Articles

Optimal selection of epitopes for TXP-immunoaffinity mass spectrometry

Mass spectrometry (MS) based protein profiling has become one of the key technologies in biomedical research and biomarker discovery. One bottleneck in MS-based protein analysis is sample preparation and an ef...

Authors: Hannes Planatscher, Jochen Supper, Oliver Poetz, Dieter Stoll, Thomas Joos, Markus F Templin and Andreas Zell

Inverse folding of RNA pseudoknot structures

RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and G-U-base pairings (secondary structure) and additional cross-serial base pair...

Authors: James ZM Gao, Linda YM Li and Christian M Reidys

On the use of cartographic projections in visualizing phylo-genetic tree space

Phylogenetic analysis is becoming an increasingly important tool for biological research. Applications include epidemiological studies, drug development, and evolutionary analysis. Phylogenetic search is a kno...

Authors: Kenneth Sundberg, Mark Clement and Quinn Snell

Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees

The Maximal Pairing Problem (MPP) is the prototype of a class of combinatorial optimization problems that are of considerable interest in bioinformatics: Given an arbitrary phylogenetic tree T and weights ω _...

Authors: Christian Arnold and Peter F Stadler

AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences

Multiple sequence alignments are used to study gene or protein function, phylogenetic relations, genome evolution hypotheses and even gene polymorphisms. Virtually without exception, all available tools focus ...

Authors: Darío Guerrero, Rocío Bautista, David P Villalobos, Francisco R Cantón and M Gonzalo Claros

Differential co-expression framework to quantify goodness of biclusters and compare biclustering algorithms

Biclustering is an important analysis procedure to understand the biological mechanisms from microarray gene expression data. Several algorithms have been proposed to identify biclusters, but very little effor...

Authors: Burton Kuan Hui Chia and R Krishna Murthy Karuturi

Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions

Many regulatory non-coding RNAs (ncRNAs) function through complementary binding with mRNAs or other ncRNAs, e.g., microRNAs, snoRNAs and bacterial sRNAs. Predicting these RNA interactions is essential for functio...

Authors: Stefan E Seemann, Andreas S Richter, Jan Gorodkin and Rolf Backofen

Sequence embedding for fast construction of guide trees for multiple sequence alignment

The most widely used multiple sequence alignment methods require sequences to be clustered as an initial step. Most sequence clustering methods require a full distance matrix to be computed between all pairs o...

Authors: Gordon Blackshields, Fabian Sievers, Weifeng Shi, Andreas Wilm and Desmond G Higgins

Challenges in experimental data integration within genome-scale metabolic models

A report of the meeting "Challenges in experimental data integration within genome-scale metabolic models", Institut Henri Poincaré, Paris, October 10-11 2009, organized by the CNRS-MPG joint program in System...

Authors: Pierre-Yves Bourguignon, Areejit Samal, François Képès, Jürgen Jost and Olivier C Martin

Distinguishing between hot-spots and melting-pots of genetic diversity using haplotype connectivity

We introduce a method to help identify how the genetic diversity of a species within a geographic region might have arisen. This problem appears, for example, in the context of identifying refugia in phylogeog...

Authors: Binh Nguyen, Andreas Spillner, Brent C Emerson and Vincent Moulton

Robinson-Foulds Supertrees

Supertree methods synthesize collections of small phylogenetic trees with incomplete taxon overlap into comprehensive trees, or supertrees, that include all taxa found in the input trees. Supertree methods bas...

Authors: Mukul S Bansal, J Gordon Burleigh, Oliver Eulenstein and David Fernández-Baca

Association of repeatedly measured intermediate risk factors for complex diseases with high dimensional SNP data

The causes of complex diseases are difficult to grasp since many different factors play a role in their onset. To find a common genetic background, many of the existing studies divide their population into con...

Authors: Sandra Waaijenborg and Aeilko H Zwinderman

Jane: a new tool for the cophylogeny reconstruction problem

This paper describes the theory and implementation of a new software tool, called Jane, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites), molecul...

Authors: Chris Conow, Daniel Fielder, Yaniv Ovadia and Ran Libeskind-Hadas

Exact distribution of a pattern in a set of random sequences generated by a Markov source: applications to biological data

In bioinformatics it is common to search for a pattern of interest in a potentially large set of rather short sequences (upstream gene regions, proteins, exons, etc.). Although many methodological approaches a...

Authors: Gregory Nuel, Leslie Regad, Juliette Martin and Anne-Claude Camproux

ANMM4CBR: a case-based reasoning method for gene expression data classification

Accurate classification of microarray data is critical for successful clinical diagnosis and treatment. The "curse of dimensionality" problem and noise in the data, however, undermines the performance of many ...

Authors: Bangpeng Yao and Shao Li

A simple, practical and complete O -time Algorithm for RNA folding using the Four-Russians Speedup

The problem of computationally predicting the secondary structure (or folding) of RNA molecules was first introduced more than thirty years ago and yet continues to be an area of active research and developmen...

