Publications

Papers and preprints from the lab.

Preprints (6) · Published (22)

Preprints

A generative reference grammar of healthy TCR repertoires reveals cancer-associated immune remodeling

A Balan, Y Elhanati, KE Meza Landeros, MDA Mendes, J Lai, SSA Zaidi, M Unal, BYS Kim, CHG Lucas, E Runco, VK Puduvalli, J Gantchev, CA Whittaker, P Sharma, V Tabar, MJ Cima, G Baquer, DA Reardon, … show all 29 authorsA Balan, Y Elhanati, KE Meza Landeros, MDA Mendes, J Lai, SSA Zaidi, M Unal, BYS Kim, CHG Lucas, E Runco, VK Puduvalli, J Gantchev, CA Whittaker, P Sharma, V Tabar, MJ Cima, G Baquer, DA Reardon, A Stortchevoi, A Boire, L Wang, FM White, DN Sidiropoulos, KKH Yu, EA Chiocca, V Anagnostou, Data Science Teamlab, Accelerating GBM Therapies TeamLab, R Karchin
bioRxiv (2026)
preprint

STAPLE: automating spatial transcriptomics analysis and AI interpretation

D Lvovs, J Quinn, A Forjaz, I Santana-Cruz, O Stapleton, K Vavikolanu, M Wetzel, Demystifying Pancreatic Cancer Therapies TeamLab, Data Science Hub Teamlab, V Bernard, BR Herb, A Favorov, LT Kagohara, … show all 21 authorsD Lvovs, J Quinn, A Forjaz, I Santana-Cruz, O Stapleton, K Vavikolanu, M Wetzel, Demystifying Pancreatic Cancer Therapies TeamLab, Data Science Hub Teamlab, V Bernard, BR Herb, A Favorov, LT Kagohara, AL Kiemen, A Maitra, DN Sidiropoulos, W Tansey, LD Wood, A Deshpande, M Noble, EJ Fertig
bioRxiv (2026)
doi

Deep Learning Enabled 3D Multi-Omic Analysis Reveals Molecular Signatures of Heterogeneous Response to Chemotherapy in Pancreatic Cancer

A Forjaz, H Mojdeganlou, A Valentin, M Wetzel, D Lvovs, A Deshpande, SM Shin, S Piya, KI Rajapakshe, PA Guerrero, BA Pedro, DN Sidiropoulos, PH Wu, VB Pagan, … show all 21 authorsA Forjaz, H Mojdeganlou, A Valentin, M Wetzel, D Lvovs, A Deshpande, SM Shin, S Piya, KI Rajapakshe, PA Guerrero, BA Pedro, DN Sidiropoulos, PH Wu, VB Pagan, Demystifying Pancreatic Cancer Therapies TeamLab, D Wirtz, EJ Fertig, LT Kagohara, WJ Ho, AL Kiemen, LD Wood
bioRxiv (2026)
doi

Intrinsic Gestational Timing Governs Human Cerebellar Development After Preterm Birth

G Sanidas, G Simonti, J Ghaemmaghami, K Woyshner, A Polyviou, R Vidva, C Lowe, A Vij, D Bittel, M Triantafyllou, N Wolff, R Cardenas, H Chen, F Almeida, S Sudhakar, K Mankad, I Koutroulis, … show all 22 authorsG Sanidas, G Simonti, J Ghaemmaghami, K Woyshner, A Polyviou, R Vidva, C Lowe, A Vij, D Bittel, M Triantafyllou, N Wolff, R Cardenas, H Chen, F Almeida, S Sudhakar, K Mankad, I Koutroulis, HS Pettersen, G Stein-O’Brien, DN Sidiropoulos, V Gallo, P Kratimenos
bioRxiv (2025)
doi

Prematurity insults remodel cerebellar development and behavior

G Sanidas, G Simonti, J Ghaemmaghami, K Woyshner, R Vidva, D Bittel, N Wolff, M Triantafyllou, A Polyviou, C Byrd, C Lowe, H Salisbury, E Goldstein, A Sathyanesan, I Koutroulis, G Stein-O’Brien, DN Sidiropoulos, V Gallo, P Kratimenos
bioRxiv (2025)
doi

