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  1. 1.   ERK Allosteric Activation: The Importance of Two Ordered Phosphorylation Events
  2. Regev,Clil; Jang,Hyunbum; Nussinov,Ruth
  3. Journal of Molecular Biology. 2025, Apr 09; 169130.
  1. 2.   Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model trained on a diverse dataset
  2. Conrad, Ryan; Narayan,Kedar
  3. Cell Systems. 2023, Jan 18; 14(1): 58-71.e5.
  1. 3.   QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results
  2. Mehta, Raghav; Filos, Angelos; Baid, Ujjwal; Sako, Chiharu; McKinley, Richard; Rebsamen, Michael; Dätwyler, Katrin; Meier, Raphael; Radojewski, Piotr; Murugesan, Gowtham Krishnan; Nalawade, Sahil; Ganesh, Chandan; Wagner, Ben; Yu, Fang F; Fei, Baowei; Madhuranthakam, Ananth J; Maldjian, Joseph A; Daza, Laura; Gómez, Catalina; Arbeláez, Pablo; Dai, Chengliang; Wang, Shuo; Reynaud, Hadrien; Mo, Yuanhan; Angelini, Elsa; Guo, Yike; Bai, Wenjia; Banerjee, Subhashis; Pei, Linmin; Ak, Murat; Rosas-González, Sarahi; Zemmoura, Ilyess; Tauber, Clovis; Vu, Minh H; Nyholm, Tufve; Löfstedt, Tommy; Ballestar, Laura Mora; Vilaplana, Veronica; McHugh, Hugh; Maso Talou, Gonzalo; Wang, Alan; Patel, Jay; Chang, Ken; Hoebel, Katharina; Gidwani, Mishka; Arun, Nishanth; Gupta, Sharut; Aggarwal, Mehak; Singh, Praveer; Gerstner, Elizabeth R; Kalpathy-Cramer, Jayashree; Boutry, Nicolas; Huard, Alexis; Vidyaratne, Lasitha; Rahman, Md Monibor; Iftekharuddin, Khan M; Chazalon, Joseph; Puybareau, Elodie; Tochon, Guillaume; Ma, Jun; Cabezas, Mariano; Llado, Xavier; Oliver, Arnau; Valencia, Liliana; Valverde, Sergi; Amian, Mehdi; Soltaninejad, Mohammadreza; Myronenko, Andriy; Hatamizadeh, Ali; Feng, Xue; Dou, Quan; Tustison, Nicholas; Meyer, Craig; Shah, Nisarg A; Talbar, Sanjay; Weber, Marc-André; Mahajan, Abhishek; Jakab, Andras; Wiest, Roland; Fathallah-Shaykh, Hassan M; Nazeri, Arash; Milchenko, Mikhail; Marcus, Daniel; Kotrotsou, Aikaterini; Colen, Rivka; Freymann,John; Kirby,Justin; Davatzikos, Christos; Menze, Bjoern; Bakas, Spyridon; Gal, Yarin; Arbel, Tal
  3. The journal of Machine Learning for Biomedical Imaging. 2022, Aug; 2022
  1. 4.   QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results
  2. Mehta, Raghav; Filos, Angelos; Baid, Ujjwal; Sako, Chiharu; McKinley, Richard; Rebsamen, Michael; Dätwyler, Katrin; Meier, Raphael; Radojewski, Piotr; Murugesan, Gowtham Krishnan; Nalawade, Sahil; Ganesh, Chandan; Wagner, Ben; Yu, Fang F; Fei, Baowei; Madhuranthakam, Ananth J; Maldjian, Joseph A; Daza, Laura; Gómez, Catalina; Arbeláez, Pablo; Dai, Chengliang; Wang, Shuo; Reynaud, Hadrien; Mo, Yuanhan; Angelini, Elsa; Guo, Yike; Bai, Wenjia; Banerjee, Subhashis; Pei, Linmin; Ak, Murat; Rosas-González, Sarahi; Zemmoura, Ilyess; Tauber, Clovis; Vu, Minh H; Nyholm, Tufve; Löfstedt, Tommy; Ballestar, Laura Mora; Vilaplana, Veronica; McHugh, Hugh; Maso Talou, Gonzalo; Wang, Alan; Patel, Jay; Chang, Ken; Hoebel, Katharina; Gidwani, Mishka; Arun, Nishanth; Gupta, Sharut; Aggarwal, Mehak; Singh, Praveer; Gerstner, Elizabeth