Authors: Yelena Frid and Dan Gusfield

FlexSnap: Flexible Non-sequential Protein Structure Alignment

Proteins have evolved subject to energetic selection pressure for stability and flexibility. Structural similarity between proteins that have gone through conformational changes can be captured effectively if ...

Authors: Saeed Salem, Mohammed J Zaki and Chris Bystroff

Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes

Segmental duplications, or low-copy repeats, are common in mammalian genomes. In the human genome, most segmental duplications are mosaics comprised of multiple duplicated fragments. This complex genomic organ...

Authors: Crystal L Kahn, Shay Mozes and Benjamin J Raphael

A markov classification model for metabolic pathways

This paper considers the problem of identifying pathways through metabolic networks that relate to a specific biological response. Our proposed model, HME3M, first identifies frequently traversed network paths...

Authors: Timothy Hancock and Hiroshi Mamitsuka

A tree-based method for the rapid screening of chemical fingerprints

The fingerprint of a molecule is a bitstring based on its structure, constructed such that structurally similar molecules will have similar fingerprints. Molecular fingerprints can be used in an initial phase ...

Authors: Thomas G Kristensen, Jesper Nielsen and Christian NS Pedersen

A simulation study comparing supertree and combined analysis methods using SMIDGen

Supertree methods comprise one approach to reconstructing large molecular phylogenies given multi-marker datasets: trees are estimated on each marker and then combined into a tree (the "supertree") on the enti...

Authors: M Shel Swenson, François Barbançon, Tandy Warnow and C Randal Linder

Linear-time protein 3-D structure searching with insertions and deletions

Two biomolecular 3-D structures are said to be similar if the RMSD (root mean square deviation) between the two molecules' sequences of 3-D coordinates is less than or equal to some given constant bound. Tools...

Authors: Tetsuo Shibuya, Jesper Jansson and Kunihiko Sadakane

Back-translation for discovering distant protein homologies in the presence of frameshift mutations

Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Mor...

Authors: Marta Gîrdea, Laurent Noé and Gregory Kucherov

Fast prediction of RNA-RNA interaction

Regulatory antisense RNAs are a class of ncRNAs that regulate gene expression by prohibiting the translation of an mRNA by establishing stable interactions with a target sequence. There is great demand for eff...

Authors: Raheleh Salari, Rolf Backofen and S Cenk Sahinalp

Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction

Functionally related genes tend to be correlated in their expression patterns across multiple conditions and/or tissue-types. Thus co-expression networks are often used to investigate functional groups of gene...

Authors: Matthew Hansen, Logan Everett, Larry Singh and Sridhar Hannenhalli

Phylogenetic comparative assembly

Recent high throughput sequencing technologies are capable of generating a huge amount of data for bacterial genome sequencing projects. Although current sequence assemblers successfully merge the overlapping ...

Authors: Peter Husemann and Jens Stoye

Constructing majority-rule supertrees

Supertree methods combine the phylogenetic information from multiple partially-overlapping trees into a larger phylogenetic tree called a supertree. Several supertree construction methods have been proposed to...

Authors: Jianrong Dong, David Fernández-Baca and FR McMorris

Refining transcriptional regulatory networks using network evolutionary models and gene histories

Computational inference of transcriptional regulatory networks remains a challenging problem, in part due to the lack of strong network models. In this paper we present evolutionary approaches to improve the i...

Authors: Xiuwei Zhang and Bernard ME Moret

An asymmetric approach to preserve common intervals while sorting by reversals

The reversal distance and optimal sequences of reversals to transform a genome into another are useful tools to analyse evolutionary scenarios. However, the number of sequences is huge and some additional crit...

Authors: Marília DV Braga, Christian Gautier and Marie-France Sagot

Linear model for fast background subtraction in oligonucleotide microarrays

One important preprocessing step in the analysis of microarray data is background subtraction. In high-density oligonucleotide arrays this is recognized as a crucial step for the global performance of the data...

Authors: K Myriam Kroll, Gerard T Barkema and Enrico Carlon

iTriplet, a rule-based nucleic acid sequence motif finder

With the advent of high throughput sequencing techniques, large amounts of sequencing data are readily available for analysis. Natural biological signals are intrinsically highly variable making their complete...

Authors: Eric S Ho, Christopher D Jakubowski and Samuel I Gunderson

Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications

Discriminative models are designed to naturally address classification tasks. However, some applications require the inclusion of grammar rules, and in these cases generative models, such as Hidden Markov Mode...

Authors: Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli and Rita Casadio

Breaking the hierarchy - a new cluster selection mechanism for hierarchical clustering methods

Hierarchical clustering methods like Ward's method have been used since decades to understand biological and chemical data sets. In order to get a partition of the data set, it is necessary to choose an optima...

Authors: László A Zahoránszky, Gyula Y Katona, Péter Hári, András Málnási-Csizmadia, Katharina A Zweig and Gergely Zahoránszky-Köhalmi

Modeling genetic imprinting effects of DNA sequences with multilocus polymorphism data

Single nucleotide polymorphisms (SNPs) represent the most widespread type of DNA sequence variation in the human genome and they have recently emerged as valuable genetic markers for revealing the genetic arch...

