Frank Alber

Summary

Affiliation: University of Southern California
Country: USA

Publications

  1. pmc High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization
    Min Xu
    Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
    BMC Syst Biol 6:S18. 2012
  2. doi request reprint Integrating diverse data for structure determination of macromolecular assemblies
    Frank Alber
    Department of Biopharmaceutical Sciences, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158 2330, USA
    Annu Rev Biochem 77:443-77. 2008
  3. ncbi request reprint The molecular architecture of the nuclear pore complex
    Frank Alber
    Department of Bioengineering and Therapeutic Sciences, and California Institute for Quantitative Biosciences, Mission Bay QB3, 1700 4th Street, Suite 503B, University of California at San Francisco, San Francisco, California 94158 2330, USA
    Nature 450:695-701. 2007
  4. pmc Simple fold composition and modular architecture of the nuclear pore complex
    Damien Devos
    Department of Biopharmaceutical Sciences, University of California, Mission Bay QB3, 1700 4th Street, Suite 503B, San Francisco, CA 94143 2552, USA
    Proc Natl Acad Sci U S A 103:2172-7. 2006
  5. ncbi request reprint Determining the architectures of macromolecular assemblies
    Frank Alber
    Department of Bioengineering and Therapeutic Sciences, and California Institute for Quantitative Biosciences, Byers Hall, Suite 503B, 1700 4th Street, University of California at San Francisco, San Francisco, California 94158 2330, USA
    Nature 450:683-94. 2007
  6. pmc Physical tethering and volume exclusion determine higher-order genome organization in budding yeast
    Harianto Tjong
    Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    Genome Res 22:1295-305. 2012
  7. doi request reprint High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching
    Min Xu
    Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
    J Struct Biol 178:152-64. 2012
  8. pmc A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps
    Shihua Zhang
    Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
    Bioinformatics 26:i261-8. 2010
  9. pmc Components of coated vesicles and nuclear pore complexes share a common molecular architecture
    Damien Devos
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, University of California, San Francisco, USA
    PLoS Biol 2:e380. 2004
  10. pmc A computational approach to increase time scales in Brownian dynamics-based reaction-diffusion modeling
    Zachary Frazier
    Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
    J Comput Biol 19:606-18. 2012

Collaborators

Detail Information

Publications14

  1. pmc High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization
    Min Xu
    Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
    BMC Syst Biol 6:S18. 2012
    ..Existing methods for obtaining the optimal alignments are mostly based on an exhaustive scanning of all but discrete relative rigid transformations (i.e. rotations and translations) of one subtomogram with respect to the other...
  2. doi request reprint Integrating diverse data for structure determination of macromolecular assemblies
    Frank Alber
    Department of Biopharmaceutical Sciences, and California Institute for Quantitative Biosciences, University of California at San Francisco, CA 94158 2330, USA
    Annu Rev Biochem 77:443-77. 2008
    ..With these tools, we are poised to integrate structural information gathered at multiple levels of the biological hierarchy--from atoms to cells--into a common framework...
  3. ncbi request reprint The molecular architecture of the nuclear pore complex
    Frank Alber
    Department of Bioengineering and Therapeutic Sciences, and California Institute for Quantitative Biosciences, Mission Bay QB3, 1700 4th Street, Suite 503B, University of California at San Francisco, San Francisco, California 94158 2330, USA
    Nature 450:695-701. 2007
    ..These findings provide clues to the evolutionary origins of the NPC...
  4. pmc Simple fold composition and modular architecture of the nuclear pore complex
    Damien Devos
    Department of Biopharmaceutical Sciences, University of California, Mission Bay QB3, 1700 4th Street, Suite 503B, San Francisco, CA 94143 2552, USA
    Proc Natl Acad Sci U S A 103:2172-7. 2006
    ..The small number of predicted fold types in the NPC and their internal symmetries suggest that the bulk of the NPC structure has evolved through extensive motif and gene duplication from a simple precursor set of only a few proteins...
  5. ncbi request reprint Determining the architectures of macromolecular assemblies
    Frank Alber
    Department of Bioengineering and Therapeutic Sciences, and California Institute for Quantitative Biosciences, Byers Hall, Suite 503B, 1700 4th Street, University of California at San Francisco, San Francisco, California 94158 2330, USA
    Nature 450:683-94. 2007
    ..The present approach should be applicable to many other macromolecular assemblies...
  6. pmc Physical tethering and volume exclusion determine higher-order genome organization in budding yeast
    Harianto Tjong
    Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
    Genome Res 22:1295-305. 2012
    ....
  7. doi request reprint High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching
    Min Xu
    Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
    J Struct Biol 178:152-64. 2012
    ..As a proof of principle, we can demonstrate that the automatic method can successfully classify a large number of experimental subtomograms without the need of a reference structure...
  8. pmc A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps
    Shihua Zhang
    Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
    Bioinformatics 26:i261-8. 2010
    ..Optimizing the quality-of-fit of all components simultaneously is challenging due to the large search space that makes the exhaustive search over all possible component configurations computationally unfeasible...
  9. pmc Components of coated vesicles and nuclear pore complexes share a common molecular architecture
    Damien Devos
    Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, University of California, San Francisco, USA
    PLoS Biol 2:e380. 2004
    ..These similarities suggest a common evolutionary origin for nuclear pore complexes and coated vesicles in an early membrane-curving module that led to the formation of the internal membrane systems in modern eukaryotes...
  10. pmc A computational approach to increase time scales in Brownian dynamics-based reaction-diffusion modeling
    Zachary Frazier
    Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
    J Comput Biol 19:606-18. 2012
    ..We can show that for reaction-diffusion processes of particles mimicking proteins, the method can increase the typical BD time step by an order of magnitude while maintaining similar accuracy in the reaction diffusion modelling...
  11. pmc Template-free detection of macromolecular complexes in cryo electron tomograms
    Min Xu
    Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
    Bioinformatics 27:i69-76. 2011
    ..It is, therefore, of great importance to develop template-free methods for the discovery of previously unknown protein complexes in cryo electron tomograms...
  12. pmc Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms
    Min Xu
    University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA
    Bioinformatics 29:i274-82. 2013
    ..However, alignment methods generally assume that each subtomogram only contains one complex. Automatic methods are needed to identify the target complexes in a subtomogram even when its shape is unknown...
  13. pmc Genome architectures revealed by tethered chromosome conformation capture and population-based modeling
    Reza Kalhor
    Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
    Nat Biotechnol 30:90-8. 2012
    ..Statistical analysis of the resulting population demonstrates that the indiscriminate properties of interchromosomal interactions are consistent with the well-known architectural features of the human genome...
  14. ncbi request reprint A structural perspective on protein-protein interactions
    Robert B Russell
    EMBL, Heidelberg, Germany
    Curr Opin Struct Biol 14:313-24. 2004
    ..Recent advances and applications of these methods emphasize the need for hybrid approaches that combine a variety of data to achieve better efficiency, accuracy, resolution and completeness...