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Qi, Jinyi

TitleComputer Scientist Faculty
InstitutionLawrence Berkeley National Lab
DepartmentMolecular Biophys & Integ Bio
Address1 Cyclotron Road
Berkeley CA 94720
Phone510/486-4695
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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. Zhang X, Badawi RD, Cherry SR, Qi J. Theoretical study of the benefit of long axial field-of-view PET on region of interest quantification. Phys Med Biol. 2018 May 25. PMID: 29799814.
      View in: PubMed
    2. Shen A, Nieves-Cintron M, Deng Y, Shi Q, Chowdhury D, Qi J, Hell JW, Navedo MF, Xiang YK. Functionally distinct and selectively phosphorylated GPCR subpopulations co-exist in a single cell. Nat Commun. 2018 03 13; 9(1):1050. PMID: 29535304.
      View in: PubMed
    3. Zhang X, Peng Q, Zhou J, Huber JS, Moses WW, Qi J. Lesion detection and quantification performance of the Tachyon-I time-of-flight PET scanner: phantom and human studies. Phys Med Biol. 2018 Feb 20. PMID: 29461254.
      View in: PubMed
    4. Wang G, Zhou J, Yu Z, Wang W, Qi J. Hybrid Pre-Log and Post-Log Image Reconstruction for Computed Tomography. IEEE Trans Med Imaging. 2017 12; 36(12):2457-2465. PMID: 28920898.
      View in: PubMed
    5. Kyme AZ, Judenhofer MS, Gong K, Bec J, Selfridge A, Du J, Qi J, Cherry SR, Meikle SR. Open-field mouse brain PET: design optimisation and detector characterisation. Phys Med Biol. 2017 Jul 13; 62(15):6207-6225. PMID: 28475491.
      View in: PubMed
    6. Gong K, Zhou J, Tohme M, Judenhofer M, Yang Y, Qi J. Sinogram Blurring Matrix Estimation From Point Sources Measurements With Rank-One Approximation for Fully 3-D PET. IEEE Trans Med Imaging. 2017 10; 36(10):2179-2188. PMID: 28613163.
      View in: PubMed
    7. Zhang M, Zhou J, Niu X, Asma E, Wang W, Qi J. Regularization parameter selection for penalized-likelihood list-mode image reconstruction in PET. Phys Med Biol. 2017 Jun 21; 62(12):5114-5130. PMID: 28402287.
      View in: PubMed
    8. Zhang X, Zhou J, Cherry SR, Badawi RD, Qi J. Quantitative image reconstruction for total-body PET imaging using the 2-meter long EXPLORER scanner. Phys Med Biol. 2017 Mar 21; 62(6):2465-2485. PMID: 28240215.
      View in: PubMed
    9. Ma D, Liu J, Qi J, Marcu L. Reply to Comment: 'A novel method for fast and robust estimation of fluorescence decay dynamics using constrained least-square deconvolution with Laguerre expansion'. Phys Med Biol. 2017 02 21; 62(4):1637-1641. PMID: 28145280.
      View in: PubMed
    10. Hutchcroft W, Wang G, Chen KT, Catana C, Qi J. Anatomically-aided PET reconstruction using the kernel method. Phys Med Biol. 2016 Sep 21; 61(18):6668-6683. PMID: 27541810.
      View in: PubMed
    11. Berg E, Roncali E, Hutchcroft W, Qi J, Cherry SR. Improving Depth, Energy and Timing Estimation in PET Detectors with Deconvolution and Maximum Likelihood Pulse Shape Discrimination. IEEE Trans Med Imaging. 2016 11; 35(11):2436-2446. PMID: 27295658.
      View in: PubMed
    12. Gong K, Majewski S, Kinahan PE, Harrison RL, Elston BF, Manjeshwar R, Dolinsky S, Stolin AV, Brefczynski-Lewis JA, Qi J. Designing a compact high performance brain PET scanner-simulation study. Phys Med Biol. 2016 05 21; 61(10):3681-97. PMID: 27081753; PMCID: PMC4863179 [Available on 05/21/17].
