STONY BROOK MEDICINE

Department of Biomedical Informatics

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FACULTY PROFILE · REVIEW PREVIEW

Tahsin Kurc

Department of Biomedical Informatics

Publications

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RankByGene: GeneGene-Guided Histopathology Representation Learning Through Cross-Modal Ranking Consistency

Wentao Huang, Meilong Xu, Xiaoling Hu, Shahira Abousamra, Aniruddha Ganguly, Saarthak Kapse, Alisa Yurovsky, Prateek Prasanna, Tahsin Kurç, Joel Saltz, Michael L. Miller, Chao Chen

ORCID match IEEE Transactions on Medical Imaging · 2026 · Found in OpenAlex

DOI: 10.1109/tmi.2026.3725898

Choose for “RankByGene: GeneGene-Guided Histopathology Representation Learning Through Cross-Modal Ranking Consistency”

MRI-based patient selection for active surveillance in prostate cancer using U-Found: a generalized deep learning model.

Noah C. Lowry, Adrian Breto, Veronica Wallaengen, Ahmad Algohary, Nicolas Tapia-Stoll, Sandra M. Gaston, Nachiketh S. Prakash, Pedro F. S. Freitas, Oleksandr N. Kryvenko, Patricia Castillo, Joel Saltz, Tahsin Kurç, Chad R. Ritch, Bruno Nahar, Mark L. Gonzalgo, Dipen J. Parekh, Brandon Mahal, B. Spieler, Alan Dal Pra, Matthew C. Abramowitz, A. Pollack, Sanoj Punnen, Radka Stoyanova

ORCID match Cancer imaging : the official publication of the International Cancer Imaging Society · 2026 · Found in OpenAlex, PubMed

DOI: 10.1186/s40644-026-00988-z

Choose for “MRI-based patient selection for active surveillance in prostate cancer using U-Found: a generalized deep learning model.”

Label-Efficient Deep Color Deconvolution of Brightfield Multiplex IHC Images

Shahira Abousamra, Danielle Fassler, Rajarsi Gupta, Tahsin Kurç, Luisa F. Escobar‐Hoyos, Dimitris Samaras, Kenneth R. Shroyer, Joel Saltz, Chao Chen

ORCID match IEEE Transactions on Medical Imaging · 2026 · Found in OpenAlex

DOI: 10.1109/tmi.2025.3609245

Choose for “Label-Efficient Deep Color Deconvolution of Brightfield Multiplex IHC Images”

Abstract 691: Visualizing differential prostate cancer lesion growth in longitudinal MRIs of patients on active surveillance: Quantitative mapping by Habitat Risk Score and digital pathology.

Sandra M. Gaston, Yuwei Zhang, Veronica Wallaengen, Amanda Galvez, Leonard Salcedo, Adrian Breto, Ahmad Algohary, Noah C. Lowry, Jakub Karczmarzyk, Gupta Rajarsi, Erich Bremer, Tahsin Kurç, Benjamin O. Spieler, Oleksandr N. Kryvenko, A. Pollack, Sanoj Punnen, J. H. Saltz, Radka Stoyanova

ORCID match Cancer Research · 2026 · Found in OpenAlex

DOI: 10.1158/1538-7445.am2026-691

Choose for “Abstract 691: Visualizing differential prostate cancer lesion growth in longitudinal MRIs of patients on active surveillance: Quantitative mapping by Habitat Risk Score and digital pathology.”

Segmentation and Classification in Digital Pathology for Glioma Research: Challenges and Deep Learning Approaches

Alexandre Momeni, Qian Wang, Avinash Kori, Mahendra Khened, Tianhao Zhao, Keyvan Farahani, Rajarsi Gupta, Qi Qi, Yunlong Zhang, Spyridon Bakas, Joel Saltz, Yue Huang, Lichi Zhang, Aditya Bagari, Xinghao Ding, Ganapathy Krishnamurthi, Tahsin Kurç, Dinggang Shen, Xuhua Ren, Jayashree Kalpathy–Cramer, James Davis, Olivier Gevaert, Ashish Kumar, Marc Thibault

ORCID match Carolina Digital Repository (University of North Carolina at Chapel Hill) · 2025 · Found in OpenAlex

DOI: 10.17615/k55d-nq81

Choose for “Segmentation and Classification in Digital Pathology for Glioma Research: Challenges and Deep Learning Approaches”

PixCell: A generative foundation model for digital histopathology images.

Srikar Yellapragada, Alexandros Graikos, Zilinghan Li, Kostas Triaridis, Varun Belagali, Saarthak Kapse, Tarak Nandi, Ravi Madduri, Prateek Prasanna, Tahsin Kurç, Rajarsi Gupta, Joel Saltz, Dimitris Samaras

ORCID match PubMed · 2025 · Found in OpenAlex, PubMed

Choose for “PixCell: A generative foundation model for digital histopathology images.”

Pathomics Image Analysis of Tumor Infiltrating Lymphocytes (TILs) in Colon Cancer

Yuwei Zhang, Shahira Abousamra, Mahmudul Hasan, Luke A. Torre-Healy, Spencer Krichevsky, Sampurna Shrestha, Erich Bremer, Derek A. Oldridge, Andrew J. Rech, Emma E. Furth, Thèrése Bocklage, Justin S. Levens, Isaac Hands, Eric B. Durbin, Dimitris Samaras, Tahsin Kurç, Joel Saltz, Rajarsi Gupta

ORCID match Research Square · 2025 · Found in OpenAlex

DOI: 10.21203/rs.3.rs-6173056/v1

Choose for “Pathomics Image Analysis of Tumor Infiltrating Lymphocytes (TILs) in Colon Cancer”

Early Detection of Prostate Cancer Immune Response to Radiation and Androgen Deprivation Therapy: Unleashing the Power of HRS Mpmri Imaging, Molecular Biomarkers and Digital Pathology

Sandra M. Gaston, Radka Stoyanova, Oleksandr N. Kryvenko, Matthew C. Abramowitz, Adrian Breto, Everaldo Jerez Hernández, V.T. Clonch, Christopher P. Anderson, A. Galvez, Adam C. Bartley, L. Salcedo, Joel Saltz, Yuesheng Zhang, Rajarsi Gupta, Tahsin Kurç, Brandon Mahal, A. Dal Pra, I Mihaylov, Andrew Pollack, B. Spieler

ORCID match International Journal of Radiation Oncology*Biology*Physics · 2025 · Found in OpenAlex

DOI: 10.1016/j.ijrobp.2025.06.2880

Choose for “Early Detection of Prostate Cancer Immune Response to Radiation and Androgen Deprivation Therapy: Unleashing the Power of HRS Mpmri Imaging, Molecular Biomarkers and Digital Pathology”

Abstract 5315: Mapping tumor infiltrating lymphocytes in whole prostatectomy specimens to visualize and quantify the immune microenvironment of prostate cancer

Yuwei Zhang, Rajarsi Gupta, Joel Saltz, Tahsin Kurç, Jakub Kaczmarzyk, Erich Bremer, Veronica Wallaengen, Amanda Gálvez Mariscal, Abigail Bartley, Leonard Salcedo, A. Pollack, Sanoj Punnen, Oleksandr N. Kryvenko, Radka Stoyanova, Sandra M. Gaston

ORCID match Cancer Research · 2025 · Found in OpenAlex

DOI: 10.1158/1538-7445.am2025-5315

Choose for “Abstract 5315: Mapping tumor infiltrating lymphocytes in whole prostatectomy specimens to visualize and quantify the immune microenvironment of prostate cancer”

Understanding metric-related pitfalls in image analysis validation.

Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Acion, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Florian Buettner, M Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A Cimini, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Jens Kleesiek, Florian Kofler, Thijs Kooi, Annette Kopp-Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern Menze, Karel G M Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir Rajpoot, Mauricio Reyes, Michael A Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Ronald M Summers, Abdel A Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gaël Varoquaux, Ziv R Yaniv, Paul F Jäger, Lena Maier-Hein

Name match · unconfirmed Nature methods · 2024 · Found in PubMed

DOI: 10.1038/s41592-023-02150-0

Choose for “Understanding metric-related pitfalls in image analysis validation.”

Understanding metric-related pitfalls in image analysis validation

Annika Reinke, Minu D. Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Ali Emre Kavur, Tim Rädsch, Carole H. Sudre, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Florian Buettner, M. Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A. Cimini, Keyvan Farahani, Luciana Ferrer, Adrián Galdrán, Bram van Ginneken, Ben Glocker, Patrick Godau, Daniel A. Hashimoto, Michael M. Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Jens Kleesiek, Florian Kofler, Thijs Kooi, Annette Kopp‐Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurç, Bennett A. Landman, Geert Litjens, Amin Madani, Klaus Maier‐Hein, Anne L. Martel, Erik Meijering, Bjoern Menze, Karel G. M. Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M. Rafelski, Nasir Rajpoot, Mauricio Reyes, Michael A. Riegler, Nicola Rieke, Julio Sáez-Rodríguez, Clara I. Sá‎nchez, Shravya Shetty, Ronald M. Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A. Tsaftaris, Ben Van Calster, Gaël Varoquaux, Ziv Yaniv, Paul F. Jäger, Lena Maier‐Hein

ORCID match Nature Methods · 2024 · Found in OpenAlex

DOI: 10.1038/s41592-023-02150-0

Choose for “Understanding metric-related pitfalls in image analysis validation”

Uncertainty Estimation for Tumor Prediction with Unlabeled Data

Ju‐Young Yun, Shahira Abousamra, Li Chen, Rajarsi Gupta, Tahsin Kurç, Dimitris Samaras, Alison L. Van Dyke, Joel Saltz, Chao Chen

ORCID match Conference on Computer Vision and Pattern Recognition Workshops. IEEE Computer Society Conference on Computer Vision and Pattern Recognition. Workshops · 2024 · Found in OpenAlex, PubMed

DOI: 10.1109/cvprw63382.2024.00688

Choose for “Uncertainty Estimation for Tumor Prediction with Unlabeled Data”

RankByGene: Gene-Guided Histopathology Representation Learning Through Cross-Modal Ranking Consistency

Wentao Huang, Meilong Xu, Hu, Xiaoling, Shahira Abousamra, Aniruddha Ganguly, Saarthak Kapse, Alisa Yurovsky, Prateek Prasanna, Tahsin Kurç, Joel Saltz, M. L. Miller, Chao Chen

ORCID match arXiv (Cornell University) · 2024 · Found in OpenAlex

DOI: 10.48550/arxiv.2411.15076

Choose for “RankByGene: Gene-Guided Histopathology Representation Learning Through Cross-Modal Ranking Consistency”

PathLDM: Text conditioned Latent Diffusion Model for Histopathology

Srikar Yellapragada, Alexandros Graikos, Prateek Prasanna, Tahsin Kurç, Joel Saltz, Dimitris Samaras

ORCID match IEEE Winter Conference on Applications of Computer Vision. IEEE Winter Conference on Applications of Computer Vision · 2024 · Found in OpenAlex, PubMed

DOI: 10.1109/wacv57701.2024.00510

Choose for “PathLDM: Text conditioned Latent Diffusion Model for Histopathology”

Pan-Cancer Tumor Infiltrating Lymphocyte Detection based on Federated Learning

Ujjwal Baid, Sarthak Pati, Tahsin Kurç, Rajarsi Gupta, Erich Bremer, Shahira Abousamra, Siddhesh Thakur, Joel Saltz, Spyridon Bakas

ORCID match · 2024 · Found in OpenAlex

DOI: 10.1109/bigdata62323.2024.10825083

Choose for “Pan-Cancer Tumor Infiltrating Lymphocyte Detection based on Federated Learning”

Optimized Whole-Slide-Image H&E Stain Normalization: A Step Towards Big Data Integration in Digital Pathology

Jose L. Agraz, Carlos Agraz, Andrew A. Chen, Charles L. Rice, Robert S. Pozos, Sven Aelterman, Amanda Tan, Angela N. Viaene, MacLean P. Nasrallah, Parth Sharma, Caleb M. Grenko, Tahsin Kurç, Joel Saltz, Michael D. Feldman, Hamed Akbari, Russell T. Shinohara, Spyridon Bakas, Parker C. Wilson

ORCID match IEEE Open Journal of Engineering in Medicine and Biology · 2024 · Found in OpenAlex, PubMed

DOI: 10.1109/ojemb.2024.3455011

Choose for “Optimized Whole-Slide-Image H&E Stain Normalization: A Step Towards Big Data Integration in Digital Pathology”

Open and reusable deep learning for pathology with WSInfer and QuPath

Jakub Kaczmarzyk, Alan O’Callaghan, Fiona Inglis, Swarad Gat, Tahsin Kurç, Rajarsi Gupta, Erich Bremer, Peter Bankhead, Joel Saltz

ORCID match npj Precision Oncology · 2024 · Found in OpenAlex, PubMed

DOI: 10.1038/s41698-024-00499-9

Choose for “Open and reusable deep learning for pathology with WSInfer and QuPath”

Metrics reloaded: recommendations for image analysis validation

Lena Maier‐Hein, Annika Reinke, Patrick Godau, Minu D. Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A. Riegler, Manuel Wiesenfarth, A. Emre Kavur, Carole H. Sudre, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Tim Rädsch, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B. Blaschko, M. Jorge Cardoso, Veronika Cheplygina, Beth A. Cimini, Professor Gary S. Collins, Keyvan Farahani, Luciana Ferrer, Adrián Galdrán, Bram van Ginneken, Robert Haase, Daniel A. Hashimoto, Michael M. Hoffman, Merel Huisman, Pierre Jannin, Charles E. Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Florian Kofler, Annette Kopp‐Schneider, Anna Kreshuk, Tahsin Kurç, Bennett A. Landman, Geert Litjens, Amin Madani, Klaus Maier‐Hein, Anne L. Martel, Peter Mattson, Erik Meijering, Bjoern Menze, Karel G. M. Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir Rajpoot, Nicola Rieke, Julio Sáez-Rodríguez, Clara I. Sá‎nchez, Shravya Shetty, Maarten van Smeden, Ronald M. Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A. Tsaftaris, Ben Van Calster, Gaël Varoquaux, Paul F. Jäger

ORCID match Nature Methods · 2024 · Found in OpenAlex, PubMed

DOI: 10.1038/s41592-023-02151-z

Choose for “Metrics reloaded: recommendations for image analysis validation”

Linking The Cancer Imaging Archive and GenBank to the National Clinical Cohort Collaborative

