BMC Bioinformatics, Volume 17 - Supplements

Volume 17, Number S-1, January 2016

Selected articles from the Fourteenth Asia Pacific Bioinformatics Conference (APBC 2016): Bioinformatics

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  Suvir Jain, Kashyap R., Tsung-Ting Kuo, Shitij Bhargava, Gordon Lin, Chun-Nan Hsu:
  Weakly supervised learning of biomedical information extraction from curated data. 1
• 
  Chien-Hung Huang, Peter Mu-Hsin Chang, Chia-Wei Hsu, Chi-Ying F. Huang, Ka-Lok Ng:
  Drug repositioning for non-small cell lung cancer by using machine learning algorithms and topological graph theory. 2
• 
  Shih-Wei Lee, Lawrence Shih-Hsin Wu, Guan-Mau Huang, Kai-Yao Huang, Tzong-Yi Lee, Julia Tzu-Ya Weng:
  Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis. 3
• 
  Sunil Kumar, Philipp Bucher:
  Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features. 4
• 
  Yafei Lyu, Qunhua Li:
  A semi-parametric statistical model for integrating gene expression profiles across different platforms. 5
• 
  Moraima Pagan, Richard T. Kloos, Chu-Fang Lin, Kevin J. Travers, Hajime Matsuzaki, Ed Y. Tom, Su Yeon Kim, Mei G. Wong, Andrew C. Stewart, Jing Huang, P. Sean Walsh, Robert J. Monroe, Giulia C. Kennedy:
  The diagnostic application of RNA sequencing in patients with thyroid cancer: an analysis of 851 variants and 133 fusions in 524 genes. 6
• 
  Henan Wang, Chong He, Garima Kushwaha, Dong Xu, Jing Qiu:
  A full Bayesian partition model for identifying hypo- and hyper-methylated loci from single nucleotide resolution sequencing data. 7
• 
  Chao Fan, Diwei Liu, Rui Huang, Zhigang Chen, Lei Deng:
  PredRSA: a gradient boosted regression trees approach for predicting protein solvent accessibility. 8
• 
  Lujia Chen, Chunhui Cai, Vicky Chen, Xinghua Lu:
  Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model. 9
• 
  Yang Yang, Zhuangdi Xu, Dandan Song:
  Missing value imputation for microRNA expression data by using a GO-based similarity measure. 10

Volume 17, Number S-2, January 2016

Bringing Maths to Life (BMTL)

• 
  Said el Bouhaddani, Jeanine J. Houwing-Duistermaat, Perttu Salo, Markus Perola, Geurt Jongbloed, Hae-Won Uh:
  Evaluation of O2PLS in Omics data integration. 11
• 
  Séverine Affeldt, Louis Verny, Hervé Isambert:
  3off2: A network reconstruction algorithm based on 2-point and 3-point information statistics. 12
• 
  Yasaman Karami, Elodie Laine, Alessandra Carbone:
  Dissecting protein architecture with communication blocks and communicating segment pairs. 13
• 
  Marcella Vacca, Kumar Parijat Tripathi, Luisa Speranza, Riccardo Aiese Cigliano, Francesco Scalabrì, Federico Marracino, Michele Madonna, Walter Sanseverino, Carla Perrone-Capano, Mario Rosario Guarracino, Maurizio D'Esposito:
  Effects of Mecp2 loss of function in embryonic cortical neurons: a bioinformatics strategy to sort out non-neuronal cells variability from transcriptome profiling. 14
• 
  Matteo Bersanelli, Ettore Mosca, Daniel Remondini, Enrico Giampieri, Claudia Sala, Gastone C. Castellani, Luciano Milanesi:
  Methods for the integration of multi-omics data: mathematical aspects. 15
• 
  Claudia Sala, Silvia Vitali, Enrico Giampieri, Ìtalo Faria do Valle, Daniel Remondini, Paolo Garagnani, Matteo Bersanelli, Ettore Mosca, Luciano Milanesi, Gastone C. Castellani:
  Stochastic neutral modelling of the Gut Microbiota's relative species abundance from next generation sequencing data. 16

Volume 17, Number S-3, February 2016

• 
  Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob B. Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan F. DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman, Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau, Nagarajan Raju, Sonia P. Chothani, C. Ramakrishnan, Masakazu Sekijima, M. Michael Gromiha, Paddy J. Slator, Nigel J. Burroughs, Przemyslaw Szalaj, Zhonghui Tang, Paul J. Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski, Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens, Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic:
  Highlights from the 11th ISCB Student Council Symposium 2015: Dublin, Ireland. 10 July 2015.

