Metabolic modeling of single Th17 cells reveals regulators of autoimmunity

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106

Trimmomatic: a flexible trimmer for Illumina sequence data

Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548

Fast gapped-read alignment with Bowtie 2

Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625

limma powers differential expression analyses for RNA-sequencing and microarray studies

Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv007 · Cited by 40,458

Model-based Analysis of ChIP-Seq (MACS)

Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386

Near-optimal probabilistic RNA-seq quantification

Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016) · Nature Biotechnology · doi:10.1038/nbt.3519 · Cited by 9,723

KEGG: new perspectives on genomes, pathways, diseases and drugs

Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y., & Morishima, K. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1092 · Cited by 8,865

Spatial reconstruction of single-cell gene expression data

Satija, R., Farrell, J. A., Gennert, D., Schier, A. F., & Regev, A. (2015) · Nature Biotechnology · doi:10.1038/nbt.3192 · Cited by 7,055

Reciprocal developmental pathways for the generation of pathogenic effector TH17 and regulatory T cells

Bettelli, E., Carrier, Y., Gao, W., Korn, T., Strom, T. B., Oukka, M., Weiner, H. L., & Kuchroo, V. K. (2006) · Nature · doi:10.1038/nature04753 · Cited by 6,992

Adaptive immunity and metabolism

Verbist, K., Sharma, P., Beere, H. M., & Green, D. R. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-15447-8.00008-8 · Cited by 1

Computational modeling of metabolism in oncology

Fong, L. E., Jin, M., Kharbanda, S., Creixell, M., Wu, X., Zhang, D., Dubrot, J., Yates, K. B., Manguso, R. T., Kaufmann-Malaga, B., et al. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-15447-8.00005-2 · Cited by 1

A gene-expression module identifies circulating immune cells with enhanced recruitment to sites of inflammation

Debajyoti, S., Laurent, T., Broquet, A. H., Fourgeux, C., Letellier, T., Tilly, G., Bruneau, S., Ville, S., Bouchet‐Delbos, L., Brancherau, J., et al. (2025) · iScience · doi:10.1016/j.isci.2025.114227 · Cited by 1

Understanding the Role and Prognostic Significance of Prostaglandin D2 Signaling in Lung Adenocarcinoma

Ferreira, L., Cunha, A., Lopes, R., Azevedo, B., & Rocha, M. (2022) · Specialty journal of Pharmacognosy Phytochemistry and Biotechnology · doi:10.51847/ukpc3yl5ui · Cited by 1

TNF alpha unmasks enteric malate aspartate shuttle dysfunction bridging Parkinson disease and intestinal inflammation

Ghirotto, B., Gonçalves, L. E., Ruder, V., James, C., Gerasimova, E. M., Rizo, T., Wend, H., Farrell, M., Gerez, J., Prymaczok, N. C., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-71317-y · Cited by 2

2-DG Re-Normalized IFN-γ Production in T Cells Excluding TEMRA Cells from Patients with Aplastic Anemia

Zhang, Y., Zhang, Y., Li, X., Chen, X., Zhang, Y., Liu, X., Wu, S., Li, Y., & Li, B. (2023) · Immunological Investigations · doi:10.1080/08820139.2023.2195436 · Cited by 1

PhyloVision : Interactive Software for Integrated Analysis of Single-Cell Transcriptomic and Phylogenetic DataPreprint

Jones, M. G., Rosen, Y., & Yosef, N. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.13.460142 · Cited by 1

Characterizing metabolism from bulk and single-cell RNA-seq data using METAFluxPreprint

Huang, Y., Mohanty, V., Dede, M., Daher, M., Li, L., Rezvani, K., & Chen, K. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.18.492580 · Cited by 1

Alternative paths to immune activation: the role of costimulatory risk genes for polygenic inflammatory disease in T helper cellsPreprint

Voda, A.-I., Correa, K., Hamp, J., Moscrop, C., Dustin, M. L., & Jostins-Dean, L. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.23.517727 · Cited by 1

Identification of novel myeloid-derived cell states with implication in cancer outcomePreprint

Guimarães, G. R., Maklouf, G. R., Teixeira, C. E., Santos, L. D. O., Tessarollo, N. G., Pretti, M. A. M., de Toledo, N. E., da Cruz, J. G. V., Falchetti, M., Dimas, M. M., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.01.04.522727 · Cited by 1