Ahmad Baghal, Joel Saltz, Tahsin Kurç, Prateek Prasanna, Samantha Baghal, Janos Hajagos, Erich Bremer, Shaymaa Al‐Shukri, Joshua L. Kennedy, Michael Rutherford, Tracy S. Nolan, Kirk Smith, Christopher G. Chute, Fred Prior

ORCID match Learning Health Systems · 2024 · Found in OpenAlex, PubMed

DOI: 10.1002/lrh2.10457

Choose for “Linking The Cancer Imaging Archive and GenBank to the National Clinical Cohort Collaborative”

Keratin 17 modulates the immune topography of pancreatic cancer

Lyanne A. Delgado-Coka, Michael Horowitz, Mariana Torrente-Goncalves, Lucia Roa‐Peña, Cindy V. Leiton, Mahmudul Hasan, Sruthi Babu, Danielle Fassler, Jaymie Oentoro, Ji-Dong Karen Bai, Emanuel F. Petricoin, Lynn M. Matrisian, Edik M. Blais, Natalia Marchenko, Felicia D. Allard, Wei Jiang, Brent K. Larson, Andrew Hendifar, Chao Chen, Shahira Abousamra, Dimitris Samaras, Tahsin Kurç, Joel Saltz, Luisa F. Escobar‐Hoyos, Kenneth R. Shroyer

ORCID match Journal of Translational Medicine · 2024 · Found in OpenAlex, PubMed

DOI: 10.1186/s12967-024-05252-1

Choose for “Keratin 17 modulates the immune topography of pancreatic cancer”

Keratin 17 modulates the immune topography of pancreatic cancer

Lyanne A. Delgado-Coka, Michael Horowitz, Mariana Torrente-Goncalves, Lucia Roa‐Peña, Cindy V. Leiton, Mahmudul Hasan, Sruthi Babu, Danielle Fassler, Jaymie Oentoro, Ji-Dong Karen Bai, Emanuel F. Petricoin, Lynn M. Matrisian, Edik M. Blais, Natalia Marchenko, Felicia D. Allard, Wei Jiang, Brent K. Larson, Andrew Hendifar, Chao Chen, Shahira Abousamra, Dimitris Samaras, Tahsin Kurç, Joel Saltz, Luisa F. Escobar‐Hoyos, Kenneth R. Shroyer

ORCID match Research Square · 2024 · Found in OpenAlex, PubMed

DOI: 10.21203/rs.3.rs-3886691/v1

Choose for “Keratin 17 modulates the immune topography of pancreatic cancer”

Contributors

Jacob T. Abel, Tanishq Mathew Abraham, Ognjen Arandjelović, Ulysses J. Balis, Peter D. Caie, Chhavi Chauhan, Jerome Cheng, Marion C. Cohen, Stanley Cohen, Neofytos Dimitriou, Michael Donovan, Gerardo Fernández, Rama R. Gullapalli, Rajarsi Gupta, David Harris‐Birtill, Tahsin Kurç, Richard M. Levenson, Zaibo Li, Abishek Sainath Madduri, Bahram Marami, David S. McClintock, Benjamin R. Mitchell, David Morrison, Daniel A. Orringer, Liron Pantanowitz, Anil V. Parwani, Marcel Prastawa, Joel Saltz, Richard T. Scott, Hamid R. Tizhoosh, Austin Todd, John E. Tomaszewski, Jack Zeineh

ORCID match Elsevier eBooks · 2024 · Found in OpenAlex

DOI: 10.1016/b978-0-323-95359-7.09997-0

Choose for “Contributors”

An Intelligent Search & Retrieval System (IRIS) and Clinical and Research Repository for Decision Support Based on Machine Learning and Joint Kernel-based Supervised Hashing

David J. Foran, Wenjin Chen, Tahsin Kurç, Rajarshi Gupta, Jakub Kaczmarzyk, Luke A. Torre-Healy, Erich Bremer, Samuel Ajjarapu, Nhan Do, Gerald Harris, Antoinette M. Stroup, Eric B. Durbin, Joel Saltz

ORCID match Cancer Informatics · 2024 · Found in OpenAlex, PubMed

DOI: 10.1177/11769351231223806

Choose for “An Intelligent Search & Retrieval System (IRIS) and Clinical and Research Repository for Decision Support Based on Machine Learning and Joint Kernel-based Supervised Hashing”

Abstract B082: Early risk stratification of ER+/HER2– breast cancer patients using digital pathology and multi-task, weakly-supervised deep learning

Jakub Kaczmarzyk, Luke A. Torre-Healy, Richard A. Moffitt, Rajarsi Gupta, Alina M. Hamilton, Tahsin Kurç, Katherine A. Hoadley, Melissa A. Troester, Joel Saltz

ORCID match Cancer Research · 2024 · Found in OpenAlex

DOI: 10.1158/1538-7445.advbc23-b082

Choose for “Abstract B082: Early risk stratification of ER+/HER2– breast cancer patients using digital pathology and multi-task, weakly-supervised deep learning”

Abstract B041: Keratin 17 excludes CD8-positive T cells and recruits CD163-positive macrophages in pancreatic ductal adenocarcinoma

Lyanne Oblein, Sruthi Babu, Mariana Torrente-Goncalves, Lucia Roa, Michael Horowitz, Mahmudul Hasan, Danielle Fassler, Jaymie Oentoro, Emanuel Petricoin, Lynn M. Matrisian, Natalia Marchenko, Edik M. Blais, Felicia D. Allard, Ali Alkalin, Wei Jiang, Brent K. Larson, Andrew Hendifar, Chao Chen, Shahira Abousamra, Dimitris Samaras, Tahsin Kurç, Joel Saltz, Luisa F. Escobar‐Hoyos, Kenneth R. Shroyer

ORCID match Cancer Research · 2024 · Found in OpenAlex

DOI: 10.1158/1538-7445.panca2023-b041

Choose for “Abstract B041: Keratin 17 excludes CD8-positive T cells and recruits CD163-positive macrophages in pancreatic ductal adenocarcinoma”

Understanding metric-related pitfalls in image analysis validation

Annika Reinke, Minu D. Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Ali Emre Kavur, Tim Rädsch, Carole H. Sudre, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B. Blaschko, Florian Buettner, M. Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A. Cimini, Professor Gary S. Collins, Keyvan Farahani, Luciana Ferrer, Adrián Galdrán, Bram van Ginneken, Ben Glocker, Patrick Godau, Robert Haase, Daniel A. Hashimoto, Michael M. Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Hannes Kenngott, Jens Kleesiek, Florian Kofler, Thijs Kooi, Annette Kopp‐Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurç, Bennett A. Landman, Geert Litjens, Amin Madani, Klaus Maier‐Hein, Anne L. Martel, Peter Mattson, Erik Meijering, Bjoern Menze, Karel G. M. Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M. Rafelski, Nasir Rajpoot, Mauricio Reyes, Michael A. Riegler, Nicola Rieke, Julio Sáez-Rodríguez, Clara I. Sá‎nchez, Shravya Shetty, van Smeden, Maarten, Ronald M. Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A. Tsaftaris, Ben Van Calster, Gaël Varoquaux, Wiesenfarth, Manuel, Ziv Yaniv, Paul F. Jäger, Lena Maier‐Hein

ORCID match arXiv (Cornell University) · 2023 · Found in OpenAlex

DOI: 10.48550/arxiv.2302.01790

Choose for “Understanding metric-related pitfalls in image analysis validation”

Topology-Guided Multi-Class Cell Context Generation for Digital Pathology

Shahira Abousamra, Rajarsi Gupta, Tahsin Kurç, Dimitris Samaras, Joel Saltz, Chao Chen

ORCID match Proceedings. IEEE Computer Society Conference on Computer Vision and Pattern Recognition · 2023 · Found in OpenAlex, PubMed

DOI: 10.1109/cvpr52729.2023.00324

Choose for “Topology-Guided Multi-Class Cell Context Generation for Digital Pathology”

PathLDM: Text conditioned Latent Diffusion Model for Histopathology

Srikar Yellapragada, Alexandros Graikos, Prateek Prasanna, Tahsin Kurç, Joel Saltz, Dimitris Samaras

ORCID match arXiv (Cornell University) · 2023 · Found in OpenAlex

DOI: 10.48550/arxiv.2309.00748

Choose for “PathLDM: Text conditioned Latent Diffusion Model for Histopathology”

Open and reusable deep learning for pathology with WSInfer and QuPath

Jakub Kaczmarzyk, Alan O’Callaghan, Fiona Inglis, Tahsin Kurç, Rajarsi Gupta, Erich Bremer, Peter Bankhead, Joel Saltz

ORCID match arXiv (Cornell University) · 2023 · Found in OpenAlex

DOI: 10.48550/arxiv.2309.04631

Choose for “Open and reusable deep learning for pathology with WSInfer and QuPath”

GaNDLF: the generally nuanced deep learning framework for scalable end-to-end clinical workflows

Sarthak Pati, Siddhesh Thakur, İbrahim Ethem Hamamcı, Ujjwal Baid, Bhakti Baheti, Megh Bhalerao, Orhun Güley, Sofia Mouchtaris, David Lang, Spyridon Thermos, Karol Gotkowski, Camila González, Caleb M. Grenko, Alexander Getka, Brandon Edwards, Micah Sheller, Junwen Wu, Deepthi Karkada, Ravi Panchumarthy, Vinayak S. Ahluwalia, Chunrui Zou, Vishnu Bashyam, Yuemeng Li, Babak Haghighi, Rhea Chitalia, Shahira Abousamra, Tahsin Kurç, Aimilia Gastounioti, Sezgin Er, Mark Bergman, Joel Saltz, Yong Fan, Prashant Shah, Anirban Mukhopadhyay, Sotirios A. Tsaftaris, Bjoern Menze, Christos Davatzikos, Despina Kontos, Alexandros Karargyris, Renato Umeton, Peter Mattson, Spyridon Bakas

ORCID match Communications Engineering · 2023 · Found in OpenAlex

DOI: 10.1038/s44172-023-00066-3

Choose for “GaNDLF: the generally nuanced deep learning framework for scalable end-to-end clinical workflows”

Data from A Containerized Software System for Generation, Management, and Exploration of Features from Whole Slide Tissue Images

Joel Saltz, Ashish Sharma, Ganesh Iyer, Erich Bremer, Feiqiao Wang, Alina Jasniewski, Tammy DiPrima, Jonas S. Almeida, Yi Qin Gao, Tianhao Zhao, Mary Saltz, Tahsin Kurç

ORCID match · 2023 · Found in OpenAlex

DOI: 10.1158/0008-5472.c.6510269.v1

Choose for “Data from A Containerized Software System for Generation, Management, and Exploration of Features from Whole Slide Tissue Images”

Data from A Containerized Software System for Generation, Management, and Exploration of Features from Whole Slide Tissue Images

Joel Saltz, Ashish Sharma, Ganesh Iyer, Erich Bremer, Feiqiao Wang, Alina Jasniewski, Tammy DiPrima, Jonas S. Almeida, Yi Qin Gao, Tianhao Zhao, Mary Saltz, Tahsin Kurç

ORCID match · 2023 · Found in OpenAlex

DOI: 10.1158/0008-5472.c.6510269

Choose for “Data from A Containerized Software System for Generation, Management, and Exploration of Features from Whole Slide Tissue Images”

Author Correction: Federated learning enables big data for rare cancer boundary detection

Sarthak Pati, Ujjwal Baid, Brandon Edwards, Micah Sheller, Shih-Han Wang, G. Anthony Reina, Patrick Foley, Alexey Gruzdev, Deepthi Karkada, Christos Davatzikos, Chiharu Sako, Satyam Ghodasara, Michel Bilello, Suyash Mohan, Philipp Vollmuth, Gianluca Brugnara, Chandrakanth Jayachandran Preetha, Felix Sahm, Klaus Maier‐Hein, Maximilian Zenk, Martin Bendszus, Wolfgang Wick, Evan Calabrese, Jeffrey D. Rudie, Javier Villanueva‐Meyer, Soonmee Cha, Madhura Ingalhalikar, Manali Jadhav, Umang Pandey, Jitender Saini, John W. Garrett, Matthew Larson, Robert Jeraj, Stuart Currie, Russell Frood, Kavi Fatania, Raymond Y. Huang, Ken Chang, Carmen Balañá, Jaume Capellades, Josep Puig, Johannes Trenkler, Josef Pichler, Georg Necker, Andreas Haunschmidt, Stephan Meckel, Gaurav Shukla, Spencer Liem, Gregory S. Alexander, Joseph Lombardo, Joshua D. Palmer, Adam E. Flanders, Adam P. Dicker, Haris I. Sair, Craig Jones, Archana Venkataraman, Meirui Jiang, Tiffany Y. So, Cheng Chen, Pheng‐Ann Heng, Qi Dou, Michal Kozubek, Filip Lux, Jan Michálek, Petr Matula, Miloš Keřkovský, Tereza Kopřivová, Marek Dostál, Václav Vybíhal, Michael A. Vogelbaum, J. Ross Mitchell, Joaquim M. Farinhas, Joseph A. Maldjian, Chandan Ganesh Bangalore Yogananda, Marco C. Pinho, Divya Reddy, James M. Holcomb, Benjamin Wagner, Benjamin M. Ellingson, Timothy F. Cloughesy, Catalina Raymond, Talia C. Oughourlian, Akifumi Hagiwara, Chencai Wang, Minh‐Son To, Sargam Bhardwaj, Chee Chong, Marc Agzarian, Alexandre X. Falcão, Samuel Botter Martins, Bernardo Corrêa de Almeida Teixeira, F Sprenger, David Menotti, Diego Rafael Lucio, Pamela LaMontagne, Daniel Marcus, Benedikt Wiestler, Florian Kofler, Ivan Ezhov, Marie Metz

ORCID match Nature Communications · 2023 · Found in OpenAlex, PubMed

DOI: 10.1038/s41467-023-36188-7

Choose for “Author Correction: Federated learning enables big data for rare cancer boundary detection”

AI and Pathology: Steering Treatment and Predicting Outcomes

Rajarsi Gupta, Jakub Kaczmarzyk, Soma Kobayashi, Tahsin Kurç, Joel Saltz

ORCID match WORLD SCIENTIFIC eBooks · 2023 · Found in OpenAlex

DOI: 10.1142/9789811265679_0019

Choose for “AI and Pathology: Steering Treatment and Predicting Outcomes”

