Software

SurvivalNet

SurvivalNet is a Python package that enables training, hyperparameter optimization, and model interpretation for Cox regression neural networks and genomic/clinical data. This project is actively maintained as an open-source project on GitHub, and a Docker container is provided to simplify installation and use.

S Yousefi, F Amrollahi, M Amgad, C Dong, JE Lewis, C Song, DA Gutman, S Halani, JE Velazquez-Vega, DJ Brat, LAD Cooper, Predicting clinical outcomes from large scale cancer genomic profiles with deep survival models, Scientific Reports, 7(11707), September 2017, PMID: 28916782

HistomicsTK / Digital Slide Archive

The Digital Slide Archive and HistomicsTK provide a web-based platform for the management, sharing, annotation, and analysis of digital pathology datasets. Developed in collaboration with Kitware using an open-source model, these projects are hosted on GitHub with Docker images available for easy deployment.

DA Gutman, M Khalilia , S Lee , M Nalisnik , Z Mullen , J Beezley , D Chittajallu , D Manthey, LAD Cooper, The Digital Slide Archive: A Software Platform for Management, Integration and Analysis of Histology for Cancer Research, Cancer Research, 77(21), pp. 75-78, November 2017, PMID: 29092945

HistomicsML

HistomicsML is a web-based platform that enables users to interact with powerful machine-learning algorithms in digital pathology images. HistomicsML uses active learning to create highly accurate classifiers to identify structures and tissue regions. A Docker image is available for easy deployment.

M Nalisnik, M Amgad, S Lee, SH Halani, JE Velazquez-Vega, DJ Brat, DA Gutman, LAD Cooper, Interactive phenotyping of large-scale histology imaging data with HistomicsML, Scientific Reports, 7(14588), November 2017, PMID: 29109450

Publications

LAD Cooper, EG Demicco, JH Saltz, RT Powell, A Rao, AJ Lazar, PanCancer insights from The Cancer Genome Atlas: the pathologist’s perspective, Journal of Pathology (Annual Review Issue), 244(5), pp. 512-524, April 2018, PMID: 29288495

P Mobadersany, S Yousefi, M Amgad, DA Gutman, JS Barnholtz-Sloan, JE Velazquez-Vega, DJ Brat, LAD Cooper, Predicting cancer outcomes from histology and genomics using convolutional networks, PNAS, 115(13), pp. 2970-2979, March 2018, PMID: 29531073

S Gurbani, E Schreibmann, AA Maudsley, JS Cordova, BK Soher, G Verma, P Barker, H Shim, LAD Cooper, A Convolutional Neural Network to Filter Artifacts in Spectroscopic Magnetic Resonance Imaging, Magnetic Resonance in Medicine, March 2018, PMID: 29520831

J Jordan, JS Goldstein, D Jaye, M Gurcan, CR Flowers, LAD Cooper, Informatics Approaches to Address New Challenges in the Classification of Lymphoid Malignancies, Journal of Clinical Oncology - Clinical Cancer Informatics, Published online February 2018, DOI: 10.1200/CCI.17.00039

AA Ivanov, B Revennaugh, L Rusnak, V Gonzalez-Pecchi, X Mo, MA Johns, Y Du, LAD Cooper, CS Moreno, FR Khuri, H Fu, The OncoPPi Portal: an integrative resource to explore and prioritize protein-protein interactions for cancer target discovery, Bioinformatics, November 2017, PMID: 29186335

M Nalisnik, M Amgad, S Lee, SH Halani, JE Velazquez-Vega, DJ Brat, DA Gutman, LAD Cooper, Interactive phenotyping of large-scale histology imaging data with HistomicsML, Scientific Reports, 7(14588), November 2017, PMID: 29109450

The Cancer Genome Atlas Research Network Comprehensive and integrated genomic characterization of adult soft tissue sarcomas, Cell, 171(4), pp. 950-965, November 2017, PMID: 29100075