CellHeap: A scRNA-seq workflow for large-scale bioinformatics data analysisPreprint

Castro, M. C., Silva, V. S., Costa, M. D. O. C. E., Silva, H. S. I. L., Walter, M. E. M. T., de Melo, A. C. M. A., Ocaña, K., dos Santos, M. T., Nicolas, M. F., Carvalho, A. C. C., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.04.19.537508 · Cited by 1

FABP7 Progenitors are a Targetable Metabolic Root in the BRCA1 BreastPreprint

McCloskey, C. W., Zhang, B., Waas, M., Abazari, G., Vyas, F., Aliar, K., Tharmapalan, P., Kuttanamkuzhi, A., Narala, S., Cruikshank, J., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.02.565360 · Cited by 1

Metabolic shift to serine pathway induced by lipids confers oncogenic properties in non-transformed breast cellsPreprint

Eduardo, M. B., Cottone, G., McCloskey, C. W., Liu, S., Zappia, M. P., Benevolenskaya, E. V., Islam, A. B. M. M. K., Frolov, M. V., Palma, F. R., Gao, P., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.21.581404 · Cited by 1

BLOC1S1 control of vacuolar organelle fidelity modulates T H 2 cell immunity and allergy susceptibilityPreprint

Sharma, R., Wu, K., Han, K., Russo, A. C., Dagur, P. K., Combs, C. A., & Sack, M. N. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.21.586144 · Cited by 1

A dominant role of TGFβ in regulating T-cell size and physiologyPreprint

Eizenberg-Magar, I., Rimer, J., Miller, S., Elyahu, Y., Mark, M., Porat, Z., Reich-Zeliger, S., Monsonego, A., Antebi, Y. E., & Friedman, N. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.02.597009 · Cited by 1

The glycolytic reaction PGAM unexpectedly restrains Th17 pathogenicity and Th17-dependent autoimmunityPreprint

Wang, C., Wagner, A., Fessler, J., DeTomaso, D., Zaghouani, S., Zhou, Y., Pierce, K. A., Sobel, R. A., Clish, C. B., Yosef, N., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.18.607992 · Cited by 1

Yeast-MetaTwin for Systematically Exploring Yeast Metabolism through Retrobiosynthesis and Deep LearningPreprint

Wu, K., Liu, H., Sun, M., Mao, R., Jiang, Y., Kerkhoven, E. J., Chen, Y., Nielsen, J., & Li, F. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.02.610684 · Cited by 1

Secreted phospholipase PLA2G12A-driven lysophospholipid signaling via lipolytic modification of extracellular vesicles facilitates pathogenic Th17 differentiationPreprint

Mochizuki, C., Taketomi, Y., Irie, A., Kano, K., Nagasaki, Y., Miki, Y., Ono, T., Nishito, Y., Nakajima, T., Tomabechi, Y., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.27.620543 · Cited by 1

S100a4+ alveolar macrophages accelerate the progression of precancerous atypical adenomatous hyperplasia by promoting fatty acid metabolismPreprint

Huang, H., Yang, Y., Zhang, Q., Yang, Y., Xiong, Z., Mao, S., Song, T., Wang, Y., Liu, Z., Bu, H., et al. (2024) · eLife · doi:10.7554/elife.101731.1 · Cited by 1

CD38 expression by neonatal human naïve CD4 + T cells shapes their distinct metabolic state and tolerogenic potentialPreprint

Dwyer, L. R., DeRogatis, A. M., Clancy, S., Gouirand, V., Chien, C., Rogers, E. E., Oltman, S. P., Jelliffe‐Pawlowski, L. L., Lynch, S. V., Rutishauser, R. L., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.02.631038 · Cited by 1

Reconstituting Mouse Embryogenesis Ex Utero from Gastrulation to Fetal Development Reveals Maternally Independent Metabolic ProgramsPreprint

Lokshtanov, D., Gao, S. M., Xu, W., Kosman, A., Roncato, F., Cruz, N. D. L., Khan, N. A., Woods, A., Campbell, I. J., Woehler, A., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.17.710314 · Cited by 1

