BMC Bioinformatics, Volume 14 - Supplements

Volume 14, Number S-1, January 2013

Computational Intelligence in Bioinformatics and Biostatistics: new trends from the CIBB conference series
Seventh International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2010), Palermo, Italy, September 16-18, 2010

• 
  Riccardo Rizzo, Paulo J. G. Lisboa:
  Introduction. I1
• 
  Giuseppe Agapito, Pietro Hiram Guzzi, Mario Cannataro:
  Visualization of protein interaction networks: problems and solutions. S1
• 
  Luis Carlos Belarmino, Roberta Lane de Oliveira Silva, Nina da Mota Soares-Cavalcanti, Nicolas Krezdorn, Ederson Akio Kido, Ralf Horres, Peter Winter, Günter Kahl, Ana Maria Benko-Iseppon:
  SymGRASS: a database of sugarcane orthologous genes involved in arbuscular mycorrhiza and root nodule symbiosis. S2
• 
  Luigi Cerulo, Vincenzo Paduano, Pietro Zoppoli, Michele Ceccarelli:
  A negative selection heuristic to predict new transcriptional targets. S3
• 
  Antonio d'Acierno, Massimo Esposito, Giuseppe De Pietro:
  An extensible six-step methodology to automatically generate fuzzy DSSs for diagnostic applications. S4
• 
  Antonino Fiannaca, Massimo La Rosa, Alfonso Urso, Riccardo Rizzo, Salvatore Gaglio:
  A knowledge-based decision support system in bioinformatics: an application to protein complex extraction. S5
• 
  Raffaele Giancarlo, Giosuè Lo Bosco, Luca Pinello, Filippo Utro:
  A methodology to assess the intrinsic discriminative ability of a distance function and its interplay with clustering algorithms for microarray data analysis. S6
• 
  Ederson Akio Kido, José R. C. Ferreira Neto, Roberta L. O. Silva, Luis Carlos Belarmino, João P. Bezerra Neto, Nina da Mota Soares-Cavalcanti, Valesca Pandolfi, Manassés D. Silva, Alexandre L. Nepomuceno, Ana Maria Benko-Iseppon:
  Expression dynamics and genome distribution of osmoprotectants in soybean: identifying important components to face abiotic stress. S7
• 
  Paulo J. G. Lisboa, Terence A. Etchells, Ian H. Jarman, Simon J. Chambers:
  Finding reproducible cluster partitions for the k-means algorithm. S8
• 
  Ivan Merelli, Andrea Calabria, Paolo Cozzi, Federica Viti, Ettore Mosca, Luciano Milanesi:
  SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS. S9
• 
  Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio:
  Prediction of disulfide connectivity in proteins with machine-learning methods and correlated mutations. S10
• 
  Viola Volpato, Alessandro Adelfio, Gianluca Pollastri:
  Accurate prediction of protein enzymatic class by N-to-1 Neural Networks. S11

Volume 14, Number S-2, January 2013

Selected articles from the Eleventh Asia Pacific Bioinformatics Conference (APBC 2013): Bioinformatics

• 
  Rujira Achawanantakun, Yanni Sun:
  Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM. S1
• 
  Kaushalya C. Amarasinghe, Jason Li, Saman K. Halgamuge:
  CoNVEX: copy number variation estimation in exome sequencing data using HMM. S2
• 
  Joseph W. Carl, Joanne Trgovcich, Sridhar Hannenhalli:
  Widespread evidence of viral miRNAs targeting host pathways. S3
• 
  Tzu-Hao Chang, Hsi-Yuan Huang, Justin Bo-Kai Hsu, Shun-Long Weng, Jorng-Tzong Horng, Hsien-Da Huang:
  An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. S4
• 
  Chi-Wei Chen, Jerome Lin, Yen-Wei Chu:
  iStable: off-the-shelf predictor integration for predicting protein stability changes. S5
• 
  Lukas Folkman, Bela Stantic, Abdul Sattar:
  Sequence-only evolutionary and predicted structural features for the prediction of stability changes in protein mutants. S6
• 
  Raj K. Gaire, Lorey Smith, Patrick Humbert, James Bailey, Peter J. Stuckey, Izhak Haviv:
  Discovery and analysis of consistent active sub-networks in cancers. S7
• 
  Chen Gu, Huang-Wei Chang, Lutz Maibaum, Vijay S. Pande, Gunnar E. Carlsson, Leonidas J. Guibas:
  Building Markov state models with solvent dynamics. S8
• 
  Eric S. Ho, Samuel I. Gunderson, Siobain Duffy:
  A multispecies polyadenylation site model. S9
• 
  Scott Lin, Cheng-Wei Cheng, Emily Chia-Yu Su:
  Prediction of B-cell epitopes using evolutionary information and propensity scales. S10
• 
  Chun-Yu Lin, Yung-Chiang Chen, Yu-Shu Lo, Jinn-Moon Yang:
  Inferring homologous protein-protein interactions through pair position specific scoring matrix. S11
• 
  Cheng-Yu Ma, Shu-Hsi Lin, Chi-Ching Lee, Chuan Yi Tang, Bonnie Berger, Chung-Shou Liao:
  Reconstruction of phyletic trees by global alignment of multiple metabolic networks. S12
• 
  Cem Meydan, Hasan H. Otu, Osman Ugur Sezerman:
  Prediction of peptides binding to MHC class I and II alleles by temporal motif mining. S13
• 
  Xuan Vinh Nguyen, Madhu Chetty, Ross L. Coppel, Sandeep Gaudana, Pramod P. Wangikar:
  A model of the circadian clock in the cyanobacterium Cyanothece sp. ATCC 51142. S14
• 
  Jiajie Peng, Jin Chen, Yadong Wang:
  Identifying cross-category relations in gene ontology and constructing genome-specific term association networks. S15
• 
  Mahmood A. Rashid, M. A. Hakim Newton, Tamjidul Hoque, Swakkhar Shatabda, Duc Nghia Pham, Abdul Sattar:
  Spiral search: a hydrophobic-core directed local search for simplified PSP on 3D FCC lattice. S16
• 
  Shaogang Ren, Bo Zeng, Xiaoning Qian:
  Adaptive bi-level programming for optimal gene knockouts for targeted overproduction under phenotypic constraints. S17
• 
  Andreas Sand, Gerth Stølting Brodal, Rolf Fagerberg, Christian N. S. Pedersen, Thomas Mailund:
  A practical O(n log² n) time algorithm for computing the triplet distance on binary trees. S18
• 
  Swakkhar Shatabda, M. A. Hakim Newton, Mahmood A. Rashid, Duc Nghia Pham, Abdul Sattar:
  The road not taken: retreat and diverge in local search for simplified protein structure prediction. S19
• 
  Rahul Singh, William Murad:
  Protein disulfide topology determination through the fusion of mass spectrometric analysis and sequence-based prediction using Dempster-Shafer theory. S20
• 
  Chinh T. T. Su, Christian Schönbach, Chee Keong Kwoh:
  Molecular docking analysis of 2009-H1N1 and 2004-H5N1 influenza virus HLA-B*4405-restricted HA epitope candidates: implications for TCR cross-recognition and vaccine development. S21
• 
  Zsuzsanna Sükösd, Bjarne Knudsen, James W. J. Anderson, Ádám Novák, Jørgen Kjems, Christian N. S. Pedersen:
  Characterising RNA secondary structure space using information entropy. S22
• 
  Yijie Wang, Xiaoning Qian:
  A novel subgradient-based optimization algorithm for blockmodel functional module identification. S23
• 
  Penghao Wang, Susan R. Wilson:
  Mass spectrometry-based protein identification by integrating de novo sequencing with database searching. S24
• 
  Cheng Yuan, Yanni Sun:
  Efficient known ncRNA search including pseudoknots. S25
• 
  Kaushalya C. Amarasinghe, Jason Li, Saman K. Halgamuge:
  Correction: CoNVEX: copy number variation estimation in exome sequencing data using HMM. S26