Volume 17, Number S-4, March 2016

NETTAB 2014. From structural bioinformatics to integrative systems biology

• 
  Arnaud Céol, Lisette G. G. C. Verhoef, Mark Wade, Heiko Müller:
  Genome and network visualization facilitates the analyses of the effects of drugs and mutations on protein-protein and drug-protein networks. 54
• 
  Federica Chiappori, Luca Mattiazzi, Luciano Milanesi, Ivan Merelli:
  A novel molecular dynamics approach to evaluate the effect of phosphorylation on multimeric protein interface: the αB-Crystallin case study. 57
• 
  Paolo Romano, Aldo Profumo, Mattia Rocco, Rosa Mangerini, Fabio Ferri, Angelo M. Facchiano:
  Geena 2, improved automated analysis of MALDI/TOF mass spectra. 61
• 
  Paolo Romano, Francesca Cordero:
  NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology. 62
• 
  Nicola Prezza, Francesco Vezzi, Max Käller, Alberto Policriti:
  Fast, accurate, and lightweight analysis of BS-treated reads with ERNE 2. 69
• 
  Claudio Angione, Maxwell Conway, Pietro Liò:
  Multiplex methods provide effective integration of multi-omic data in genome-scale models. 83

Volume 17, Number S-5, June 2016

Selected articles from Statistical Methods for Omics Data Integration and Analysis 2014

• 
  Ioannis Kavakiotis, Aliki Xochelli, Andreas Agathangelidis, Grigorios Tsoumakas, Nicos Maglaveras, Kostas Stamatopoulos, Anastasia Hadzidimitriou, Ioannis P. Vlahavas, Ioanna Chouvarda:
  Integrating multiple immunogenetic data sources for feature extraction and mining somatic hypermutation patterns: the case of "towards analysis" in chronic lymphocytic leukaemia. 173
• 
  Sebastián Moschen, Janet Higgins, Julio A. Di Rienzo, Ruth A. Heinz, Norma Paniego, Paula Fernandez:
  Network and biosignature analysis for the integration of transcriptomic and metabolomic data to characterize leaf senescence process in sunflower. 174
• 
  Andrew J. Sedgewick, Ivy Shi, Rory M. Donovan, Panayiotis V. Benos:
  Learning mixed graphical models with separate sparsity parameters and stability-based model selection. S175
• 
  Animesh Acharjee, Bjorn Kloosterman, Richard G. F. Visser, Chris Maliepaard:
  Integration of multi-omics data for prediction of phenotypic traits using random forest. 180
• 
  Panagiotis Chouvardas, George Kollias, Christoforos Nikolaou:
  Inferring active regulatory networks from gene expression data using a combination of prior knowledge and enrichment analysis. 181
• 
  Nikolas Papanikolaou, Georgios A. Pavlopoulos, Theodosios Theodosiou, Ioannis S. Vizirianakis, Ioannis Iliopoulos:
  DrugQuest - a text mining workflow for drug association discovery. 182
• 
  Costas Bouyioukos, Mohamed Elati, François Képès:
  Analysis tools for the interplay between genome layout and regulation. 191
• 
  Vincenzo Lagani, Argyro D. Karozou, David Gomez-Cabrero, Gilad Silberberg, Ioannis Tsamardinos:
  A comparative evaluation of data-merging and meta-analysis methods for reconstructing gene-gene interactions. S194
• 
  Frans M. van der Kloet, Patricia Sebastián-León, Ana Conesa, Age K. Smilde, Johan A. Westerhuis:
  Separating common from distinctive variation. S195
• 
  Esteban Vegas, Josep M. Oller, Ferran Reverter:
  Inferring differentially expressed pathways using kernel maximum mean discrepancy-based test. 205
• 
  Francesco Strino, Michael Lappe:
  Identifying peaks in *-seq data using shape information. S206

Volume 17, Number S-6, July 2016

Proceedings of the ACM Ninth International Workshop on Data and Text Mining in Biomedical Informatics: bioinformatics

• 
  Jongsoo Keum, Sunyong Yoo, Doheon Lee, Hojung Nam:
  Prediction of compound-target interactions of natural products using large-scale drug and protein information. 219
• 
  Kimin Oh, Gwan-Su Yi:
  Prediction of scaffold proteins based on protein interaction and domain architectures. 220
• 
  Woochang Hwang, Jaejoon Choi, Mijin Kwon, Doheon Lee:
  Context-specific functional module based drug efficacy prediction. 275

Volume 17, Number S-7, July 2016

Selected articles from the 12th Annual Biotechnology and Bioinformatics Symposium: bioinformatics