Impaired Lipoprotein Secretion by APOE4 Leads to Lysosomal and Mitochondrial Dysfunction in Human MicrogliaPreprint

Revanna, J. S., Wessendorf-Rodriguez, K. A., Xiao, Q., Sabedot, T. S., Cuoco, M. S., Sarkar, S., Zhou-Yang, L., Lim, C. K., Prozapas, V. N., Wooldridge, R., et al. (2026) · SSRN Electronic Journal · doi:10.64898/2026.05.12.724612 · Cited by 2

PhyloVision: Interactive Software for Integrated Analysis of Single-Cell Transcriptomic and Phylogenetic DataPreprint

Jones, M. G., Rosen, Y., & Yosef, N. (2021) · SSRN Electronic Journal · doi:10.2139/ssrn.3951492

"El milagro de la palmera" o Calahorra y Ciudadano Kane.

Adán, M. A. S. F. (2007) · Dialnet (Universidad de la Rioja)

γ-aminobutyrate (GAB) functions as a bioenergetic and signaling gatekeeper to control T cell inflammationPreprint

Kang, S., Liu, L., Wang, T., Cannon, M. V., Lin, P., Fan, T. W. ‐., Scott, D. A., Wu, H.-J. J., Lane, A. N., & Wang, R. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.17.480926

Helicobacter chronic stage inflammation undergoes fluctuations that are altered in tlpA mutantsPreprint

Johnson, K. S., Yang, C., Carter, J. E., Worthington, A. K., Robinson, E. K., Lopez-Magaña, R., Salgado, F., Arnold, I. C., & Ottemann, K. M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.01.502425

Advances in Tumor Microenvironment Immune Profiling

Blake, M. K., O’Connell, P. M., & Aldhamen, Y. A. (2022) · Springer eBooks · doi:10.1007/978-3-030-80962-1_85-1

A multiomics approach to understanding pathology of Combined D,L-2- Hydroxyglutaric Aciduria and phenylbutyrate as potential treatmentPreprint

Phua, Y. L., D’Annibale, O., Karunanidhi, A., Mohsen, A.-W. A., Kirmse, B., Dobrowolski, S. F., & Vockley, J. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.02.02.526527

Androgen Signaling Restricts Glutaminolysis to Drive Sex-Specific Th17 MetabolismPreprint

Chowdhury, N. U., Cephus, J.-Y., Madden, M. Z., Wolf, M. M., Chi, C., Sugiura, A., Stier, M. T., Voss, K., Ye, X., Kuehnle, S. N., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.02.10.527741

Systems biology and real-world data as drivers of change in drug research and development

Sivananthan, A. (2023) · Medical Writing · doi:10.56012/awvf3242

Data from Mitochondria Transfer from Mesenchymal Stem Cells Confers Chemoresistance to Glioblastoma Stem Cells through Metabolic Rewiring

Nakhle, J., Khattar, K., Özkan, T., Boughlita, A., Moussa, D. A., Darlix, A., Lorcy, F., Rigau, V., Bauchet, L., Gerbal‐Chaloin, S., et al. (2023) · doi:10.1158/2767-9764.c.6664816

Data from Mitochondria transfer from mesenchymal stem cells confers chemoresistance to Glioblastoma stem cells through metabolic rewiring

Nakhle, J., Khattar, K., Özkan, T., Boughlita, A., Moussa, D. A., Darlix, A., Lorcy, F., Rigau, V., Bauchet, L., Gerbal‐Chaloin, S., et al. (2023) · doi:10.1158/2767-9764.c.6664816.v1

Flux estimation analysis systematically characterizes the metabolic shifts of the central metabolism pathway in human cancer

Yang, G. M., Huang, S., Hu, K., Lu, A. Z., Yang, J., Meroueh, N., Dang, P., Wang, Y., Zhu, H., Cao, S., et al. (2023) · Frontiers in Oncology · doi:10.3389/fonc.2023.1117810

Alternative paths to immune activation: the role of costimulatory risk genes for polygenic inflammatory disease in T helper cellsPreprint

Voda, A.-I., Correa, K., Hamp, J., Moscrop, C., Dustin, M. L., & Jostins-Dean, L. (2023) · doi:10.7554/elife.86891.1

Alternative paths to immune activation: the role of costimulatory risk genes for polygenic inflammatory disease in T helper cellsPreprint

