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1. Surgical Site Infections in Simultaneous Colorectal and Liver Resections for Metastatic Colorectal Adenocarcinoma

Author

Schleimer, Lauren E., Hakki, Lynn, Seier, Kenneth, Seo, Susan K., Cohen, Nina, Usiak, Shauna, Romero, Tiffany, Kamboj, Mini, Ilagan, Crisanta, Saadat, Lily V., Alessandris, Remo, Soares, Kevin C., Drebin, Jeffrey, Wei, Alice C., Widmar, Maria, Wei, Iris H., Smith, J. Joshua, Pappou, Emmanouil P., Paty, Philip B., Nash, Garrett M., Jarnagin, William R., Garcia-Aguilar, Julio, Gonen, Mithat, Kingham, T. Peter, Weiser, Martin R., and D’Angelica, Michael I.

Published
2025
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2. Robotic Versus Open Placement of Hepatic Artery Infusion Pumps

Author

Schleimer, Lauren E., Liu, Annie, Kalvin, Hannah L., Barekzai, Ahmad Bashir, Choubey, Ankur P., Jung, Joslyn, Haque, Rubiya, Jarnagin, William R., Balachandran, Vinod P., Geevarghese, Ruben, Marinelli, Brett, Gonen, Mithat, Drebin, Jeffrey, Allen, Peter J., D’Angelica, Michael I., Wei, Alice C., Zani, Sabino, Kingham, T. Peter, Lidsky, Michael E., and Soares, Kevin C.

Published
2025
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3. Adjuvant Cytotoxic Chemotherapy may not be Associated with a Survival Advantage for Resected Intrahepatic Cholangiocarcinoma

Author

Sharib, Jeremy, Rhodin, Kristen E., Liu, Annie, McIntyre, Sarah, Bartholomew, Alex, Masoud, Sabran, DeLaura, Isabel, Kemeny, Nancy E., Cercek, Andrea, Harding, James J., O’Reilly, Eileen M., Abou-Alfa, Ghassan K., Reidy-Lagunes, Diane, Connell, Louise Catherine, Dika, Imane El, Balachandran, Vinod P., Drebin, Jeffrey, Soares, Kevin C., Wei, Alice C., Kingham, T. Peter, D’Angelica, Michael I., Uronis, Hope, Strickler, John, Hsu, S. David, Morse, Michael, Zani, Sabino, Allen, Peter J., Jarnagin, William R., and Lidsky, Michael E.

Published
2025
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4. Clinicogenomic landscape of pancreatic adenocarcinoma identifies KRAS mutant dosage as prognostic of overall survival

Author

Varghese, Anna M., Perry, Maria A., Chou, Joanne F., Nandakumar, Subhiksha, Muldoon, Daniel, Erakky, Amanda, Zucker, Amanda, Fong, Christopher, Mehine, Miika, Nguyen, Bastien, Basturk, Olca, Balogun, Fiyinfolu, Kelsen, David P., Brannon, A. Rose, Mandelker, Diana, Vakiani, Efsevia, Park, Wungki, Yu, Kenneth H., Stadler, Zsofia K., Schattner, Mark A., Jarnagin, William R., Wei, Alice C., Chakravarty, Debyani, Capanu, Marinela, Schultz, Nikolaus, Berger, Michael F., Iacobuzio-Donahue, Christine A., Bandlamudi, Chaitanya, and O’Reilly, Eileen M.

Published
2025
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6. Computed Tomography-Based Radiomics with Machine Learning Outperforms Radiologist Assessment in Estimating Colorectal Liver Metastases Pathologic Response After Chemotherapy

Author

Karagkounis, Georgios, Horvat, Natally, Danilova, Sofia, Chhabra, Salini, Narayan, Raja R., Barekzai, Ahmad B., Kleshchelski, Adam, Joanne, Chou, Gonen, Mithat, Balachandran, Vinod, Soares, Kevin C., Wei, Alice C., Kingham, T. Peter, Jarnagin, William R., Shia, Jinru, Chakraborty, Jayasree, and D’Angelica, Michael I.