R; Kalpathy-Cramer, Jayashree; Boutry, Nicolas; Huard, Alexis; Vidyaratne, Lasitha; Rahman, Md Monibor; Iftekharuddin, Khan M; Chazalon, Joseph; Puybareau, Elodie; Tochon, Guillaume; Ma, Jun; Cabezas, Mariano; Llado, Xavier; Oliver, Arnau; Valencia, Liliana; Valverde, Sergi; Amian, Mehdi; Soltaninejad, Mohammadreza; Myronenko, Andriy; Hatamizadeh, Ali; Feng, Xue; Dou, Quan; Tustison, Nicholas; Meyer, Craig; Shah, Nisarg A; Talbar, Sanjay; Weber, Marc-André; Mahajan, Abhishek; Jakab, Andras; Wiest, Roland; Fathallah-Shaykh, Hassan M; Nazeri, Arash; Milchenko, Mikhail; Marcus, Daniel; Kotrotsou, Aikaterini; Colen, Rivka; Freymann,John; Kirby,Justin; Davatzikos, Christos; Menze, Bjoern; Bakas, Spyridon; Gal, Yarin; Arbel, Tal
  3. The Journal of Machine Learning for Biomedical Imaging. 2022, Aug; 2022
  1. 5.   MoNuSAC2020: A Multi-Organ Nuclei Segmentation and Classification Challenge
  2. Verma, Ruchika; Kumar, Neeraj; Patil, Abhijeet; Kurian, Nikhil Cherian; Rane, Swapnil; Graham, Simon; Zwager, Mieke; Raza, Shan E. Ahmed; Rajpoot, Nasir; Wu, Xiyi; Chen, Huai; Huang, Yijie; Wang, Lisheng; Jung,Hyun; Brown, G. Thomas; Liu,Yanling; Liu, Shuolin; Jahromi, Seyed Alireza Fatemi; Khani, Ali Asghar; Montahaei, Ehsan; Baghshah, Mahdieh Soleymani; Behroozi, Hamid; Semkin, Pavel; Rassadin, Alexandr; Dutande, Prasad; Lodaya, Romil; Baid, Ujjwal; Baheti, Bhakti; Talbar, Sanjay; Mahbod, Amirreza; Ecker, Rupert; Ellinger, Isabella; Luo, Zhipeng; Dong, Bin; Xu, Zhengyu; Yao, Yuehan; Lv, Shuai; Feng, Ming; Xu, Kele; Zunair, Hasib; Ben Hamza, Abdessamad; Smiley, Steven; Yin, Tang-Kai; Fang, Qi-Rui; Srivastava, Shikhar; Mahapatra, Dwarikanath; Trnavska, Lubomira; Zhang, Hanyun; Narayanan, Priya Lakshmi; Law, Justin; Yuan, Yinyin; Tejomay, Abhiroop; Mitkari, Aditya; Koka, Dinesh; Ramachandra, Vikas; Kini, Lata; Sethi, Amit
  3. IEEE Transactions on Medical Imaging. 2021, June 4; 40(12): 3413-3423.
  1. 6.   FIB-SEM as a Volume Electron Microscopy Approach to Study Cellular Architectures in SARS-CoV-2 and Other Viral Infections: A Practical Primer for a Virologist
  2. Baena Echeverri,Valentina; Conrad,Ryan; Friday, Patrick; Fitzgerald, Ella; Kim, Taeeun; Bernbaum, John; Berensmann, Heather; Harned,Adam; Nagashima,Kunio; Narayan,Kedar
  3. Viruses. 2021, Apr 2; 13(4):
  1. 7.   PAIP 2019: Liver cancer segmentation challenge
  2. Kim, Yoo Jung; Jang, Hyungjoon; Lee, Kyoungbun; Park, Seongkeun; Min, Sung-Gyu; Hong, Choyeon; Park, Jeong Hwan; Lee, Kanggeun; Kim, Jisoo; Hong, Wonjae; Jung,Hyun; Liu,Yanling; Rajkumar, Haran; Khened, Mahendra; Krishnamurthi, Ganapathy; Yang, Sen; Wang, Xiyue; Han, Chang Hee; Kwak, Jin Tae; Ma, Jianqiang; Tang, Zhe; Marami, Bahram; Zeineh, Jack; Zhao, Zixu; Heng, Pheng-Ann; Schmitz, Rüdiger; Madesta, Frederic; Rösch, Thomas; Werner, Rene; Tian, Jie; Puybareau, Elodie; Bovio, Matteo; Zhang, Xiufeng; Zhu, Yifeng; Chun, Se Young; Jeong, Won-Ki; Park, Peom; Choi, Jinwook