Voda, A.-I., Correa, K., Hamp, J., Moscrop, C., Dustin, M. L., & Jostins-Dean, L. (2023) · doi:10.7554/elife.86891

A via de sinalização de STING limita o potencial patogênico de células TH17

Damasceno, L. E. A. (2023) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.17.2023.tde-30062023-093518

1284 Computational approaches for metabolic target discovery in immuno-oncology

Fong, L. E., Jin, M., Kharbanda, S., Wu, X., Creixell, M., Kaufmann-Malaga, B., & Powell, J. D. (2023) · Regular and Young Investigator Award Abstracts · doi:10.1136/jitc-2023-sitc2023.1284

Calibrated Identification of Feature Dependencies in Single-cell MultiomicsPreprint

Boyeau, P., Bates, S., Ergen, C., Jordan, M. I., & Yosef, N. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.03.565520

Sysrecon: A systematic data-driven tool for genome-scale metabolic reconstructionsPreprint

Ouyang, S., Li, Z., Hu, J., Cao, M., Wang, X., Sun, H., Feng, Y., & Mao, L. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.13.571370 · Cited by 1

A method to identify high consensus predictions of single-cell metabolic fluxPreprint

Amiss, M., Lum, J. J., & Jabbari, H. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.01.15.572211

Spermidine/spermine N1-acetyltransferase controls tissue-specific regulatory T cell function in chronic inflammationPreprint

Neuwirth, T., Malzl, D., Knapp, K., Tsokkou, P., Kleißl, L., Redl, A., Freystätter, C., Marella, N., Kutschat, A. P., Ponweiser, E., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.25.586519

scFBApy: A Python Framework for Super-Network Flux Balance Analysis

Galuzzi, B. G., & Damiani, C. (2024) · Communications in computer and information science · doi:10.1007/978-3-031-57430-6_8

Microbial Antioxidants and Their Interactions with Gastrointestinal Tract Epithelial Cells in the CattlePreprint

Sun, H., Zhu, S., Jia, M., Li, H., Han, B., Shi, T., Zhang, Q., Zheng, W., Xu, J., Chen, L., et al. (2024) · Research Square · doi:10.21203/rs.3.rs-4193125/v1

scRNA-seq and spatial transcriptomics reveal neuroendocrine-like cancer cells promote angiogenesis and EMT through neural signaling pathways in male breast cancerPreprint

Zhang, X., Sh, Y., Cai, S., Xu, B., Wang, H., Cui, J., Yang, Z., Chen, S., Zhou, Z., Cai, Y., et al. (2024) · Research Square · doi:10.21203/rs.3.rs-4291684/v1

Inferring metabolite states from spatial transcriptomes using multiple graph neural networkPreprint

Luo, J., Ai, D., & Sun, W. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.12.598759

Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in ratsPreprint

Yang, H., Zhang, C., Kim, W., Shi, M., Kılıçlıoğlu, M., Bayram, C., Bolat, İ., Tozlu, Ö. Ö., Baba, C., Yuksel, N., et al. (2024) · eLife · doi:10.7554/elife.98427.1

Pre-implantation embryo metabolism identified by PEMA reveals endogenous lactate insufficiency contributes to pre-implantation development arrest

Li, J., Hou, W., Zhao, Q., Xi, H., Liu, W., Xiao, S., Song, E., Zhu, L., Cai, Y., Zong, M., et al. (2024) · Fundamental Research · doi:10.1016/j.fmre.2024.10.005

Systems-Wide Analyses of Immune Programming of Regulatory T Cells in Early Life Providing Lifelong Protection from Diseases

Dehli, R. I., & Brix, S. (2024) · RNA technologies · doi:10.1007/978-3-031-62178-9_15

Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in ratsPreprint

Yang, H., Zhang, C., Kim, W., Shi, M., Kılıçlıoğlu, M., Bayram, C., Bolat, İ., Tozlu, Ö. Ö., Baba, C., Yuksel, N., et al. (2025) · eLife · doi:10.7554/elife.98427.2 · Cited by 1

Spermine attenuates TGF-β-induced EMT by downregulating fibronectin

Liu, H., & Chen, Y. (2025) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2025.108352