Published
2024
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7. Survival Outcomes and Genetic Characteristics of Resected Pancreatic Acinar Cell Carcinoma

Author

Blair, Alex B., Radomski, Shannon N., Chou, Joanne, Liu, Mengyuan, Howell, Thomas Clark, Park, Wungki, O’Reilly, Eileen M., Zheng, Lei, Balachandran, Vinod P., Wei, Alice C., Kingham, T. Peter, D’Angelica, Michael I., Drebin, Jeffrey, Zani, Sabino, Blazer, III, Dan G., Burkhart, Richard A., Burns, III, William R., Lafaro, Kelly J., Allen, Peter J., Jarnagin, William R., Lidsky, Michael E., He, Jin, and Soares, Kevin C.

Published
2024
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8. Failure to Rescue After Resection of Perhilar Cholangiocarcinoma in an International Multicenter Cohort

Author

Olthof, Pim B., Bouwense, Stefan A. W., Bednarsch, Jan, Dewulf, Maxime, Kazemier, Geert, Maithel, Shishir, Jarnagin, William R., Aldrighetti, Luca, Roberts, Keith J., Troisi, Roberto I., Malago, Massimo M., Lang, Hauke, Alikhanov, Ruslan, Ruzzenente, Andrea, Malik, Hassan, Charco, Ramón, Sparrelid, Ernesto, Pratschke, Johann, Cescon, Matteo, Nadalin, Silvio, Hagendoorn, Jeroen, Schadde, Erik, Hoogwater, Frederik J. H., Schnitzbauer, Andreas A., Topal, Baki, Lodge, Peter, Olde Damink, Steven W. M., Neumann, Ulf P., and Groot Koerkamp, Bas

Published
2024
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12. ASO Visual Abstract: Adjuvant Cytotoxic Chemotherapy May Not Be Associated with a Survival Advantage for Resected Intrahepatic Cholangiocarcinoma

Author

Sharib, Jeremy, Rhodin, Kristen E., Liu, Annie, McIntyre, Sarah, Bartholomew, Alex, Masoud, Sabran, DeLaura, Isabel, Kemeny, Nancy E., Cercek, Andrea, Harding, James J., O’Reilly, Eileen M., Abou-Alfa, Ghassan K., Reidy-Lagunes, Diane, Connell, Louise Catherine, El Dika, Imane, Balachandran, Vinod P., Drebin, Jeffrey, Soares, Kevin C., Wei, Alice C., Kingham, T. Peter, D’Angelica, Michael I., Uronis, Hope, Strickler, John, Hsu, S. David, Morse, Michael, Zani, Sabino, Allen, Peter J., Jarnagin, William R., and Lidsky, Michael E.

Published
2025
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13. ASO Visual Abstract: Survival of Patients with Resected Microsatellite Instability-High, Mismatch Repair Deficient, and Lynch Syndrome-Associated Pancreatic Ductal Adenocarcinomas

Author

Eikenboom, Ellis L., Nasar, Naaz, Seier, Kenneth, Gönen, Mithat, Spaander, Manon C. W., O’Reilly, Eileen M., Jarnagin, William R., Drebin, Jeffrey, D’Angelica, Michael I., Kingham, T. Peter, Balachandran, Vinod P., Soares, Kevin C., Wagner, Anja, and Wei, Alice C.

Published
2025
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14. ASO Visual Abstract: Surgical Site Infections in Simultaneous Colorectal and Liver Resections for Metastatic Colorectal Adenocarcinoma

Author

Schleimer, Lauren E., Hakki, Lynn, Seier, Kenneth, Seo, Susan K., Cohen, Nina, Usiak, Shauna, Romero, Tiffany, Kamboj, Mini, Ilagan, Crisanta, Saadat, Lily V., Alessandris, Remo, Soares, Kevin C., Drebin, Jeffrey, Wei, Alice C., Widmar, Maria, Wei, Iris H., Joshua Smith, J., Pappou, Emmanouil P., Paty, Philip B., Nash, Garrett M., Jarnagin, William R., Garcia-Aguilar, Julio, Gonen, Mithat, Kingham, T. Peter, Weiser, Martin R., and D’Angelica, Michael I.

