UCell: Robust and scalable single-cell gene signature scoring

Integrated analysis of multimodal single-cell data

Hao, Y., Hao, S., Andersen-Nissen, E., Mauck, W. M., Zheng, S., Butler, A., Lee, M. J., Wilk, A. J., Darby, C., Zagar, M., et al. (2020) · doi:10.1101/2020.10.12.335331 · Cited by 15,508

Comprehensive Integration of Single-Cell Data

Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., Hao, Y., Stoeckius, M., Smibert, P., & Satija, R. (2019) · Cell · doi:10.1016/j.cell.2019.05.031 · Cited by 15,453

On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other

Mann, H. B., & Whitney, D. R. (1947) · The Annals of Mathematical Statistics · doi:10.1214/aoms/1177730491 · Cited by 14,320

The Molecular Signatures Database Hallmark Gene Set Collection

Liberzon, A., Birger, C., Thorvaldsdóttir, H., Ghandi, M., Mesirov, J. P., & Tamayo, P. (2015) · Cell Systems · doi:10.1016/j.cels.2015.12.004 · Cited by 13,807

Scenic: single-cell regulatory network inference and clustering.

Aibar, S., González-Blas, C. B., Moerman, T., Huynh-Thu, V. A., Imrichova, H., Hulselmans, G., Rambow, F., Marine, J.-C., Geurts, P., Aerts, J., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4463 · Cited by 6,520

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

Tirosh, I., Izar, B., Prakadan, S. M., Wadsworth, M. H., Treacy, D., Trombetta, J. J., Rotem, A., Rodman, C., Lian, C., Murphy, G., et al. (2016) · Science · doi:10.1126/science.aad0501 · Cited by 4,944

The human cell atlas

Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C., Birney, E., Bodenmiller, B., Campbell, P., Carninci, P., Clatworthy, M., et al. (2017) · eLife · doi:10.7554/elife.27041 · Cited by 2,232

The Human Cell Atlas

Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C. O., Birney, E., Bodenmiller, B., & al, E. (2017) · Zurich Open Repository and Archive (University of Zurich) · doi:10.5167/uzh-162597 · Cited by 1,457

Construction of a human cell landscape at single-cell level

Han, X., Zhou, Z., Fei, L., Sun, H., Wang, R., Chen, Y., Chen, H., Wang, J., Tang, H., Ge, W., et al. (2020) · Nature · doi:10.1038/s41586-020-2157-4 · Cited by 1,087

Areas beneath the relative operating characteristics (ROC) and relative operating levels (ROL) curves: Statistical significance and interpretation

Mason, S. J., & Graham, N. E. (2002) · Quarterly Journal of the Royal Meteorological Society · doi:10.1256/003590002320603584 · Cited by 860

Single-cell transcriptomics uncovers HPV-driven immune evasion and establishes a TAB2-based prognostic signature in cervical cancer

Mi, J., Guo, W., Li, L., Wang, S., Wang, B., Fu, Y., Hu, N., He, H., Li, B., Wang, W., et al. (2026) · Translational Oncology · doi:10.1016/j.tranon.2026.102935 · Cited by 1

NF-κB-active tumors with matrix CAFs and suppressive immunity as key resistance mechanisms to chemoradiation in rectal cancer

Park, J., Shin, S. Y., Kim, J. W., Kim, D., Cho, S., Kim, H. H., An, C., & Lee, S. H. (2026) · Experimental & Molecular Medicine · doi:10.1038/s12276-026-01792-2 · Cited by 1

Long-lasting extracellular matrix modifications reshape intestinal stem cell fate and promote chronic inflammation

Adir, I., Sochen, C., Gelb, S., Menachem, A. H., Lebon, S., Toval, B., Holiar, V. V., Davidzohn, N., Salame, T., Rosenhek‐Goldian, I., et al. (2026) · Immunity · doi:10.1016/j.immuni.2026.07.022 · Cited by 5

Gliomas phenocopy an inborn error of metabolism to drive neuronal activity and tumor growth

Abdullah, K. G., Miki, K., Edgar, C. K., Wu, S. A., Xiao, Y., Huang, Y.-T., Drexler, R., Krishna, S., Puliyappadamba, V. T., Tay, L. W. R., et al. (2026) · Cell · doi:10.1016/j.cell.2026.08.037 · Cited by 2

IL-2-producing TFH cells sustain Treg cell homeostasis and immune tolerance in the gut

Dave, S., Bachus, H., Santiago, N., Meloun, A., Smelkinson, M. G., Foote, J. B., Hill, T., Fucile, C., Rosenberg, A. F., & Ballesteros‐Tato, A. (2026) · Nature Immunology · doi:10.1038/s41590-026-02690-5 · Cited by 1