S100a4+ alveolar macrophages accelerate the progression of precancerous atypical adenomatous hyperplasia by promoting the angiogenic function regulated by fatty acid metabolismPreprint

Huang, H., Yang, Y., Zhang, Q., Yang, Y., Xiong, Z., Mao, S., Song, T., Wang, Y., Liu, Z., Bu, H., et al. (2025) · eLife · doi:10.7554/elife.101731.2

Using Specific Reporter Mice to Assess CD4+ T Cell Transdifferentiation

Nawrocki, M., & Huber, S. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4414-0_9

Identification of Immune Characteristics of 2 Subtypes of Breast Cancer by Combining Polyamine Metabolism-related Genes to Help With Immunotherapy

Yi, X., Tang, B., Mo, Q., Tang, Y., Fu, W., Zhang, L., & Xie, L. (2025) · Journal of Immunotherapy · doi:10.1097/cji.0000000000000559

Th17 and Th22 Cells

Schnell, A., Burkett, P. R., Lee, Y., Peters, A., & Kuchroo, V. K. (2025) · Elsevier eBooks · doi:10.1016/b978-0-12-824465-4.00274-x

Immunometabolism Governs T Cell Immunity

Raynor, J. L., Shi, H., & Chi, H. (2025) · Elsevier eBooks · doi:10.1016/b978-0-12-824465-4.00275-1

Systems biology methods to study the epigenome and metabolic-epigenetic interactions

Manjunatha, P. B., Bhowmick, R., & Chandrasekaran, S. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-26759-8.00006-0

A Polyamine Takes the Fast Track to Attack Crystal‐Induced Inflammation

Gumá, M., & Terkeltaub, R. A. (2025) · Arthritis & Rheumatology · doi:10.1002/art.43405

Targeting PKLR and lipogenic enzymes through JNK inhibition to develop a therapeutic strategy for MASLD and MASHPreprint

Mardinoğlu, A., Kim, W., Li, M., Liao, X., Özmen, S., Yıldız, E., Saraçoğlu, M., Baba, C., Çelikezen, F. Ç., Atalay, S. A., et al. (2025) · Research Square · doi:10.21203/rs.3.rs-7114368/v1

Advances in Tumor Microenvironment Immune Profiling

Blake, M. K., O’Connell, P., & Aldhamen, Y. A. (2025) · Springer eBooks · doi:10.1007/978-3-032-00761-2_85

Exosome miR‐6990‐5p from MMP14 high Macrophage Promotes Fibrosis Through Th17 Cell Differentiation in Hypersensitivity Pneumonia

Peng, D., Li, J., Qin, B., Xiong, A., Ran, Q., Bai, L., He, X., Li, X., Zhang, L., Arooj, M., et al. (2025) · European Journal of Immunology · doi:10.1002/eji.70048

Metabolic zonation and characterization of tissue slices with spatial transcriptomicsPreprint

Arrastoa, O. E., Pirona, A. C., Wagner, A., & Yosef, N. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.11.687271

PNS Alleviates Rheumatoid Arthritis by Regulating HIF-1α/PKM2-mediated Glycolysis to Inhibit Th17 DifferentiationPreprint

Bao, Y., Chen, S., Ge, Y., Zhang, Q., Wang, F., Jiang, B., & Zhou, L. (2025) · Research Square · doi:10.21203/rs.3.rs-7840833/v1

Multi-omics analysis identified spermidine as a potential compound against aortic aneurysm rupture

Zhao, J., Liu, S., Xiong, Y., Liu, Y., Liu, T., Sun, J., & Wang, W. (2025) · JVS-Vascular Insights · doi:10.1016/j.jvsvi.2025.100324

hypeR-GEM: connecting metabolite signatures to enzyme-coding genes via genome-scale metabolic models

Huang, Z., Perls, T. T., Sebastiani, P., Segrè, D., & Monti, S. (2026) · Bioinformatics · doi:10.1093/bioinformatics/btag588

SLC39-driven zinc influx orchestrates pleiotropic tumor–immune crosstalk to establish an immune-suppressive microenvironment in colorectal cancerPreprint

Hong, S., Park, S., Kim, S., Park, Y. I., Kang, M., Lee, J., Hemberg, M., Kim, S. E., & Kim, K. (2025) · Research Square · doi:10.21203/rs.3.rs-8267774/v1

