| # | Title | Authors | Journal | Year | |
|---|---|---|---|---|---|
| 43 | Precision targeting of autoreactive B cells in systemic lupus erythematosus using anti-9G4 idiotope synthetic immune receptor T cells | J. Liu, Y. Xia, B. J. Mog, C. Gliech, E. Shaw, D. Ferris, B. Moritz, T. O. Awosika, S. R. DiNapoli, S. Glavaris, K. J. Kaeo, X. Li, N. Marcou, A. H. Pearlman, T. S. Ahmedna, R. Bugrovsky, I. Sanz, C. Bettegowda, S. Paul, V. D. Alvarado, D. Wirtz, D. Goldman, M. Petri, K. W. Kinzler, S. Zhou, F. Andrade, B. Vogelstein, and M. F. Konig | BioRxiv | 2025 | |
| 42 | NLTD 2.0: A nonlinear framework for robust and customizable color deconvolution in histopathology | F. Selaru, J.M. Phillip, D. Wirtz, and P.-H. Wu | BioRxiv | 2025 | |
| 41 | Hyper-migratory CAR T cells alleviate ovarian cancer metastatic burden and improve prognosis | P. R. Nair, E. Hanna, S. Joshi, V. Duarte-Alvarado, C. L. Bonifant, and D. Wirtz | BioRxiv | 2025 | |
| 40 | Solving the “Blind men and the elephant problem”: Additive deep learning of complex high dimensional models from partial faceted datasets | Y. Wu, P.-H. Wu, A. Chambliss, D. Wirtz, and S.X. Sun | BioRxiv | 2025 | |
| 39 | Integration of nuclear morphology and 3D imaging to profile cellular neighborhoods | A. Forjaz, D. Kramer, Y. Shen, H. Bea, M. Tsapatsis, J. Ping, V. Queiroga, K. Sang Han, S. Joshi, C. Grubel, M.L. Beery, I. Kusmartseva, M.A. Atkinson, A.L. Kiemen, and D. Wirtz | BioRxiv | 2025 | |
| 38 | 3D map-guided modeling of functional endometrial tissue using multi-compartment assembloids | K.A. Ren,V. Duarte-Alvarado, X.D. Zhou, B. Ho,A. Forjaz, A.J. Crawford, G.M. Alicea-Rebecca, S. Joshi, P. Nair, E.A. Hanna, and D. Wirtz | BioRxiv | 2025 | |
| 37 | 3D multi-omic mapping of whole nondiseased human fallopian tubes at cellular resolution reveals a large incidence of ovarian cancer precursors | A. Forjaz, V. Queiroga, Y. Li, A. Hernandez, A. Crawford,X. Qin, M. Zhong, M. Tsapatsis, S. Joshi, D. Kramer, O. Nizet, H. Bea, Y. Li, S. Qin, R. O’Flynn, M. Yang, B. Pratt, F. Wu, P. Gensbigler, M. Blecher, P.-H. Wu, L. T. Kagohara11,12, I.-M. Shih, D. Zwicker, M. Atkinson, L. Shi, R. Fan, A.L. Kiemen, and D. Wirtz | BioRxiv | 2025 | |
| 36 | PIVOT: an open-source tool for multi-omic spatial data registration | A. Forjaz, V.M. Romero, I. Reucroft, M. Eminizer, D. Kramer, D. Higuera, H. Mojdeganlou, P.A. Guerrero, J. Min, M. Wetzel, D. Lvovs, A. Valentin, S.M. Shin, X. Yuan, R.C. Sears, K. Chin, A. Maitra, E.J. Fertig, W\.J. Ho, L.T. Kagohara, L.D. Wood, D. Wirtz, D.N. Sidiropoulos, and A.L. Kiemen | BioRxiv | 2025 | |
| 35 | CODAvision: best practices and a user-friendly interface for rapid, customizable segmentation of medical images | V. Matos-Romero, J. Gomez-Becerril, A. Forjaz, L. Dequiedt, T. Newton, S. Joshi, Y. Shen, E. Hanna, P.R. Nair, A. Sivasubramanian, J. Wang, E.L. Lasse-Opsahl, A.T.F. Bell, Julianna Czum, Charles Steenbergen, Dao-Fu Dai, Laura D Wood, Luciane T. Kagohara, E.J. Fertig, M.Pasca di Magliano, J. Shatzel, O.J. McCarty, Jamie O Lo, A. Rosenberg, R..H. Hruban, A. Munoz-Barrutia, D. Wirtz, A. L Kiemen | BioRxiv | 2025 | |
