Published in PLoS Comput Biol on December 20, 2012
Robust enumeration of cell subsets from tissue expression profiles. Nat Methods (2015) 2.30
Computational deconvolution: extracting cell type-specific information from heterogeneous samples. Curr Opin Immunol (2013) 1.40
Systematic pan-cancer analysis of tumour purity. Nat Commun (2015) 1.35
Digital sorting of complex tissues for cell type-specific gene expression profiles. BMC Bioinformatics (2013) 1.18
DeMix: deconvolution for mixed cancer transcriptomes using raw measured data. Bioinformatics (2013) 1.08
An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples. Brief Bioinform (2014) 1.03
Intercellular network structure and regulatory motifs in the human hematopoietic system. Mol Syst Biol (2014) 0.96
Immune cell subsets and their gene expression profiles from human PBMC isolated by Vacutainer Cell Preparation Tube (CPT™) and standard density gradient. BMC Immunol (2015) 0.85
ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles. BMC Bioinformatics (2015) 0.78
Quality cell therapy manufacturing by design. Nat Biotechnol (2016) 0.78
Topic model-based mass spectrometric data analysis in cancer biomarker discovery studies. BMC Genomics (2016) 0.75
Synergistic Communication between CD4+ T Cells and Monocytes Impacts the Cytokine Environment. Sci Rep (2016) 0.75
Inference of immune cell composition on the expression profiles of mouse tissue. Sci Rep (2017) 0.75
Gene Expression Deconvolution for Uncovering Molecular Signatures in Response to Therapy in Juvenile Idiopathic Arthritis. PLoS One (2016) 0.75
Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies. Genome Biol (2017) 0.75
Personalized medicine: from genotypes and molecular phenotypes towards therapy- session introduction. Pac Symp Biocomput (2014) 0.75
Detect tissue heterogeneity in gene expression data with BioQC. BMC Genomics (2017) 0.75
Visualizing the structure of RNA-seq expression data using grade of membership models. PLoS Genet (2017) 0.75
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics (2003) 100.88
Using GOstats to test gene lists for GO term association. Bioinformatics (2006) 12.58
Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell (2011) 7.03
Individuality and variation in gene expression patterns in human blood. Proc Natl Acad Sci U S A (2003) 6.49
Rosetta error model for gene expression analysis. Bioinformatics (2006) 4.67
Isolation of single human hematopoietic stem cells capable of long-term multilineage engraftment. Science (2011) 3.89
Most random gene expression signatures are significantly associated with breast cancer outcome. PLoS Comput Biol (2011) 3.33
Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations. Proc Natl Acad Sci U S A (2003) 3.19
Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus. PLoS One (2009) 2.98
Quantitative noise analysis for gene expression microarray experiments. Proc Natl Acad Sci U S A (2002) 2.66
Comparison of different isolation techniques prior gene expression profiling of blood derived cells: impact on physiological responses, on overall expression and the role of different cell types. Pharmacogenomics J (2004) 2.60
Separation of samples into their constituents using gene expression data. Bioinformatics (2001) 2.02
Supervised normalization of microarrays. Bioinformatics (2010) 2.00
Optimal deconvolution of transcriptional profiling data using quadratic programming with application to complex clinical blood samples. PLoS One (2011) 1.62
Dynamic interaction networks in a hierarchically organized tissue. Mol Syst Biol (2010) 1.51
Cell-cell interaction networks regulate blood stem and progenitor cell fate. Mol Syst Biol (2009) 1.49
ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing. Bioinformatics (2009) 1.22
A note on oligonucleotide expression values not being normally distributed. Biostatistics (2009) 1.01
Biological assessment of robust noise models in microarray data analysis. Bioinformatics (2011) 1.00
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res (2010) 10.97
Cytoscape Web: an interactive web-based network browser. Bioinformatics (2010) 10.03
Diversity and complexity in DNA recognition by transcription factors. Science (2009) 9.07
Growth factors, matrices, and forces combine and control stem cells. Science (2009) 8.46
FTO Obesity Variant Circuitry and Adipocyte Browning in Humans. N Engl J Med (2015) 6.48
GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biol (2008) 5.94
Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell (2006) 5.72
Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol (2009) 5.41
Exploration of essential gene functions via titratable promoter alleles. Cell (2004) 5.21
Probing microRNAs with microarrays: tissue specificity and functional inference. RNA (2004) 4.91