DA Gutman, M Khalilia , S Lee , M Nalisnik , Z Mullen , J Beezley , D Chittajallu , D Manthey, LAD Cooper, The Digital Slide Archive: A Software Platform for Management, Integration and Analysis of Histology for Cancer Research, Cancer Research, 77(21), pp. 75-78, November 2017, PMID: 29092945

J Ross, LAD Cooper, DA Gutman, J Kong, M Williams, C Tucker-Burden, M McCrary, A Bouras, M Kaluzova, W Dunn, D Duong, C Hadjipanayis, DJ Brat, 5-Aminolevulinic Acid Guided Sampling of Glioblastoma Microenvironments Identifies Pro-Survival Signaling at Infiltrative Margins, Scientific Reports, 7(15593), November 2017, PMID: 29142297

LM Poisson, DJ Brat, Y Zhou, LAD Cooper, M Snuderl, C Thomas, AM Franceschi, B Griffith, A Flanders, JG Golfinos, AS Chi, R Jain, T2-FLAIR Mismatch, an Imaging Biomarker for IDH and 1p/19q Status in Lower Grade Gliomas: A TCGA/TCIA Project, Clinical Cancer Research, 23(20), October 2017, PMID: 28751449

S Yousefi, F Amrollahi, M Amgad, C Dong, JE Lewis, C Song, DA Gutman, S Halani, JE Velazquez-Vega, DJ Brat, LAD Cooper, Predicting clinical outcomes from large scale cancer genomic profiles with deep survival models, Scientific Reports, 7(11707), September 2017, PMID: 28916782

S Harati, LAD Cooper, JD Moran, Y Du, AA Ivanov, MA Johns, FR Khuri, H Fu, CS Moreno, MEDICI: Mining Essentiality Data to Identify Critical Interactions for Cancer Drug Target Discovery and Development, PLoS One, 12(1), January 2017, PMID: 28118365

S Wilkinson, Y Hou, JT Zoine, J Saltz, LAD Cooper, AI Marcus, Coordinated cell motility is regulated by a combination of LKB1 farnesylation and kinase activity, Scientific Reports, 7(40929), January 2017, PMID: 28102310

L Zenggang, AA Ivanov, S Rina, Q Qi, P Webber, E McMillan, V Gonzalez-Pecchi, C Pham, X Cheng, C Li, X Dong, XL Mo, S Liu, B Revennaugh, W Zhou, A Marcus, S Harati, X Chen, M Johns, M White, CS Moreno, LAD Cooper, Y Du, F Khuri, H Fu, The OncoPPi Network of Cancer-focused Protein-Protein Interactions to Inform Biological Insights and Therapeutic Strategies, Nature Communications, 8(14356), February 2017, PMID: 28205554

XL Mo, Q Qi, AA Ivanov, Q Niu, Y Luo, J Havel, R Goetze, S Bell, CS Moreno, LAD Cooper, MA Johns, FR Khuri, Y Du, H Fu, AKT1, LKB1, and YAP1 revealed as MYC interactors with NanoLuc-based protein-fragment complementation assay, Molecular Pharmacology, 91(4), pp. 339- 47, April 2017, PMID: 28087810

AE Kersh, M Sasaki, LAD Cooper, HT Kissick, BP Pollack, Understanding the impact of ErbB activating events and signal transduction on antigen processing and presentation: MHC expression as a model, Frontiers in Pharmacology, Cancer Molecular Targets and Therapeutics, 7(32), September 2016, PMID: 27729860

K Huang, Y Liu, Y Huang, L Li, LAD Cooper, J Ruan, Z Zhao, Intelligent biology and medicine in 2015: advancing interdisciplinary education, collaboration, and data science, BMC Genomics, 17 Supplement 7, August 2016, PMID: 27556295

JS Cordova, CG Hadjipanayis, Z Liang, SS Gurbani, LAD Cooper, CA Holder, JJ Olson, E Schreibmann, S Neill, HG Shu, H Shim, Whole-brain, volumetric spectroscopic MRI identifies infiltrating margins in glioblastoma, Neuro-Oncology, 18(8), pp. 1180-9, March 2016, PMID: 26984746

