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    Hamann, Bernd

    TitleComputer Scientist Faculty
    SchoolLawrence Berkeley National Lab
    DepartmentComputational Research
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/486-6135
    vCardDownload vCard

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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Gimenez AA, Gamblin T, Jusufi I, Bhatele A, Schulz M, Bremer PT, Hamann B. MemAxes: Visualization and Analytics for Characterizing Complex Memory Performance Behaviors. IEEE Trans Vis Comput Graph. 2017 Jun 22. PMID: 28650817.
        View in: PubMed
      2. Murugesan S, Bouchard K, Chang E, Dougherty M, Hamann B, Weber GH. Multi-scale visual analysis of time-varying electrocorticography data via clustering of brain regions. BMC Bioinformatics. 2017 Jun 06; 18(Suppl 6):236. PMID: 28617218.
        View in: PubMed
      3. Borges V, Ferreira de Oliveira MC, Silva T, Vieira A, Hamann B. Region Growing for Segmenting Green Microalgae Images. IEEE/ACM Trans Comput Biol Bioinform. 2016 Oct 06. PMID: 27723599.
        View in: PubMed
      4. Murugesan S, Bouchard K, Brown JA, Hamann B, Seeley WW, Trujillo A, Weber GH. Brain Modulyzer: Interactive Visual Analysis of Functional Brain Connectivity. IEEE/ACM Trans Comput Biol Bioinform. 2016 May 09. PMID: 27244747.
        View in: PubMed
      5. Murugesan S, Bouchard K, Brown JA, Hamann B, Seeley WW, Trujillo A, Weber GH. Brain Modulyzer: Interactive Visual Analysis of Functional Brain Connectivity. IEEE/ACM Trans Comput Biol Bioinform. 2016 May 09. PMID: 28113724.
        View in: PubMed
      6. Isaacs KE, Bremer PT, Jusufi I, Gamblin T, Bhatele A, Schulz M, Hamann B. Combing the Communication Hairball: Visualizing Parallel Execution Traces using Logical Time. IEEE Trans Vis Comput Graph. 2014 Dec; 20(12):2349-58. PMID: 26356949.
        View in: PubMed
      7. Zawadzki RJ, Capps AG, Kim DY, Panorgias A, Stevenson SB, Hamann B, Werner JS. Progress on Developing Adaptive Optics-Optical Coherence Tomography for In Vivo Retinal Imaging: Monitoring and Correction of Eye Motion Artifacts. IEEE J Sel Top Quantum Electron. 2014 Mar; 20(2). PMID: 25544826.
        View in: PubMed
      8. Shafii S, Obermaier H, Linn R, Koo E, Hlawitschka M, Garth C, Hamann B, Joy KI. Visualization and analysis of vortex-turbine intersections in wind farms. IEEE Trans Vis Comput Graph. 2013 Sep; 19(9):1579-91. PMID: 23846101.
        View in: PubMed
      9. Shafii S, Obermaier H, Linn R, Koo E, Hlawitschka M, Garth C, Hamann B, Joy K. Visualization and Analysis of Vortex-Turbine Intersections in Wind Farms. IEEE Trans Vis Comput Graph. 2013 Feb 13. PMID: 23420226.
        View in: PubMed
      10. Westerteiger R, Compton T, Bernadin T, Cowgill E, Gwinner K, Hamann B, Gerndt A, Hagen H. Interactive Retro-Deformation of Terrain for Reconstructing 3D Fault Displacements. IEEE Trans Vis Comput Graph. 2012 Dec; 18(12):2208-15. PMID: 26357128.
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      11. Engel D, Greff K, Garth C, Bein K, Wexler A, Hamann B, Hagen H. Visual Steering and Verification of Mass Spectrometry Data Factorization in Air Quality Research. IEEE Trans Vis Comput Graph. 2012 Dec; 18(12):2275-84. PMID: 26357135.
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      12. Williams S, Petersen M, Bremer PT, Hecht M, Pascucci V, Ahrens J, Hlawitschka M, Hamann B. Adaptive extraction and quantification of geophysical vortices. IEEE Trans Vis Comput Graph. 2011 Dec; 17(12):2088-95. PMID: 22034327.
        View in: PubMed
      13. Stevens EW, Sumner DY, Harwood CL, Crutchfield JP, Hamann B, Kreylos O, Puckett E, Senge P. Understanding microbialite morphology using a comprehensive suite of three-dimensional analysis tools. Astrobiology. 2011 Jul-Aug; 11(6):509-18. PMID: 21740150.
