Anne E Carpenter

Summary

Publications

  1. pmc Screening cellular feature measurements for image-based assay development
    David J Logan
    Imaging Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
    J Biomol Screen 15:840-6. 2010
  2. pmc A call for bioimaging software usability
    Anne E Carpenter
    Imaging Platform, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
    Nat Methods 9:666-70. 2012
  3. pmc Workflow and metrics for image quality control in large-scale high-content screens
    Mark Anthony Bray
    Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
    J Biomol Screen 17:266-74. 2012
  4. pmc Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning
    Thouis R Jones
    The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 106:1826-31. 2009
  5. pmc CellProfiler Analyst: data exploration and analysis software for complex image-based screens
    Thouis R Jones
    Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    BMC Bioinformatics 9:482. 2008
  6. pmc Genome-scale RNAi on living-cell microarrays identifies novel regulators of Drosophila melanogaster TORC1-S6K pathway signaling
    Robert A Lindquist
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Genome Res 21:433-46. 2011
  7. pmc Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software
    Lee Kamentsky
    Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
    Bioinformatics 27:1179-80. 2011
  8. pmc Small molecules discovered in a pathway screen target the Rho pathway in cytokinesis
    Adam B Castoreno
    Dana Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
    Nat Chem Biol 6:457-63. 2010
  9. pmc High- and low-throughput scoring of fat mass and body fat distribution in C. elegans
    Carolina Wählby
    Centre for Image Analysis and Science for Life Laboratory, Uppsala University, Uppsala, Sweden Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA Electronic address
    Methods 68:492-9. 2014
  10. doi request reprint Extracting rich information from images
    Anne E Carpenter
    Imaging Platform, Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA, 02142, USA
    Methods Mol Biol 486:193-211. 2009

