Sanjay Jain

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Sanjay Jain

Professor of Medicine, Professor of Pediatrics, Professor of Pathology and Immunology

 https://orcid.org/0000-0003-2804-127X

    Willing to Mentor

    Available to Mentor:

    Health Professions (Medical, OT, PT, Dental, Audiology, etc.) Students, High School Students, PhD/MSTP Students, Post-Baccalaureate Students, Postdocs, Residents and Fellows, Undergraduate Students

    • 7936
      Citations
    1990 …2024

    Research activity per year

    Search results

    • 2024

      CODEX and H&E Imaging: Cell Type Mapping, Analysis, and Visualization Pipeline

      Maragall, J. A., Lucarelli, N., Naglah, A., Border, S., Winfree, S., Laszik, Z., Eadon, M., El-Achkar, T. M., Jain, S. & Sarder, P., 2024, Medical Imaging 2024: Digital and Computational Pathology. Tomaszewski, J. E. & Ward, A. D. (eds.). SPIE, 129330W. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 12933).

      Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    • Computational Integration of CODEX and Brightfield Histology for Cell Annotation using Deep Learning

      Lucarelli, N., Laszik, Z., Winfree, S., El-Achkar, T. M., Eadon, M., Jain, S. & Sarder, P., 2024, Medical Imaging 2024: Digital and Computational Pathology. Tomaszewski, J. E. & Ward, A. D. (eds.). SPIE, 129331F. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 12933).

      Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

    • Correction to: Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP) (Nature Cell Biology, (2023), 25, 8, (1089-1100), 10.1038/s41556-023-01194-w)

      HuBMAP Consortium, Jain, S., Pei, L., Spraggins, J. M., Angelo, M., Carson, J. P., Gehlenborg, N., Ginty, F., Gonçalves, J. P., Hagood, J. S., Hickey, J. W., Kelleher, N. L., Laurent, L. C., Lin, S., Lin, Y., Liu, H., Naba, A., Nakayasu, E. S., Qian, W. J. & Radtke, A. & 181 others, Robson, P., Stockwell, B. R., Van de Plas, R., Vlachos, I. S., Zhou, M., Börner, K., Snyder, M. P., Ahn, K. J., Allen, J., Anderson, D. M., Anderton, C. R., Curcio, C., Angelin, A., Arvanitis, C., Atta, L., Awosika-Olumo, D., Bahmani, A., Bai, H., Balderrama, K., Balzano, L., Bandyopadhyay, G., Bandyopadhyay, S., Bar-Joseph, Z., Barnhart, K., Barwinska, D., Becich, M., Becker, L., Becker, W., Bedi, K., Bendall, S., Benninger, K., Betancur, D., Bettinger, K., Billings, S., Blood, P., Bolin, D., Border, S., Bosse, M., Bramer, L., Brewer, M., Brusko, M., Bueckle, A., Burke, K., Burnum-Johnson, K., Butcher, E., Butterworth, E., Cai, L., Calandrelli, R., Caldwell, M., Campbell-Thompson, M., Cao, D., Cao-Berg, I., Caprioli, R., Caraccio, C., Caron, A., Carroll, M., Chadwick, C., Chen, A., Chen, D., Chen, F., Chen, H., Chen, J., Chen, L., Chen, L., Chiacchia, K., Cho, S., Chou, P., Choy, L., Cisar, C., Clair, G., Clarke, L., Clouthier, K. A., Colley, M. E., Conlon, K., Conroy, J., Contrepois, K., Corbett, A., Corwin, A., Cotter, D., Courtois, E., Cruz, A., Csonka, C., Czupil, K., Daiya, V., Dale, K., Davanagere, S. A., Dayao, M., de Caestecker, M. P., Decker, A., Deems, S., Degnan, D., Desai, T., Deshpande, V., Deutsch, G., Devlin, M., Diep, D., Dodd, C., Donahue, S., Dong, W., dos Santos Peixoto, R., Duffy, M., Dufresne, M., Duong, T. E., Dutra, J., Eadon, M. T., El-Achkar, T. M., Enninful, A., Eraslan, G., Eshelman, D., Espin-Perez, A., Esplin, E. D., Esselman, A., Falo, L. D., Falo, L., Fan, J., Fan, R., Farrow, M. A., Farzad, N., Favaro, P., Fermin, J., Filiz, F., Filus, S., Fisch, K., Fisher, E., Fisher, S., Flowers, K., Flynn, W. F., Fogo, A. B., Fu, D., Fulcher, J., Fung, A., Furst, D., Gallant, M., Gao, F., Gao, Y., Gaulton, K., Gaut, J. P., Gee, J., Ghag, R. R., Ghazanfar, S., Ghose, S., Gisch, D., Gold, I., Gondalia, A., Gorman, B., Greenleaf, W., Greenwald, N., Gregory, B., Guo, R., Gupta, R., Hakimian, H., Haltom, J., Halushka, M., Han, K. S., Hanson, C., Harbury, P., Hardi, J., Harlan, L., Harris, R. C., Hartman, A., Heidari, E., Helfer, J., Helminiak, D., Hemberg, M., Henning, N., Herr, B. W., Ho, J., Holden-Wiltse, J., Hong, S. H., Hong, Y. K., Honick, B., Hood, G., Hu, P., Hu, Q., Huang, M., Huyck, H., Imtiaz, T., Isberg, O. G., Itkin, M., Jackson, D. & Jacobs, M., May 2024, In: Nature Cell Biology. 26, 5, p. 839 1 p.

      Research output: Contribution to journal › Comment/debate

      Open Access
      1 Scopus citations

    • Label-Free 3D Microscopy Platform Confirms and Uncovers Biomarkers of Kidney Nephropathy and Liver Cancer

      Fung, A. A., Jain, S. & Shi, L., 2024.