A Containerized Software System for Generation, Management and Exploration of Features from Whole Slide Tissue Images from A Containerized Software System for Generation, Management, and Exploration of Features from Whole Slide Tissue Images

Joel Saltz, Ashish Sharma, Ganesh Iyer, Erich Bremer, Feiqiao Wang, Alina Jasniewski, Tammy DiPrima, Jonas S. Almeida, Yi Qin Gao, Tianhao Zhao, Mary Saltz, Tahsin Kurç

ORCID match · 2023 · Found in OpenAlex

DOI: 10.1158/0008-5472.22418981

Choose for “A Containerized Software System for Generation, Management and Exploration of Features from Whole Slide Tissue Images from A Containerized Software System for Generation, Management, and Exploration of Features from Whole Slide Tissue Images”

A Containerized Software System for Generation, Management and Exploration of Features from Whole Slide Tissue Images from A Containerized Software System for Generation, Management, and Exploration of Features from Whole Slide Tissue Images

Joel Saltz, Ashish Sharma, Ganesh Iyer, Erich Bremer, Feiqiao Wang, Alina Jasniewski, Tammy DiPrima, Jonas S. Almeida, Yi Qin Gao, Tianhao Zhao, Mary Saltz, Tahsin Kurç

ORCID match · 2023 · Found in OpenAlex

DOI: 10.1158/0008-5472.22418981.v1

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Understanding and Leveraging the I/O Patterns of Emerging Machine Learning Analytics

Ana Gainaru, Dmitry Ganyushin, Bing Xie, Tahsin Kurç, Joel Saltz, Sarp Oral, Norbert Podhorszki, Franz Poeschel, Axel Huebl, Scott Klasky

ORCID match Communications in computer and information science · 2022 · Found in OpenAlex

DOI: 10.1007/978-3-030-96498-6_7

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Spatial Characterization of Tumor-Infiltrating Lymphocytes and Breast Cancer Progression

Danielle Fassler, Luke A. Torre-Healy, Rajarsi Gupta, Alina M. Hamilton, Soma Kobayashi, Sarah C. Van Alsten, Yuwei Zhang, Tahsin Kurç, Richard A. Moffitt, Melissa A. Troester, Katherine A. Hoadley, Joel Saltz

ORCID match Cancers · 2022 · Found in OpenAlex, PubMed

DOI: 10.3390/cancers14092148

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Spatial Characterization of Tumor-Infiltrating Lymphocytes and Breast Cancer Progression

Luke A. Torre-Healy, Melissa A. Troester, Soma Kobayashi, Sarah C. Van Alsten, Rajarsi Gupta, Katherine A. Hoadley, Yuwei Zhang, Alina M. Hamilton, Tahsin Kurç, Danielle Fassler, Joel Saltz, Richard A. Moffitt

ORCID match Carolina Digital Repository (University of North Carolina at Chapel Hill) · 2022 · Found in OpenAlex

DOI: 10.17615/yqef-6n73

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Robust Image Population Based Stain Color Normalization: How Many Reference Slides Are Enough?

Jose L. Agraz, Caleb M. Grenko, Andrew A. Chen, Angela N. Viaene, MacLean D. Nasrallah, Sarthak Pati, Tahsin Kurç, Joel Saltz, Michael D. Feldman, Hamed Akbari, Parth Sharma, Russell T. Shinohara, Spyridon Bakas

ORCID match IEEE Open Journal of Engineering in Medicine and Biology · 2022 · Found in OpenAlex, PubMed

DOI: 10.1109/ojemb.2023.3234443

Choose for “Robust Image Population Based Stain Color Normalization: How Many Reference Slides Are Enough?”

Metrics reloaded: Recommendations for image analysis validation

Lena Maier‐Hein, Annika Reinke, Patrick Godau, Minu D. Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A. Riegler, Manuel Wiesenfarth, Ali Emre Kavur, Carole H. Sudre, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Tim Rädsch, Laura Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B. Blaschko, M. Jorge Cardoso, Veronika Cheplygina, Beth A. Cimini, Professor Gary S. Collins, Keyvan Farahani, Luciana Ferrer, Adrián Galdrán, Bram van Ginneken, Robert Haase, Daniel A. Hashimoto, Michael M. Hoffman, Merel Huisman, Pierre Jannin, Charles E. Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Hannes Kenngott, Florian Kofler, Annette Kopp‐Schneider, Anna Kreshuk, Tahsin Kurç, Bennett A. Landman, Geert Litjens, Amin Madani, Klaus Maier‐Hein, Anne L. Martel, Peter Mattson, Erik Meijering, Bjoern Menze, Karel G. M. Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir Rajpoot, Nicola Rieke, Julio Sáez-Rodríguez, Clara I. Sá‎nchez, Shravya Shetty, Maarten van Smeden, Ronald M. Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A. Tsaftaris, Ben Van Calster, Gaël Varoquaux, Paul F. Jäger

ORCID match arXiv (Cornell University) · 2022 · Found in OpenAlex

DOI: 10.48550/arxiv.2206.01653

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Learning Topological Interactions for Multi-Class Medical Image Segmentation

Saumya Gupta, Xiaoling Hu, James Kaan, Michael Jin, Mutshipay Mpoy, Katherine Chung, Gagandeep Singh, Mary Saltz, Tahsin Kurç, Joel Saltz, Apostolos K. Tassiopoulos, Prateek Prasanna, Chao Chen

ORCID match arXiv (Cornell University) · 2022 · Found in OpenAlex

DOI: 10.48550/arxiv.2207.09654

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Learning Topological Interactions for Multi-Class Medical Image Segmentation

Saumya Gupta, Xiaoling Hu, James Kaan, Michael Jin, Mutshipay Mpoy, Katherine Chung, Gagandeep Singh, Mary Saltz, Tahsin Kurç, Joel Saltz, Apostolos K. Tassiopoulos, Prateek Prasanna, Chao Chen

ORCID match Lecture notes in computer science · 2022 · Found in OpenAlex

DOI: 10.1007/978-3-031-19818-2_40

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Federated learning enables big data for rare cancer boundary detection

Sarthak Pati, Ujjwal Baid, Brandon Edwards, Micah Sheller, Shih‐Han Wang, G. Anthony Reina, Patrick Foley, А. Д. Груздев, Deepthi Karkada, Christos Davatzikos, Chiharu Sako, Satyam Ghodasara, Michel Bilello, Suyash Mohan, Philipp Vollmuth, Gianluca Brugnara, Chandrakanth Jayachandran Preetha, Felix Sahm, Klaus Maier‐Hein, Maximilian Zenk, Martin Bendszus, Wolfgang Wick, Evan Calabrese, Jeffrey D. Rudie, Javier Villanueva‐Meyer, Soonmee Cha, Madhura Ingalhalikar, Manali Jadhav, Umang Pandey, Jitender Saini, John W. Garrett, Matthew Larson, Robert Jeraj, Stuart Currie, Russell Frood, Kavi Fatania, Raymond Y. Huang, Ken Chang, Carmen Balañá, Jaume Capellades, Josep Puig, Johannes Trenkler, Josef Pichler, Georg Necker, Andreas Haunschmidt, Stephan Meckel, Gaurav Shukla, Spencer Liem, Gregory S. Alexander, Joseph S. Lombardo, Joshua D. Palmer, Adam E. Flanders, Adam P. Dicker, Haris I. Sair, Craig Jones, Archana Venkataraman, Meirui Jiang, Tiffany Y. So, Cheng Chen, Pheng‐Ann Heng, Qi Dou, Michal Kozubek, Filip Lux, Jan Michálek, Petr Matula, Miloš Keřkovský, Tereza Kopřivová, Marek Dostál, Václav Vybíhal, Michael A. Vogelbaum, J. Ross Mitchell, Joaquim M. Farinhas, Joseph A. Maldjian, Chandan Ganesh Bangalore Yogananda, Marco C. Pinho, Divya Reddy, James Holcomb, Benjamin Wagner, Benjamin M. Ellingson, Timothy F. Cloughesy, Catalina Raymond, Talia C. Oughourlian, Akifumi Hagiwara, Chencai Wang, Minh‐Son To, Sargam Bhardwaj, Chee Chong, Marc Agzarian, Alexandre X. Falcão, Samuel Botter Martins, Bernardo Corrêa de Almeida Teixeira, F Sprenger, David Menotti, Diego Rafael Lucio, Pamela LaMontagne, Daniel S. Marcus, Benedikt Wiestler, Florian Kofler, Ivan Ezhov, Marie Metz

ORCID match Nature Communications · 2022 · Found in OpenAlex, PubMed

DOI: 10.1038/s41467-022-33407-5

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Federated Learning for the Classification of Tumor Infiltrating Lymphocytes

Ujjwal Baid, Sarthak Pati, Tahsin Kurç, Rajarsi Gupta, Erich Bremer, Shahira Abousamra, Siddhesh Thakur, Joel Saltz, Spyridon Bakas

ORCID match arXiv (Cornell University) · 2022 · Found in OpenAlex

DOI: 10.48550/arxiv.2203.16622

Choose for “Federated Learning for the Classification of Tumor Infiltrating Lymphocytes”

Evaluating histopathology transfer learning with ChampKit

Jakub Kaczmarzyk, Tahsin Kurç, Shahira Abousamra, Rajarsi Gupta, Joel Saltz, Peter K. Koo

ORCID match arXiv (Cornell University) · 2022 · Found in OpenAlex

DOI: 10.48550/arxiv.2206.06862

Choose for “Evaluating histopathology transfer learning with ChampKit”

An Expandable Informatics Framework for Enhancing Central Cancer Registries with Digital Pathology Specimens, Computational Imaging Tools, and Advanced Mining Capabilities.

D.J. Foran, Eric B. Durbin, Wenjin Chen, Evita Sadimin, Ashish Sharma, Imon Banerjee, Tahsin Kurç, Nan Li, Antoinette M. Stroup, Gerald Harris, Annie Gu, Maria J. Schymura, Rajarsi Gupta, Erich Bremer, Joseph Balsamo, Tammy DiPrima, Feiqiao Wang, Shahira Abousamra, Dimitris Samaras, Isaac Hands, Kevin C. Ward, Joel H. Saltz

ORCID match Journal of pathology informatics · 2022 · Found in OpenAlex, PubMed

DOI: 10.4103/jpi.jpi_31_21

Choose for “An Expandable Informatics Framework for Enhancing Central Cancer Registries with Digital Pathology Specimens, Computational Imaging Tools, and Advanced Mining Capabilities.”

AI and Pathology: Steering Treatment and Predicting Outcomes

Rajarsi Gupta, Jakub Kaczmarzyk, Soma Kobayashi, Tahsin Kurç, Joel Saltz

ORCID match arXiv (Cornell University) · 2022 · Found in OpenAlex

DOI: 10.48550/arxiv.2206.07573

Choose for “AI and Pathology: Steering Treatment and Predicting Outcomes”

A Novel Framework for Characterization of Tumor-Immune Spatial Relationships in Tumor Microenvironment

Mahmudul Hasan, Jakub Kaczmarzyk, David Paredes, Lyanne Oblein, Jaymie Oentoro, Shahira Abousamra, Michael Horowitz, Dimitris Samaras, Chao Chen, Tahsin Kurç, Kenneth R. Shroyer, Joel Saltz

ORCID match arXiv (Cornell University) · 2022 · Found in OpenAlex

DOI: 10.48550/arxiv.2204.12283

Choose for “A Novel Framework for Characterization of Tumor-Immune Spatial Relationships in Tumor Microenvironment”

Multi-Class Cell Detection Using Spatial Context Representation

Shahira Abousamra, David Belinsky, John Van Arnam, Felicia D. Allard, Eric U. Yee, Rajarsi Gupta, Tahsin Kurç, Dimitris Samaras, Joel Saltz, Chao Chen

ORCID match 2021 IEEE/CVF International Conference on Computer Vision (ICCV) · 2021 · Found in OpenAlex, PubMed

DOI: 10.1109/iccv48922.2021.00397

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Multi-Class Cell Detection Using Spatial Context Representation

Shahira Abousamra, David Belinsky, John Van Arnam, Felicia D. Allard, Eric U. Yee, Rajarsi Gupta, Tahsin Kurç, Dimitris Samaras, Joel Saltz, Chao Chen

ORCID match arXiv (Cornell University) · 2021 · Found in OpenAlex

DOI: 10.48550/arxiv.2110.04886

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Common limitations of performance metrics in biomedical image analysis

Annika Reinke, Matthias Eisenmann, Minu D. Tizabi, Carole H. Sudre, Tim Rädsch, Michela Antonelli, Tal Arbel, Spyridon Bakas, M. Jorge Cardoso, Veronika Cheplygina, Keyvan Farahani, Ben Glocker, Doreen Heckmann-Nötzel, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Jens Kleesiek, Tahsin Kurç, Michal Kozubek, Bennett A. Landman, Geert Litjens, Klaus Maier‐Hein, Anne Lousise Martel, Bjoern Menze, Henning Müller, Jens Petersen, Mauricio Reyes, Nicola Rieke, Bram Stieltjes, Ronald M. Summers, Sotirios A. Tsaftaris, Bram van Ginneken, Annette Kopp‐Schneider, Paul F. Jäger, Lena Maier‐Hein

ORCID match ArODES (HES-SO (https://www.hes-so.ch/)) · 2021 · Found in OpenAlex

Choose for “Common limitations of performance metrics in biomedical image analysis”