Research Grants

Collaborators

Detail Information

Publications30

  1. pmc Screening cellular feature measurements for image-based assay development
    David J Logan
    Imaging Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
    J Biomol Screen 15:840-6. 2010
    ..The authors present the resulting assay quality measures as a baseline for future algorithm comparisons, and all software, methods, and images they present are freely available...
  2. pmc A call for bioimaging software usability
    Anne E Carpenter
    Imaging Platform, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
    Nat Methods 9:666-70. 2012
    ..We suggest that, to maximize both the public's and researchers' investments, usability should be a more highly valued goal. We describe specific characteristics of usability toward which bioimaging software projects should aim...
  3. pmc Workflow and metrics for image quality control in large-scale high-content screens
    Mark Anthony Bray
    Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
    J Biomol Screen 17:266-74. 2012
    ..They have implemented these as a versatile, open-source toolbox of algorithms and metrics readily usable by biologists to improve data quality in a wide variety of biological experiments...
  4. pmc Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning
    Thouis R Jones
    The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 106:1826-31. 2009
    ..By using this approach, we successfully scored images in RNA interference screens in 2 organisms for the prevalence of 15 diverse cellular morphologies, some of which were previously intractable...
  5. pmc CellProfiler Analyst: data exploration and analysis software for complex image-based screens
    Thouis R Jones
    Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    BMC Bioinformatics 9:482. 2008
    ..Image-based screens can produce hundreds of measured features for each of hundreds of millions of individual cells in a single experiment...
  6. pmc Genome-scale RNAi on living-cell microarrays identifies novel regulators of Drosophila melanogaster TORC1-S6K pathway signaling
    Robert A Lindquist
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Genome Res 21:433-46. 2011
    ..We conclude that cell-based microarrays are a useful platform for genome-scale and secondary screening in Drosophila, revealing regulators that may represent drug targets for cancers and other diseases of deregulated TORC1 signaling...
  7. pmc Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software
    Lee Kamentsky
    Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
    Bioinformatics 27:1179-80. 2011
    ..It is more robust and user friendly, with new algorithms and features to facilitate high-throughput work. ImageJ plugins can now be run within a CellProfiler pipeline...
  8. pmc Small molecules discovered in a pathway screen target the Rho pathway in cytokinesis
    Adam B Castoreno
    Dana Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
    Nat Chem Biol 6:457-63. 2010
    ..Rhodblocks differentially perturb Rho pathway proteins in cells and can be used to dissect the mechanism of the Rho pathway during cytokinesis...
  9. pmc High- and low-throughput scoring of fat mass and body fat distribution in C. elegans
    Carolina Wählby
    Centre for Image Analysis and Science for Life Laboratory, Uppsala University, Uppsala, Sweden Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA Electronic address
    Methods 68:492-9. 2014
    ..Thus we present a feasible approach to small-scale phenotyping and large-scale screening for genetic and/or chemical perturbations that lead to alterations in fat quantity and distribution in whole animals. ..
  10. doi request reprint Extracting rich information from images
    Anne E Carpenter
    Imaging Platform, Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA, 02142, USA
    Methods Mol Biol 486:193-211. 2009
    ..We use as an example publicly available images from a cytoplasm-to-nucleus translocation assay...
  11. pmc Identification of small molecules for human hepatocyte expansion and iPS differentiation
    Jing Shan
    Harvard Massachusetts Institute of Technology Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts, USA
    Nat Chem Biol 9:514-20. 2013
    ..The identification of these small molecules can help address a major challenge affecting many facets of liver research and may lead to the development of new therapeutics for liver diseases. ..
  12. ncbi request reprint Image-based chemical screening
    Anne E Carpenter
    Broad Institute Imaging Platform, 7 Cambridge Center, Room 6011, Cambridge, Massachusetts 02142, USA
    Nat Chem Biol 3:461-5. 2007
    ..In this Perspective, I highlight the key steps necessary for conducting a high-throughput image-based chemical compound screen...
  13. ncbi request reprint CellProfiler: free, versatile software for automated biological image analysis
    Michael R Lamprecht
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Biotechniques 42:71-5. 2007
    ....
  14. pmc An image analysis toolbox for high-throughput C. elegans assays
    Carolina Wählby
    Imaging Platform, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
    Nat Methods 9:714-6. 2012
    ..elegans for the study of diverse biological pathways that are relevant to human disease...
  15. doi request reprint Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution
    Bjorn Nilsson
    Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
    Bioinformatics 25:1078-9. 2009
    ..However, the data generated by these arrays are several-fold larger than data from earlier platforms, creating a need for efficient analysis tools that scale robustly with data size...
  16. pmc CellProfiler: image analysis software for identifying and quantifying cell phenotypes
    Anne E Carpenter
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Genome Biol 7:R100. 2006
    ....
  17. pmc Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment
    Vebjorn Ljosa
    1Broad Institute of MIT and Harvard, Cambridge, MA, USA
    J Biomol Screen 18:1321-9. 2013
    ....
  18. pmc The bromodomain protein Brd4 insulates chromatin from DNA damage signalling
    Scott R Floyd
    Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Nature 498:246-50. 2013
    ..These data implicate Brd4, previously known for its role in transcriptional control, as an insulator of chromatin that can modulate the signalling response to DNA damage...
  19. pmc High content image analysis identifies novel regulators of synaptogenesis in a high-throughput RNAi screen of primary neurons
    Thomas J F Nieland
    Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
    PLoS ONE 9:e91744. 2014
    ..This methodology is broadly applicable for high-throughput screening of genes and drugs that may rescue or improve synaptic dysfunction associated with cognitive function and neurological disorders. ..
  20. ncbi request reprint A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen
    Jason Moffat
    Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
    Cell 124:1283-98. 2006
    ..This work provides a widely applicable resource for loss-of-function screens, as well as a roadmap for its application to biological discovery...
  21. doi request reprint Using CellProfiler for automatic identification and measurement of biological objects in images
    Martha S Vokes
    Broad Institute Imaging Platform, Cambridge, Massachusetts, USA
    Curr Protoc Mol Biol . 2008
    ..The flexibility of the software allows users to tailor pipelines of adjustable modules to fit different biological experiments, to generate accurate measurements from dozens or even hundreds of thousands of images...
  22. pmc mTOR complex 1 regulates lipin 1 localization to control the SREBP pathway
    Timothy R Peterson
    Whitehead Institute for Biomedical Research, Koch Center for Integrative Cancer Research at MIT, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
    Cell 146:408-20. 2011
    ..These findings establish lipin 1 as a key component of the mTORC1-SREBP pathway...
  23. ncbi request reprint Microarrays of lentiviruses for gene function screens in immortalized and primary cells
    Steve N Bailey
    Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology Department of Biology, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Methods 3:117-22. 2006
    ..Because lentiviruses have a wide cellular tropism, including primary cells, lentivirus-infected cell microarrays can be used as a platform for high-throughput screening in a variety of cell types...
  24. pmc The Spemann organizer gene, Goosecoid, promotes tumor metastasis
    Kimberly A Hartwell
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 103:18969-74. 2006
    ..These results demonstrate that Goosecoid promotes tumor cell malignancy and suggest that other conserved organizer genes may function similarly in human cancer...
  25. pmc Niche-based screening identifies small-molecule inhibitors of leukemia stem cells
    Kimberly A Hartwell
    1 Broad Institute, Cambridge, Massachusetts, USA 2 Department of Medicine, Division of Hematology, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts, USA 3 Harvard Medical School, Boston, Massachusetts, USA 4
    Nat Chem Biol 9:840-8. 2013
    ..Mechanistic studies demonstrated that the effect was on target, via inhibition of HMG-CoA reductase. These results illustrate the power of merging physiologically relevant models with high-throughput screening. ..
  26. pmc Identification of host-targeted small molecules that restrict intracellular Mycobacterium tuberculosis growth
    Sarah A Stanley
    The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
    PLoS Pathog 10:e1003946. 2014
    ..Given the existing experience with some of our identified compounds for other therapeutic indications, further clinically-directed study of these compounds is merited. ..
  27. pmc Multiplex cytological profiling assay to measure diverse cellular states
    Sigrun M Gustafsdottir
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
    PLoS ONE 8:e80999. 2013
    ..This image-based assay provides an unbiased approach to characterize compound- and disease-associated cell states to support future probe discovery...
  28. pmc A microscale human liver platform that supports the hepatic stages of Plasmodium falciparum and vivax
    Sandra March
    Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Cell Host Microbe 14:104-15. 2013
    ..vivax. Finally, we validate the potential of this platform as a tool for medium-throughput antimalarial drug screening and vaccine development. ..
  29. pmc A chemical screen probing the relationship between mitochondrial content and cell size
    Toshimori Kitami
    Broad Institute, Cambridge, Massachusetts, United States of America
    PLoS ONE 7:e33755. 2012
    ..At present the molecular target of BRD6897 remains to be elucidated, but if identified, could reveal an important additional mechanism that governs mitochondrial biogenesis and turnover...

Research Grants1

  1. Continued development of CellProfiler cell image analysis software
    Anne E Carpenter; Fiscal Year: 2010
    ..public health relevance: ..