Authors: Sheron Wen, Chenguang Wang, Arthur Berg, Yao Li, Myron M Chang, Roger B Fillingim, Margaret R Wallace, Roland Staud, Lee Kaplan and Rongling Wu

Tracking cells in Life Cell Imaging videos using topological alignments

With the increasing availability of live cell imaging technology, tracking cells and other moving objects in live cell videos has become a major challenge for bioimage informatics. An inherent problem for most...

Authors: Axel Mosig, Stefan Jäger, Chaofeng Wang, Sumit Nath, Ilker Ersoy, Kannap-pan Palaniappan and Su-Shing Chen

Review of “Bioinformatics: A Computing Perspective” edited by Shuba Gopal, Anne Haake, Rhys Price Jones and Paul Tymann

Authors: Dae-Won Kim and Hong-Seog Park

A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series

The ability to monitor the change in expression patterns over time, and to observe the emergence of coherent temporal responses using gene expression time series, obtained from microarray experiments, is criti...

Authors: Sara C Madeira and Arlindo L Oliveira

Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity

To identify differentially expressed genes (DEGs) from microarray data, users of the Affymetrix GeneChip system need to select both a preprocessing algorithm to obtain expression-level measurements and a way o...

Authors: Koji Kadota, Yuji Nakai and Kentaro Shimizu

Evolving DNA motifs to predict GeneChip probe performance

Affymetrix High Density Oligonuclotide Arrays (HDONA) simultaneously measure expression of thousands of genes using millions of probes. We use correlations between measurements for the same gene across 6685 hu...

Authors: WB Langdon and AP Harrison

A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data

A genetic network can be represented as a directed graph in which a node corresponds to a gene and a directed edge specifies the direction of influence of one gene on another. The reconstruction of such networ...

Authors: Sahely Bhadra, Chiranjib Bhattacharyya, Nagasuma R Chandra and I Saira Mian

An image processing approach to computing distances between RNA secondary structures dot plots

Computing the distance between two RNA secondary structures can contribute in understanding the functional relationship between them. When used repeatedly, such a procedure may lead to finding a query RNA stru...

Authors: Tor Ivry, Shahar Michal, Assaf Avihoo, Guillermo Sapiro and Danny Barash

Lossless filter for multiple repeats with bounded edit distance

Identifying local similarity between two or more sequences, or identifying repeats occurring at least twice in a sequence, is an essential part in the analysis of biological sequences and of their phylogenetic...

Authors: Pierre Peterlongo, Gustavo Akio Tominaga Sacomoto, Alair Pereira do Lago, Nadia Pisanti and Marie-France Sagot

CHSMiner: a GUI tool to identify chromosomal homologous segments

The identification of chromosomal homologous segments (CHS) within and between genomes is essential for comparative genomics. Various processes including insertion/deletion and inversion could cause the degene...

Authors: Zhen Wang, Guohui Ding, Zhonghao Yu, Lei Liu and Yixue Li

Auto-validating von Neumann rejection sampling from small phylogenetic tree spaces

In phylogenetic inference one is interested in obtaining samples from the posterior distribution over the tree space on the basis of some observed DNA sequence data. One of the simplest sampling methods is the...

Authors: Raazesh Sainudiin and Thomas York

HuMiTar: A sequence-based method for prediction of human microRNA targets

MicroRNAs (miRs) are small noncoding RNAs that bind to complementary/partially complementary sites in the 3' untranslated regions of target genes to regulate protein production of the target transcript and to ...

Authors: Jishou Ruan, Hanzhe Chen, Lukasz Kurgan, Ke Chen, Chunsheng Kang and Peiyu Pu

Stability of multiple alignments and phylogenetic trees: an analysis of ABC-transporter proteins family

Sequence-based phylogeny reconstruction is a fundamental task in Bioinformatics. Practically all methods for phylogeny reconstruction are based on multiple alignments. The quality and stability of the underlyi...

Authors: Holger Wagner, Burkhard Morgenstern and Andreas Dress

Syntenator: Multiple gene order alignments with a gene-specific scoring function

Identification of homologous regions or conserved syntenies across genomes is one crucial step in comparative genomics. This task is usually performed by genome alignment softwares like WABA or blastz. In case...

Authors: Christian Rödelsperger and Christoph Dieterich

Fast algorithms for computing sequence distances by exhaustive substring composition

The increasing throughput of sequencing raises growing needs for methods of sequence analysis and comparison on a genomic scale, notably, in connection with phylogenetic tree reconstruction. Such needs are har...

Authors: Alberto Apostolico and Olgert Denas

"Hook"-calibration of GeneChip-microarrays: Theory and algorithm

The improvement of microarray calibration methods is an essential prerequisite for quantitative expression analysis. This issue requires the formulation of an appropriate model describing the basic relationshi...

Authors: Hans Binder and Stephan Preibisch

"Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures

Microarray experiments rely on several critical steps that may introduce biases and uncertainty in downstream analyses. These steps include mRNA sample extraction, amplification and labelling, hybridization, a...

Authors: Hans Binder, Knut Krohn and Stephan Preibisch