Common Limitations of Image Processing Metrics: A Picture Story

Annika Reinke, Minu D. Tizabi, Carole H. Sudre, Matthias Eisenmann, Tim Rädsch, Baumgartner, Michael, Acion, Laura, Michela Antonelli, Tal Arbel, Spyridon Bakas, Bankhead, Peter, Benis, Arriel, Blaschko, Matthew, Buettner, Florian, M. Jorge Cardoso, Chen, Jianxu, Veronika Cheplygina, Christodoulou, Evangelia, Cimini, Beth, Collins, Gary S., Engelhardt, Sandy, Keyvan Farahani, Ferrer, Luciana, Galdran, Adrian, Bram van Ginneken, Ben Glocker, Godau, Patrick, Haase, Robert, Hamprecht, Fred, Hashimoto, Daniel A., Doreen Heckmann-Nötzel, Hirsch, Peter, Hoffman, Michael M., Huisman, Merel, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Kainmueller, Dagmar, Kainz, Bernhard, Karargyris, Alexandros, Karthikesalingam, Alan, Kavur, A. Emre, Kenngott, Hannes, Jens Kleesiek, Kleppe, Andreas, Kohler, Sven, Kofler, Florian, Annette Kopp‐Schneider, Kooi, Thijs, Michal Kozubek, Kreshuk, Anna, Tahsin Kurç, Bennett A. Landman, Geert Litjens, Madani, Amin, Klaus Maier‐Hein, Martel, Anne L., Mattson, Peter, Meijering, Erik, Bjoern Menze, Moher, David, Moons, Karel G. M., Henning Müller, Nichyporuk, Brennan, Nickel, Felix, Noyan, M. Alican, Jens Petersen, Polat, Gorkem, Rafelski, Susanne M., Rajpoot, Nasir, Mauricio Reyes, Nicola Rieke, Riegler, Michael, Rivaz, Hassan, Saez-Rodriguez, Julio, Sánchez, Clara I., Schroeter, Julien, Saha, Anindo, Selver, M. Alper, Sharan, Lalith, Shetty, Shravya, van Smeden, Maarten, Bram Stieltjes, Ronald M. Summers, Taha, Abdel A., Tiulpin, Aleksei, Sotirios A. Tsaftaris, Van Calster, Ben, Varoquaux, Gaël, Wiesenfarth, Manuel, Yaniv, Ziv R., Paul F. Jäger, Lena Maier‐Hein

ORCID match arXiv (Cornell University) · 2021 · Found in OpenAlex

DOI: 10.48550/arxiv.2104.05642

Choose for “Common Limitations of Image Processing Metrics: A Picture Story”

Building robust pathology image analyses with uncertainty quantification

Jeremias Gomes, Jun Kong, Tahsin Kurç, Alba Cristina Magalhães Alves de Melo, Renato Cordeiro Ferreira, Joel Saltz, George Teodoro

ORCID match Computer Methods and Programs in Biomedicine · 2021 · Found in OpenAlex, PubMed

DOI: 10.1016/j.cmpb.2021.106291

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Automated digital TIL analysis (ADTA) adds prognostic value to standard assessment of depth and ulceration in primary melanoma

Michael Moore, Isabel D. Friesner, Emanuelle M. Rizk, Benjamin T. Fullerton, Manas Mondal, Megan H. Trager, Karen Mendelson, Ijeuru Chikeka, Tahsin Kurç, Rajarsi Gupta, Bethany R. Rohr, Eric Robinson, Balázs Ács, Rui Chang, Harriet M. Kluger, Bret Taback, Larisa J. Geskin, Basil A. Horst, Kevin Gardner, George Niedt, Jülide Tok Çelebi, Robyn D. Gartrell‐Corrado, Jane L. Messina, Tammie Ferringer, David L. Rimm, Joel Saltz, Jing Wang, R. Vanguri, Yvonne M. Saenger

ORCID match Scientific Reports · 2021 · Found in OpenAlex, PubMed

DOI: 10.1038/s41598-021-82305-1

Choose for “Automated digital TIL analysis (ADTA) adds prognostic value to standard assessment of depth and ulceration in primary melanoma”

Weakly-Supervised Deep Stain Decomposition for Multiplex IHC Images

Shahira Abousamra, Danielle Fassler, Le Hou, Yuwei Zhang, Rajarsi Gupta, Tahsin Kurç, Luisa F. Escobar‐Hoyos, Dimitris Samaras, Beatrice Knudson, Kenneth R. Shroyer, Joel Saltz, Chao Chen

ORCID match · 2020 · Found in OpenAlex

DOI: 10.1109/isbi45749.2020.9098652

Choose for “Weakly-Supervised Deep Stain Decomposition for Multiplex IHC Images”

Utilizing Automated Breast Cancer Detection to Identify Spatial Distributions of Tumor-Infiltrating Lymphocytes in Invasive Breast Cancer

Han Le, Rajarsi Gupta, Le Hou, Shahira Abousamra, Danielle Fassler, Luke A. Torre-Healy, Richard A. Moffitt, Tahsin Kurç, Dimitris Samaras, Rebecca Batiste, Tianhao Zhao, Arvind Rao, Alison L. Van Dyke, Ashish Sharma, Erich Bremer, Jonas S. Almeida, Joel Saltz

ORCID match American Journal Of Pathology · 2020 · Found in OpenAlex, PubMed

DOI: 10.1016/j.ajpath.2020.03.012

Choose for “Utilizing Automated Breast Cancer Detection to Identify Spatial Distributions of Tumor-Infiltrating Lymphocytes in Invasive Breast Cancer”

Segmentation and Classification in Digital Pathology for Glioma Research: Challenges and Deep Learning Approaches

Tahsin Kurç, Spyridon Bakas, Xuhua Ren, Aditya Bagari, Alexandre Momeni, Yue Huang, Lichi Zhang, Ashish Kumar, Marc Thibault, Qi Qi, Qian Wang, Avinash Kori, Olivier Gevaert, Yunlong Zhang, Dinggang Shen, Mahendra Khened, Xinghao Ding, Ganapathy Krishnamurthi, Jayashree Kalpathy–Cramer, James Davis, Tianhao Zhao, Rajarsi Gupta, Joel Saltz, Keyvan Farahani

ORCID match Frontiers in Neuroscience · 2020 · Found in OpenAlex, PubMed

DOI: 10.3389/fnins.2020.00027

Choose for “Segmentation and Classification in Digital Pathology for Glioma Research: Challenges and Deep Learning Approaches”

Publisher Correction to: Deep learning-based image analysis methods for brightfield-acquired multiplex immunohistochemistry images

Danielle Fassler, Shahira Abousamra, Rajarsi Gupta, Chao Chen, Maozheng Zhao, David Paredes, Syeda Areeha Batool, Beatrice S. Knudsen, Luisa F. Escobar‐Hoyos, Kenneth R. Shroyer, Dimitris Samaras, Tahsin Kurç, Joel Saltz

ORCID match Diagnostic Pathology · 2020 · Found in OpenAlex, PubMed

DOI: 10.1186/s13000-020-01021-y

Choose for “Publisher Correction to: Deep learning-based image analysis methods for brightfield-acquired multiplex immunohistochemistry images”

Preoperative Pembrolizumab Treatment Changes Tils in Naïve Stage I/IIA TNBC Patients Within a Window of Opportunity Trial

Q. Wang, R. Vanguri, Hua Guo, Shuobo Boboila, Tahsin Kurç, Han Le, Shahira Abousamra, Le Hou, Dimitris Samaras, Rajarsi Gupta, Joel Saltz, Kevin Gardner, Hanina Hibshoosh, Kevin Kalinsky, Eileen P. Connolly

ORCID match International Journal of Radiation Oncology*Biology*Physics · 2020 · Found in OpenAlex

DOI: 10.1016/j.ijrobp.2020.07.1091

Choose for “Preoperative Pembrolizumab Treatment Changes Tils in Naïve Stage I/IIA TNBC Patients Within a Window of Opportunity Trial”

PRISM: A Platform for Imaging in Precision Medicine

Ashish Sharma, Lawrence Tarbox, Tahsin Kurç, Jonathan P. Bona, Kirk Smith, Pradeeban Kathiravelu, Erich Bremer, Joel Saltz, Fred Prior

ORCID match JCO Clinical Cancer Informatics · 2020 · Found in OpenAlex, PubMed

DOI: 10.1200/cci.20.00001

Choose for “PRISM: A Platform for Imaging in Precision Medicine”

Geospatial Distribution and Predictors of Mortality in Hospitalized Patients With COVID-19: A Cohort Study

Sandeep K. Mallipattu, Randeep S. Jawa, Richard A. Moffitt, Janos Hajagos, Bettina C. Fries, Sharon Nachman, Tong J. Gan, Mary Saltz, Joel Saltz, Kenneth Kaushansky, Hal A. Skopicki, Kayley Abell-Hart, Irtaza Chaudhri, Juan Deng, Víctor García, Sujoy Gayen, Tahsin Kurç, Olena Bolotova, Jeanwoo Yoo, Simrat Dhaliwal, Nisha Nataraj, Siao Sun, C Tsai, Y Wang, Sadia Abbasi, Rang Abdullah, Sahar Ahmad, K Bai, Elliott Bennett‐Guerrero, Alicia S. Chua, Carol A. Gomes, Martin I. Griffel, Andreas P. Kalogeropoulos, D Kiamanesh, N Kim, Farrukh M. Koraishy, V Lingham, Mohamed G. Mansour, Luis A. Marcos, Joshua D. Miller, S Poovathor, Jerry A. Rubano, Daniel N. Rutigliano, M Sands, Carolyn Santora, Jonathon Schwartz, Kenneth R. Shroyer, Sonja Spitzer, Alison Stopeck, Mark A. Talamini, Mathew Tharakan, James A. Vosswinkel, William A. Wertheim, Sandeep K. Mallipattu, Randeep S. Jawa, Richard A. Moffitt, Janos Hajagos, Bettina C. Fries, Sharon Nachman, Tong J. Gan, Mary Saltz, Joel Saltz, Kenneth Kaushansky, Hal A. Skopicki, Kayley Abell-Hart, Irtaza Chaudhri, Juan Deng, Víctor García, Sujoy Gayen, Tahsin Kurç, Olena Bolotova, Jeanwoo Yoo, Simrat Dhaliwal, Nisha Nataraj, Siao Sun, C Tsai, Y Wang, Sadia Abbasi, Rang Abdullah, Sahar Ahmad, K Bai, Elliott Bennett‐Guerrero, Alicia S. Chua, Carol A. Gomes, Martin I. Griffel, Andreas P. Kalogeropoulos, D Kiamanesh, N Kim, Farrukh M. Koraishy, V Lingham, Mohamed G. Mansour, Luis A. Marcos, Joshua D. Miller, S Poovathor, Jerry A. Rubano, Daniel N. Rutigliano, M Sands, Carolyn Santora, Jonathon Schwartz, Kenneth R. Shroyer

ORCID match Open Forum Infectious Diseases · 2020 · Found in OpenAlex

DOI: 10.1093/ofid/ofaa436

Choose for “Geospatial Distribution and Predictors of Mortality in Hospitalized Patients With COVID-19: A Cohort Study”

From Whole Slide Tissues to Knowledge: Mapping Sub-cellular Morphology of Cancer

Tahsin Kurç, Ashish Sharma, Rajarsi Gupta, Le Hou, Han Le, Shahira Abousamra, Erich Bremer, Ryan Birmingham, Tammy DiPrima, Nan Li, Feiqiao Wang, Joseph Balsamo, Whitney Bremer, Dimitris Samaras, Joel Saltz

ORCID match Lecture notes in computer science · 2020 · Found in OpenAlex

DOI: 10.1007/978-3-030-46643-5_37

Choose for “From Whole Slide Tissues to Knowledge: Mapping Sub-cellular Morphology of Cancer”

Extending the Publish/Subscribe Abstraction for High-Performance I/O and Data Management at Extreme Scale.

Jeremy Logan, Mark Ainsworth, Chuck Atkins, Jieyang Chen, Jong Choi, Junmin Gu, James Kress, Greg Eisenhauer, Berk Geveci, William F. Godoy, Mark Kim, Tahsin Kurç, Qing Liu, Kshitij Mehta, George Ostrouchov, Norbert Podhorszki, David Pugmire, E. Suchyta, Nicholas Thompson, Ozan Tuğluk, Lipeng Wan, Ruonan Wang, Ben Whitney, Matthew Wolf, Kesheng Wu, Scott Klasky

ORCID match OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) · 2020 · Found in OpenAlex

Choose for “Extending the Publish/Subscribe Abstraction for High-Performance I/O and Data Management at Extreme Scale.”

Effect of automated TIL quantification in early-stage melanoma on accuracy of standard T staging using AJCC guidelines.

Michael Moore, Isabel D. Friesner, Emanuelle M. Rizk, Megan H. Trager, Jülide Tok Çelebi, Jeani Rich, Ijeuru Chikeka, Tahsin Kurç, Jing Wang, Bethany R. Rohr, Eric M. Robinson, Larisa J. Geskin, Basil A. Horst, Kevin Gardner, George Niedt, Jane L. Messina, Tammy C. Ferringer, Joel Saltz, R. Vanguri, Yvonne M. Saenger

ORCID match Journal of Clinical Oncology · 2020 · Found in OpenAlex

DOI: 10.1200/jco.2020.38.15_suppl.10076

Choose for “Effect of automated TIL quantification in early-stage melanoma on accuracy of standard T staging using AJCC guidelines.”

