Journal Articles (Peer-Reviewed)

39. B. Shepard, J. Chau, R. Kurtz, A. Z. Rosenberg, P. Sarder, S. P. Border^†, B. Ginley^§, O. Rodriguez, C. Albanese, G. Knoer, A. Greene, A. Maria A. de Souza, S. Ranjit, M. Levi, and C. Ecelbarger, “Nascent shifts in renal cellular metabolism, structure, and function due to chronic empagliflozin in pre-diabetic mice” in revision for American Physiological Society.

38. T. Yoshida, K. Z. Latt, A. Z. Rosenberg, B. A. Santo^†, K. Myakala, Y. Ishimoto, Y. Zhao, S. Shrivastav, B. A. Jones, X. Yang, X. X. Wang, V. M. Tutino, P. Sarder, M. Levi, K. Okamoto, C. A. Winkler, and J. B. Kopp, “PKR activation-induced mitochondrial dysfunction in HIV-transgenic mice with nephropathy,” to appear in eLife.

37. C. Roufosse, M. Naesens, M. Haas, C. Lefaucheur, R. B. Mannon, M. Afrouzian, N. Alachkar, O. Aubert, S. M. Bagnasco, I. Batal, C. O. C. Bellamy, V. Broecker, K. Budde, M. Clahsen-Van Groningen, S. M. Coley, L. D. Cornell, D. Dadhania, A. J. Demetris, G. Einecke, A. B. Farris, A. B. Fogo, J. Friedewald, I. W. Gibson, C. Horsfield, E. Huang, S. A. Husain, A. M. Jackson, J. Kers, Z. Kikic, A. Klein, N. Kozakowski, H. Liapis, M. Mangiola, R. A. Montgomery, B. Nankinvell, D. A. H. Neil, P. Nickerson, M. Rabant, P. Randhawa, L. V. Riella, I. Rosales, V. Royal, R. Sapir-Pichhadze, P. Sarder, M. Sarwal, C. Schinstock, M. Stegall, K. Solez, J. van der Laak, C. Wiebe, R. B. Colvin, A. Loupy, and M. Mengel, “The Banff 2022 Kidney Meeting Work Plan: Data-driven refinement of the Banff Classification for renal allografts,” American Journal of Transplantation, vol. 24, pp. 350-361, Mar. 2024.

36. N. Lucarelli^†, B. Ginley^§, J. Zee, S. Mimar^Ω, A. S. Paul^Ω, S. Jain, S. S. Han, L. Rodrigeus, T. Ozrazgat-Baslanti, M. L. Wong, G. Nadkarni, W. L. Clapp, K. Y. Jen, and P. Sarder, “Correlating deep learning-based automated reference kidney histomorphometry with patient demographics and creatinine,” Kidney 360, vol. 4, pp. 1726-1737, Dec. 2023. [Selected to be on the cover of the respective issue.]

35. A. B. Farris, M. P. Alexander, U. G. J. Balis, L. Barisoni, P. Boor, R. D. Bülow, L. D. Cornell, A. J. Demtris, E. Farkash, M. Hermsen, J. Hogan, R. Kain, J. Kers, J. Kong, R. M. Levenson, A. Loupy, M. Naesens, P. Sarder, J. E. Tomaszewski, J. van der Laak, D. van Midden, Y. Yagi, and K. Solez, “Banff Digital Pathology Working Group: Image Bank, Artificial Intelligence Algorithm, and Challenge Trial Developments,” Transplant International, vol. 36, pp. 11783: 1-9, Oct. 2023.

34. K. Myakala, X. X. Wang, N. V. Shults, E. Krawczyk, B. A. Jones, X. Yang, A. Z. Rosenberg, B. Ginley^†, P. Sarder, L. Brodsky, Y. Jang, C. H. Na, Y. Qi, X. Zhang, U. Guha, C. Wu, S. Bansal, J. Ma, A. Cheema, C. Albanese, M. D. Hirschey, T. Yoshida, J. B. Kopp, J. Panov, and M. Levi, “NAD metabolism modulates inflammation and mitochondria function in diabetic kidney disease,” Journal of Biological Chemistry, vol. 299, no. 8, pp. 1-28, Aug. 2023.