PIVOT: an open-source tool for multi-omic spatial data registration

A Forjaz, VM Romero, I Reucroft, M Eminizer, D Kramer, D Higuera, H Mojdeganlou, PA Guerrero, J Min, M Wetzel, D Lvovs, A Valentin, SM Shin, X Yuan, RC Sears, K Chin, A Maitra, EJ Fertig, WJ Ho, … show all 24 authorsA Forjaz, VM Romero, I Reucroft, M Eminizer, D Kramer, D Higuera, H Mojdeganlou, PA Guerrero, J Min, M Wetzel, D Lvovs, A Valentin, SM Shin, X Yuan, RC Sears, K Chin, A Maitra, EJ Fertig, WJ Ho, LT Kagohara, LD Wood, D Wirtz, DN Sidiropoulos, AL Kiemen
bioRxiv (2025)
doi

Published

2026

Clinical, genomic, and spatial transcriptomic features of pancreatic adenosquamous carcinoma support subtype-specific therapeutic strategies

SD Haldar, M Wetzel, J Lu, JW Lee, H Sinan, CD Jakubowski, F Saj, D Pavlick, RP Graf, J Quintanilha, G Li, J Mitchell, JS Ross, A Maitra, M Javle, S Pant, H Wang, R Burkhart, DA Laheru, EM Jaffee, … show all 25 authorsSD Haldar, M Wetzel, J Lu, JW Lee, H Sinan, CD Jakubowski, F Saj, D Pavlick, RP Graf, J Quintanilha, G Li, J Mitchell, JS Ross, A Maitra, M Javle, S Pant, H Wang, R Burkhart, DA Laheru, EM Jaffee, EJ Fertig, ED Thompson, DN Sidiropoulos, LT Kagohara, NS Azad
Clinical Cancer Research
pubmeddoi

First-in-human testing of a mutant KRAS vaccine for pancreatic cancer interception in high-risk cohorts

SD Haldar, AL Huff, HH Wang, Z Zhu, M Berg, J Lu, N Sun, E Abou Diwan, H Sinan, CJ Thoburn, MZ Guo, T Yoshida, LC Chu, AK Ferguson, DN Sidiropoulos, LT Kagohara, WJ Ho, KM Bever, M Baretti, M Yarchoan, … show all 28 authorsSD Haldar, AL Huff, HH Wang, Z Zhu, M Berg, J Lu, N Sun, E Abou Diwan, H Sinan, CJ Thoburn, MZ Guo, T Yoshida, LC Chu, AK Ferguson, DN Sidiropoulos, LT Kagohara, WJ Ho, KM Bever, M Baretti, M Yarchoan, DA Laheru, JM Nauroth, AM Thomas, H Wang, NS Azad, MG Goggins, EM Jaffee, N Zaidi
Cancer Discovery
pubmeddoi

B Cells and Tertiary Lymphoid Structures as Integral Components of the Cancer Immunity Cycle

DN Sidiropoulos, WJ Ho
Cancer Immunology Research, 14(5): 716–717
pubmeddoi

The Seven Ps of Cancer Interception

DN Sidiropoulos, N Zaidi, M Yarchoan, EM Jaffee
Cancer Discovery, 16(4): 651–655
pubmeddoi

Cytometric atlas of combination immunotherapy in pancreatic cancer: blood-based signatures reveal vaccine and checkpoint inhibitor responses

DN Sidiropoulos, Z Zhang, JN Durham, S Charmsaz, NE Gross, JW Lee, Y Sun, S Perikala, JA Tandurella, D Lvovs, A Mitschang, G Lemson, SM Shin, AG Hernandez, S Mitchell, JM Leatherman, L Danilova, … show all 23 authorsDN Sidiropoulos, Z Zhang, JN Durham, S Charmsaz, NE Gross, JW Lee, Y Sun, S Perikala, JA Tandurella, D Lvovs, A Mitschang, G Lemson, SM Shin, AG Hernandez, S Mitchell, JM Leatherman, L Danilova, H Wang, EJ Fertig, EM Jaffee, KM Bever, DT Le, WJ Ho
Cancer Immunology Research, 14(3): 399–410
pubmeddoi