    13. Yang Y, Bec J, Zhou J, Zhang M, Judenhofer MS, Bai X, Di K, Wu Y, Rodriguez M, Dokhale P, Shah KS, Farrell R, Qi J, Cherry SR. A Prototype High-Resolution Small-Animal PET Scanner Dedicated to Mouse Brain Imaging. J Nucl Med. 2016 07; 57(7):1130-5. PMID: 27013696.
      View in: PubMed
    14. Gong K, Cherry SR, Qi J. On the assessment of spatial resolution of PET systems with iterative image reconstruction. Phys Med Biol. 2016 Mar 07; 61(5):N193-202. PMID: 26864088.
      View in: PubMed
    15. Zhang M, Zhou J, Yang Y, Rodríguez-Villafuerte M, Qi J. Efficient system modeling for a small animal PET scanner with tapered DOI detectors. Phys Med Biol. 2016 Jan 21; 61(2):461-74. PMID: 26682623; PMCID: PMC4874520 [Available on 01/21/17].
    16. Yang L, Wang G, Qi J. Theoretical Analysis of Penalized Maximum-Likelihood Patlak Parametric Image Reconstruction in Dynamic PET for Lesion Detection. IEEE Trans Med Imaging. 2016 Apr; 35(4):947-56. PMID: 26625407; PMCID: PMC4996625 [Available on 04/01/17].
    17. Peng Q, Choong WS, Vu C, Huber JS, Janecek M, Wilson D, Huesman RH, Qi J, Zhou J, Moses WW. Performance of the Tachyon Time-of-Flight PET Camera. IEEE Trans Nucl Sci. 2015 Feb; 62(1):111-119. PMID: 26594057.
      View in: PubMed
    18. Poon JK, Dahlbom ML, Casey ME, Qi J, Cherry SR, Badawi RD. Validation of the SimSET simulation package for modeling the Siemens Biograph mCT PET scanner. Phys Med Biol. 2015 Feb 07; 60(3):N35-45. PMID: 25586800.
      View in: PubMed
    19. Yang L, Ferrero A, Hagge RJ, Badawi RD, Qi J. Evaluation of penalty design in penalized maximum-likelihood image reconstruction for lesion detection. J Med Imaging (Bellingham). 2014 Oct; 1(3):035501. PMID: 26158072; PMCID: PMC4286231.
    20. Wang G, Qi J. Edge-preserving PET image reconstruction using trust optimization transfer. IEEE Trans Med Imaging. 2015 Apr; 34(4):930-9. PMID: 25438302; PMCID: PMC4385498.
    21. Wang G, Qi J. PET image reconstruction using kernel method. IEEE Trans Med Imaging. 2015 Jan; 34(1):61-71. PMID: 25095249; PMCID: PMC4280333.
    22. Zhou J, Qi J. Efficient fully 3D list-mode TOF PET image reconstruction using a factorized system matrix with an image domain resolution model. Phys Med Biol. 2014 Feb 07; 59(3):541-59. PMID: 24434568; PMCID: PMC4182441.
    23. Yang L, Zhou J, Ferrero A, Badawi RD, Qi J. Regularization design in penalized maximum-likelihood image reconstruction for lesion detection in 3D PET. Phys Med Biol. 2014 Jan 20; 59(2):403-19. PMID: 24351981; PMCID: PMC4254853.
    24. Wang G, Qi J. Direct estimation of kinetic parametric images for dynamic PET. Theranostics. 2013 Nov 20; 3(10):802-15. PMID: 24396500; PMCID: PMC3879057.
    25. Wang G, Qi J. An optimization transfer algorithm for nonlinear parametric image reconstruction from dynamic PET data. IEEE Trans Med Imaging. 2012 Oct; 31(10):1977-88. PMID: 22893380; PMCID: PMC4086832.
    26. Wang G, Qi J. Penalized likelihood PET image reconstruction using patch-based edge-preserving regularization. IEEE Trans Med Imaging. 2012 Dec; 31(12):2194-204. PMID: 22875244; PMCID: PMC4080915.