33. G. Vasquez-Rios, W. Oh, S. Lee, P. Bhatraju, S. G. Mansour, D. G. Moledina, F. F. Gulamali, E. Siew, A. X. Garg, P. Sarder, V. M. Chinchilli, J. S. Kaufman, C. Y. Hsu, K. D. Liu, P. L. Kimmel, A. S. Go, M. M. Wurfel, J. Himmelfarb, C. R. Parikh, S. G. Coca, and G. N. Nadkarni, “Joint modeling of clinical and biomarker data in acute kidney injury defines unique sub-phenotypes with differing outcomes,” Clinical Journal of the American Society of Nephrology, vol. 18, no. 6, pp. 716-726, Jun. 2023.

32. X. Zheng, L. Higdon, A. Gaudet, M. Shah, A. Balistieri, C. Li, P. Nadai, L. Palaniappan, X. Yang, B. A. Santo^†, B. Ginley^†, X. X. Wang, K. Myakala, P. Nallagatla, M. Levi, P. Sarder, A. Rosenberg, J. S. Maltzman, N. de Freitas Caires, and V. Bhalla, “Endothelial cell-specific molecule-1 inhibits albuminuria in diabetic mice,” Kidney360, vol. 3, no. 12, pp. 2059-2076, Jul. 2022. [Editorial on this article: J. H. Holthoff, K. Chandrashekar, and L. A. Juncos, “The role of Esm-1 in diabetic kidney disease: More than just a biomarker,” Kidney360, vol. 3, no. 12, pp. 1998–2000, Dec. 2022.]

31. M. Andrews, T. Yoshida, C. M. Henderson, H. Pflaum, A. McGregor, J. A. Lieberman, I. H. de Boer, T. Vaisar, J. Himmelfarb, B. Kestenbaum, J. Y. Chung, S. M. Hewitt, B. A. Santo^†, B. Ginley^†, P. Sarder, A.Z. Rosenberg, T. Murakami, J. B. Kopp, Z. Kuklenyik, and A. N. Hoofnagle, “Variant APOL1 protein in plasma associates with larger particles in humans and mouse models of kidney injury,” Plos One, vol. 17, no. 10, pp. e0276649: 1-20, Oct. 2022.

30. B. Lutnick^†, D. Manthey, J. U. Becker, B. Ginley^†, K. Moos, J. E. Zuckerman, L. Rodrigues, A. J. Gallan, L. Barisoni, C. E. Alpers, X. X. Wang, K. Myakala, B. A. Jones, M. Levi, J. B. Kopp, T. Yoshida, S. S. Han, S. Jain, A. Z. Rosenberg, K. Y. Jen, and P. Sarder, for the Kidney Precision Medicine Project, “A user-friendly tool for cloud-based whole slide image segmentation, with examples from renal histopathology,” Communications Medicine (London), vol. 2, pp. 105: 1-15, Aug. 2022.

29. B. A. Santo^†, D. Govind^†, P. Daneshpajouhnejad, X. Yang, X. X. Wang, K. Myakala, B. A. Jones, M. Levi, J. B. Kopp, L. J. Niedernhofer, D. Manthey, K. C. Moon, S. S. Han, J. Zee, A. Z. Rosenberg, and P. Sarder, “PodoCount: A robust, fully automated whole-slide podocyte quantification tool,” Kidney International Reports, vol. 7, no. 6, pp. 1377-92, Jun. 2022.

28. B. Lutnick^†, D. Manthey, J. U. Becker, J. E. Zuckerman, L. Rodrigues, K. Y. Jen, and P. Sarder, “A tool for federated training of segmentation models on whole slide images,” Journal of Pathology Informatics – Elsevier, vol. 13, pp. 100101: 1-7, May 2022.

27. U. Muhammad, Md. Z. Hoque, M. Oussalah, A. Keskinarkaus, T. Seppänena, and P. Sarder, “SAM: Self-augmentation mechanism for COVID-19 detection using chest X-ray images,” Knowledge-Based Systems – Elsevier, vol. 241, pp. 108207: 1-12, Apr. 2022.

26. B. Lutnick^†, L. K. Murali^†, B. Ginley^†, A. Z. Rosenberg, and P. Sarder, “Histo-fetch – On-the-fly processing of gigapixel whole slide images simplifies and speeds neural network training,” Journal of Pathology Informatics – Elsevier, vol. 13, no. 7, pp. 1-5, Jan. 2022.

25. D. Govind^†, J. U. Becker, J. Miecznikowski, A. Z. Rosenberg, J. Dang, P. L. Tharaux, R. Yacoub, F. Thaiss, P. F. Hoyer, D. Manthey, B. Lutnick, A. M. Worral, I. Mohammad, V. Walavalkar, J. E. Tomaszewski, K. Y. Jen, and P. Sarder, “PodoSighter: A cloud-based tool for label-free podocyte detection in kidney whole-slide images,” Journal of the American Society of Nephrology, vol. 32, no. 11, pp. 2795–2813, Nov. 2021. [Selected to be on the cover of the respective issue.]