JS Cordova, SS Gurbani, JJ Olson, Z Liang, LAD Cooper, HG Shu, E Schreibmann, S Neill, CG Hadjipanayis, CA Holder, H Shim, A systemic pipeline for the objective comparison of whole-brain spectroscopic MRI with histology in biopsy specimens from grade III glioma, Tomography, 2(2), pp. 106-16, June 2016, PMID: 27489883

M Ceccarelli, FP Barthel, TM Malta, TS Sabedot, SR Salama, SM Pagnotta, BA Murray, O Mo- rozova, Y Newton, J Wang, DJ Brat, P Zoppoli, R Akbani, AD Cherniack, H Zhang, L Posson, T Mikelsen, WKA Yung, J Huse, CC Lau, A Rao, M Grifford, M Wrensch, R Beroukhim, LAD Cooper, R Rabadan, KD Aldape, PW Laird, DH Gutmann, H Noushmehr, A Iavarone, RGW Ver- haak, The Cancer Genome Atlas Research Network, Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma, Cell, 164(3), pp. 550-63, January 2016, PMID: 26824661

BH Hinrichs, S Newman, CL Appin, W Dunn, LAD Cooper, R Pauly, J Kowalski, M Rossi, DJ Brat, Farewell to GBM-O: Genomic and Transcriptomic Profiling of Glioblastoma with Oligodendroglioma Component Reveals Distinct Molecular Subtypes, Acta Neuropathologica Communications, 4(4), January 2016, PMID: 26757882

T Kurc, X Qi, D Wang, G Teodoro, LAD Cooper, M Nalisnik, L Yang, JH Saltz, DJ Foran, Scalable analysis of Big pathology image data cohorts using efficient methods and high-performance computing strategies, BMC Bioinformatics, 16(1), Dec 2015, PMID: 26627175

DA Gutman, WD Dunn, P Grossmann, LAD Cooper, CA Holder, KL Ligon, BM Alexander, HL Aerts, Somatic mutations associated with MRI-derived volumetric features in glioblastoma, Neuroradiology, 57(12), pp. 1227-37, Dec 2015, PMID: 26337765

The Cancer Genome Atlas Research Network, Comprehensive and Integrative Genomic Characterization of Diffuse Lower Grade Gliomas, New England Journal of Medicine, 372, pp. 2481-98, June 2015, PMID: 26061751

LAD Cooper, J Kong, DA Gutman, WD Dunn, M Nalisnik, DJ Brat, Novel genotype-phenotype associations in human cancers enabled by advanced molecular platforms and computational analysis of whole slide images, Laboratory Investigation, 95(4), pp. 366-76, April 2015, PMID: 25599536

J Kong, LAD Cooper, F Wang, J Gao, G Teodoro, L Scarpace, T Mikkelsen, MJ Schniederjan, CS Moreno, JH Saltz, DJ Brat, Machine-based morphologic analysis of glioblastoma using whole-slide pathology images uncovers clinically relevant molecular correlates, PLoS One, 8(11), pp. e81049, doi: 10.1371/journal.pone.0081049, November 2013, PMID: 24236209

DA Gutman, J Cobb, D Somanna, Y Park, F Wang, T Kurc, JH Saltz, DJ Brat, LAD Cooper, Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of Revised January 30, 2018 TCGA pathology data, JAMIA, 20(6), pp. 1091-98, November 2013, PMID: 23893318

WC Rutledge, J Kong, J Gao, DA Gutman, LAD Cooper, C Appin, Y Park, L Scarpace, T Mikkelsen, ML Cohen, KD Aldape, RE McLendon, NL Lehman, CR Miller, MJ Schniederjan, CW Brennan, CS Moreno, JH Saltz, DJ Brat, Tumor-infiltrating lymphocytes in glioblastoma are associated with specific genomic alterations and related to transcriptional class, Clinical Cancer Research, 19(18), pp. 4951-60, September 2013, PMID: 23864165