Deciphering glycosylation-driven prognostic insights and therapeutic prospects in glioblastoma through a comprehensive regulatory model

Jin, X., Chen, Z., & Zhao, H. (2024) · Frontiers in Oncology · doi:10.3389/fonc.2024.1288820 · Cited by 1

Integrated Analysis of Single-Cell and Bulk RNA Data Reveals Complexity and Significance of the Melanoma Interactome

Diaz, M. J., Tran, J. T., Samia, A. M., Forouzandeh, M., Grant-Kels, J. M., & Montanez-Wiscovich, M. E. (2025) · Cancers · doi:10.3390/cancers17010148 · Cited by 1

Pathway Enrichment-Based Unsupervised Learning Identifies Novel Subtypes of Cancer-Associated Fibroblasts in Pancreatic Ductal Adenocarcinoma

Ai, H., Nie, R., & Wang, X. (2025) · Interdisciplinary Sciences Computational Life Sciences · doi:10.1007/s12539-025-00705-7 · Cited by 1

SCENE : Signature Collection for Endometrial Cancer Prognosis

Dugo, E., Piva, F., Giulietti, M., Giannella, L., & Ciavattini, A. (2025) · Journal of Cellular and Molecular Medicine · doi:10.1111/jcmm.70762 · Cited by 1

DeepPathway: predicting pathway expression from histopathology images

Ahsan, M., Hanley, K. P., Fergie, M., O’Leary, C., Borst, G. R., Roncaroli, F., Minhas, F., Rattray, M., Iqbal, M., & Baker, S. M. (2026) · Bioinformatics · doi:10.1093/bioinformatics/btag643 · Cited by 1

Identification and Experimental Validation of OS-Related Gene Sets Based on Integrated Analysis of Single-Cell and Bulk RNA Sequencing Data with Machine Learning in Patients with Sepsis

Tao, L., Tian, W., Li, P., Chen, Y., & Liu, J. (2025) · Inflammation · doi:10.1007/s10753-025-02346-w · 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

Finding Significantly Enriched Cells in Single-Cell RNA Sequencing by Single-Sample Approaches

Mrukwa, A., Marczyk, M., & Żyła, J. (2022) · Lecture notes in computer science · doi:10.1007/978-3-031-07802-6_3 · Cited by 1

Context-dependent triggering of STING-interferon signaling by CD11b agonists supports anti-tumor immunity in mouse models and human cancer patientsPreprint

Liu, X., Hogg, G. D., Zuo, C., Baer, J. M., Lander, V. E., Kang, L., Borcherding, N. C., Knolhoff, B. L., Osterhout, R. E., Galkin, A., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.22.485233 · Cited by 1

Identifying commonalities between cell lines and tumors at the single cell level using Sobolev Alignment of deep generative modelsPreprint

Mourragui, S. M. C., Siefert, J. C., Reinders, M. J. T., Loog, M., & Wessels, L. F. A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.08.483431 · Cited by 1

Single-Cell Analysis of Cell-Type Specific Immune Response in Pneumococcal MeningitisPreprint

Zhang, Y., Duan, J., Lin, S., Wen, J., & Liao, J. (2022) · Research Square · doi:10.21203/rs.3.rs-1834120/v1 · Cited by 1

Upregulation of CD55 complement regulator in distinct PBMC subpopulations of COVID-19 patients is associated with suppression of interferon responsesPreprint

Detsika, M. G., Σάκκου, Μ., Triantafillidou, V., Konstantopoulos, D., Grigoriou, E., Psarra, K., Jahaj, E., Dimopoulou, I., Orfanos, S. E., Tsirogianni, A., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.07.510750 · 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

Dendrimeric DNA Coordinate Barcoding Design for Spatial RNA SequencingPreprint

Cao, J., Zheng, Z., Sun, D., Chen, X., Cheng, R., Lv, T., An, Y., Zheng, J., Song, J. T., Wu, L., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.26.546618 · Cited by 1

Targeting CD74-positive macrophages improves neoadjuvant therapy in cervical cancer as revealed by single-cell transcriptomics analysisPreprint

Wang, Z., Wang, B., Feng, Y., Ye, J., Mao, Z., Zhang, T., Xu, M., Zhang, W., Jiao, X., Zhang, Y., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.09.566505 · Cited by 1

A distinct subpopulation of adipocytes in adult perirenal adipose tissue arises through brown-to-white conversion but reverts to a thermogenic phenotype upon cold exposurePreprint

Zhang, H., Li, Y., Ibáñez, C. F., & Xie, M. (2024) · eLife · doi:10.7554/elife.93151.2 · Cited by 1

Androgen Receptor interacts with c-Myc to regulate macrophage-osteoclast axis and drive bone metastasis in Triple Negative Breast CancerPreprint