      Research output: Contribution to conference › Paper › peer-review

    • Mapping human tissues with highly multiplexed RNA in situ hybridization

      Kalhor, K., Chen, C. J., Lee, H. S., Cai, M., Nafisi, M., Que, R., Palmer, C. R., Yuan, Y., Zhang, Y., Li, X., Song, J., Knoten, A., Lake, B. B., Gaut, J. P., Keene, C. D., Lein, E., Kharchenko, P. V., Chun, J., Jain, S. & Fan, J. B. & 1 others, Zhang, K., Dec 2024, In: Nature communications. 15, 1, 2511.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      9 Scopus citations

    • Molecular Signatures of Glomerular Neovascularization in a Patient with Diabetic Kidney Disease

      Kidney Precision Medicine Project, Ferkowicz, M. J., Verma, A., Barwinska, D., Melo Ferreira, R., Henderson, J. M., Kirkpatrick, M., Silva, P. S., Steenkamp, D. W., Phillips, C. L., Waikar, S. S., Sutton, T. A., Lake, B., Zhang, K., Lecker, S., Morales, A., Stillman, I., Bogen, S., Amodu, A. A. & Beck, L. & 181 others, Henderson, J., Ilori, T., Maikhor, S., Onul, I., Schmidt, I., Verma, A., Waikar, S., Yadati, P., Yu, G., Colona, M. R., McMahon, G., Weins, A., Hacohen, N., Greka, A., Hoover, P. J., Marshall, J. L., Aulisio, M., Bush, W., Chen, Y., Crawford, D., Madabhushi, A., Viswanathan, V. S., Bush, L., Cooperman, L., Gadegbeku, C., Herlitz, L., Jolly, S., Nguyen, J., O'Malley, C., O'Toole, J., Palmer, E., Poggio, E., Spates-Harden, K., Sedor, J., Sendrey, D., Taliercio, J., Appelbaum, P., Balderes, O., Barasch, J., Berroue, C., Bomback, A., Canetta, P. A., D'Agati, V., Kiryluk, K., Kudose, S., Mehl, K., Sabatello, M., Shang, N., Varela, G., De Pinho Gonçalves, J., Lardenoije, R., Migas, L., Van De Plas, R., Barisoni, L., Rennke, H., Azeloglu, E., Campbell, K., Coca, S., He, C., He, J., Iyengar, S. R., Lefferts, S., Nadkarni, G., Patel, M., Tokita, J., Ward, S., Xiong, Y., Verdoes, A., Sabo, A., Barwinska, D., Gisch, D. L., Williams, J., Kelly, K., Dunn, K., Asghari, M., Eadon, M., Ferkowicz, M., Dagher, P., Ferreira, R. M., Winfree, S., Bledsoe, S., Wofford, S., El-Achkar, T., Sutton, T., Bowen, W., Cheng, Y. H., Slade, A., Record, E., Cheng, Y., Borner, K., Herr, B., Jain, Y., Quardokus, E., Atta, M., Bernard, L., Menez, S., Parikh, C., Corona Villalobos, C. P., Wang, A., Wen, Y., Xu, A., Chen, S., Donohoe, I., Johansen, C., Rosas, S., Sun, J., Ardayfio, J., Bebiak, J., Brown, K., Campbell, T., Fox, M., Hayashi, L., Jefferson, N., Richard Knight, J. J., Koewler, R., Pinkeney, R., Saul, J., Shpigel, A., Stutzke, C., Prasad, P., Madhavan, S. M., Parikh, S., Rovin, B., Shapiro, J. P., Anderton, C., Lukowski, J., Pasa-Tolic, L., Velickovic, D., Oliver, G., Mao, W., Sealfon, R., Troyanskaya, O., Wong, A., Pollack, A., Goltsev, Y., Ginley, B., Lutnick, B., Anjani, K., Laszik, Z. G., Mukatash, T., Nolan, G., Beyda, D., Bracamonte, E., Brosius, F., Campos, B., Marquez, N., Mendoza, K., Scott, R., Thajudeen, B., Tsosie, R., Woodhead, G., Saunders, M., Alloway, R. R., Lee, P. J., Rike, A., Shi, T., Woodle, E. S., Bjornstad, P., Hsieh, E., Kendrick, J., Pyle, L., Thurman, J., Vinovskis, C., Wrobel, J., Lucarelli, N., Sarder, P., Bui, J., Carmona-Powell, E., Gaba, R., Kelly, T., Lash, J., Meza, N., Redmond, D., Renteria, A., Ricardo, A., Setty, S., Rosengart, M., Basta, J., Gaut, J., Jain, S. & Vijayan, A., Feb 2024, In: Clinical Journal of the American Society of Nephrology. 19, 2, p. 266-275 10 p.

      Research output: Contribution to journal › Article › peer-review

      3 Scopus citations

    • Multi-molecular hyperspectral PRM-SRS microscopy

      Zhang, W., Li, Y., Fung, A. A., Li, Z., Jang, H., Zha, H., Chen, X., Gao, F., Wu, J. Y., Sheng, H., Yao, J., Skowronska-Krawczyk, D., Jain, S. & Shi, L., Dec 2024, In: Nature communications. 15, 1, 1599.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      8 Scopus citations

    • Precision Medicine in Nephrology: An Integrative Framework of Multidimensional Data in the Kidney Precision Medicine Project

      Kidney Precision Medicine Project, Mar 2024, In: American Journal of Kidney Diseases. 83, 3, p. 402-410 9 p.

      Research output: Contribution to journal › Article › peer-review

      7 Scopus citations

    • Protein N-Glycans in Healthy and Sclerotic Glomeruli in Diabetic Kidney Disease

      Kidney Precision Medicine Project, Sep 1 2024, In: Journal of the American Society of Nephrology. 35, 9, p. 1198-1207 10 p.