24. B. Ginley^†,*, K. Y. Jen^*, S. S. Han, L. Rodrigues, S. Jain, A. Fogo, J. Zuckerman, V. Walavalkar, J. C. Miecznikowski, Y. Wen, F. Yen, D. Yun, K. C. Moon, A. Rosenberg, C. Parikh, and P. Sarder, “Automated computational detection of interstitial fibrosis, tubular atrophy, and glomerulosclerosis,” Journal of the American Society of Nephrology, vol. 32, no. 4, pp. 837–50, Apr. 2021. [Featured article of the respective issue. Editorial on this article: J. B. Hodgin and L.H. Mariani, “Automated quantification of chronic changes in the kidney biopsy: Another step in the right direction,” Journal of the American Society of Nephrology, vol. 32, no. 4, pp. 767-68, Apr. 2021.]

23. D. Govind^†,*, K. Y. Jen^*, K. Matsukuma, G. Gao, K. A. Olson, D. Gui, G. Wilding, S. P. Border^†, and P. Sarder, “Improving the accuracy of gastrointestinal neuroendocrine tumor grading with deep learning,” Scientific Reports – Nature, vol. 10, pp. 11064: 1–12, Jul. 2020.

22. B. Ginley^†, B. Lutnick^†, K. Y. Jen, A. Fogo, S. Jain, A. Rosenberg, V. Walavalkar, G. Wilding, J. E. Tomaszewski, R. Yacoub, G. M. Rossi, and P. Sarder, “Computational segmentation and classification of diabetic glomerulosclerosis,” Journal of the American Society of Nephrology, vol. 30, no. 10, pp. 1953–67, Oct. 2019. [Featured article of the respective issue. The article was selected for the Best of American Society of Nephrology (ASN) Journals: Clinical Journal of ASN (CJASN) & JASN in 2019. Editorial on this article: K. V. Lemley, “Machine learning comes to nephrology,” Journal of the American Society of Nephrology, vol. 30, no. 10, pp. 1780-81, Oct. 2019.]

21. B. Lutnick^†, B. Ginley^†, D. Govind^†, S. D. McGarry, P. S. LaViolette, R. Yacoub, S. Jain, J. E. Tomaszewski, K. Y. Jen, and P. Sarder, “An integrated iterative annotation technique for easing neural network training in medical image analysis,” Nature Machine Intelligence, vol. 1, no. 2, pp. 112–19, Feb. 2019.

20. D. Maji, J. Lu, P. Sarder, A. H. Schmieder, G. Cui, X. Yang, D. Pan, M. D. Lew, S. Achilefu, and G. M. Lanza, “Cellular trafficking of Sn-2 phosphatidylcholine prodrugs studied with fluorescence lifetime imaging and super-resolution microscopy,” Prec. Nanomed., vol. 1, no. 2, pp. 127–45, Jul. 2018. [Selected as Feature Article for the 2018(2) issue.]

19. D. Govind^†, B. Lutnick^†, J. E. Tomaszewski, and P. Sarder, “Automated erythrocyte detection and classification from whole slide images,” Journal of Medical Imaging – SPIE, vol. 5, no. 2, pp. 027501:1–11, Apr. 2018.

18. O. Simon^†, R. Yacoub, S. Jain, J. E. Tomaszewski, and P. Sarder, “Multi-radial LBP features as a tool for rapid glomerular detection and assessment in whole slide histopathology images,” Scientific Reports – Nature, vol. 8, pp. 2032:1–11, Feb. 2018.

17. B. Ginley^†, T. Emmons, B. Lutnick^†, C. Urban, B. H. Segal, and P. Sarder, “Computational detection and quantification of human and mouse neutrophil extracellular traps in flow cytometry and confocal microscopy,” Scientific Reports – Nature, vol. 7, pp. 17755:1–11, Dec. 2017.

16. E. K. Stachowiak, C. A. Benson, S. T. Narla, A. Dimitri, L. Chuye, S. Dhiman, K. Harikrishnan, S. Elahi, D. Freedman, K. Brennard, P. Sarder, and M. K. Stachowiak, “Cerebral organoids reveal early cortical maldevelopment in schizophrenia — computational anatomy and genomics, role of FGFR1,” Translational Psychiatry – Nature, vol. 7, no. 6, pp. 1–24, Nov. 2017.