| 34 | Accelerated Discovery of Cell Migration Regulators Using Label-Free Deep Learning-Based Automated Tracking | T. Chu, Y. Lim, Y. Sun, D. Wirtz,* P.-H. Wu* | BioRxiv | 2025 | |
| 33 | Integration of nuclear morphology and 3D imaging to profile cellular neighborhoods | A. Forjaz, D. Kramer, Y. Shen, H. Bea, M. Tsapatsis, J. Ping, V. Queiroga, K. Sang Han, S. Joshi, C. Grubel, M.L. Beery, I. Kusmartseva, M.A. Atkinson, A.L. Kiemen, D. Wirtz | BioRxiv | 2025 | |
| 32 | qMAP enabled microanatomical mapping of human skin aging | K. Sang Han, I. B. Sander, J. Kumer, E. Resnick, C. Booth, G. Cheng, Y. Im, B. Starich, A. L. Kiemen, J. M. Philip, S. Reddy, C. E. Joshu, J. C. Sunshine, J. D. Walston, D. Wirtz, P.-H. Wu | BioRxiv | 2024 | |
| 31 | Digitize your Biology! Modeling multicellular systems through interpretable cell behavior | J.A.I. Johnson, G.L. Stein-O’Brien, M. Booth, R. Heiland, F. Kurtoglu, D.R. Bergman, E. Bucher, A. Deshpande, A. Forjaz, M. Getz, I. Godet, M. Lyman, J. Metzcar, J. Mitchell, A. Raddatz, H. Rocha, J. Solorzano, A. Sundus, Y. Wang, D. Gilkes, L.T. Kagohara, A.L. Kiemen, E.D. Thompson, D. Wirtz, P.-H. Wu, D. Zaidi, L. Zheng, J.W. Zimmerman, E.M. Jaffee, Y.H. Chang, L.M. Coussens, J.W. Gray, L.M. Heiser, E.J. Fertig, and P. Macklin | BioRxiv | 2023 | |
| 30 | Generative interpolation and restoration of images using deep learning for improved 3D tissue mapping | S. Joshi, A. Forjaz, K. SangHan, Y. Shen, D. Xenes, J. Matelsky, B. Wester, A. Munoz-Barrutia, A.L. Kiemen, P.-H. Wu, and D. Wirtz | BioRxiv | 2024 | |
| 29 | Serine synthesis pathway upregulated by E-cadherin is essential for the proliferation and metastasis of breast cancers | G. Lee, C. Wong, A. Cho, J.J. West, A. J. Crawford, G.C. Russo, B.R. Si, J. Kim, L. Hoffner, C. Jang, M. Jung, R.D. Leone, K. Konstantopoulos, A. J. Ewald, D. Wirtz, and S. Jeong | Cancer Research | 2024 | |
| 28 | A TBX5-dependent compartment boundary patterns the cardiac interventricular septum | S. Kathiriya, M.H. Dominguez, K.S. Rao, J.M. Muncie-Vasic, W.P. Devine, K.M. Hu, S.K. Hota, B.I. Garay, D. Quintero, P. Goyal, M.N. Matthews, R. Thomas, T. Sukonnik, D. Miguel-Perez, S. Winchester, E.F. Brower, A. Forjaz, P.-H. Wu, D. Wirtz, A.L. Kiemen, and B.G. Bruneau | BioRxiv | 2024 | |
| 27 | Substrate stiffness modulates the emergence and magnitude of senescence phenotypes | B. Starich, F. Yang, D. Tanrioven, H.-C. Kung, J. Baek, P. R. Nair, P. Kamat, N. Macaluso, J. Eoh, K. Sang Han,L. Gu, S.X. Sun, P-H. Wu, D. Wirtz, and J. M. Phillip | BioRxiv | 2024 | |
| 26 | Engineering self-propelled tumor-infiltrating CAR T cells using synthetic velocity receptors | A.C. Johnston, G.M. Alicea, C.C. Lee, P.V. Patel, E.A. Hanna, E. Vaz, A. Forjaz, Z. Wan, P.R. Nair, Y. Lim, T. Chen, W. Du, D. Kim, T.D. Nichakawade, V.W. Rebecca, C.L. Bonifant, R. Fan, A.L. Kiemen, P.-H. Wu, and D. Wirtz | BioRxiv | 2023 | |
| 25 | Three-dimensional reconstruction of fetal rhesus macaque kidneys at single-cell resolution reveals complex inter-relation of structures. | L. Dequiedt, A.Forjaz, J. O. Lo, O. McCarty, P-H. Wu, A. Rosenberg, D. Wirtz, and A. Kiemen | BioRxiv | 2023 | |