Mapping multipathology via spatial omic integration

R Palaganas, DN Sidiropoulos, M Morris, GL Stein-O’Brien
Current Opinion in Biotechnology, 97: 103398
pubmeddoi

2025

Neoadjuvant immunotherapy promotes the formation of mature tertiary lymphoid structures in a remodeled pancreatic tumor microenvironment

DN Sidiropoulos, SM Shin, M Wetzel, AA Girgis, D Bergman, L Danilova, S Perikala, D Shu, JM Montagne, A Deshpande, J Leatherman, L Dequiedt, V Jacobs, A Ogurtsova, G Mo, X Yuan, D Lvovs, … show all 29 authorsDN Sidiropoulos, SM Shin, M Wetzel, AA Girgis, D Bergman, L Danilova, S Perikala, D Shu, JM Montagne, A Deshpande, J Leatherman, L Dequiedt, V Jacobs, A Ogurtsova, G Mo, X Yuan, D Lvovs, G Stein-O’Brien, M Yarchoan, Q Zhu, EI Harper, AT Weeraratna, AL Kiemen, EM Jaffee, L Zheng, WJ Ho, RA Anders, EJ Fertig, LT Kagohara
Cancer Immunology Research, 13(11): 1716–1731
pubmeddoi

BIWT: a bioinformatics walkthrough for embedding spatial multiomics in agent-based models for virtual cells

DR Bergman, JAI Johnson, M Naji, M Booth, H Lima da Rocha, A Deshpande, DN Sidiropoulos, T Lopez-Vidal, R Heiland, LT Kagohara, RA Anders, L Zheng, EM Jaffee, G Stein-O’Brien, P Macklin, EJ Fertig
Bioinformatics, 41(11): btaf571
pubmeddoi

Entinostat in combination with nivolumab for patients with advanced cholangiocarcinoma: a phase 2 clinical trial

E Hallab, JN Durham, R Walker, L Cope, S Charmsaz, NE Gross, DN Sidiropoulos, A Hernandez, J Leatherman, S Mitchell, M Yarchoan, WJ Ho, NS Azad, M Baretti
Epigenetics Communications, 5(1): 6
doi

CD137 agonism enhances anti-PD1 induced activation of expanded CD8+ T cell clones in a neoadjuvant pancreatic cancer clinical trial

JM Montagne, JT Mitchell, JA Tandurella, ES Christenson, LV Danilova, A Deshpande, M Loth, DN Sidiropoulos, E Davis-Marcisak, DR Bergman, Q Zhu, H Wang, LT Kagohara, LL Engle, BF Green, AV Favorov, … show all 34 authorsJM Montagne, JT Mitchell, JA Tandurella, ES Christenson, LV Danilova, A Deshpande, M Loth, DN Sidiropoulos, E Davis-Marcisak, DR Bergman, Q Zhu, H Wang, LT Kagohara, LL Engle, BF Green, AV Favorov, WJ Ho, SJ Lim, R Zhang, P Li, J Gai, G Mo, S Mitchell, R Wang, A Vaghasia, W Hou, Y Xu, JW Zimmerman, JH Elisseeff, S Yegnasubramanian, RA Anders, EM Jaffee, L Zheng, EJ Fertig
iScience, 28(1)
pubmeddoi

2024

Entinostat in combination with nivolumab in metastatic pancreatic ductal adenocarcinoma: a phase 2 clinical trial