    27. Liu J, Sun Y, Qi J, Marcu L. A novel method for fast and robust estimation of fluorescence decay dynamics using constrained least-squares deconvolution with Laguerre expansion. Phys Med Biol. 2012 Feb 21; 57(4):843-65. PMID: 22290334; PMCID: PMC3407553.
    28. Zhou J, Qi J. Fast and efficient fully 3D PET image reconstruction using sparse system matrix factorization with GPU acceleration. Phys Med Biol. 2011 Oct 21; 56(20):6739-57. PMID: 21970864; PMCID: PMC4080908.
    29. Cheng-Liao J, Qi J. PET image reconstruction with anatomical edge guided level set prior. Phys Med Biol. 2011 Nov 07; 56(21):6899-918. PMID: 21983558; PMCID: PMC3393853.
    30. Qi J, Yang Y, Zhou J, Wu Y, Cherry SR. Experimental assessment of resolution improvement of a zoom-in PET. Phys Med Biol. 2011 Sep 07; 56(17):N165-74. PMID: 21828899.
      View in: PubMed
    31. Yang Y, James SS, Wu Y, Du H, Qi J, Farrell R, Dokhale PA, Shah KS, Vaigneur K, Cherry SR. Tapered LSO arrays for small animal PET. Phys Med Biol. 2011 Jan 07; 56(1):139-53. PMID: 21119228; PMCID: PMC3117425.
    32. Cao N, Huesman RH, Moses WW, Qi J. Detection performance analysis for time-of-flight PET. Phys Med Biol. 2010 Nov 21; 55(22):6931-50. PMID: 21048292; PMCID: PMC3132876.
    33. Cheng-Liao J, Qi J. Segmentation of mouse dynamic PET images using a multiphase level set method. Phys Med Biol. 2010 Nov 07; 55(21):6549-69. PMID: 20959689; PMCID: PMC3410969.
    34. Tohme MS, Qi J. Iterative reconstruction of Fourier-rebinned PET data using sinogram blurring function estimated from point source scans. Med Phys. 2010 Oct; 37(10):5530-40. PMID: 21089788; PMCID: PMC2962665.
    35. Zhou J, Qi J. Adaptive imaging for lesion detection using a zoom-in PET system. IEEE Trans Med Imaging. 2011 Jan; 30(1):119-30. PMID: 20699208; PMCID: PMC3014423.
    36. Wang G, Qi J. Acceleration of the direct reconstruction of linear parametric images using nested algorithms. Phys Med Biol. 2010 Mar 07; 55(5):1505-17. PMID: 20157226; PMCID: PMC2952886.
    37. Fu L, Qi J. A residual correction method for high-resolution PET reconstruction with application to on-the-fly Monte Carlo based model of positron range. Med Phys. 2010 Feb; 37(2):704-13. PMID: 20229880; PMCID: PMC2821421.
    38. St James S, Yang Y, Bowen SL, Qi J, Cherry SR. Simulation study of spatial resolution and sensitivity for the tapered depth of interaction PET detectors for small animal imaging. Phys Med Biol. 2010 Jan 21; 55(2):N63-74. PMID: 20023331; PMCID: PMC3136367.
    39. Li C, Wang G, Qi J, Cherry SR. Three-dimensional fluorescence optical tomography in small-animal imaging using simultaneous positron-emission-tomography priors. Opt Lett. 2009 Oct 01; 34(19):2933-5. PMID: 19794772; PMCID: PMC2856619.
    40. Zhou J, Qi J. Theoretical analysis and simulation study of a high-resolution zoom-in PET system. Phys Med Biol. 2009 Sep 07; 54(17):5193-208. PMID: 19671969.
      View in: PubMed
    41. Cao N, Huesman RH, Moses WW, Qi J. DETECTION PERFORMANCE ANALYSIS FOR TIME-OF-FLIGHT PET. Proc IEEE Int Symp Biomed Imaging. 2009 Aug 07; June 28 2009-July 1 2009:402-405. PMID: 20936051.