| 24 | Three-dimensional assessments are necessary to determine the true spatial tissue composition of diseased tissues | A. Forjaz, E. Vaz, V. Matos Romero, S. Joshi, A. M. Braxton, A. C. Jiang, K. Fujikura, T. Cornish, S.-M. Hong, R. H. Hruban, P.-H. Wu, L. D. Wood, A. L. Kiemen, D. Wirtz | BioRxiv | 2023 | |
| 23 | Power-law growth models explain incidences and sizes of pancreatic cancer precursor lesions and confirm spatial genomic findings | A.L. Kiemen, P.-H. Wu, A.M. Braxton, T.C. Cornish, R.H. Hruban, L. Wood, D. Wirtz, and D. Zwicker | BioRxiv | 2023 | |
| 22 | Serine synthesis pathway upregulated by E-cadherin is essential for the proliferation and metastasis of breast cancers | G. Lee, C. Wong, A. Cho, J.J. West, A. J. Crawford, G.C. Russo, B.R. Si, J. Kim, L. Hoffner, C. Jang, M. Jung, R.D. Leone, K. Konstantopoulos, A. J. Ewald, D. Wirtz, and S. Jeong | BioRxiv | 2023 | |
| 21 | Mechano-induced homotypic patterned domain formation by monocytes | W. Du, J. Zhu, Y. Wu, A. L. Kiemen, S.X. Sun, D. Wirtz | BioRxiv | 2023 | |
| 20 | Precision-engineered biomimetics: the human fallopian tube | A.J. Crawford, A. Forjaz, I. Bhorkar, T. Roy, D. Schell, V. Queiroga, K. Ren, D. Kramer, J. Bons, W. Huang, G.C. Russo, M.-H. Lee, B. Schilling, P.-H. Wu, I.-M. Shih, T.-L. Wang, A. Kiemen, and D. Wirtz | BioRxiv | 2023 | |
| 19 | Age-related increases in IGFBP2 increase melanoma cell invasion and lipid synthesis | G.M. Alicea, M.E. Portuallo, P. Patel, M.E. Fane, A. Carey, D.W. Speicher, A. Kossenkov, V. W. Rebecca III, D. Wirtz, and A.T. Weeraratna | BioRxiv | 2023 | |
| 18 | Three-dimensional genomic mapping of human pancreatic tissue reveals striking multifocality and genetic heterogeneity in precancerous lesions | A.M. Braxton, A.L. Kiemen, M.P. Grahn, A. Forjaz, J.M. Babu, L. Zheng, L. Jiang, H. Cheng, Q. Song, R. Reichel, S. Graham, A.I. Damanakis, C.G. Fischer, S. Mo, C. Metz, J. Granger, X.D. Liu, N. Bachmann, C. AlmagroPérez, A.C.Jiang, J. Yoo, B. Kim, S. Du, E. Foster, J.Y. Hsu, P.A. Rivera, L.C. Chu, F. Liu, N. Niknafs, E.K. Fishman, A. Yuille, N.J. Roberts, E.D. Thompson, R.B. Scharpf, T.C. Cornish, Y. Jiao, R. Karchin, R.H. Hruban, P.-H. Wu, D. Wirtz, and L.D. Wood | BioRxiv | 2023 | |
| 17 | PanIN and CAF transitions in pancreatic carcinogenesis revealed with spatial data integration | A. T.F. Bell,J.T. Mitchell, A.L. Kiemen, K. Fujikura, H. Fedor, B. Gambichler, A. Deshpande, P.-H. Wu, D.N. Sidiropoulos, R. Erbe, J. Stern, R. Chan, S. Williams, J.M. Chell, J.W. Zimmerman, D. Wirtz, E. M. Jaffee, L.D. Wood, E. J. Fertig, L.T. Kagohara | BioRxiv | 2022 | |
| 16 | Tumor proliferation and invasion are coupled through cell-extracellular matrix friction | A. J. Crawford, C. Gomez-Cruz, G. C. Russo, W. Huang, I. Bhorkar, A. Munoz-Barrutia, D. Wirtz and D. Garcia-Gonzalez | BioRxiv | 2022 | |
| 15 | MLL1 regulates cytokine-driven cell migration and metastasis | P.R. Nair, L. Danilova, E. Gomez-de-Mariscal, A. Munoz-Barrutia, E.J. Fertig, D. Wirtz | BioRxiv | 2022 | |
| 14 | Mechanotransductive feedback control of endothelial cell motility and vascular morphogenesis | D.E. Mason, M. Goeckel, S.L. Vega, P.-H. Wu, D. Johnson, S.-J. Heo, D. Wirtz, J.A. Burdick, L. Wood, B.Y. Chow, A.N. Stratman, and J.D. Boerckel | BioRxiv | 2022 | |