Deep learning-based image analysis methods for brightfield-acquired multiplex immunohistochemistry images

Danielle Fassler, Shahira Abousamra, Rajarsi Gupta, Chao Chen, Maozheng Zhao, David Paredes, Syeda Areeha Batool, Beatrice S. Knudsen, Luisa F. Escobar‐Hoyos, Kenneth R. Shroyer, Dimitris Samaras, Tahsin Kurç, Joel Saltz

ORCID match Diagnostic Pathology · 2020 · Found in OpenAlex, PubMed

DOI: 10.1186/s13000-020-01003-0

Choose for “Deep learning-based image analysis methods for brightfield-acquired multiplex immunohistochemistry images”

Computational Precision Medicine Radiology-Pathology challenge on Brain Tumor Classification 2020

Keyvan Farahani, Tahsin Kurç, Spyridon Bakas, Benjamin Bearce, Jayashree Kalpathy–Cramer, John Freymann, Joel Saltz, Eric Stahlberg, George Zaki, MacLean P. Nasrallah, Russell T. Shinohara

ORCID match Zenodo (CERN European Organization for Nuclear Research) · 2020 · Found in OpenAlex

DOI: 10.5281/zenodo.3718894

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Automated Assessment of the Curliness of Collagen Fiber in Breast Cancer

David Paredes, Prateek Prasanna, Christina Preece, Rajarsi Gupta, Farzad Fereidouni, Dimitris Samaras, Tahsin Kurç, Richard M. Levenson, Patricia Thompson-Carino, Joel Saltz, Chao Chen

ORCID match Lecture notes in computer science · 2020 · Found in OpenAlex

DOI: 10.1007/978-3-030-66415-2_17

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Abstract P3-09-17: Preoperative pembrolizumab increases sTILs in treatment naïve stage I/IIA TNBC patients in a window of opportunity trial

R. Vanguri, Hua Guo, Shuobo Boboila, Tahsin Kurç, Han Le, Shahira Abousamra, Le Hou, Dimitris Samaras, Rajarsi Gupta, Joel Saltz, Kevin Gardner, Hanina Hibshoosh, Kevin Kalinsky, Eileen P. Connolly

ORCID match Cancer Research · 2020 · Found in OpenAlex

DOI: 10.1158/1538-7445.sabcs19-p3-09-17

Choose for “Abstract P3-09-17: Preoperative pembrolizumab increases sTILs in treatment naïve stage I/IIA TNBC patients in a window of opportunity trial”

AI in Medical Imaging Informatics: Current Challenges and Future Directions

Andreas S. Panayides, Amir A. Amini, Nenad Filipović, Ashish Sharma, Sotirios A. Tsaftaris, Alistair A. Young, David J. Foran, Nhan Do, Spyretta Golemati, Tahsin Kurç, Kun Huang, Konstantina S. Nikita, Ben P. Veasey, Michalis Zervakis, Joel Saltz, Constantinos S. Pattichis

ORCID match IEEE Journal of Biomedical and Health Informatics · 2020 · Found in OpenAlex

DOI: 10.1109/jbhi.2020.2991043

Choose for “AI in Medical Imaging Informatics: Current Challenges and Future Directions”

ADIOS 2: The Adaptable Input Output System. A framework for high-performance data management

William F. Godoy, Norbert Podhorszki, Ruonan Wang, Chuck Atkins, Greg Eisenhauer, Junmin Gu, Philip E. Davis, Jong Youl Choi, K. Germaschewski, Kevin Huck, Axel Huebl, Mark Kim, James Kress, Tahsin Kurç, Qing Liu, Jeremy Logan, Kshitij Mehta, George Ostrouchov, Manish Parashar, Franz Poeschel, David Pugmire, E. Suchyta, Keichi Takahashi, Nick Thompson, Seiji Tsutsumi, Lipeng Wan, Matthew Wolf, Kesheng Wu, Scott Klasky

ORCID match SoftwareX · 2020 · Found in OpenAlex

DOI: 10.1016/j.softx.2020.100561

Choose for “ADIOS 2: The Adaptable Input Output System. A framework for high-performance data management”

Utilizing Automated Breast Cancer Detection to Identify Spatial Distributions of Tumor Infiltrating Lymphocytes in Invasive Breast Cancer

Han Le, Rajarsi Gupta, Le Hou, Shahira Abousamra, Danielle Fassler, Tahsin Kurç, Dimitris Samaras, Rebecca Batiste, Tianhao Zhao, Arvind Rao, Alison L. Van Dyke, Ashish Sharma, Erich Bremer, Jonas S. Almeida, Joel Saltz

ORCID match arXiv (Cornell University) · 2019 · Found in OpenAlex

DOI: 10.48550/arxiv.1905.10841

Choose for “Utilizing Automated Breast Cancer Detection to Identify Spatial Distributions of Tumor Infiltrating Lymphocytes in Invasive Breast Cancer”

The Emergence of Pathomics

Rajarsi Gupta, Tahsin Kurç, Ashish Sharma, Jonas S. Almeida, Joel Saltz

ORCID match Current Pathobiology Reports · 2019 · Found in OpenAlex

DOI: 10.1007/s40139-019-00200-x

Choose for “The Emergence of Pathomics”

Run-time Parameter Sensitivity Analysis Optimizations

Eduardo Scartezini, Willian Barreiros, Tahsin Kurç, Jun Kong, Alba Cristina Magalhães Alves de Melo, Joel Saltz, George Teodoro

ORCID match arXiv (Cornell University) · 2019 · Found in OpenAlex

DOI: 10.48550/arxiv.1910.14548

Choose for “Run-time Parameter Sensitivity Analysis Optimizations”

Robust Histopathology Image Analysis: To Label or to Synthesize?

Le Hou, Ayush Agarwal, Dimitris Samaras, Tahsin Kurç, Rajarsi Gupta, Joel Saltz

ORCID match Proceedings. IEEE Computer Society Conference on Computer Vision and Pattern Recognition · 2019 · Found in OpenAlex, PubMed

DOI: 10.1109/cvpr.2019.00873

Choose for “Robust Histopathology Image Analysis: To Label or to Synthesize?”

Optimizing parameter sensitivity analysis of large‐scale microscopy image analysis workflows with multilevel computation reuse

Willian Barreiros, Jeremías Moreira, Tahsin Kurç, Jun Kong, Alba Cristina Magalhães Alves de Melo, Joel Saltz, George Teodoro

ORCID match Concurrency and Computation Practice and Experience · 2019 · Found in OpenAlex, PubMed

DOI: 10.1002/cpe.5403

Choose for “Optimizing parameter sensitivity analysis of large‐scale microscopy image analysis workflows with multilevel computation reuse”

Methods for Segmentation and Classification of Digital Microscopy Tissue Images

Quoc Dang Vu, Simon Graham, Tahsin Kurç, Minh Nguyen Nhat To, Muhammad Shaban, Talha Qaiser, Navid Alemi Koohbanani, Syed Ali Khurram, Jayashree Kalpathy-Cramer, Tianhao Zhao, Rajarsi Gupta, Jin Tae Kwak, Nasir Rajpoot, Joel Saltz, Keyvan Farahani

ORCID match Frontiers in Bioengineering and Biotechnology · 2019 · Found in OpenAlex, PubMed

DOI: 10.3389/fbioe.2019.00053

Choose for “Methods for Segmentation and Classification of Digital Microscopy Tissue Images”

Learning from Thresholds: Fully Automated Classification of Tumor Infiltrating Lymphocytes for Multiple Cancer Types

Shahira Abousamra, Le Hou, Rajarsi Gupta, Chao Chen, Dimitris Samaras, Tahsin Kurç, Rebecca Batiste, Tianhao Zhao, Shroyer Kenneth, Joel Saltz

ORCID match arXiv (Cornell University) · 2019 · Found in OpenAlex

DOI: 10.48550/arxiv.1907.03960

Choose for “Learning from Thresholds: Fully Automated Classification of Tumor Infiltrating Lymphocytes for Multiple Cancer Types”

Label Super Resolution with Inter-Instance Loss

Maozheng Zhao, Le Hou, Han Le, Dimitris Samaras, Nebojša Jojić, Danielle Fassler, Tahsin Kurç, Rajarsi Gupta, Kolya Malkin, Shroyer Kenneth, Joel Saltz

ORCID match arXiv (Cornell University) · 2019 · Found in OpenAlex

DOI: 10.48550/arxiv.1904.04429

Choose for “Label Super Resolution with Inter-Instance Loss”

Abstract A27: Deep learning for analysis of tumor-lymphocyte interactions in pancreatic ductal adenocarcinoma

Soma Kobayashi, Le Han, Lucie Chrastecka, Rajarsi Gupta, Le Hou, Shahira Abousamra, Danielle Fassler, Kenneth R. Shroyer, Dimitris Samaras, Tahsin Kurç, Richard A. Moffitt, Joel Saltz

ORCID match Cancer Research · 2019 · Found in OpenAlex

DOI: 10.1158/1538-7445.panca19-a27

Choose for “Abstract A27: Deep learning for analysis of tumor-lymphocyte interactions in pancreatic ductal adenocarcinoma”

A Vision for Managing Extreme-Scale Data Hoards

Jeremy Logan, Kshitij Mehta, Gerd Heber, Scott Klasky, Tahsin Kurç, Norbert Podhorszki, Patrick Widener, Matthew Wolf

ORCID match · 2019 · Found in OpenAlex

DOI: 10.1109/icdcs.2019.00179

Choose for “A Vision for Managing Extreme-Scale Data Hoards”

Twenty Years of Digital Pathology: An Overview of the Road Travelled, What is on the Horizon, and the Emergence of Vendor-Neutral Archives

Liron Pantanowitz, Ashish Sharma, Alexis B. Carter, Tahsin Kurç, Alan Sussman, Joel Saltz

ORCID match Journal of Pathology Informatics · 2018 · Found in OpenAlex, PubMed

DOI: 10.4103/jpi.jpi_69_18

Choose for “Twenty Years of Digital Pathology: An Overview of the Road Travelled, What is on the Horizon, and the Emergence of Vendor-Neutral Archives”

Tuning for Tissue Image Segmentation Workflows for Accuracy and Performance

Luis F. R. Taveira, Tahsin Kurç, Alba Cristina Magalhães Alves de Melo, Jun Kong, Erich Bremer, Joel Saltz, George Teodoro

ORCID match arXiv (Cornell University) · 2018 · Found in OpenAlex

DOI: 10.48550/arxiv.1810.02911

Choose for “Tuning for Tissue Image Segmentation Workflows for Accuracy and Performance”

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Joel Saltz, Rajarsi Gupta, Le Hou, Tahsin Kurç, Pankaj K. Singh, Vu Nguyen, Dimitris Samaras, Kenneth R. Shroyer, Tianhao Zhao, Rebecca Batiste, John Van Arnam, Rory Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy Defreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila M. Reynolds, Ilya Shmulevich, Vésteinn Thórsson, Vésteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Han Liang, Shiyun Ling, Shiyun Ling, Yiling Lu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary Heins, Ritika Kundra, Marc Ladanyi, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang

ORCID match Cell Reports · 2018 · Found in OpenAlex, PubMed

DOI: 10.1016/j.celrep.2018.03.086

Choose for “Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images”

Multi-objective Parameter Auto-tuning for Tissue Image Segmentation Workflows

Luis F. R. Taveira, Tahsin Kurç, Alba Cristina Magalhães Alves de Melo, Jun Kong, Erich Bremer, Joel Saltz, George Teodoro

ORCID match Journal of Imaging Informatics in Medicine · 2018 · Found in OpenAlex, PubMed

DOI: 10.1007/s10278-018-0138-z

Choose for “Multi-objective Parameter Auto-tuning for Tissue Image Segmentation Workflows”

Methods for Segmentation and Classification of Digital Microscopy Tissue\n Images

Quoc Dang Vu, Simon Graham, Minh Nguyen Nhat To, Muhammad Shaban, Talha Qaiser, Navid Alemi Koohbanani, Syed Ali Khurram, Tahsin Kurç, Keyvan Farahani, Tianhao Zhao, Rajarsi Gupta, Jin Tae Kwak, Nasir Rajpoot, Joel Saltz

ORCID match arXiv (Cornell University) · 2018 · Found in OpenAlex

DOI: 10.48550/arxiv.1810.13230

Choose for “Methods for Segmentation and Classification of Digital Microscopy Tissue\n Images”

Cooperative and out‐of‐core execution of the irregular wavefront propagation pattern on hybrid machines with Intel® Xeon Phi™

Jeremias Gomes, Alba Cristina Magalhães Alves de Melo, Jun Kong, Tahsin Kurç, Joel Saltz, George Teodoro

ORCID match Concurrency and Computation Practice and Experience · 2018 · Found in OpenAlex, PubMed

DOI: 10.1002/cpe.4425

Choose for “Cooperative and out‐of‐core execution of the irregular wavefront propagation pattern on hybrid machines with Intel® Xeon Phi™”

A View from ORNL: Scientific Data Research Opportunities in the Big Data Age

Scott Klasky, Matthew Wolf, Mark Ainsworth, Chuck Atkins, Jong Youl Choi, Greg Eisenhauer, Berk Geveci, William F. Godoy, Mark Kim, James Kress, Tahsin Kurç, Qing Liu, Jeremy Logan, Arthur B. Maccabe, Kshitij Mehta, George Ostrouchov, Manish Parashar, Norbert Podhorszki, David Pugmire, E. Suchyta, Lipeng Wan, Ruonan Wang

ORCID match · 2018 · Found in OpenAlex

DOI: 10.1109/icdcs.2018.00136

Choose for “A View from ORNL: Scientific Data Research Opportunities in the Big Data Age”

Unsupervised Histopathology Image Synthesis

Le Hou, Ayush Agarwal, Dimitris Samaras, Tahsin Kurç, Rajarsi Gupta, Joel Saltz

ORCID match arXiv (Cornell University) · 2017 · Found in OpenAlex

DOI: 10.48550/arxiv.1712.05021

Choose for “Unsupervised Histopathology Image Synthesis”

TGE: Machine Learning Based Task Graph Embedding for Large-Scale Topology Mapping

Jong Youl Choi, Jeremy Logan, Matthew Wolf, George Ostrouchov, Tahsin Kurç, Qing Liu, Norbert Podhorszki, Scott Klasky, Melissa Romanus, Qian Sun, Manish Parashar, R.M. Churchill, C. S. Chang

ORCID match · 2017 · Found in OpenAlex

DOI: 10.1109/cluster.2017.67

Choose for “TGE: Machine Learning Based Task Graph Embedding for Large-Scale Topology Mapping”

SparkGIS: Resource Aware Efficient In-Memory Spatial Query Processing.

Furqan Baig, Hoang Vo, Tahsin Kurc, Joel Saltz, Fusheng Wang

Name match · unconfirmed Proceedings of the ... ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems : ACM GIS. ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems · 2017 · Found in PubMed

Choose for “SparkGIS: Resource Aware Efficient In-Memory Spatial Query Processing.”

