Volume 10 Supplement 1
Selected papers from the Seventh Asia-Pacific Bioinformatics Conference (APBC 2009)
Research
Edited by Michael Q Zhang, Michael S Waterman and Xuegong Zhang
The Seventh Asia Pacific Bioinformatics Conference (APBC 2009). Go to conference site.
Beijing, China13-16 January 2009
Page 1 of 2
-
Citation: BMC Bioinformatics 2009 10(Suppl 1):S1
-
Genome aliquoting with double cut and join
The genome aliquoting probem is, given an observed genome A with n copies of each gene, presumed to descend from an n-way polyploidization event from an ordinary diploid genome B, followed by a history of chromos...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S2 -
Pathogenic Bacillus anthracis in the progressive gene losses and gains in adaptive evolution
Sequence mutations represent a driving force of adaptive evolution in bacterial pathogens. It is especially evident in reductive genome evolution where bacteria underwent lifestyles shifting from a free-living...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S3 -
SE: an algorithm for deriving sequence alignment from a pair of superimposed structures
Generating sequence alignments from superimposed structures is an important part of many structure comparison programs. The accuracy of the alignment affects structure recognition, classification and possibly ...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S4 -
ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets
With the increasing availability of whole genome sequences, it is becoming more and more important to use complete genome sequences for inferring species phylogenies. We developed a new tool ComPhy, 'Composite...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S5 -
Maximum independent sets of commuting and noninterfering inversions
Given three signed permutations, an inversion median is a fourth permutation that minimizes the sum of the pairwise inversion distances between it and the three others. This problem is NP-hard as well as hard ...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S6 -
Inversion-based genomic signatures
Reconstructing complete ancestral genomes (at least in terms of their gene inventory and arrangement) is attracting much interest due to the rapidly increasing availability of whole genome sequences. While mod...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S7 -
Triplet supertree heuristics for the tree of life
There is much interest in developing fast and accurate supertree methods to infer the tree of life. Supertree methods combine smaller input trees with overlapping sets of taxa to make a comprehensive phylogene...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S8 -
Sorting by reversals, block interchanges, tandem duplications, and deletions
Finding sequences of evolutionary operations that transform one genome into another is a classic problem in comparative genomics. While most of the genome rearrangement algorithms assume that there is exactly ...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S9 -
Improved algorithms for approximate string matching (extended abstract)
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorith...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S10 -
Simultaneous phylogeny reconstruction and multiple sequence alignment
A phylogeny is the evolutionary history of a group of organisms. To date, sequence data is still the most used data type for phylogenetic reconstruction. Before any sequences can be used for phylogeny reconstr...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S11 -
Methods for comparative metagenomics
Metagenomics is a rapidly growing field of research that aims at studying uncultured organisms to understand the true diversity of microbes, their functions, cooperation and evolution, in environments such as ...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S12 -
DNA motif alignment by evolving a population of Markov chains
Deciphering cis-regulatory elements or de novo motif-finding in genomes still remains elusive although much algorithmic effort has been expended. The Markov chain Monte Carlo (MCMC) method such as Gibbs motif sam...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S13 -
Parallel short sequence assembly of transcriptomes
The de novo assembly of genomes and transcriptomes from short sequences is a challenging problem. Because of the high coverage needed to assemble short sequences as well as the overhead of modeling the assembly p...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S14 -
Finding optimal threshold for correction error reads in DNA assembling
DNA assembling is the problem of determining the nucleotide sequence of a genome from its substrings, called reads. In the experiments, there may be some errors on the reads which affect the performance of the DN...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S15 -
Crystallizing short-read assemblies around seeds
New short-read sequencing technologies produce enormous volumes of 25–30 base paired-end reads. The resulting reads have vastly different characteristics than produced by Sanger sequencing, and require differe...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S16 -
Short read DNA fragment anchoring algorithm
The emerging next-generation sequencing method based on PCR technology boosts genome sequencing speed considerably, the expense is also get decreased. It has been utilized to address a broad range of bioinform...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S17 -
REMAS: a new regression model to identify alternative splicing events from exon array data
Alternative splicing (AS) is an important regulatory mechanism for gene expression and protein diversity in eukaryotes. Previous studies have demonstrated that it can be causative for, or specific to splicing-...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S18 -
