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 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
•