SparkGIS

Furqan Baig, Hoang Vo, Tahsin Kurç, Joel Saltz, Fusheng Wang

ORCID match · 2017 · Found in OpenAlex

DOI: 10.1145/3139958.3140019

Choose for “SparkGIS”

Evaluation of nucleus segmentation in digital pathology images through large scale image synthesis

Naiyun Zhou, Xiaxia Yu, Tianhao Zhao, Si Wen, Fusheng Wang, Wei Zhu, Tahsin Kurç, Allen Tannenbaum, Joel Saltz, Yi Gao

ORCID match Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE · 2017 · Found in OpenAlex, PubMed

DOI: 10.1117/12.2254220

Choose for “Evaluation of nucleus segmentation in digital pathology images through large scale image synthesis”

Computing Just What You Need: Online Data Analysis and Reduction at Extreme Scales

Ian Foster, Mark Ainsworth, Bryce Allen, Julie Bessac, Franck Cappello, Jong Youl Choi, Emil M. Constantinescu, Philip E. Davis, Sheng Di, Wendy Di, Hanqi Guo, Scott Klasky, Kerstin Kleese van Dam, Tahsin Kurç, Qing Liu, Abid M. Malik, Kshitij Mehta, Klaus Mueller, Todd Munson, George Ostouchov, Manish Parashar, Tom Peterka, Line Pouchard, Dingwen Tao, Ozan Tuğluk, Stefan M. Wild, Matthew Wolf, Justin M. Wozniak, Wei Xu, Shinjae Yoo

ORCID match Lecture notes in computer science · 2017 · Found in OpenAlex

DOI: 10.1007/978-3-319-64203-1_1

Choose for “Computing Just What You Need: Online Data Analysis and Reduction at Extreme Scales”

A Containerized Software System for Generation, Management, and Exploration of Features from Whole Slide Tissue Images

Joel Saltz, Ashish Sharma, Ganesh R Iyer, Erich Bremer, Feiqiao Wang, Alina Jasniewski, Tammy DiPrima, Jonas S. Almeida, Yi Gao, Tianhao Zhao, Mary Saltz, Tahsin Kurç

ORCID match Cancer Research · 2017 · Found in OpenAlex, PubMed

DOI: 10.1158/0008-5472.can-17-0316

Choose for “A Containerized Software System for Generation, Management, and Exploration of Features from Whole Slide Tissue Images”

Visualization and Analysis for Near-Real-Time Decision Making in Distributed Workflows

David Pugmire, James Kress, Jong Choi, Scott Klasky, Tahsin Kurç, R.M. Churchill, Matthew Wolf, Greg Eisenhower, Hank Childs, Kesheng Wu, Alex Sim, Junmin Gu, Jonathan Low

ORCID match · 2016 · Found in OpenAlex

DOI: 10.1109/ipdpsw.2016.175

Choose for “Visualization and Analysis for Near-Real-Time Decision Making in Distributed Workflows”

Stream processing for near real-time scientific data analysis

Jong Youl Choi, Tahsin Kurç, Jeremy Logan, Matthew Wolf, E. Suchyta, James Kress, David Pugmire, Norbert Podhorszki, Eun-Kyu Byun, Mark Ainsworth, Manish Parashar, Scott Klasky

ORCID match · 2016 · Found in OpenAlex

DOI: 10.1109/nysds.2016.7747804

Choose for “Stream processing for near real-time scientific data analysis”

Patch-Based Convolutional Neural Network for Whole Slide Tissue Image Classification

Le Hou, Dimitris Samaras, Tahsin Kurç, Yi Gao, James Davis, Joel Saltz

ORCID match Proceedings. IEEE Computer Society Conference on Computer Vision and Pattern Recognition · 2016 · Found in OpenAlex, PubMed

DOI: 10.1109/cvpr.2016.266

Choose for “Patch-Based Convolutional Neural Network for Whole Slide Tissue Image Classification”

Multi-scale learning based segmentation of glands in digital colonrectal pathology images

Yi Gao, William Liu, Shipra Arjun, Liangjia Zhu, Vadim Ratner, Tahsin Kurç, Joel Saltz, Allen Tannenbaum

ORCID match Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE · 2016 · Found in OpenAlex, PubMed

DOI: 10.1117/12.2216790

Choose for “Multi-scale learning based segmentation of glands in digital colonrectal pathology images”

Large-Scale Microscopy Imaging Analytics for In Silico Biomedicine

Joel Saltz, Fusheng Wang, George Teodoro, Lee Cooper, Patrick Widener, Jun Kong, David A. Gutman, Tony Pan, Sharath R. Cholleti, Ashish Sharma, Daniel J. Brat, Tahsin Kurç

ORCID match · 2016 · Found in OpenAlex

DOI: 10.1201/b14935-3

Choose for “Large-Scale Microscopy Imaging Analytics for In Silico Biomedicine”

Hierarchical nucleus segmentation in digital pathology images

Yi Gao, Vadim Ratner, Liangjia Zhu, Tammy DiPrima, Tahsin Kurç, Allen Tannenbaum, Joel Saltz

ORCID match Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE · 2016 · Found in OpenAlex, PubMed

DOI: 10.1117/12.2217029

Choose for “Hierarchical nucleus segmentation in digital pathology images”

Exascale Storage Systems the SIRIUS Way

Scott Klasky, Hasan Abbasi, Mark Ainsworth, Jong Youl Choi, Matthew Curry, Tahsin Kurç, Qingxiu Liu, Jay Lofstead, Carlos Maltzahn, Manish Parashar, Norbert Podhorszki, E. Suchyta, F Wang, Matthew Wolf, C. S. Chang, R.M. Churchill, S. Ethier

ORCID match Journal of Physics Conference Series · 2016 · Found in OpenAlex

DOI: 10.1088/1742-6596/759/1/012095

Choose for “Exascale Storage Systems the SIRIUS Way”

Automatic histopathology image analysis with CNNs

Le Hou, K. Ranjith Singh, Dimitris Samaras, Tahsin Kurç, Yi Gao, Roberta Seidman, Joel Saltz

ORCID match · 2016 · Found in OpenAlex

DOI: 10.1109/nysds.2016.7747812

Choose for “Automatic histopathology image analysis with CNNs”

Efficient Irregular Wavefront Propagation Algorithms on Intel(R) Xeon Phi(TM)

Jeremias M. Gomes, George Teodoro, Alba Cristina Magalhães Alves de Melo, Jun Kong, Tahsin Kurç, Joel Saltz

ORCID match Proceedings. Symposium on Computer Architecture and High Performance Computing · 2015 · Found in OpenAlex, PubMed

DOI: 10.1109/sbac-pad.2015.13

Choose for “Efficient Irregular Wavefront Propagation Algorithms on Intel(R) Xeon Phi(TM)”

Application performance analysis and efficient execution on systems with multi-core CPUs, GPUs and MICs: a case study with microscopy image analysis

George Teodoro, Tahsin Kurç, Guilherme Andrade, Jun Kong, Renato Ferreira, Joel Saltz

ORCID match The International Journal of High Performance Computing Applications · 2015 · Found in OpenAlex, PubMed

DOI: 10.1177/1094342015594519

Choose for “Application performance analysis and efficient execution on systems with multi-core CPUs, GPUs and MICs: a case study with microscopy image analysis”

Temporal abstraction-based clinical phenotyping with Eureka!

Andrew R. Post, Tahsin Kurç, Richie Willard, Himanshu Rathod, Michel Theodor Mansour, Akshatha Kalsanka Pai, William M. Torian, Sanjay Agravat, Suzanne Sturm, Joel Saltz

ORCID match PubMed · 2013 · Found in OpenAlex

Choose for “Temporal abstraction-based clinical phenotyping with Eureka!”

SEMANTICALLY INTEROPERABLE XML DATA

Cristobal Vergara-Niedermayr, Fusheng Wang, Tony Pan, Tahsin Kurç, Joel Saltz

ORCID match International Journal of Semantic Computing · 2013 · Found in OpenAlex

DOI: 10.1142/s1793351x13500037

Choose for “SEMANTICALLY INTEROPERABLE XML DATA”

High-performance computational analysis of glioblastoma pathology images with database support identifies molecular and survival correlates

Jun Kong, Fusheng Wang, George Teodoro, Lee Cooper, Carlos S. Moreno, Tahsin Kurç, Tony Pan, Joel Saltz, Daniel J. Brat

ORCID match Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013 · 2013 · Found in OpenAlex

DOI: 10.1109/bibm.2013.6732495

Choose for “High-performance computational analysis of glioblastoma pathology images with database support identifies molecular and survival correlates”

Clinical Phenotyping with the Analytic Information Warehouse.

Andrew R. Post, Tahsin Kurç, Richie Willard, Himanshu Rathod, Michel Theodor Mansour, Akshatha Kalsanka Pai, William M. Torian, Sanjay Agravat, Suzanne Sturm, Joel H. Saltz

ORCID match AMIA · 2013 · Found in OpenAlex

Choose for “Clinical Phenotyping with the Analytic Information Warehouse.”

Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data

David A. Gutman, Jake Cobb, Dhananjaya Somanna, Yuna Park, Fusheng Wang, Tahsin Kurç, Joel Saltz, Daniel J. Brat, Lee Cooper, Jun Kong

ORCID match Journal of the American Medical Informatics Association · 2013 · Found in OpenAlex

DOI: 10.1136/amiajnl-2012-001469

Choose for “Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data”

A high-performance spatial database based approach for pathology imaging algorithm evaluation

Fusheng Wang, Jun Kong, Jingjing Gao, Lee Cooper, Tahsin Kurç, Zhengwen Zhou, David Adler, Cristobal Vergara-Niedermayr, Bryan Katigbak, Daniel J. Brat, Joel Saltz

ORCID match Journal of Pathology Informatics · 2013 · Found in OpenAlex

DOI: 10.4103/2153-3539.108543

Choose for “A high-performance spatial database based approach for pathology imaging algorithm evaluation”

The Tumor Microenvironment Strongly Impacts Master Transcriptional Regulators and Gene Expression Class of Glioblastoma

Lee Cooper, David A. Gutman, C Chisolm, Christina Appin, Jun Kong, Yuan Rong, Tahsin Kurç, Erwin G. Van Meir, Joel Saltz, Carlos S. Moreno, Daniel J. Brat

ORCID match American Journal Of Pathology · 2012 · Found in OpenAlex

DOI: 10.1016/j.ajpath.2012.01.040

Choose for “The Tumor Microenvironment Strongly Impacts Master Transcriptional Regulators and Gene Expression Class of Glioblastoma”

Managing and querying whole slide images

Fusheng Wang, Tae Woo Oh, Cristobal Vergara-Niedermayr, Tahsin Kurç, Joel Saltz

ORCID match Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE · 2012 · Found in OpenAlex

DOI: 10.1117/12.912388

Choose for “Managing and querying whole slide images”

Integrated morphologic analysis for the identification and characterization of disease subtypes

Lee Cooper, Jun Kong, D. Gutman, Fusheng Wang, Jingjing Gao, Christina Appin, Sharath R. Cholleti, Tony Pan, Ashish Sharma, Lisa Scarpace, Tom Mikkelsen, Tahsin Kurç, Carlos S. Moreno, Daniel J. Brat, Joel H. Saltz

ORCID match Journal of the American Medical Informatics Association · 2012 · Found in OpenAlex

DOI: 10.1136/amiajnl-2011-000700

Choose for “Integrated morphologic analysis for the identification and characterization of disease subtypes”

High Performance Computing Techniques for Scaling Image Analysis Workflows

Patrick Widener, Tahsin Kurç, Wenjin Chen, Fusheng Wang, Lin F. Yang, Jun Hu, Vijay Kumar, Vicky Chu, Lee Cooper, Jun Kong, Ashish Sharma, Tony Pan, Joel Saltz, David J. Foran

ORCID match Lecture notes in computer science · 2012 · Found in OpenAlex

DOI: 10.1007/978-3-642-28145-7_7

Choose for “High Performance Computing Techniques for Scaling Image Analysis Workflows”

Efficient regression testing of ontology-driven systems

Mijung Kim, Jake Cobb, Mary Jean Harrold, Tahsin Kurç, Alessandro Orso, Joel Saltz, Andrew Post, Kunal Malhotra, Shamkant B. Navathe

ORCID match · 2012 · Found in OpenAlex

DOI: 10.1145/2338965.2336792

Choose for “Efficient regression testing of ontology-driven systems”

Digital Pathology: Data-Intensive Frontier in Medical Imaging

Lee Cooper, Alexis B. Carter, Alton B. Farris, Fusheng Wang, Jun Kong, David A. Gutman, Patrick Widener, Tony Pan, Sharath R. Cholleti, Ashish Sharma, Tahsin Kurç, Daniel J. Brat, Joel Saltz

ORCID match Proceedings of the IEEE · 2012 · Found in OpenAlex

DOI: 10.1109/jproc.2011.2182074

Choose for “Digital Pathology: Data-Intensive Frontier in Medical Imaging”

Morphological signatures and genomic correlates in glioblastoma

Lee Cooper, Jun Kong, Fusheng Wang, Tahsin Kurç, Carlos S. Moreno, Daniel J. Brat, Joel H. Saltz

ORCID match Proceedings - International Symposium on Biomedical Imaging · 2011 · Found in OpenAlex

DOI: 10.1109/isbi.2011.5872714

Choose for “Morphological signatures and genomic correlates in glioblastoma”

Integrative, Multimodal Analysis of Glioblastoma Using TCGA Molecular Data, Pathology Images, and Clinical Outcomes

Jun Kong, Lee Cooper, Fusheng Wang, David A. Gutman, Jingjing Gao, C Chisolm, Ashish Sharma, Tony Pan, Erwin G. Van Meir, Tahsin Kurç, Carlos S. Moreno, Joel Saltz, Daniel J. Brat

ORCID match IEEE Transactions on Biomedical Engineering · 2011 · Found in OpenAlex

DOI: 10.1109/tbme.2011.2169256

Choose for “Integrative, Multimodal Analysis of Glioblastoma Using TCGA Molecular Data, Pathology Images, and Clinical Outcomes”

In silico analysis of nuclei in glioblastoma using large-scale microscopy images improves prediction of treatment response

Jun Kong, Lee Cooper, Carlos S. Moreno, Fusheng Wang, Tahsin Kurç, Joel Saltz, Daniel J. Brat

ORCID match Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS · 2011 · Found in OpenAlex

DOI: 10.1109/iembs.2011.6089903

Choose for “In silico analysis of nuclei in glioblastoma using large-scale microscopy images improves prediction of treatment response”

ImageMiner: a software system for comparative analysis of tissue microarrays using content-based image retrieval, high-performance computing, and grid technology

David J. Foran, Lin Yang, Wenjin Chen, Jun Hu, Lauri Goodell, Michael Reiß, Fusheng Wang, Tahsin Kurç, Tony Pan, Ashish Sharma, Joel Saltz

ORCID match Journal of the American Medical Informatics Association · 2011 · Found in OpenAlex

DOI: 10.1136/amiajnl-2011-000170

Choose for “ImageMiner: a software system for comparative analysis of tissue microarrays using content-based image retrieval, high-performance computing, and grid technology”

A new steerable pressure force for parametric deformable models

Jun Kong, Lee Cooper, Ashish Sharma, Tahsin Kurç, Daniel J. Brat, Joel Saltz

ORCID match Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE · 2011 · Found in OpenAlex

DOI: 10.1117/12.877700

Choose for “A new steerable pressure force for parametric deformable models”

A data model and database for high-resolution pathology analytical image informatics

Fusheng Wang, Jun Kong, Lee Cooper, Tony Pan, Tahsin Kurç, Wenjin Chen, Ashish Sharma, Cristobal Niedermayr, Tae Woo Oh, Daniel J. Brat, Alton B. Farris, David J. Foran, Joel Saltz

ORCID match Journal of Pathology Informatics · 2011 · Found in OpenAlex

DOI: 10.4103/2153-3539.83192

Choose for “A data model and database for high-resolution pathology analytical image informatics”

A comprehensive framework for classification of nuclei in digital microscopy imaging: An application to diffuse gliomas

Jun Kong, Lee Cooper, Fusheng Wang, C Chisolm, Carlos S. Moreno, Tahsin Kurç, Patrick Widener, Daniel J. Brat, Joel Saltz

ORCID match Proceedings - International Symposium on Biomedical Imaging · 2011 · Found in OpenAlex

DOI: 10.1109/isbi.2011.5872833

Choose for “A comprehensive framework for classification of nuclei in digital microscopy imaging: An application to diffuse gliomas”

A Temporal Abstraction-based Extract, Transform and Load Process for Creating Registry Databases for Research.