• 
  Yijia Zhang, Hongfei Lin, Zhihao Yang, Jian Wang, Yiwei Liu, Shengtian Sang:
  A method for predicting protein complex in dynamic PPI networks. 229
• 
  Ahmed AbdoAziz Ahmed Abdulla, Hongfei Lin, Bo Xu, Santosh Kumar Banbhrani:
  Improving biomedical information retrieval by linear combinations of different query expansion techniques. 238
• 
  Mark T. W. Ebbert, Mark E. Wadsworth, Lyndsay A. Staley, Kaitlyn L. Hoyt, Brandon D. Pickett, Justin Miller, John Duce, John S. K. Kauwe, Perry G. Ridge:
  Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches. 239
• 
  Wenpin Hou, Yushan Qiu, Nobuyuki Hashimoto, Wai-Ki Ching, Kiyoko F. Aoki-Kinoshita:
  A systematic framework to derive N-glycan biosynthesis process and the automated construction of glycosylation networks. 240
• 
  Aaron R. Sharp, Joshua Udall:
  OMWare: a tool for efficient assembly of genome-wide physical maps. 241
• 
  Arman Sargolzaei, Mohamed N. Abdelghani, Kang K. Yen, Saman Sargolzaei:
  Sensorimotor control: computing the immediate future from the delayed present. 245
• 
  Thi Thanh Thuy Phan, Takenao Ohkawa:
  Protein-protein interaction extraction with feature selection by evaluating contribution levels of groups consisting of related features. 246
• 
  Paul M. Bodily, M. Stanley Fujimoto, Justin T. Page, Mark J. Clement, Mark T. W. Ebbert, Perry G. Ridge:
  A novel approach for multi-SNP GWAS and its application in Alzheimer's disease. 268
• 
  Emad Y. Ramadan, Ahmed Naef, Moataz A. Ahmed:
  Protein complexes predictions within protein interaction networks using genetic algorithms. 269
• 
  Emad Y. Ramadan, Sadiq Al-Insaif, Md. Rafiul Hassan:
  Network topology measures for identifying disease-gene association in breast cancer. 274

Volume 17, Number S-8, August 2016

Selected articles from the 11th International Symposium on Bioinformatics Research and Applications (ISBRA '15): bioinformatics

• 
  Leonid Zaslavsky, Stacy Ciufo, Boris Fedorov, Tatiana A. Tatusova:
  Clustering analysis of proteins from microbial genomes at multiple levels of resolution. 276
• 
  Sefa Kiliç, Ivan Erill:
  Assessment of transfer methods for comparative genomics of regulatory networks in bacteria. 277
• 
  ChenHsiang Shen, Xiaxia Yu, Robert W. Harrison, Irene T. Weber:
  Automated prediction of HIV drug resistance from genotype data. 278
• 
  Gaoshi Li, Min Li, Jianxin Wang, Jingli Wu, Fang-Xiang Wu, Yi Pan:
  Predicting essential proteins based on subcellular localization, orthology and PPI networks. 279
• 
  Xiaojun Xu, Hong Thai, Kathryn M. Kitrinos, Guo-liang Xia, Anuj Gaggar, Matthew Paulson, Lilia Ganova-Raeva, Yury Khudyakov, James Lara:
  Modeling the functional state of the reverse transcriptase of hepatitis B virus and its application to probing drug-protein interaction. 280
• 
  Ashraf Yaseen, Mais Nijim, Brandon Williams, Lei Qian, Min Li, Jianxin Wang, Yaohang Li:
  FLEXc: protein flexibility prediction using context-based statistics, predicted structural features, and sequence information. 281
• 
  Jianyu Shi, Jia-Xin Li, Hui-Meng Lu:
  Predicting existing targets for new drugs base on strategies for missing interactions. 282
• 
  Cuncong Zhong, Youngik Yang, Shibu Yooseph:
  GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly. 283
• 
  Stéphane Chrétien, Christophe Guyeux, Bastien Conesa, Régis Delage-Mouroux, Michèle Jouvenot, Philippe Huetz, Françoise Descôtes:
  A Bregman-proximal point algorithm for robust non-negative matrix factorization with possible missing values and outliers - application to gene expression analysis. 284
• 
  Yongtao Ye, Tak Wah Lam, Hing-Fung Ting:
  PnpProbs: a better multiple sequence alignment tool by better handling of guide trees. 285

Volume 17, Number S-9, July 2016

Selected articles from the IEEE International Conference on Bioinformatics and Biomedicine 2015: bioinformatics

• 
  Yanqing Ji, Hao Ying, John Tran, Peter Dews, R. Michael Massanari:
  Integrating unified medical language system and association mining techniques into relevance feedback for biomedical literature search. 264
• 
  Tian Bai, Leiguang Gong, Ye Wang, Yan Wang, Casimir A. Kulikowski, Lan Huang:
  A method for exploring implicit concept relatedness in biomedical knowledge network. 265
• 
  Qiang Yu, Hongwei Huo, Ruixing Zhao, Dazheng Feng, Jeffrey Scott Vitter, Jun Huan:
  RefSelect: a reference sequence selection algorithm for planted (l, d) motif search. 266
• 
  Haidong Lan, Yuandong Chan, Kai Xu, Bertil Schmidt, Shaoliang Peng, Weiguo Liu:
  Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters. 267
• 
  Dan He, Laxmi Parida:
  Does encoding matter? A novel view on the quantitative genetic trait prediction problem. 272