Guan, X., Liu, Y., Fan, L., Zhao, Y., Zhu, Y., Yang, Y., Ye, F., Gu, Y., & Xu, F. (2024) · Research Square · doi:10.21203/rs.3.rs-4318418/v1 · Cited by 1

ctQC improves biological inferences from single cell and spatial transcriptomics dataPreprint

Lakshmanan, V., Kahraman, M., Macalinao, D. C., Gunn, N. A. L., Venkatesh, P. N., Chang, M., Fu, C. W. P., Qiang, L. W., Tan, I. B., & Prabhakar, S. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.23.594978 · Cited by 1

Profiling ranked list enrichment scoring in sparse data elucidates algorithmic tradeoffsPreprint

Wenzel, A. T., Jun, J., Liefeld, T., Tamayo, P., & Mesirov, J. P. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.03.597180 · Cited by 1

Single-Nucleus RNA Sequencing Reveals Spatiotemporal Dynamics of Disease-Associated Microglia in Amyotrophic Lateral SclerosisPreprint

Chen, L., Zhang, M.-D., Xu, H., Ye, H.-Q., Chen, D.-F., Wang, P., Bao, Z.-W., Zou, S.-M., Lv, Y.-T., Wu, Z., et al. (2024) · SSRN Electronic Journal · doi:10.2139/ssrn.4861071 · Cited by 1

Aberrant STAT signaling drives T cell dysregulation in a targetable pediatric sepsis endotypePreprint

Lindell, R. B., Sayed, S. U., Campos, J. S., Sheetz, S. A., Babu, A., Knight, M., Mauracher, A. A., Hay, C. A., Conrey, P. E., Fitzgerald, J. C., et al. (2024) · medRxiv · doi:10.1101/2024.06.11.24308709 · Cited by 1

Data from Paradoxical Activation of Oncogenic Signaling as a Cancer Treatment Strategy

Dias, M. H., Friskes, A., Wang, S., Neto, J. M. F., van Gemert, F. P. A., Mourragui, S. M. C., Papagianni, C., Kuiken, H. J., Mainardi, S., Villanueva, D. A., et al. (2024) · doi:10.1158/2159-8290.c.7309549.v1 · Cited by 1

An integrated multi-omics investigation of W-NK1, a cytokine-primed non-engineered natural killer cell therapy productPreprint

Arthur, L., Mahajan, N., Vadakekolathu, J. N., Leedom, T. A., Boocock, D. J., Coveney, C., Hamil, A., Magee, K. L., Dean, J., Schramm, E. C., et al. (2024) · medRxiv · doi:10.1101/2024.07.08.24310018 · Cited by 1

Ex vivo Model of Functioning Human Lymph Node Reveals Pivotal Role for Innate Lymphoid Cells and Stromal Populations in Response to Vaccine AdjuvantPreprint

Fergusson, J. R., Siu, J. H. Y., Gupta, N., Nee, E., Reinke, S., Ströbel, T., Bhalla, A., Kandage, S. M., Courant, T., Hill, S., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.21.608943 · Cited by 1

The mitochondrial unfolded protein response in human microglia disrupts neuronal-glial communication and promotes senescencePreprint

Maria Jose Perez, J., Lam, A., Weissleder, C., Bertoli, F., Raji, H., Bosch, M., Nemazanyy, I., Kalb, S., Kehili, M., Hirschberg, I., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.03.610925 · Cited by 1

Cell types associated with human brain functional connectomes and their implications in psychiatric diseasesPreprint

Nie, P., Zhan, Y., Chen, R., Qi, R., Liu, C., & Wang, G.-Z. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.11.627878 · Cited by 1

Spatial transcriptomics exploration of the primary neuroblastoma microenvironment unveils novel paracrine interactionsPreprint

Siaw, J. T., Merseburger, P., Borenäs, M., Jansson, C., Karlsson, J., Claeys, A., Jennische, E., Lind, D. E., Nord, D. G., Palmer, R. H., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.21.629891 · Cited by 1

Single-Cell Analysis of Microglia and Monocyte Dynamics Uncover Distinct TNF-α-driven Neuroimmune Signatures after Intracerebral HemorrhagePreprint

Kawamura, Y., Johnson, C. W., DeLong, J. H., Camillo, L. P. D. L., Velazquez, S. E., Takahashi, M., Beatty, H. E., Herbert, R., Cord, B. J., Matouk, C. C., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.24.630187 · Cited by 1

Mapping the ISR Landscape in Cognitive Disorders via single-cell multi-omicsPreprint

Torkenczy, K. A., Reineke, L. C., Dooling, S. W., Henderson, B., Itzhak, D. N., Yang, B. A., He, D., Myers, R., Walter, P., Tyanova, S., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.28.640905 · Cited by 1