M Baretti, L Danilova, JN Durham, CB Betts, L Cope, DN Sidiropoulos, JA Tandurella, S Charmsaz, N Gross, A Hernandez, WJ Ho, C Thoburn, R Walker, J Leatherman, S Mitchell, B Christmas, A Saeed, … show all 24 authorsM Baretti, L Danilova, JN Durham, CB Betts, L Cope, DN Sidiropoulos, JA Tandurella, S Charmsaz, N Gross, A Hernandez, WJ Ho, C Thoburn, R Walker, J Leatherman, S Mitchell, B Christmas, A Saeed, DA Gaykalova, S Yegnasubramanian, EJ Fertig, LM Coussens, M Yarchoan, E Jaffee, NS Azad
Nature Communications, 15(1): 9801
pubmeddoi

Maturation of tertiary lymphoid structures

DH Shu, DN Sidiropoulos
Methods in Molecular Biology, 43–55
pubmeddoi

Immunotherapy response induces divergent tertiary lymphoid structure morphologies in hepatocellular carcinoma

DH Shu, WJ Ho, LT Kagohara, A Girgis, SM Shin, L Danilova, JW Lee, DN Sidiropoulos, S Mitchell, K Munjal, K Howe, KJ Bendinelli, E Kartalia, H Qi, G Mo, J Montagne, JM Leatherman, TY Lopez-Vidal, … show all 39 authorsDH Shu, WJ Ho, LT Kagohara, A Girgis, SM Shin, L Danilova, JW Lee, DN Sidiropoulos, S Mitchell, K Munjal, K Howe, KJ Bendinelli, E Kartalia, H Qi, G Mo, J Montagne, JM Leatherman, TY Lopez-Vidal, Q Zhu, AL Huff, X Yuan, A Hernandez, EM Coyne, N Zaidi, DJ Zabransky, LL Engle, A Ogurtsova, M Baretti, D Laheru, JN Durham, H Wang, JC Sunshine, RJ Johnston, JS Deutsch, JM Taube, RA Anders, EM Jaffee, EJ Fertig, M Yarchoan
Nature Immunology, 25(11): 2110–2123
pubmeddoi

PanIN and CAF transitions in pancreatic carcinogenesis revealed with spatial data integration

AT Bell, JT Mitchell, AL Kiemen, M Lyman, K Fujikura, JW Lee, E Coyne, SM Shin, S Nagaraj, A Deshpande, PH Wu, DN Sidiropoulos, R Erbe, J Stern, R Chan, S Williams, JM Chell, L Ciotti, JW Zimmerman, … show all 27 authorsAT Bell, JT Mitchell, AL Kiemen, M Lyman, K Fujikura, JW Lee, E Coyne, SM Shin, S Nagaraj, A Deshpande, PH Wu, DN Sidiropoulos, R Erbe, J Stern, R Chan, S Williams, JM Chell, L Ciotti, JW Zimmerman, D Wirtz, WJ Ho, N Zaidi, E Thompson, EM Jaffee, LD Wood, EJ Fertig, LT Kagohara
Cell Systems, 15(8): 753–769.e5
pubmeddoi

Phosphodiesterase-5 inhibition collaborates with vaccine-based immunotherapy to reprogram myeloid cells in pancreatic ductal adenocarcinoma

NE Gross, Z Zhang, JT Mitchell, S Charmsaz, AG Hernandez, EM Coyne, SM Shin, DC Vargas Carvajal, DN Sidiropoulos, Y Cho, G Mo, X Yuan, C Cannon, J Suresh Babu, MR Lyman, T Armstrong, LT Kagohara, KM Bever, DT Le, EM Jaffee, EJ Fertig, WJ Ho
JCI Insight, 9(18): e179292
pubmeddoi

Transfer learning reveals cancer-associated fibroblasts are associated with epithelial–mesenchymal transition and inflammation in cancer cells in pancreatic ductal adenocarcinoma