  3. Medical Image Analysis. 2021, Jan; 67: 101854.
  1. 8.   Data Augmentation and Transfer Learning to Improve Generalizability of an Automated Prostate Segmentation Model
  2. Sanford, Thomas H.; Zhang, Ling; Harmon,Stephanie; Sackett, Jonathan; Yang, Dong; Roth, Holger; Xu, Ziyue; Kesani, Deepak; Mehralivand, Sherif; Baroni, Ronaldo H.; Barrett, Tristan; Girometti, Rossano; Oto, Aytekin; Purysko, Andrei S.; Xu, Sheng; Pinto, Peter A.; Xu, Daguang; Wood, Bradford J.; Choyke, Peter L.; Turkbey, Baris
  3. AMERICAN JOURNAL OF ROENTGENOLOGY. 2020, DEC; 215(6): 1403-1410.
  1. 9.   A Deep Learning Pipeline for Nucleus Segmentation
  2. Zaki,George; Gudla, Prabhakar R; Lee, Kyunghun; Kim, Justin; Ozbun, Laurent; Shachar, Sigal; Gadkari, Manasi; Sun, Jing; Fraser, Iain D C; Franco, Luis M; Misteli, Tom; Pegoraro, Gianluca
  3. CYTOMETRY PART A. 2020, NOV 19;
  1. 10.   Deep Learning for Automated Liver Segmentation to Aid in the Study of Infectious Diseases in Nonhuman Primates
  2. Reza, Syed M S; Bradley, Dara; Aiosa, Nina; Castro, Marcelo; Lee, Ji Hyun; Lee, Byeong-Yeul; Bennett, Richard S; Hensley, Lisa E; Cong, Yu; Johnson, Reed; Hammoud, Dima; Feuerstein, Irwin; Solomon,Jeffrey
  3. Academic radiology. 2020, Nov; 28(Supplement 1): pii: S1076-6332(20)30504-3.
  1. 11.   Translating Embryogenesis to Generate Organoids: Novel Approaches to Personalized Medicine
  2. Sahu,Sounak; Sharan,Shyam
  3. iScience. 2020, SEP 25; 23(9):
  1. 12.   High throughput assessment of biomarkers in tissue microarrays using artificial intelligence: PTEN loss as a proof-of-principle in multi-center prostate cancer cohorts
  2. Harmon,Stephanie; Patel, Palak G; Sanford, Thomas H; Caven, Isabelle; Iseman, Rachael; Vidotto, Thiago; Picanço, Clarissa; Squire, Jeremy A; Masoudi, Samira; Mehralivand, Sherif; Choyke, Peter L; Berman, David M; Turkbey, Baris; Jamaspishvili, Tamara
  3. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc. 2020, Sep 03;
  1. 13.   Atlas-based liver segmentation for nonhuman primate research
  2. Solomon,Jeffrey; Aiosa, Nina; Bradley, Dara; Castro, Marcelo A.; Reza, Syed; Bartos, Christopher; Sayre, Philip; Lee, Ji Hyun; Sword, Jennifer; Holbrook, Michael R.; Bennett, Richard S.; Hammoud, Dima A.; Johnson, Reed F.; Feuerstein, Irwin
  3. INTERNATIONAL JOURNAL OF COMPUTER ASSISTED RADIOLOGY AND SURGERY. 2020, JUL 9;
  1. 14.   Disruption of MAGI2-RapGEF2-Rap1 signaling contributes to podocyte dysfunction in congenital nephrotic syndrome caused by mutations in MAGI2
  2. Zhu, Bingbing; Cao, Aili; Li, Jianhua; Young, James; Wong, Jenny; Ashraf, Shazia; Bierzynska, Agnieszka; Menon, Madhav C; Hou,Steven; Sawyers, Charles; Campbell, Kirk N; Saleem, Moin A; He, John C; Hildebrandt, Friedhelm; D'Agati, Vivette D; Peng, Wen; Kaufman, Lewis
  3. Kidney international. 2019, Sep; 96(3): 642-655.
  1. 15.   Automated Computational Detection, Quantitation, and Mapping of Mitosis in Whole-Slide Images for Clinically Actionable Surgical Pathology Decision Support
  2. Puri, Munish; Hoover, Shelley B; Hewitt, Stephen M; Wei,Bih; Adissu, Hibret Amare; Halsey, Charles H C; Beck, Jessica; Bradley, Charles; Cramer, Sarah D; Durham, Amy C; Esplin, D Glen; Frank, Chad; Lyle, L Tiffany; McGill, Lawrence D; Sánchez, Melissa D; Schaffer, Paula A; Traslavina, Ryan P; Buza, Elizabeth; Yang, Howard H; Lee, Maxwell P; Dwyer, Jennifer E; Simpson, R Mark