Mast cell extracellular granules are bioactive condensates driven by heparin and polyaminePreprint

Xiong, Y., Tomares, D. T., Guo, J., Satoh, K., Zeng, L., Tian, Y., Su, M., Albis, A., Pant, A., Pappu, R. V., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.25.696514

Suppression of electron transport chain Complex III assembly is an adaptive mechanism to reduce host inflammation during viral infectionPreprint

Beh, S., Lee, C. Q. E., Shen, K., Zhong, C., Mantri, C. K., Liang, C., Lim, R., Yi, T. K., Sobota, R. M., Chen, J., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.30.702752

An Integrated Pipeline for Cell-Type Annotation, Metabolic Profiling, and Spatial Communication Analysis in the Liver using Spatial TranscriptomicsPreprint

Zhang, C. X., Li, J., Luo, O., Fu, X., Andrews, T. S., Steinberg, G. R., & Wang, D. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.07.704573

Systematic Analysis of Human Tissue- and Cell-Specific Metabolic Models Identifies High-Sugar, High-Fat Diet–Induced Liver DysregulationPreprint

Li, M., Shi, M., Zhang, C., Türkez, H., Uhlén, M., & Mardinoğlu, A. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.18.706568

Protocol for single-cell optimization objective and trade-off inference

Lin, D.-W., Teixeira, C., Chung, C. H., Roy, S. S., Ghosh, A., & Chandrasekaran, S. (2026) · STAR Protocols · doi:10.1016/j.xpro.2026.104373

Immunometabolic and Spatiotemporal Control of Tissue‐Resident Memory T Cell Biology

Raynor, J. L., & Chi, H. (2026) · Barrier Immunity · doi:10.1002/dni2.70007 · Cited by 1

Inhibition of T cell polyamine metabolism promotes transplant acceptance by modulating cytotoxic CD8+ T cell differentiation

Tang, R., Chang, Y., An, Y., Shan, D., Song, S., Xing, K., Li, P., Zhang, H., Hua, X., Chen, X., et al. (2026) · American Journal of Transplantation · doi:10.1016/j.ajt.2026.02.038

Single-cell genomics highlight MYC-associated metabolic activation and altered cell interactions in T-prolymphocytic leukemia progression

Wahnschaffe, L., Jungherz, D., Müller, T. A., Pemovska, T., Pichler, A., Poulain, S., Julia, E., Timonen, S., Böttcher, M., Jiang, Q., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-70185-w

Towards single-cell modelling of tumour metabolism

Pacheco, M. P., Gonzalez, E., & Sauter, T. (2026) · Biocatalysis and Biotransformation · doi:10.1080/10242422.2026.2645236

Multi‐Omics Profiling Uncovers Predictive Factors for Tumor‐Infiltrating Lymphocyte Therapy in Ovarian Cancer

Wang, X., Hou, R., Chen, J., He, B., Liu, P., Zhu, G., Lan, H., & Zhu, W. (2026) · Journal of Clinical Laboratory Analysis · doi:10.1002/jcla.70196

Étude multi-omics des mutations des isocitrates déshydrogénases dans les leucémies aiguës myéloïdes

Hucteau, A. (2023) · theses.fr (ABES) · doi:10.70675/2ddbfecfzaa70z4d57z87cbzbcc9f3c01cc6

The role of R-loop aberrations in lower-grade gliomas: prognostic, immune, and metabolic implications from multi-omics and machine learning analysis

Huang, R., Lin, B.-B., Huang, H., Li, C., Zhuang, S., Wei, N., Yu, Y., Zhou, W., Qiu, Y., Lu, Z., et al. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1758954

PIM1 kinase–regulated cellular metabolism sustains differentiation and function of effector CD8+ T cells during chronic viral infection

Brown, A. K., Niu, H., Shen, J., Zhang, Y., de Castro, P. A. S. V., Kasmani, M. Y., Lin, S., Topchyan, P., Mani, N. L., Volberding, P. J., et al. (2026) · The Journal of Immunology · doi:10.1093/jimmun/vkag062

Metabolic-secretory decoupling defines a disease-intrinsic state in rheumatoid arthritis monocytesPreprint

