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  1. Article

    Open Access

    Enhancing cancer clonality analysis with integrative genomics

    It is understood that cancer is a clonal disease initiated by a single cell, and that metastasis, which is the spread of cancer from the primary site, is also initiated by a single cell. The seemingly natural ...

    Erich A Peterson, Michael A Bauer, Shweta S Chavan, Cody Ashby in BMC Bioinformatics (2015)

  2. Article

    Open Access

    Leveraging the new with the old: providing a framework for the integration of historic microarray studies with next generation sequencing

    Next Generation Sequencing (NGS) methods are rapidly providing remarkable advances in our ability to study the molecular profiles of human cancers. However, the scientific discovery offered by NGS also include...

    Michael A Bauer, Shweta S Chavan, Erich A Peterson, Christoph J Heuck in BMC Bioinformatics (2014)

  3. Article

    Open Access

    Revealing the inherent heterogeneity of human malignancies by variant consensus strategies coupled with cancer clonal analysis

    Tumors are heterogeneous in composition. They are composed of cancer cells proper, along with stromal elements that collectively form a microenvironment, all of which are necessary to nurture the malignant pro...

    Erich A Peterson, Shweta S Chavan, Michael A Bauer, Christoph J Heuck in BMC Bioinformatics (2014)

  4. Article

    Open Access

    Towards the integration, annotation and association of historical microarray experiments with RNA-seq

    Transcriptome analysis by microarrays has produced important advances in biomedicine. For instance in multiple myeloma (MM), microarray approaches led to the development of an effective disease subty** via c...

    Shweta S Chavan, Michael A Bauer, Erich A Peterson, Christoph J Heuck in BMC Bioinformatics (2013)

  5. Article

    Open Access

    NATbox: a network analysis toolbox in R

    There has been recent interest in capturing the functional relationships (FRs) from high-throughput assays using suitable computational techniques. FRs elucidate the working of genes in concert as a system as ...

    Shweta S Chavan, Michael A Bauer, Marco Scutari in BMC Bioinformatics (2009)