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
TAZ controls Smad nucleocytoplasmic shuttling and regulates human embryonic stem-cell self-renewal. Nat Cell Biol (2008) 3.44
Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nat Biotechnol (2009) 3.44
A panoramic view of yeast noncoding RNA processing. Cell (2003) 3.11
Reproducible, ultra high-throughput formation of multicellular organization from single cell suspension-derived human embryonic stem cell aggregates. PLoS One (2008) 3.08
Niche-mediated control of human embryonic stem cell self-renewal and differentiation. EMBO J (2007) 2.91
An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming. Cell (2011) 2.89
GeneMANIA prediction server 2013 update. Nucleic Acids Res (2013) 2.74
Brain-wide pathway for waste clearance captured by contrast-enhanced MRI. J Clin Invest (2013) 2.66
Rapid expansion of human hematopoietic stem cells by automated control of inhibitory feedback signaling. Cell Stem Cell (2012) 2.58
RBPDB: a database of RNA-binding specificities. Nucleic Acids Res (2010) 2.42
Control of human embryonic stem cell colony and aggregate size heterogeneity influences differentiation trajectories. Stem Cells (2008) 2.34
Alternative splicing of conserved exons is frequently species-specific in human and mouse. Trends Genet (2005) 2.26
Fast integration of heterogeneous data sources for predicting gene function with limited annotation. Bioinformatics (2010) 2.26
A microfabricated platform to measure and manipulate the mechanics of engineered cardiac microtissues. Tissue Eng Part A (2012) 1.95
LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance. Mol Cell (2012) 1.93
Controlled, scalable embryonic stem cell differentiation culture. Stem Cells (2004) 1.87
Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure. RNA (2010) 1.87
RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. Bioinformatics (2007) 1.86
Efficiency of embryoid body formation and hematopoietic development from embryonic stem cells in different culture systems. Biotechnol Bioeng (2002) 1.85
In Vivo 3D Digital Atlas Database of the Adult C57BL/6J Mouse Brain by Magnetic Resonance Microscopy. Front Neuroanat (2008) 1.85
RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins. PLoS Comput Biol (2010) 1.78
Pegasys: software for executing and integrating analyses of biological sequences. BMC Bioinformatics (2004) 1.74
The systematic production of cells for cell therapies. Cell Stem Cell (2008) 1.71
Development of alopecia areata is associated with higher central and peripheral hypothalamic-pituitary-adrenal tone in the skin graft induced C3H/HeJ mouse model. J Invest Dermatol (2008) 1.62
Generation of human embryonic stem cell-derived mesoderm and cardiac cells using size-specified aggregates in an oxygen-controlled bioreactor. Biotechnol Bioeng (2009) 1.61
Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitment. Cell Stem Cell (2007) 1.56
Transcriptional networks: reverse-engineering gene regulation on a global scale. Curr Opin Microbiol (2004) 1.54
Polo-like kinase 2 (PLK2) phosphorylates alpha-synuclein at serine 129 in central nervous system. J Biol Chem (2008) 1.54
Functional immobilization of signaling proteins enables control of stem cell fate. Nat Methods (2008) 1.52
Dynamic interaction networks in a hierarchically organized tissue. Mol Syst Biol (2010) 1.51
STAT5 protein negatively regulates T follicular helper (Tfh) cell generation and function. J Biol Chem (2012) 1.51
Shear-controlled single-step mouse embryonic stem cell expansion and embryoid body-based differentiation. Stem Cells (2005) 1.51
Cell-cell interaction networks regulate blood stem and progenitor cell fate. Mol Syst Biol (2009) 1.49
Hair follicles from alopecia areata patients exhibit alterations in immune privilege-associated gene expression in advance of hair loss. J Invest Dermatol (2010) 1.48
Genome-wide analysis of alternative splicing in Caenorhabditis elegans. Genome Res (2010) 1.46
The beneficial effects of the herbal medicine Free and Easy Wanderer Plus (FEWP) and fluoxetine on post-stroke depression. J Altern Complement Med (2008) 1.43
A global assessment of stem cell engineering. Tissue Eng Part A (2014) 1.38
High-throughput generation of hydrogel microbeads with varying elasticity for cell encapsulation. Biomaterials (2010) 1.37
Alternative induced pluripotent stem cell characterization criteria for in vitro applications. Cell Stem Cell (2009) 1.36
MicroRNA-223 regulates FOXO1 expression and cell proliferation. FEBS Lett (2012) 1.35
Incorporation of biomaterials in multicellular aggregates modulates pluripotent stem cell differentiation. Biomaterials (2010) 1.35
Don't look: growing clonal versus nonclonal neural stem cell colonies. Stem Cells (2008) 1.33