Published
2024
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15. ASO Visual Abstract: Computed Tomography-Based Radiomics with Machine Learning Outperforms Radiologist Assessment in Estimating Colorectal Liver Metastases Pathologic Response After Chemotherapy

Author

Karagkounis, Georgios, Horvat, Natally, Danilova, Sofia, Chhabra, Salini, Narayan, Raja R., Barekzai, Ahmad B., Kleshchelski, Adam, Joanne, Chou, Gonen, Mithat, Balachandran, Vinod, Soares, Kevin C., Wei, Alice C., Kingham, T. Peter, Jarnagin, William R., Shia, Jinru, Chakraborty, Jayasree, and D’Angelica, Michael I.

Published
2024
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16. Multi-parametric atlas of the pre-metastatic liver for prediction of metastatic outcome in early-stage pancreatic cancer

Author

Bojmar, Linda, Zambirinis, Constantinos P., Hernandez, Jonathan M., Chakraborty, Jayasree, Shaashua, Lee, Kim, Junbum, Johnson, Kofi Ennu, Hanna, Samer, Askan, Gokce, Burman, Jonas, Ravichandran, Hiranmayi, Zheng, Jian, Jolissaint, Joshua S., Srouji, Rami, Song, Yi, Choubey, Ankur, Kim, Han Sang, Cioffi, Michele, van Beek, Elke, Sigel, Carlie, Jessurun, Jose, Velasco Riestra, Paulina, Blomstrand, Hakon, Jönsson, Carolin, Jönsson, Anette, Lauritzen, Pernille, Buehring, Weston, Ararso, Yonathan, Hernandez, Dylanne, Vinagolu-Baur, Jessica P., Friedman, Madison, Glidden, Caroline, Firmenich, Laetitia, Lieberman, Grace, Mejia, Dianna L., Nasar, Naaz, Mutvei, Anders P., Paul, Doru M., Bram, Yaron, Costa-Silva, Bruno, Basturk, Olca, Boudreau, Nancy, Zhang, Haiying, Matei, Irina R., Hoshino, Ayuko, Kelsen, David, Sagi, Irit, Scherz, Avigdor, Scherz-Shouval, Ruth, Yarden, Yosef, Oren, Moshe, Egeblad, Mikala, Lewis, Jason S., Keshari, Kayvan, Grandgenett, Paul M., Hollingsworth, Michael A., Rajasekhar, Vinagolu K., Healey, John H., Björnsson, Bergthor, Simeone, Diane M., Tuveson, David A., Iacobuzio-Donahue, Christine A., Bromberg, Jaqueline, Vincent, C. Theresa, O’Reilly, Eileen M., DeMatteo, Ronald P., Balachandran, Vinod P., D’Angelica, Michael I., Kingham, T. Peter, Allen, Peter J., Simpson, Amber L., Elemento, Olivier, Sandström, Per, Schwartz, Robert E., Jarnagin, William R., and Lyden, David

Published
2024
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17. Higher Postoperative Mortality and Inferior Survival After Right-Sided Liver Resection for Perihilar Cholangiocarcinoma: Left-Sided Resection is Preferred When Possible

Author

Olthof, Pim B., Erdmann, Joris I., Alikhanov, Ruslan, Charco, Ramón, Guglielmi, Alfredo, Hagendoorn, Jeroen, Hakeem, Abdul, Hoogwater, Frederik J. H., Jarnagin, William R., Kazemier, Geert, Lang, Hauke, Maithel, Shishir K., Malago, Massimo, Malik, Hassan Z., Nadalin, Silvio, Neumann, Ulf, Olde Damink, Steven W. M., Pratschke, Johann, Ratti, Francesca, Ravaioli, Matteo, Roberts, Keith J., Schadde, Erik, Schnitzbauer, Andreas A., Sparrelid, Ernesto, Topal, Baki, Troisi, Roberto I., and Groot Koerkamp, Bas

Published
2024
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18. ASO Visual Abstract: Has Management of Intrahepatic Cholangiocarcinoma Evolved with the Evidence? Trends and Practice Patterns from the National Cancer Database

Author

Schleimer, Lauren E., Kalvin, Hannah L., Ellis, Ryan J., Kingham, T. Peter, Soares, Kevin C., D’Angelica, Michael I., Balachandran, Vinod P., Drebin, Jeffrey, Cercek, Andrea, Abou-Alfa, Ghassan K., O’Reilly, Eileen M., Harding, James J., Gönen, Mithat, Wei, Alice C., and Jarnagin, William R.