      Research output: Contribution to journal › Article › peer-review

      4 Scopus citations

    • Role of Artificial Intelligence in Kidney Pathology: Promises and Pitfalls

      Goodman, K., Sarullo, K., Swamidass, S. J., Gaut, J. P. & Jain, S., Jul 1 2024, In: Kidney360. 5, 7, p. 1044-1046 3 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      1 Scopus citations

    • Sensory neurons promote immune homeostasis in the lung

      Tamari, M., Del Bel, K. L., Ver Heul, A. M., Zamidar, L., Orimo, K., Hoshi, M., Trier, A. M., Yano, H., Yang, T. L., Biggs, C. M., Motomura, K., Shibuya, R., Yu, C. D., Xie, Z., Iriki, H., Wang, Z., Auyeung, K., Damle, G., Demircioglu, D. & Gregory, J. K. & 13 others, Hasson, D., Dai, J., Chang, R. B., Morita, H., Matsumoto, K., Jain, S., Van Dyken, S., Milner, J. D., Bogunovic, D., Hu, H., Artis, D., Turvey, S. E. & Kim, B. S., Jan 4 2024, In: Cell. 187, 1, p. 44-61.e17

      Research output: Contribution to journal › Article › peer-review

      Open Access
      28 Scopus citations

    • Spatial transcriptomics in health and disease

      Jain, S. & Eadon, M. T., Oct 2024, In: Nature Reviews Nephrology. 20, 10, p. 659-671 13 p.

      Research output: Contribution to journal › Review article › peer-review

      16 Scopus citations

    • The chromatin landscape of healthy and injured cell types in the human kidney

      Gisch, D. L., Brennan, M., Lake, B. B., Basta, J., Keller, M. S., Melo Ferreira, R., Akilesh, S., Ghag, R., Lu, C., Cheng, Y. H., Collins, K. S., Parikh, S. V., Rovin, B. H., Robbins, L., Stout, L., Conklin, K. Y., Diep, D., Zhang, B., Knoten, A. & Barwinska, D. & 332 others, Asghari, M., Sabo, A. R., Ferkowicz, M. J., Sutton, T. A., Kelly, K. J., De Boer, I. H., Rosas, S. E., Kiryluk, K., Hodgin, J. B., Alakwaa, F., Winfree, S., Jefferson, N., Türkmen, A., Gaut, J. P., Gehlenborg, N., Phillips, C. L., El-Achkar, T. M., Dagher, P. C., Hato, T., Zhang, K., Himmelfarb, J., Kretzler, M., Mollah, S., Lake, B., Morales, A., Stillman, I., Lecker, S., Bogen, S., Verma, A., Yu, G., Schmidt, I., Henderson, J., Beck, L., Yadati, P., Waikar, S., Amodu, A. A., Maikhor, S., Ilori, T., Colona, M. R., Weins, A., McMahon, G., Hacohen, N., Greka, A., Marshall, J. L., Hoover, P. J., Viswanathan, V. S., Crawford, D., Aulisio, M., Bush, W., Chen, Y., Madabhushi, A., O’Malley, C., Gadegbeku, C., Sendrey, D., Poggio, E., O’Toole, J., Sedor, J., Taliercio, J., Bush, L., Herlitz, L., Palmer, E., Nguyen, J., Spates-Harden, K., Cooperman, L., Jolly, S., Vinovskis, C., Bomback, A., Barasch, J., Kiryluk, K., Appelbaum, P., D’Agati, V., Berrouet, C., Mehl, K., Sabatello, M., Shang, N., Balderes, O., Canetta, P. A., Kudose, S., de Pinho Gonçalves, J., Migas, L., Van de Plas, R., Lardenoije, R., Barisoni, L., Rennke, H., Verdoes, A., Sabo, A., Gisch, D. L., Williams, J., Kelly, K., Dunn, K., Eadon, M., Ferkowicz, M., Dagher, P., Winfree, S., Bledsoe, S., Wofford, S., (El-Achkar), T. A., Sutton, T., Bowen, W., Slade, A., Record, E., Cheng, Y., Jain, Y., Herr, B., Quardokus, E., Wang, A., Villalobos, C. P. C., Parikh, C., Atta, M., Menez, S., Wen, Y., Xu, A., Bernard, L., Johansen, C., Chen, S., Rosas, S., Donohoe, I., Sun, J., Knight, R., Shpigel, A., Bebiak, J., Saul, J., Ardayfio, J., Koewler, R., Pinkeney, R., Campbell, T., Azeloglu, E., Nadkarni, G., He, J., Tokita, J., Campbell, K., Patel, M., Lefferts, S., Iyengar, S. R., Ward, S., Coca, S., He, C., Xiong, Y., Prasad, P., Rovin, B., Shapiro, J. P., Parikh, S., Madhavan, S. M., Lukowski, J., Velickovic, D., Pasa-Tolic, L., Oliver, G., Troyanskaya, O., Sealfon, R., Mao, W., Wong, A., Pollack, A., Goltsev, Y., Ginley, B., Lutnick, B., Nolan, G., Anjani, K., Mukatash, T., Laszik, Z. G., Campos, B., Thajudeen, B., Beyda, D., Bracamonte, E., Brosius, F., Woodhead, G., Mendoza, K., Marquez, N., Scott, R., Tsosie, R., Saunders, M., Rike, A., Woodle, E. S., Lee, P. J., Alloway, R. R., Shi, T., Hsieh, E., Kendrick, J., Thurman, J., Wrobel, J., Pyle, L., Bjornstad, P., Lucarelli, N., Sarder, P., Renteria, A., Ricardo, A., Srivastava, A., Redmond, D., Carmona-Powell, E., Bui, J., Lash, J., Fox, M., Meza, N., Gaba, R., Setty, S., Kelly, T., Lienczewski, C., Demeke, D., Otto, E., Ascani, H., Hodgin, J., Schaub, J., Hartman, J., Mariani, L., Bitzer, M., Rose, M., Bonevich, N., Conser, N., McCown, P., Dull, R., Menon, R., Reamy, R., Eddy, S., Balis, U., Blanc, V., Nair, V., He, Y. O., Wright, Z., Steck, B., Luo, J., Frey, R., Coleman, A., Henderson-Brown, D., Berge, J., Caramori, M. L., Adeyi, O., Nachman, P., Safadi, S., Flanagan, S., Ma, S., Klett, S., Wolf, S., Harindhanavudhi, T., Rao, V., Mottl, A., Froment, A., Zeitler, E., Bream, P., Kelley, S., Rosengart, M., Elder, M., Palevsky, P., Murugan, R., Hall, D. E., Bender, F., Winters, J., Kellum, J. A., Gilliam, M., Tublin, M., Tan, R., Zhang, G., Sharma, K., Venkatachalam, M., Hendricks, A., Kermani, A., Torrealba, J., Vazquez, M., Wang, N., Cai, Q., Miller, R. T., Ma, S., Hedayati, S., Hoofnagle, A., Wangperawong, A., Berglund, A., Dighe, A. L., Young, B., Larson, B., Berry, B., Alpers, C., Limonte, C., Stutzke, C., Roberts, G., de Boer, I., Snyder, J., Phuong, J., Carson, J., Rezaei, K., Tuttle, K., Brown, K., Blank, K., Sarkisova, N., Jefferson, N., McClelland, R., Mooney, S., Nam, Y., Wilcox, A., Park, C., Dowd, F., Williams, K., Grewenow, S. M., Daniel, S., Shankland, S., Pamreddy, A., Ye, H., Montellano, R., Bansal, S., Pillai, A., Zhang, D., Park, H., Patel, J., Sambandam, K., Basit, M., Wen, N., Moe, O. W., Toto, R. D., Lee, S. C., Sharman, K., Caprioli, R. M., Fogo, A., Allen, J., Spraggins, J., Djambazova, K., de Caestecker, M., Dufresne, M., Farrow, M., Vijayan, A., Minor, B., Nwanne, G., Gaut, J., Conlon, K., Kaushal, M., Diettman, S. M., Victoria Castro, A. M., Moledina, D., Wilson, F. P., Moeckel, G., Cantley, L., Shaw, M., Kakade, V., Arora, T., Jain, S. & Rauchman, M., Dec 2024, In: Nature communications. 15, 1, 433.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      13 Scopus citations
    • 2023

