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Making drugs from T cells: The quantitative pharmacology of engineered T cell therapeutics npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-03-18 Daniel C. Kirouac, Cole Zmurchok, Denise Morris
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A robust ultrasensitive transcriptional switch in noisy cellular environments npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-03-16 Eui Min Jeong, Jae Kyoung Kim
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GO2Sum: generating human-readable functional summary of proteins from GO terms npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-03-15 Swagarika Jaharlal Giri, Nabil Ibtehaz, Daisuke Kihara
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Detecting and understanding meaningful cancerous mutations based on computational models of mRNA splicing npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-03-07 Nicolas Lynn, Tamir Tuller
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Multivariate canonical correlation analysis identifies additional genetic variants for chronic kidney disease npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-03-09 Amy J. Osborne, Agnieszka Bierzynska, Elizabeth Colby, Uwe Andag, Philip A. Kalra, Olivier Radresa, Philipp Skroblin, Maarten W. Taal, Gavin I. Welsh, Moin A. Saleem, Colin Campbell
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Data-driven energy landscape reveals critical genes in cancer progression npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-03-08 Juntan Liu, Chunhe Li
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Morphological entropy encodes cellular migration strategies on multiple length scales npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-03-07 Yanping Liu, Yang Jiao, Qihui Fan, Xinwei Li, Zhichao Liu, Dui Qin, Jun Hu, Liyu Liu, Jianwei Shuai, Zhangyong Li
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Integration of graph neural networks and genome-scale metabolic models for predicting gene essentiality npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-03-06 Ramin Hasibi, Tom Michoel, Diego A. Oyarzún
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Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-03-02 Saurabh Singh, Sarika Yadav, Celine Cavallo, Durgesh Mourya, Ishu Singh, Vijay Kumar, Sachin Shukla, Pallavi Shukla, Romil Chaudhary, Gyan Prakash Maurya, Ronja Lea Jennifer Müller, Lilly Rohde, Aradhana Mishra, Olaf Wolkenhauer, Shailendra Gupta, Anurag Tripathi
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Do calcium channel blockers applied to cardiomyocytes cause increased channel expression resulting in reduced efficacy? npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-03-01 Karoline Horgmo Jæger, Verena Charwat, Samuel Wall, Kevin E. Healy, Aslak Tveito
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Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-02-28 Harshi Weerakoon, Ahmed Mohamed, Yide Wong, Jinjin Chen, Bhagya Senadheera, Oscar Haigh, Thomas S. Watkins, Stephen Kazakoff, Pamela Mukhopadhyay, Jason Mulvenna, John J. Miles, Michelle M. Hill, Ailin Lepletier
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Agent-based modeling of the prostate tumor microenvironment uncovers spatial tumor growth constraints and immunomodulatory properties npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-02-21 Maisa N. G. van Genderen, Jeroen Kneppers, Anniek Zaalberg, Elise M. Bekers, Andries M. Bergman, Wilbert Zwart, Federica Eduati
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Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-02-19 Kozo Nishida, Junichi Maruyama, Kazunari Kaizu, Koichi Takahashi, Katsuyuki Yugi
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Forum on immune digital twins: a meeting report npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-02-16 Reinhard Laubenbacher, Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luis L. Fonseca, James Glazier, Tomas Helikar, Marti Jett-Tilton, Denise Kirschner, Paul Macklin, Borna Mehrad, Beth Moore, Virginia Pasour, Ilya Shmulevich, Amber Smith, Isabel Voigt, Thomas E. Yankeelov, Tjalf Ziemssen
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Evaluation of single-sample network inference methods for precision oncology npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-02-15 Joke Deschildre, Boris Vandemoortele, Jens Uwe Loers, Katleen De Preter, Vanessa Vermeirssen
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MarkerMap: nonlinear marker selection for single-cell studies npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-02-14 Wilson Gregory, Nabeel Sarwar, George Kevrekidis, Soledad Villar, Bianca Dumitrascu
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Crop-GPA: an integrated platform of crop gene-phenotype associations npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-02-12 Yujia Gao, Qian Zhou, Jiaxin Luo, Chuan Xia, Youhua Zhang, Zhenyu Yue
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Mitigating non-genetic resistance to checkpoint inhibition based on multiple states of immune exhaustion npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-02-09 Irina Kareva, Jana L. Gevertz
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AutoTransOP: translating omics signatures without orthologue requirements using deep learning npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-01-29 Nikolaos Meimetis, Krista M. Pullen, Daniel Y. Zhu, Avlant Nilsson, Trong Nghia Hoang, Sara Magliacane, Douglas A. Lauffenburger
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An architecture for collaboration in systems biology at the age of the Metaverse npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-01-27 Eliott Jacopin, Yuki Sakamoto, Kozo Nishida, Kazunari Kaizu, Koichi Takahashi