Volume 17, Number S-10, August 2016

• 
  Eric C. Rouchka, Julia H. Chariker, Benjamin J. Harrison, Juw Won Park, Xueyuan Cao, Stanley Pounds, Susana C. Raimondi, James R. Downing, Raul C. Ribeiro, Jeffrey Rubnitz, Jatinder Lamba, Bernie J. Daigle Jr., Deborah Burgess, Stephanie Gehrlich, John C. Carmen, Nicholas Johnson, Chandrakanth Emani, Kalpani De Silva, Michael P. Heaton, Theodore S. Kalbfleisch, Teeradache Viangteeravat, Rahul Mudunuri, Oluwaseun Ajayi, Fatih Sen, Eunice Y. Huang, Mohammad Mohebbi, Luaire Florian, Douglas J. Jackson, John F. Naber, Akm Sabbir, Sally R. Ellingson, Yuping Lu, Charles A. Phillips, Michael A. Langston, Rahul Kumar Sevakula, Raghuveer Thirukovalluru, Nishchal K. Verma, Yan Cui, Mohammed Sayed, Jing Wang, Qi Liu, Yu Shyr, Xiaofei Zhang, Naresh Prodduturi, Gavin R. Oliver, Diane Grill, Jie Na, Jeanette Eckel-Passow, Eric W. Klee, Michael M. Goodin, Mark L. Farman, Harrison Inocencio, Chanyong Jang, Jerzy W. Jaromczyk, Neil Moore, Kelly L. Sovacool, Leon Dent, Mike Izban, Sammed N. Mandape, Shruti S. Sakhare, Siddharth Pratap, Dana Marshall, M. Scotty Depriest, James N. MacLeod, Hanady Adam, Ethan Blandford, Joel Campbell, Joshua Castlen, Brittany Dixon, Ginger Gilbert, Aaron Hall, Philip Kreisle, Jessica Lasher, Bethany Oakes, Allison Speer, Maximilian Valentine, Naga Satya Venkateswara Ra Nagisetty, Rony Jose, Robert W. Rooney, David Hains:
  Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016: Cadiz, KY, USA. 8-10 April 2016.

Volume 17, Number S-11, September 2016

Selected articles from the 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2014)

• 
  Hongjian Li, Kwong-Sak Leung, Man Hon Wong, Pedro J. Ballester:
  Correcting the impact of docking pose generation error on binding affinity prediction. 308
• 
  Danilo Pellin, Clelia Di Serio:
  A novel scan statistics approach for clustering identification and comparison in binary genomic data. 320
• 
  Antonino Fiannaca, Massimo La Rosa, Laura La Paglia, Riccardo Rizzo, Alfonso Urso:
  MiRNATIP: a SOM-based miRNA-target interactions predictor. 321
• 
  Andrea Bracciali, Marco Aldinucci, Murray Patterson, Tobias Marschall, Nadia Pisanti, Ivan Merelli, Massimo Torquati:
  PWHATSHAP: efficient haplotyping for future generation sequencing. 342
• 
  Daniela Evangelista, Kumar Parijat Tripathi, Mario Rosario Guarracino:
  An Atlas of annotations of Hydra vulgaris transcriptome. 360

Volume 17, Number S-12, October 2016

Italian Society of Bioinformatics (BITS): Annual Meeting 2015

• 
  Luciano Milanesi, Alessandro Guffanti, Giancarlo Mauri, Marco Masseroli:
  BITS 2015: the annual meeting of the Italian Society of Bioinformatics. 1-4
• 
  Angelo Nuzzo, Giovanni Carapezza, Sebastiano Di Bella, Alfredo Pulvirenti, Antonella Isacchi, Roberta Bosotti:
  KAOS: a new automated computational method for the identification of overexpressed genes. 5-14
• 
  Susanna Zucca, Margherita Villaraggia, Stella Gagliardi, Gaetano Salvatore Grieco, Marialuisa Valente, Cristina Cereda, Paolo Magni:
  Analysis of amplicon-based NGS data from neurological disease gene panels: a new method for allele drop-out management. 15-26
• 
  Ìtalo Faria do Valle, Enrico Giampieri, Giorgia Simonetti, Antonella Padella, Marco Manfrini, Anna Ferrari, Cristina Papayannidis, Isabella Zironi, Marianna Garonzi, Simona Bernardi, Massimo Delledonne, Giovanni Martinelli, Daniel Remondini, Gastone C. Castellani:
  Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data. 27-35
• 
  Marco Pellegrini, Miriam Baglioni, Filippo Geraci:
  Protein complex prediction for large protein protein interaction networks with the Core&Peel method. 37-58
• 
  Andrea Manconi, Marco Moscatelli, Giuliano Armano, Matteo Gnocchi, Alessandro Orro, Luciano Milanesi:
  Removing duplicate reads using graphics processing units. 59-71
• 
  Maria Angela Diroma, Paolo Lubisco, Marcella Attimonelli:
  A comprehensive collection of annotations to interpret sequence variation in human mitochondrial transfer RNAs. 73-82
• 
  Davide Cangelosi, Simone Pelassa, Martina Morini, Massimo Conte, Maria Bosco, Alessandra Eva, Angela Rita Sementa, Luigi Varesio:
  Artificial neural network classifier predicts neuroblastoma patients' outcome. 83-93
• 
  Arianna Consiglio, Corrado Mencar, Giorgio Grillo, Flaviana Marzano, Mariano Francesco Caratozzolo, Sabino Liuni:
  A fuzzy method for RNA-Seq differential expression analysis in presence of multireads. 95-110
• 
  Claudia Cava, Antonio Colaprico, Gloria Bertoli, Gianluca Bontempi, Giancarlo Mauri, Isabella Castiglioni:
  How interacting pathways are regulated by miRNAs in breast cancer subtypes. 111-133
• 
  Ilaria Granata, Mara Sangiovanni, Francesco Maiorano, Marco Miele, Mario Rosario Guarracino:
  Var2GO: a web-based tool for gene variants selection. 135-140

