 
  Yerko Escalona, José Antonio Garate, Tomás Pérez-Acle:
  Exploring the membrane potential of a simple dual membrane system by using a constant electric field. A5
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  Franco L. Simonetti, Martin Banchero, Ariel J. Berenstein, Ariel Chernomoretz, Cristina Marino Buslje:
  Using coevolution to improve protein subfamily classification. A6
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  Jan Engelhardt, Peter F. Stadler:
  Evolution of 3'UTR-associated RNAs. A7
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  Javier Cáceres, Romina Sepúlveda, Camila Navas, Ramón Latorre, Fernando D. González Nilo:
  Rational discovery of new capsaicin analogues as TRPV1 activators. A8

Volume 16, Number S-9, June 2015

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  Angelo M. Facchiano, Claudia Angelini, Roberta Bosotti, Alessandro Guffanti, Anna Marabotti, Roberto Marangoni, Stefano Pascarella, Paolo Romano, Andreas Zanzoni, Manuela Helmer-Citterich:
  Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics. S1
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  Matteo Carrara, Josephine Lum, Francesca Cordero, Marco Beccuti, Michael Poidinger, Susanna Donatelli, Raffaele A. Calogero, Francesca Zolezzi:
  Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis. S2
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  Stefano Parodi, Rosa Filiberti, Paola Marroni, Roberta Libener, Giovanni Ivaldi, Michele Mussap, Enrico Ferrari, Chiara Manneschi, Erika Montani, Marco Muselli:
  Differential diagnosis of pleural mesothelioma using Logic Learning Machine. S3
• 
  Alberto Policriti, Nicola Prezza:
  Fast randomized approximate string matching with succinct hash data structures. S4
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  Andrea Calabria, Giulio Spinozzi, Fabrizio Benedicenti, Erika Tenderini, Eugenio Montini:
  adLIMS: a customized open source software that allows bridging clinical and basic molecular research studies. S5
• 
  Francesco Di Palma, Sandro Bottaro, Giovanni Bussi:
  Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations. S6
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  Gianvito Pio, Michelangelo Ceci, Donato Malerba, Domenica D'Elia:
  ComiRNet: a web-based system for the analysis of miRNA-gene regulatory networks. S7
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  Giulio Caravagna, Luca De Sano, Marco Antoniotti:
  Automatising the analysis of stochastic biochemical time-series. S8

Volume 16, Number S10, December 2015

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  Robert Bossy, Wiktoria Golik, Zorana Ratkovic, Dialekti Valsamou, Philippe Bessières, Claire Nédellec:
  Overview of the gene regulation network and the bacteria biotope tasks in BioNLP'13 shared task. S1
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  Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Andrew Rowley, Hong-Woo Chun, Sung-Jae Jung, Sung-Pil Choi, Jun'ichi Tsujii, Sophia Ananiadou:
  Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013. S2
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  Jin-Dong Kim, Jung-Jae Kim, Xu Han, Dietrich Rebholz-Schuhmann:
  Extending the evaluation of Genia Event task toward knowledge base construction and comparison to Gene Regulation Ontology task. S3
• 
  Thomas Provoost, Marie-Francine Moens:
  Semi-supervised Learning for the BioNLP Gene Regulation Network. S4
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  Ilknur Karadeniz, Arzucan Özgür:
  Detection and categorization of bacteria habitats using shallow linguistic analysis. S5
• 
  Thomas Lavergne, Cyril Grouin, Pierre Zweigenbaum:
  The contribution of co-reference resolution to supervised relation detection between bacteria and biotopes entities. S6
• 
  Makoto Miwa, Sophia Ananiadou:
  Adaptable, high recall, event extraction system with minimal configuration. S7
• 
  Xiao Liu, Antoine Bordes, Yves Grandvalet:
  Extracting biomedical events from pairs of text entities. S8