      Aberrant centrosome biogenesis disrupts nephron and collecting duct progenitor growth and fate resulting in fibrocystic kidney disease

      Cheng, T., Agwu, C., Shim, K., Wang, B., Jain, S. & Mahjoub, M. R., Dec 2023, In: Development (Cambridge). 150, 24

      Research output: Contribution to journal › Article › peer-review

      Open Access
      3 Scopus citations

    • Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)

      Jain, S., Pei, L., Spraggins, J. M., Angelo, M., Carson, J. P., Gehlenborg, N., Ginty, F., Gonçalves, J. P., Hagood, J. S., Hickey, J. W., Kelleher, N. L., Laurent, L. C., Lin, S., Lin, Y., Liu, H., Naba, A., Nakayasu, E. S., Qian, W. J., Radtke, A. & Robson, P. & 464 others, Stockwell, B. R., Van de Plas, R., Vlachos, I. S., Zhou, M., Ahn, K. J., Allen, J., Anderson, D. M., Anderton, C. R., Curcio, C., Angelin, A., Arvanitis, C., Atta, L., Awosika-Olumo, D., Bahmani, A., Bai, H., Balderrama, K., Balzano, L., Bandyopadhyay, G., Bandyopadhyay, S., Bar-Joseph, Z., Barnhart, K., Barwinska, D., Becich, M., Becker, L., Becker, W., Bedi, K., Bendall, S., Benninger, K., Betancur, D., Bettinger, K., Billings, S., Blood, P., Bolin, D., Border, S., Bosse, M., Bramer, L., Brewer, M., Brusko, M., Bueckle, A., Burke, K., Burnum-Johnson, K., Butcher, E., Butterworth, E., Cai, L., Calandrelli, R., Caldwell, M., Campbell-Thompson, M., Cao, D., Cao-Berg, I., Caprioli, R., Caraccio, C., Caron, A., Carroll, M., Chadwick, C., Chen, A., Chen, D., Chen, F., Chen, H., Chen, J., Chen, L., Chen, L., Chiacchia, K., Cho, S., Chou, P., Choy, L., Cisar, C., Clair, G., Clarke, L., Clouthier, K. A., Colley, M. E., Conlon, K., Conroy, J., Contrepois, K., Corbett, A., Corwin, A., Cotter, D., Courtois, E., Cruz, A., Csonka, C., Czupil, K., Daiya, V., Dale, K., Davanagere, S. A., Dayao, M., de Caestecker, M. P., Decker, A., Deems, S., Degnan, D., Desai, T., Deshpande, V., Deutsch, G., Devlin, M., Diep, D., Dodd, C., Donahue, S., Dong, W., dos Santos Peixoto, R., Duffy, M., Dufresne, M., Duong, T. E., Dutra, J., Eadon, M. T., El-Achkar, T. M., Enninful, A., Eraslan, G., Eshelman, D., Espin-Perez, A., Esplin, E. D., Esselman, A., Falo, L. D., Falo, L., Fan, J., Fan, R., Farrow, M. A., Farzad, N., Favaro, P., Fermin, J., Filiz, F., Filus, S., Fisch, K., Fisher, E., Fisher, S., Flowers, K., Flynn, W. F., Fogo, A. B., Fu, D., Fulcher, J., Fung, A., Furst, D., Gallant, M., Gao, F., Gao, Y., Gaulton, K., Gaut, J. P., Gee, J., Ghag, R. R., Ghazanfar, S., Ghose, S., Gisch, D., Gold, I., Gondalia, A., Gorman, B., Greenleaf, W., Greenwald, N., Gregory, B., Guo, R., Gupta, R., Hakimian, H., Haltom, J., Halushka, M., Han, K. S., Hanson, C., Harbury, P., Hardi, J., Harlan, L., Harris, R. C., Hartman, A., Heidari, E., Helfer, J., Helminiak, D., Hemberg, M., Henning, N., Herr, B. W., Ho, J., Holden-Wiltse, J., Hong, S. H., Hong, Y. K., Honick, B., Hood, G., Hu, P., Hu, Q., Huang, M., Huyck, H., Imtiaz, T., Isberg, O. G., Itkin, M., Jackson, D., Jacobs, M., Jain, Y., Jewell, D., Jiang, L., Jiang, Z. G., Johnston, S., Joshi, P., Ju, Y., Judd, A., Kagel, A., Kahn, A., Kalavros, N., Kalhor, K., Karagkouni, D., Karathanos, T., Karunamurthy, A., Katari, S., Kates, H., Kaushal, M., Keener, N., Keller, M., Kenney, M., Kern, C., Kharchenko, P., Kim, J., Kingsford, C., Kirwan, J., Kiselev, V., Kishi, J., Kitata, R. B., Knoten, A., Kollar, C., Krishnamoorthy, P., Kruse, A. R. S., Da, K., Kundaje, A., Kutschera, E., Kwon, Y., Lake, B. B., Lancaster, S., Langlieb, J., Lardenoije, R., Laronda, M., Laskin, J., Lau, K., Lee, H., Lee, M., Lee, M., Strekalova, Y. L., Li, D., Li, J., Li, J., Li, X., Li, Z., Liao, Y. C., Liaw, T., Lin, P., Lin, Y., Lindsay, S., Liu, C., Liu, Y., Liu, Y., Lott, M., Lotz, M., Lowery, L., Lu, P., Lu, X., Lucarelli, N., Lun, X., Luo, Z., Ma, J., Macosko, E., Mahajan, M., Maier, L., Makowski, D., Malek, M., Manthey, D., Manz, T., Margulies, K., Marioni, J., Martindale, M., Mason, C., Mathews, C., Maye, P., McCallum, C., McDonough, E., McDonough, L., Mcdowell, H., Meads, M., Medina-Serpas, M., Ferreira, R. M., Messinger, J., Metis, K., Migas, L. G., Miller, B., Mimar, S., Minor, B., Misra, R., Missarova, A., Mistretta, C., Moens, R., Moerth, E., Moffitt, J., Molla, G., Monroe, M., Monte, E., Morgan, M., Muraro, D., Murphy, B., Murray, E., Musen, M. A., Naglah, A., Nasamran, C., Neelakantan, T., Nevins, S., Nguyen, H., Nguyen, N., Nguyen, T., Nguyen, T., Nigra, D., Nofal, M., Nolan, G., Nwanne, G., O’Connor, M., Okuda, K., Olmer, M., O’Neill, K., Otaluka, N., Pang, M., Parast, M., Pasa-Tolic, L., Paten, B., Patterson, N. H., Peng, T., Phillips, G., Pichavant, M., Piehowski, P., Pilner, H., Pingry, E., Pita-Juarez, Y., Plevritis, S., Ploumakis, A., Pouch, A., Pryhuber, G., Puerto, J., Qaurooni, D., Qin, L., Quardokus, E. M., Rajbhandari, P., Rakow-Penner, R., Ramasamy, R., Read, D., Record, E. G., Reeves, D., Ricarte, A., Rodríguez-Soto, A., Ropelewski, A., Rosario, J., Roselkis, M. A., Rowe, D., Roy, T. K., Ruffalo, M., Ruschman, N., Sabo, A., Sachdev, N., Saka, S., Salamon, D., Sarder, P., Sasaki, H., Satija, R., Saunders, D., Sawka, R., Schey, K., Schlehlein, H., Scholten, D., Schultz, S., Schwartz, L., Schwenk, M., Scibek, R., Segre, A., Serrata, M., Shands, W., Shen, X., Shendure, J., Shephard, H., Shi, L., Shi, T., Shin, D. G., Shirey, B., Sibilla, M., Silber, M., Silverstein, J., Simmel, D., Simmons, A., Singhal, D., Sivajothi, S., Smits, T., Soncin, F., Song, Q., Stanley, V., Stuart, T., Su, H., Su, P., Sun, X., Surrette, C., Swahn, H., Tan, K., Teichmann, S., Tejomay, A., Tellides, G., Thomas, K., Thomas, T., Thompson, M., Tian, H., Tideman, L., Trapnell, C., Tsai, A. G., Tsai, C. F., Tsai, L., Tsui, E., Tsui, T., Tung, J., Turner, M., Uranic, J., Vaishnav, E. D., Varra, S. R., Vaskivskyi, V., Velickovic, D., Velickovic, M., Verheyden, J., Waldrip, J., Wallace, D., Wan, X., Wang, A., Wang, F., Wang, M., Wang, S., Wang, X., Wasserfall, C., Wayne, L., Webber, J., Weber, G. M., Wei, B., Wei, J. J., Weimer, A., Welling, J., Wen, X., Wen, Z., Williams, M. K., Winfree, S., Winograd, N., Woodard, A., Wright, D., Wu, F., Wu, P. H., Wu, Q., Wu, X., Xing, Y., Xu, T., Yang, M., Yang, M., Yap, J., Ye, D. H., Yin, P., Yuan, Z., Yun, C., Zahraei, A., Zemaitis, K., Zhang, B., Zhang, C., Zhang, C., Zhang, C., Zhang, K., Zhang, S., Zhang, T., Zhang, Y., Zhao, B., Zhao, W., Zheng, J. W., Zhong, S., Zhu, B., Zhu, C., Zhu, D., Zhu, Q., Zhu, Y., Börner, K. & Snyder, M. P., Aug 2023, In: Nature Cell Biology. 25, 8, p. 1089-1100 12 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      50 Scopus citations

    • An atlas of healthy and injured cell states and niches in the human kidney

      KPMP Consortium, Jul 20 2023, In: Nature. 619, 7970, p. 585-594 10 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      207 Scopus citations

    • A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease

      the Kidney Precision Medicine Project, Dec 2023, In: Nature communications. 14, 1, 4140.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      30 Scopus citations

    • Automated Reference Kidney Histomorphometry using a Panoptic Segmentation Neural Network Correlates to Patient Demographics and Creatinine

      Ginley, B., Lucarelli, N., Zee, J., Jain, S., Han, S. S., Rodrigues, L., Wong, M. L., Jen, K. Y. & Sarder, P., 2023, Medical Imaging 2023: Digital and Computational Pathology. Tomaszewski, J. E. & Ward, A. D. (eds.). SPIE, 124711R. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 12471).

      Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

      2 Scopus citations

    • Characterization of Glomerular and Tubulointerstitial Proteomes in a Case of Nonsteroidal Anti-Inflammatory Drug–Attributed Acute Kidney Injury A Clinical Pathologic Molecular Correlation

      the Kidney Precision Medicine Project, Mar 2023, In: Clinical Journal of the American Society of Nephrology. 18, 3, p. 402-410 9 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      4 Scopus citations

    • Computational Pathology Fusing Spatial Technologies

      Border, S., Lucarelli, N., Eadon, M. T., El-Achkar, T. M., Jain, S. & Sarder, P., May 2023, In: Clinical Journal of the American Society of Nephrology. 18, 5, p. 675-677 3 p.

      Research output: Contribution to journal › Comment/debate

      Open Access
      1 Scopus citations

    • Conundrums of choice of 'normal' kidney tissue for single cell studies

      Jain, S., May 1 2023, In: Current Opinion in Nephrology and Hypertension. 32, 3, p. 249-256 8 p.

      Research output: Contribution to journal › Review article › peer-review

      Open Access
      1 Scopus citations

    • Correlating Deep Learning-Based Automated Reference Kidney Histomorphometry with Patient Demographics and Creatinine

      Lucarelli, N., Ginley, B., Zee, J., Mimar, S., Paul, A. S., Jain, S., Han, S. S., Rodrigues, L., Ozrazgat-Baslanti, T., Wong, M. L., Nadkarni, G., Clapp, W. L., Jen, K. Y. & Sarder, P., Dec 1 2023, In: Kidney360. 4, 12, p. 1726-1737 12 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      6 Scopus citations

    • Erratum: 89 Bridging Cell Biology and Engineering Sciences: Interdisciplinary Team-based Training in Computational Pathology (Journal of Clinical and Translational Science (2023) 7: s1 ( 25) DOI: 10.1017/cts.2023.172)

      Tan, M. J. T., Gupta, A., Fermin, J. L., Border, S. P., Jain, S., Tomaszewski, J. E., Levites Strekalova, Y. A. & Sarder, P., Jun 14 2023, In: Journal of Clinical and Translational Science. 7, 1, e133.

      Research output: Contribution to journal › Comment/debate

    • Evaluation of Plasma Biomarkers to Predict Major Adverse Kidney Events in Hospitalized Patients With COVID-19

      TRIKIC Consortium, Sep 2023, In: American Journal of Kidney Diseases. 82, 3, p. 322-332.e1

      Research output: Contribution to journal › Article › peer-review

      Open Access
      6 Scopus citations

    • Lethal neonatal respiratory failure due to biallelic variants in BBS1 and monoallelic variant in TTC21B

      Viehl, L., Wegner, D. J., Hmiel, S. P., White, F. V., Jain, S., Cole, F. S. & Wambach, J. A., Feb 2023, In: Pediatric Nephrology. 38, 2, p. 605-609 5 p.

      Research output: Contribution to journal › Article › peer-review

      1 Scopus citations

    • Navigating the kidney organoid: insights into assessment and enhancement of nephron function

      Tabibzadeh, N., Satlin, L. M., Jain, S. & Morizane, R., Dec 2023, In: American Journal of Physiology - Renal Fluid and Electrolyte Physiology. 325, 6, p. F695-F706

      Research output: Contribution to journal › Article › peer-review

      Open Access
      8 Scopus citations

    • Shank2 identifies a subset of glycinergic neurons involved in altered nociception in an autism model

      Olde Heuvel, F., Ouali Alami, N., Aousji, O., Pogatzki-Zahn, E., Zahn, P. K., Wilhelm, H., Deshpande, D., Khatamsaz, E., Catanese, A., Woelfle, S., Schön, M., Jain, S., Grabrucker, S., Ludolph, A. C., Verpelli, C., Michaelis, J., Boeckers, T. M. & Roselli, F., Dec 2023, In: Molecular Autism. 14, 1, 21.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      3 Scopus citations
    • 2022

      An ex vivo culture model of kidney podocyte injury reveals mechanosensitive, synaptopodin-templating, sarcomere-like structures

      Jiang, S., Alisafaei, F., Huang, Y. Y., Hong, Y., Peng, X., Qu, C., Puapatanakul, P., Jain, S., Miner, J. H., Genin, G. M. & Suleiman, H. Y., Sep 2022, In: Science Advances. 8, 35, eabn6027.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      4 Scopus citations

    • A Participant-Centered Approach to Understanding Risks and Benefits of Participation in Research Informed by the Kidney Precision Medicine Project

      Kidney Precision Medicine Project, Jul 2022, In: American Journal of Kidney Diseases. 80, 1, p. 132-138 7 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      5 Scopus citations

    • A reference tissue atlas for the human kidney

      Kidney Precision Medicine Project, Jun 2022, In: Science Advances. 8, 23, eabn4965.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      83 Scopus citations