A voting approach to identify a small number of highly predictive genes using multiple classifiers
Microarray gene expression profiling has provided extensive datasets that can describe characteristics of cancer patients. An important challenge for this type of data is the discovery of gene sets which can b...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S19 -
Knowledge driven decomposition of tumor expression profiles
Tumors have been hypothesized to be the result of a mixture of oncogenic events, some of which will be reflected in the gene expression of the tumor. Based on this hypothesis a variety of data-driven methods h...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S20 -
Network-based support vector machine for classification of microarray samples
The importance of network-based approach to identifying biological markers for diagnostic classification and prognostic assessment in the context of microarray data has been increasingly recognized. To our kno...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S21 -
Using random forest for reliable classification and cost-sensitive learning for medical diagnosis
Most machine-learning classifiers output label predictions for new instances without indicating how reliable the predictions are. The applicability of these classifiers is limited in critical domains where inc...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S22 -
A statistical framework for integrating two microarray data sets in differential expression analysis
Different microarray data sets can be collected for studying the same or similar diseases. We expect to achieve a more efficient analysis of differential expression if an efficient statistical method can be de...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S23 -
Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations
Gene expression microarray technologies are widely used across most areas of biological and medical research. Comparing and integrating microarray data from different experiments would be very useful, but is c...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S24 -
Integrative disease classification based on cross-platform microarray data
Disease classification has been an important application of microarray technology. However, most microarray-based classifiers can only handle data generated within the same study, since microarray data generat...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S25 -
Principal component tests: applied to temporal gene expression data
Clustering analysis is a common statistical tool for knowledge discovery. It is mainly conducted when a project still is in the exploratory phase without any priori hypotheses. However, the statistical signifi...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S26 -
Biclustering of gene expression data using reactive greedy randomized adaptive search procedure
Biclustering algorithms belong to a distinct class of clustering algorithms that perform simultaneous clustering of both rows and columns of the gene expression matrix and can be a very useful analysis tool wh...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S27 -
Identification of histone modifications in biomedical text for supporting epigenomic research
Posttranslational modifications of histones influence the structure of chromatine and in such a way take part in the regulation of gene expression. Certain histone modification patterns, distributed over the g...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S28 -
Searching for bidirectional promoters in Arabidopsis thaliana
A "bidirectional gene pair" is defined as two adjacent genes which are located on opposite strands of DNA with transcription start sites (TSSs) not more than 1000 base pairs apart and the intergenic region bet...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S29 -
ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules
The detection of cis-regulatory modules (CRMs) that mediate transcriptional responses in eukaryotes remains a key challenge in the postgenomic era. A CRM is characterized by a set of co-occurring transcription fa...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S30 -
Transcriptional interaction-assisted identification of dynamic nucleosome positioning
Nucleosomes regulate DNA accessibility and therefore play a central role in transcription control. Computational methods have been developed to predict static nucleosome positions from DNA sequences, but nucle...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S31 -
Predicting microRNA targets in time-series microarray experiments via functional data analysis
MicroRNA (miRNA) target prediction is an important component in understanding gene regulation. One approach is computational: searching nucleotide sequences for miRNA complementary base pairing. An alternative...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S32 -
A structural interpretation of the effect of GC-content on efficiency of RNA interference
RNA interference (RNAi) mediated by small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) has become a powerful technique for eukaryotic gene knockdown. siRNA GC-content negatively correlates with RNA...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S33 -
Computational identification of condition-specific miRNA targets based on gene expression profiles and sequence information
MicroRNAs (miRNAs) are small and noncoding RNAs that play important roles in various biological processes. They regulate target mRNAs post-transcriptionally through complementary base pairing. Since the change...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S34 -
HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models
