Published in Bioinformatics on February 10, 2005
Modeling cancer progression via pathway dependencies. PLoS Comput Biol (2008) 2.12
Quantifying cancer progression with conjunctive Bayesian networks. Bioinformatics (2009) 1.37
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
Algorithms to model single gene, single chromosome, and whole genome copy number changes jointly in tumor phylogenetics. PLoS Comput Biol (2014) 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
A new model of time scheme for progression of colorectal cancer. BMC Syst Biol (2014) 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
Detection of novel amplicons in prostate cancer by comprehensive genomic profiling of prostate cancer cell lines using oligonucleotide-based arrayCGH. PLoS One (2007) 0.79
Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores. Bioinformatics (2008) 0.78
Defining order and timing of mutations during cancer progression: the TO-DAG probabilistic graphical model. Front Genet (2015) 0.77
Computational Cancer Biology: An Evolutionary Perspective. PLoS Comput Biol (2016) 0.76
The evolution of tumour phylogenetics: principles and practice. Nat Rev Genet (2017) 0.75
ROCR: visualizing classifier performance in R. Bioinformatics (2005) 19.60
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
Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature (2012) 10.99
Comparative lesion sequencing provides insights into tumor evolution. Proc Natl Acad Sci U S A (2008) 10.52
Gene expression-based classification of malignant gliomas correlates better with survival than histological classification. Cancer Res (2003) 8.06
Analysis of the IDH1 codon 132 mutation in brain tumors. Acta Neuropathol (2008) 7.79
Type and frequency of IDH1 and IDH2 mutations are related to astrocytic and oligodendroglial differentiation and age: a study of 1,010 diffuse gliomas. Acta Neuropathol (2009) 7.73
Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma. Cancer Cell (2012) 6.71
Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell (2012) 6.07
BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics (2005) 5.95
Viral population estimation using pyrosequencing. PLoS Comput Biol (2008) 5.89
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71
Computing topological parameters of biological networks. Bioinformatics (2007) 5.36
A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics (2006) 4.82
Dissecting the genomic complexity underlying medulloblastoma. Nature (2012) 4.77
An endogenous tumour-promoting ligand of the human aryl hydrocarbon receptor. Nature (2011) 4.63
Long-term survival with glioblastoma multiforme. Brain (2007) 4.51
NOA-04 randomized phase III trial of sequential radiochemotherapy of anaplastic glioma with procarbazine, lomustine, and vincristine or temozolomide. J Clin Oncol (2009) 4.32
Sarcoidosis is associated with a truncating splice site mutation in BTNL2. Nat Genet (2005) 4.23
K27M mutation in histone H3.3 defines clinically and biologically distinct subgroups of pediatric diffuse intrinsic pontine gliomas. Acta Neuropathol (2012) 4.00
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
Analysis of BRAF V600E mutation in 1,320 nervous system tumors reveals high mutation frequencies in pleomorphic xanthoastrocytoma, ganglioglioma and extra-cerebellar pilocytic astrocytoma. Acta Neuropathol (2011) 3.66
Molecular predictors of progression-free and overall survival in patients with newly diagnosed glioblastoma: a prospective translational study of the German Glioma Network. J Clin Oncol (2009) 3.65
Farewell to oligoastrocytoma: in situ molecular genetics favor classification as either oligodendroglioma or astrocytoma. Acta Neuropathol (2014) 3.52
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
High prevalence of BRAF V600E mutations in Erdheim-Chester disease but not in other non-Langerhans cell histiocytoses. Blood (2012) 3.44
Monoclonal antibody specific for IDH1 R132H mutation. Acta Neuropathol (2009) 3.38
FSTL5 is a marker of poor prognosis in non-WNT/non-SHH medulloblastoma. J Clin Oncol (2011) 3.33
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
International Society Of Neuropathology--Haarlem consensus guidelines for nervous system tumor classification and grading. Brain Pathol (2014) 3.21
Genetic variation in DLG5 is associated with inflammatory bowel disease. Nat Genet (2004) 3.19
Delineation of two clinically and molecularly distinct subgroups of posterior fossa ependymoma. Cancer Cell (2011) 3.11
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
Characterization of R132H mutation-specific IDH1 antibody binding in brain tumors. Brain Pathol (2009) 2.77
Patients with IDH1 wild type anaplastic astrocytomas exhibit worse prognosis than IDH1-mutated glioblastomas, and IDH1 mutation status accounts for the unfavorable prognostic effect of higher age: implications for classification of gliomas. Acta Neuropathol (2010) 2.71
CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet (2006) 2.66
ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. BMC Bioinformatics (2011) 2.60
Assessment of BRAF V600E mutation status by immunohistochemistry with a mutation-specific monoclonal antibody. Acta Neuropathol (2011) 2.53
Reduced H3K27me3 and DNA hypomethylation are major drivers of gene expression in K27M mutant pediatric high-grade gliomas. Cancer Cell (2013) 2.50
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
Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma. Nat Genet (2013) 2.42
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Res (2010) 2.41
Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes. Nucleic Acids Res (2003) 2.37
Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction. J Comput Biol (2010) 2.37
Tumour class prediction and discovery by microarray-based DNA methylation analysis. Nucleic Acids Res (2002) 2.34
Targeting the BRAF V600E mutation in multiple myeloma. Cancer Discov (2013) 2.32
Molecular staging of intracranial ependymoma in children and adults. J Clin Oncol (2010) 2.27
The HIN domain of IFI-200 proteins consists of two OB folds. Biochem Biophys Res Commun (2005) 2.25
Intracranial thermotherapy using magnetic nanoparticles combined with external beam radiotherapy: results of a feasibility study on patients with glioblastoma multiforme. J Neurooncol (2006) 2.22
Yes and PI3K bind CD95 to signal invasion of glioblastoma. Cancer Cell (2008) 2.21
Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping. Nucleic Acids Res (2008) 2.19
A DNA methylation fingerprint of 1628 human samples. Genome Res (2011) 2.16
Toward the blood-borne miRNome of human diseases. Nat Methods (2011) 2.14
Co-clustering of biological networks and gene expression data. Bioinformatics (2002) 2.12
Choreoathetosis, hypothyroidism, and pulmonary alterations due to human NKX2-1 haploinsufficiency. J Clin Invest (2002) 2.09
Distinct requirement for an intact dimer interface in wild-type, V600E and kinase-dead B-Raf signalling. EMBO J (2012) 2.09
Adult medulloblastoma comprises three major molecular variants. J Clin Oncol (2011) 2.07
Reliable detection of subclonal single-nucleotide variants in tumour cell populations. Nat Commun (2012) 2.06
Desmoplastic infantile astrocytoma with multiple intracranial and intraspinal localizations at presentation. Childs Nerv Syst (2015) 2.00
Prognostic or predictive value of MGMT promoter methylation in gliomas depends on IDH1 mutation. Neurology (2013) 1.98
Causes and consequences of DNA hypomethylation in human cancer. Biochem Cell Biol (2005) 1.94
Combined molecular analysis of BRAF and IDH1 distinguishes pilocytic astrocytoma from diffuse astrocytoma. Acta Neuropathol (2009) 1.93
Computational epigenetics. Bioinformatics (2007) 1.92
Immunohistochemical testing of BRAF V600E status in 1,120 tumor tissue samples of patients with brain metastases. Acta Neuropathol (2011) 1.91
Oncogenic FAM131B-BRAF fusion resulting from 7q34 deletion comprises an alternative mechanism of MAPK pathway activation in pilocytic astrocytoma. Acta Neuropathol (2011) 1.90
BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing. Nucleic Acids Res (2011) 1.90
The effect of thermotherapy using magnetic nanoparticles on rat malignant glioma. J Neurooncol (2005) 1.89
24 hours in the life of HIV-1 in a T cell line. PLoS Pathog (2013) 1.89
Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays. PLoS Med (2005) 1.88
Transitional cell carcinoma of the ureter: prognostic factors influencing progression and survival. Eur Urol (2006) 1.86
NOXclass: prediction of protein-protein interaction types. BMC Bioinformatics (2006) 1.85
TP53 mutation is frequently associated with CTNNB1 mutation or MYCN amplification and is compatible with long-term survival in medulloblastoma. J Clin Oncol (2010) 1.83
EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data. Genome Biol (2009) 1.83
Focal genomic amplification at 19q13.42 comprises a powerful diagnostic marker for embryonal tumors with ependymoblastic rosettes. Acta Neuropathol (2010) 1.82
Immunohistochemistry is highly sensitive and specific for the detection of V600E BRAF mutation in melanoma. Am J Surg Pathol (2013) 1.80
A new clinico-pathological classification system for mesial temporal sclerosis. Acta Neuropathol (2007) 1.77
The microRNA profile of prostate carcinoma obtained by deep sequencing. Mol Cancer Res (2010) 1.75
Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation. Plant Physiol (2006) 1.75
Learning multiple evolutionary pathways from cross-sectional data. J Comput Biol (2005) 1.74
Histone deacetylase 8 in neuroblastoma tumorigenesis. Clin Cancer Res (2009) 1.71
Embryonal tumor with abundant neuropil and true rosettes (ETANTR), ependymoblastoma, and medulloepithelioma share molecular similarity and comprise a single clinicopathological entity. Acta Neuropathol (2013) 1.68
Recco: recombination analysis using cost optimization. Bioinformatics (2006) 1.68