Volume 16, Number S11, December 2015

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  Jan Aerts, G. Elisabeta Marai, Kay Nieselt, Cydney B. Nielsen, Marc Streit, Daniel Weiskopf:
  Highlights from the 5th Symposium on Biological Data Visualization: Part 1. S1
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  Hamid Younesy, Torsten Möller, Matthew C. Lorincz, Mohammad M. Karimi, Steven J. M. Jones:
  VisRseq: R-based visual framework for analysis of sequencing data. S2
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  André Hennig, Jörg Bernhardt, Kay Nieselt:
  Pan-Tetris: an interactive visualisation for Pan-genomes. S3
• 
  Florin Chelaru, Héctor Corrada Bravo:
  Epiviz: a view inside the design of an integrated visual analysis software for genomics. S4
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  Sehi L'Yi, Bongkyung Ko, DongHwa Shin, Young-Joon Cho, Jaeyong Lee, Bohyoung Kim, Jinwook Seo:
  XCluSim: a visual analytics tool for interactively comparing multiple clustering results of bioinformatics data. S5
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  Jillian Aurisano, Khairi Reda, Andrew E. Johnson, G. Elisabeta Marai, Jason Leigh:
  BactoGeNIE: a large-scale comparative genome visualization for big displays. S6
• 
  Christian Stolte, Kenneth Sabir, Julian Heinrich, Christopher J. Hammang, Andrea Schafferhans, Seán I. O'Donoghue:
  Integrated visual analysis of protein structures, sequences, and feature data. S7
• 
  Marwan Abdellah, Ahmet Bilgili, Stefan Eilemann, Henry Markram, Felix Schürmann:
  Physically-based in silico light sheet microscopy for visualizing fluorescent brain models. S8
• 
  A. Johannes Pretorius, Y. Zhou, Roy A. Ruddle:
  Visual parameter optimisation for biomedical image processing. S9
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  Hao Ding, Chao Wang, Kun Huang, Raghu Machiraju:
  GRAPHIE: graph based histology image explorer. S10

Volume 16, Number S12, December 2015

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  Xiao Wang, Jun Zhang, Guo-Zheng Li:
  Multi-location gram-positive and gram-negative bacterial protein subcellular localization using gene ontology and multi-label classifier ensemble. S1
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  Yongguo Mei, Vida Abedi, Adria Carbo, Xiaoying Zhang, Pinyi Lu, Casandra W. Philipson, Raquel Hontecillas, Stefan Hoops, Nathan Liles, Josep Bassaganya-Riera:
  Multiscale modeling of mucosal immune responses. S2
• 
  Fengying Yu, Zhihao Yang, Xiaohua Hu, Yuanyuan Sun, Hongfei Lin, Jian Wang:
  Protein complex detection in PPI networks based on data integration and supervised learning method. S3
• 
  Hao Chen, Josiah Poon, Simon K. Poon, Lizhi Cui, Kei Fan, Daniel Man-yuen Sze:
  Ensemble learning for prediction of the bioactivity capacity of herbal medicines from chromatographic fingerprints. S4
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  Xianjun Shen, Li Yi, Yang Yi, Jincai Yang, Tingting He, Xiaohua Hu:
  Dynamic identifying protein functional modules based on adaptive density modularity in protein-protein interaction networks. S5

Volume 16, Number S13, December 2015

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  Roozbeh Dehghannasiri, Byung-Jun Yoon, Edward R. Dougherty:
  Efficient experimental design for uncertainty reduction in gene regulatory networks. S2
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  Daniel N. Mohsenizadeh, Jianping Hua, Michael L. Bittner, Edward R. Dougherty:
  Dynamical modeling of uncertain interaction-based genomic networks. S3
• 
  Hui Huang, Thanh Nguyen, Sara Ibrahim, Sandeep Shantharam, Zongliang Yue, Jake Y. Chen:
  DMAP: a connectivity map database to enable identification of novel drug repositioning candidates. S4
• 
  James Lemon, Sinan Kockara, Tansel Halic, Mutlu Mete:
  Density-based parallel skin lesion border detection with webCL. S5
• 
  Weizhong Zhao, James J. Chen, Roger Perkins, Zhichao Liu, Weigong Ge, Yijun Ding, Wen Zou:
  A heuristic approach to determine an appropriate number of topics in topic modeling. S8
• 
  Heng Luo, Hao Ye, Hui Wen Ng, Leming Shi, Weida Tong, William Mattes, Donna Mendrick, Huixiao Hong:
  Understanding and predicting binding between human leukocyte antigens (HLAs) and peptides by network analysis. S9
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  Mikhail G. Dozmorov, Indra Adrianto, Cory B. Giles, Edmund R. Glass, Stuart B. Glenn, Courtney Montgomery, Kathy L. Sivils, Lorin E. Olson, Tomoaki Iwayama, Willard M. Freeman, Christopher J. Lessard, Jonathan D. Wren:
  Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data. S10
• 
  Jakob Dohrmann, Juris Puchin, Rahul Singh:
  Global multiple protein-protein interaction network alignment by combining pairwise network alignments. S11
• 
  Mansuck Kim, Huan Zhang, Charles Woloshuk, Won-Bo Shim, Byung-Jun Yoon:
  Computational identification of genetic subnetwork modules associated with maize defense response to Fusarium verticillioides. S12
•