Volume 17, Number S-13, October 2016

Proceedings of the 13th Annual MCBIOS conference

• 
  Inimary T. Toby, Mikhail K. Levin, Edward Salinas, Scott Christley, Sanchita Bhattacharya, Felix Breden, Adam Buntzman, Brian Corrie, John M. Fonner, Namita T. Gupta, Uri Hershberg, Nishanth Marthandan, Aaron M. Rosenfeld, William Rounds, Florian Rubelt, Walter Scarborough, Jamie K. Scott, Mohamed Uduman, Jason A. Vander Heiden, Richard H. Scheuermann, Nancy Monson, Steven H. Kleinstein, Lindsay G. Cowell:
  VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. 333
• 
  Edmund R. Glass, Mikhail G. Dozmorov:
  Improving sensitivity of linear regression-based cell type-specific differential expression deconvolution with per-gene vs. global significance threshold. 334
• 
  Ryan Eshleman, Rahul Singh:
  Leveraging graph topology and semantic context for pharmacovigilance through twitter-streams. 335
• 
  Yongsheng Bai, Lizhong Ding, Steve Baker, Jenny M. Bai, Ethan Rath, Feng Jiang, Jianghong Wu, Hui Jiang, Gary W. Stuart:
  Dissecting the biological relationship between TCGA miRNA and mRNA sequencing data using MMiRNA-Viewer. 336
• 
  Yang Liu, Saad M. Khan, Juexin Wang, Mats Rynge, Yuanxun Zhang, Shuai Zeng, Shiyuan Chen, João V. Maldonado dos Santos, Babu Valliyodan, Prasad Calyam, Nirav C. Merchant, Henry T. Nguyen, Dong Xu, Trupti Joshi:
  PGen: large-scale genomic variations analysis workflow and browser in SoyKB. 337
• 
  Quang Tran, Shanshan Gao, Vinhthuy Phan:
  Analysis of optimal alignments unfolds aligners' bias in existing variant profiles. 349
• 
  Sujoy Roy, Brandon C. Curry, Behrouz Madahian, Ramin Homayouni:
  Prioritization, clustering and functional annotation of MicroRNAs using latent semantic indexing of MEDLINE abstracts. 350
• 
  Navadon Khunlertgit, Byung-Jun Yoon:
  Incorporating topological information for predicting robust cancer subnetwork markers in human protein-protein interaction network. 351
• 
  Jonathan D. Wren, Inimary T. Toby, Huxiao Hong, Bindu Nanduri, Rakesh Kaundal, Mikhail G. Dozmorov, Shraddha Thakkar:
  Proceedings of the 2016 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. 356
• 
  Mutlu Mete, Ünal Sakoglu, Jeffrey S. Spence, Michael Devous, Thomas S. Harris, Bryon Adinoff:
  Successful classification of cocaine dependence using brain imaging: a generalizable machine learning approach. 357
• 
  Sertan Kaya, Mustafa Bayraktar, Sinan Kockara, Mutlu Mete, Tansel Halic, Halle E. Field, Henry K. Wong:
  Abrupt skin lesion border cutoff measurement for malignancy detection in dermoscopy images. 367
• 
  Mikyung Lee, Zhichao Liu, Ruili Huang, Weida Tong:
  Application of dynamic topic models to toxicogenomics data. 368
• 
  Si Chen, Lih-Yuan Deng, Dale Bowman, Jyh-Jen Horng Shiau, Tit-Yee Wong, Behrouz Madahian, Henry Horng-Shing Lu:
  Phylogenetic tree construction using trinucleotide usage profile (TUP). 381
• 
  Xueyuan Cao, Kristine R. Crews, James R. Downing, Jatinder Lamba, Stanley Pounds:
  CC-PROMISE effectively integrates two forms of molecular data with multiple biologically related endpoints. 382
• 
  Hyundoo Jeong, Xiaoning Qian, Byung-Jun Yoon:
  Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model. 395

