Published in J Comput Biol on August 19, 2005
HIV-1 subtype B protease and reverse transcriptase amino acid covariation. PLoS Comput Biol (2007) 1.78
Cancer evolution: mathematical models and computational inference. Syst Biol (2014) 1.36
The temporal order of genetic and pathway alterations in tumorigenesis. PLoS One (2011) 1.20
Inferring differentiation pathways from gene expression. Bioinformatics (2008) 1.09
A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis. PLoS Comput Biol (2012) 1.07
Comparison of classifier fusion methods for predicting response to anti HIV-1 therapy. PLoS One (2008) 1.07
The mathematics of cancer: integrating quantitative models. Nat Rev Cancer (2015) 1.00
Algorithms to model single gene, single chromosome, and whole genome copy number changes jointly in tumor phylogenetics. PLoS Comput Biol (2014) 0.98
A differentiation-based phylogeny of cancer subtypes. PLoS Comput Biol (2010) 0.98
Construction of oncogenetic tree models reveals multiple pathways of oral cancer progression. Int J Cancer (2009) 0.97
Stability analysis of mixtures of mutagenetic trees. BMC Bioinformatics (2008) 0.87
Drug-class specific impact of antivirals on the reproductive capacity of HIV. PLoS Comput Biol (2010) 0.86
Learning oncogenetic networks by reducing to mixed integer linear programming. PLoS One (2013) 0.86
Models of RNA virus evolution and their roles in vaccine design. Immunome Res (2010) 0.83
Inferring tree causal models of cancer progression with probability raising. PLoS One (2014) 0.83
Learning oncogenic pathways from binary genomic instability data. Biometrics (2011) 0.83
A phylogenetic and Markov model approach for the reconstruction of mutational pathways of drug resistance. Bioinformatics (2009) 0.82
Differences in reversion of resistance mutations to wild-type under structured treatment interruption and related increase in replication capacity. PLoS One (2011) 0.82
Methods and challenges in timing chromosomal abnormalities within cancer samples. Bioinformatics (2013) 0.81
Simultaneous inference of cancer pathways and tumor progression from cross-sectional mutation data. J Comput Biol (2015) 0.80
A new ensemble coevolution system for detecting HIV-1 protein coevolution. Biol Direct (2015) 0.80
Bayesian methods for fitting mixture models that characterize branching tree processes: An application to development of resistant TB strains. Stat Med (2011) 0.79
Algorithmic methods to infer the evolutionary trajectories in cancer progression. Proc Natl Acad Sci U S A (2016) 0.79
Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores. Bioinformatics (2008) 0.78
Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling. BMC Bioinformatics (2015) 0.77
HIV-1 mutational pathways under multidrug therapy. AIDS Res Ther (2011) 0.77
Genome instability model of metastatic neuroblastoma tumorigenesis by a dictionary learning algorithm. BMC Med Genomics (2015) 0.77
Phylogenetic analysis of multiple FISH markers in oral tongue squamous cell carcinoma suggests that a diverse distribution of copy number changes is associated with poor prognosis. Int J Cancer (2015) 0.76
Bayesian estimation of mixture models with prespecified elements to compare drug resistance in treatment-naïve and experienced tuberculosis cases. PLoS Comput Biol (2013) 0.76
Temporal ordering of cancer microarray data through a reinforcement learning based approach. PLoS One (2013) 0.75
The evolution of tumour phylogenetics: principles and practice. Nat Rev Genet (2017) 0.75
Variable selection for disease progression models: methods for oncogenetic trees and application to cancer and HIV. BMC Bioinformatics (2017) 0.75
ROCR: visualizing classifier performance in R. Bioinformatics (2005) 19.60
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J (2004) 15.51
A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet (2006) 15.14
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics (2006) 11.33
BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics (2005) 5.95
Computing topological parameters of biological networks. Bioinformatics (2007) 5.36
Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions. J Clin Invest (2009) 5.07
A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics (2006) 4.82
Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses. Plant Physiol (2005) 4.34
Sarcoidosis is associated with a truncating splice site mutation in BTNL2. Nat Genet (2005) 4.23
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
pcaMethods--a bioconductor package providing PCA methods for incomplete data. Bioinformatics (2007) 3.84
Bioinformatics prediction of HIV coreceptor usage. Nat Biotechnol (2007) 3.64
Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype. Proc Natl Acad Sci U S A (2002) 3.46
Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies. Nucleic Acids Res (2010) 3.31
BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol (2012) 3.24
Genetic variation in DLG5 is associated with inflammatory bowel disease. Nat Genet (2004) 3.19
Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment. Cell Host Microbe (2011) 3.05
CpG island mapping by epigenome prediction. PLoS Comput Biol (2007) 3.02
Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLoS Genet (2011) 2.98
Estimating mutual information using B-spline functions--an improved similarity measure for analysing gene expression data. BMC Bioinformatics (2004) 2.83
CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet (2006) 2.66
Predicting HIV coreceptor usage on the basis of genetic and clinical covariates. Antivir Ther (2007) 2.49
Calculating the statistical significance of changes in pathway activity from gene expression data. Stat Appl Genet Mol Biol (2004) 2.48
Starch as a major integrator in the regulation of plant growth. Proc Natl Acad Sci U S A (2009) 2.47