Single-Cell Transcriptomics of Multi-Site Cell Therapy in Osteoarthritis: Tissue-Specific Traits and Treatment CorrelationsPreprint

Chatterjee, P., Stevens, H. Y., Kippner, L. E., Yeago, C., Drissi, H., Mautner, K., Boden, S. D., Gibson, G. C., & Roy, K. (2025) · medRxiv · doi:10.1101/2025.04.14.25325743 · Cited by 1

Splicing variants in MYRF cause partial loss of function in the retinal pigment epitheliumPreprint

Rozumek, G. M., Brinkmeier, M. L., Guan, B., Wang, S. Q., Tower, C. A., Yang, N. T., Lim, R., Dong, L., Hannum, D. F., Moroi, S. E., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.21.649840 · Cited by 1

GDF15 reprograms the microenvironment to drive the development of uveal melanoma liver metastasesPreprint

Sriramareddy, S. N., Siddarajappa, N., Park, J. S., Nguyen, T., Kuznetsoff, J. N., Kurtenbach, S., Dollar, J. J., Adams, D., Licht, J. D., Corrêa, Z. M., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.07.652654 · Cited by 1

Cell Type-Specific Effects of miR-21 Loss Attenuate Tumor Progression in MYC-Driven Prostate CancerPreprint

Zennami, K., Graham, M. K., Chikara, S., Sysa‐Shah, P., Rafiqi, F., Wang, R., Abel, B., Zeng, Q., Krueger, T. E. G., Brennen, W. N., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.14.654101 · Cited by 2

Persistent ECM Scarring Reprograms Intestinal Stem Cells to Drive Chronic InflammationPreprint

Adir, I., Sochen, C., Menachem, A. H., Lebon, S., Toval, B., Holiar, V. V., Davidzohn, N., Salame, T., Rosenhek‐Goldian, I., Savickas, S., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.08.658481 · Cited by 1

Integrated Single Cell Analysis Identifies CD39+ Tumor-Associated NK Cells with Cytotoxic Potential in Lung CancerPreprint

Serger, C., Rebuffet, L., Sandholzer, M. T., Fusi, I., Oelgarth, N., Tundo, S., Luu, T. T., Hojski, A., Lardinois, D., Trefny, M. P., et al. (2025) · SSRN Electronic Journal · doi:10.2139/ssrn.5356127 · Cited by 1

Distinct myeloid precursors and their interaction with mesenchymal cells orchestrate the spreading of psoriatic disease from the skin to the jointsPreprint

Raimondo, M. G., Mohammadian, H., Angeli, M. R., Alivernini, S., Fedorchenko, V., Huang, K., Demmler, R., Rhein, P., Xu, C., Li, Y., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.14.665302 · Cited by 1

The nuclear receptor NR4A1 serves as a neutrophil-intrinsic regulator mitigating stroke severityPreprint

Strecker, J., Schmidt, Y., Liebmann, M., Walter, C., Roth, S., Aleth, H., Börsch, A.-L., Schmidt‐Pogoda, A., Beuker, C., Yusuf, A. M., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.19.677282 · Cited by 1

Spatial Transcriptomics of Glioblastoma Defines Spatially Anchored Transcriptional Activity Informing Therapeutic Vulnerability and ResistancePreprint

Ravikumar, V., Maddox, A., Kulkarni, R., Hara, T., Rao, A. U. K., & Al‐Holou, W. N. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.17.683110 · Cited by 1

Chronic sensing of host-derived lipids is an all-in-one signal that primes and activates NLRP3Preprint

Dufies, O., Gioia, M. D., Spreafico, R., Tan, P. J., Springstead, J. R., Prell, S. A., Case, J., Gao, C., Wei, K., Wu, H., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.29.685328 · Cited by 1

Dysregulation of transcription networks regulating oligodendrogenesis in age-related decline in CNS remyelinationPreprint

Dimas, P., Morabito, S., Rawji, K. S., Wang, Q., Krause, F. N., Cubillos, J. F., Belaadi, N., Assinck, P., Shi, Z., Cao, Z., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.14.688494 · Cited by 3

Reconstructing developmental and disease progression with sample-level embeddingsPreprint

Jiang, L., Tan, Z. C., Grabski, I. N., Hao, Y., Nakatsuka, N. J., Sarkar, S., Shenoy, A., & Satija, R. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.10.693462 · Cited by 2

Selective infection and loss of PRDM1+ LN Tfh cells in uncontrolled HIV infection precludes formation of Tfh reservoirs under ARTPreprint

Wu, V. H., Nordin, J. M. L., Pampena, M. B., Rachimi, S., Burgess, W. L., Clark, M., Robinson, J. A., Estrada, P. M. D. R., Schleimann, M. H., Torres-Ruiz, F., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.11.693731 · Cited by 1