Volume 17, Number S-14, November 2016

• 
  Pedro Feijão, Eloi Araujo:
  Fast ancestral gene order reconstruction of genomes with unequal gene content. 187-200
• 
  Ashok Rajaraman, Jian Ma:
  Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction. 201-212
• 
  Nikita Alexeev, Pavel Avdeyev, Max A. Alekseyev:
  Comparative genomics meets topology: a novel view on genome median and halving problems. 213-223
• 
  Laurent Bulteau, Guillaume Fertin, Eric Tannier:
  Genome rearrangements with indels in intergenes restrict the scenario space. 225-231
• 
  Zhe Yu, David Sankoff:
  A continuous analog of run length distributions reflecting accumulated fractionation events. 233-240
• 
  Lawrence H. Uricchio, Tandy J. Warnow, Noah A. Rosenberg:
  An analytical upper bound on the number of loci required for all splits of a species tree to appear in a set of gene trees. 241-250
• 
  Mark Jones, Christophe Paul, Céline Scornavacca:
  On the consistency of orthology relationships. 251-262
• 
  Mehmood Alam Khan, Owais Mahmudi, Ikram Ullah, Lars Arvestad, Jens Lagergren:
  Probabilistic inference of lateral gene transfer events. 263-270
• 
  Jiafan Zhu, Yun Yu, Luay Nakhleh:
  In the light of deep coalescence: revisiting trees within networks. 271-282

Volume 17, Number S-15, November 2016

Proceedings of Statistical Methods for Omics Data Integration and Analysis 2015

• 
  Pedro Furió-Tarí, Ana Conesa, Sonia Tarazona:
  RGmatch: matching genomic regions to proximal genes in omics data integration. 1-10
• 
  Sara Aibar, María Abáigar, Francisco J. Campos-Laborie, Jose Manuel Sánchez-Santos, Jesus M. Hernandez-Rivas, Javier De Las Rivas:
  Identification of expression patterns in the progression of disease stages by integration of transcriptomic data. 11-21
• 
  David Gomez-Cabrero, Jörg Menche, Claudia Vargas, Isaac Cano, Dieter Maier, Albert-László Barabási, Jesper Tegnér, Josep Roca:
  From comorbidities of chronic obstructive pulmonary disease to identification of shared molecular mechanisms by data integration. 23-35
• 
  Animesh Acharjee, Zsuzsanna Ament, James A. West, Elizabeth Stanley, Julian L. Griffin:
  Integration of metabolomics, lipidomics and clinical data using a machine learning method. 37-49

Volume 17, Number S-16, December 2016

Proceedings of the Tenth International Workshop on Machine Learning in Systems Biology (MLSB 2016)

• 
  Aalt D. J. van Dijk, Harri Lähdesmäki, Dick de Ridder, Juho Rousu:
  Selected proceedings of Machine Learning in Systems Biology: MLSB 2016. 51-52
• 
  Saulius Lukauskas, Roberto Visintainer, Guido Sanguinetti, Gabriele Beate Schweikert:
  DGW: an exploratory data analysis tool for clustering and visualisation of epigenomic marks. 53-63
• 
  Sung Hee Park, Sunmin Lee, Young-Joon Kim, Sangsoo Kim:
  ChARM: Discovery of combinatorial chromatin modification patterns in hepatitis B virus X-transformed mouse liver cancer using association rule mining. 65-83
• 
  Séverine Affeldt, Nataliya Sokolovska, Edi Prifti, Jean-Daniel Zucker:
  Spectral consensus strategy for accurate reconstruction of large biological networks. 85-97
• 
  Otte Heinävaara, Janne Leppä-aho, Jukka Corander, Antti Honkela:
  On the inconsistency of ℓ 1-penalised sparse precision matrix estimation. 99-107
• 
  André Veríssimo, Arlindo Limede Oliveira, Marie-France Sagot, Susana Vinga:
  DegreeCox - a network-based regularization method for survival analysis. 109-121
• 
  Mehmet Gönen:
  Integrating gene set analysis and nonlinear predictive modeling of disease phenotypes using a Bayesian multitask formulation. 123-135

Volume 17, Number S-17, December 2016

Proceedings of the 27th International Conference on Genome Informatics: bioinformatics