The metabolic signature related to high plant growth rate in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2007) 2.44
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Res (2010) 2.41
PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor. Nucleic Acids Res (2007) 2.40
Shift of HIV tropism in stem-cell transplantation with CCR5 Delta32 mutation. N Engl J Med (2014) 2.39
Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes. Nucleic Acids Res (2003) 2.37
The HIN domain of IFI-200 proteins consists of two OB folds. Biochem Biophys Res Commun (2005) 2.25
Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping. Nucleic Acids Res (2008) 2.19
Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach. Arch Toxicol (2012) 2.17
A DNA methylation fingerprint of 1628 human samples. Genome Res (2011) 2.16
Co-clustering of biological networks and gene expression data. Bioinformatics (2002) 2.12
Metabolomic and transcriptomic stress response of Escherichia coli. Mol Syst Biol (2010) 2.04
Phase I dose escalation and pharmacokinetic study of BI 2536, a novel Polo-like kinase 1 inhibitor, in patients with advanced solid tumors. J Clin Oncol (2008) 1.98
Computational epigenetics. Bioinformatics (2007) 1.92
BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing. Nucleic Acids Res (2011) 1.90
Structural kinetic modeling of metabolic networks. Proc Natl Acad Sci U S A (2006) 1.88
Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays. PLoS Med (2005) 1.88
Metabolomics of temperature stress. Physiol Plant (2008) 1.87
Arabidopsis female gametophyte gene expression map reveals similarities between plant and animal gametes. Curr Biol (2010) 1.85
NOXclass: prediction of protein-protein interaction types. BMC Bioinformatics (2006) 1.85
HIV-1 suppression and durable control by combining single broadly neutralizing antibodies and antiretroviral drugs in humanized mice. Proc Natl Acad Sci U S A (2013) 1.85
EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data. Genome Biol (2009) 1.83
A comprehensive analysis of human gene expression profiles identifies stromal immunoglobulin κ C as a compatible prognostic marker in human solid tumors. Clin Cancer Res (2012) 1.83
Robin: an intuitive wizard application for R-based expression microarray quality assessment and analysis. Plant Physiol (2010) 1.82
Parallel analysis of transcript and metabolic profiles: a new approach in systems biology. EMBO Rep (2003) 1.76
Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation. Plant Physiol (2006) 1.75
Identification of metabolic and biomass QTL in Arabidopsis thaliana in a parallel analysis of RIL and IL populations. Plant J (2007) 1.74
ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites. BMC Bioinformatics (2007) 1.71
Recco: recombination analysis using cost optimization. Bioinformatics (2006) 1.68
Functional evaluation of domain-domain interactions and human protein interaction networks. Bioinformatics (2007) 1.65
DASMI: exchanging, annotating and assessing molecular interaction data. Bioinformatics (2009) 1.64
Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis, and tissue microarray validation. Clin Cancer Res (2012) 1.63
Mode of inheritance of primary metabolic traits in tomato. Plant Cell (2008) 1.56
Primary HIV drug resistance and efficacy of first-line antiretroviral therapy guided by resistance testing. J Acquir Immune Defic Syndr (2006) 1.53
Computational analysis of human protein interaction networks. Proteomics (2007) 1.53
Decision tree supported substructure prediction of metabolites from GC-MS profiles. Metabolomics (2010) 1.51
HIV-2EU: supporting standardized HIV-2 drug resistance interpretation in Europe. Clin Infect Dis (2013) 1.49
Correspondence of tumor localization with tumor recurrence and cytogenetic progression in meningiomas. Neurosurgery (2008) 1.44
The metabolic response of heterotrophic Arabidopsis cells to oxidative stress. Plant Physiol (2006) 1.43
Toxicogenomics directory of chemically exposed human hepatocytes. Arch Toxicol (2014) 1.43
YLoc--an interpretable web server for predicting subcellular localization. Nucleic Acids Res (2010) 1.43
ERBB2 and TOP2A in breast cancer: a comprehensive analysis of gene amplification, RNA levels, and protein expression and their influence on prognosis and prediction. Clin Cancer Res (2010) 1.41
Mtreemix: a software package for learning and using mixture models of mutagenetic trees. Bioinformatics (2005) 1.41
EpiExplorer: live exploration and global analysis of large epigenomic datasets. Genome Biol (2012) 1.40
Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage. PLoS Comput Biol (2007) 1.39
Novel Sm-like proteins with long C-terminal tails and associated methyltransferases. FEBS Lett (2004) 1.38
Improving disease gene prioritization using the semantic similarity of Gene Ontology terms. Bioinformatics (2010) 1.37
Compensatory mutations at the HIV cleavage sites p7/p1 and p1/p6-gag in therapy-naive and therapy-experienced patients. Antivir Ther (2006) 1.37
Evolution of raltegravir resistance during therapy. J Antimicrob Chemother (2009) 1.33
Permutation importance: a corrected feature importance measure. Bioinformatics (2010) 1.32
Going from where to why--interpretable prediction of protein subcellular localization. Bioinformatics (2010) 1.32
Phase I study of the angiogenesis inhibitor BIBF 1120 in patients with advanced solid tumors. Clin Cancer Res (2009) 1.32
Backbone rigidity and static presentation of guanidinium groups increases cellular uptake of arginine-rich cell-penetrating peptides. Nat Commun (2011) 1.30
Role of thioredoxin reductase 1 and thioredoxin interacting protein in prognosis of breast cancer. Breast Cancer Res (2010) 1.30
Biomarker discovery in heterogeneous tissue samples -taking the in-silico deconfounding approach. BMC Bioinformatics (2010) 1.30
Predicting Bevirimat resistance of HIV-1 from genotype. BMC Bioinformatics (2010) 1.30