My Bibliography

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Yellapragada S, Graikos A, Prasanna P, Kurc T, Saltz J, Samaras D. PathLDM: Text conditioned Latent Diffusion Model for Histopathology. IEEE Winter Conf Appl Comput Vis. 2024 Jan;2024:5170-5179. doi: 10.1109/wacv57701.2024.00510. Epub 2024 Apr 9. PubMed PMID: 38808304; PubMed Central PMCID: PMC11131586.

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Kapse S, Das S, Zhang J, Gupta RR, Saltz J, Samaras D, Prasanna P. Attention De-sparsification Matters: Inducing diversity in digital pathology representation learning. Med Image Anal. 2024 Apr;93:103070. doi: 10.1016/j.media.2023.103070. Epub 2023 Dec 28. PubMed PMID: 38176354; PubMed Central PMCID: PMC11150864.

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Delgado-Coka LA, Horowitz M, Torrente-Goncalves M, Roa-Peña L, Leiton CV, Hasan M, Babu S, Fassler D, Oentoro J, Karen Bai JD, Petricoin EF, Matrisian LM, Blais EM, Marchenko N, Allard FD, Jiang W, Larson B, Hendifar A, Chen C, Abousamra S, Samaras D, Kurc T, Saltz J, Escobar-Hoyos LF, Shroyer K. Keratin 17 modulates the immune topography of pancreatic cancer. Res Sq. 2024 Feb 20;. doi: 10.21203/rs.3.rs-3886691/v1. PubMed PMID: 38464123; PubMed Central PMCID: PMC10925455.

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Foran DJ, Chen W, Kurc T, Gupta R, Kaczmarzyk JR, Torre-Healy LA, Bremer E, Ajjarapu S, Do N, Harris G, Stroup A, Durbin E, Saltz JH. An Intelligent Search & Retrieval System (IRIS) and Clinical and Research Repository for Decision Support Based on Machine Learning and Joint Kernel-based Supervised Hashing. Cancer Inform. 2024;23:11769351231223806. doi: 10.1177/11769351231223806. eCollection 2024. PubMed PMID: 38322427; PubMed Central PMCID: PMC10840403.

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Kaczmarzyk JR, O'Callaghan A, Inglis F, Gat S, Kurc T, Gupta R, Bremer E, Bankhead P, Saltz JH. Open and reusable deep learning for pathology with WSInfer and QuPath. NPJ Precis Oncol. 2024 Jan 10;8(1):9. doi: 10.1038/s41698-024-00499-9. PubMed PMID: 38200147; PubMed Central PMCID: PMC10781748.

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van Assen M, Tariq A, Razavi AC, Yang C, Banerjee I, De Cecco CN. Fusion Modeling: Combining Clinical and Imaging Data to Advance Cardiac Care. Circ Cardiovasc Imaging. 2023 Dec;16(12):e014533. doi: 10.1161/CIRCIMAGING.122.014533. Epub 2023 Dec 11. Review. PubMed PMID: 38073535; PubMed Central PMCID: PMC10754220.

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Hart S, Garcia V, Dudgeon S, Hanna M, Li X, Blenman K, Elfer K, Ly A, Salgado R, Saltz J, Gupta R, Hytopoulos E, Larsimont D, Lennerz J, Gallas B. Initial interactions with the <scp>FDA</scp> on developing a validation dataset as a medical device development tool. The Journal of Pathology. 2023 October; :-. doi: 10.1002/path.6208.

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Kaczmarzyk J, Gupta R, Kurc T, Abousamra S, Saltz J, Koo P. ChampKit: A framework for rapid evaluation of deep neural networks for patch-based histopathology classification. Computer Methods and Programs in Biomedicine. 2023 September; 239:107631-. doi: 10.1016/j.cmpb.2023.107631.

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Kaczmarzyk JR, Gupta R, Kurc TM, Abousamra S, Saltz JH, Koo PK. ChampKit: A framework for rapid evaluation of deep neural networks for patch-based histopathology classification. Comput Methods Programs Biomed. 2023 Sep;239:107631. doi: 10.1016/j.cmpb.2023.107631. Epub 2023 May 30. PubMed PMID: 37271050; PubMed Central PMCID: PMC11093625.

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Abousamra S, Gupta R, Kurc T, Samaras D, Saltz J, Chen C. Topology-Guided Multi-Class Cell Context Generation for Digital Pathology. Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2023 Jun;2023:3323-3333. doi: 10.1109/cvpr52729.2023.00324. Epub 2023 Aug 22. PubMed PMID: 38741683; PubMed Central PMCID: PMC11090253.

