Published in BMC Bioinformatics on June 15, 2006
Combining family- and population-based imputation data for association analysis of rare and common variants in large pedigrees. Genet Epidemiol (2014) 0.93
Genetics of migraine and pharmacogenomics: some considerations. J Headache Pain (2007) 0.83
Multilocus association testing of quantitative traits based on partial least-squares analysis. PLoS One (2011) 0.82
MarkerSet: a marker selection tool based on markers location and informativity in experimental designs. BMC Res Notes (2008) 0.81
Increasing the number of SNP loci does not necessarily improve prediction power at least in the comparison of MTHFR SNP and haplotypes. J Epidemiol (2008) 0.79
Modeling associations between genetic markers using Bayesian networks. Bioinformatics (2010) 0.76
The International HapMap Project. Nature (2003) 73.65
The structure of haplotype blocks in the human genome. Science (2002) 50.88
Genome-wide association studies for common diseases and complex traits. Nat Rev Genet (2005) 33.96
Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol (1995) 30.55
Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet (2003) 21.52
High-resolution haplotype structure in the human genome. Nat Genet (2001) 20.51
Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics (2003) 17.73
The fine-scale structure of recombination rate variation in the human genome. Science (2004) 17.05
Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science (2001) 15.54
Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am J Hum Genet (2005) 14.09
Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet (2003) 13.60
Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am J Hum Genet (2001) 10.48
Mapping complex disease loci in whole-genome association studies. Nature (2004) 7.31
Evidence for substantial fine-scale variation in recombination rates across the human genome. Nat Genet (2004) 6.99
A dynamic programming algorithm for haplotype block partitioning. Proc Natl Acad Sci U S A (2002) 5.12
A comparison of estimators of the population recombination rate. Mol Biol Evol (2000) 4.84
Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populations. Am J Hum Genet (2004) 3.91
Selection of genetic markers for association analyses, using linkage disequilibrium and haplotypes. Am J Hum Genet (2003) 2.94
Haplotype block structure and its applications to association studies: power and study designs. Am J Hum Genet (2002) 2.88
The impact of SNP density on fine-scale patterns of linkage disequilibrium. Hum Mol Genet (2004) 2.78
Assessing the performance of the haplotype block model of linkage disequilibrium. Am J Hum Genet (2003) 2.59
Graphical modeling of the joint distribution of alleles at associated loci. Am J Hum Genet (2004) 2.50
An MDL method for finding haplotype blocks and for estimating the strength of haplotype block boundaries. Pac Symp Biocomput (2003) 2.45
Absence of the TAP2 human recombination hotspot in chimpanzees. PLoS Biol (2004) 2.22
HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics (2004) 1.86
Finding haplotype block boundaries by using the minimum-description-length principle. Am J Hum Genet (2003) 1.71
Haplotype and missing data inference in nuclear families. Genome Res (2004) 1.69
Multilocus LD measure and tagging SNP selection with generalized mutual information. Genet Epidemiol (2005) 1.33
Optimal haplotype block-free selection of tagging SNPs for genome-wide association studies. Genome Res (2004) 1.28
Optimal selection of SNP markers for disease association studies. Hum Hered (2004) 1.07
Is haplotype block identification useful for association mapping studies? Genet Epidemiol (2004) 1.00
Defining haplotype blocks and tag single-nucleotide polymorphisms in the human genome. Hum Mol Genet (2003) 0.93
Retracted Minimum description length block finder, a method to identify haplotype blocks and to compare the strength of block boundaries. Am J Hum Genet (2003) 0.93
The effect of single-nucleotide polymorphism marker selection on patterns of haplotype blocks and haplotype frequency estimates. Am J Hum Genet (2005) 0.92
The impact of sample size and marker selection on the study of haplotype structures. Hum Genomics (2004) 0.91
Informativeness of genetic markers for inference of ancestry. Am J Hum Genet (2003) 6.90
A dynamic programming algorithm for haplotype block partitioning. Proc Natl Acad Sci U S A (2002) 5.12
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
Inferring domain-domain interactions from protein-protein interactions. Genome Res (2002) 4.36
Haplotype block structure and its applications to association studies: power and study designs. Am J Hum Genet (2002) 2.88