    • A user-friendly tool for cloud-based whole slide image segmentation with examples from renal histopathology

      the Kidney Precision Medicine Project, Lutnick, B., Manthey, D., Becker, J. U., Ginley, B., Moos, K., Zuckerman, J. E., Rodrigues, L., Gallan, A. J., Barisoni, L., Alpers, C. E., Wang, X. X., Myakala, K., Jones, B. A., Levi, M., Kopp, J. B., Yoshida, T., Zee, J., Han, S. S. & Jain, S. & 181 others, Rosenberg, A. Z., Jen, K. Y., Sarder, P., Lutnick, B., Ginley, B., Knight, R., Lecker, S. H., Stillman, I., Bogen, S., Amodu, A. A., Ilori, T., Schmidt, I., Maikhor, S., Beck, L. H., Verma, A., Henderson, J. M., Onul, I., Waikar, S., McMahon, G. M., Weins, A., Colona, M. R., Valerius, M. T., Hacohen, N., Hoover, P. J., Greka, A., Marshall, J. L., Aulisio, M., Chen, Y. M., Janowczyk, A., Jayapandian, C., Viswanathan, V. S., Bush, W. S., Crawford, D. C., Madabhushi, A., O’toole, J., Poggio, E., Sedor, J., Cooperman, L., Jolly, S., Herlitz, L., Nguyen, J., Gonzalez-Vicente, A., Palmer, E., Sendrey, D., Taliercio, J., Bush, L., Spates-Harden, K., Vinovskis, C., Bjornstad, P. M., Pyle, L., Appelbaum, P., Barasch, J. M., Bomback, A. S., D’Agati, V. D., Kiryluk, K., Mehl, K., Canetta, P. A., Shang, N., Balderes, O., Kudose, S., Alexandrov, T., Rennke, H., El-Achkar, T. M., Cheng, Y., Dagher, P. C., Eadon, M. T., Dunn, K. W., Kelly, K. J., Sutton, T. A., Barwinska, D., Ferkowicz, M. J., Winfree, S., Bledsoe, S., Rivera, M., Williams, J. C., Ferreira, R. M., Borner, K., Bueckle, A., Herr, B. W., Quardokus, E. M., Record, E., Su, J., Gisch, D., Wofford, S., Jain, Y., Parikh, C. R., Corona-Villalobos, C. P., Menez, S., Wen, Y., Johansen, C., Rosas, S. E., Roy, N., Williams, M., Sun, J., Ardayfio, J., Bebiak, J., Brown, K., Campbell, C. E., Saul, J., Shpigel, A., Stutzke, C., Koewler, R., Campbell, T., Hayashi, L., Jefferson, N., Roberts, G. V., Pinkeney, R., Azeloglu, E. U., He, C., Iyengar, R., Hansen, J., Xiong, Y., Prasad, P., Srivastava, A., Rovin, B., Parikh, S., Shapiro, J. P., Madhavan, S. M., Anderton, C. R., Pasa-Tolic, L., Velickovic, D., Lukowski, J., Oliver, G. H., Troyanskaya, O., Sealfon, R., Wong, A., Tuttle, K. R., Pollack, A., Goltsev, Y., Zhang, K., Lake, B. B., Laszik, Z. G., Nolan, G., Boada, P., Sarwal, M., Anjani, K., Sigdel, T., Mukatash, T., Lee, P. J., Alloway, R. R., Woodle, E. S., Burg, A. R., Rike, A., Shi, T., Ascani, H., Balis, U. G. J., Hodgin, J. B., Kretzler, M., Lienczewski, C., Mariani, L. H., Menon, R., Steck, B., He, Y., Otto, E., Schaub, J., Blanc, V. M., Eddy, S., Conser, N. C., Luo, J., Frey, R., Palevsky, P. M., Rosengart, M., Kellum, J. A., Hall, D. E., Randhawa, P., Tublin, M., Murugan, R., Elder, M. M., Winters, J., Vita, T., Bender, F., Tan, R., Gilliam, M., Blank, K. N., Carson, J., De Boer, I. H., Dighe, A. L., Shankland, S., Vijayan, A., Gaut, J. P. & Rauchman, M. I., Dec 2022, In: Communications Medicine. 2, 1, 105.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      20 Scopus citations

    • Integrated single-cell sequencing and histopathological analyses reveal diverse injury and repair responses in a participant with acute kidney injury: a clinical-molecular-pathologic correlation

      Kidney Precision Medicine Project, Jun 2022, In: Kidney International. 101, 6, p. 1116-1125 10 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      10 Scopus citations

    • NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health

      Stanford TDA, University of Connecticut TMC, University of Michigan TDA, University of Minnesota TMC, University of Pittsburgh TMC, University of Washington TDA, Washington University TMC, Yale TMC, SenNet Consortium, Writing Group, Brown University TDA, Buck Institute for Research on Aging TMC/TDA, Consortium Organization and Data Coordinating Center (CODCC), Columbia TMC, Duke University TMC, Massachusetts General Hospital TDA, Mayo Clinic TDA & National Institute of Health (NIH), Dec 2022, In: Nature Aging. 2, 12, p. 1090-1100 11 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      58 Scopus citations

    • Tissue registration and exploration user interfaces in support of a human reference atlas

      Börner, K., Bueckle, A., Herr, B. W., Cross, L. E., Quardokus, E. M., Record, E. G., Ju, Y., Silverstein, J. C., Browne, K. M., Jain, S., Wasserfall, C. H., Jorgensen, M. L., Spraggins, J. M., Patterson, N. H. & Weber, G. M., Dec 2022, In: Communications Biology. 5, 1, 1369.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      6 Scopus citations
    • 2021

      A multimodal and integrated approach to interrogate human kidney biopsies with rigor and reproducibility: Guidelines from the kidney precision medicine project

      Kidney Precision Medicine Project, 2021, In: Physiological genomics. 53, 1, p. 1-11 11 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      51 Scopus citations

    • Anatomical structures, cell types and biomarkers of the Human Reference Atlas

      Börner, K., Teichmann, S. A., Quardokus, E. M., Gee, J. C., Browne, K., Osumi-Sutherland, D., Herr, B. W., Bueckle, A., Paul, H., Haniffa, M., Jardine, L., Bernard, A., Ding, S. L., Miller, J. A., Lin, S., Halushka, M. K., Boppana, A., Longacre, T. A., Hickey, J. & Lin, Y. & 16 others, Valerius, M. T., He, Y., Pryhuber, G., Sun, X., Jorgensen, M., Radtke, A. J., Wasserfall, C., Ginty, F., Ho, J., Sunshine, J., Beuschel, R. T., Brusko, M., Lee, S., Malhotra, R., Jain, S. & Weber, G., Nov 2021, In: Nature Cell Biology. 23, 11, p. 1117-1128 12 p.