Volume 14, Number S-3, February 2013

Selected proceedings from the Automated Function Prediction Meeting 2011

• 
  Domenico Cozzetto, Daniel W. A. Buchan, Kevin Bryson, David T. Jones:
  Protein function prediction by massive integration of evolutionary analyses and multiple data sources. S1
• 
  Meghana Chitale, Ishita K. Khan, Daisuke Kihara:
  In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment. S2
• 
  Zheng Wang, Renzhi Cao, Jianlin Cheng:
  Three-Level Prediction of Protein Function by Combining Profile-Sequence Search, Profile-Profile Search, and Domain Co-Occurrence Networks. S3
• 
  Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Giuseppe Profiti, Andrea Zauli, Ivan Rossi, Rita Casadio:
  How to inherit statistically validated annotation within BAR+ protein clusters. S4
• 
  Robert Rentzsch, Christine A. Orengo:
  Protein function prediction using domain families. S5
• 
  Serkan Erdin, Eric Venner, Andreas Martin Lisewski, Olivier Lichtarge:
  Function prediction from networks of local evolutionary similarity in protein structure. S6
• 
  Tobias Hamp, Rebecca Kassner, Stefan Seemayer, Esmeralda Vicedo, Christian Schaefer, Dominik Achten, Florian Auer, Ariane Boehm, Tatjana Braun, Maximilian Hecht, Mark Heron, Peter Hönigschmid, Thomas A. Hopf, Stefanie Kaufmann, Michael Kiening, Denis Krompass, Cedric Landerer, Yannick Mahlich, Manfred Roos, Burkhard Rost:
  Homology-based inference sets the bar high for protein function prediction. S7
• 
  Liang Lan, Nemanja Djuric, Yuhong Guo, Slobodan Vucetic:
  MS-kNN: protein function prediction by integrating multiple data sources. S8
• 
  Hai Fang, Julian Gough:
  A domain-centric solution to functional genomics via dcGO Predictor. S9
• 
  Artem Sokolov, Christopher S. Funk, Kiley Graim, Karin Verspoor, Asa Ben-Hur:
  Combining heterogeneous data sources for accurate functional annotation of proteins. S10
• 
  Nadav Rappoport, Michal Linial:
  Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex. S11
• 
  Daniel Lopez, Florencio Pazos:
  Concomitant prediction of function and fold at the domain level with GO-based profiles. S12
• 
  Zhouxi Wang, Pengcheng Yin, Joslynn S. Lee, Ramya Parasuram, Srinivas Somarowthu, Mary Jo Ondrechen:
  Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs). S13
• 
  Andrew Wong, Hagit Shatkay:
  Protein Function Prediction using Text-based Features extracted from the Biomedical Literature: The CAFA Challenge. S14
• 
  Jesse A. Gillis, Paul Pavlidis:
  Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA). S15

Volume 14, Number S-4, March 2013

Selected Articles on Computational Vaccinology

• 
  Yongqun He, Zhiwei Cao, Anne S. De Groot, Vladimir Brusic, Christian Schönbach, Nikolai Petrovsky:
  Computational vaccinology and the ICoVax 2012 workshop. I1
• 
  Jing Wang, Yabin Yu, Yunan Zhao, Dabing Zhang, Jing Li:
  Evaluation and integration of existing methods for computational prediction of allergens. S1
• 
  Zuoshuang Xiang, Yongqun He:
  Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology. S2
• 
  Ying-Tsang Lo, Tun-Wen Pai, Wei-Kuo Wu, Hao-Teng Chang:
  Prediction of conformational epitopes with the use of a knowledge-based energy function and geometrically related neighboring residue characteristics. S3
• 
  Ying-Tsang Lo, Hsin-Wei Wang, Tun-Wen Pai, Wen-Shyong Tzou, Hui-Huang Hsu, Hao-Teng Chang:
  Protein-ligand binding region prediction (PLB-SAVE) based on geometric features and CUDA acceleration. S4
• 
  Liping Chen, Di Wu, Lei Ji, Xiaofang Wu, Deshun Xu, Zhi-Wei Cao, Jiankang Han:
  Bioinformatics analysis of the epitope regions for norovirus capsid protein. S5

