SciFive: a text-to-text transformer model for biomedical literature

Authors: Phan, Long N., Anibal, James T., Tran, Hieu, Chanana, Shaurya, Bahadroglu, Erol, Peltekian, Alec, Altan-Bonnet, Grégoire

Subject Terms: Computer Science - Computation and Language, Computer Science - Artificial Intelligence, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2106.03598

Manufacture of CD22 CAR T cells following positive versus negative selection results in distinct cytokine secretion profiles and γδ T cell output

Authors: Song, Hannah W., Benzaoui, Mehdi, Dwivedi, Alka, Underwood, Sarah, Shao, Lipei, Achar, Sooraj, Posarac, Vesna, Remley, Victoria A., Prochazkova, Michaela, Cai, Yihua, Jin, Ping, Somerville, Robert P., Stroncek, David F., Altan-Bonnet, Grégoire, Shah, Nirali N., Chien, Christopher D., Taylor, Naomi, Highfill, Steven L.

Source: In Molecular Therapy - Methods & Clinical Development 14 March 2024 32(1)

Quantitative Immunology for Physicists

Authors: Altan-Bonnet, Grégoire, Mora, Thierry, Walczak, Aleksandra M.

Source: Physics Reports 849, 1--83 (2020)

Subject Terms: Quantitative Biology - Quantitative Methods, Quantitative Biology - Genomics, Quantitative Biology - Molecular Networks, Quantitative Biology - Subcellular Processes

Access URL: http://arxiv.org/abs/1907.03891

A stem cell epigenome is associated with primary nonresponse to CD19 CAR T cells in pediatric acute lymphoblastic leukemia

Authors: Masih, Katherine E., Gardner, Rebecca A., Chou, Hsien-Chao, Abdelmaksoud, Abdalla, Song, Young K., Mariani, Luca, Gangalapudi, Vineela, Gryder, Berkley E., Wilson, Ashley L., Adebola, Serifat O., Stanton, Benjamin Z., Wang, Chaoyu, Milewski, David, Kim, Yong Yean, Tian, Meijie, Cheuk, Adam Tai-Chi, Wen, Xinyu, Zhang, Yue, Altan-Bonnet, Grégoire, Kelly, Michael C., Wei, Jun S., Bulyk, Martha L., Jensen, Michael C., Orentas, Rimas J., Khan, Javed

Source: In Blood Advances 8 August 2023 7(15):4218-4232

Biochemical feedback and its application to immune cells II: dynamics and critical slowing down

Authors: Byrd, Tommy A., Erez, Amir, Vogel, Robert M., Peterson, Curtis, Vennettilli, Michael, Altan-Bonnet, Grégoire, Mugler, Andrew

Source: Phys. Rev. E 100, 022415 (2019)

Subject Terms: Physics - Biological Physics, Condensed Matter - Statistical Mechanics, Quantitative Biology - Molecular Networks

Access URL: http://arxiv.org/abs/1902.02444

CD19/22 CAR T cells in children and young adults with B-ALL: phase 1 results and development of a novel bicistronic CAR

Authors: Shalabi, Haneen, Qin, Haiying, Su, Angela, Yates, Bonnie, Wolters, Pamela L., Steinberg, Seth M., Ligon, John A., Silbert, Sara, DéDé, Kniya, Benzaoui, Mehdi, Goldberg, Sophia, Achar, Sooraj, Schneider, Dina, Shahani, Shilpa A., Little, Lauren, Foley, Toni, Molina, John C., Panch, Sandhya, Mackall, Crystal L., Lee, Daniel W., Chien, Christopher D., Pouzolles, Marie, Ahlman, Mark, Yuan, Constance M., Wang, Hao-Wei, Wang, Yanyu, Inglefield, Jon, Toledo-Tamula, Mary Anne, Martin, Staci, Highfill, Steven L., Altan-Bonnet, Gregoire, Stroncek, David, Fry, Terry J., Taylor, Naomi, Shah, Nirali N.

Source: Blood. 140(5):451-463

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100183235785.0x000001&indx=1&recIds=ETOCvdc_100183235785.0x000001

Universality of biochemical feedback and its application to immune cells

Authors: Erez, Amir, Byrd, Tommy A., Vogel, Robert M., Altan-Bonnet, Grégoire, Mugler, Andrew

Source: Phys. Rev. E 99, 022422 (2019)

Subject Terms: Physics - Biological Physics, Quantitative Biology - Molecular Networks

Access URL: http://arxiv.org/abs/1703.04194

A local regulatory T cell feedback circuit maintains immune homeostasis by pruning self-activated T cells

Authors: Wong, Harikesh S., Park, Kyemyung, Gola, Anita, Baptista, Antonio P., Miller, Christine H., Deep, Deeksha, Lou, Meng, Boyd, Lisa F., Rudensky, Alexander Y., Savage, Peter A., Altan-Bonnet, Grégoire, Tsang, John S., Germain, Ronald N.

