Anshul Kundaje

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements
    Anshul Kundaje
    Department of Computer Science, Stanford University, Stanford, California 94305, USA
    Genome Res 22:1735-47. 2012
  2. pmc Modeling gene expression using chromatin features in various cellular contexts
    Xianjun Dong
    Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Genome Biol 13:R53. 2012
  3. pmc Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
    Kevin Y Yip
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Genome Biol 13:R48. 2012
  4. ncbi request reprint Learning regulatory programs that accurately predict differential expression with MEDUSA
    Anshul Kundaje
    Department of Computer Science, Center for Computational Learning Systems, Columbia University, New York, NY 10065, USA
    Ann N Y Acad Sci 1115:178-202. 2007
  5. pmc Extensive variation in chromatin states across humans
    Maya Kasowski
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Science 342:750-2. 2013
  6. ncbi request reprint Combining sequence and time series expression data to learn transcriptional modules
    Anshul Kundaje
    Department of Computer Science, Columbia University, New York 10027, USA
    IEEE/ACM Trans Comput Biol Bioinform 2:194-202. 2005
  7. pmc Linking disease associations with regulatory information in the human genome
    Marc A Schaub
    Department of Computer Science, Stanford University, Stanford, California 94305, USA
    Genome Res 22:1748-59. 2012
  8. pmc STAT3 targets suggest mechanisms of aggressive tumorigenesis in diffuse large B-cell lymphoma
    Jennifer Hardee
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305
    G3 (Bethesda) 3:2173-85. 2013
  9. pmc ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
    Stephen G Landt
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genome Res 22:1813-31. 2012
  10. pmc Principles of regulatory information conservation between mouse and human
    Yong Cheng
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Nature 515:371-5. 2014

Collaborators

Detail Information

Publications13

  1. pmc Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements
    Anshul Kundaje
    Department of Computer Science, Stanford University, Stanford, California 94305, USA
    Genome Res 22:1735-47. 2012
    ..Meta-analyses of the signal profiles revealed a common vocabulary of chromatin signals shared across multiple cell lines and binding proteins...
  2. pmc Modeling gene expression using chromatin features in various cellular contexts
    Xianjun Dong
    Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Genome Biol 13:R53. 2012
    ..ENCODE also generated the genome-wide mapping of eleven histone marks, one histone variant, and DNase I hypersensitivity sites in seven cell lines...
  3. pmc Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
    Kevin Y Yip
    Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
    Genome Biol 13:R48. 2012
    ..While this large amount of data creates a valuable resource, it is nonetheless overwhelmingly complex and simultaneously incomplete since it covers only a small fraction of all human transcription factors...
  4. ncbi request reprint Learning regulatory programs that accurately predict differential expression with MEDUSA
    Anshul Kundaje
    Department of Computer Science, Center for Computational Learning Systems, Columbia University, New York, NY 10065, USA
    Ann N Y Acad Sci 1115:178-202. 2007
    ..With MEDUSA, statistical validation becomes a prerequisite for hypothesis generation and network building rather than a secondary consideration...
  5. pmc Extensive variation in chromatin states across humans
    Maya Kasowski
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Science 342:750-2. 2013
    ..Overall, our results provide insights into chromatin variation among humans. ..
  6. ncbi request reprint Combining sequence and time series expression data to learn transcriptional modules
    Anshul Kundaje
    Department of Computer Science, Columbia University, New York 10027, USA
    IEEE/ACM Trans Comput Biol Bioinform 2:194-202. 2005
    ....
  7. pmc Linking disease associations with regulatory information in the human genome
    Marc A Schaub
    Department of Computer Science, Stanford University, Stanford, California 94305, USA
    Genome Res 22:1748-59. 2012
    ..Our results show that the experimental data sets generated by the ENCODE Consortium can be successfully used to suggest functional hypotheses for variants associated with diseases and other phenotypes...
  8. pmc STAT3 targets suggest mechanisms of aggressive tumorigenesis in diffuse large B-cell lymphoma
    Jennifer Hardee
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305
    G3 (Bethesda) 3:2173-85. 2013
    ..Novel treatments aimed at these pathways may increase the survivability of activated B-cell-like diffuse large B-cell lymphoma. ..
  9. pmc ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
    Stephen G Landt
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genome Res 22:1813-31. 2012
    ..All data sets used in the analysis have been deposited for public viewing and downloading at the ENCODE (http://encodeproject.org/ENCODE/) and modENCODE (http://www.modencode.org/) portals...
  10. pmc Principles of regulatory information conservation between mouse and human
    Yong Cheng
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Nature 515:371-5. 2014
    ..Single nucleotide variants at sites with potential regulatory functions are enriched in occupancy-conserved TF-occupied sequences. ..
  11. pmc Comparative analysis of regulatory information and circuits across distant species
    Alan P Boyle
    1 Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA 2
    Nature 512:453-6. 2014
    ..The comparative maps of regulatory circuitry provided here will drive an improved understanding of the regulatory underpinnings of model organism biology and how these relate to human biology, development and disease. ..
  12. doi request reprint Integrative analysis of 111 reference human epigenomes
    Anshul Kundaje
    1 Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA 2 The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA 3 Department of Genetics, Department of Computer Science, 300 Pasteur Dr, Lane Building, L301, Stanford, California 94305 5120, USA
    Nature 518:317-30. 2015
    ..Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease. ..
  13. pmc A classification-based framework for predicting and analyzing gene regulatory response
    Anshul Kundaje
    Department of Computer Science, Columbia University, New York, NY 10027, USA
    BMC Bioinformatics 7:S5. 2006
    ..Using the Adaboost algorithm, GeneClass learns a prediction function in the form of an alternating decision tree, a margin-based generalization of a decision tree...