| 13 | Spatial transcriptomics of FFPE pancreatic intraepithelial neoplasias reveals cellular and molecular alterations of progression to pancreatic ductal carcinoma | A. T.F. Bell, J. T. Mitchell, A. L. Kiemen, K. Fujikura, H. Fedor, B. Gambichler, A. Deshpande, P.-H. Wu, D. N. Sidiropoulos, R. Erbe, J. Stern, R. Chan, S. Williams, J. M. Chell, J. W. Zimmerman, D. Wirtz, E. M. Jaffee, L. D. Wood, E. J. Fertig, and L T. Kagohara | BioRxiv | 2022 | |
| 12 | Search for temporal cell segmentation robustness in phase-contrast microscopy videos | E. Gómez‐de‐Mariscal, H. Jayatilaka, O. Cicek, T. Brox, D. Wirtz, and A. Muñoz‐Barrutia, | ArXiv | 2021 | |
| 11 | Senescent stroma induces nuclear deformations in cancer cells via the inhibition of RhoA/ROCK/myosin II-based cytoskeletal tension | I. Aifuwa, J.M. Philip, B. Choul Kim, T.R. Luperchio, A. Jimenez, T. Perestrelo, S.-H. Lee, N. Longe, K. Reddy, T.J. Ha, D. Wirtz | BioRxiv | 2020 | |
| 10 | Multi-compartments organoids | M.-H. Lee, Y.S. Rahmanto, G.C. Russo, P.-H. Wu, D. Gilkes, A. Kiemen, T. Miyamoto, Y. Yu, M. Habibi, I.-M. Shih, T.-L. Wang, and D. Wirtz | BioRxiv | 2020 | |
| 9 | E-cadherin interacts with EGFR resulting in hyper-activation of ERK in multiple models of breast cancer | G.C Russo, A.J. Crawford, D. Clark, J. Cui, R, Carney, M.N. Karl, B. Su, B.A Starich, T.-S. Lih, Q. Zhang, P.-H. Wu, M.-H. Lee, H.S. Leong, H. Zhang, D. Wirtz. | BioRxiv | 2020 | |
| 8 | Deep learning identification of stiffness markers in breast cancer | A. Sneider, J. H. Kim, A. Kiemen, P.-H. Wu, M. Habibi, M. White, J. M.Phillip, L. Gu, and D. Wirtz | BioRxiv | 2020 | |
| 7 | In situ characterization of the 3D microanatomy of the pancreas and pancreatic cancer at single cell resolution | A.L. Kiemen, A.M. Braxton, M.P. Grahn, K.S. Han, J. Mahesh Babu, R. Reichel, F. Amoa, S.M. Hong, T.C. Cornish, E.D. Thompson, L.D. Wood, R.H. Hruban, P.H. Wu, D. Wirtz | BioRxiv | 2020 | |
| 6 | Fractional re-distribution among cell motility states during ageing | J. M. Phillip, N. Zamponi, M.P. Phillip, J. Daya, S. McGovern, W. Williams, K. Tschudi, H. Jayatilaka, P.-H. Wu, J. Walston, and D. Wirtz | BioRxiv | 2020 | |
| 5 | The role of integrin av and CD44 in GBM migration in human brain | Z.A. Binder, S.H.J Kim, P.-H. Wu, A. Giri, G.L. Galia, C.A. Pardo, and D. Wirtz | BioRxiv | 2019 | |
| 4 | Use of the p-value as a size-dependent function to address practical differences when analyzing large datasets | E. Gómez-de-Mariscal, V. Guerrero, A. Sneider, H. Jayatilaka, J. M. Phillip, D. Wirtz, and A. Muñoz-Barrutia | BioRxiv | 2019 | |
| 3 | YAP/TAZ as a novel regulator of cell volume | N.A. Perez-Gonzalez, N.D. Rochman, K. Yao, J. Tao, M.-T. Le, S. Flanary, L. Sablich, B. Toler, E. Crentsil, F. Takaesu, B. Lambrus, J. Huang, V. Fu, A.J. Holland, S. An, D. Wirtz, K.-L. Guan, S.X. Sun | BioRxiv | 2019 | |
| 2 | Role of Membrane-tension gated Ca flux in cell mechanosensation | L. He, J. Tao, F. Si, Y. Wu, T. Wu, V. Prasath, D. Wirtz, and S.X. Sun | BioRxiv | 2017 | |
| 1 | Computational discovery of tissue morphology biomarkers in very long-term survivors with pancreatic ductal adenocarcinoma | J.S. Sarnecki, L.D. Wood, C.L. Wolfgang, R.H. Hruban, A. Maitra, D. Wirtz, and P.-H. Wu | BioRxiv | 2017 |
Chemical & Biomolecular Engineering