Published
2024
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20. Tumoral Intraductal Neoplasms of the Bile Ducts Comprise Morphologically and Genetically Distinct Entities

Author

Wang, Tao, Askan, Gokce, Ozcan, Kerem, Rana, Satshil, Zehir, Ahmet, Bhanot, Umeshkumar K., Yantiss, Rhonda K., Rao, Deepthi S., Wahl, Samuel J., Bagci, Pelin, Balci, Serdar, Balachandran, Vinod, Jarnagin, William R., Adsay, N. Volkan, Klimstra, David S., and Basturk, Olca

Subjects
Gene mutations, Tumors, Tumor proteins, Dysplasia, Health, World Health Organization
Abstract

* Context.--Tumoral (grossly visible) intraductal neoplasms of the bile ducts are still being characterized. Objective.--To investigate their morphologic, immunohistochemical, and molecular features. Design.--Forty-one cases were classified as gastric-, intestinal-, pancreatobiliary-type intraductal papillary neoplasm (IPN), intraductal oncocytic papillary neoplasm (IOPN), or intraductal tubulopapillary neoplasm (ITPN) on the basis of histology. All neoplasms were subjected to targeted next-generation sequencing. Results.--The mean age at diagnosis was 69 years (4281 years); male to female ratio was 1.3. Most neoplasms (n = 23, 56%) were extrahepatic/large (mean size, 4.6 cm). The majority (n = 32, 78%) contained high-grade dysplasia, and 68% (n = 28) revealed invasion. All gastric-type IPNs (n = 9) and most ITPNs/IOPNs showed consistent colabeling for CK7/MUC6, which was less common among others (P = .004). Intestinal-type IPNs (n = 5) showed higher rates of CK20 expression than others (P < .001). Overall, the most commonly mutated genes included TP53 and APC, while copy number variants affected ELF3 and CDKN2A/B. All gastric-type IPNs contained an alteration affecting the Wnt signaling pathway; 7 of 9 (78%) showed aberrations in the MAPK pathway. Mutations in APC and KRAS were common in gastric-type IPNs as compared with others (P = .01 for both). SMAD4 was more frequently mutated in intestinaltype IPNs (P = .02). Pancreatobiliary-type IPNs (n = 14) exhibited frequent alterations in tumor suppressor genes including TP53, CDKN2A/B, and ARID2 (P = .04, P = .01 and P = .002, respectively). Of 6 IOPNs analyzed, 3 (50%) revealed ATP1B1-PRKACB fusion. ITPNs (n = 6) showed relatively few recurrent genetic aberrations. Follow-up information was available for 38 patients (median, 58.5 months). The ratio of disease-related deaths was higher for the cases with invasion (56% versus 10%). Conclusions.--Tumoral intraductal neoplasms of the bile ducts, similar to their counterparts in the pancreas, are morphologically and genetically heterogeneous. (Arch Pathol Lab Med. 2023;147:1390-1401; doi: 10.5858/arpa.2022-0343-OA), Tumoral (grossly visible) intraductal neoplasms of the bile ducts are rare tumors, which exhibit variable histomorphology and behavior. The nomenclature for these biliary neoplasms has been inconsistent, and they have [...]