Source: In Cell 22 July 2021 184(15):3981-3997

The case for absolute ligand discrimination : modeling information processing and decision by immune T cells

Authors: François, Paul, Altan-Bonnet, Grégoire

Subject Terms: Quantitative Biology - Cell Behavior, Quantitative Biology - Molecular Networks

Access URL: http://arxiv.org/abs/1505.03095

β-Coronaviruses Use Lysosomes for Egress Instead of the Biosynthetic Secretory Pathway

Authors: Ghosh, Sourish, Dellibovi-Ragheb, Teegan A., Kerviel, Adeline, Pak, Eowyn, Qiu, Qi, Fisher, Matthew, Takvorian, Peter M., Bleck, Christopher, Hsu, Victor W., Fehr, Anthony R., Perlman, Stanley, Achar, Sooraj R., Straus, Marco R., Whittaker, Gary R., de Haan, Cornelis A.M., Kehrl, John, Altan-Bonnet, Grégoire, Altan-Bonnet, Nihal

Source: In Cell 10 December 2020 183(6):1520-1535

Inducible nitric oxide synthase-derived extracellular nitric oxide flux regulates proinflammatory responses at the single cell level

Authors: Somasundaram, Veena, Gilmore, Anne C., Basudhar, Debashree, Palmieri, Erika Mariana, Scheiblin, David A., Heinz, William F., Cheng, Robert.Y.S., Ridnour, Lisa A., Altan-Bonnet, Grégoire, Lockett, Stephen J., McVicar, Daniel W., Wink, David A.

Source: In Redox Biology January 2020 28

Constitutive Activation of the B Cell Receptor Underlies Dysfunctional Signaling in Chronic Lymphocytic Leukemia

Authors: Ziegler, Carly G.K., Kim, Joel, Piersanti, Kelly, Oyler-Yaniv, Alon, Argyropoulos, Kimon V., van den Brink, Marcel R.M., Palomba, M. Lia, Altan-Bonnet, Nihal, Altan-Bonnet, Grégoire

Source: In Cell Reports 23 July 2019 28(4):923-937

Discerning Aggregation in Homogeneous Ensembles: A General Description of Photon Counting Spectroscopy in Diffusing Systems

Authors: Ren, Hai-cang, Goddard, Noel L., Altan-Bonnet, Gregoire, Libchaber, Albert

Subject Terms: Physics - Biological Physics, Condensed Matter - Soft Condensed Matter

Access URL: http://arxiv.org/abs/physics/0404093

Catch and Release of Cytokines Mediated by Tumor Phosphatidylserine Converts Transient Exposure into Long-Lived Inflammation

Authors: Oyler-Yaniv, Jennifer, Oyler-Yaniv, Alon, Shakiba, Mojdeh, Min, Nina K., Chen, Ying-Han, Cheng, Sheue-yann, Krichevsky, Oleg, Altan-Bonnet, Nihal, Altan-Bonnet, Grégoire

Source: In Molecular Cell 1 June 2017 66(5):635-647

A Tunable Diffusion-Consumption Mechanism of Cytokine Propagation Enables Plasticity in Cell-to-Cell Communication in the Immune System

Authors: Oyler-Yaniv, Alon, Oyler-Yaniv, Jennifer, Whitlock, Benjamin M., Liu, Zhiduo, Germain, Ronald N., Huse, Morgan, Altan-Bonnet, Grégoire, Krichevsky, Oleg

Source: In Immunity 18 April 2017 46(4):609-620

Clonal Abundance of Tumor-Specific CD4+ T Cells Potentiates Efficacy and Alters Susceptibility to Exhaustion

Authors: Malandro, Nicole, Budhu, Sadna, Kuhn, Nicholas F., Liu, Cailian, Murphy, Judith T., Cortez, Czrina, Zhong, Hong, Yang, Xia, Rizzuto, Gabrielle, Altan-Bonnet, Grégoire, Merghoub, Taha, Wolchok, Jedd D.

Source: In Immunity 19 January 2016 44(1):179-193

T Cells Integrate Local and Global Cues to Discriminate between Structurally Similar Antigens

Authors: Voisinne, Guillaume, Nixon, Briana G., Melbinger, Anna, Gasteiger, Georg, Vergassola, Massimo, Altan-Bonnet, Grégoire

Source: In Cell Reports 26 May 2015 11(8):1208-1219

EGFR and PDGFRA co-expression and heterodimerization in glioblastoma tumor sphere lines

Authors: Chakravarty, Debyani, Pedraza, Alicia, Cotari, Jesse, Liu, Angela, Punko, Diana, Kokroo, Aushim, Huse, Jason, Altan-Bonnet, Gregoire, Brennan, Cameron

Source: Scientific reports. 7(1):1-10

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100175688044.0x000001&indx=1&recIds=ETOCvdc_100175688044.0x000001

Phosphatidylserine Vesicles Enable Efficient En Bloc Transmission of Enteroviruses

Authors: Chen, Ying-Han, Du, WenLi, Hagemeijer, Marne C., Takvorian, Peter M., Pau, Cyrilla, Cali, Ann, Brantner, Christine A., Stempinski, Erin S., Connelly, Patricia S., Ma, Hsin-Chieh, Jiang, Ping, Wimmer, Eckard, Altan-Bonnet, Grégoire, Altan-Bonnet, Nihal

Source: In Cell 12 February 2015 160(4):619-630

Diversity training for signal transduction: leveraging cell-to-cell variability to dissect cellular signaling, differentiation and death

Authors: Cotari, Jesse W, Voisinne, Guillaume, Altan-Bonnet, Grégoire

Source: In Current Opinion in Biotechnology August 2013 24(4):760-766