      View in: PubMed
    42. Wang G, Qi J. DIRECT RECONSTRUCTION OF DYNAMIC PET PARAMETRIC IMAGES USING SPARSE SPECTRAL REPRESENTATION. Proc IEEE Int Symp Biomed Imaging. 2009 Aug 07; 2009:867-870. PMID: 21278825.
      View in: PubMed
    43. Wu Y, Bowen SL, Yang K, Packard N, Fu L, Burkett G, Qi J, Boone JM, Cherry SR, Badawi RD. PET characteristics of a dedicated breast PET/CT scanner prototype. Phys Med Biol. 2009 Jul 07; 54(13):4273-87. PMID: 19531852; PMCID: PMC2738997.
    44. Wu Y, Catana C, Farrell R, Dokhale PA, Shah KS, Qi J, Cherry SR. PET Performance Evaluation of an MR-Compatible PET Insert. IEEE Trans Nucl Sci. 2009 Jun 16; 56(3):574-580. PMID: 21072320.
      View in: PubMed
    45. Tohme MS, Qi J. Iterative image reconstruction for positron emission tomography based on a detector response function estimated from point source measurements. Phys Med Biol. 2009 Jun 21; 54(12):3709-25. PMID: 19478379; PMCID: PMC2901798.
    46. Wang G, Qi J. Generalized algorithms for direct reconstruction of parametric images from dynamic PET data. IEEE Trans Med Imaging. 2009 Nov; 28(11):1717-26. PMID: 19447699; PMCID: PMC2901800.
    47. Wang G, Schultz LJ, Qi J. Bayesian image reconstruction for improving detection performance of muon tomography. IEEE Trans Image Process. 2009 May; 18(5):1080-9. PMID: 19342340.
      View in: PubMed
    48. Wang G, Qi J. Analysis of penalized likelihood image reconstruction for dynamic PET quantification. IEEE Trans Med Imaging. 2009 Apr; 28(4):608-20. PMID: 19211345; PMCID: PMC2792209.
    49. Zhou J, Qi J. High-resolution adaptive PET imaging. Inf Process Med Imaging. 2009; 21:26-37. PMID: 19694250.
      View in: PubMed
    50. Yang Y, Qi J, Wu Y, St James S, Farrell R, Dokhale PA, Shah KS, Cherry SR. Depth of interaction calibration for PET detectors with dual-ended readout by PSAPDs. Phys Med Biol. 2009 Jan 21; 54(2):433-45. PMID: 19098356; PMCID: PMC2631388.
    51. Catana C, Procissi D, Wu Y, Judenhofer MS, Qi J, Pichler BJ, Jacobs RE, Cherry SR. Simultaneous in vivo positron emission tomography and magnetic resonance imaging. Proc Natl Acad Sci U S A. 2008 Mar 11; 105(10):3705-10. PMID: 18319342; PMCID: PMC2268792.
    52. Zhang H, Kusunose J, Kheirolomoom A, Seo JW, Qi J, Watson KD, Lindfors HA, Ruoslahti E, Sutcliffe JL, Ferrara KW. Dynamic imaging of arginine-rich heart-targeted vehicles in a mouse model. Biomaterials. 2008 Apr; 29(12):1976-88. PMID: 18255141; PMCID: PMC2475513.
    53. Wang G, Fu L, Qi J. Maximum a posteriori reconstruction of the Patlak parametric image from sinograms in dynamic PET. Phys Med Biol. 2008 Feb 07; 53(3):593-604. PMID: 18199904.
      View in: PubMed
    54. Catana C, Wu Y, Judenhofer MS, Qi J, Pichler BJ, Cherry SR. Simultaneous acquisition of multislice PET and MR images: initial results with a MR-compatible PET scanner. J Nucl Med. 2006 Dec; 47(12):1968-76. PMID: 17138739.
      View in: PubMed
    55. Qi J, Huesman RH. Penalized maximum-likelihood image reconstruction for lesion detection. Phys Med Biol. 2006 Aug 21; 51(16):4017-29. PMID: 16885621.