Volume 14, Number S-5, April 2013

Proceedings of the Third Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq 2013)

• 
  Manuel Allhoff, Alexander Schönhuth, Marcel Martin, Ivan G. Costa, Sven Rahmann, Tobias Marschall:
  Discovering motifs that induce sequencing errors. S1
• 
  Christina Ander, Ole Schulz-Trieglaff, Jens Stoye, Anthony J. Cox:
  metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences. S2
• 
  Eric Bareke, Virginie Saillour, Jean-François Spinella, Ramon Vidal, Jasmine Healy, Daniel Sinnett, Miklós Csürös:
  Joint genotype inference with germline and somatic mutations. S3
• 
  Jacob Biesinger, Yuanfeng Wang, Xiaohui Xie:
  Discovering and mapping chromatin states using a tree hidden Markov model. S4
• 
  Jie Zhu, Yufang Qin, Taigang Liu, Jun Wang, Xiaoqi Zheng:
  Prioritization of candidate disease genes by topological similarity between disease and protein diffusion profiles. S5
• 
  Matthew Hayes, Jing Li:
  Bellerophon: a hybrid method for detecting interchromo-somal rearrangements at base pair resolution using next-generation sequencing data. S6
• 
  Evgeny Kapun, Fedor Tsarev:
  De Bruijn Superwalk with Multiplicities Problem is NP-hard. S7
• 
  Roy R. Lederman:
  A random-permutations-based approach to fast read alignment. S8
• 
  Chi-Long Li, Kun-Tze Chen, Chin Lung Lu:
  Assembling contigs in draft genomes using reversals and block-interchanges. S9
• 
  Sheng Li, Francine E. Garrett-Bakelman, Altuna Akalin, Paul Zumbo, Ross L. Levine, Bik L. To, Ian D. Lewis, Anna L. Brown, Richard J. D'Andrea, Ari Melnick, Christopher E. Mason:
  An optimized algorithm for detecting and annotating regional differential methylation. S10
• 
  Yi Li, Xiaohui Xie:
  A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues. S11
• 
  Yongchu Liu, Jiangtao Guo, Gang-Qing Hu, Huaiqiu Zhu:
  Gene prediction in metagenomic fragments based on the SVM algorithm. S12
• 
  Christine Lo, Sangwoo Kim, Shay Zakov, Vineet Bafna:
  Evaluating genome architecture of a complex region via generalized bipartite matching. S13
• 
  Li Song, Liliana Florea:
  CLASS: constrained transcript assembly of RNA-seq reads. S14
• 
  Alexandru I. Tomescu, Anna Kuosmanen, Romeo Rizzi, Veli Mäkinen:
  A novel min-cost flow method for estimating transcript expression with RNA-Seq. S15
• 
  Xi Wang, Murray J. Cairns:
  Gene set enrichment analysis of RNA-Seq data: integrating differential expression and splicing. S16
• 
  Yu Zhang:
  De novo inference of stratification and local admixture in sequencing studies. S17

Volume 14, Number S-6, April 2013

Selected articles from the 10th International Conference on Artificial Immune Systems (ICARIS)

• 
  Elena Zaslavsky, German Nudelman, Susanna Marquez, Uri Hershberg, Boris M. Hartmann, Juilee Thakar, Stuart C. Sealfon, Steven H. Kleinstein:
  Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection. S1
• 
  Vladimir Sarpe, Christian Jacob:
  Simulating the decentralized processes of the human immune system in a virtual anatomy model. S2
• 
  Thomas E. Todd, Omar Tibi, Yu Lin, Samantha Sayers, Denise N. Bronner, Zuoshuang Xiang, Yongqun He:
  Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates. S3
• 
  Ivan Dimitrov, Darren R. Flower, Irini A. Doytchinova:
  AllerTOP - a server for in silico prediction of allergens. S4
• 
  David N. Olivieri, Merly Escalona, José Faro:
  Software tool for 3D extraction of germinal centers. S5
• 
  Grazziela P. Figueredo, Peer-Olaf Siebers, Uwe Aickelin:
  Investigating mathematical models of immuno-interactions with early-stage cancer under an agent-based modelling perspective. S6
• 
  Alexandre Bittencourt Pigozzo, Gilson Costa Macedo, Rodrigo Weber dos Santos, Marcelo Lobosco:
  On the computational modeling of the innate immune system. S7
• 
  José Faro, Michal Or-Guil:
  How oligoclonal are germinal centers? A new method for estimating clonal diversity from immunohistological sections. S8
• 
  Richard Alun Williams, Richard B. Greaves, Mark Read, Jon Timmis, Paul S. Andrews, Vipin Kumar:
  In silico investigation into dendritic cell regulation of CD8Treg mediated killing of Th1 cells in murine experimental autoimmune encephalomyelitis. S9
• 
  Johannes Textor, Mathieu Sinn, Rob J. De Boer:
  Analytical results on the Beauchemin model of lymphocyte migration. S10
• 
  Francesca Cordero, Marco Beccuti, Chiara Fornari, Stefania Lanzardo, Laura Conti, Federica Cavallo, Gianfranco Balbo, Raffaele A. Calogero:
  Multi-level model for the investigation of oncoantigen-driven vaccination effect. S11

