Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 64

1.

Deep Fusion of Contextual and Object-based Representations for Delineation of Multiple Nuclear Phenotypes.

Khoshdeli M, Winkelmaier G, Parvin B.

Bioinformatics. 2019 May 28. pii: btz430. doi: 10.1093/bioinformatics/btz430. [Epub ahead of print]

PMID:
31135022
2.

Deep Learning Models Differentiate Tumor Grades from H&E Stained Histology Sections.

Khoshdeli M, Borowsky A, Parvin B.

Conf Proc IEEE Eng Med Biol Soc. 2018 Jul;2018:620-623. doi: 10.1109/EMBC.2018.8512357.

PMID:
30440473
3.

Fusion of encoder-decoder deep networks improves delineation of multiple nuclear phenotypes.

Khoshdeli M, Winkelmaier G, Parvin B.

BMC Bioinformatics. 2018 Aug 7;19(1):294. doi: 10.1186/s12859-018-2285-0.

4.

High-Dimensional Phenotyping Identifies Age-Emergent Cells in Human Mammary Epithelia.

Pelissier Vatter FA, Schapiro D, Chang H, Borowsky AD, Lee JK, Parvin B, Stampfer MR, LaBarge MA, Bodenmiller B, Lorens JB.

Cell Rep. 2018 Apr 24;23(4):1205-1219. doi: 10.1016/j.celrep.2018.03.114.

5.

Feature-Based Representation Improves Color Decomposition and Nuclear Detection Using a Convolutional Neural Network.

Khoshdeli M, Parvin B.

IEEE Trans Biomed Eng. 2018 Mar;65(3):625-634. doi: 10.1109/TBME.2017.2711529.

6.

Buckyballs conjugated with nucleic acid sequences identifies microorganisms in live cell assays.

Cheng Q, Parvin B.

J Nanobiotechnology. 2017 Nov 9;15(1):78. doi: 10.1186/s12951-017-0315-0.

7.

Detection of Nuclei in H&E Stained Sections Using Convolutional Neural Networks.

Khoshdeli M, Cong R, Parvin B.

IEEE EMBS Int Conf Biomed Health Inform. 2017 Feb;2017:105-108. doi: 10.1109/BHI.2017.7897216. Epub 2017 Apr 13.

8.

Atypical Presentation of Acute Freiberg Disease.

Kenny L, Purushothaman B, Teasdale R, El-Hassany M, Parvin B.

J Foot Ankle Surg. 2017 Mar - Apr;56(2):385-389. doi: 10.1053/j.jfas.2016.11.001.

PMID:
28231970
9.

Integrative Analysis of Cellular Morphometric Context Reveals Clinically Relevant Signatures in Lower Grade Glioma.

Han J, Wang Y, Cai W, Borowsky A, Parvin B, Chang H.

Med Image Comput Comput Assist Interv. 2016 Oct;9900:72-80. doi: 10.1007/978-3-319-46720-7_9. Epub 2016 Oct 2.

10.

When machine vision meets histology: A comparative evaluation of model architecture for classification of histology sections.

Zhong C, Han J, Borowsky A, Parvin B, Wang Y, Chang H.

Med Image Anal. 2017 Jan;35:530-543. doi: 10.1016/j.media.2016.08.010. Epub 2016 Sep 9.

11.

Erratum: Stiffness of the microenvironment upregulates ERBB2 expression in 3D cultures of MCF10A within the range of mammographic density.

Cheng Q, Bilgin CC, Fontenay G, Chang H, Henderson M, Han J, Parvin B.

Sci Rep. 2016 Aug 24;6:31680. doi: 10.1038/srep31680. No abstract available.

12.

Stiffness of the microenvironment upregulates ERBB2 expression in 3D cultures of MCF10A within the range of mammographic density.

Cheng Q, Bilgin CC, Fontenay G, Chang H, Henderson M, Han J, Parvin B.

Sci Rep. 2016 Jul 7;6:28987. doi: 10.1038/srep28987. Erratum in: Sci Rep. 2016 Aug 24;6:31680.

13.

BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models.

Bilgin CC, Fontenay G, Cheng Q, Chang H, Han J, Parvin B.