Teoh, S. T., Malkewitz, S., Iperi, C., Makowiec, C., Kakale, A., Duphey, S. M., Börsch, A., Buczak, K., Wolski, W., Yang, M., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.23.720351

Macronutrient Composition and Genetic Background Determine the Response to a Ketogenic DietPreprint

Zhang, Z., Moura‐Assis, A., Liu, S., Millet, A., Shaked, J., Rajan, D., Alwaseem, H., Viscio, M. I.-D., Molina, H., Birsoy, K., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.23.720368

Roles of gut metabolites on bone mineralization and remodeling: impact of metabolic dysregulation on the gut-immune-bone axis

Basak, S., Hridayanka, K. S. N., & Duttaroy, A. K. (2026) · Frontiers in Endocrinology · doi:10.3389/fendo.2026.1774824

SLC7A7 Downregulation in Monocytes Drives Immunosuppression and Osteosarcoma Progression

Jiang, B., Zhu, H., & Zhang, Z. (2026) · International Journal of Genomics · doi:10.1155/ijog/8314828

Aberrant CD4 + T cell refeeding response impairs neuro-immune crosstalk in Parkinson’s diseasePreprint

Austin‐Muttitt, K., David, B. R., Sassi, M., Agarwal, R., Sabedot, T. S., Jones, J. R., Cuoco, M. S., Jenkins, B. J., Roberts, L. D., Harris, L., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.06.723248

MechAInistic: A Reviewer-Supervised Multi-Agent LLM System for Auditable Mechanistic Drug-Hypothesis GenerationPreprint

Loecker, J., Pujara, N., Bryant, W., Puniya, B. L., Packrisamy, P., Hamed, A. A., & Helikar, T. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.11.723319

Deciphering tumor metabolites: emerging technologies shaping clinical implications

Zhu, X., Huang, L., Tian, P., Shao, Z. M., & Xiao, Y. (2026) · Trends in cancer · doi:10.1016/j.trecan.2026.04.004

Senescent cells induce vascular MHC II to recruit CD4 + T cells and drive inflammation in aging adipose tissuePreprint

Xie, Q., Lin, T., Jang, S., Jan, C. H., Selahi, A., Nyberg, K. D., Wendorff, A. A., Hake, K., Lefebvre, A. E. Y. T., Jin, M., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.13.724992

Immunosenescence and Vaccine Efficacy in Aging: Dynamic Interplay of Gut Microbiota and mTOR Signaling Pathways

Li, J. J., Zhang, Y., Yu, D., Li, J., Chen, K., & 储利胜 (2026) · Aging Cell · doi:10.1111/acel.70548

Critical illness expands a transcriptionally distinct hypometabolic CD8 + T effector program associated with respiratory failure and mortalityPreprint

Nichols, C. M., Mwizerwa, E. L., Sim, C. Y., Obeidalla, S. N., Cephus, J.-Y., Roe, C. E., Irish, J. M., Newcomb, D. C., Kerchberger, V. E., Bastarache, J. A., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.28.728555

Human Genome-Scale Models of Metabolism and Gene Expression Reveal Resource Constraints of Cancer Cell LinesPreprint

Baghdassarian, H., Giusto, P. D., Tibocha‐Bonilla, J. D., Armingol, E., Gopalakrishnan, S., Dworkin, L. A., Yang, L. M., & Lewis, N. E. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.30.728988

Aging reprograms the functional, epigenetic, and metabolic landscape of macrophagesPreprint

Suresh, M., Tapia-Belmonte, F., Weselman, B. T., Li, X., Durr, M., Duchovny, I., Yanitza, G.-M., Hepp, M. I., Noonepalle, S. K. R., Salas-Burgos, A., et al. (2026) · Research Square · doi:10.21203/rs.3.rs-10155437/v1

Genetically informed single-cell and spatial mapping of metabolic programs in human health and diseasePreprint

Xu, H., Huang, G., Zhang, L., Liu, W., Wu, Q., Chen, M., Zhao, D., Zhang, Y., & Xu, A. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.25.734643

Targeting PKLR and lipogenic enzymes through JNK inhibition to develop a therapeutic strategy for MASLD and MASH

