James Hicks

Summary

Affiliation: Cold Spring Harbor Laboratory
Country: USA

Publications

  1. pmc Future medical applications of single-cell sequencing in cancer
    Nicholas Navin
    Department of Genetics, MD Anderson Cancer Center, Houston, TX 77030, USA
    Genome Med 3:31. 2011
  2. pmc Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors
    L O Baumbusch
    Department of Genetics, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, 0310 Oslo, Norway
    BMC Genomics 9:379. 2008
  3. pmc Novel patterns of genome rearrangement and their association with survival in breast cancer
    James Hicks
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 16:1465-79. 2006
  4. doi request reprint Tumour evolution inferred by single-cell sequencing
    Nicholas Navin
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Nature 472:90-4. 2011
  5. pmc Strong association of de novo copy number mutations with autism
    Jonathan Sebat
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Science 316:445-9. 2007
  6. pmc Inferring tumor progression from genomic heterogeneity
    Nicholas Navin
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 20:68-80. 2010
  7. pmc Tracing the tumor lineage
    Nicholas E Navin
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Mol Oncol 4:267-83. 2010
  8. doi request reprint Genome-wide copy number analysis of single cells
    Timour Baslan
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    Nat Protoc 7:1024-41. 2012
  9. pmc A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions
    Wen Xue
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Proc Natl Acad Sci U S A 109:8212-7. 2012
  10. pmc Functional identification of tumor-suppressor genes through an in vivo RNA interference screen in a mouse lymphoma model
    Anka Bric
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Cancer Cell 16:324-35. 2009

Collaborators

Detail Information

Publications14

  1. pmc Future medical applications of single-cell sequencing in cancer
    Nicholas Navin
    Department of Genetics, MD Anderson Cancer Center, Houston, TX 77030, USA
    Genome Med 3:31. 2011
    ..In this review we discuss the challenges and technical aspects of single-cell sequencing, with a strong focus on genomic copy number, and discuss how this information can be used to diagnose and treat cancer patients...
  2. pmc Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors
    L O Baumbusch
    Department of Genetics, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, 0310 Oslo, Norway
    BMC Genomics 9:379. 2008
    ..Various platforms, brands and underlying technologies are available, facing the user with many choices regarding platform sensitivity and number, localization, and density distribution of probes...
  3. pmc Novel patterns of genome rearrangement and their association with survival in breast cancer
    James Hicks
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 16:1465-79. 2006
    ....
  4. doi request reprint Tumour evolution inferred by single-cell sequencing
    Nicholas Navin
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Nature 472:90-4. 2011
    ..In contrast to gradual models of tumour progression, our data indicate that tumours grow by punctuated clonal expansions with few persistent intermediates...
  5. pmc Strong association of de novo copy number mutations with autism
    Jonathan Sebat
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Science 316:445-9. 2007
    ..Affected genomic regions were highly heterogeneous and included mutations of single genes. These findings establish de novo germline mutation as a more significant risk factor for ASD than previously recognized...
  6. pmc Inferring tumor progression from genomic heterogeneity
    Nicholas Navin
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Genome Res 20:68-80. 2010
    ..By comparing multiple subpopulations from different anatomic locations, we have inferred pathways of cancer progression and the organization of tumor growth...
  7. pmc Tracing the tumor lineage
    Nicholas E Navin
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Mol Oncol 4:267-83. 2010
    ..Finally, we discuss how recent technical advances in single cell genomics will herald a new era in understanding the fundamental basis of tumor heterogeneity and progression...
  8. doi request reprint Genome-wide copy number analysis of single cells
    Timour Baslan
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    Nat Protoc 7:1024-41. 2012
    ..All together, the protocol takes ∼3 d from flow cytometry to sequence-ready DNA libraries...
  9. pmc A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions
    Wen Xue
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Proc Natl Acad Sci U S A 109:8212-7. 2012
    ..Our data imply that large cancer-associated deletions can produce phenotypes distinct from those arising through loss of a single TSG, and as such should be considered and studied as distinct mutational events...
  10. pmc Functional identification of tumor-suppressor genes through an in vivo RNA interference screen in a mouse lymphoma model
    Anka Bric
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Cancer Cell 16:324-35. 2009
    ..Our results emphasize the utility of in vivo RNAi screens, identify and validate a diverse set of tumor suppressors, and have therapeutic implications...
  11. ncbi request reprint Large-scale copy number polymorphism in the human genome
    Jonathan Sebat
    Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
    Science 305:525-8. 2004
    ..We observed copy number variation of 70 different genes within CNP intervals, including genes involved in neurological function, regulation of cell growth, regulation of metabolism, and several genes known to be associated with disease...
  12. pmc DDX5 regulates DNA replication and is required for cell proliferation in a subset of breast cancer cells
    Anthony Mazurek
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Cancer Discov 2:812-25. 2012
    ....
  13. pmc An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer
    Lars Zender
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    Cell 135:852-64. 2008
    ..Our results establish the feasibility of in vivo RNAi screens and illustrate how combining cancer genomics, RNA interference, and mosaic mouse models can facilitate the functional annotation of the cancer genome...
  14. pmc Identification of alterations in DNA copy number in host stromal cells during tumor progression
    Robert J Pelham
    Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 103:19848-53. 2006
    ..We show that numerous amplifications and deletions are found within the host stromal microenvironment, suggesting that alterations in host DNA copy number can occur and may play a significant role in modifying tumor-stromal interactions...