Publications

Journals Articles:

1. A radiogenomic dataset of non-small cell lung cancer

S Bakr, O Gevaert, S Echegaray, K Ayers, M Zhou, M Shafiq, H Zheng, ...

Scientific data 5 (1), 1-9

2. Noninvasive radiomics signature based on quantitative analysis of computed tomography images as a surrogate for microvascular invasion in hepatocellular carcinoma: a pilot study

S Bakr, S Echegaray, R Shah, A Kamaya, J Louie, S Napel, N Kothary, ...

Journal of Medical Imaging 4 (4), 041303-041303

3. GFPT2-Expressing Cancer-Associated Fibroblasts Mediate Metabolic Reprogramming in Human Lung Adenocarcinoma

W Zhang, G Bouchard, A Yu, M Shafiq, M Jamali, JB Shrager, K Ayers, ...

Cancer research 78 (13), 3445-3457

4. Data for NSCLC radiogenomics collection

S Bakr, O Gevaert, S Echegaray, K Ayers, M Zhou, M Shafiq, H Zheng, ...

The Cancer Imaging Archive

5. Quantitative Image Feature Engine (QIFE): an open-source, modular engine for 3D quantitative feature extraction from volumetric medical images

S Echegaray, S Bakr, DL Rubin, S Napel

Journal of digital imaging 31, 403-414

6. [18F] FDG Positron emission tomography (PET) tumor and penumbra imaging features predict recurrence in non–small cell lung cancer

SA Mattonen, GA Davidzon, S Bakr, S Echegaray, ANC Leung, ...

Tomography 5 (1), 145-153

7. Quantitative imaging feature pipeline: a web-based tool for utilizing, sharing, and building image-processing pipelines

SA Mattonen, D Gude, S Echegaray, S Bakr, DL Rubin, S Napel

Journal of Medical Imaging 7 (4), 042803-042803

8. Imaging-AMARETTO: an imaging genomics software tool to interrogate multiomics networks for relevance to radiography and histopathology imaging biomarkers of clinical outcomes

O Gevaert, M Nabian, S Bakr, C Everaert, J Shinde, A Manukyan, ...

JCO clinical cancer informatics 4, 421-435

9. Data for NSCLC Radiogenomics Collection. The Cancer Imaging Archive. 2017

S Bakr, O Gevaert, S Echegaray, K Ayers, M Zhou, M Shafiq, H Zheng, ...

10. Interreader variability in semantic annotation of microvascular invasion in hepatocellular carcinoma on contrast-enhanced triphasic CT images

S Bakr, O Gevaert, B Patel, A Kesselman, R Shah, S Napel, N Kothary

Radiology: Imaging Cancer 2 (3), e190062

11. A radiogenomic dataset of non-small cell lung cancer. Sci Data. 2018; 5: 180202

S Bakr, O Gevaert, S Echegaray, K Ayers, M Zhou, M Shafiq, H Zheng, ...

Epub 2018/10/17. doi: 10.1038/sdata. 2018.202. PubMed PMID: 30325352

12. Data for NSCLC Radiogenomics collection. The Cancer Imaging Archive

S Bakr, O Gevaert, S Echegaray, K Ayers, M Zhou, M Shafiq, H Zheng, ...

13. Identifying key multifunctional components shared by critical cancer and normal liver pathways via sparseGMM

S Bakr, K Brennan, P Mukherjee, J Argemi, M Hernaez, O Gevaert

Cell Reports Methods, 100392

14. Characterization and Linking of Imaging and Molecular Patterns in Hepatocellular Carcinoma

SHA Bakr

Stanford University

15. Introduction to AMARETTO

J Shinde, C Everaert, S Bakr, M Nabian, J Xu, V Carey, N Pochet, ...

16. Positron Emission Tomography (PET) Tumor Penumbra Imaging Features Predict Outcome in Non-Small Cell Lung Cancer

S Mattonen, GA Davidzon, S Bakr, M Vasanawala, GS Horng, S Napel, ...

D99. CLINICALLY INFORMATIVE BIOMARKERS IN LUNG CANCER: A NEEDLE IN A …

17. Imaging-AMARETTO: a software tool for imaging genomics in cancer

O Gevaert, M Nabian, S Bakr, C Everaert, J Shinde, A Manukyan, ...

Conference Presentations and Abstracts:

1. Identifying key multifunctional components shared by critical cancer and normal liver pathways via sparseGMM, International Society for Computational Biology, ISMB , Madison, WI, July 2022.

2. Positron Emission Tomography (PET) Tumor Penumbra Imaging Features Predict Outcome in Non-Small Cell Lung Cancer, submitted to American Thoracic Society Annual Meeting, San Diego, CA, May 2018.

3. A Size-independent Radiomics Model for Classification of Indeterminate Pulmonary Nodules Seen at CT, RSNA 2017, November 2017

4. Radiogenomics data set for Non-Small Cell Lung Cancer, Radiomics 2016, October 2016

5. Solving Larger IMRT Problems by Enhanced Reduced-Order Constrained Optimization, AAPM 57th Annual Meeting & Exhibition, July 2016

6. ROCO optimization for IMRT treatment Planning, Stanford University, March 2015

7. Integration of Reduced Order Constrained Optimization for IMRT Planning into the Eclipse Treatment Planning System, AAPM Spring Clinical meeting, March 2015