• 
  Guangyong Zheng, Yaochen Xu, Xiujun Zhang, Zhi-Ping Liu, Zhuo Wang, Luonan Chen, Xin-Guang Zhu:
  CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data. 137-144
• 
  Mengmeng Wu, Ting Chen, Rui Jiang:
  Global inference of disease-causing single nucleotide variants from exome sequencing data. 145-157
• 
  Jihyeob Mun, Dong-Uk Kim, Kwang-Lae Hoe, Seon-Young Kim:
  Genome-wide functional analysis using the barcode sequence alignment and statistical analysis (Barcas) tool. 159-167
• 
  Abha Belorkar, Limsoon Wong:
  GFS: fuzzy preprocessing for effective gene expression analysis. 169-184
• 
  Kun-Tze Chen, Cheih-Jung Chen, Hsin-Ting Shen, Chia-Liang Liu, Shang-Hao Huang, Chin Lung Lu:
  Multi-CAR: a tool of contig scaffolding using multiple references. 185-192
• 
  Song Liu, Yi Wang, Fei Wang:
  A fast read alignment method based on seed-and-vote for next generation sequencing. 193-203
• 
  Yan Yan, Kaizhong Zhang:
  Spectra library assisted de novo peptide sequencing for HCD and ETD spectra pairs. 205-211
• 
  Yanglan Gan, Han Tao, Guobing Zou, Cairong Yan, Jihong Guan:
  Dynamic epigenetic mode analysis using spatial temporal clustering. 213-220
• 
  Pi-Jing Wei, Di Zhang, Junfeng Xia, Chun-Hou Zheng:
  LNDriver: identifying driver genes by integrating mutation and expression data based on gene-gene interaction network. 221-230
• 
  Qiaosheng Zhang, Jie Li, Haozhe Xie, Hanqing Xue, Yadong Wang:
  A network-based pathway-expanding approach for pathway analysis. 231-241
• 
  Yuchen Yuan, Yi Shi, Changyang Li, Jinman Kim, Weidong Cai, Zeguang Han, David Dagan Feng:
  DeepGene: an advanced cancer type classifier based on deep learning and somatic point mutations. 243-256
• 
  Jusang Lee, Kyuri Jo, Sunwon Lee, Jaewoo Kang, Sun Kim:
  Prioritizing biological pathways by recognizing context in time-series gene expression data. 257-268
• 
  Hui Liu, Yinglong Song, Jihong Guan, Libo Luo, Ziheng Zhuang:
  Inferring new indications for approved drugs via random walk on drug-disease heterogenous networks. 269-277
• 
  Onkar Singh, Emily Chia-Yu Su:
  Prediction of HIV-1 protease cleavage site using a combination of sequence, structural, and physicochemical features. 279-289
• 
  Nan Meng, Raghu Machiraju, Kun Huang:
  Identification of recurrent combinatorial patterns of chromatin modifications at promoters across various tissue types. 291-303

Volume 17, Number S-18, December 2016

Proceedings of X-meeting 2015: 11th International Conference of the AB3C + Brazilian Symposium on Bioinformatics: bioinformatics

• 
  Elisa Terumi Rubel, Roberto Tadeu Raittz, Nilson Antônio da Rocha Coimbra, Michelly Alves Coutinho Gehlen, Fábio de Oliveira Pedrosa:
  ProClaT, a new bioinformatics tool for in silico protein reclassification: case study of DraB, a protein coded from the draTGB operon in Azospirillum brasilense. 1-10
• 
  Rayane Nunes Lima, Muhammad Faheem, João Alexandre Ribeiro Gonçalves Barbosa, Marcelo Depólo Polêto, Hugo Verli, Fernando Lucas Melo, Renato Oliveira Resende:
  Homology modeling and molecular dynamics provide structural insights into tospovirus nucleoprotein. 11-17
• 
  Caroline Anne Larlee, Alex Brandts, David Sankoff:
  Compromise or optimize? The breakpoint anti-median. 19-23
• 
  Fabio Ribeiro Cerqueira, Adilson Mendes Ricardo, Alcione de Paiva Oliveira, Armin Graber, Christian Baumgartner:
  MUMAL2: Improving sensitivity in shotgun proteomics using cost sensitive artificial neural networks and a threshold selector algorithm. 25-38
• 
  Emmanuel Bresso, Roberto C. Togawa, Kim E. Hammond-Kosack, Martin Urban, Bernard Maigret, Natália Florencio Martins:
  GPCRs from fusarium graminearum detection, modeling and virtual screening - the search for new routes to control head blight disease. 39-52
• 
  Yuri Bento Marques, Alcione de Paiva Oliveira, Ana Tereza Ribeiro de Vasconcelos, Fabio Ribeiro Cerqueira:
  Mirnacle: machine learning with SMOTE and random forest for improving selectivity in pre-miRNA ab initio prediction. 53-63
• 
  Diego C. B. Mariano, Felipe L. Pereira, Edgar L. Aguiar, Letícia de Castro Oliveira, Leandro Benevides, Luis Guimarães, Edson Luiz Folador, Thiago J. Sousa, Preetam Ghosh, Debmalya Barh, Henrique C. P. Figueiredo, Artur Silva, Rommel Ramos, Vasco Ariston de Carvalho Azevedo:
  SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology. 65-72
• 
  João Victor de Araújo Oliveira, Fabrizio Costa, Rolf Backofen, Peter F. Stadler, Maria Emília Telles Walter, Jana Hertel:
  SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification. 73-86