Scalable high-fidelity human vascularized cortical assembloids recapitulate neurovascular co-development and cell specializationPreprint

Bhalla, S., Gülsuyu, B., Sanchez, D., Ross, J. M., Arul, S., Gopinadhan, A., Öztürk, M. M., Mukhtar, T., Augustin, J. J., Wang, J., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.09.698753 · Cited by 2

A reproducible human brain tissue model to study physiological and disease-associated microglia phenotypesPreprint

Klimmt, J., Gonçalves, C. C., Montgomery, J. V., Müller, S. A., Bublitz, M., Filser, S., Paeger, L., Nuscher, B., Dannert, A., Roeber, S., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.20.699077 · Cited by 1

Federated single-cell QTL meta-analysis reveals novel disease mechanismsPreprint

Kaptijn, D., Michielsen, L., Neavin, D. R., Ripoll-Cladellas, A., Alquicira-Hernández, J., Korshevniuk, M., Lee, J. T. H., Oelen, R., Vochteloo, M., Warmerdam, R., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.20.700519 · Cited by 2

Cell-type specific impact of opioid use disorder and HIV on the human forebrain and cerebellumPreprint

Green, A. A., Vashist, T. D., Jakhmola, S., Chen, X., Baidwan, G., Buchanan, J., Tiwari, S. K., Griffin, E. N., Howell, A., Lee, Y., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.01.708876 · Cited by 1

Midgestation metabolic constraint in purine metabolism drives distinct strategies for placenta and fetal growthPreprint

Xu, W., Cruz, N. D. L., Woods, A., Lokshtanov, D., Gao, S. M., Khan, N. A., Wright, S., Rodriguez, M. E. F., McIntire, D. D., Duryea, E. L., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.18.712680 · Cited by 1

Multi-omic profiling of human antibody-secreting cells reveals diverse subsets sustain durable humoral immunityPreprint

Glass, D. R., Dornisch, E. M., Yin, H., Ludmann, S. A., Samudre, A., Kuhl, S., Malone, J., Chander, A., Kaul, N., Phalen, C. G., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.13.717827 · Cited by 1

Single-nucleus profiling reveals age-associated remodeling opposed by parity in the postmenopausal human ovaryPreprint

Byrne, J., Martin, N., Watson, M. A., Soygur, B., Devrukhkar, P. R., Tran, T., Shanes, E. D., Pavone, M. E., Duncan, F. E., & Schilling, B. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.11.724381 · Cited by 1

Transient MYC Mimicking the Exercise Response Orchestrates Multifaceted Skeletal Muscle AdaptationsPreprint

Jones, R. G., Koopmans, P. J., Serrano, N., Cabrera, A. R., Morena, F., Chambers, T. L., Walters, R., Borowik, A., Taylor, M. E., Wohlgemuth, R. P., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.29.735332 · Cited by 1

Systematic CRISPRi perturbation of 1,408 autism risk genes maps multilevel transcriptional convergence in human cortical neuronsPreprint

Gogate, A., Chen, W.-C., Nzima, M., Takeuchi, C., Zhao, H., Wang, L., Sivakumar, S., Deng, M., Kaur, K. J., Kraus, W. L., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.09.02.748925 · Cited by 1

PhenoMapR: scalable mapping of sample phenotypes to single-cell, spatial, and bulk transcriptomics dataPreprint

Benard, B. A., Lalgudi, C. K., Azizi, A., & Gentles, A. J. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.09.08.749933 · Cited by 1

Physis come ereingnis

Moli, A. L. (1998) · Giornale di Metafisica: revista bimestrale di filosofia

Integrated single-cell (phospho-)protein and RNA detection uncovers phenotypic characteristics of human antibody secreting cellsPreprint

van Buijtenen, E., Janssen, W., Vink, P. M., Habraken, M., Wingens, L. J. A., van Elsas, A., Huck, W. T. S., van Buggenum, J. A. G. L., & van Eenennaam, H. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.31.486501

Dynamic Single-Cell RNA Sequencing Reveals that Intravenous BCG Vaccination Curtails SARS-CoV-2 Induced Disease Severity and Lung InflammationPreprint

Singh, A. K., Wang, R., Lombardo, K. A., Praharaj, M., Bullen, C. K., Um, P. K., Davis, S. L., Komm, O. D., Illei, P. B., Ordoñez, A. A., et al. (2022) · SSRN Electronic Journal · doi:10.2139/ssrn.4199633

Single Cell Profiling Reveals Strain-Specific Differences in Myeloid Inflammatory Potential in the Rat LiverPreprint

Pouyabahar, D., Chung, S., Pezzutti, O. I., Perciani, C. T., Wang, X., Ma, X., Jiang, C., Camat, D., Chung, T., Sekhon, M., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.11.516225

