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BMC Bioinformatics, Volume 14 - Supplements
Volume 14, Number S-1, January 2013
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
- 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
- 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
- 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
- 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
- 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
- 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
- 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