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Items: 30

1.

The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos.

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.

Nat Commun. 2019 Oct 3;10(1):4486. doi: 10.1038/s41467-019-12211-8.

2.

Deep Learning-Based Gleason Grading of Prostate Cancer from Histopathology Images - Role of Multiscale Decision Aggregation and Data Augmentation.

Karimi D, Nir G, Fazli L, Black PC, Goldenberg L, Salcudean SE.

IEEE J Biomed Health Inform. 2019 Sep 30. doi: 10.1109/JBHI.2019.2944643. [Epub ahead of print]

PMID:
31567104
3.

A new era: artificial intelligence and machine learning in prostate cancer.

Goldenberg SL, Nir G, Salcudean SE.

Nat Rev Urol. 2019 Jul;16(7):391-403. doi: 10.1038/s41585-019-0193-3. Review.

PMID:
31092914
4.

A multiplexed DNA FISH strategy for assessing genome architecture in Caenorhabditis elegans.

Fields BD, Nguyen SC, Nir G, Kennedy S.

Elife. 2019 May 14;8. pii: e42823. doi: 10.7554/eLife.42823.

5.

Comparison of Artificial Intelligence Techniques to Evaluate Performance of a Classifier for Automatic Grading of Prostate Cancer From Digitized Histopathologic Images.

Nir G, Karimi D, Goldenberg SL, Fazli L, Skinnider BF, Tavassoli P, Turbin D, Villamil CF, Wang G, Thompson DJS, Black PC, Salcudean SE.

JAMA Netw Open. 2019 Mar 1;2(3):e190442. doi: 10.1001/jamanetworkopen.2019.0442.

6.

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling.

Nir G, Farabella I, PĂ©rez 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.

PLoS Genet. 2018 Dec 26;14(12):e1007872. doi: 10.1371/journal.pgen.1007872. eCollection 2018 Dec.

7.

An End-to-end System for Automatic Characterization of Iba1 Immunopositive Microglia in Whole Slide Imaging.

Kyriazis AD, Noroozizadeh S, Refaee A, Choi W, Chu LT, Bashir A, Cheng WH, Zhao R, Namjoshi DR, Salcudean SE, Wellington CL, Nir G.

Neuroinformatics. 2019 Jul;17(3):373-389. doi: 10.1007/s12021-018-9405-x.

PMID:
30406865
8.

Automatic grading of prostate cancer in digitized histopathology images: Learning from multiple experts.

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.

Med Image Anal. 2018 Dec;50:167-180. doi: 10.1016/j.media.2018.09.005. Epub 2018 Sep 24.

PMID:
30340027
9.

Prostate segmentation in MRI using a convolutional neural network architecture and training strategy based on statistical shape models.

Karimi D, Samei G, Kesch C, Nir G, Salcudean SE.

Int J Comput Assist Radiol Surg. 2018 Aug;13(8):1211-1219. doi: 10.1007/s11548-018-1785-8. Epub 2018 May 15.

PMID:
29766373
10.

Investigation of Physical Phenomena Underlying Temporal-Enhanced Ultrasound as a New Diagnostic Imaging Technique: Theory and Simulations.

Bayat S, Azizi S, Daoud MI, Nir G, Imani F, Gerardo CD, Yan P, Tahmasebi A, Vignon F, Sojoudi S, Wilson S, Iczkowski KA, Lucia MS, Goldenberg L, Salcudean SE, Abolmaesumi P, Mousavi P.

IEEE Trans Ultrason Ferroelectr Freq Control. 2018 Mar;65(3):400-410. doi: 10.1109/TUFFC.2017.2785230.

PMID:
29505407
11.

OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes.

Beliveau BJ, Kishi JY, Nir G, Sasaki HM, Saka SK, Nguyen SC, Wu CT, Yin P.

Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2183-E2192. doi: 10.1073/pnas.1714530115. Epub 2018 Feb 20.

12.

The role of near-wall drag effects in the dynamics of tethered DNA under shear flow.

Nir G, Chetrit E, Vivante A, Garini Y, Berkovich R.

Soft Matter. 2018 Mar 28;14(12):2219-2226. doi: 10.1039/c7sm01328k. Epub 2018 Feb 16.

PMID:
29451293
13.

In Situ Super-Resolution Imaging of Genomic DNA with OligoSTORM and OligoDNA-PAINT.

Beliveau BJ, Boettiger AN, Nir G, Bintu B, Yin P, Zhuang X, Wu CT.

Methods Mol Biol. 2017;1663:231-252. doi: 10.1007/978-1-4939-7265-4_19.

14.

Focal application of low-dose-rate brachytherapy for prostate cancer: a pilot study.

Mahdavi SS, Spadinger IT, Salcudean SE, Kozlowski P, Chang SD, Ng T, Lobo J, Nir G, Moradi H, Peacock M, Morris WJ.

J Contemp Brachytherapy. 2017 Jun;9(3):197-208. doi: 10.5114/jcb.2017.68424. Epub 2017 Jun 13.

15.

Detection and grading of prostate cancer using temporal enhanced ultrasound: combining deep neural networks and tissue mimicking simulations.

Azizi S, Bayat S, Yan P, Tahmasebi A, Nir G, Kwak JT, Xu S, Wilson S, Iczkowski KA, Lucia MS, Goldenberg L, Salcudean SE, Pinto PA, Wood B, Abolmaesumi P, Mousavi P.

