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Guy Nir, Ph.D.

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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Shao Y, Nir G, Fazli L, Goldenberg L, Gleave M, Black P, Wang J, Salcudean S. Improving prostate cancer classification in H&E tissue micro arrays using Ki67 and P63 histopathology. Comput Biol Med. 2020 Oct 14; 127:104053. PMID: 33126125.
    Citations:    
  2. Nguyen HQ, Chattoraj S, Castillo D, Nguyen SC, Nir G, Lioutas A, Hershberg EA, Martins NMC, Reginato PL, Hannan M, Beliveau BJ, Church GM, Daugharthy ER, Marti-Renom MA, Wu CT. 3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing. Nat Methods. 2020 08; 17(8):822-832. PMID: 32719531.
    Citations:    Fields:    
  3. Erceg J, AlHaj Abed J, Goloborodko A, Lajoie BR, Fudenberg G, Abdennur N, Imakaev M, McCole RB, Nguyen SC, Saylor W, Joyce EF, Senaratne TN, Hannan MA, Nir G, Dekker J, Mirny LA, Wu CT. The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos. Nat Commun. 2019 10 03; 10(1):4486. PMID: 31582744.
    Citations: 5     Fields:    Translation:AnimalsCells
  4. Karimi D, Nir G, Fazli L, Black PC, Goldenberg L, Salcudean SE. Deep Learning-Based Gleason Grading of Prostate Cancer From Histopathology Images-Role of Multiscale Decision Aggregation and Data Augmentation. IEEE J Biomed Health Inform. 2020 05; 24(5):1413-1426. PMID: 31567104.
    Citations: 3     Fields:    
  5. Kyriazis AD, Noroozizadeh S, Refaee A, Choi W, Chu LT, Bashir A, Cheng WH, Zhao R, Namjoshi DR, Salcudean SE, Wellington CL, Nir G. An End-to-end System for Automatic Characterization of Iba1 Immunopositive Microglia in Whole Slide Imaging. Neuroinformatics. 2019 07; 17(3):373-389. PMID: 30406865.
    Citations: 1     Fields:    Translation:AnimalsCells
  6. Goldenberg SL, Nir G, Salcudean SE. A new era: artificial intelligence and machine learning in prostate cancer. Nat Rev Urol. 2019 07; 16(7):391-403. PMID: 31092914.
    Citations: 6     Fields:    Translation:Humans
  7. Fields BD, Nguyen SC, Nir G, Kennedy S. A multiplexed DNA FISH strategy for assessing genome architecture in Caenorhabditis elegans. Elife. 2019 05 14; 8. PMID: 31084706.
    Citations: 6     Fields:    Translation:Animals
  8. Nir G, Karimi D, Goldenberg SL, Fazli L, Skinnider BF, Tavassoli P, Turbin D, Villamil CF, Wang G, Thompson DJS, Black PC, Salcudean SE. Comparison of Artificial Intelligence Techniques to Evaluate Performance of a Classifier for Automatic Grading of Prostate Cancer From Digitized Histopathologic Images. JAMA Netw Open. 2019 03 01; 2(3):e190442. PMID: 30848813.
    Citations: 5     Fields:    Translation:Humans
  9. Nir G, Farabella I, Pérez Estrada C, Ebeling CG, Beliveau BJ, Sasaki HM, Lee SD, Nguyen SC, McCole RB, Chattoraj S, Erceg J, AlHaj Abed J, Martins NMC, Nguyen HQ, Hannan MA, Russell S, Durand NC, Rao SSP, Kishi JY, Soler-Vila P, Di Pierro M, Onuchic JN, Callahan SP, Schreiner JM, Stuckey JA, Yin P, Aiden EL, Marti-Renom MA, Wu CT. Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. PLoS Genet. 2018 12; 14(12):e1007872. PMID: 30586358.
    Citations: 17     Fields:    Translation:HumansCells
  10. Nir G, Hor S, Karimi D, Fazli L, Skinnider BF, Tavassoli P, Turbin D, Villamil CF, Wang G, Wilson RS, Iczkowski KA, Lucia MS, Black PC, Abolmaesumi P, Goldenberg SL, Salcudean SE. Automatic grading of prostate cancer in digitized histopathology images: Learning from multiple experts. Med Image Anal. 2018 12; 50:167-180. PMID: 30340027.
    Citations: 10     Fields:    Translation:Humans
  11. Karimi D, Samei G, Kesch C, Nir G, Salcudean SE. Prostate segmentation in MRI using a convolutional neural network architecture and training strategy based on statistical shape models. Int J Comput Assist Radiol Surg. 2018 Aug; 13(8):1211-1219. PMID: 29766373.
    Citations: 3     Fields:    Translation:Humans
  12. Beliveau BJ, Kishi JY, Nir G, Sasaki HM, Saka SK, Nguyen SC, Wu CT, Yin P. OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes. Proc Natl Acad Sci U S A. 2018 03 06; 115(10):E2183-E2192. PMID: 29463736.
    Citations: 16     Fields:    Translation:HumansAnimals
  13. Nir G, Chetrit E, Vivante A, Garini Y, Berkovich R. The role of near-wall drag effects in the dynamics of tethered DNA under shear flow. Soft Matter. 2018 Mar 28; 14(12):2219-2226. PMID: 29451293.
    Citations:    Fields:    Translation:Cells
  14. Beliveau BJ, Boettiger AN, Nir G, Bintu B, Yin P, Zhuang X, Wu CT. In Situ Super-Resolution Imaging of Genomic DNA with OligoSTORM and OligoDNA-PAINT. Methods Mol Biol. 2017; 1663:231-252. PMID: 28924672.
    Citations: 9     Fields:    Translation:HumansAnimals
  15. Lindner M, Nir G, Vivante A, Young IT, Garini Y. Dynamic analysis of a diffusing particle in a trapping potential. Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Feb; 87(2):022716. PMID: 23496557.
    Citations: 9     Fields:    Translation:Cells
  16. Nir G, Lindner M, Dietrich HRC, Girshevitz O, Vorgias CE, Garini Y. HU protein induces incoherent DNA persistence length. Biophys J. 2011 Feb 02; 100(3):784-790. PMID: 21281594.
    Citations: 6     Fields:    Translation:Cells
  17. Lindner M, Nir G, Medalion S, Dietrich HR, Rabin Y, Garini Y. Force-free measurements of the conformations of DNA molecules tethered to a wall. Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Jan; 83(1 Pt 1):011916. PMID: 21405722.
    Citations: 9     Fields:    Translation:Cells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.