PLoS One. 2016 Mar 15;11(3):e0148379. doi: 10.1371/journal.pone.0148379. eCollection 2016.

14.

Machine Learning and Data Mining in Medical Imaging.

Shen D, Zhang D, Young A, Parvin B.

IEEE J Biomed Health Inform. 2015 Sep;19(5):1587-8. No abstract available.

PMID:
26574616
15.

Functionalized Buckyballs for Visualizing Microbial Species in Different States and Environments.

Cheng Q, Aravind A, Buckley M, Gifford A, Parvin B.

Sci Rep. 2015 Sep 8;5:13685. doi: 10.1038/srep13685.

16.

Stacked Predictive Sparse Decomposition for Classification of Histology Sections.

Chang H, Zhou Y, Borowsky A, Barner K, Spellman P, Parvin B.

Int J Comput Vis. 2015 May;113(1):3-18. Epub 2014 Dec 23.

17.

NUCLEI SEGMENTATION VIA SPARSITY CONSTRAINED CONVOLUTIONAL REGRESSION.

Zhou Y, Chang H, Barner KE, Parvin B.

Proc IEEE Int Symp Biomed Imaging. 2015 Apr;2015:1284-1287. doi: 10.1109/ISBI.2015.7164109. Epub 2015 Jul 23.

18.
19.

Scaling up graph-based semisupervised learning via prototype vector machines.

Zhang K, Lan L, Kwok JT, Vucetic S, Parvin B.

IEEE Trans Neural Netw Learn Syst. 2015 Mar;26(3):444-57. doi: 10.1109/TNNLS.2014.2315526.

20.

Classification of Histology Sections via Multispectral Convolutional Sparse Coding.

Zhou Y, Chang H, Barner K, Spellman P, Parvin B.

Conf Comput Vis Pattern Recognit Workshops. 2014 Jun;2014:3081-3088.

21.
22.

Stress signaling from human mammary epithelial cells contributes to phenotypes of mammographic density.

DeFilippis RA, Fordyce C, Patten K, Chang H, Zhao J, Fontenay GV, Kerlikowske K, Parvin B, Tlsty TD.

Cancer Res. 2014 Sep 15;74(18):5032-5044. doi: 10.1158/0008-5472.CAN-13-3390. Epub 2014 Aug 29.

23.

Molecular deconstruction, detection, and computational prediction of microenvironment-modulated cellular responses to cancer therapeutics.

Labarge MA, Parvin B, Lorens JB.

Adv Drug Deliv Rev. 2014 Apr;69-70:123-31. doi: 10.1016/j.addr.2014.02.009. Epub 2014 Feb 26. Review.

24.

Characterization of tissue histopathology via predictive sparse decomposition and spatial pyramid matching.

Chang H, Nayak N, Spellman PT, Parvin B.

Med Image Comput Comput Assist Interv. 2013;16(Pt 2):91-8.

25.

CLASSIFICATION OF TUMOR HISTOPATHOLOGY VIA SPARSE FEATURE LEARNING.

Nayak N, Chang H, Borowsky A, Spellman P, Parvin B.

Proc IEEE Int Symp Biomed Imaging. 2013 Apr;2013. doi: 10.1109/ISBI.2013.6556499.

26.

Classification of Tumor Histology via Morphometric Context.

Chang H, Borowsky A, Spellman P, Parvin B.

Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2013 Jun 23;2013. doi: 10.1109/CVPR.2013.286.

27.

Integrated profiling of three dimensional cell culture models and 3D microscopy.

Bilgin CC, Kim S, Leung E, Chang H, Parvin B.

Bioinformatics. 2013 Dec 1;29(23):3087-93. doi: 10.1093/bioinformatics/btt535. Epub 2013 Sep 16.

28.

Breast fibroblasts modulate early dissemination, tumorigenesis, and metastasis through alteration of extracellular matrix characteristics.

Dumont N, Liu B, Defilippis RA, Chang H, Rabban JT, Karnezis AN, Tjoe JA, Marx J, Parvin B, Tlsty TD.

Neoplasia. 2013 Mar;15(3):249-62.