Int J Comput Assist Radiol Surg. 2017 Aug;12(8):1293-1305. doi: 10.1007/s11548-017-1627-0. Epub 2017 Jun 20.

PMID:
28634789
16.

MR elastography of prostate cancer: quantitative comparison with histopathology and repeatability of methods.

Sahebjavaher RS, Nir G, Honarvar M, Gagnon LO, Ischia J, Jones EC, Chang SD, Fazli L, Goldenberg SL, Rohling R, Kozlowski P, Sinkus R, Salcudean SE.

NMR Biomed. 2015 Jan;28(1):124-39. doi: 10.1002/nbm.3218. Epub 2014 Nov 14.

PMID:
25395244
17.

MR elastography and diffusion-weighted imaging of ex vivo prostate cancer: quantitative comparison to histopathology.

Sahebjavaher RS, Nir G, Gagnon LO, Ischia J, Jones EC, Chang SD, Yung A, Honarvar M, Fazli L, Goldenberg SL, Rohling R, Sinkus R, Kozlowski P, Salcudean SE.

NMR Biomed. 2015 Jan;28(1):89-100. doi: 10.1002/nbm.3203. Epub 2014 Nov 10.

18.

Multi-parametric 3D quantitative ultrasound vibro-elastography imaging for detecting palpable prostate tumors.

Mohareri O, Ruszkowski A, Lobo J, Ischia J, Baghani A, Nir G, Eskandari H, Jones E, Fazli L, Goldenberg L, Moradi M, Salcudean S.

Med Image Comput Comput Assist Interv. 2014;17(Pt 1):561-8.

PMID:
25333163
19.

Air quality and social deprivation in four French metropolitan areas--a localized spatio-temporal environmental inequality analysis.

Padilla CM, Kihal-Talantikite W, Vieira VM, Rossello P, Le Nir G, Zmirou-Navier D, Deguen S.

Environ Res. 2014 Oct;134:315-24. doi: 10.1016/j.envres.2014.07.017. Epub 2014 Sep 7.

20.

Multiparametric 3D in vivo ultrasound vibroelastography imaging of prostate cancer: Preliminary results.

Moradi M, Mahdavi SS, Nir G, Mohareri O, Koupparis A, Gagnon LO, Fazli L, Casey RG, Ischia J, Jones EC, Goldenberg SL, Salcudean SE.

Med Phys. 2014 Jul;41(7):073505. doi: 10.1118/1.4884226.

PMID:
24989419
21.

A framework for optimization-based design of motion encoding in magnetic resonance elastography.

Nir G, Sahebjavaher RS, Sinkus R, Salcudean SE.

Magn Reson Med. 2015 Apr;73(4):1514-25. doi: 10.1002/mrm.25280. Epub 2014 May 6.

PMID:
24803300
22.

Registration of whole-mount histology and volumetric imaging of the prostate using particle filtering.

Nir G, Sahebjavaher RS, Kozlowski P, Chang SD, Jones EC, Goldenberg SL, Salcudean SE.

IEEE Trans Med Imaging. 2014 Aug;33(8):1601-13. doi: 10.1109/TMI.2014.2319231. Epub 2014 Apr 22.

PMID:
24771576
23.

Model-based registration of ex vivo and in vivo MRI of the prostate using elastography*.

Nir G, Sahebjavaher RS, Kozlowski P, Chang SD, Sinkus R, Goldenberg SL, Salcudean SE.

IEEE Trans Med Imaging. 2013 Jul;32(7):1349-61. doi: 10.1109/TMI.2013.2269174.

PMID:
23807814
24.

Dynamic analysis of a diffusing particle in a trapping potential.

Lindner M, Nir G, Vivante A, Young IT, Garini Y.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Feb;87(2):022716. Epub 2013 Feb 25.

PMID:
23496557
25.

Model-based registration of ex vivo and in vivo MRI of the prostate using elastography.

Nir G, Sahebjavaher RS, Kozlowski P, Chang SD, Sinkus R.

IEEE Trans Med Imaging. 2013 Jun;32(6):1068-80. doi: 10.1109/TMI.2013.2251469. Epub 2013 Mar 7.

PMID:
23475353
26.

Force-free measurements of the conformations of DNA molecules tethered to a wall.

Lindner M, Nir G, Medalion S, Dietrich HR, Rabin Y, Garini Y.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Jan;83(1 Pt 1):011916. Epub 2011 Jan 27.

PMID:
21405722
27.

HU protein induces incoherent DNA persistence length.

Nir G, Lindner M, Dietrich HRC, Girshevitz O, Vorgias CE, Garini Y.

Biophys J. 2011 Feb 2;100(3):784-790. doi: 10.1016/j.bpj.2010.12.3687.

28.

TEMPORAL REGISTRATION OF PARTIAL DATA USING PARTICLE FILTERING.

Nir G, Tannenbaum A.

Proc Int Conf Image Proc. 2011:2177-2180.

29.

Second-hand prostatism: effects of prostatic symptoms on spouses' quality of life, daily routines and family relationships.

Shvartzman P, Borkan JM, Stoliar L, Peleg A, Nakar S, Nir G, Tabenkin H.

Fam Pract. 2001 Dec;18(6):610-3.

PMID:
11739347
30.

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