Content-based retrieval of focal liver lesions using bag-of-visual-words representations of single- and multiphase contrast-enhanced CT images. J Digit Imaging (2012) 1.33
Phospholipase C{gamma}1 is essential for T cell development, activation, and tolerance. J Exp Med (2010) 1.32
Autographa californica multiple nucleopolyhedrovirus nucleocapsid assembly is interrupted upon deletion of the 38K gene. J Virol (2006) 1.31
Enabling stem cell therapies through synthetic stem cell-niche engineering. J Clin Invest (2010) 1.31
Design and formulation of functional pluripotent stem cell-derived cardiac microtissues. Proc Natl Acad Sci U S A (2013) 1.29
Development of a perfusion fed bioreactor for embryonic stem cell-derived cardiomyocyte generation: oxygen-mediated enhancement of cardiomyocyte output. Biotechnol Bioeng (2005) 1.28
LongSAGE analysis of skeletal muscle at three prenatal stages in Tongcheng and Landrace pigs. Genome Biol (2007) 1.25
Understanding cellular networks to improve hematopoietic stem cell expansion cultures. Curr Opin Biotechnol (2006) 1.25
High-throughput combinatorial cell co-culture using microfluidics. Integr Biol (Camb) (2011) 1.25
Development of robust hepatitis C virus genotype 4 subgenomic replicons. Gastroenterology (2012) 1.25
Spatial organization of embryonic stem cell responsiveness to autocrine gp130 ligands reveals an autoregulatory stem cell niche. Stem Cells (2006) 1.24
Derivation, expansion and differentiation of induced pluripotent stem cells in continuous suspension cultures. Nat Methods (2012) 1.23
ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing. Bioinformatics (2009) 1.22
Sensitivity analysis of intracellular signaling pathway kinetics predicts targets for stem cell fate control. PLoS Comput Biol (2007) 1.22
LIF-mediated control of embryonic stem cell self-renewal emerges due to an autoregulatory loop. FASEB J (2007) 1.21
Melittin prevents liver cancer cell metastasis through inhibition of the Rac1-dependent pathway. Hepatology (2008) 1.17
PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors. Genome Biol (2015) 1.17
MEF2 activation in differentiated primary human skeletal muscle cultures requires coordinated involvement of parallel pathways. Am J Physiol Cell Physiol (2004) 1.16
Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein. Genome Biol (2014) 1.15
CXCR3/ligands are significantly involved in the tumorigenesis of basal cell carcinomas. Am J Pathol (2010) 1.15
The benefits of selecting phenotype-specific variants for applications of mixed models in genomics. Sci Rep (2013) 1.13
A critical role of Rap1b in B-cell trafficking and marginal zone B-cell development. Blood (2008) 1.12
Sustained in vitro expansion of bone progenitors is cell density dependent. Stem Cells (2004) 1.12
Geometric control of cardiomyogenic induction in human pluripotent stem cells. Tissue Eng Part A (2011) 1.11
Interrogating functional integration between injected pluripotent stem cell-derived cells and surrogate cardiac tissue. Proc Natl Acad Sci U S A (2009) 1.10
Combining many interaction networks to predict gene function and analyze gene lists. Proteomics (2012) 1.09
Ligand/receptor signaling threshold (LIST) model accounts for gp130-mediated embryonic stem cell self-renewal responses to LIF and HIL-6. Stem Cells (2002) 1.09
Dynamic changes in cellular and microenvironmental composition can be controlled to elicit in vitro human hematopoietic stem cell expansion. Exp Hematol (2005) 1.09
Genetic variation and relationships of eighteen Chinese indigenous pig breeds. Genet Sel Evol (2003) 1.08
A critical role of TAK1 in B-cell receptor-mediated nuclear factor kappaB activation. Blood (2009) 1.07
An improved strategy for high-level production of TEV protease in Escherichia coli and its purification and characterization. Protein Expr Purif (2006) 1.07
Cocaine increases the intracellular calcium concentration in brain independently of its cerebrovascular effects. J Neurosci (2006) 1.07
Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction. Genome Med (2013) 1.05
Manipulation of signaling thresholds in "engineered stem cell niches" identifies design criteria for pluripotent stem cell screens. PLoS One (2009) 1.03
Adult human bone marrow-derived mesenchymal progenitor cells are capable of adhesion-independent survival and expansion. Exp Hematol (2003) 1.02
The use of vascular endothelial growth factor functionalized agarose to guide pluripotent stem cell aggregates toward blood progenitor cells. Biomaterials (2010) 1.01
Genetic relationships among twelve Chinese indigenous goat populations based on microsatellite analysis. Genet Sel Evol (2002) 1.01
The Centre for Modeling Human Disease Gene Trap resource. Nucleic Acids Res (2004) 1.00
Predictive microfluidic control of regulatory ligand trajectories in individual pluripotent cells. Proc Natl Acad Sci U S A (2012) 1.00