Volume 14, Number S-7, April 2013

Italian Society of Bioinformatics (BITS): Annual Meeting 2012

• 
  Carmela Gissi, Paolo Romano, Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti, Angelo M. Facchiano, Manuela Helmer-Citterich:
  Bioinformatics in Italy: BITS 2012, the ninth annual meeting of the Italian Society of Bioinformatics. S1
• 
  Matteo Carrara, Marco Beccuti, Federica Cavallo, Susanna Donatelli, Fulvio Lazzarato, Francesca Cordero, Raffaele A. Calogero:
  State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues? S2
• 
  Tomás Di Domenico, Ian Walsh, Silvio C. E. Tosatto:
  Analysis and consensus of currently available intrinsic protein disorder annotation sources in the MobiDB database. S3
• 
  Massimo La Rosa, Antonino Fiannaca, Riccardo Rizzo, Alfonso Urso:
  Alignment-free analysis of barcode sequences by means of compression-based methods. S4
• 
  Rosario Distefano, Giovanni Nigita, Valentina Macca, Alessandro Laganà, Rosalba Giugno, Alfredo Pulvirenti, Alfredo Ferro:
  VIRGO: visualization of A-to-I RNA editing sites in genomic sequences. S5
• 
  Riccardo Vicedomini, Francesco Vezzi, Simone Scalabrin, Lars Arvestad, Alberto Policriti:
  GAM-NGS: genomic assemblies merger for next generation sequencing. S6
• 
  Lorenzo Calviello, Pasquale Stano, Fabio Mavelli, Pier Luigi Luisi, Roberto Marangoni:
  Quasi-cellular systems: stochastic simulation analysis at nanoscale range. S7
• 
  Gianvito Pio, Michelangelo Ceci, Domenica D'Elia, Corrado Loglisci, Donato Malerba:
  A Novel Biclustering Algorithm for the Discovery of Meaningful Biological Correlations between microRNAs and their Target Genes. S8
• 
  Marco Cammisa, Antonella Correra, Giuseppina Andreotti, Maria Vittoria Cubellis:
  Identification and analysis of conserved pockets on protein surfaces. S9
• 
  Ilenia Boria, Lara Boatti, Graziano Pesole, Flavio Mignone:
  NGS-Trex: Next Generation Sequencing Transcriptome profile explorer. S10
• 
  Mattia D'Antonio, Paolo D'Onorio De Meo, Daniele Paoletti, Berardino Elmi, Matteo Pallocca, Nico Sanna, Ernesto Picardi, Graziano Pesole, Tiziana Castrignanò:
  WEP: a high-performance analysis pipeline for whole-exome data. S11
• 
  Davide Cangelosi, Fabiola Blengio, Rogier Versteeg, Angelika Eggert, Alberto Garaventa, Claudio Gambini, Massimo Conte, Alessandra Eva, Marco Muselli, Luigi Varesio:
  Logic Learning Machine creates explicit and stable rules stratifying neuroblastoma patients. S12
• 
  Vincenzo Bonnici, Rosalba Giugno, Alfredo Pulvirenti, Dennis E. Shasha, Alfredo Ferro:
  A subgraph isomorphism algorithm and its application to biochemical data. S13
• 
  Swaraj Basu, Ferenc Müller, Remo Sanges:
  Examples of sequence conservation analyses capture a subset of mouse long non-coding RNAs sharing homology with fish conserved genomic elements. S14

Volume 14, Number S-8, May 2013

Proceedings of the 2012 International Conference on Intelligent Computing (ICIC 2012)

• 
  Fei Luo, Yangyang Gao, Yongqiong Zhu, Juan Liu:
  Integrating peptides' sequence and energy of contact residues information improves prediction of peptide and HLA-I binding with unknown alleles. S1
• 
  Hui Zhang, Qing Guo, Costas S. Iliopoulos:
  Locating tandem repeats in weighted sequences in proteins. S2
• 
  Jin-Xing Liu, Yutian Wang, Chun-Hou Zheng, Wen Sha, Jian-Xun Mi, Yong Xu:
  Robust PCA based method for discovering differentially expressed genes. S3
• 
  Xiao-hua Xu, Lin Lu, Ping He, Ling Chen:
  Protein localization prediction using random walks on graphs. S4
• 
  Vitoantonio Bevilacqua, Paolo Pannarale:
  Scalable high-throughput identification of genetic targets by network filtering. S5
• 
  A. Mary Thangakani, Sandeep Kumar, Devadasan Velmurugan, M. Michael Gromiha:
  Distinct position-specific sequence features of hexa-peptides that form amyloid-fibrils: application to discriminate between amyloid fibril and amorphous β-aggregate forming peptide sequences. S6
• 
  Youhei Namiki, Takashi Ishida, Yutaka Akiyama:
  Acceleration of sequence clustering using longest common subsequence filtering. S7
• 
  Ben Niu, Hong Wang, Qiqi Duan, Li Li:
  Biomimicry of quorum sensing using bacterial lifecycle model. S8
• 
  Bing Wang, Jun Zhang, Peng Chen, Zhiwei Ji, Shuping Deng, Chi Li:
  Prediction of peptide drift time in ion mobility mass spectrometry from sequence-based features. S9
• 
  Zhu-Hong You, Ying-Ke Lei, Lin Zhu, Junfeng Xia, Bing Wang:
  Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis. S10
• 
  Shu-Lin Wang, Yaping Fang, Jianwen Fang:
  Diagnostic prediction of complex diseases using phase-only correlation based on virtual sample template. S11

Volume 14, Number S-9, June 2013

Selected articles from the 8th International Symposium on Bioinformatics Research and Applications (ISBRA'12)

• 
  Xiao Xu, Yuanhao Zhang, Jennie Williams, Eric Antoniou, W. Richard McCombie, Song Wu, Wei Zhu, Nicholas O. Davidson, Paula Denoya, Ellen Li:
  Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets. S1
• 
  Pavel Skums, Nicholas Mancuso, Alexander Artyomenko, Bassam Tork, Ion I. Mandoiu, Yuri Khudyakov, Alex Zelikovsky:
  Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows. S2
• 
  Bhanu Rekepalli, Paul Giblock, Christopher M. Reardon:
  PoPLAR: Portal for Petascale Lifescience Applications and Research. S3
• 
  Ghada Badr, Isra Al-Turaiki, Hassan Mathkour:
  Classification and assessment tools for structural motif discovery algorithms. S4
• 
  Shouguo Gao, Xujing Wang:
  Identification of highly synchronized subnetworks from gene expression data. S5
• 
  Achraf El Allali, John R. Rose:
  MGC: a metagenomic gene caller. S6
• 
  Michael Souza, Carlile Lavor, Albert Muritiba, Nelson Maculan:
  Solving the molecular distance geometry problem with inaccurate distance data. S7