MicroRNA s (miRNAs) are small non-coding single-stranded RNAs (20–23 nts) that are known to act as post-transcriptional and translational regulators of gene expression. Although, they were initially overlooked, t...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S35 -
Computational prediction of novel non-coding RNAs in Arabidopsis thaliana
Non-coding RNA (ncRNA) genes do not encode proteins but produce functional RNA molecules that play crucial roles in many key biological processes. Recent genome-wide transcriptional profiling studies using til...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S36 -
Fine-grained parallel RNAalifold algorithm for RNA secondary structure prediction on FPGA
In the field of RNA secondary structure prediction, the RNAalifold algorithm is one of the most popular methods using free energy minimization. However, general-purpose computers including parallel computers o...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S37 -
Prediction of RNA secondary structure with pseudoknots using integer programming
RNA secondary structure prediction is one major task in bioinformatics, and various computational methods have been proposed so far. Pseudoknot is one of the typical substructures appearing in several RNAs, an...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S38 -
Sequence-structure relations of pseudoknot RNA
The analysis of sequence-structure relations of RNA is based on a specific notion and folding of RNA structure. The notion of coarse grained structure employed here is that of canonical RNA pseudoknot contact-...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S39 -
Reduction of the secondary structure topological space through direct estimation of the contact energy formed by the secondary structures
Electron cryomicroscopy is a fast developing technique aiming at the determination of the 3-dimensional structures of large protein complexes. Using this technique, protein density maps can be generated with 6...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S40 -
Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses
In pandemic and epidemic forms, avian and human influenza viruses often cause significant damage to human society and economics. Gradually accumulated mutations on hemagglutinin (HA) cause immunologically dist...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S41 -
Predicting disordered regions in proteins using the profiles of amino acid indices
Intrinsically unstructured or disordered proteins are common and functionally important. Prediction of disordered regions in proteins can provide useful information for understanding protein function and for h...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S42 -
A method to improve protein subcellular localization prediction by integrating various biological data sources
Protein subcellular localization is crucial information to elucidate protein functions. Owing to the need for large-scale genome analysis, computational method for efficiently predicting protein subcellular lo...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S43 -
Studying the unfolding process of protein G and protein L under physical property space
The studies on protein folding/unfolding indicate that the native state topology is an important determinant of protein folding mechanism. The folding/unfolding behaviors of proteins which have similar topolog...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S44 -
Prediction of amyloid fibril-forming segments based on a support vector machine
Amyloid fibrillar aggregates of proteins or polypeptides are known to be associated with many human diseases. Recent studies suggest that short protein regions trigger this aggregation. Thus, identifying these...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S45 -
Towards comprehensive structural motif mining for better fold annotation in the "twilight zone" of sequence dissimilarity
Automatic identification of structure fingerprints from a group of diverse protein structures is challenging, especially for proteins whose divergent amino acid sequences may fall into the "twilight-" or "midn...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S46 -
Semi-supervised protein subcellular localization
Protein subcellular localization is concerned with predicting the location of a protein within a cell using computational method. The location information can indicate key functionalities of proteins. Accurate...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S47 -
A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction: implication for structure and active site binding mechanism
SARS coronavirus main proteinase (SARS CoVMpro) is an important enzyme for the replication of Severe Acute Respiratory Syndrome virus. The active site region of SARS CoVMpro is divided into 8 subsites. Underst...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S48 -
Quality assessment of tandem mass spectra using support vector machine (SVM)
Tandem mass spectrometry has become particularly useful for the rapid identification and characterization of protein components of complex biological mixtures. Powerful database search methods have been develo...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S49 -
Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences
Peptide identification via tandem mass spectrometry is the basic task of current proteomics research. Due to the complexity of mass spectra, the majority of mass spectra cannot be interpreted at present. The e...
Citation: BMC Bioinformatics 2009 10(Suppl 1):S50
Annual Journal Metrics
-
2022 Citation Impact
3.0 - 2-year Impact Factor
4.3 - 5-year Impact Factor
0.938 - SNIP (Source Normalized Impact per Paper)
1.100 - SJR (SCImago Journal Rank)2022 Speed
18 days submission to first editorial decision for all manuscripts (Median)
135 days submission to accept (Median)2022 Usage
6,060,124 downloads
14,511 Altmetric mentions