Published
2023
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22. Gemcitabine with Cisplatin Versus Hepatic Arterial Infusion Pump Chemotherapy for Liver-Confined Unresectable Intrahepatic Cholangiocarcinoma

Author

Franssen, Stijn, Holster, Jessica J., Jolissaint, Joshua S., Nooijen, Lynn E., Cercek, Andrea, D’Angelica, Michael I., Homs, Marjolein Y. V., Wei, Alice C., Balachandran, Vinod P., Drebin, Jeffrey A., Harding, James J., Kemeny, Nancy E., Kingham, T. Peter, Klümpen, Heinz-Josef, Mostert, Bianca, Swijnenburg, Rutger-Jan, Soares, Kevin C., Jarnagin, William R., and Groot Koerkamp, Bas

Published
2024
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25. Distinct clinical outcomes and biological features of specific KRAS mutants in human pancreatic cancer

Author

McIntyre, Caitlin A., Grimont, Adrien, Park, Jiwoon, Meng, Yinuo, Sisso, Whitney J., Seier, Kenneth, Jang, Gun Ho, Walch, Henry, Aveson, Victoria G., Falvo, David J., Fall, William B., Chan, Christopher W., Wenger, Andrew, Ecker, Brett L., Pulvirenti, Alessandra, Gelfer, Rebecca, Zafra, Maria Paz, Schultz, Nikolaus, Park, Wungki, O’Reilly, Eileen M., Houlihan, Shauna L., Alonso, Alicia, Hissong, Erika, Church, George M., Mason, Christopher E., Siolas, Despina, Notta, Faiyaz, Gonen, Mithat, Dow, Lukas E., Jarnagin, William R., and Chandwani, Rohit

Published
2024
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29. The Medical Segmentation Decathlon

Author

Antonelli, Michela, Reinke, Annika, Bakas, Spyridon, Farahani, Keyvan, AnnetteKopp-Schneider, Landman, Bennett A., Litjens, Geert, Menze, Bjoern, Ronneberger, Olaf, Summers, Ronald M., van Ginneken, Bram, Bilello, Michel, Bilic, Patrick, Christ, Patrick F., Do, Richard K. G., Gollub, Marc J., Heckers, Stephan H., Huisman, Henkjan, Jarnagin, William R., McHugo, Maureen K., Napel, Sandy, Pernicka, Jennifer S. Goli, Rhode, Kawal, Tobon-Gomez, Catalina, Vorontsov, Eugene, Meakin, James A., Ourselin, Sebastien, Wiesenfarth, Manuel, Arbelaez, Pablo, Bae, Byeonguk, Chen, Sihong, Daza, Laura, Feng, Jianjiang, He, Baochun, Isensee, Fabian, Ji, Yuanfeng, Jia, Fucang, Kim, Namkug, Kim, Ildoo, Merhof, Dorit, Pai, Akshay, Park, Beomhee, Perslev, Mathias, Rezaiifar, Ramin, Rippel, Oliver, Sarasua, Ignacio, Shen, Wei, Son, Jaemin, Wachinger, Christian, Wang, Liansheng, Wang, Yan, Xia, Yingda, Xu, Daguang, Xu, Zhanwei, Zheng, Yefeng, Simpson, Amber L., Maier-Hein, Lena, and Cardoso, M. Jorge

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, 68T07
Abstract

International challenges have become the de facto standard for comparative assessment of image analysis algorithms given a specific task. Segmentation is so far the most widely investigated medical image processing task, but the various segmentation challenges have typically been organized in isolation, such that algorithm development was driven by the need to tackle a single specific clinical problem. We hypothesized that a method capable of performing well on multiple tasks will generalize well to a previously unseen task and potentially outperform a custom-designed solution. To investigate the hypothesis, we organized the Medical Segmentation Decathlon (MSD) - a biomedical image analysis challenge, in which algorithms compete in a multitude of both tasks and modalities. The underlying data set was designed to explore the axis of difficulties typically encountered when dealing with medical images, such as small data sets, unbalanced labels, multi-site data and small objects. The MSD challenge confirmed that algorithms with a consistent good performance on a set of tasks preserved their good average performance on a different set of previously unseen tasks. Moreover, by monitoring the MSD winner for two years, we found that this algorithm continued generalizing well to a wide range of other clinical problems, further confirming our hypothesis. Three main conclusions can be drawn from this study: (1) state-of-the-art image segmentation algorithms are mature, accurate, and generalize well when retrained on unseen tasks; (2) consistent algorithmic performance across multiple tasks is a strong surrogate of algorithmic generalizability; (3) the training of accurate AI segmentation models is now commoditized to non AI experts.

