Published in Nucleic Acids Res on May 21, 2007
CDX2 as a Prognostic Biomarker in Stage II and Stage III Colon Cancer. N Engl J Med (2016) 8.53
Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nat Biotechnol (2011) 7.84
Genome-wide measurement of RNA folding energies. Mol Cell (2012) 2.85
Gene Expression Commons: an open platform for absolute gene expression profiling. PLoS One (2012) 1.96
Boolean implication networks derived from large scale, whole genome microarray datasets. Genome Biol (2008) 1.91
Genomic and proteomic analysis reveals a threshold level of MYC required for tumor maintenance. Cancer Res (2008) 1.58
Combined analysis of murine and human microarrays and ChIP analysis reveals genes associated with the ability of MYC to maintain tumorigenesis. PLoS Genet (2008) 1.23
Reverse engineering dynamic temporal models of biological processes and their relationships. Proc Natl Acad Sci U S A (2010) 1.09
Zebrafish Pou5f1-dependent transcriptional networks in temporal control of early development. Mol Syst Biol (2010) 1.08
Temporal changes in gene expression induced by sulforaphane in human prostate cancer cells. Prostate (2009) 1.04
Adaptive control of the false discovery rate in voxel-based morphometry. Hum Brain Mapp (2009) 1.04
Temporal patterns of gene expression in developing maize endosperm identified through transcriptome sequencing. Proc Natl Acad Sci U S A (2014) 1.04
Discriminating cellular heterogeneity using microwell-based RNA cytometry. Nat Commun (2014) 0.92
A cell of origin gene signature indicates human bladder cancer has distinct cellular progenitors. Stem Cells (2014) 0.90
The C228T mutation of TERT promoter frequently occurs in bladder cancer stem cells and contributes to tumorigenesis of bladder cancer. Oncotarget (2015) 0.89
Statecharts for gene network modeling. PLoS One (2010) 0.84
Identification of thresholds for dichotomizing DNA methylation data. EURASIP J Bioinform Syst Biol (2013) 0.80
Deciphering Transcriptional Programming during Pod and Seed Development Using RNA-Seq in Pigeonpea (Cajanus cajan). PLoS One (2016) 0.78
Modelling gene expression profiles related to prostate tumor progression using binary states. Theor Biol Med Model (2013) 0.78
Mining TCGA data using Boolean implications. PLoS One (2014) 0.78
The power of boolean implication networks. Front Physiol (2012) 0.76
Assessing the evolution of gene expression using microarray data. Evol Bioinform Online (2008) 0.75
OLFM4, KNG1 and Sec24C identified by proteomics and immunohistochemistry as potential markers of early colorectal cancer stages. Clin Proteomics (2017) 0.75
CLUSTERnGO: a user-defined modelling platform for two-stage clustering of time-series data. Bioinformatics (2015) 0.75
Rapid Chromatin Switch in the Direct Reprogramming of Fibroblasts to Neurons. Cell Rep (2017) 0.75
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A (1998) 192.97
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
Java Treeview--extensible visualization of microarray data. Bioinformatics (2004) 24.12
Missing value estimation methods for DNA microarrays. Bioinformatics (2001) 20.84
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet (2003) 14.56
WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res (2005) 12.88
Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol (2004) 9.38
Significance analysis of time course microarray experiments. Proc Natl Acad Sci U S A (2005) 8.65
The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res (2003) 6.31
ErmineJ: tool for functional analysis of gene expression data sets. BMC Bioinformatics (2005) 4.98
Clustering of time-course gene expression data using a mixed-effects model with B-splines. Bioinformatics (2003) 4.15
Cluster analysis of gene expression dynamics. Proc Natl Acad Sci U S A (2002) 3.83
Clustering short time series gene expression data. Bioinformatics (2005) 3.48
Analyzing time series gene expression data. Bioinformatics (2004) 3.45
Continuous representations of time-series gene expression data. J Comput Biol (2003) 3.32
Aligning gene expression time series with time warping algorithms. Bioinformatics (2001) 2.82
Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures. Mol Biol Cell (2005) 2.30
Statistical tests for identifying differentially expressed genes in time-course microarray experiments. Bioinformatics (2003) 2.22
A data-driven clustering method for time course gene expression data. Nucleic Acids Res (2006) 2.20
Using hidden Markov models to analyze gene expression time course data. Bioinformatics (2003) 2.10
Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes. Proc Natl Acad Sci U S A (2003) 2.10