      View in: PubMed
    56. Qi J, Leahy RM. Iterative reconstruction techniques in emission computed tomography. Phys Med Biol. 2006 Aug 07; 51(15):R541-78. PMID: 16861768.
      View in: PubMed
    57. Qi J. Comparison of Lesion Detection and Quantification in MAP Reconstruction with Gaussian and Non-Gaussian Priors. Int J Biomed Imaging. 2006; 2006:87567. PMID: 23165056; PMCID: PMC2324047.
    58. Qi J, Huesman RH. Theoretical study of penalized-likelihood image reconstruction for region of interest quantification. IEEE Trans Med Imaging. 2006 May; 25(5):640-8. PMID: 16689267.
      View in: PubMed
    59. Qi J. Maximum-likelihood estimation of detector response for PET image reconstruction. Conf Proc IEEE Eng Med Biol Soc. 2006; 1:2530-3. PMID: 17946519.
      View in: PubMed
    60. Huber JS, Moses WW, Wang GC, Derenzo SE, Huesman RH, Qi J, Virador P, Choong WS, Mandelli E, Beuville E, Pedrali-Noy M, Krieger B, Meddeler GJ. A retrospective on the LBNL PEM project. Phys Med. 2006; 21 Suppl 1:60-3. PMID: 17645996.
      View in: PubMed
    61. Qi J, Huesman RH. Effect of errors in the system matrix on maximum a posteriori image reconstruction. Phys Med Biol. 2005 Jul 21; 50(14):3297-312. PMID: 16177510; PMCID: PMC1382175.
    62. Hu J, Tam K, Qi J. An approximate short scan helical FDK cone beam algorithm based on nutating curved surfaces satisfying the Tuy's condition. Med Phys. 2005 Jun; 32(6):1529-36. PMID: 16013710.
      View in: PubMed
    63. Qi J, Huesman RH. Propagation of errors from the sensitivity image in list mode reconstruction. IEEE Trans Med Imaging. 2004 Sep; 23(9):1094-9. PMID: 15377118.
      View in: PubMed
    64. Li Q, Asma E, Qi J, Bading JR, Leahy RM. Accurate estimation of the Fisher information matrix for the PET image reconstruction problem. IEEE Trans Med Imaging. 2004 Sep; 23(9):1057-64. PMID: 15377114.
      View in: PubMed
    65. Qi J. Analysis of lesion detectability in Bayesian emission reconstruction with nonstationary object variability. IEEE Trans Med Imaging. 2004 Mar; 23(3):321-9. PMID: 15027525.
      View in: PubMed
    66. Qi J. Optimization of a PET scanner design for prostate lesion detection. Conf Proc IEEE Eng Med Biol Soc. 2004; 2:1357-60. PMID: 17271944.
      View in: PubMed
    67. Qi J. A unified noise analysis for iterative image estimation. Phys Med Biol. 2003 Nov 07; 48(21):3505-19. PMID: 14653559.
      View in: PubMed
    68. Qi J. Theoretical evaluation of the detectability of random lesions in Bayesian emission reconstruction. Inf Process Med Imaging. 2003 Jul; 18:354-65. PMID: 15344471.
      View in: PubMed
    69. Qi J, Huesman RH. Scatter correction for positron emission mammography. Phys Med Biol. 2002 Aug 07; 47(15):2759-71. PMID: 12200937.
      View in: PubMed
    70. Nichols TE, Qi J, Asma E, Leahy RM. Spatiotemporal reconstruction of list-mode PET data. IEEE Trans Med Imaging. 2002 Apr; 21(4):396-404. PMID: 12022627.
      View in: PubMed
    71. Qi J, Huesman RH. Theoretical study of lesion detectability of MAP reconstruction using computer observers. IEEE Trans Med Imaging. 2001 Aug; 20(8):815-22. PMID: 11513032.
      View in: PubMed
    72. Qi J, Leahy RM. Resolution and noise properties of MAP reconstruction for fully 3-D PET. IEEE Trans Med Imaging. 2000 May; 19(5):493-506. PMID: 11021692.
      View in: PubMed

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