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Abousamra S, Fassler D, Yao J, Gupta R, Kurc T, Escobar-Hoyos L, Samaras D, Shroyer K, Saltz J, Chen C. Unsupervised Stain Decomposition via Inversion Regulation for Multiplex Immunohistochemistry Images. Proc Mach Learn Res. 2023 Jul;227:74-94. PubMed PMID: 38817539; PubMed Central PMCID: PMC11138139.

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Smith K, Ulin K, Knopp M, Kry S, Xiao Y, Rosen M, Michalski J, Iandoli M, Laurie F, Quigley J, Reifler H, Santiago J, Briggs K, Kirby S, Schmitter K, Prior F, Saltz J, Sharma A, Bishop-Jodoin M, Moni J, Cicchetti MG, FitzGerald TJ. Quality improvements in radiation oncology clinical trials. Front Oncol. 2023;13:1015596. doi: 10.3389/fonc.2023.1015596. eCollection 2023. Review. PubMed PMID: 36776318; PubMed Central PMCID: PMC9911211.

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Yoo Y, Wilkins K, Alakwaa F, Liu F, Torre-Healy L, Krichevsky S, Hong S, Sakhuja A, Potu C, Saltz J, Saran R, Zhu R, Setoguchi S, Kane-Gill S, Mallipattu S, He Y, Ellison D, Byrd J, Parikh C, Moffitt R, Koraishy F. COVID-19-associated AKI in hospitalized US patients: incidence, temporal trends, geographical distribution, risk factors and mortality. [preprint]. 2022 September. doi: 10.1101/2022.09.02.22279398.

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Kobayashi S, Shieh J, Ruiz de Sabando A, Kim J, Liu Y, Zee SY, Prasanna P, Bialkowska AB, Saltz JH, Yang VW. Deep learning-based approach to the characterization and quantification of histopathology in mouse models of colitis. PLoS One. 2022;17(8):e0268954. doi: 10.1371/journal.pone.0268954. eCollection 2022. PubMed PMID: 36037173; PubMed Central PMCID: PMC9423669.

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Ding L, Bradford C, Kuo IL, Fan Y, Ulin K, Khalifeh A, Yu S, Liu F, Saleeby J, Bushe H, Smith K, Bianciu C, LaRosa S, Prior F, Saltz J, Sharma A, Smyczynski M, Bishop-Jodoin M, Laurie F, Iandoli M, Moni J, Cicchetti MG, FitzGerald TJ. Radiation Oncology: Future Vision for Quality Assurance and Data Management in Clinical Trials and Translational Science. Front Oncol. 2022;12:931294. doi: 10.3389/fonc.2022.931294. eCollection 2022. Review. PubMed PMID: 36033446; PubMed Central PMCID: PMC9399423.

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Barreiros W, Melo A, Kong J, Ferreira R, Kurc T, Saltz J, Teodoro G. Efficient microscopy image analysis on CPU-GPU systems with cost-aware irregular data partitioning. Journal of Parallel and Distributed Computing. 2022 June; 164:40-54. doi: 10.1016/j.jpdc.2022.02.004.

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Fassler DJ, Torre-Healy LA, Gupta R, Hamilton AM, Kobayashi S, Van Alsten SC, Zhang Y, Kurc T, Moffitt RA, Troester MA, Hoadley KA, Saltz J. Spatial Characterization of Tumor-Infiltrating Lymphocytes and Breast Cancer Progression. Cancers (Basel). 2022 Apr 26;14(9). doi: 10.3390/cancers14092148. PubMed PMID: 35565277; PubMed Central PMCID: PMC9105398.

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Abousamra S, Belinsky D, Van Arnam J, Allard F, Yee E, Gupta R, Kurc T, Samaras D, Saltz J, Chen C. Multi-Class Cell Detection Using Spatial Context Representation. Proc IEEE Int Conf Comput Vis. 2021 Oct;2021:3985-3994. doi: 10.1109/iccv48922.2021.00397. Epub 2022 Feb 28. PubMed PMID: 38783989; PubMed Central PMCID: PMC11114143.

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Kathiravelu P, Zaiman Z, Gichoya J, Veiga L, Banerjee I. Towards an internet-scale overlay network for latency-aware decentralized workflows at the edge. Comput Netw. 2022 Feb 11;203. doi: 10.1016/j.comnet.2021.108654. Epub 2021 Dec 11. PubMed PMID: 35082552; PubMed Central PMCID: PMC8785248.