Data from Checkpoint Blockade–Induced Dermatitis and Colitis Are Dominated by Tissue-Resident Memory T Cells and Th1/Tc1 Cytokines

Reschke, R., Shapiro, J. W., Yu, J., Rouhani, S. J., Olson, D. J., Zha, Y., & Gajewski, T. F. (2023) · doi:10.1158/2326-6066.c.6550938.v1

Deciphering the gene regulatory circuitry governing chemoresistance in Triple-Negative Breast CancerPreprint

Lusby, R., Zhang, Z., Mahesh, A., & Tiwari, V. K. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.05.539623

Switching of RNA splicing regulators in immature neuroblasts: a key step in adult neurogenesisPreprint

Bernou, C., Mouthon, M., Daynac, M., Demaille, B., Barroca, V., Couillard‐Després, S., Déchamps, N., Ménard, V., Bellenger, L., Antoniewski, C., et al. (2023) · eLife · doi:10.7554/elife.87083.1

Prominent contributions of selective neuronal subtypes to pediatric drug-resistant focal dysplasiaPreprint

Zhang, Y., Li, L., Zhu, F., Zhang, X., Xia, D., Zhong, C., Liang, S., Cao, D., Zou, H., Duan, J., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.21.549980

Bulk and Single-Cell Transcriptome Analysis Reveal Shared Key Genes and Patterns of Immune Dysregulation in Sepsis and Systemic Lupus ErythematosusPreprint

Wen, X., Bai, S., Zhang, K., Li, S., Li, J., Yang, J. A., Yu, Q., Cao, L., Cai, Z., & Zhang, G. (2023) · Research Square · doi:10.21203/rs.3.rs-3113873/v1

Phenotypic plasticity, spatial niches and cancer-associated fibroblast/mural cell interactions define the human prostate cancer microenvironmentPreprint

Sampson, N., Brunner, E., Damisch, E., Fotakis, G., Trajanoski, Z., Schäfer, G., Nommensen, L., Neumann, L., Puhr, M., Čulig, Z., et al. (2023) · Research Square · doi:10.21203/rs.3.rs-3258823/v1

The interferon/STAT1 signaling axis is a common feature of tumor-initiating cells in breast cancerPreprint

Souto, E. P., Gong, P., Landua, J. D., Srinivasan, R. R., Ganesan, A., Dobrolecki, L. E., Purdy, S. C., Pan, X., Zeosky, M., Chung, A., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.15.557958

Comprehensive Single-Cell Transcriptomic Profiling Identifies Molecular Subtypes and Prognostic Biomarkers in Esophageal Squamous Cell Carcinoma: Implications for Targeted TherapyPreprint

Zhang, D., Zhao, F., Guo, P., Li, Z., & Li, S. (2023) · Research Square · doi:10.21203/rs.3.rs-3313878/v1

A distinct subpopulation of adipocytes in adult perirenal adipose tissue arises through brown-to-white conversion but reverts to a thermogenic phenotype upon cold exposurePreprint

Zhang, H., Li, Y., Ibáñez, C. F., & Xie, M. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.11.561821

A distinct subpopulation of adipocytes in adult perirenal adipose tissue arises through brown-to-white conversion but reverts to a thermogenic phenotype upon cold exposurePreprint

Zhang, H., Li, Y., Ibáñez, C. F., & Xie, M. (2024) · eLife · doi:10.7554/elife.93151.1

Sox9 links biliary maturation to branching morphogenesisPreprint

Hrncir, H. R., Bombin, S., Goodloe, B., Hogan, C. B., Jadi, O., & Gracz, A. D. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.01.15.574730

A single-cell transcriptomic analysis of Neuroblastomas revealed a selective cGAS-STING pathway suppression in malignant cells

Sibilio, P., Funari, A., Veschi, V., Giulio, S. D., Paci, P., & Giannini, G. (2023) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm58861.2023.10385378

Integrative single-cell multi-omics of CD19-CAR pos and CAR neg T cells suggest drivers of immunotherapy response in B-cell neoplasiasPreprint

Guerrero-Murillo, M., Rill, A., Trincado, J. L., Bataller, Á., Ortiz‐Maldonado, V., Benítez‐Ribas, D., Español‐Rego, M., González, E. A., Martínez‐Cibrián, N., Marchese, D., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.01.23.576878

Switching of RNA splicing regulators in immature neuroblasts: a key step in adult neurogenesisPreprint

Bernou, C., Mouthon, M., Daynac, M., Kortulewski, T., Demaille, B., Barroca, V., Couillard‐Després, S., Déchamps, N., Ménard, V., Bellenger, L., et al. (2024) · eLife · doi:10.7554/elife.87083.2