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Large-scale computational modelling of the M1 and M2 synovial macrophages in rheumatoid arthritis npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-01-26 Naouel Zerrouk, Rachel Alcraft, Benjamin A. Hall, Franck Augé, Anna Niarakis
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“Digital twins elucidate critical role of Tscm in clinical persistence of TCR-engineered cell therapy” npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-01-26 Louis R. Joslyn, Weize Huang, Dale Miles, Iraj Hosseini, Saroja Ramanujan
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Measuring criticality in control of complex biological networks npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-01-20 Wataru Someya, Tatsuya Akutsu, Jean-Marc Schwartz, Jose C. Nacher
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Representation and quantification of module activity from omics data with rROMA npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-01-19 Matthieu Najm, Matthieu Cornet, Luca Albergante, Andrei Zinovyev, Isabelle Sermet-Gaudelus, Véronique Stoven, Laurence Calzone, Loredana Martignetti
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Ecological disruptive selection acting on quantitative loci can drive sympatric speciation npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-01-15 Pavithra Venkataraman, Supreet Saini
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GINv2.0: a comprehensive topological network integrating molecular interactions from multiple knowledge bases npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-01-13 Xiao Chang, Shen Yan, Yizheng Zhang, Yingchun Zhang, Luyang Li, Zhanyu Gao, Xuefei Lin, Xu Chi
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The antidepressive mechanism of Longya Lilium combined with Fluoxetine in mice with depression-like behaviors npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-01-13 Huina Ma, Hehua Huang, Chenyu Li, Shasha Li, Juefang Gan, Chunrong Lian, Yanwu Ling
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Minimally sufficient experimental design using identifiability analysis npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-01-06 Jana L. Gevertz, Irina Kareva
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Epigenetic OCT4 regulatory network: stochastic analysis of cellular reprogramming npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-01-06 Simone Bruno, Thorsten M. Schlaeger, Domitilla Del Vecchio
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Exploring chronic and transient tumor hypoxia for predicting the efficacy of hypoxia-activated pro-drugs npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2024-01-05 Shreya Mathur, Shannon Chen, Katarzyna A. Rejniak
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Asking the right questions for mutagenicity prediction from BioMedical text npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-12-18 Sathwik Acharya, Nicolas K. Shinada, Naoki Koyama, Megumi Ikemori, Tomoki Nishioka, Seiji Hitaoka, Atsushi Hakura, Shoji Asakura, Yukiko Matsuoka, Sucheendra K. Palaniappan
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Transcriptional profiling upon T cell stimulation reveals down-regulation of inflammatory pathways in T and B cells in SLE versus Sjögren’s syndrome npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-12-15 Gino Kwon, Annika Wiedemann, Lisa M. Steinheuer, Ana-Luisa Stefanski, Franziska Szelinski, Tomas Racek, Andreas Philipp Frei, Klas Hatje, Tony Kam-Thong, David Schubert, Thomas Schindler, Thomas Dörner, Kevin Thurley
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Mesenchymal ovarian cancer cells promote CD8+ T cell exhaustion through the LGALS3-LAG3 axis npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-12-12 Edward Yakubovich, David P. Cook, Galaxia M. Rodriguez, Barbara C. Vanderhyden
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Harnessing synthetic biology for advancing RNA therapeutics and vaccine design npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-11-30 Blaine A. Pfeifer, Marie Beitelshees, Andrew Hill, Justin Bassett, Charles H. Jones
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Few-shot prediction of amyloid β accumulation from mainly unpaired data on biomarker candidates npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-11-23 Yuichiro Yada, Honda Naoki
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Explainable deep learning for tumor dynamic modeling and overall survival prediction using Neural-ODE npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-11-18 Mark Laurie, James Lu
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Modulating the dynamics of NFκB and PI3K enhances the ensemble-level TNFR1 signaling mediated apoptotic response npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-11-16 Shubhank Sherekar, Chaitra S. Todankar, Ganesh A. Viswanathan
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An integrated study to decipher immunosuppressive cellular communication in the PDAC environment npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-11-10 Gülben AVŞAR, Pınar PİR
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Data-driven structural analysis of small cell lung cancer transcription factor network suggests potential subtype regulators and transition pathways npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-10-31 Mustafa Ozen, Carlos F. Lopez