Published
2021
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32. EPIC-Survival: End-to-end Part Inferred Clustering for Survival Analysis, Featuring Prognostic Stratification Boosting

Author

Muhammad, Hassan, Xie, Chensu, Sigel, Carlie S., Doukas, Michael, Alpert, Lindsay, Jarnagin, William R., Simpson, Amber, and Fuchs, Thomas J.

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Histopathology-based survival modelling has two major hurdles. Firstly, a well-performing survival model has minimal clinical application if it does not contribute to the stratification of a cancer patient cohort into different risk groups, preferably driven by histologic morphologies. In the clinical setting, individuals are not given specific prognostic predictions, but are rather predicted to lie within a risk group which has a general survival trend. Thus, It is imperative that a survival model produces well-stratified risk groups. Secondly, until now, survival modelling was done in a two-stage approach (encoding and aggregation). The massive amount of pixels in digitized whole slide images were never utilized to their fullest extent due to technological constraints on data processing, forcing decoupled learning. EPIC-Survival bridges encoding and aggregation into an end-to-end survival modelling approach, while introducing stratification boosting to encourage the model to not only optimize ranking, but also to discriminate between risk groups. In this study we show that EPIC-Survival performs better than other approaches in modelling intrahepatic cholangiocarcinoma, a historically difficult cancer to model. Further, we show that stratification boosting improves further improves model performance, resulting in a concordance-index of 0.880 on a held-out test set. Finally, we were able to identify specific histologic differences, not commonly sought out in ICC, between low and high risk groups., Comment: co-first authors: Hassan Muhammad and Chensu Xie

Published
2021

34. Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer

Author

Rojas, Luis A., Sethna, Zachary, Soares, Kevin C., Olcese, Cristina, Pang, Nan, Patterson, Erin, Lihm, Jayon, Ceglia, Nicholas, Guasp, Pablo, Chu, Alexander, Yu, Rebecca, Chandra, Adrienne Kaya, Waters, Theresa, Ruan, Jennifer, Amisaki, Masataka, Zebboudj, Abderezak, Odgerel, Zagaa, Payne, George, Derhovanessian, Evelyna, Müller, Felicitas, Rhee, Ina, Yadav, Mahesh, Dobrin, Anton, Sadelain, Michel, Łuksza, Marta, Cohen, Noah, Tang, Laura, Basturk, Olca, Gönen, Mithat, Katz, Seth, Do, Richard Kinh, Epstein, Andrew S., Momtaz, Parisa, Park, Wungki, Sugarman, Ryan, Varghese, Anna M., Won, Elizabeth, Desai, Avni, Wei, Alice C., D’Angelica, Michael I., Kingham, T. Peter, Mellman, Ira, Merghoub, Taha, Wolchok, Jedd D., Sahin, Ugur, Türeci, Özlem, Greenbaum, Benjamin D., Jarnagin, William R., Drebin, Jeffrey, O’Reilly, Eileen M., and Balachandran, Vinod P.

Published
2023
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35. Leveraging Contrastive Learning with SimSiam for the Classification of Primary and Secondary Liver Cancers

Author

Mojtahedi, Ramtin, Hamghalam, Mohammad, Jarnagin, William R., Do, Richard K. G., Simpson, Amber L., Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Woo, Jonghye, editor, Hering, Alessa, editor, Silva, Wilson, editor, Li, Xiang, editor, Fu, Huazhu, editor, Liu, Xiaofeng, editor, Xing, Fangxu, editor, Purushotham, Sanjay, editor, Mathai, Tejas S., editor, Mukherjee, Pritam, editor, De Grauw, Max, editor, Beets Tan, Regina, editor, Corbetta, Valentina, editor, Kotter, Elmar, editor, Reyes, Mauricio, editor, Baumgartner, Christian F., editor, Li, Quanzheng, editor, Leahy, Richard, editor, Dong, Bin, editor, Chen, Hao, editor, Huo, Yuankai, editor, Lv, Jinglei, editor, Xu, Xinxing, editor, Li, Xiaomeng, editor, Mahapatra, Dwarikanath, editor, Cheng, Li, editor, Petitjean, Caroline, editor, and Presles, Benoît, editor