15. S. Narla, Y-W. Lee, C. A. Benson, P. Sarder, K. J. Brennand, E. K. Stachowiak, and M. K. Stachowiak, “Common developmental genome deprogramming in schizophrenia — Role of Integrative Nuclear FGFR1 Signaling (INFS),” Schizophrenia Research, vol. 185, pp. 17–32, Jul. 2017.

14. B. Ginley^†, J. E. Tomaszewski, R. Yacoub, F. Chen, and P. Sarder, “Unsupervised labeling of glomerular boundaries using Gabor filters and statistical testing in renal histology,” Journal of Medical Imaging – SPIE, vol. 4, no. 2, pp. 021102:1–13, Feb. 2017.

13. E. Ringhausen, T. Wang, J. Pitts, P. Sarder, and W. Akers, “Evaluation of dynamic optical projection of acquired luminescence for sentinel lymph node biopsy in large animals,” Technology in Cancer Research & Treatment, vol. 15, no. 6, pp. 787–795, Dec. 2016.

12. R. Gilson, R. Tang, A. Som, C. Klajer, P. Sarder, G. Sudlow, W. Akers, and S. Achilefu, “Protonation and trapping of a small pH-sensitive near-infrared fluorescent molecule in acidic tumor environment delineates diverse tumors in vivo,” Molecular Pharmaceutics, vol. 12, no. 12, pp. 4237–4246, Oct. 2015.

11. X. Xu, Z. Li, P. Sarder, N. Kotagiri, and A. Nehorai, “Simultaneous detection of multiple biological targets using optimized microfluidic microsphere-trap arrays,” Journal of Micro/Nanolithography, MEMS, and MOEMS, vol. 13, no. 1, pp. 13017:1–10, Jan. 2014.

10. D. Hu^*, P. Sarder^*, P. Ronhovde, S. Orthaus, S. Achilefu, and Z. Nussinov, “Automatic segmentation of fluorescence lifetime microscopy images of cells using multiresolution community detection–a first study,” Journal of Microscopy, vol. 253, no. 1, pp. 54–64, Jan. 2014.

9. P. Sarder, K. Gullicksrud, S. Mondal, G. Sudlow, S. Achilefu, and W. Akers, “Dynamic optical projection of acquired luminescence for aiding oncologic surgery,” Journal of Biomedical Optics, vol. 253, no. 12, pp. 12501:1–3, Dec. 2013.

8. P. Sarder, S. Yazdanfar, W. Akers, R. Tang, G. Sudlow, C. Egbulefu, and S. Achilefu, “All–near-infrared multiphoton microscopy interrogates intact tissues at deeper imaging depths than conventional single and two photon near-infrared excitation microscopes,” Journal of Biomedical Optics, vol. 18, no. 10, pp. 106012:1–11, Oct. 2013.

7. X. Xu, P. Sarder, N. Kotagiri, S. Achilefu, and A. Nehorai, “Performance analysis and design of position-encoded microsphere arrays using the Ziv-Zakai bound,” IEEE Trans. on NanoBioscience, vol. 12, no. 1, pp. 29–40, Mar. 2013.

6. X. Xu^*, P. Sarder^*, Z. Li^*, and A. Nehorai, “Optimization of microfluidic microsphere-trap arrays,” Biomicrofluidics, vol. 7, no. 1, pp. 014112:1–16, Feb. 2013.

5. R. Nothdurft*, P. Sarder^*, S. Bloch, J. Culver, and S. Achilefu, “Fluorescence lifetime imaging microscopy using near-infrared contrast agents,” Journal of Microscopy, vol. 247, no. 2, pp. 202–207, Aug. 2012.

4. P. Sarder, and A. Nehorai, “Statistical design of position-encoded microsphere arrays,” IEEE Trans. on NanoBioscience, vol. 10, no. 1, pp. 16–29, Mar. 2011.

3. P. Sarder, W. Schierding, J. P. Cobb, and A. Nehorai, “Estimating sparse gene regulatory networks using a Bayesian linear regression,” IEEE Trans. on NanoBioscience, vol. 9, no. 2, pp. 121–131, June 2010.

2. P. Sarder, and A. Nehorai, “Estimating locations of quantum-dot–encoded microparticles from ultra-high density 3D microarrays,” IEEE Trans. on NanoBioscience, vol. 7, no. 4, pp. 284–297, Dec. 2008.

1. P. Sarder, A. Nehorai, P. H. Davis, and S. Stanley, “Estimating gene signals from noisy microarray images,” IEEE Trans. on NanoBioscience, vol. 7, no. 2, pp. 142–153, June 2008.