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Coupled two-way clustering analysis of gene microarray data.
We present a coupled two-way clustering approach to gene microarray data analysis. The main idea is to identify subsets of the genes and samples, such that when one of these is used to cluster theExpand
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Stem cell-related "self-renewal" signature and high epidermal growth factor receptor expression associated with resistance to concomitant chemoradiotherapy in glioblastoma.
PURPOSE Glioblastomas are notorious for resistance to therapy, which has been attributed to DNA-repair proficiency, a multitude of deregulated molecular pathways, and, more recently, to theExpand
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A module of negative feedback regulators defines growth factor signaling
Signaling pathways invoke interplays between forward signaling and feedback to drive robust cellular response. In this study, we address the dynamics of growth factor signaling through profiling ofExpand
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Pathway-based personalized analysis of cancer
We introduce Pathifier, an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for everyExpand
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Association of survival and disease progression with chromosomal instability: A genomic exploration of colorectal cancer
During disease progression the cells that comprise solid malignancies undergo significant changes in gene copy number and chromosome structure. Colorectal cancer provides an excellent model to studyExpand
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A distinctive DNA damage response in human hematopoietic stem cells reveals an apoptosis-independent role for p53 in self-renewal.
Highly regenerative tissues such as blood must possess effective DNA damage responses (DDR) that balance long-term regeneration with protection from leukemogenesis. Hematopoietic stem cells (HSCs)Expand
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Resampling Method for Unsupervised Estimation of Cluster Validity
We introduce a method for validation of results obtained by clustering analysis of data. Expand
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RNF20 and USP44 regulate stem cell differentiation by modulating H2B monoubiquitylation.
Embryonic stem cells (ESCs) maintain high genomic plasticity, which is essential for their capacity to enter diverse differentiation pathways. Posttranscriptional modifications of chromatin histonesExpand
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Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
MOTIVATION Genes are often characterized dichotomously as either housekeeping or single-tissue specific. Expand
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Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes
BackgroundThe human genome contains over one million Alu repeat elements whose distribution is not uniform. While metabolism-related genes were shown to be enriched with Alu, in structural genes AluExpand
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