29.

Stacked Predictive Sparse Coding for Classification of Distinct Regions of Tumor Histopathology.

Chang H, Zhou Y, Spellman P, Parvin B.

Proc IEEE Int Conf Comput Vis. 2013:169-176.

30.

Invariant delineation of nuclear architecture in glioblastoma multiforme for clinical and molecular association.

Chang H, Han J, Borowsky A, Loss L, Gray JW, Spellman PT, Parvin B.

IEEE Trans Med Imaging. 2013 Apr;32(4):670-82. doi: 10.1109/TMI.2012.2231420. Epub 2012 Dec 4.

31.

Automatic Segmentation and Quantification of Filamentous Structures in Electron Tomography.

Loss LA, Bebis G, Chang H, Auer M, Sarkar P, Parvin B.

ACM BCB. 2012 Oct;2012:170-177. doi: 10.1145/2382936.2382958.

32.

Multireference level set for the characterization of nuclear morphology in glioblastoma multiforme.

Chang H, Han J, Spellman PT, Parvin B.

IEEE Trans Biomed Eng. 2012 Dec;59(12):3460-7. doi: 10.1109/TBME.2012.2218107. Epub 2012 Sep 10.

33.

Inference of causal networks from time-varying transcriptome data via sparse coding.

Zhang K, Han J, Groesser T, Fontenay G, Parvin B.

PLoS One. 2012;7(8):e42306. doi: 10.1371/journal.pone.0042306. Epub 2012 Aug 20.

34.

A molecular method for the delivery of small molecules and proteins across the cell wall of algae using molecular transporters.

Hyman JM, Geihe EI, Trantow BM, Parvin B, Wender PA.

Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13225-30. doi: 10.1073/pnas.1202509109. Epub 2012 Jul 30.

35.

CD36 repression activates a multicellular stromal program shared by high mammographic density and tumor tissues.

DeFilippis RA, Chang H, Dumont N, Rabban JT, Chen YY, Fontenay GV, Berman HK, Gauthier ML, Zhao J, Hu D, Marx JJ, Tjoe JA, Ziv E, Febbraio M, Kerlikowske K, Parvin B, Tlsty TD.

Cancer Discov. 2012 Sep;2(9):826-39. Epub 2012 Jul 9.

36.

Histomorphometric study of lumen of human vermiform appendix.

Rahman MM, Khalil M, Sultana SZ, Jahan MK, Shafiquzzaman M, Parvin B, Islam MT.

Mymensingh Med J. 2012 Jan;21(1):39-43.

PMID:
22314452
37.

Identification of fluorescent compounds with non-specific binding property via high throughput live cell microscopy.

Nath S, Spencer VA, Han J, Chang H, Zhang K, Fontenay GV, Anderson C, Hyman JM, Nilsen-Hamilton M, Chang YT, Parvin B.

PLoS One. 2012;7(1):e28802. doi: 10.1371/journal.pone.0028802. Epub 2012 Jan 5.

38.

Morphometic analysis of TCGA glioblastoma multiforme.

Chang H, Fontenay GV, Han J, Cong G, Baehner FL, Gray JW, Spellman PT, Parvin B.

BMC Bioinformatics. 2011 Dec 20;12:484. doi: 10.1186/1471-2105-12-484.

39.

COMPARISON OF SPARSE CODING AND KERNEL METHODS FOR HISTOPATHOLOGICAL CLASSIFICATION OF GLIOBASTOMA MULTIFORME.

Han J, Chang H, Loss L, Zhang K, Baehner FL, Gray JW, Spellman P, Parvin B.

Proc IEEE Int Symp Biomed Imaging. 2011 Jun 9;2011:711-714.

40.

Iterative tensor voting for perceptual grouping of ill-defined curvilinear structures.

Loss LA, Bebis G, Parvin B.

IEEE Trans Med Imaging. 2011 Aug;30(8):1503-13. doi: 10.1109/TMI.2011.2129526. Epub 2011 Mar 17.

41.

Persistence of γ-H2AX and 53BP1 foci in proliferating and non-proliferating human mammary epithelial cells after exposure to γ-rays or iron ions.