Volume 14, Number S-10, August 2013

Selected articles from the 10th International Workshop on Computational Systems Biology (WCSB) 2013: Bioinformatics

• 
  Helena Skutkova, Martin Vítek, Petr Babula, René Kizek, Ivo Provazník:
  Classification of genomic signals using dynamic time warping. S1
• 
  Juhani Kähärä, Harri Lähdesmäki:
  Evaluating a linear k-mer model for protein-DNA interactions using high-throughput SELEX data. S2
• 
  Catherine F. Higham, Dirk Husmeier:
  A Bayesian approach for parameter estimation in the extended clock gene circuit of Arabidopsis thaliana. S3
• 
  Johannes Georg Klotz, Martin Bossert, Steffen Schober:
  Computing preimages of Boolean networks. S4
• 
  Teppo Annila, Eero Lihavainen, Ines J. Marques, Darren R. Williams, Olli Yli-Harja, Andre S. Ribeiro:
  ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis. S5
• 
  Muhammad Farhan, Pekka Ruusuvuori, Mario Emmenlauer, Pauli Rämö, Christoph Dehio, Olli Yli-Harja:
  Multi-scale Gaussian representation and outline-learning based cell image segmentation. S6
• 
  Sabrina Hock, Jan Hasenauer, Fabian J. Theis:
  Modeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability analysis. S7
• 
  Sharif Chowdhury, Meenakshisundaram Kandhavelu, Olli Yli-Harja, Andre S. Ribeiro:
  Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE). S8
• 
  Heinz Koeppl, Marc Hafner, James Lu:
  Mapping behavioral specifications to model parameters in synthetic biology. S9

Volume 14, Number S-11, September 2013

Selected articles from The Second Workshop on Data Mining of Next-Generation Sequencing in conjunction with the 2012 IEEE International Conference on Bioinformatics and Biomedicine

• 
  Min Zhao, Qingguo Wang, Quan Wang, Peilin Jia, Zhongming Zhao:
  Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. S1
• 
  Anurag Nagar, Michael Hahsler:
  Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment. S2
• 
  Zhe Zhang, Jeremy Leipzig, Ariella Sasson, Angela M. Yu, Juan C. Perin, Hongbo M. Xie, Mahdi Sarmady, Patrick V. Warren, Peter S. White:
  Efficient digest of high-throughput sequencing data in a reproducible report. S3
• 
  Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis:
  libgapmis: extending short-read alignments. S4
• 
  Oliver Bonham-Carter, Hesham H. Ali, Dhundy Bastola:
  A base composition analysis of natural patterns for the preprocessing of metagenome sequences. S5
• 
  Renato de Paula, Maristela Holanda, Luciana S. A. Gomes, Sérgio Lifschitz, Maria Emília M. T. Walter:
  Provenance in bioinformatics workflows. S6
• 
  Julia Warnke, Hesham H. Ali:
  An efficient and scalable graph modeling approach for capturing information at different levels in next generation sequencing reads. S7
• 
  Po-Yen Wu, John H. Phan, May D. Wang:
  Assessing the impact of human genome annotation choice on RNA-seq expression estimates. S8

Volume 14, Number S-12, September 2013

Selected articles from the IEEE International Conference on Bioinformatics and Biomedicine 2012: Bioinformatics

• 
  Mohammed Al-Shalalfa, Reda Alhajj:
  Using context-specific effect of miRNAs to identify functional associations between miRNAs and gene signatures. S1
• 
  Hong Cai, Changjin Hong, Timothy G. Lilburn, Armando L. Rodriguez, Sheng Chen, Jianying Gu, Rui Kuang, Yufeng Wang:
  A novel subnetwork alignment approach predicts new components of the cell cycle regulatory apparatus in Plasmodium falciparum. S2
• 
  Chun-Pei Cheng, Yu-Cheng Liu, Yi-Lin Tsai, Vincent S. Tseng:
  An efficient method for mining cross-timepoint gene regulation sequential patterns from time course gene expression datasets. S3
• 
  Wei Xiong, Hui Liu, Jihong Guan, Shuigeng Zhou:
  Protein function prediction by collective classification with explicit and implicit edges in protein-protein interaction networks. S4
• 
  Ping Zhang, Weidan Cao, Zoran Obradovic:
  Learning by aggregating experts and filtering novices: a solution to crowdsourcing problems in bioinformatics. S5
• 
  Xionghui Zhou, Juan Liu, Xinghuo Ye, Wei Wang, Jianghui Xiong:
  Ensemble classifier based on context specific miRNA regulation modules: a new method for cancer outcome prediction. S6

Volume 14, Number S-13, October 2013

Selected articles from the 9th Annual Biotechnology and Bioinformatics Symposium (BIOT 2012)