Binary analysis and optimization-based normalization of gene expression data. Bioinformatics (2002) 2.10
A practical false discovery rate approach to identifying patterns of differential expression in microarray data. Bioinformatics (2005) 1.94
DnaA coordinates replication initiation and cell cycle transcription in Caulobacter crescentus. Mol Microbiol (2005) 1.71
The Graphical Query Language: a tool for analysis of gene expression time-courses. Bioinformatics (2005) 1.28
Analysis techniques for microarray time-series data. J Comput Biol (2002) 1.14
Extracting transcriptional events from temporal gene expression patterns during Dictyostelium development. Bioinformatics (2002) 1.08
A multi-step approach to time series analysis and gene expression clustering. Bioinformatics (2006) 1.03
Identifying genes from up-down properties of microarray expression series. Bioinformatics (2005) 0.94
Time ordering of gene coexpression. Biostatistics (2006) 0.91
Regularization Paths for Generalized Linear Models via Coordinate Descent. J Stat Softw (2010) 38.65
Effect of screening and adjuvant therapy on mortality from breast cancer. N Engl J Med (2005) 16.70
Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science (2011) 15.45
Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes. N Engl J Med (2004) 6.91
Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE. Nat Biotechnol (2011) 5.46
Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome. Am J Pathol (2002) 5.20
Effects of mammography screening under different screening schedules: model estimates of potential benefits and harms. Ann Intern Med (2009) 4.60
Different gene expression patterns in invasive lobular and ductal carcinomas of the breast. Mol Biol Cell (2004) 3.73
Association of a leukemic stem cell gene expression signature with clinical outcomes in acute myeloid leukemia. JAMA (2010) 3.25
Non-small cell lung cancer: identifying prognostic imaging biomarkers by leveraging public gene expression microarray data--methods and preliminary results. Radiology (2012) 2.98
Benefits and harms of computed tomography lung cancer screening strategies: a comparative modeling study for the U.S. Preventive Services Task Force. Ann Intern Med (2013) 2.77
Survival analysis of cancer risk reduction strategies for BRCA1/2 mutation carriers. J Clin Oncol (2009) 2.74
Ly6d marks the earliest stage of B-cell specification and identifies the branchpoint between B-cell and T-cell development. Genes Dev (2009) 2.46
Gene Expression Commons: an open platform for absolute gene expression profiling. PLoS One (2012) 1.96
Boolean implication networks derived from large scale, whole genome microarray datasets. Genome Biol (2008) 1.91
Hierarchy in somatic mutations arising during genomic evolution and progression of follicular lymphoma. Blood (2013) 1.86
A pluripotency signature predicts histologic transformation and influences survival in follicular lymphoma patients. Blood (2009) 1.74
Discovering biological progression underlying microarray samples. PLoS Comput Biol (2011) 1.65
Genomic and proteomic analysis reveals a threshold level of MYC required for tumor maintenance. Cancer Res (2008) 1.58
Multiplexed proximity ligation assays to profile putative plasma biomarkers relevant to pancreatic and ovarian cancer. Clin Chem (2008) 1.57
Paraffin-based 6-gene model predicts outcome in diffuse large B-cell lymphoma patients treated with R-CHOP. Blood (2008) 1.55
Prediction of survival in diffuse large B-cell lymphoma based on the expression of 2 genes reflecting tumor and microenvironment. Blood (2011) 1.41
Glioblastoma multiforme: exploratory radiogenomic analysis by using quantitative image features. Radiology (2014) 1.36
Online tool to guide decisions for BRCA1/2 mutation carriers. J Clin Oncol (2012) 1.35
Analysis of factorial time-course microarrays with application to a clinical study of burn injury. Proc Natl Acad Sci U S A (2010) 1.33
Oncogenic regulators and substrates of the anaphase promoting complex/cyclosome are frequently overexpressed in malignant tumors. Am J Pathol (2007) 1.28
Prognostic PET 18F-FDG uptake imaging features are associated with major oncogenomic alterations in patients with resected non-small cell lung cancer. Cancer Res (2012) 1.28
Impact of adjuvant therapy and mammography on U.S. mortality from 1975 to 2000: comparison of mortality results from the cisnet breast cancer base case analysis. J Natl Cancer Inst Monogr (2006) 1.23
Combined analysis of murine and human microarrays and ChIP analysis reveals genes associated with the ability of MYC to maintain tumorigenesis. PLoS Genet (2008) 1.23