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Sun S, Annadi R, Chaudhri I, Munir K, Hajagos J, Saltz J, Hoai M, Mallipattu S, Moffitt R, Koraishy F. Short- and Long-Term Recovery after Moderate/Severe AKI in Patients with and without COVID-19. Kidney360. 2022 February; 3(2):242-257. doi: 10.34067/KID.0005342021.

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Foran DJ, Durbin EB, Chen W, Sadimin E, Sharma A, Banerjee I, Kurc T, Li N, Stroup AM, Harris G, Gu A, Schymura M, Gupta R, Bremer E, Balsamo J, DiPrima T, Wang F, Abousamra S, Samaras D, Hands I, Ward K, Saltz JH. An Expandable Informatics Framework for Enhancing Central Cancer Registries with Digital Pathology Specimens, Computational Imaging Tools, and Advanced Mining Capabilities. J Pathol Inform. 2022;13:5. doi: 10.4103/jpi.jpi_31_21. eCollection 2022. PubMed PMID: 35136672; PubMed Central PMCID: PMC8794027.

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Agraz J, Grenko C, Chen A, Viaene A, Nasrallah M, Pati S, Kurc T, Saltz J, Feldman M, Akbari H, Sharma P, Shinohara R, Bakas S. Robust Image Population Based Stain Color Normalization: How Many Reference Slides Are Enough?. IEEE Open Journal of Engineering in Medicine and Biology. 2022; 3:218-226. doi: 10.1109/OJEMB.2023.3234443.

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Saha M, Guo X, Sharma A. TilGAN: GAN for Facilitating Tumor-Infiltrating Lymphocyte Pathology Image Synthesis With Improved Image Classification. IEEE Access. 2021;9:79829-79840. doi: 10.1109/access.2021.3084597. Epub 2021 May 28. PubMed PMID: 34178560; PubMed Central PMCID: PMC8224465.

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Haendel M, Chute C, Bennett T, Eichmann D, Guinney J, Kibbe W, Payne P, Pfaff E, Robinson P, Saltz J, Spratt H, Suver C, Wilbanks J, Wilcox A, Williams A, Wu C, Blacketer C, Bradford R, Cimino J, Clark M, Colmenares E, Francis P, Gabriel D, Graves A, Hemadri R, Hong S, Hripscak G, Jiao D, Klann J, Kostka K, Lee A, Lehmann H, Lingrey L, Miller R, Morris M, Murphy S, Natarajan K, Palchuk M, Sheikh U, Solbrig H, Visweswaran S, Walden A, Walters K, Weber G, Zhang X, Zhu R, Amor B, Girvin A, Manna A, Qureshi N, Kurilla M, Michael S, Portilla L, Rutter J, Austin C, Gersing K. The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment. Journal of the American Medical Informatics Association. 2021 March; 28(3):427-443. doi: 10.1093/jamia/ocaa196.

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Kathiravelu P, Sharma A, Sharma P. Understanding Scanner Utilization With Real-Time DICOM Metadata Extraction. IEEE Access. 2021;9:10621-10633. doi: 10.1109/access.2021.3050467. Epub 2021 Jan 11. PubMed PMID: 35966128; PubMed Central PMCID: PMC9373881.

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Fedorov A, Hancock M, Clunie D, Brochhausen M, Bona J, Kirby J, Freymann J, Pieper S, J W L Aerts H, Kikinis R, Prior F. DICOM re-encoding of volumetrically annotated Lung Imaging Database Consortium (LIDC) nodules. Med Phys. 2020 Nov;47(11):5953-5965. doi: 10.1002/mp.14445. Epub 2020 Sep 6. PubMed PMID: 32772385; PubMed Central PMCID: PMC7721965.

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Fassler DJ, Abousamra S, Gupta R, Chen C, Zhao M, Paredes D, Batool SA, Knudsen BS, Escobar-Hoyos L, Shroyer KR, Samaras D, Kurc T, Saltz J. Deep learning-based image analysis methods for brightfield-acquired multiplex immunohistochemistry images. Diagn Pathol. 2020 Jul 28;15(1):100. doi: 10.1186/s13000-020-01003-0. PubMed PMID: 32723384; PubMed Central PMCID: PMC7385962.