Kim, W., Li, M., Liao, X., Özmen, S., Yıldız, E., Saraçoğlu, M., Baba, C., Çelikezen, F. Ç., Atalay, S. A., Akkuş, A. T., et al. (2026) · Frontiers in Pharmacology · doi:10.3389/fphar.2026.1823203

S100A8+S100A9+ transitional macrophages are associated with pulmonary fibrosis progression by integrating immunometabolism and fibrogenic crosstalk

林岑珊, Wu, M., Zhang, Z., Zheng, M., Li, H., 王余芳, Du, Z., Wu, L., Dai, J., Yu, Y. P., et al. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1832940

Panax notoginseng saponins (PNS)alleviates rheumatoid arthritis by regulating HIF-1α/PKM2-mediated glycolysis to inhibit Th17 differentiation

Bao, Y., Chen, S., Ge, Y., Zhang, Q., Wang, F., Jiang, B., & Zhou, L. (2026) · Molecular Biology Reports · doi:10.1007/s11033-026-12314-8

A Single-Cell Perturbation Analysis Framework Integrating Metabolic Constraints and Chain-Based Interpretability

Zheng, R., Huang, J., Liu, F., Xiang, J., & Li, M. (2026) · Lecture notes in computer science · doi:10.1007/978-981-92-3719-7_26

Association of serum spermidine level with vascular calcification in peritoneal dialysis patients

Luo, D., Liu, X., Chen, J., Luo, Q., Li, S., Jia, Z., Liu, M., & Dou, X. (2026) · Renal Failure · doi:10.1080/0886022x.2026.2686026

The next-generation virtual cell: From spatiotemporal transcriptomic modeling to closed-loop target discovery in complex diseases

Zhao, M., Ma, X., Shi, W., & Sun, Y. (2026) · Life Sciences · doi:10.1016/j.lfs.2026.124600 · Cited by 1

Deep learning as a bridge between sequencing-derived biological data and functional interpretation

Hong, H., Liu, L., Liao, W., Zhao, J., Liu, Y., He, X., Li, J., He, R., Jin, Y., Sha, L., et al. (2026) · Discover Artificial Intelligence · doi:10.1007/s44163-026-01739-6

Converging quality by design, artificial intelligence, and biofoundry automation: A new paradigm for scalable circular biomanufacturing

Belloch-Molina, C., da Silva, F. V. S., Morrissey, J. P., & Sousa-Gallagher, M. J. (2026) · Biotechnology Advances · doi:10.1016/j.biotechadv.2026.109001

Amino acid metabolic regulatory network in tumor immune escape: mechanistic exploration and intervention directions

Liu, Z., He, L., Tian, Y., Feng, S., Yang, X., Wu, H., Pu, Q., Wang, Y., & Yuan, X. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1871598

In Silico Metabolic Modeling of Single Th17 Cells Reveals Regulators of Autoimmunity

Wagner, A. (2021) · eScholarship (California Digital Library)

Cell-specific metabolic models reveal novel metabolic regulators of Th17 pathogenicity: from single-cell RNA-Seq to actionable metabolic targets

Wagner, A., Wang, C., DeTomaso, D., Koul, A., Regev, A., Kuchroo, V. K., & Yosef, N. (2018) · The Journal of Immunology · doi:10.4049/jimmunol.200.supp.163.21

In Silico Modeling of Metabolic State in Single Th17 Cells Reveals Novel Regulators of Inflammation and Autoimmunity

Wagner, A., Wang, C., DeTomaso, D., Ávila-Pacheco, J., Zaghouani, S., Fessler, J., Akama‐Garren, E. H., Pierce, K. A., Ron‐Harel, N., Haigis, M. C., et al. (2020) · The Journal of Immunology · doi:10.4049/jimmunol.204.supp.150.22 · Cited by 4

Metabolic and Epigenomic Regulation of Th17/Treg Balance by the Polyamine PathwayPreprint

Wang, C., Wagner, A., Fessler, J., Ávila-Pacheco, J., Karminski, J., Thakore, P. I., Zaghouani, S., Pierce, K. A., Bod, L., Schnell, A., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.01.23.911966 · Cited by 6

A Compass to Guide Insights into TH17 Cellular Metabolism and Autoimmunity

Wilson, A., Mosure, S., & Solt, L. A. (2021) · Immunometabolism · doi:10.20900/immunometab20220001 · Cited by 2