      Research output: Contribution to journal › Review article › peer-review

      Open Access
      56 Scopus citations

    • A Pilot Study of Urine Proteomics in COVID-19–Associated Acute Kidney Injury

      Ye, Y., Swensen, A. C., Wang, Y., Kaushal, M., Salamon, D., Knoten, A., Nicora, C. D., Marks, L., Gaut, J. P., Vijayan, A., Orton, D. J., Mudd, P. A., Parikh, C. R., Qian, W. J., O'Halloran, J. A., Piehowski, P. D. & Jain, S., Dec 2021, In: Kidney International Reports. 6, 12, p. 3064-3069 6 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      4 Scopus citations

    • Automated Computational Detection of Interstitial Fibrosis, Tubular Atrophy, and Glomerulosclerosis

      Ginley, B., Jen, K. Y., Han, S. S., Rodrigues, L., Jain, S., Fogo, A. B., Zuckerman, J., Walavalkar, V., Miecznikowski, J. C., Wen, Y., Yen, F., Yun, D., Moon, K. C., Rosenberg, A., Parikh, C. & Sarder, P., Apr 1 2021, In: Journal of the American Society of Nephrology : JASN. 32, 4, p. 837-850 14 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      61 Scopus citations

    • Cadherin-11, Sparc-related modular calcium binding protein-2, and Pigment epithelium-derived factor are promising non-invasive biomarkers of kidney fibrosis

      Kidney Precision Medicine Project (KPMP), Sep 2021, In: Kidney International. 100, 3, p. 672-683 12 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      29 Scopus citations

    • Large-scale, three-dimensional tissue cytometry of the human kidney: a complete and accessible pipeline

      for the Kidney Precision Medicine Project, May 2021, In: Laboratory Investigation. 101, 5, p. 661-676 16 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      18 Scopus citations

    • Ontology-based Modeling, Representation, and Analysis of Biomarkers in Healthy and Disease Kidney Tissue

      Kidney Precision Medicine Project, 2021, In: CEUR Workshop Proceedings. 3073, p. 70-76 7 p.

      Research output: Contribution to journal › Conference article › peer-review

      1 Scopus citations

    • Patient perspectives and involvement in precision medicine research

      Kidney Precision Medicine Project, Mar 2021, In: Kidney International. 99, 3, p. 511-514 4 p.

      Research output: Contribution to journal › Comment/debate

      7 Scopus citations

    • Plasticity of distal nephron epithelia from human kidney organoids enables the induction of ureteric tip and stalk

      Howden, S. E., Wilson, S. B., Groenewegen, E., Starks, L., Forbes, T. A., Tan, K. S., Vanslambrouck, J. M., Holloway, E. M., Chen, Y. H., Jain, S., Spence, J. R. & Little, M. H., Apr 1 2021, In: Cell Stem Cell. 28, 4, p. 671-684.e6

      Research output: Contribution to journal › Article › peer-review

      Open Access
      79 Scopus citations

    • Rationale and design of the Kidney Precision Medicine Project

      Kidney Precision Medicine Project, Mar 2021, In: Kidney International. 99, 3, p. 498-510 13 p.

      Research output: Contribution to journal › Comment/debate

      Open Access
      103 Scopus citations
    • 2020

      Fully automated classification of glomerular lesions in lupus nephritis

      Ginley, B., Jen, K. Y., Rosenberg, A., Rossi, G. M., Jain, S. & Sarder, P., 2020, Medical Imaging 2020: Digital Pathology. Tomaszewski, J. E. & Ward, A. D. (eds.). SPIE, 113200Y. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 11320).

      Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

      8 Scopus citations

    • Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project

      Kidney Precision Medicine Project, Nov 1 2020, In: Nature Reviews Nephrology. 16, 11, p. 686-696 11 p.

      Research output: Contribution to journal › Review article › peer-review

      Open Access
      47 Scopus citations

    • Neutrophil Extracellular Traps (NETs): An unexplored territory in renal pathobiology, a pilot computational study

      Santo, B. A., Segal, B. H., Tomaszewski, J. E., Mohammad, I., Worral, A. M., Jain, S., Visser, M. B. & Sarder, P., 2020, Medical Imaging 2020: Digital Pathology. Tomaszewski, J. E. & Ward, A. D. (eds.). SPIE, 1132012. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 11320).

      Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

      4 Scopus citations

    • Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker

      Kidney Precision Medicine Project (KPMP),5 and Nephrotic Syndrome Study Network (NEPTUNE), Mar 26 2020, In: JCI Insight. 5, 6, e133267.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      108 Scopus citations
    • 2019

      An integrated iterative annotation technique for easing neural network training in medical image analysis

      Lutnick, B., Ginley, B., Govind, D., McGarry, S. D., LaViolette, P. S., Yacoub, R., Jain, S., Tomaszewski, J. E., Jen, K. Y. & Sarder, P., Feb 1 2019, In: Nature Machine Intelligence. 1, 2, p. 112-119 8 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      109 Scopus citations

    • A single-nucleus RNA-sequencing pipeline to decipher the molecular anatomy and pathophysiology of human kidneys

      Lake, B. B., Chen, S., Hoshi, M., Plongthongkum, N., Salamon, D., Knoten, A., Vijayan, A., Venkatesh, R., Kim, E. H., Gao, D., Gaut, J., Zhang, K. & Jain, S., Dec 1 2019, In: Nature communications. 10, 1, 2832.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      197 Scopus citations