Published
2023
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39. ASO Visual Abstract: Gemcitabine with Cisplatin Versus Hepatic Arterial Infusion Pump Chemotherapy for Liver-Confined Unresectable Intrahepatic Cholangiocarcinoma

Author

Franssen, Stijn, Holster, Jessica J., Jolissaint, Joshua S., Nooijen, Lynn E., Cercek, Andrea, D’Angelica, Michael I., Homs, Marjolein Y. V., Wei, Alice C., Balachandran, Vinod P., Drebin, Jeffrey A., Harding, James J., Kemeny, Nancy E., Kingham, T. Peter, Klümpen, Heinz-Josef, Mostert, Bianca, Swijnenburg, Rutger-Jan, Soares, Kevin C., Jarnagin, William R., and Groot Koerkamp, Bas

Published
2024
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40. ASO Visual Abstract: Combined Hepatic Artery Infusion Pump and Systemic Chemotherapy in the Modern Era for Chemotherapy-Naive Patients with Unresectable Colorectal Liver Metastases

Author

Verheij, Floris S., Kuhlmann, Koert F. D., Silliman, Danielle R., Soares, Kevin C., Kingham, T. Peter, Balachandran, Vinod P., Drebin, Jeffrey A., Wei, Alice C., Jarnagin, William R., Cercek, Andrea, Kok, Niels F. M., Kemeny, Nancy E., and D’Angelica, Michael I.

Published
2023
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41. Towards Unsupervised Cancer Subtyping: Predicting Prognosis Using A Histologic Visual Dictionary

Author

Muhammad, Hassan, Sigel, Carlie S., Campanella, Gabriele, Boerner, Thomas, Pak, Linda M., Büttner, Stefan, IJzermans, Jan N. M., Koerkamp, Bas Groot, Doukas, Michael, Jarnagin, William R., Simpson, Amber, and Fuchs, Thomas J.

Subjects
Computer Science - Computer Vision and Pattern Recognition, Quantitative Biology - Tissues and Organs, Statistics - Machine Learning
Abstract

Unlike common cancers, such as those of the prostate and breast, tumor grading in rare cancers is difficult and largely undefined because of small sample sizes, the sheer volume of time needed to undertake on such a task, and the inherent difficulty of extracting human-observed patterns. One of the most challenging examples is intrahepatic cholangiocarcinoma (ICC), a primary liver cancer arising from the biliary system, for which there is well-recognized tumor heterogeneity and no grading paradigm or prognostic biomarkers. In this paper, we propose a new unsupervised deep convolutional autoencoder-based clustering model that groups together cellular and structural morphologies of tumor in 246 ICC digitized whole slides, based on visual similarity. From this visual dictionary of histologic patterns, we use the clusters as covariates to train Cox-proportional hazard survival models. In univariate analysis, three clusters were significantly associated with recurrence-free survival. Combinations of these clusters were significant in multivariate analysis. In a multivariate analysis of all clusters, five showed significance to recurrence-free survival, however the overall model was not measured to be significant. Finally, a pathologist assigned clinical terminology to the significant clusters in the visual dictionary and found evidence supporting the hypothesis that collagen-enriched fibrosis plays a role in disease severity. These results offer insight into the future of cancer subtyping and show that computational pathology can contribute to disease prognostication, especially in rare cancers., Comment: 10 pages, 6 figures

Published
2019

43. Concordance in Oncogenic Alterations Between the Primary Tumor and Advanced Disease: Insights Into the Heterogeneity of Intrahepatic Cholangiocarcinoma

Author

McIntyre, Sarah M., Preston, William A., Walch, Henry, Sharib, Jeremy, Kundra, Ritika, Sigel, Carlie, Lidsky, Michael E., Allen, Peter J., Morse, Michael A., Chen, Wei, Cercek, Andrea, Harding, James J., Abou-Alfa, Ghassan K., OʼReilly, Eileen M., Park, Wungki, Balachandran, Vinod P., Drebin, Jeffrey, Soares, Kevin C., Wei, Alice, Kingham, T. Peter, DʼAngelica, Michael I., Iacobuzio-Donahue, Christine, and Jarnagin, William R.

