CAT: a conditional association test for microbiome data using a leave-out approach

Authors: Shi, Yushu, Zhang, Liangliang, Do, Kim-Anh, Jenq, Robert R., Peterson, Christine B.

Subject Terms: Statistics - Methodology

Access URL: http://arxiv.org/abs/2309.08109

survivalContour: Visualizing predicted survival via colored contour plots

Authors: Shi, Yushu, Zhang, Liangliang, Do, Kim-Anh, Jenq, Robert R., Peterson, Christine B.

Subject Terms: Statistics - Applications

Access URL: http://arxiv.org/abs/2308.13737

Antibiotic-induced loss of gut microbiome metabolic output correlates with clinical responses to CAR T-cell therapy

Authors: Prasad, Rishika ¹, Rehman, Abdur ², Rehman, Lubna ², Darbaniyan, Faezeh ², Blumenberg, Viktoria ^{3, 4, 5}, Schubert, Maria-Luisa ⁶, Mor, Uria ⁷, Zamir, Eli ⁸, Schmidt, Sabine ⁸, Hayase, Tomo ¹, Chang, Chia-Chi ¹, McDaniel, Lauren ¹, Flores, Ivonne ¹, Strati, Paolo ², Nair, Ranjit ², Chihara, Dai ², Fayad, Luis E. ², Ahmed, Sairah ², Iyer, Swaminathan P. ², Wang, Michael ², Jain, Preetesh ², Nastoupil, Loretta J. ², Westin, Jason ², Arora, Reetakshi ², Turner, Joel ⁹, Khawaja, Fareed ¹⁰, Wu, Ranran ¹¹, Dennison, Jennifer B. ¹¹, Menges, Meghan ⁹, Hidalgo-Vargas, Melanie ⁹, Reid, Kayla ⁹, Davila, Marco L. ¹², Dreger, Peter ⁶, Korell, Felix ⁶, Schmitt, Anita ⁶, Tanner, Mark R. ¹³, Champlin, Richard E. ¹³, Flowers, Christopher R. ², Shpall, Elizabeth J. ¹³, Hanash, Samir ¹¹, Neelapu, Sattva S. ², Schmitt, Michael ⁶, Subklewe, Marion ^{3, 4, 5}, Francois-Fahrmann, Johannes ¹¹, Stein-Thoeringer, C. K. ^{14, 15}, Elinav, Eran ^{7, 8}, Jain, Michael D. ⁹, Hayase, Eiko ¹, Jenq, Robert R. ^{1, 13}, Saini, Neeraj Y. ^{2, 13, ∗}

Source: In Blood 20 February 2025 145(8):823-839

Longitudinal analysis of gut microbiome and metabolome correlates of response and toxicity with idecabtagene vicleucel

Authors: Saha, Satabdi ¹, Rehman, Lubna ², Rehman, Abdur ², Darbaniyan, Faezeh ³, Weber, Donna M. ², Becnel, Melody ², Gaballa, Mahmoud ², Thomas, Sheeba K. ², Lee, Hans C. ², Chang, Chia-Chi ⁴, Arora, Reetakshi ², Menges, Meghan ⁵, Corallo, Sal ⁵, Davila, Marco L. ⁶, Locke, Frederick L. ⁵, Tanner, Mark R. ⁷, Neelapu, Sattva S. ², Shpall, Elizabeth J. ⁷, Flowers, Christopher R. ², Orlowski, Robert Z. ^{2, 8}, Jenq, Robert R. ^{4, 7}, Jain, Michael D. ⁵, Peterson, Christine ^{1, ∗}, Hansen, Doris K. ^{5, ∗∗}, Saini, Neeraj Y. ^{2, 7, ∗∗∗}, Patel, Krina K. ^{2, ∗∗∗∗}

Source: In Blood Advances March 2025

Review and revamp of compositional data transformation: A new framework combining proportion conversion and contrast transformation

Authors: Zhang, Yiqian ^{a, b}, Schluter, Jonas ^c, Zhang, Lijun ^a, Cao, Xuan ^d, Jenq, Robert R. ^e, Feng, Hao ^a, Haines, Jonathan ^a, Zhang, Liangliang ^{a, f, ⁎}

Source: In Computational and Structural Biotechnology Journal December 2024 23:4088-4107

Inflammation-induced epigenetic imprinting regulates intestinal stem cells

Authors: Zhao, Dongchang ¹, Ravikumar, Visweswaran ², Leach, Tyler J. ¹, Kraushaar, Daniel ¹, Lauder, Emma ^{1, 3}, Li, Lu ¹, Sun, Yaping ¹, Oravecz-Wilson, Katherine ³, Keller, Evan T. ⁴, Chen, Fengju ¹, Maneix, Laure ¹, Jenq, Robert R. ⁵, Britton, Robert ¹, King, Katherine Y. ¹, Santibanez, Ana E. ¹, Creighton, Chad J. ¹, Rao, Arvind ², Reddy, Pavan ^{1, 3, 6, ∗}