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Le H, Gupta R, Hou L, Abousamra S, Fassler D, Torre-Healy L, Moffitt RA, Kurc T, Samaras D, Batiste R, Zhao T, Rao A, Van Dyke AL, Sharma A, Bremer E, Almeida JS, Saltz J. Utilizing Automated Breast Cancer Detection to Identify Spatial Distributions of Tumor-Infiltrating Lymphocytes in Invasive Breast Cancer. Am J Pathol. 2020 Jul;190(7):1491-1504. doi: 10.1016/j.ajpath.2020.03.012. Epub 2020 Apr 8. PubMed PMID: 32277893; PubMed Central PMCID: PMC7369575.

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Panayides AS, Amini A, Filipovic ND, Sharma A, Tsaftaris SA, Young A, Foran D, Do N, Golemati S, Kurc T, Huang K, Nikita KS, Veasey BP, Zervakis M, Saltz JH, Pattichis CS. AI in Medical Imaging Informatics: Current Challenges and Future Directions. IEEE J Biomed Health Inform. 2020 Jul;24(7):1837-1857. doi: 10.1109/JBHI.2020.2991043. PubMed PMID: 32609615; PubMed Central PMCID: PMC8580417.

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Hou L, Gupta R, Van Arnam JS, Zhang Y, Sivalenka K, Samaras D, Kurc TM, Saltz JH. Dataset of segmented nuclei in hematoxylin and eosin stained histopathology images of ten cancer types. Sci Data. 2020 Jun 19;7(1):185. doi: 10.1038/s41597-020-0528-1. PubMed PMID: 32561748; PubMed Central PMCID: PMC7305328.

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Hou L, Agarwal A, Samaras D, Kurc TM, Gupta RR, Saltz JH. Robust Histopathology Image Analysis: to Label or to Synthesize?. Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2019 Jun;2019:8533-8542. doi: 10.1109/CVPR.2019.00873. Epub 2020 Jan 9. PubMed PMID: 34025103; PubMed Central PMCID: PMC8139403.

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Wong C, Tang LH, Davidson C, Vosburgh E, Chen W, Foran DJ, Notterman DA, Levine AJ, Xu EY. Two well-differentiated pancreatic neuroendocrine tumor mouse models. Cell Death Differ. 2020 Jan;27(1):269-283. doi: 10.1038/s41418-019-0355-0. Epub 2019 Jun 3. PubMed PMID: 31160716; PubMed Central PMCID: PMC7206057.

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Barnette DA, Davis MA, Flynn N, Pidugu AS, Swamidass SJ, Miller GP. Comprehensive kinetic and modeling analyses revealed CYP2C9 and 3A4 determine terbinafine metabolic clearance and bioactivation. Biochem Pharmacol. 2019 Dec;170:113661. doi: 10.1016/j.bcp.2019.113661. Epub 2019 Oct 9. PubMed PMID: 31605674; PubMed Central PMCID: PMC6905088.

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Kurc T, Sharma A, Gupta R, Hou L, Le H, Abousamra S, Bremer E, Birmingham R, DiPrima T, Li N, Wang F. From Whole Slide Tissues to Knowledge: Mapping Sub-cellular Morphology of Cancer. Springer Cham. 2019 October.

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Le H, Samaras D, Kurc T, Gupta R, Shroyer K, Saltz J. Pancreatic cancer detection in whole slide images using noisy label annotations. Springer Cham. 2019 October.

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Ren J, Singer EA, Sadimin E, Foran DJ, Qi X. Statistical Analysis of Survival Models Using Feature Quantification on Prostate Cancer Histopathological Images. J Pathol Inform. 2019;10:30. doi: 10.4103/jpi.jpi_85_18. eCollection 2019. PubMed PMID: 31620309; PubMed Central PMCID: PMC6788183.

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Taveira LFR, Kurc T, Melo ACMA, Kong J, Bremer E, Saltz JH, Teodoro G. Multi-objective Parameter Auto-tuning for Tissue Image Segmentation Workflows. J Digit Imaging. 2019 Jun;32(3):521-533. doi: 10.1007/s10278-018-0138-z. PubMed PMID: 30402669; PubMed Central PMCID: PMC6499855.

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Ren J, Hacihaliloglu I, Singer EA, Foran DJ, Qi X. Unsupervised Domain Adaptation for Classification of Histopathology Whole-Slide Images. Front Bioeng Biotechnol. 2019;7:102. doi: 10.3389/fbioe.2019.00102. eCollection 2019. PubMed PMID: 31158269; PubMed Central PMCID: PMC6529804.

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Gomes J, Barreiros W Jr, Kurc T, Melo ACMA, Kong J, Saltz JH, Teodoro G. Sensitivity analysis in digital pathology: Handling large number of parameters with compute expensive workflows. Comput Biol Med. 2019 May;108:371-381. doi: 10.1016/j.compbiomed.2019.03.006. Epub 2019 Mar 13. PubMed PMID: 31054503; PubMed Central PMCID: PMC7363453.