S Guinn, B Kinny-Köster, JA Tandurella, JT Mitchell, DN Sidiropoulos, M Loth, MR Lyman, AB Pucsek, DJ Zabransky, JW Lee, E Kartalia, M Ramani, TT Seppälä, C Cherry, R Suri, H Zlomke, J Patel, J He, … show all 34 authorsS Guinn, B Kinny-Köster, JA Tandurella, JT Mitchell, DN Sidiropoulos, M Loth, MR Lyman, AB Pucsek, DJ Zabransky, JW Lee, E Kartalia, M Ramani, TT Seppälä, C Cherry, R Suri, H Zlomke, J Patel, J He, CL Wolfgang, J Yu, L Zheng, DP Ryan, DT Ting, A Kimmelman, A Gupta, L Danilova, JH Elisseeff, LD Wood, G Stein-O'Brien, LT Kagohara, EM Jaffee, RA Burkhart, EJ Fertig, JW Zimmerman
Cancer Research, 84(9): 1517–1533
pubmeddoi

2023

Systems immunology spanning tumors, lymph nodes, and periphery

DN Sidiropoulos, WJ Ho, EM Jaffee, LT Kagohara, EJ Fertig
Cell Reports Methods, 3(12)
pubmeddoi

Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces

A Deshpande, M Loth, DN Sidiropoulos, S Zhang, L Yuan, AT Bell, Q Zhu, WJ Ho, C Santa-Maria, DM Gilkes, SR Williams, CR Uytingco, J Chew, A Hartnett, ZW Bent, AV Favorov, AS Popel, M Yarchoan, … show all 30 authorsA Deshpande, M Loth, DN Sidiropoulos, S Zhang, L Yuan, AT Bell, Q Zhu, WJ Ho, C Santa-Maria, DM Gilkes, SR Williams, CR Uytingco, J Chew, A Hartnett, ZW Bent, AV Favorov, AS Popel, M Yarchoan, A Kiemen, PH Wu, K Fujikura, D Wirtz, LD Wood, L Zheng, EM Jaffee, RA Anders, L Danilova, G Stein-O’Brien, LT Kagohara, EJ Fertig
Cell Systems, 14(4): 285–301.e4
pubmeddoi

2022

Integrated T cell cytometry metrics for immune-monitoring applications in immunotherapy clinical trials

DN Sidiropoulos, GL Stein-O’Brien, L Danilova, NE Gross, S Charmsaz, S Xavier, J Leatherman, H Wang, M Yarchoan, EM Jaffee, EJ Fertig, WJ Ho
JCI Insight, 7(19): e160398
pubmeddoi

Entinostat Decreases Immune Suppression to Promote Antitumor Responses in a HER2+ Breast Tumor Microenvironment

DN Sidiropoulos, CI Rafie, JK Jang, S Castanon, AG Baugh, E Gonzalez, BJ Christmas, VH Narumi, EF Davis-Marcisak, G Sharma, E Bigelow, A Vaghasia, A Gupta, A Skaist, M Considine, SJ Wheelan, … show all 26 authorsDN Sidiropoulos, CI Rafie, JK Jang, S Castanon, AG Baugh, E Gonzalez, BJ Christmas, VH Narumi, EF Davis-Marcisak, G Sharma, E Bigelow, A Vaghasia, A Gupta, A Skaist, M Considine, SJ Wheelan, SK Ganesan, M Yu, S Yegnasubramanian, V Stearns, RM Connolly, DA Gaykalova, LT Kagohara, EM Jaffee, EJ Fertig, ET Roussos Torres
Cancer Immunology Research, 10(5): 656–669
pubmeddoi

2020

Wild primate microbiomes prevent weight gain in germ-free mice

DN Sidiropoulos, GA Al-Ghalith, RR Shields-Cutler, TL Ward, AJ Johnson, P Vangay, D Knights, PC Kashyap, Y Xian, AE Ramer-Tait, JB Clayton
Animal Microbiome, 2(1): 16
pubmeddoi

2018

Fecal microbiota transplantation reverses antibiotic and chemotherapy-induced gut dysbiosis in mice

Q Le Bastard, T Ward, D Sidiropoulos, BM Hillmann, CL Chun, MJ Sadowsky, D Knights, E Montassier
Scientific Reports, 8(1): 6219
pubmeddoi