Additional file 6 of Spatially resolved transcriptomic profiles reveal unique defining molecular features of infiltrative 5ALA-metabolizing cells associated with glioblastoma recurrence

Andrieux, G., Das, T., Griffin, M., Straehle, J., Paine, S., Beck, J., Boerries, M., Heiland, D. H., Smith, S. J., Rahman, R., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23665189

Additional file 5 of Spatially resolved transcriptomic profiles reveal unique defining molecular features of infiltrative 5ALA-metabolizing cells associated with glioblastoma recurrence

Andrieux, G., Das, T., Griffin, M., Straehle, J., Paine, S., Beck, J., Boerries, M., Heiland, D. H., Smith, S. J., Rahman, R., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23665183

Additional file 9 of Spatially resolved transcriptomic profiles reveal unique defining molecular features of infiltrative 5ALA-metabolizing cells associated with glioblastoma recurrence

Andrieux, G., Das, T., Griffin, M., Straehle, J., Paine, S., Beck, J., Boerries, M., Heiland, D. H., Smith, S. J., Rahman, R., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23665198

Additional file 13 of Spatially resolved transcriptomic profiles reveal unique defining molecular features of infiltrative 5ALA-metabolizing cells associated with glioblastoma recurrence

Andrieux, G., Das, T., Griffin, M., Straehle, J., Paine, S., Beck, J., Boerries, M., Heiland, D. H., Smith, S. J., Rahman, R., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23665216

Additional file 8 of Spatially resolved transcriptomic profiles reveal unique defining molecular features of infiltrative 5ALA-metabolizing cells associated with glioblastoma recurrence

Andrieux, G., Das, T., Griffin, M., Straehle, J., Paine, S., Beck, J., Boerries, M., Heiland, D. H., Smith, S. J., Rahman, R., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23665195

Additional file 11 of Spatially resolved transcriptomic profiles reveal unique defining molecular features of infiltrative 5ALA-metabolizing cells associated with glioblastoma recurrence

Andrieux, G., Das, T., Griffin, M., Straehle, J., Paine, S., Beck, J., Boerries, M., Heiland, D. H., Smith, S. J., Rahman, R., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23665207

Additional file 12 of Spatially resolved transcriptomic profiles reveal unique defining molecular features of infiltrative 5ALA-metabolizing cells associated with glioblastoma recurrence

Andrieux, G., Das, T., Griffin, M., Straehle, J., Paine, S., Beck, J., Boerries, M., Heiland, D. H., Smith, S. J., Rahman, R., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23665210

Additional file 4 of Spatially resolved transcriptomic profiles reveal unique defining molecular features of infiltrative 5ALA-metabolizing cells associated with glioblastoma recurrence

Andrieux, G., Das, T., Griffin, M., Straehle, J., Paine, S., Beck, J., Boerries, M., Heiland, D. H., Smith, S. J., Rahman, R., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23665180

Additional file 3 of Spatially resolved transcriptomic profiles reveal unique defining molecular features of infiltrative 5ALA-metabolizing cells associated with glioblastoma recurrence

Andrieux, G., Das, T., Griffin, M., Straehle, J., Paine, S., Beck, J., Boerries, M., Heiland, D. H., Smith, S. J., Rahman, R., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23665177

Additional file 2 of Spatially resolved transcriptomic profiles reveal unique defining molecular features of infiltrative 5ALA-metabolizing cells associated with glioblastoma recurrence

Andrieux, G., Das, T., Griffin, M., Straehle, J., Paine, S., Beck, J., Boerries, M., Heiland, D. H., Smith, S. J., Rahman, R., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23665174

Additional file 7 of Spatially resolved transcriptomic profiles reveal unique defining molecular features of infiltrative 5ALA-metabolizing cells associated with glioblastoma recurrence

Andrieux, G., Das, T., Griffin, M., Straehle, J., Paine, S., Beck, J., Boerries, M., Heiland, D. H., Smith, S. J., Rahman, R., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23665192

Additional file 10 of Spatially resolved transcriptomic profiles reveal unique defining molecular features of infiltrative 5ALA-metabolizing cells associated with glioblastoma recurrence

Andrieux, G., Das, T., Griffin, M., Straehle, J., Paine, S., Beck, J., Boerries, M., Heiland, D. H., Smith, S. J., Rahman, R., et al. (2023) · Figshare · doi:10.6084/m9.figshare.23665201

A Single-cell Census of Pulmonary Endarterectomies Tissue Across Different Anatomical Regions in Chronic Thromboembolic Pulmonary Hypertension

Zhang, R., Zhang, Y., Li, H., Zhang, J., Han, S., Cheng, X., Zhao, Q., He, J., 罗祠军, Qiu, H., et al. (2024) · Clinical and Translational Medicine · doi:10.1002/ctm2.70864