Andrew R. Post, Tahsin Kurç, Marc Overcash, Dedra Cantrell, Tim Morris, Kristi Eckerson, Circe Tsui, Terry Willey, Arshed A. Quyyumi, Danny J. Eapen, Guillermo E. Umpierrez, David C. Ziemer, Joel Saltz

ORCID match PubMed · 2011 · Found in OpenAlex

Choose for “A Temporal Abstraction-based Extract, Transform and Load Process for Creating Registry Databases for Research.”

Middleware Architecture Approaches for Collaborative Cancer Research

Tahsin Kurç, Ashish Sharma, Scott Oster, Tony Pan, Shannon Hastings, Stephen Langella, David Ervin, Justin Permar, Daniel J. Brat, Thomas J. FitzGerald, James A. Purdy, Walter Bosch, Joel Saltz

ORCID match · 2010 · Found in OpenAlex

DOI: 10.1007/978-1-4419-5714-6_4

Choose for “Middleware Architecture Approaches for Collaborative Cancer Research”

High-Performance Systems for in Silico Microscopy Imaging Studies

Fusheng Wang, Tahsin Kurç, Patrick Widener, Tony Pan, Jun Kong, Lee Cooper, David A. Gutman, Ashish Sharma, Sharath R. Cholleti, Vijay Kumar, Joel Saltz

ORCID match Lecture notes in computer science · 2010 · Found in OpenAlex

DOI: 10.1007/978-3-642-15120-0_2

Choose for “High-Performance Systems for in Silico Microscopy Imaging Studies”

An Integrative Approach for In Silico Glioma Research

Lee Cooper, Jun Kong, David A. Gutman, Fusheng Wang, Sharath R. Cholleti, Tony Pan, Patrick Widener, Ashish Sharma, Tom Mikkelsen, Adam E. Flanders, Daniel L. Rubin, Erwin G. Van Meir, Tahsin Kurç, Carlos S. Moreno, Daniel J. Brat, Joel H. Saltz

ORCID match IEEE Transactions on Biomedical Engineering · 2010 · Found in OpenAlex

DOI: 10.1109/tbme.2010.2060338

Choose for “An Integrative Approach for In Silico Glioma Research”

Parallel materialization of large ABoxes

Sivaramakrishnan Narayanan, Ümit V. Çatalyürek, Tahsin Kurç, Joel Saltz

ORCID match · 2009 · Found in OpenAlex

DOI: 10.1145/1529282.1529564

Choose for “Parallel materialization of large ABoxes”

HPC and Grid Computing for Integrative Biomedical Research

Tahsin Kurç, Shannon Hastings, Vijay Kumar, Stephen Langella, Ashish Sharma, Tony Pan, Scott Oster, David Ervin, Justin Permar, Sivaramakrishnan Narayanan, Yolanda Gil, Ewa Deelman, Mary Hall, Joel Saltz

ORCID match The International Journal of High Performance Computing Applications · 2009 · Found in OpenAlex

DOI: 10.1177/1094342009106192

Choose for “HPC and Grid Computing for Integrative Biomedical Research”

Enabling Data Analysis on High-Throughput Data in Large Data Depository Using Web-Based Analysis Platform - A Case Study on Integrating QUEST with GenePattern in Epigenetics Research

Terry Camerlengo, Hatice Gülçin Özer, Pearlly S. Yan, Jeffrey D. Parvin, Tim H.‐M. Huang, Kun Huang, Mingxiang Teng, Lang Li, Yunlong Liu, Francisco Pérez, Tahsin Kurç

ORCID match · 2009 · Found in OpenAlex

DOI: 10.1109/bibm.2009.84

Choose for “Enabling Data Analysis on High-Throughput Data in Large Data Depository Using Web-Based Analysis Platform - A Case Study on Integrating QUEST with GenePattern in Epigenetics Research”

e-Science, caGrid, and Translational Biomedical Research

Joel Saltz, Tahsin Kurç, S. Hastings, Stephen Langella, Scott Oster, David Ervin, Ashish Sharma, Tony Pan, Metin N. Gürcan, Justin Permar, Renato Ferreira, Philip Payne, Ümit V. Çatalyürek, E. Caserta, Giovanni Leone, Michael C. Ostrowski, Ravi Madduri, Ian Foster, Subha Madhavan

ORCID match Computer · 2008 · Found in OpenAlex

DOI: 10.1109/mc.2008.459

Choose for “e-Science, caGrid, and Translational Biomedical Research”

Translational research design templates, Grid computing, and HPC

Joel Saltz, Scott Oster, Shannon Hastings, Stephen Langella, Renato Ferreira, Justin Permar, Ashish Sharma, David Ervin, Tony Pan, Ümit V. Çatalyürek, Tahsin Kurç

ORCID match · 2008 · Found in OpenAlex

DOI: 10.1109/ipdps.2008.4536089

Choose for “Translational research design templates, Grid computing, and HPC”

Sharing Data and Analytical Resources Securely in a Biomedical Research Grid Environment

Stephen Langella, S. Hastings, Scott Oster, Tony Pan, Ashish Sharma, Justin Permar, David Ervin, B. Barla Cambazoğlu, Tahsin Kurç, Joel Saltz

ORCID match Journal of the American Medical Informatics Association · 2008 · Found in OpenAlex

DOI: 10.1197/jamia.m2662

Choose for “Sharing Data and Analytical Resources Securely in a Biomedical Research Grid Environment”

Large-Scale Biomedical Image Analysis in Grid Environments

Vijay Kumar, Benjamin Rutt, Tahsin Kurç, Ümit V. Çatalyürek, Tony Pan, Sunny K. Chow, Stephan Lamont, Maryann E. Martone, Joel H. Saltz

ORCID match IEEE Transactions on Information Technology in Biomedicine · 2008 · Found in OpenAlex

DOI: 10.1109/titb.2007.908466

Choose for “Large-Scale Biomedical Image Analysis in Grid Environments”

Global Healthgrid: e-Science Meets Biomedical Informatics

Joel Saltz, Shannon Hastings, Stephen Langella, Scott Oster, Tahsin Kurç, Philip Payne, Renato A. Ferreira, Beth Plale, Carole Goble, David Ervin, Ashish Sharma, Tony Pan, Justin Permar, Peter Brezány, F. Siebenlist, Ravi Madduri, Ian Foster, Krishnakant Shanbhag, Charlie Mead, Neil Chue Hong

ORCID match · 2008 · Found in OpenAlex

Choose for “Global Healthgrid: e-Science Meets Biomedical Informatics”

An imaging workflow for characterizing phenotypical change in large histological mouse model datasets

Kishore Mosaliganti, Tony Pan, Randall Ridgway, Richard Sharp, Lee Cooper, Alex Gulacy, Ashish Sharma, Okan Irfanoglu, Raghu Machiraju, Tahsin Kurç, Alain de Bruin, Pamela L. Wenzel, Gustavo Leone, Joel Saltz, Kun Huang

ORCID match Journal of Biomedical Informatics · 2008 · Found in OpenAlex

DOI: 10.1016/j.jbi.2008.03.013

Choose for “An imaging workflow for characterizing phenotypical change in large histological mouse model datasets”

An Evaluation of Database Solutions to Spatial Object Association

Vijay Kumar, Tahsin Kurç, Joel Saltz, Ghaleb Abdulla, Scott R. Kohn, Celeste Matarazzo

ORCID match OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) · 2008 · Found in OpenAlex

Choose for “An Evaluation of Database Solutions to Spatial Object Association”

An Application of a Service-oriented System to Support ArrayAnnotation in Custom Chip Design for Epigenomic Analysis

Junghee Han, Dustin Potter, Tahsin Kurç, Greg Singer, Pearlly S. Yan, Hao Sun, Shannon Hastings, Stephen Langella, Scott Oster, Ramana V. Davuluri, Tim H.M. Huang, Joel H. Saltz

ORCID match Cancer Informatics · 2008 · Found in OpenAlex

DOI: 10.1177/117693510800600005

Choose for “An Application of a Service-oriented System to Support ArrayAnnotation in Custom Chip Design for Epigenomic Analysis”

A roadmap for caGrid, an enterprise Grid architecture for biomedical research.

Joel Saltz, Shannon Hastings, Stephen Langella, Scott Oster, Tahsin Kurç, Philip Payne, Renato Ferreira, Beth Plale, Carole Goble, David Ervin, Ashish Sharma, Tony Pan, Justin Permar, Peter Brezány, F. Siebenlist, Ravi Madduri, Ian Foster, Krishnakant Shanbhag, Charlie Mead, Neil Chue Hong

ORCID match PubMed · 2008 · Found in OpenAlex

Choose for “A roadmap for caGrid, an enterprise Grid architecture for biomedical research.”

A dynamic scheduling approach for coordinated wide-area data transfers using GridFTP

Gaurav Khanna, Ümit V. Çatalyürek, Tahsin Kurç, Rajkumar Kettimuthu, P. Sadayappan, Joel Saltz

ORCID match Proceedings - IEEE International Parallel and Distributed Processing Symposium · 2008 · Found in OpenAlex

DOI: 10.1109/ipdps.2008.4536325

Choose for “A dynamic scheduling approach for coordinated wide-area data transfers using GridFTP”

caGrid 1.0: a Grid enterprise architecture for cancer research.

Scott Oster, Stephen Langella, Shannon Hastings, David Ervin, Ravi Madduri, Tahsin Kurç, F. Siebenlist, Peter A. Covitz, Krishnakant Shanbhag, Ian Foster, Joel Saltz

ORCID match PubMed · 2007 · Found in OpenAlex

Choose for “caGrid 1.0: a Grid enterprise architecture for cancer research.”

caGrid 1.0: An Enterprise Grid Infrastructure for Biomedical Research

Scott Oster, Stephen Langella, S. Hastings, David Ervin, Ravi Madduri, Jeffrey Phillips, Tahsin Kurç, F. Siebenlist, Peter A. Covitz, Kaustubh R. Shanbhag, Ian Foster, Joel Saltz

ORCID match Journal of the American Medical Informatics Association · 2007 · Found in OpenAlex

DOI: 10.1197/jamia.m2522

Choose for “caGrid 1.0: An Enterprise Grid Infrastructure for Biomedical Research”

Toward terabyte pattern mining

Gregory Buehrer, Srinivasan Parthasarathy, Shirish Tatikonda, Tahsin Kurç, Joel Saltz

ORCID match · 2007 · Found in OpenAlex

DOI: 10.1145/1229428.1229432

Choose for “Toward terabyte pattern mining”

Malignant‐lesion segmentation using 4D co‐occurrence texture analysis applied to dynamic contrast‐enhanced magnetic resonance breast image data

Brent Woods, Bradley D. Clymer, Tahsin Kurç, Johannes T. Heverhagen, Robert Stevens, Adem Orsdemir, Orhan Bulan, Michael V. Knopp

ORCID match Journal of Magnetic Resonance Imaging · 2007 · Found in OpenAlex

DOI: 10.1002/jmri.20837

Choose for “Malignant‐lesion segmentation using 4D co‐occurrence texture analysis applied to dynamic contrast‐enhanced magnetic resonance breast image data”

Intelligent Optimization of Parallel and Distributed Applications

Bhupesh Bansal, Ümit V. Çatalyürek, Jacqueline Chame, Chun Chen, Ewa Deelman, Yolanda Gil, Mary Hall, Vijay Kumar, Tahsin Kurç, Kristina Lerman, Aiichiro Nakano, Yoonju Lee Nelson, Joel Saltz, Ashish Sharma, Priya Vashishta

ORCID match · 2007 · Found in OpenAlex

DOI: 10.1109/ipdps.2007.370490

Choose for “Intelligent Optimization of Parallel and Distributed Applications”

GridIMAGE: A Novel Use of Grid Computing to Support Interactive Human and Computer-Assisted Detection Decision Support

Metin N. Gürcan, Tony Pan, Ashish Sharma, Tahsin Kurç, Scott Oster, Stephen Langella, Shannon Hastings, Khan Siddiqui, Eliot L. Siegel, Joel Saltz

ORCID match Journal of Imaging Informatics in Medicine · 2007 · Found in OpenAlex

DOI: 10.1007/s10278-007-9020-0

Choose for “GridIMAGE: A Novel Use of Grid Computing to Support Interactive Human and Computer-Assisted Detection Decision Support”

GridCAD: Grid-based Computer-aided Detection System

Tony Pan, Metin N. Gürcan, Stephen Langella, Scott Oster, Shannon Hastings, Ashish Sharma, Benjamin Rutt, David Ervin, Tahsin Kurç, Khan Siddiqui, Joel Saltz, Eliot L. Siegel

ORCID match Radiographics · 2007 · Found in OpenAlex

DOI: 10.1148/rg.273065153

Choose for “GridCAD: Grid-based Computer-aided Detection System”

Dynamic Data-Driven Systems Approach for Simulation Based Optimizations

Tahsin Kurç, Xi Zhang, Manish Parashar, Héctor Klíe, Mary F. Wheeler, Ümit V. Çatalyürek, Joel Saltz

ORCID match Lecture notes in computer science · 2007 · Found in OpenAlex

DOI: 10.1007/978-3-540-72584-8_158

Choose for “Dynamic Data-Driven Systems Approach for Simulation Based Optimizations”

An Efficient and Reliable Scientific Workflow System

Tulio Tavares, Steve Langella, Joel Saltz, George Teodoro, Tahsin Kurç, Renato Ferreira, Dorgival Guedes, Wagner Meira, Ümit V. Çatalyürek, Shannon Hastings, Scott Oster

ORCID match · 2007 · Found in OpenAlex

DOI: 10.1109/ccgrid.2007.20

Choose for “An Efficient and Reliable Scientific Workflow System”

Towards Dynamic Data-Driven Management of the Ruby Gulch Waste Repository

Manish Parashar, V. Matossian, Héctor Klíe, Sunil G. Thomas, Mary F. Wheeler, Tahsin Kurç, Joel Saltz, Roelof Versteeg

ORCID match Lecture notes in computer science · 2006 · Found in OpenAlex

DOI: 10.1007/11758532_52

Choose for “Towards Dynamic Data-Driven Management of the Ruby Gulch Waste Repository”

TRIPS and TIDES

Shirish Tatikonda, Srinivasan Parthasarathy, Tahsin Kurç

ORCID match · 2006 · Found in OpenAlex

DOI: 10.1145/1183614.1183680

Choose for “TRIPS and TIDES”

Service-Based Access to and Processing of Large Scientific Datasets.