• 
  Brendan D. O'Fallon, Whitney Wooderchak-Donahue, Pinar Bayrak-Toydemir, David K. Crockett:
  VarRanker: rapid prioritization of sequence variations associated with human disease. S1
• 
  Jacob Durtschi, Rebecca L. Margraf, Emily M. Coonrod, Kalyan C. Mallempati, Karl V. Voelkerding:
  VarBin, a novel method for classifying true and false positive variants in NGS data. S2
• 
  Mohsen Hajiloo, Babak Damavandi, Metanat HooshSadat, Farzad Sangi, John R. Mackey, Carol E. Cass, Russell Greiner, Sambasivarao Damaraju:
  Breast cancer prediction using genome wide single nucleotide polymorphism data. S3
• 
  Mohsen Hajiloo, Hamid R. Rabiee, Mahdi Anooshahpour:
  Fuzzy support vector machine: an efficient rule-based classification technique for microarrays. S4
• 
  James D. Jensen, Daniel M. Jensen, Mark J. Clement, Quinn O. Snell:
  Probabilistic inference and ranking of gene regulatory pathways as a shortest-path problem. S5
• 
  David A. McClellan:
  Directional Darwinian Selection in proteins. S6
• 
  Ximeng Zheng, Etsuko N. Moriyama:
  Comparative studies of differential gene calling using RNA-Seq data. S7
• 
  Wenting Wang, Veerabhadran Baladandayuthapani, Chris C. Holmes, Kim-Anh Do:
  Integrative network-based Bayesian analysis of diverse genomics data. S8
• 
  Ashraf Yaseen, Yaohang Li:
  Dinosolve: a protein disulfide bonding prediction server using context-based features to enhance prediction accuracy. S9
• 
  Tao Lu, Yongchao Dou, Chi Zhang:
  Fuzzy clustering of CPP family in plants with evolution and interaction analyses. S10

Volume 14, Number S-14, October 2013

Proceedings of the Tenth Annual MCBIOS Conference

• 
  Jonathan D. Wren, Mikhail G. Dozmorov, Dennis Burian, Rakesh Kaundal, Andy D. Perkins, Edward J. Perkins, Doris M. Kupfer, Gordon K. Springer:
  Proceedings of the 2013 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. S1
• 
  Mikhail G. Dozmorov, Cory B. Giles, Kristi A. Koelsch, Jonathan D. Wren:
  Systematic classification of non-coding RNAs by epigenomic similarity. S2
• 
  Yi Yang, Andrew S. Maxwell, Xiaowei Zhang, Nan Wang, Edward J. Perkins, Chaoyang Zhang, Ping Gong:
  Differential reconstructed gene interaction networks for deriving toxicity threshold in chemical risk assessment. S3
• 
  Shweta S. Chavan, Michael A. Bauer, Erich A. Peterson, Christoph J. Heuck, Donald J. Johann:
  Towards the integration, annotation and association of historical microarray experiments with RNA-seq. S4
• 
  Jason Hennessey, Steven X. Ge:
  A cross disciplinary study of link decay and the effectiveness of mitigation techniques. S5
• 
  Jie Shen, Wenqian Zhang, Hong Fang, Roger Perkins, Weida Tong, Huixiao Hong:
  Homology modeling, molecular docking, and molecular dynamics simulations elucidated α-fetoprotein binding modes. S6
• 
  Rakesh Kaundal, Sitanshu S. Sahu, Ruchi Verma, Tyler Weirick:
  Identification and characterization of plastid-type proteins from sequence-attributed features using machine learning. S7
• 
  Jialiang Yang, Jun Li, Stefan Grünewald, Xiu-Feng Wan:
  BinAligner: a heuristic method to align biological networks. S8
• 
  Firoz Ahmed, Rakesh Kaundal, Gajendra P. S. Raghava:
  PHDcleav: a SVM based method for predicting human Dicer cleavage sites using sequence and secondary structure of miRNA precursors. S9
• 
  Rahul Singh, Hui Yang, Ben Dalziel, Daniel Asarnow, William Murad, David Foote, Matthew Gormley, Jonathan Stillman, Susan Fisher:
  Towards human-computer synergetic analysis of large-scale biological data. S10
• 
  Halil Bisgin, Minjun Chen, Yuping Wang, Reagan Kelly, Hong Fang, Xiaowei Xu, Weida Tong:
  A systems approach for analysis of high content screening assay data with topic modeling. S11
• 
  Jesse Eickholt, Jianlin Cheng:
  A study and benchmark of DNcon: a method for protein residue-residue contact prediction using deep networks. S12
• 
  Fan Zhang, Renee Drabier:
  SASD: the Synthetic Alternative Splicing Database for identifying novel isoform from proteomics. S13
• 
  R. Shyama Prasad Rao, Dong Xu, Jay J. Thelen, Ján A. Miernyk:
  Circles within circles: crosstalk between protein Ser/Thr/Tyr-phosphorylation and Met oxidation. S14
• 
  Wen Zou, Hailin Tang, Weizhong Zhao, Joe Meehan, Steven L. Foley, Wei-Jiun Lin, Hung-Chia Chen, Hong Fang, Rajesh Nayak, James J. Chen:
  Data mining tools for Salmonella characterization: application to gel-based fingerprinting analysis. S15
• 
  Zhendong Zhao, Gang Fu, Sheng Liu, Khaled M. Elokely, Robert J. Doerksen, Yixin Chen, Dawn Wilkins:
  Drug activity prediction using multiple-instance learning via joint instance and feature selection. S16
• 
  Cory B. Giles, Reshmi Girijadevi, Mikhail G. Dozmorov, Jonathan D. Wren:
  mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis. S17

Volume 14, Number S-15, October 2013

Proceedings of the Eleventh Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics

• 
  Hadas Zur, Tamir Tuller:
  Transcript features alone enable accurate prediction and understanding of gene expression in S. cerevisiae. S1
• 
  Chris A. Nasrallah:
  The dynamics of alternative pathways to compensatory substitution. S2
• 
  Eyla Willing, Simone Zaccaria, Marília D. V. Braga, Jens Stoye:
  On the inversion-indel distance. S3
• 
  Murray Patterson, Gergely J. Szöllosi, Vincent Daubin, Eric Tannier:
  Lateral gene transfer, rearrangement, reconciliation. S4
• 
  Manuel Lafond, Magali Semeria, Krister M. Swenson, Eric Tannier, Nadia El-Mabrouk:
  Gene tree correction guided by orthology. S5
• 
  Yun Yu, Nikola Ristic, Luay Nakhleh:
  Fast algorithms and heuristics for phylogenomics under ILS and hybridization. S6
• 
  Arash Jamshidpey, David Sankoff:
  Phase change for the accuracy of the median value in estimating divergence time. S7
• 
  Chunfang Zheng, David Sankoff:
  Practical aliquoting of flowering plant genomes. S8
• 
  Mingfu Shao, Yu Lin, Bernard M. E. Moret:
  Sorting genomes with rearrangements and segmental duplications through trajectory graphs. S9
• 
  Owais Mahmudi, Joel Sjöstrand, Bengt Sennblad, Jens Lagergren:
  Genome-wide probabilistic reconciliation analysis across vertebrates. S10
• 
  Bérénice Batut, David P. Parsons, Stephan Fischer, Guillaume Beslon, Carole Knibbe:
  In silico experimental evolution: a tool to test evolutionary scenarios. S11
• 
  Raja Ali, Sayyed Muhammad, Mehmood Alam Khan, Lars Arvestad:
  Quantitative synteny scoring improves homology inference and partitioning of gene families. S12
• 
  Veli Mäkinen, Jani Rahkola:
  Haploid to diploid alignment for variation calling assessment. S13
• 
  Katharina Jahn, Sascha Winter, Jens Stoye, Sebastian Böcker:
  Statistics for approximate gene clusters. S14
• 
  Vincent Ranwez, Yan Holtz, Gautier Sarah, Morgane Ardisson, Sylvain Santoni, Sylvain Glemin, Muriel Tavaud-Pirra, Jacques David:
  Disentangling homeologous contigs in allo-tetraploid assembly: application to durum wheat. S15
• 
  Hayssam Soueidan, Florence Maurier, Alexis Groppi, Pascal Sirand-Pugnet, Florence Tardy, Christine Citti, Virginie Dupuy, Macha Nikolski:
  Finishing bacterial genome assemblies with Mix. S16
• 
  Krister M. Swenson, Paul Guertin, Hugo Deschênes, Anne Bergeron:
  Reconstructing the modular recombination history of Staphylococcus aureus phages. S17
• 
  Mohammed El-Kebir, Tobias Marschall, Inken Wohlers, Murray Patterson, Jaap Heringa, Alexander Schönhuth, Gunnar W. Klau:
  Mapping proteins in the presence of paralogs using units of coevolution. S18
• 
  Eric C. H. Chen, Carlos Fernando Buen Abad Najar, Chunfang Zheng, Alex Brandts, Eric Lyons, Haibao Tang, Lorenzo Carretero-Paulet, Victor A. Albert, David Sankoff:
  The dynamics of functional classes of plant genes in rediploidized ancient polyploids. S19

Volume 14, Number S-16, October 2013

Twelfth International Conference on Bioinformatics (InCoB2013): Bioinformatics

• 
  Min-Gang Su, Tzong-Yi Lee:
  Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures. S2
• 
  Jiao Li, Zhiyong Lu:
  Pathway-based drug repositioning using causal inference. S3
• 
  Danai Laksameethanasan, Rui Tan, Geraldine Toh, Lit-Hsin Loo:
  cellXpress: a fast and user-friendly software platform for profiling cellular phenotypes. S4
• 
  Austin W. T. Chiang, Ming-Jing Hwang:
  A computational pipeline for identifying kinetic motifs to aid in the design and improvement of synthetic gene circuits. S5
• 
  Yue Wang, Wilson Wen Bin Goh, Limsoon Wong, Giovanni Montana:
  Random forests on Hadoop for genome-wide association studies of multivariate neuroimaging phenotypes. S6
• 
  Chinh Tran To Su, Xuchang Ouyang, Jie Zheng, Chee Keong Kwoh:
  Structural analysis of the novel influenza A (H7N9) viral Neuraminidase interactions with current approved neuraminidase inhibitors Oseltamivir, Zanamivir, and Peramivir in the presence of mutation R289K. S7
• 
  Phi-Vu Nguyen, Sriganesh Srihari, Hon Wai Leong:
  Identifying conserved protein complexes between species by constructing interolog networks. S8
• 
  Marzio Pennisi, Abdul Mateen Rajput, Luca Toldo, Francesco Pappalardo:
  Agent based modeling of Treg-Teff cross regulation in relapsing-remitting multiple sclerosis. S9
• 
  Kai-Yao Huang, Cheng-Tsung Lu, Neil Arvin Bretaña, Tzong-Yi Lee, Tzu-Hao Chang:
  ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins. S10
• 
  Zhenhua Li, Ying He, Qian Liu, Liang Zhao, Limsoon Wong, Chee Keong Kwoh, Hung T. Nguyen, Jinyan Li:
  Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding. S11
• 
  Phasit Charoenkwan, Eric Hwang, Robert W. Cutler, Hua-Chin Lee, Li-Wei Ko, Hui-Ling Huang, Shinn-Ying Ho:
  HCS-Neurons: identifying phenotypic changes in multi-neuron images upon drug treatments of high-content screening. S12
• 
  Ravi Uttamatanin, Peerapol Yuvapoositanon, Apichart Intarapanich, Saowaluck Kaewkamnerd, Ratsapan Phuksaritanon, Anunchai Assawamakin, Sissades Tongsima:
  MetaSel: a metaphase selection tool using a Gaussian-based classification technique. S13
• 
  Piyush B. Madhamshettiwar, Stefan Maetschke, Melissa J. Davis, Mark A. Ragan:
  RMaNI: Regulatory Module Network Inference framework. S14