  3. Journal of pathology informatics. 2019, Feb; 10: 4.
  1. 16.   Auto-segmentation for Thoracic Radiation Treatment Planning: A Grand Challenge at AAPM 2017
  2. Yang, Jinzhong; Veeraraghavan, Harini; Armato, Samuel G; Farahani, Keyvan; Kirby, Justin; Kalpathy-Kramer, Jayashree; van Elmpt, Wouter; Dekker, Andre; Han, Xiao; Feng, Xue; Aljabar, Paul; Oliveira, Bruno; van der Heyden, Brent; Zamdborg, Leonid; Lam, Dao; Gooding, Mark; Sharp, Gregory C
  3. Medical Physics. 2018, Oct; 45(10): 4568-4581.
  1. 17.   Design and performance of the micro-dose calibrator
  2. Adler, Stephen; Choyke, Peter
  3. Physics in Medicine and Biology. 2018, Sep 10; 63(18):
  1. 18.   Therapeutics for APOL1 nephropathies: putting out the fire in the podocyte
  2. Heymann, Jurgen; Winkler, Cheryl; Hoek, Maarten; Susztak, Katalin; Kopp, Jeffrey B.
  3. NEPHROLOGY DIALYSIS TRANSPLANTATION. 2017, Jan 01; 32(Supplement: 1): i65-i70.
  1. 19.   FGF4 and FGF8 comprise the wavefront activity that controls somitogenesis
  2. Naiche, L. A.; Holder, N.; Lewandoski, M.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2011, Mar; 108(10): 4018-4023.
  1. 20.   Mosaic Uniparental Disomies and Aneuploidies as Large Structural Variants of the Human Genome
  2. Rodriguez-Santiago, B.; Malats, N.; Rothman, N.; Armengol, L.; Garcia-Closas, M.; Kogevinas, M.; Villa, O.; Hutchinson, A.; Earl, J.; Marenne, G.; Jacobs, K.; Rico, D.; Tardon, A.; Carrato, A.; Thomas, G.; Valencia, A.; Silverman, D.; Real, F. X.; Chanock, S. J.; Perez-Jurado, L. A.
  3. American Journal of Human Genetics. 2010, Jul; 87(1): 129-138.
  1. 21.   MYH9 Genetic Variants Associated With Glomerular Disease: What Is the Role for Genetic Testing?
  2. Kopp, J. B.; Winkler, C. A.; Nelson, G. W.
  3. Seminars in Nephrology. 2010, Jul; 30(4): 409-417.
  1. 22.   African ancestry allelic variation at the MYH9 gene contributes to increased susceptibility to non-diabetic end-stage kidney disease in Hispanic Americans
  2. Behar, D. M.; Rosset, S.; Tzur, S.; Selig, S.; Yudkovsky, G.; Bercovici, S.; Kopp, J. B.; Winkler, C. A.; Nelson, G. W.; Wasser, W. G.; Skorecki, K.
  3. Human Molecular Genetics. 2010, May; 19(9): 1816-1827.
  1. 23.   Tailored synthesis of nitric oxide-releasing polyurethanes using O-2-protected diazeniumdiolated chain extenders
  2. Reynolds, M. M.; Saavedra, J. E.; Showalter, B. M.; Valdez, C. A.; Shanklin, A. P.; Oh, B. K.; Keefer, L. K.; Meyerhoff, M. E.
  3. Journal of Materials Chemistry. 2010, Mar 21; 20(15): 3107-3114.
  1. 24.   Is There a Genetic Basis for Health Disparities in Human Immunodeficiency Virus Disease?
  2. Winkler, C.
  3. Mount Sinai Journal of Medicine. 2010, Mar-Apr; 77(2): 149-159.
  1. 25.   Peloruside B, A Potent Antitumor Macrolide from the New Zealand Marine Sponge Mycale hentscheli: Isolation, Structure, Total Synthesis, and Bioactivity
  2. Singh, A. J.; Xu, C. X.; Xu, X. M.; West, L. M.; Wilmes, A.; Chan, A.; Hamel, E.; Miller, J. H.; Northcote, P. T.; Ghosh, A. K.
  3. Journal of Organic Chemistry. 2010, Jan; 75(1): 2-10.
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