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PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-10-30 Miguel Ponce-de-Leon, Arnau Montagud, Vincent Noël, Annika Meert, Gerard Pradas, Emmanuel Barillot, Laurence Calzone, Alfonso Valencia
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‘Social’ versus ‘asocial’ cells—dynamic competition flux balance analysis npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-10-28 Yanhua Liu, Hans V. Westerhoff
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The modular biochemical reaction network structure of cellular translation npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-10-26 Bruno Cuevas-Zuviría, Evrim Fer, Zachary R. Adam, Betül Kaçar
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Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-10-19 Daniel Kim, Andy Tran, Hani Jieun Kim, Yingxin Lin, Jean Yee Hwa Yang, Pengyi Yang
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Reliable interpretability of biology-inspired deep neural networks npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-10-10 Wolfgang Esser-Skala, Nikolaus Fortelny
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Proteomic meta-study harmonization, mechanotyping and drug repurposing candidate prediction with ProHarMeD npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-10-10 Klaudia Adamowicz, Lis Arend, Andreas Maier, Johannes R. Schmidt, Bernhard Kuster, Olga Tsoy, Olga Zolotareva, Jan Baumbach, Tanja Laske
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Understanding and leveraging phenotypic plasticity during metastasis formation npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-10-06 Saumil Shah, Lisa-Marie Philipp, Stefano Giaimo, Susanne Sebens, Arne Traulsen, Michael Raatz
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Optimal energy and redox metabolism in the cyanobacterium Synechocystis sp. PCC 6803 npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-09-22 Amit Kugler, Karin Stensjö
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BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-09-22 John Wu, William C. L. Stewart, Ciriyam Jayaprakash, Jayajit Das
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Experiment-based computational model predicts that IL-6 classic and trans-signaling exhibit similar potency in inducing downstream signaling in endothelial cells npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-09-21 Min Song, Youli Wang, Brian H. Annex, Aleksander S. Popel
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Self-reproduction and doubling time limits of different cellular subsystems npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-09-20 Kristo Abner, Peter Šverns, Janar Arold, Indrek Morell, Taivo Lints, Sander Medri, Andrus Seiman, Kaarel Adamberg, Raivo Vilu
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Topological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-09-14 Dhananjay Bhaskar, William Y. Zhang, Alexandria Volkening, Björn Sandstede, Ian Y. Wong
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Metabolomics and transcriptomics based multi-omics integration reveals radiation-induced altered pathway networking and underlying mechanism npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-09-09 Kiran Maan, Ruchi Baghel, Seema Dhariwal, Apoorva Sharma, Radhika Bakhshi, Poonam Rana
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Potential value of high-throughput single-cell DNA sequencing of Juvenile myelomonocytic leukemia: report of two cases npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-09-09 E. V. Volchkov, A. A. Khozyainova, M. Kh. Gurzhikhanova, I. V. Larionova, V. E. Matveev, D. A. Evseev, A. K. Ignatova, M. E. Menyailo, D. A. Venyov, R. S. Vorobev, A. A. Semchenkova, Yu. V. Olshanskaya, E. V. Denisov, M. A. Maschan
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Quantitative systems-based prediction of antimicrobial resistance evolution npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-09-07 Daniel A. Charlebois
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Amplitude response and singularity behavior of circadian clock to external stimuli npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-08-12 Tao Zhang, Yu Liu, Ling Yang
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Extending the landscape of omics technologies by pathomics npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-08-07 Roman D. Bülow, David L. Hölscher, Ivan G. Costa, Peter Boor
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Knowledge-based mechanistic modeling accurately predicts disease progression with gefitinib in EGFR-mutant lung adenocarcinoma npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-07-31 Adèle L’Hostis, Jean-Louis Palgen, Angélique Perrillat-Mercerot, Emmanuel Peyronnet, Evgueni Jacob, James Bosley, Michaël Duruisseaux, Raphaël Toueg, Lucile Lefèvre, Riad Kahoul, Nicoletta Ceres, Claudio Monteiro
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A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-07-31 Geena V. Ildefonso, Stacey D. Finley
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Growth exponents reflect evolutionary processes and treatment response in brain metastases npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-07-21 Beatriz Ocaña-Tienda, Julián Pérez-Beteta, Juan Jiménez-Sánchez, David Molina-García, Ana Ortiz de Mendivil, Beatriz Asenjo, David Albillo, Luis A. Pérez-Romasanta, Manuel Valiente, Lucía Zhu, Pedro García-Gómez, Elisabet González-Del Portillo, Manuel Llorente, Natalia Carballo, Estanislao Arana, Víctor M. Pérez-García
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Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling npj Syst. Biol. Appl. (IF 4.0) Pub Date : 2023-07-17 A. Leung, P. Rangamani