Ümit V. Çatalyürek, Sivaramakrishnan Narayanan, Olcay Sertel, Jun Kong, B. Barla Cambazoğlu, Tony Pan, Ashish K. Sharma, Shannon Hastings, Stephen Langella, Scott Oster, Tahsin Kurç, Metin N. Gürcan, Joel Saltz

ORCID match IEEE International Conference on High Performance Computing, Data, and Analytics · 2006 · Found in OpenAlex

Choose for “Service-Based Access to and Processing of Large Scientific Datasets.”

Scheduling of tasks with batch-shared I/O on heterogeneous systems

Nagavijayalakshmi Vydyanathan, Gaurav Khanna, Ümit V. Çatalyürek, Tahsin Kurç, P. Sadayappan, Joel Saltz

ORCID match · 2006 · Found in OpenAlex

DOI: 10.5555/1898953.1899083

Choose for “Scheduling of tasks with batch-shared I/O on heterogeneous systems”

Models, methods and middleware for grid-enabled multiphysics oil reservoir management

Héctor Klíe, Wolfgang Bangerth, Xiaodong Gai, Mary F. Wheeler, Paul L. Stoffa, Mrinal K. Sen, Manish Parashar, Ümit V. Çatalyürek, Joel Saltz, Tahsin Kurç

ORCID match Engineering With Computers · 2006 · Found in OpenAlex

DOI: 10.1007/s00366-006-0035-9

Choose for “Models, methods and middleware for grid-enabled multiphysics oil reservoir management”

Large Image Correction and Warping in a Cluster Environment

Vijay Kumar, Benjamin Rutt, Tahsin Kurç, Ümit V. Çatalyürek, Joel Saltz, Sunny K. Chow, Stephan Lamont, Maryann E. Martone

ORCID match · 2006 · Found in OpenAlex

DOI: 10.1109/sc.2006.39

Choose for “Large Image Correction and Warping in a Cluster Environment”

An XML-based System for Synthesis of Data from Disparate Databases

Tahsin Kurç, Daniel Janies, Andrew D. Johnson, Stephen Langella, Scott Oster, S. Hastings, F.K. Habib, Terry Camerlengo, David Ervin, Ümit V. Çatalyürek, Joel H. Saltz

ORCID match Journal of the American Medical Informatics Association · 2006 · Found in OpenAlex

DOI: 10.1197/jamia.m1848

Choose for “An XML-based System for Synthesis of Data from Disparate Databases”

XML database support for distributed execution of data-intensive scientific workflows

Shannon Hastings, Matheus Ribeiro, Stephen Langella, Scott Oster, Ümit V. Çatalyürek, Tony Pan, Kun Huang, Renato Ferreira, Joel Saltz, Tahsin Kurç

ORCID match ACM SIGMOD Record · 2005 · Found in OpenAlex

DOI: 10.1145/1084805.1084815

Choose for “XML database support for distributed execution of data-intensive scientific workflows”

Virtual Microscopy: Distributed Image Storage, Retrieval, Analysis, and Visualization

Tony Pan, S. Jewel, Ümit V. Çatalyürek, Pamela L. Wenzel, Giuseppe Leone, S. Hastings, Scott Oster, Stephen Langella, Tahsin Kurç, Joel Saltz, Daniel Cowden

ORCID match · 2005 · Found in OpenAlex

DOI: 10.1002/0471756504.ch29

Choose for “Virtual Microscopy: Distributed Image Storage, Retrieval, Analysis, and Visualization”

Use of PVFS for Efficient Execution of Jobs with Pipeline-Shared I/O

Naga Vydyanathan, Gaurav Khanna, Tahsin Kurç, Ümit V. Çatalyürek, Pete Wyckoff, Joel Saltz, P. Sadayappan

ORCID match · 2005 · Found in OpenAlex

DOI: 10.1109/grid.2004.63

Choose for “Use of PVFS for Efficient Execution of Jobs with Pipeline-Shared I/O”

Towards Dynamic Data-Driven Optimization of Oil Well Placement

Manish Parashar, V. Matossian, Wolfgang Bangerth, Héctor Klíe, Benjamin Rutt, Tahsin Kurç, Ümit V. Çatalyürek, Joel Saltz, Mary F. Wheeler

ORCID match Lecture notes in computer science · 2005 · Found in OpenAlex

DOI: 10.1007/11428848_85

Choose for “Towards Dynamic Data-Driven Optimization of Oil Well Placement”

Tools for efficient subsetting and pipelined processing of large scale, distributed biomedical image data

Matheus Ribeiro, Tahsin Kurç, Tony Pan, Kun Huang, Ümit V. Çatalyürek, Xi Zhang, Steve Langella, Shannon Hastings, Scott Oster, Renato Ferreira, Joel Saltz

ORCID match Advances in parallel computing · 2005 · Found in OpenAlex

DOI: 10.1016/s0927-5452(05)80020-6

Choose for “Tools for efficient subsetting and pipelined processing of large scale, distributed biomedical image data”

The Virtual Microscope

Ümit V. Çatalyürek, Michael D. Beynon, Chia‐Lin Chang, Tahsin Kurç, Alan Sussman, Joel Saltz

ORCID match · 2005 · Found in OpenAlex

DOI: 10.21236/ada440466

Choose for “The Virtual Microscope”

Supporting Large Scale Medical and Scientific Datasets.

Ümit V. Çatalyürek, Shannon Hastings, Kun Huang, Vijay Kumar, Tahsin Kurç, Stephen Langella, Sivaramakrishnan Narayanan, Scott Oster, Tony Pan, Benjamin Rutt, Xi Zhang, Joel Saltz

ORCID match · 2005 · Found in OpenAlex

Choose for “Supporting Large Scale Medical and Scientific Datasets.”

A simulation and data analysis system for large‐scale, data‐driven oil reservoir simulation studies

Tahsin Kurç, Ümit V. Çatalyürek, Xi Zhang, Joel Saltz, Ryan Martino, Mary F. Wheeler, Małgorzata Peszyńska, Alan Sussman, Christian Hansen, Mrinal K. Sen, Roustam K. Seifoullaev, Paul L. Stoffa, Carlos Torres‐Verdín, Manish Parashar

ORCID match Concurrency and Computation Practice and Experience · 2005 · Found in OpenAlex

DOI: 10.1002/cpe.898

Choose for “A simulation and data analysis system for large‐scale, data‐driven oil reservoir simulation studies”

A simulation and data analysis system for large-scale, data-driven oil reservoir simulation studies: Research Articles

Tahsin Kurç, Ümit V. Çatalyürek, Xi Zhang, Joel Saltz, Ryan Martino, Mary F. Wheeler, Małgorzata Peszyńska, Alan Sussman, Christian Hansen, Mrinal K. Sen, Roustam K. Seifoullaev, Paul L. Stoffa, Carlos Torres‐Verdín, Manish Parashar

ORCID match IEEE International Conference on High Performance Computing, Data, and Analytics · 2005 · Found in OpenAlex

Choose for “A simulation and data analysis system for large-scale, data-driven oil reservoir simulation studies: Research Articles”

An approach for automatic data virtualization

Li Weng, C. Agrawal, Ümit V. Çatalyürek, Tahsin Kurç, S. Narayanan, Joel Saltz

ORCID match · 2004 · Found in OpenAlex

DOI: 10.1109/hpdc.2004.1323476

Choose for “An approach for automatic data virtualization”

The virtual microscope

Ümit V. Çatalyürek, Michael D. Beynon, Chialin Chang, Tahsin Kurç, Alan Sussman, Joel Saltz

ORCID match IEEE Transactions on Information Technology in Biomedicine · 2003 · Found in OpenAlex

DOI: 10.1109/titb.2004.823952

Choose for “The virtual microscope”

Parallel computing in environment and energy

Mary F. Wheeler, Wonsuck Lee, Clint Dawson, Dorian Arnold, Tahsin Kurç, Manish Parashar, Joel Saltz, Alan Sussman

ORCID match · 2003 · Found in OpenAlex

Choose for “Parallel computing in environment and energy”

Optimizing Reduction Computations In a Distributed Environment

Tahsin Kurç, Feng Lee, Gagan Agrawal, Ümit V. Çatalyürek, Renato Ferreira, Joel Saltz

ORCID match · 2003 · Found in OpenAlex

DOI: 10.1145/1048935.1050160

Choose for “Optimizing Reduction Computations In a Distributed Environment”

Driving Scientific Applications by Data in Distributed Environments

Joel Saltz, Ümit V. Çatalyürek, Tahsin Kurç, Mike Gray, Shannon Hastings, Steve Langella, Sivaramakrishnan Narayanan, Ryan Martino, Steven L. Bryant, Małgorzata Peszyńska, Mary F. Wheeler, Alan Sussman, Michael D. Beynon, Christian Hansen, Don Stredney, D Sessanna

ORCID match Lecture notes in computer science · 2003 · Found in OpenAlex

DOI: 10.1007/3-540-44864-0_37

Choose for “Driving Scientific Applications by Data in Distributed Environments”

DATABASE SUPPORT FOR DATA-DRIVEN SCIENTIFIC APPLICATIONS IN THE GRID

Sivaramakrishnan Narayanan, Tahsin Kurç, Ümit V. Çatalyürek, Joel Saltz

ORCID match Parallel Processing Letters · 2003 · Found in OpenAlex

DOI: 10.1142/s0129626403001264

Choose for “DATABASE SUPPORT FOR DATA-DRIVEN SCIENTIFIC APPLICATIONS IN THE GRID”

Building Parallel Database Systems for Multidimensional Data

Chailin Chang, Tahsin Kurç, Alan Sussman, Joel Saltz

ORCID match The MIT Press eBooks · 2003 · Found in OpenAlex

DOI: 10.7551/mitpress/6038.003.0004

Choose for “Building Parallel Database Systems for Multidimensional Data”

A component-based implementation of multiple sequence alignment

Ümit V. Çatalyürek, Mike Gray, Tahsin Kurç, Joel Saltz, Eric Stahlberg, Renato Ferreira

ORCID match · 2003 · Found in OpenAlex

DOI: 10.1145/952532.952559

Choose for “A component-based implementation of multiple sequence alignment”

A component-based implementation of multiple sequence alignment

Ümit V. Çatalyürek, Mike Gray, Tahsin Kurç, Joel Saltz, Eric Stahlberg, Renato Ferreira

ORCID match Proceedings of the 2003 ACM symposium on Applied computing - SAC '03 · 2003 · Found in OpenAlex

DOI: 10.1145/952548.952559

Choose for “A component-based implementation of multiple sequence alignment”

Servicing Mixed Data Intensive Query Workloads

Henrique Andrade, Tahsin Kurç, Alan Sussman, Eugene Borovikov, Joel Saltz

ORCID match University Libraries (University of Maryland) · 2002 · Found in OpenAlex

Choose for “Servicing Mixed Data Intensive Query Workloads”

Executing Multiple Pipelined Data Analysis Operations in the Grid

M. B. Spencer, R. Ferreira, M. Beynon, Tahsin Kurç, Ümit V. Çatalyürek, Alan Sussman, Joel Saltz

ORCID match · 2002 · Found in OpenAlex

DOI: 10.1109/sc.2002.10015

Choose for “Executing Multiple Pipelined Data Analysis Operations in the Grid”

Visualization of large data sets with the Active Data Repository

Tahsin Kurç, Ümit V. Çatalyürek, Chia‐Lin Chang, Alan Sussman, Joel Saltz

ORCID match IEEE Computer Graphics and Applications · 2001 · Found in OpenAlex

DOI: 10.1109/38.933521

Choose for “Visualization of large data sets with the Active Data Repository”

Distributed processing of very large datasets with DataCutter

Michael D. Beynon, Tahsin Kurç, Ümit V. Çatalyürek, Chialin Chang, Alan Sussman, Joel Saltz

ORCID match Parallel Computing · 2001 · Found in OpenAlex

DOI: 10.1016/s0167-8191(01)00099-0

Choose for “Distributed processing of very large datasets with DataCutter”

Efficient Performance Prediction for Large-Scale, Data-Intensive Applications

Tahsin Kurç, Mustafa Uysal, Hyeonsang Eom, Jeff Hollingsworth, Joel Saltz, Alan Sussman

ORCID match The International Journal of High Performance Computing Applications · 2000 · Found in OpenAlex

DOI: 10.1177/109434200001400305

Choose for “Efficient Performance Prediction for Large-Scale, Data-Intensive Applications”

Querying very large multi-dimensional datasets in ADR

Tahsin Kurç, Chialin Chang, Renato Ferreira, Alan Sussman, Joel Saltz

ORCID match · 1999 · Found in OpenAlex

DOI: 10.1145/331532.331544

Choose for “Querying very large multi-dimensional datasets in ADR”

Object-space parallel polygon rendering on hypercubes

Tahsin Kurç, Cevdet Aykanat, Bülent Özgüç

ORCID match Computers & Graphics · 1998 · Found in OpenAlex

DOI: 10.1016/s0097-8493(98)00047-8

Choose for “Object-space parallel polygon rendering on hypercubes”

Active pixel merging on hypercube multicomputers

Tahsin Kurç, Cevdet Aykanat, Bülent Özgüç

ORCID match Lecture notes in computer science · 1996 · Found in OpenAlex

DOI: 10.1007/3-540-61142-8_565

Choose for “Active pixel merging on hypercube multicomputers”
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