Volume 14, Number S-17, October 2013

Proceedings of the 12th Annual UT-ORNL-KBRIN Bioinformatics Summit 2013

• 
  Eric C. Rouchka, Robert M. Flight:
  Proceedings of the Twelfth Annual UT-ORNL-KBRIN Bioinformatics Summit 2013. A1
• 
  Gang Wu, Iwona Pawlikowska, Tanja Gruber, James R. Downing, Jinghui Zhang, Stan Pounds:
  Subgroup and outlier detection analysis. A2
• 
  Yuan Tan, Zhifa Liu:
  Feature selection and prediction with a Markov blanket structure learning algorithm. A3
• 
  Zhifa Liu:
  A powerful association for comorbidity analysis based on score based test. A4
• 
  Teeradache Viangteeravat, Eunice Y. Huang, Grady Wade:
  Giving raw data a chance to talk: A demonstration of de-identified Pediatric Research Database (PRD) and exploratory analysis techniques for possible research cohort discovery and identifiable high risk factors for readmission. A5
• 
  Somchan Vuthipadadon, Mark Sakauye, Emanuel Villa, Emin Kuscu, Netasha Bowers, Teresa Franklin, Linda Moses-Simmons, Ian M. Brooks:
  The BLUES database: A health disparities registry for pregnant mothers. A6
• 
  Pamela D. Thompson, Amos Sakwe, Josiah Ochieng, Siddharth Pratap, Dana Marshall:
  The α2-HeremansSchmid glycoprotein (AHSG) promotes growth in head and neck squamous cell carcinoma (HNSCC). A7
• 
  Miranda L. Parrish, Claire A. Rinehart:
  Correlation of geographical distribution of mycobacteriophages with genomic clusters and genome distance. A8
• 
  Ethan S. Gill, Claire A. Rinehart:
  Comparison of codon usage in mycobacteriophages with and without tRNAs in their genomes. A9
• 
  Chiraag D. Kapadia, Claire A. Rinehart:
  Ab Initio prediction of mycobacteriophages protein structure and function. A10
• 
  Hui Yu, Zhongming Zhao:
  Differential coexpression network modules observed in human hepatocellular carcinoma progression. A11
• 
  Gipsy Majumdar, Rajendra Raghow:
  A systems biology approach to elucidating epigenetic regulation of cardiac hypertrophy. A12
• 
  Morgan Harrell, Junfeng Xia, Zhongming Zhao:
  Network analysis of gene fusions in human cancer. A13
• 
  Ramkrishna Mitra, Jingchun Sun, Min Zhao, Zhongming Zhao:
  Identifying transcription factor and microRNA mediated synergetic regulatory networks in lung cancer. A14
• 
  Huy Vuong, Zhongming Zhao:
  A short tutorial in analyzing NGS data of cancer genomes for somatic mutation calling. A15
• 
  Guolian Kang:
  Power and sample size of two-stage extreme phenotype sequencing design for next generation sequencing studies. A16
• 
  Roger G. Chui, Jerzy W. Jaromczyk, Neil Moore, Christopher L. Schardl:
  FPD2GB2: Automating a transition from a customized genome browser to GBrowse2. A17
• 
  Tyler Parke, Mark L. Farman, Elizabeth Farnsworth, Derek Fox, Jerzy W. Jaromczyk, Jolanta Jaromczyk, Neil Moore, Christopher L. Schardl, Ruriko Yoshida, Patrick Calie:
  Using HPC for teaching and learning bioinformatics software: Benefits and challenges. A18
• 
  Nisrine Enyinda, Zhifa Liu, Areg Negatu, Stan Pounds:
  Our strategy to achieve and document reproducible computing. A19
• 
  Nam S. Vo, Vinhthuy Phan:
  Using partially ordered sets to represent and predict true patterns of gene response to treatments. A20
• 
  Stan Pounds, Cuilan Lani Gao:
  Empirical Bayesian selection of hypothesis testing procedures for analysis of digital gene expression data. A21
• 
  Dana Marshall, Siddharth Pratap, Jianan Dong, Gary L. Rogers, Leon Dent:
  Genomic and proteomic characterization of multi-drug resistant Acinetobacter baumannii. A22

Volume 14, Number S-18, November 2013

Selected articles from the Second IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2012): Bioinformatics

• 
  Peikai Chen, Yubo Fan, Tsz-Kwong Man, Y. S. Hung, Ching C. Lau, Stephen T. C. Wong:
  A gene signature based method for identifying subtypes and subtype-specific drivers in cancer with an application to medulloblastoma. S1
• 
  Filip Jagodzinski, Pamela Clark, Jessica Grant, Tiffany Liu, Samantha Monastra, Ileana Streinu:
  Rigidity analysis of protein biological assemblies and periodic crystal structures. S2
• 
  Naomi Fox, Ileana Streinu:
  Towards accurate modeling of noncovalent interactions for protein rigidity analysis. S3
• 
  Martin Strauch, Julia Rein, Christian Lutz, C. Giovanni Galizia:
  Signal extraction from movies of honeybee brain activity: the ImageBee plugin for KNIME. S4
• 
  Fabrizio F. Borelli, Raphael Y. de Camargo, David Correa Martins Jr., Luiz C. S. Rozante:
  Gene regulatory networks inference using a multi-GPU exhaustive search algorithm. S5

Volume 14, Number S-19, November 2013

Highlights from the 2nd IEEE Symposium on Biological Data Visualization

• 
  Paul Craig, Alan Cannon, Robert Kukla, Jessie B. Kennedy:
  MaTSE: the gene expression time-series explorer. S1
• 
  Corinna Vehlow, Jan Hasenauer, Andrei Kramer, Andreas Raue, Sabine Hug, Jens Timmer, Nicole Radde, Fabian J. Theis, Daniel Weiskopf:
  iVUN: interactive Visualization of Uncertain biochemical reaction Networks. S2
• 
  Christian Partl, Alexander Lex, Marc Streit, Denis Kalkofen, Karl Kashofer, Dieter Schmalstieg:
  enRoute: dynamic path extraction from biological pathway maps for exploring heterogeneous experimental datasets. S3
• 
  Július Parulek, Cagatay Turkay, Nathalie Reuter, Ivan Viola:
  Visual cavity analysis in molecular simulations. S4
• 
  Norbert Lindow, Daniel Baum, Ana-Nicoleta Bondar, Hans-Christian Hege:
  Exploring cavity dynamics in biomolecular systems. S5
• 
  Martin Strauch, Clemens Müthing, Marc P. Broeg, Paul Szyszka, Daniel Münch, Thomas Laudes, Oliver Deussen, Cosmas Galizia, Dorit Merhof:
  The looks of an odour - Visualising neural odour response patterns in real time. S6