Genome-wide characterization of gene expression variations and DNA copy number changes in prostate cancer cell lines. Prostate (2005) 1.20
Improvements in observed and relative survival in follicular grade 1-2 lymphoma during 4 decades: the Stanford University experience. Blood (2013) 1.20
MicroRNAs are independent predictors of outcome in diffuse large B-cell lymphoma patients treated with R-CHOP. Clin Cancer Res (2011) 1.17
A comparative review of CISNET breast models used to analyze U.S. breast cancer incidence and mortality trends. J Natl Cancer Inst Monogr (2006) 1.15
MiDReG: a method of mining developmentally regulated genes using Boolean implications. Proc Natl Acad Sci U S A (2010) 1.15
Lymphomas that recur after MYC suppression continue to exhibit oncogene addiction. Proc Natl Acad Sci U S A (2011) 1.13
Fast calculation of pairwise mutual information for gene regulatory network reconstruction. Comput Methods Programs Biomed (2009) 1.10
Comparative analysis of 5 lung cancer natural history and screening models that reproduce outcomes of the NLST and PLCO trials. Cancer (2014) 1.08
Temporal changes in gene expression induced by sulforaphane in human prostate cancer cells. Prostate (2009) 1.04
CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data. Bioinformatics (2012) 1.04
Incidental extracardiac findings at coronary CT: clinical and economic impact. AJR Am J Roentgenol (2010) 1.01
Breast magnetic resonance image screening and ductal lavage in women at high genetic risk for breast carcinoma. Cancer (2004) 0.99
A simulation model investigating the impact of tumor volume doubling time and mammographic tumor detectability on screening outcomes in women aged 40-49 years. J Natl Cancer Inst (2010) 0.96
A simulation model to predict the impact of prophylactic surgery and screening on the life expectancy of BRCA1 and BRCA2 mutation carriers. Cancer Epidemiol Biomarkers Prev (2012) 0.91
Ductal lavage of fluid-yielding and non-fluid-yielding ducts in BRCA1 and BRCA2 mutation carriers and other women at high inherited breast cancer risk. Cancer Epidemiol Biomarkers Prev (2005) 0.90
Reconstructing directed signed gene regulatory network from microarray data. IEEE Trans Biomed Eng (2011) 0.88
Simulation-based parameter estimation for complex models: a breast cancer natural history modelling illustration. Stat Methods Med Res (2004) 0.87
Modeling the impact of population screening on breast cancer mortality in the United States. Breast (2011) 0.87
Simultaneous class discovery and classification of microarray data using spectral analysis. J Comput Biol (2009) 0.86
Timing robustness in the budding and fission yeast cell cycles. PLoS One (2010) 0.85
Bayesian gene set analysis for identifying significant biological pathways. J R Stat Soc Ser C Appl Stat (2011) 0.84
Characterization of patient specific signaling via augmentation of Bayesian networks with disease and patient state nodes. Conf Proc IEEE Eng Med Biol Soc (2009) 0.84
Modeling the transition of lung cancer from early to advanced stage. Cancer Causes Control (2009) 0.83
Opinions of women with high inherited breast cancer risk about prophylactic mastectomy: an initial evaluation from a screening trial including magnetic resonance imaging and ductal lavage. Health Expect (2005) 0.82
Identification of drug targets by chemogenomic and metabolomic profiling in yeast. Pharmacogenet Genomics (2012) 0.81
Cd14 SNPs regulate the innate immune response. Mol Immunol (2012) 0.80
Comparing the benefits of screening for breast cancer and lung cancer using a novel natural history model. Cancer Causes Control (2011) 0.80
Note on "Comparison of model selection for regression" by Vladimir Cherkassky and Yunqian Ma. Neural Comput (2003) 0.79
TreeVis: a MATLAB-based tool for tree visualization. Comput Methods Programs Biomed (2012) 0.78
The prognostic value of tumor-associated macrophages in leiomyosarcoma: a single institution study. Am J Clin Oncol (2011) 0.76
Quantitative proteomic profiling identifies protein correlates to EGFR kinase inhibition. Mol Cancer Ther (2012) 0.76
Reducing the computational complexity of information theoretic approaches for reconstructing gene regulatory networks. J Comput Biol (2010) 0.75
Feasibility evaluation of an online tool to guide decisions for BRCA1/2 mutation carriers. Fam Cancer (2013) 0.75
Raising the bar for the U.S. Preventive Services Task Force. Ann Intern Med (2014) 0.75
Ductal pattern enhancement on magnetic resonance imaging of the breast due to ductal lavage. Breast J (2007) 0.75
Glioblastoma Multiforme: Exploratory Radiogenomic Analysis by Using Quantitative Image Features. Radiology (2015) 0.75