Groesser T, Chang H, Fontenay G, Chen J, Costes SV, Helen Barcellos-Hoff M, Parvin B, Rydberg B.

Int J Radiat Biol. 2011 Jul;87(7):696-710. doi: 10.3109/09553002.2010.549535. Epub 2011 Jan 27.

PMID:
21271785
42.

Multiscale iterative voting for differential analysis of stress response for 2D and 3D cell culture models.

Han J, Chang H, Yang Q, Fontenay G, Groesser T, Barcellos-Hoff MH, Parvin B.

J Microsc. 2011 Mar;241(3):315-26. doi: 10.1111/j.1365-2818.2010.03442.x. Epub 2010 Aug 26.

43.

Linking changes in epithelial morphogenesis to cancer mutations using computational modeling.

Rejniak KA, Wang SE, Bryce NS, Chang H, Parvin B, Jourquin J, Estrada L, Gray JW, Arteaga CL, Weaver AM, Quaranta V, Anderson AR.

PLoS Comput Biol. 2010 Aug 26;6(8). pii: e1000900. doi: 10.1371/journal.pcbi.1000900.

44.

Exon-level microarray analyses identify alternative splicing programs in breast cancer.

Lapuk A, Marr H, Jakkula L, Pedro H, Bhattacharya S, Purdom E, Hu Z, Simpson K, Pachter L, Durinck S, Wang N, Parvin B, Fontenay G, Speed T, Garbe J, Stampfer M, Bayandorian H, Dorton S, Clark TA, Schweitzer A, Wyrobek A, Feiler H, Spellman P, Conboy J, Gray JW.

Mol Cancer Res. 2010 Jul;8(7):961-74. doi: 10.1158/1541-7786.MCR-09-0528. Epub 2010 Jul 6.

45.

Sparse multitask regression for identifying common mechanism of response to therapeutic targets.

Zhang K, Gray JW, Parvin B.

Bioinformatics. 2010 Jun 15;26(12):i97-105. doi: 10.1093/bioinformatics/btq181.

46.

Prediction of epigenetically regulated genes in breast cancer cell lines.

Loss LA, Sadanandam A, Durinck S, Nautiyal S, Flaucher D, Carlton VE, Moorhead M, Lu Y, Gray JW, Faham M, Spellman P, Parvin B.

BMC Bioinformatics. 2010 Jun 4;11:305. doi: 10.1186/1471-2105-11-305.

47.

Molecular predictors of 3D morphogenesis by breast cancer cell lines in 3D culture.

Han J, Chang H, Giricz O, Lee GY, Baehner FL, Gray JW, Bissell MJ, Kenny PA, Parvin B.

PLoS Comput Biol. 2010 Feb 26;6(2):e1000684. doi: 10.1371/journal.pcbi.1000684.

48.

Multidimensional profiling of cell surface proteins and nuclear markers.

Han J, Chang H, Andarawewa K, Yaswen P, Barcellos-Hoff MH, Parvin B.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Jan-Mar;7(1):80-90. doi: 10.1109/TCBB.2008.134.

PMID:
20150670
49.

MORPHOMETRIC SUBTYPING FOR A PANEL OF BREAST CANCER CELL LINES.

Han J, Chang H, Fontenay G, Wang NJ, Gray JW, Parvin B.

Proc IEEE Int Symp Biomed Imaging. 2009 Jun 28;6:791-794.

50.

Basal subtype and MAPK/ERK kinase (MEK)-phosphoinositide 3-kinase feedback signaling determine susceptibility of breast cancer cells to MEK inhibition.

Mirzoeva OK, Das D, Heiser LM, Bhattacharya S, Siwak D, Gendelman R, Bayani N, Wang NJ, Neve RM, Guan Y, Hu Z, Knight Z, Feiler HS, Gascard P, Parvin B, Spellman PT, Shokat KM, Wyrobek AJ, Bissell MJ, McCormick F, Kuo WL, Mills GB, Gray JW, Korn WM.

Cancer Res. 2009 Jan 15;69(2):565-72. doi: 10.1158/0008-5472.CAN-08-3389.

Supplemental Content

Loading ...
Support Center