Adjust quality scores from alignment and improve sequencing accuracy. Nucleic Acids Res (2004) 2.76
Mapping Gene Ontology to proteins based on protein-protein interaction data. Bioinformatics (2004) 2.63
Marine bacterial, archaeal and protistan association networks reveal ecological linkages. ISME J (2011) 2.40
Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi. Genome Res (2007) 2.37
Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA/GT)n and (A/T)n microsatellites. Nucleic Acids Res (2003) 2.28
Tor1/Sch9-regulated carbon source substitution is as effective as calorie restriction in life span extension. PLoS Genet (2009) 2.18
Alignment-free sequence comparison (I): statistics and power. J Comput Biol (2009) 2.18
HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination. Bioinformatics (2004) 2.16
Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors. Bioinformatics (2006) 2.15
Prediction of protein function using protein-protein interaction data. J Comput Biol (2003) 2.15
The relationship between microsatellite slippage mutation rate and the number of repeat units. Mol Biol Evol (2003) 2.01
Assessment of the reliability of protein-protein interactions and protein function prediction. Pac Symp Biocomput (2003) 1.89
HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics (2004) 1.86
An integrative approach for causal gene identification and gene regulatory pathway inference. Bioinformatics (2006) 1.82
Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies. Genome Res (2004) 1.74
Inferring microRNA activities by combining gene expression with microRNA target prediction. PLoS One (2008) 1.71
Further understanding human disease genes by comparing with housekeeping genes and other genes. BMC Genomics (2006) 1.68
Maternal influence on blood pressure suggests involvement of mitochondrial DNA in the pathogenesis of hypertension: the Framingham Heart Study. J Hypertens (2007) 1.67
An integrated probabilistic model for functional prediction of proteins. J Comput Biol (2004) 1.67
Diffusion kernel-based logistic regression models for protein function prediction. OMICS (2006) 1.63
Accurate genome relative abundance estimation based on shotgun metagenomic reads. PLoS One (2011) 1.62
CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data. Bioinformatics (2006) 1.55
Alignment-free sequence comparison (II): theoretical power of comparison statistics. J Comput Biol (2010) 1.52
An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics (2006) 1.52
A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila. BMC Genomics (2009) 1.27
Alignment-free sequence comparison based on next-generation sequencing reads. J Comput Biol (2013) 1.26
Sequence-based prioritization of nonsynonymous single-nucleotide polymorphisms for the study of disease mutations. Am J Hum Genet (2007) 1.20
Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. BMC Syst Biol (2011) 1.19
Efficient statistical significance approximation for local similarity analysis of high-throughput time series data. Bioinformatics (2012) 1.12
Comparison of metagenomic samples using sequence signatures. BMC Genomics (2012) 1.10
Inference of transcription modification in long-live yeast strains from their expression profiles. BMC Genomics (2007) 1.09
Somatic, germline and sex hierarchy regulated gene expression during Drosophila metamorphosis. BMC Genomics (2009) 1.08
New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. Brief Bioinform (2013) 1.07
Ecdysone receptor acts in fruitless- expressing neurons to mediate drosophila courtship behaviors. Curr Biol (2009) 1.07
Prediction of protein function using protein-protein interaction data. Proc IEEE Comput Soc Bioinform Conf (2002) 1.05
New powerful statistics for alignment-free sequence comparison under a pattern transfer model. J Theor Biol (2011) 1.05
Testing gene set enrichment for subset of genes: Sub-GSE. BMC Bioinformatics (2008) 1.03
The effects of protein interactions, gene essentiality and regulatory regions on expression variation. BMC Syst Biol (2008) 1.03
Mitochondrial genome mutations in hypertensive individuals. Am J Hypertens (2004) 1.02
Inferring activity changes of transcription factors by binding association with sorted expression profiles. BMC Bioinformatics (2007) 1.01
Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy. BMC Bioinformatics (2006) 0.99
Systematic identification of cell cycle regulated transcription factors from microarray time series data. BMC Genomics (2008) 0.98
Sub-array normalization subject to differentiation. Nucleic Acids Res (2005) 0.98
Significant and systematic expression differentiation in long-lived yeast strains. PLoS One (2007) 0.98