Source: In Cell Stem Cell 3 October 2024 31(10):1447-1464

Sparse tree-based clustering of microbiome data to characterize microbiome heterogeneity in pancreatic cancer

Authors: Shi, Yushu, Zhang, Liangliang, Do, Kim-Anh, Jenq, Robert, Peterson, Christine

Subject Terms: Statistics - Applications

Access URL: http://arxiv.org/abs/2007.15812

Third-party fecal microbiota transplantation for high-risk treatment-naïve acute GVHD of the lower GI tract

Authors: DeFilipp, Zachariah, Damania, Ashish V., Kim, Haesook T., Chang, Chia-Chi, El-Jawahri, Areej, McAfee, Steven L., Bottoms, AJ S., Toncheva, Vesselina, Smith, Melissa M., Dolaher, Maria, Perry, Lindsey, White, Meghan, Diana, Brittany, Connolly, Sheila, Dey, Bimalangshu R., Frigault, Matthew J., Newcomb, Richard A., O’Donnell, Paul V., Spitzer, Thomas R., Mansour, Michael K., Weber, Daniela, Ajami, Nadim J., Hohmann, Elizabeth, Jenq, Robert R., Chen, Yi-Bin

Source: In Blood Advances 14 May 2024 8(9):2074-2084

ProgPermute: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries

Authors: Zhang, Liangliang, Shi, Yushu, Do, Kim-Anh, Peterson, Christine B., Jenq, Robert R.

Subject Terms: Statistics - Methodology, Statistics - Applications

Access URL: http://arxiv.org/abs/2005.01169

aPCoA: Covariate Adjusted Principal Coordinates Analysis

Authors: Shi, Yushu, Zhang, Liangliang, Do, Kim-Anh, Peterson, Christine, Jenq, Robert

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2003.09544

Engineering T cells to suppress acute GVHD and leukemia relapse after allogeneic hematopoietic stem cell transplantation

Authors: Mo, Feiyan, Watanabe, Norihiro, Omdahl, Kayleigh I., Burkhardt, Phillip M., Ding, Xiaoyun, Hayase, Eiko, Panoskaltsis-Mortari, Angela, Jenq, Robert R., Heslop, Helen E., Kean, Leslie S., Brenner, Malcolm K., Tkachev, Victor, Mamonkin, Maksim

Source: In Blood 9 March 2023 141(10):1194-1208

Ambient oxygen levels regulate intestinal dysbiosis and GVHD severity after allogeneic stem cell transplantation

Authors: Seike, Keisuke, Kiledal, Anders, Fujiwara, Hideaki, Henig, Israel, Burgos da Silva, Marina, van den Brink, Marcel R.M., Hein, Robert, Hoostal, Matthew, Liu, Chen, Oravecz-Wilson, Katherine, Lauder, Emma, Li, Lu, Sun, Yaping, Schmidt, Thomas M., Shah, Yatrik M., Jenq, Robert R., Dick, Gregory, Reddy, Pavan

Source: In Immunity 14 February 2023 56(2):353-368

Mucus-degrading Bacteroides link carbapenems to aggravated graft-versus-host disease

Authors: Hayase, Eiko, Hayase, Tomo, Jamal, Mohamed A., Miyama, Takahiko, Chang, Chia-Chi, Ortega, Miriam R., Ahmed, Saira S., Karmouch, Jennifer L., Sanchez, Christopher A., Brown, Alexandria N., El-Himri, Rawan K., Flores, Ivonne I., McDaniel, Lauren K., Pham, Dung, Halsey, Taylor, Frenk, Annette C., Chapa, Valerie A., Heckel, Brooke E., Jin, Yimei, Tsai, Wen-Bin, Prasad, Rishika, Tan, Lin, Veillon, Lucas, Ajami, Nadim J., Wargo, Jennifer A., Galloway-Peña, Jessica, Shelburne, Samuel, Chemaly, Roy F., Davey, Lauren, Glowacki, Robert W.P., Liu, Chen, Rondon, Gabriela, Alousi, Amin M., Molldrem, Jeffrey J., Champlin, Richard E., Shpall, Elizabeth J., Valdivia, Raphael H., Martens, Eric C., Lorenzi, Philip L., Jenq, Robert R.

Source: In Cell 29 September 2022 185(20):3705-3719

Oncogenic collagen I homotrimers from cancer cells bind to α3β1 integrin and impact tumor microbiome and immunity to promote pancreatic cancer

Authors: Chen, Yang, Yang, Sujuan, Tavormina, Jena, Tampe, Desiree, Zeisberg, Michael, Wang, Huamin, Mahadevan, Krishnan K., Wu, Chang-Jiun, Sugimoto, Hikaru, Chang, Chia-Chi, Jenq, Robert R., McAndrews, Kathleen M., Kalluri, Raghu

Source: In Cancer Cell 8 August 2022 40(8):818-834

Dosing a synbiotic of human milk oligosaccharides and B. infantis leads to reversible engraftment in healthy adult microbiomes without antibiotics

Authors: Button, Julie E., Autran, Chloe A., Reens, Abigail L., Cosetta, Casey M., Smriga, Steven, Ericson, Megan, Pierce, Jessica V., Cook, David N., Lee, Martin L., Sun, Adam K., Alousi, Amin M., Koh, Andrew Y., Rechtman, David J., Jenq, Robert R., McKenzie, Gregory J.