Volume 17, Number S-19, December 2016

15th International Conference On Bioinformatics (InCoB 2016): Bioinformatics

• 
  Christian Schönbach, Chandra Verma, Peter J. Bond, Shoba Ranganathan:
  Bioinformatics and systems biology research update from the 15th International Conference on Bioinformatics (InCoB2016). 87-90
• 
  Marzio Pennisi, Salvatore Cavalieri, Santo Motta, Francesco Pappalardo:
  A methodological approach for using high-level Petri Nets to model the immune system response. 91-105
• 
  Arpah Abu, Lee Kien Leow, Rosli Ramli, Hasmahzaiti Omar:
  Classification of Suncus murinus species complex (Soricidae: Crocidurinae) in Peninsular Malaysia using image analysis and machine learning approaches. 107-118
• 
  Filippo Castiglione, Paolo Tieri, Alessandro Palma, Abdul Salam Jarrah:
  Statistical ensemble of gene regulatory networks of macrophage differentiation. 119-128
• 
  Josep Basha Gutierrez, Kenta Nakai:
  A study on the application of topic models to motif finding algorithms. 129-138
• 
  Mostafa M. Abbas, Hazem M. Bahig:
  A fast exact sequential algorithm for the partial digest problem. 139-148
• 
  Richie Ruei-Chi Gan, Ting-Wen Chen, Timothy H. Wu, Po-Jung Huang, Chi-Ching Lee, Yuan-Ming Yeh, Cheng-Hsun Chiu, Hsien-Da Huang, Petrus Tang:
  PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organisms. 149-158
• 
  Chaowang Lan, Qingfeng Chen, Jinyan Li:
  Grouping miRNAs of similar functions via weighted information content of gene ontology. 159-170
• 
  Yi-Fan Liou, Hui-Ling Huang, Shinn-Ying Ho:
  A hydrophobic spine stabilizes a surface-exposed α-helix according to analysis of the solvent-accessible surface area. 171-182
• 
  Nguyen-Quoc-Khanh Le, Yu-Yen Ou:
  Incorporating efficient radial basis function networks and significant amino acid pairs for predicting GTP binding sites in transport proteins. 183-192
• 
  Mogeeb A. A. Mosleh, Mohd Sapiyan Baba, Sorayya Malek, Rasheed A. Almaktari:
  Ceph-X: development and evaluation of 2D cephalometric system. 193-201
• 
  Tamara Vasylenko, Yi-Fan Liou, Po-Chin Chiou, Hsiao-Wei Chu, Yung-Sung Lai, Yu-Ling Chou, Hui-Ling Huang, Shinn-Ying Ho:
  SCMBYK: prediction and characterization of bacterial tyrosine-kinases based on propensity scores of dipeptides. 203-217
• 
  Chinh Tran To Su, Wei-Li Ling, Wai-Heng Lua, Yu-Xuan Haw, Samuel Ken-En Gan:
  Structural analyses of 2015-updated drug-resistant mutations in HIV-1 protease: an implication of protease inhibitor cross-resistance. 219-228
• 
  Apichart Intarapanich, Saowaluck Kaewkamnerd, Montri Pannarut, Philip James Shaw, Sissades Tongsima:
  Fast processing of microscopic images using object-based extended depth of field. 229-237
• 
  Dhwani Dholakia, Sukriti Goyal, Salma Jamal, Aditi Singh, Asmita Das, Abhinav Grover:
  Molecular modeling and lead design of substituted zanamivir derivatives as potent anti-influenza drugs. 239-249
• 
  Ronesh Sharma, Shiu Kumar, Tatsuhiko Tsunoda, Ashwini Patil, Alok Sharma:
  Predicting MoRFs in protein sequences using HMM profiles. 251-258
• 
  Elham Yousef Kalafi, Wooi Boon Tan, Christopher Town, Sarinder Kaur Dhillon:
  Automated identification of Monogeneans using digital image processing and K-nearest neighbour approaches. 259-266
• 
  Ali Ezzat, Min Wu, Xiaoli Li, Chee Keong Kwoh:
  Drug-target interaction prediction via class imbalance-aware ensemble learning. 267-276
• 
  Chao Xie, Chin Lui Wesley Goi, Daniel H. Huson, Peter F. R. Little, Rohan B. H. Williams:
  RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys. 277-282
• 
  Kopal Joshi, Sukriti Goyal, Sonam Grover, Salma Jamal, Aditi Singh, Pawan Dhar, Abhinav Grover:
  Novel group-based QSAR and combinatorial design of CK-1δ inhibitors as neuroprotective agents. 283-295