Published
2024
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46. A large annotated medical image dataset for the development and evaluation of segmentation algorithms

Author

Simpson, Amber L., Antonelli, Michela, Bakas, Spyridon, Bilello, Michel, Farahani, Keyvan, van Ginneken, Bram, Kopp-Schneider, Annette, Landman, Bennett A., Litjens, Geert, Menze, Bjoern, Ronneberger, Olaf, Summers, Ronald M., Bilic, Patrick, Christ, Patrick F., Do, Richard K. G., Gollub, Marc, Golia-Pernicka, Jennifer, Heckers, Stephan H., Jarnagin, William R., McHugo, Maureen K., Napel, Sandy, Vorontsov, Eugene, Maier-Hein, Lena, and Cardoso, M. Jorge

Subjects
Computer Science - Computer Vision and Pattern Recognition, Electrical Engineering and Systems Science - Image and Video Processing
Abstract

Semantic segmentation of medical images aims to associate a pixel with a label in a medical image without human initialization. The success of semantic segmentation algorithms is contingent on the availability of high-quality imaging data with corresponding labels provided by experts. We sought to create a large collection of annotated medical image datasets of various clinically relevant anatomies available under open source license to facilitate the development of semantic segmentation algorithms. Such a resource would allow: 1) objective assessment of general-purpose segmentation methods through comprehensive benchmarking and 2) open and free access to medical image data for any researcher interested in the problem domain. Through a multi-institutional effort, we generated a large, curated dataset representative of several highly variable segmentation tasks that was used in a crowd-sourced challenge - the Medical Segmentation Decathlon held during the 2018 Medical Image Computing and Computer Aided Interventions Conference in Granada, Spain. Here, we describe these ten labeled image datasets so that these data may be effectively reused by the research community.

Published
2019

47. Genomic Predictors of Recurrence Patterns After Complete Resection of Colorectal Liver Metastases and Adjuvant Hepatic Artery Infusion Chemotherapy

Author

Narayan, Raja R., Datta, Jashodeep, Goldman, Debra A., Aveson, Victoria G., Walch, Henry S., Sanchez-Vega, Francisco, Gönen, Mithat, Balachandran, Vinod P., Drebin, Jeffrey A., Jarnagin, William R., Kingham, T. Peter, Wei, Alice C., Schultz, Nikolaus, Kemeny, Nancy E., and D’Angelica, Michael I.

Published
2022
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48. Histopathological growth patterns of liver metastasis: updated consensus guidelines for pattern scoring, perspectives and recent mechanistic insights

Author

Latacz, Emily, Höppener, Diederik, Bohlok, Ali, Leduc, Sophia, Tabariès, Sébastien, Fernández Moro, Carlos, Lugassy, Claire, Nyström, Hanna, Bozóky, Béla, Floris, Giuseppe, Geyer, Natalie, Brodt, Pnina, Llado, Laura, Van Mileghem, Laura, De Schepper, Maxim, Majeed, Ali W., Lazaris, Anthoula, Dirix, Piet, Zhang, Qianni, Petrillo, Stéphanie K., Vankerckhove, Sophie, Joye, Ines, Meyer, Yannick, Gregorieff, Alexander, Roig, Nuria Ruiz, Vidal-Vanaclocha, Fernando, Denis, Larsimont, Oliveira, Rui Caetano, Metrakos, Peter, Grünhagen, Dirk J., Nagtegaal, Iris D., Mollevi, David G., Jarnagin, William R., D’Angelica, Michael I, Reynolds, Andrew R., Doukas, Michail, Desmedt, Christine, Dirix, Luc, Donckier, Vincent, Siegel, Peter M., Barnhill, Raymond, Gerling, Marco, Verhoef, Cornelis, and Vermeulen, Peter B.

Published
2022
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