DA Gutman, LAD Cooper, SN Hwang, CA Holder, J Gao, TD Aurora, WD Dunn Jr, L Scarpace, T Mikkelsen, R Jain, M Wintermark, M Jilwan, P Raghavan, E Huang, RJ Clifford, P Mongkolwat, V Kleper, J Freymann, J Kirby, PO Zinn, CS Moreno, C Jaffe, R Colen, DL Rubin, JH Saltz, A Flanders, DJ Brat, MR imaging predictors of molecular profile and survival: multi-institutional study of the TCGA glioblastoma data set, Radiology, 267(2), pp. 560-9, May 2013, PMID: 23392431

G Teodoro, T Pan, T Kurc, J Kong, LAD Cooper, JH Saltz, Efficient irregular wavefront propagation algorithms on hybrid CPU/GPU machines, Parallel Computing, 39(4-5), pp. 189-211, April 2013, PMID: 23908562

LAD Cooper, DA Gutman, C Chisolm, C Appin, J Kong, Y Rong, T Kurc, EG Van Meir, JH Saltz, CS Moreno, DJ Brat, The Tumor Microenvironment Strongly Impacts Master Transcriptional Regulators and Gene Expression Class of Glioblastoma, The American Journal of Pathology, 180(5), pp. 2108-2129, May 2012, PMID: 22440258

LAD Cooper, AB Carter, AB Farris, F Wang, J Kong, DA Gutman, P Widener, TC Pan, SR Cholleti, A Sharma, T Kurc, DJ Brat, JH Saltz, Digital Pathology: Data-Intensive Frontier in Medical Imaging, Proceedings of the IEEE, 100(4), pp. 991-1003, April 2012, PMID: 25328166

LAD Cooper, J Kong, DA Gutman, F Wang, J Gao, C Appin, S Cholleti, T Pan, A Sharma, L Scarpace, T Mikkelsen, T Kurc, CS Moreno, DJ Brat, JH Saltz, Integrated morphologic analysis for the identification and characterization of disease subtypes, JAMIA, 19(2), pp. 317-323, March-April 2012, PMID: 22278382

SM Cork, B Kaur, NS Devi, LAD Cooper, JH Saltz, EM Sandberg, S Kaluz, EG Van Meir, A proprotein convertase/MMP-14 proteolytic cascade releases a novel 40kDa vasculostatin from tumor suppressor BAI1, Oncogene, 31(50): pp. 5144-52; December 2012, PMID: 22330140

LAD Cooper, DA Gutman, Q Long, BA Johnson, SR Cholleti, T Kurc, JH Saltz, DJ Brat, CS Moreno, The Proneural Molecular Signature is Enriched in Oligodendrogliomas and Predicts Im- proved Survival among Diffuse Gliomas, PLoS ONE, 5(9), pp. e12548. doi:10.1371/journal.pone.0012548, September 2010, PMID: 20838435

LAD Cooper, J Kong, DA Gutman, F Wang, SR Cholleti, T Pan, P Widener, A Sharma, T Mikkelsen, A Flanders, D Rubin, E Van Meir, T Kurc, C Moreno, DJ Brat, JH Saltz, An Integrative Approach for In Silico Glioma Research, IEEE Transactions on Biomedical Engineering Letters, 57(10), pp.2617-21, October 2010, PMID: 20656651

K Mosaliganti, LAD Cooper, R Sharp, R Machiraju, G Leone, K Huang, JH Saltz, Reconstruction of cellular biological structures from optical microscopy data, IEEE Transaction on Visualization and Computer Graphics, 14(4), pp. 863-76, August 2008, PMID: 18467760

A Ruiz, M Ujaldon, LAD Cooper, K Huang, Non-rigid Registration for Large Set of Microscopic Images on Graphics Processors, Journal of Signal Processing Systems, 55(1), pp.229-50, April 2009, PMID: 25328635

LAD Cooper, O Sertel, J Kong, G Lozanski, K Huang, M Gurcan, Feature-Based Registration of Histopathology Images with Different Stains: An Application for Computerized Follicular Lym- phoma Prognosis, Computer Programs and Methods in Biomedicine, 96(3), pp.182-92, May 2009, PMID: 19487043