The power of detecting enriched patterns: an HMM approach. J Comput Biol (2010) 0.97
Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach. BMC Bioinformatics (2011) 0.96
Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data. Am J Hum Genet (2003) 0.96
Modeling RNA degradation for RNA-Seq with applications. Biostatistics (2012) 0.93
Defining haplotype blocks and tag single-nucleotide polymorphisms in the human genome. Hum Mol Genet (2003) 0.93
Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny. BMC Bioinformatics (2011) 0.90
Detecting susceptibility genes in case-control studies using set association. BMC Genet (2003) 0.89
Compound poisson approximation of the number of occurrences of a position frequency matrix (PFM) on both strands. J Comput Biol (2008) 0.89
The transmission disequilibrium test and imprinting effects test based on case-parent pairs. Genet Epidemiol (2007) 0.89
Accuracy assessment of diploid consensus sequences. IEEE/ACM Trans Comput Biol Bioinform (2007) 0.88
A dynamic programming algorithm for binning microbial community profiles. Bioinformatics (2006) 0.87
Network motif identification in stochastic networks. Proc Natl Acad Sci U S A (2006) 0.87
Assessing the power of tag SNPs in the mapping of quantitative trait loci (QTL) with extremal and random samples. BMC Genet (2005) 0.86
A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays. BMC Bioinformatics (2008) 0.86
Comparative analyses of time-course gene expression profiles of the long-lived sch9Delta mutant. Nucleic Acids Res (2009) 0.84
CEDER: accurate detection of differentially expressed genes by combining significance of exons using RNA-Seq. IEEE/ACM Trans Comput Biol Bioinform (2012) 0.84
Association of genetic variation in the mitochondrial genome with blood pressure and metabolic traits. Hypertension (2012) 0.84
Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks. Brief Bioinform (2013) 0.83
Sequence alignment as hypothesis testing. J Comput Biol (2011) 0.83
DomainRBF: a Bayesian regression approach to the prioritization of candidate domains for complex diseases. BMC Syst Biol (2011) 0.82
MARD: a new method to detect differential gene expression in treatment-control time courses. Bioinformatics (2006) 0.82
Systematic identification of transcription factors associated with patient survival in cancers. BMC Genomics (2009) 0.81
Detection of parent-of-origin effects for quantitative traits in complete and incomplete nuclear families with multiple children. Am J Epidemiol (2011) 0.80
Multiple alignment-free sequence comparison. Bioinformatics (2013) 0.79
HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome. Bioinformatics (2009) 0.79
Conservation and implications of eukaryote transcriptional regulatory regions across multiple species. BMC Genomics (2008) 0.78
Extreme value distribution based gene selection criteria for discriminant microarray data analysis using logistic regression. J Comput Biol (2004) 0.78
Sampling distribution for microsatellites amplified by PCR: mean field approximation and its applications to genotyping. J Theor Biol (2004) 0.78
A quantile method for sizing optical maps. J Comput Biol (2007) 0.78
Microsatellite mutations during the polymerase chain reaction: mean field approximations and their applications. J Theor Biol (2003) 0.78
Chromatin regulation and gene centrality are essential for controlling fitness pleiotropy in yeast. PLoS One (2009) 0.77
SEME: a fast mapper of Illumina sequencing reads with statistical evaluation. J Comput Biol (2013) 0.76
A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms. BMC Genomics (2013) 0.76
Normal and compound poisson approximations for pattern occurrences in NGS reads. J Comput Biol (2012) 0.76
The mutation process of microsatellites during the polymerase chain reaction. J Comput Biol (2003) 0.76
HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies. Nucleic Acids Res (2011) 0.75
Network tuned multiple rank aggregation and applications to gene ranking. BMC Bioinformatics (2015) 0.75
Computational methods for the analysis of tag sequences in metagenomics studies. Front Biosci (Schol Ed) (2012) 0.75
Finding genetic overlaps among diseases based on ranked gene lists. J Comput Biol (2015) 0.75
Prioritizing functional modules mediating genetic perturbations and their phenotypic effects: a global strategy. Genome Biol (2008) 0.75
Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach. BMC Bioinformatics (2009) 0.75
Research in Computational Molecular Biology (RECOMB 2013). J Comput Biol (2013) 0.75
In this special issue of the Journal of Computational Biology, we take great pleasure in celebrating the landmark birthdays of two leaders in our field. J Comput Biol (2012) 0.75