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Hou L, Nguyen V, Kanevsky AB, Samaras D, Kurc TM, Zhao T, Gupta RR, Gao Y, Chen W, Foran D, Saltz JH. Sparse Autoencoder for Unsupervised Nucleus Detection and Representation in Histopathology Images. Pattern Recognit. 2019 Feb;86:188-200. doi: 10.1016/j.patcog.2018.09.007. Epub 2018 Sep 13. PubMed PMID: 30631215; PubMed Central PMCID: PMC6322841.

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Malkin K, Robinson C, Hou L, Soobitsky R, Czawlytko J, Samaras D, Saltz J, Joppa L, Jolic N. Label super-Resolution Networks. ICLR 2019. 2019. NIHMSID: NIHMS1027980.

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Pandrekar S, Chen X, Gopalkrishna G, Srivastava A, Saltz M, Saltz J, Wang F. Social Media Based Analysis of Opioid Epidemic Using Reddit. AMIA Annu Symp Proc. 2018;2018:867-876. eCollection 2018. PubMed PMID: 30815129; PubMed Central PMCID: PMC6371364.

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Ren J, Karagoz K, Gatza ML, Singer EA, Sadimin E, Foran DJ, Qi X. Recurrence analysis on prostate cancer patients with Gleason score 7 using integrated histopathology whole-slide images and genomic data through deep neural networks. J Med Imaging (Bellingham). 2018 Oct;5(4):047501. doi: 10.1117/1.JMI.5.4.047501. Epub 2018 Nov 15. PubMed PMID: 30840742; PubMed Central PMCID: PMC6237203.

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Gomes J, de Melo ACMA, Kong J, Kurc T, Saltz JH, Teodoro G. Cooperative and out-of-core execution of the irregular wavefront propagation pattern on hybrid machines with Intel(Ⓡ) Xeon Phi™. Concurr Comput. 2018 Jul 25;30(14). doi: 10.1002/cpe.4425. Epub 2018 Jan 24. PubMed PMID: 30344454; PubMed Central PMCID: PMC6195363.

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Umphlett M, Nguyen V, Gupta R, Samaras D, Bell H, Saltz J, Tsankova N. Utilizing Histology to Define a Digital Signature for Cell Infiltration in Glioblastoma. JOURNAL OF NEUROPATHOLOGY AND EXPERIMENTAL NEUROLOGY. 2018 June; 77(6):495-495.

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Wen S, Kurc TM, Hou L, Saltz JH, Gupta RR, Batiste R, Zhao T, Nguyen V, Samaras D, Zhu W. Comparison of Different Classifiers with Active Learning to Support Quality Control in Nucleus Segmentation in Pathology Images. AMIA Jt Summits Transl Sci Proc. 2018;2017:227-236. eCollection 2018. PubMed PMID: 29888078; PubMed Central PMCID: PMC5961826.

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Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Mokrab Y, Newman AM, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CS, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I. The Immune Landscape of Cancer. Immunity. 2018 Apr 17;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023. Epub 2018 Apr 5. PubMed PMID: 29628290; PubMed Central PMCID: PMC5982584.

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Chen X, Wang Y, Yu X, Schoenfeld E, Saltz M, Saltz J, Wang F. Large-scale Analysis of Opioid Poisoning Related Hospital Visits in New York State. AMIA Annu Symp Proc. 2017;2017:545-554. eCollection 2017. PubMed PMID: 29854119; PubMed Central PMCID: PMC5977648.

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Saltz J, Gupta R, Hou L, Kurc T, Singh P, Nguyen V, Samaras D, Shroyer KR, Zhao T, Batiste R, Van Arnam J, Shmulevich I, Rao AUK, Lazar AJ, Sharma A, Thorsson V. Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images. Cell Rep. 2018 Apr 3;23(1):181-193.e7. doi: 10.1016/j.celrep.2018.03.086. PubMed PMID: 29617659; PubMed Central PMCID: PMC5943714.

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Cooper LA, Demicco EG, Saltz JH, Powell RT, Rao A, Lazar AJ. PanCancer insights from The Cancer Genome Atlas: the pathologist's perspective. J Pathol. 2018 Apr;244(5):512-524. doi: 10.1002/path.5028. Epub 2018 Feb 22. Review. PubMed PMID: 29288495; PubMed Central PMCID: PMC6240356.