Lipidic and senescent macrophages predict progression and response to combinatorial immunotherapy in triple-negative breast cancerPreprint

Chan, C. M. F., To, A., Zhang, S., Wong, J. W. H., Huang, Y., Chao, Y., & Sugimura, R. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.24.600550

Pathogenic variants associated with speech/cognitive delay and seizures affect genes with expression biases in excitatory neurons and microglia in developing human cortexPreprint

Russ, J. B., Stone, A. C., Maney, K., Morris, L. C., Wright, C. F., Hurst, J. H., & Cohen, J. L. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.01.601597

Dynamic Tumor Immune Microenvironment Remodeling Predicts Response of Checkpoint Inhibitor TherapyPreprint

Lin, Z., Chandra, M., Srinivas, N., Ugurel, S., Becker, J. C., & Aran, D. (2025) · bioRxiv · doi:10.1101/2024.06.30.601413

Reviewer #2 (Public Review): NK Cell Exhaustion in Wilson’s Disease Revealed by Single-cell RNA Sequencing Predicts the Prognosis of Cholecystitis

(2024) · eLife · doi:10.7554/elife.98867.1.sa0

eLife Assessment: NK Cell Exhaustion in Wilson’s Disease Revealed by Single-cell RNA Sequencing Predicts the Prognosis of Cholecystitis

Nair, S. (2024) · eLife · doi:10.7554/elife.98867.1.sa2

Reviewer #1 (Public Review): NK Cell Exhaustion in Wilson’s Disease Revealed by Single-cell RNA Sequencing Predicts the Prognosis of Cholecystitis

(2024) · eLife · doi:10.7554/elife.98867.1.sa1

NK Cell Exhaustion in Wilson’s Disease Revealed by Single-cell RNA Sequencing Predicts the Prognosis of CholecystitisPreprint

Jin, Y., Xing, J., Dai, C., Jin, L., Zhang, W., Tao, Q., Hou, M., Li, Z., Yang, W., Feng, Q., et al. (2024) · eLife · doi:10.7554/elife.98867.1

The immune landscape of tumor-associated macrophage reprogrammingPreprint

Duval, F., Lourenço, J., Hicham, M., Boivin, G., Guichard, A., Wyser-Rmili, C., Fournier, N., Palma, M. D., & Mansouri, N. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.25.614962

Pre-existing intratumoral stem-like CD8 + T-cells drive radiotherapy-induced tumor controlPreprint

Köksal, H., Herbst, M., Perreira, P., Nater, M., Regli, N., Boudjeniba, C., Borgoni, N. E., Cecconi, V., & van den Broek, M. F. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.16.618635

Type I Interferon Drives a Cellular State Inert to TCR‐Stimulation and Could Impede Effective T‐Cell Differentiation in Cancer

Corvino, D., Batstone, M. D., Hughes, B. G. M., Kempchen, T. N., Ng, S. S., Salim, N., Schneppenheim, F., Rommel, D., Kumar, A., Pearson, S., et al. (2024) · European Journal of Immunology · doi:10.1002/eji.202451371

Th1 cells are critical tissue organizers of myeloid-rich perivascular activation nichesPreprint

Bala, N., McGurk, A. I., Carter, E. M., Sidhu, I., Niak, S., Leddon, S. A., & Fowell, D. J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.24.625073

NK Cell Exhaustion in Wilson’s Disease Revealed by Single-cell RNA Sequencing Predicts the Prognosis of CholecystitisPreprint

Jin, Y., Xing, J., Dai, C., Jin, L., Zhang, W., Tao, Q., Hou, M., Li, Z., Yang, W., Feng, Q., et al. (2024) · eLife · doi:10.7554/elife.98867.2

UCell and pyUCell: single-cell gene signature scoring for R and Python

Andreatta, M., & Carmona, S. J. (2026) · Bioinformatics · doi:10.1093/bioinformatics/btag055 · Cited by 21

Single-Cell Signature Explorer for comprehensive visualization of single cell signatures across scRNA-seq datasets

Pont, F., Tosolini, M., & Fournié, J. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz601 · Cited by 132

pysigscore: gene signatures scoring across bulk and single-cell transcriptomicsPreprint

Giacomello, T., Mazzara, S., Abbruzzese, G., Barberis, A., Tangherloni, A., & Buffa, F. M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.04.742537

CanSig Benchmarks Methods for Reproducible Cancer Cell State Discovery from Single-Cell Transcriptomic Data

Barkmann, F., Yates, J., Czyż, P., Kraft, A., Glettig, M., Beerenwinkel, N., & Boeva, V. (2026) · Repository for Publications and Research Data (ETH Zurich) · doi:10.3929/ethz-c-000796281

Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID

Cortal, A., Martignetti, L., Six, E. M., & Rausell, A. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00896-6 · Cited by 165