Roded Sharan

Research interests

Publications

• Using deep learning to model the hierarchical structure and function of a cell

  Nature Methods · 2018 · https://doi.org/10.1038/nmeth.4627

• Network propagation: a universal amplifier of genetic associations

  Nature Reviews Genetics · 2017 · https://doi.org/10.1038/nrg.2017.38

• Simultaneous Identification of Multiple Driver Pathways in Cancer

  PLoS Computational Biology · 2013 · https://doi.org/10.1371/journal.pcbi.1003054

• INDI: a computational framework for inferring drug interactions and their associated recommendations

  Molecular Systems Biology · 2012 · https://doi.org/10.1038/msb.2012.26

• Competitive and cooperative metabolic interactions in bacterial communities

  Nature Communications · 2011 · https://doi.org/10.1038/ncomms1597

• PREDICT: a method for inferring novel drug indications with application to personalized medicine

  Molecular Systems Biology · 2011 · https://doi.org/10.1038/msb.2011.26

• Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect

  PLoS Computational Biology · 2011 · https://doi.org/10.1371/journal.pcbi.1002018

• Associating Genes and Protein Complexes with Disease via Network Propagation

  PLoS Computational Biology · 2010 · https://doi.org/10.1371/journal.pcbi.1000641

• The large-scale organization of the bacterial network of ecological co-occurrence interactions

  Nucleic Acids Research · 2010 · https://doi.org/10.1093/nar/gkq118

• Expander: from expression microarrays to networks and functions

  Nature Protocols · 2010 · https://doi.org/10.1038/nprot.2009.230

• Protein networks in disease

  Genome Research · 2008 · https://doi.org/10.1101/gr.071852.107

• A genome‐scale computational study of the interplay between transcriptional regulation and metabolism

  Molecular Systems Biology · 2007 · https://doi.org/10.1038/msb4100141

• Network‐based prediction of protein function

  Molecular Systems Biology · 2007 · https://doi.org/10.1038/msb4100129

• Modeling cellular machinery through biological network comparison

  Nature Biotechnology · 2006 · https://doi.org/10.1038/nbt1196

• Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks

  Journal of Computational Biology · 2006 · https://doi.org/10.1089/cmb.2006.13.133

• Conserved patterns of protein interaction in multiple species

  Proceedings of the National Academy of Sciences · 2005 · 10.1073/pnas.0409522102

• EXPANDER – an integrative program suite for microarray data analysis

  BMC Bioinformatics · 2005 · https://doi.org/10.1186/1471-2105-6-232

• An initial blueprint for myogenic differentiation

  Genes & Development · 2005 · https://doi.org/10.1101/gad.1281105

• Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data

  Proceedings of the National Academy of Sciences · 2004 · https://doi.org/10.1073/pnas.0308661100

• PathBLAST: a tool for alignment of protein interaction networks

  Nucleic Acids Research · 2004 · https://doi.org/10.1093/nar/gkh411

• Cluster graph modification problems

  Discrete Applied Mathematics · 2004 · https://doi.org/10.1016/j.dam.2004.01.007

• Conserved pathways within bacteria and yeast as revealed by global protein network alignment

  Proceedings of the National Academy of Sciences · 2003 · https://doi.org/10.1073/pnas.1534710100

• Genome-Wide In Silico Identification of Transcriptional Regulators Controlling the Cell Cycle in Human Cells

  Genome Research · 2003 · https://doi.org/10.1101/gr.947203

• CLICK and EXPANDER: a system for clustering and visualizing gene expression data

  Bioinformatics · 2003 · https://doi.org/10.1093/bioinformatics/btg232

• Discovering statistically significant biclusters in gene expression data

  Bioinformatics · 2002 · https://doi.org/10.1093/bioinformatics/18.suppl_1.s136

• CLICK: a clustering algorithm with applications to gene expression analysis.

  PubMed · 2000

Current projects

No projects listed.