        View in: PubMed
      14. Shafii S, Dillard SE, Hlawitschka M, Hamann B. The Topological Effects of Smoothing. IEEE Trans Vis Comput Graph. 2012 Jan; 18(1):160-72. PMID: 21519107.
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      15. Hummel M, Garth C, Hamann B, Hagen H, Joy KI. IRIS: illustrative rendering for integral surfaces. IEEE Trans Vis Comput Graph. 2010 Nov-Dec; 16(6):1319-28. PMID: 20975172.
        View in: PubMed
      16. Rübel O, Ahern S, Bethel EW, Biggin MD, Childs H, Cormier-Michel E, Depace A, Eisen MB, Fowlkes CC, Geddes CG, Hagen H, Hamann B, Huang MY, Keränen SV, Knowles DW, Hendriks CL, Malik J, Meredith J, Messmer P. Coupling visualization and data analysis for knowledge discovery from multi-dimensional scientific data. Procedia Comput Sci. 2010 May; 1(1):1757-1764. PMID: 23762211.
        View in: PubMed
      17. Rübel O, Weber GH, Huang MY, Bethel EW, Biggin MD, Fowlkes CC, Luengo Hendriks CL, Keränen SV, Eisen MB, Knowles DW, Malik J, Hagen H, Hamann B. Integrating data clustering and visualization for the analysis of 3D gene expression data. IEEE/ACM Trans Comput Biol Bioinform. 2010 Jan-Mar; 7(1):64-79. PMID: 20150669.
        View in: PubMed
      18. Hlawitschka M, Garth C, Tricoche X, Kindlmann G, Scheuermann G, Joy KI, Hamann B. Direct visualization of fiber information by coherence. Int J Comput Assist Radiol Surg. 2010 Mar; 5(2):125-31. PMID: 20033521.
        View in: PubMed
      19. Weber GH, Rübel O, Huang MY, DePace AH, Fowlkes CC, Keränen SV, Luengo Hendriks CL, Hagen H, Knowles DW, Malik J, Biggin MD, Hamann B. Visual exploration of three-dimensional gene expression using physical views and linked abstract views. IEEE/ACM Trans Comput Biol Bioinform. 2009 Apr-Jun; 6(2):296-309. PMID: 19407353.
        View in: PubMed
      20. Zawadzki RJ, Choi SS, Fuller AR, Evans JW, Hamann B, Werner JS. Cellular resolution volumetric in vivo retinal imaging with adaptive optics-optical coherence tomography. Opt Express. 2009 Mar 2; 17(5):4084-94. PMID: 19259248.
        View in: PubMed
      21. Gyulassy A, Bremer PT, Hamann B, Pascucci V. A practical approach to Morse-Smale complex computation: scalability and generality. IEEE Trans Vis Comput Graph. 2008 Nov-Dec; 14(6):1619-26. PMID: 18989018.
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      22. Fowlkes CC, Hendriks CL, Keränen SV, Weber GH, Rübel O, Huang MY, Chatoor S, DePace AH, Simirenko L, Henriquez C, Beaton A, Weiszmann R, Celniker S, Hamann B, Knowles DW, Biggin MD, Eisen MB, Malik J. A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell. 2008 Apr 18; 133(2):364-74. PMID: 18423206.
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      23. Feng L, Hotz I, Hamann B, Joy K. Anisotropic noise samples. IEEE Trans Vis Comput Graph. 2008 Mar-Apr; 14(2):342-54. PMID: 18192714.
        View in: PubMed
      24. Gyulassy A, Duchaineau M, Natarajan V, Pascucci V, Bringa E, Higginbotham A, Hamann B. Topologically clean distance fields. IEEE Trans Vis Comput Graph. 2007 Nov-Dec; 13(6):1432-9. PMID: 17968094.
        View in: PubMed
      25. Fuller A, Zawadzki R, Choi S, Wiley D, Werner J, Hamann B. Segmentation of three-dimensional retinal image data. IEEE Trans Vis Comput Graph. 2007 Nov-Dec; 13(6):1719-26. PMID: 17968130.
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      26. Schlemmer M, Heringer M, Morr F, Hotz I, Hering-Bertram M, Garth C, Kollmann W, Hamann B, Hagen H. Moment invariants for the analysis of 2D flow fields. IEEE Trans Vis Comput Graph. 2007 Nov-Dec; 13(6):1743-50. PMID: 17968133.
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      27. Gyulassy A, Natarajan V, Pascucci V, Hamann B. Efficient computation of Morse-Smale complexes for three-dimensional scalar functions. IEEE Trans Vis Comput Graph. 2007 Nov-Dec; 13(6):1440-7. PMID: 17968095.