Source: In Cell Host & Microbe 11 May 2022 30(5):712-725

Alloreactive T cells deficient of the short-chain fatty acid receptor GPR109A induce less graft-versus-host disease

Authors: Docampo, Melissa D., da Silva, Marina B., Lazrak, Amina, Nichols, Katherine B., Lieberman, Sophia R., Slingerland, Ann E., Armijo, Gabriel K., Shono, Yusuke, Nguyen, Chi, Monette, Sebastien, Dwomoh, Emmanuel, Lee, Nicole, Geary, Clair D., Perobelli, Suelen M., Smith, Melody, Markey, Kate A., Vardhana, Santosha A., Kousa, Anastasia I., Zamir, Eli, Greenfield, Itamar, Sun, Joseph C., Cross, Justin R., Peled, Jonathan U., Jenq, Robert R., Stein-Thoeringer, Christoph K. ^*, van den Brink, Marcel R.M. ^*

Source: In Blood 14 April 2022 139(15):2392-2405

Dietary fiber and gut bacteria shape infection susceptibility.

Authors: Mohammed, Aqsa¹ (AUTHOR), Jenq, Robert R¹ (AUTHOR) rrjenq@mdanderson.org

Source: Molecular Systems Biology. Jun2024, Vol. 20 Issue 6, p593-595. 3p.

Subject Terms: *DIETARY fiber, *GUT microbiome, *INFECTION, *BACTERIA

National Institutes of Health Consensus Development Project on Criteria for Clinical Trials in Chronic Graft-versus-Host Disease: IV. The 2020 Highly morbid forms report

Authors: Wolff, Daniel, Radojcic, Vedran, Lafyatis, Robert, Cinar, Resat, Rosenstein, Rachel K., Cowen, Edward W., Cheng, Guang-Shing, Sheshadri, Ajay, Bergeron, Anne, Williams, Kirsten M., Todd, Jamie L., Teshima, Takanori, Cuvelier, Geoffrey D.E., Holler, Ernst, McCurdy, Shannon R., Jenq, Robert R., Hanash, Alan M., Jacobsohn, David, Santomasso, Bianca D., Jain, Sandeep, Ogawa, Yoko, Steven, Philipp, Luo, Zhonghui Katie, Dietrich-Ntoukas, Tina, Saban, Daniel, Bilic, Ervina, Penack, Olaf, Griffith, Linda M., Cowden, Meredith, Martin, Paul J., Greinix, Hildegard T., Sarantopoulos, Stefanie, Socie, Gerard, Blazar, Bruce R., Pidala, Joseph, Kitko, Carrie L., Couriel, Daniel R., Cutler, Corey, Schultz, Kirk R., Pavletic, Steven Z., Lee, Stephanie J., Paczesny, Sophie

Source: In Transplantation and Cellular Therapy October 2021 27(10):817-835

Fecal microbiota diversity disruption and clinical outcomes after auto-HCT: a multicenter observational study

Authors: Khan, Niloufer, Lindner, Sarah, Gomes, Antonio L.C., Devlin, Sean M., Shah, Gunjan L., Sung, Anthony D., Sauter, Craig S., Landau, Heather J., Dahi, Parastoo B., Perales, Miguel-Angel, Chung, David J., Lesokhin, Alexander M., Dai, Anqi, Clurman, Annelie, Slingerland, John B., Slingerland, Ann E., Brereton, Daniel G., Giardina, Paul A., Maloy, Molly, Armijo, Gabriel K., Rondon-Clavo, Carlos, Fontana, Emily, Bohannon, Lauren, Ramalingam, Sendhilnathan, Bush, Amy T., Lew, Meagan V., Messina, Julia A., Littmann, Eric, Taur, Ying, Jenq, Robert R., Chao, Nelson J., Giralt, Sergio, Markey, Kate A., Pamer, Eric G., van den Brink, Marcel R.M. ^*, Peled, Jonathan U. ^{*, *}

Source: In Blood 18 March 2021 137(11):1527-1537

Refractory acute graft-versus-host disease: a new working definition beyond corticosteroid refractoriness

Authors: Mohty, Mohamad ^{1, 1}, Holler, Ernst ², Jagasia, Madan ³, Jenq, Robert ⁴, Malard, Florent ¹, Martin, Paul ^{5, 6}, Socié, Gérard ⁷, Zeiser, Robert ⁸

Source: In Blood 22 October 2020 136(17):1903-1906