        View in: PubMed
      28. Dillard S, Bingert J, Thoma D, Hamann B. Construction of simplified boundary surfaces from serial-sectioned metal micrographs. IEEE Trans Vis Comput Graph. 2007 Nov-Dec; 13(6):1528-35. PMID: 17968106.
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      29. Staadt OG, Natarajan V, Weber GH, Wiley DF, Hamann B. Interactive processing and visualization of image data for biomedical and life science applications. BMC Cell Biol. 2007; 8 Suppl 1:S10. PMID: 17634091.
        View in: PubMed
      30. Zawadzki RJ, Fuller AR, Wiley DF, Hamann B, Choi SS, Werner JS. Adaptation of a support vector machine algorithm for segmentation and visualization of retinal structures in volumetric optical coherence tomography data sets. J Biomed Opt. 2007 Jul-Aug; 12(4):041206. PMID: 17867795.
        View in: PubMed
      31. Weber GH, Dillard SE, Carr H, Pascucci V, Hamann B. Topology-controlled volume rendering. IEEE Trans Vis Comput Graph. 2007 Mar-Apr; 13(2):330-41. PMID: 17218749.
        View in: PubMed
      32. Samsioe G, Dvorak V, Genazzani AR, Hamann B, Heikkinen J, Mueck AO, Suzin J, Kawakami FT, Ferreira A, Sun D, Arguinzoniz M. One-year endometrial safety evaluation of a continuous combined transdermal matrix patch delivering low-dose estradiol-norethisterone acetate in postmenopausal women. Maturitas. 2007 Jun 20; 57(2):171-81. PMID: 17317046.
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      33. Gu S, Anderson I, Kunin V, Cipriano M, Minovitsky S, Weber G, Amenta N, Hamann B, Dubchak I. TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities. Bioinformatics. 2007 Mar 15; 23(6):764-6. PMID: 17234642.
        View in: PubMed
      34. Gyulassy A, Natarajan V, Pascucci V, Bremer PT, Society C, Hamann B. A topological approach to simplification of three-dimensional scalar functions. IEEE Trans Vis Comput Graph. 2006 Jul-Aug; 12(4):474-84. PMID: 16805257.
        View in: PubMed
      35. Park SW, Linsen L, Kreylos O, Owens JD, Hamann B. Discrete Sibson interpolation. IEEE Trans Vis Comput Graph. 2006 Mar-Apr; 12(2):243-53. PMID: 16509383.
        View in: PubMed
      36. Luengo Hendriks CL, Keränen SV, Fowlkes CC, Simirenko L, Weber GH, DePace AH, Henriquez C, Kaszuba DW, Hamann B, Eisen MB, Malik J, Sudar D, Biggin MD, Knowles DW. Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline. Genome Biol. 2006; 7(12):R123. PMID: 17184546.
        View in: PubMed
      37. Shah N, Teplitsky MV, Minovitsky S, Pennacchio LA, Hugenholtz P, Hamann B, Dubchak IL. SNP-VISTA: an interactive SNP visualization tool. BMC Bioinformatics. 2005; 6:292. PMID: 16336665.
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      38. Wiley DF, Bertram M, Hamann B. On a construction of a hierarchy of best linear spline approximations using a finite element approach. IEEE Trans Vis Comput Graph. 2004 Sep-Oct; 10(5):548-63. PMID: 15794137.
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      39. Bremer PT, Edelsbrunner H, Hamann B, Pascucci V. A topological hierarchy for functions on triangulated surfaces. IEEE Trans Vis Comput Graph. 2004 Jul-Aug; 10(4):385-96. PMID: 18579967.
        View in: PubMed
      40. Bertram M, Duchaineau MA, Hamann B, Joy KI. Generalized B-spline subdivision-surface wavelets for geometry compression. IEEE Trans Vis Comput Graph. 2004 May-Jun; 10(3):326-38. PMID: 18579963.
        View in: PubMed
      41. Crivelli S, Kreylos O, Hamann B, Max N, Bethel W. ProteinShop: a tool for interactive protein manipulation and steering. J Comput Aided Mol Des. 2004 Apr; 18(4):271-85. PMID: 15562991.
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      42. Mahrous K, Bennett J, Scheuermann G, Hamann B, Joy KI. Topological segmentation in three-dimensional vector fields. IEEE Trans Vis Comput Graph. 2004 Mar-Apr; 10(2):198-205. PMID: 15384644.
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      43. Shah N, Couronne O, Pennacchio LA, Brudno M, Batzoglou S, Bethel EW, Rubin EM, Hamann B, Dubchak I. Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinformatics. 2004 Mar 22; 20(5):636-43. PMID: 15033870.
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