Bioinformatics

Usart, M. et al. (2025) ‘Loss of Socs2 improves molecular responses to IFNα in a mouse model of myeloproliferative neoplasms driven by JAK2-V617F’, Leukemia [Preprint]. Available at: https://doi.org/10.1038/s41375-025-02550-5.

Schwayer, C. et al. (2025) ‘Cell heterogeneity and fate bistability drive tissue patterning during intestinal regeneration’, bioRxiv [Preprint]. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2025.01.14.632683.

Geng, A. et al. (2025) ‘Circulating monocytes upregulate CD52 and sustain innate immune function in cirrhosis unless acute decompensation emerges’, Journal of Hepatology [Preprint]. Available at: https://doi.org/10.1016/j.jhep.2024.12.031.

Tundo, Sofia et al. (2024) ‘Inhibition of Cbl-b restores effector functions of human intratumoral NK cells’, Journal for ImmunoTherapy of Cancer, 12(11), p. e009860. Available at: https://doi.org/10.1136/jitc-2024-009860.

Blumer, S. et al. (2024) ‘Characteristics of ectopic alveolar basal cells relative to airway basal cells in fibrosis’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2024.09.24.614660.

Kawamura, Y.K. et al. (2024) ‘Preventing CpG island hypermethylation in oocytes safeguards mouse development’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2024.05.29.595726.

Katsantoni, Maria et al. (2024) ‘ZARP: A user-friendly and versatile RNA-seq analysis workflow’, F1000Research, 13, p. 533. Available at: https://doi.org/10.12688/f1000research.149237.1.

Flint, E. et al. (2024) ‘Targeting the expansion of myeloid-derived suppressor cells in liver cirrhosis’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2024.03.29.587228.

Rai, Shivam et al. (2024) ‘IL-1β promotes MPN disease initiation by favoring early clonal expansion of JAK2-mutant hematopoietic stem cells’, Blood Advances, 8(5), pp. 1234–1249. Available at: https://doi.org/10.1182/bloodadvances.2023011338.

Elewaut, D. et al. (2024) ‘GDF15 mediates inflammation-associated bone loss through a brain-bone axis’. Research Square Platform LLC. Available at: https://doi.org/10.21203/rs.3.rs-3824212/v1.

Falcetta, Denis et al. (2024) ‘CaMKIIβ deregulation contributes to neuromuscular junction destabilization in Myotonic Dystrophy type I’, Skeletal Muscle, 14(1). Available at: https://doi.org/10.1186/s13395-024-00345-3.

Müller-Durovic, Bojana et al. (2024) ‘A metabolic dependency of EBV can be targeted to hinder B cell transformation’, Science (New York, N.Y.), 385, p. eadk4898. Available at: https://doi.org/10.1126/science.adk4898.

Schaefer, Thorsten et al. (2024) ‘Nuclear and cytosolic fractions of SOX2 synergize as transcriptional and translational co-regulators of cell fate’, Cell Reports, 43. Available at: https://doi.org/10.1016/j.celrep.2024.114807.

Usart, Marc et al. (2024) ‘Loss of Dnmt3a increases self-renewal and resistance to pegIFN-α in JAK2-V617F–positive myeloproliferative neoplasms’, Blood, 143, pp. 2490–2503. Available at: https://doi.org/10.1182/blood.2023020270.

Wieboldt, Ronja et al. (2024) ‘Engagement of sialylated glycans with Siglec receptors on suppressive myeloid cells inhibits anticancer immunity via CCL2’, Cellular and Molecular Immunology, 21, pp. 495–509. Available at: https://doi.org/10.1038/s41423-024-01142-0.

Trefny, Marcel P. et al. (2023) ‘Deletion of SNX9 alleviates CD8 T cell exhaustion for effective cellular cancer immunotherapy’, Nature Communications, 14(1). Available at: https://doi.org/10.1038/s41467-022-35583-w.

Trefny, Marcel P. et al. (2023) ‘Deletion of SNX9 alleviates CD8 T cell exhaustion for effective cellular cancer immunotherapy’, Nature Communications, 14(1). Available at: https://doi.org/10.1038/s41467-022-35583-w.

Klein, Fabian et al. (2023) ‘Combined multidimensional single-cell protein and RNA profiling dissects the cellular and functional heterogeneity of thymic epithelial cells’, Nature Communications, 14. Available at: https://doi.org/10.1038/s41467-023-39722-9.

Bentaleb, C. et al. (2022) ‘The endocytic recycling compartment serves as a viral factory for hepatitis E virus’, Cellular and Molecular Life Sciences, 79(12). Available at: https://doi.org/10.1007/s00018-022-04646-y.

Ham DJ et al. (2022) ‘Author Correction: Distinct and additive effects of calorie restriction and rapamycin in aging skeletal muscle.’, 13(1). Available at: https://doi.org/10.1038/s41467-022-30189-8.

Bentaleb, C. et al. (2021) ‘The Endocytic Recycling Compartment Serves as a Viral Factory for Hepatitis E Virus’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2021.10.14.464345.

Melhem, H. et al. (2021) ‘Epithelial GPR35 protects from Citrobacter rodentium infection by preserving goblet cells and mucosal barrier integrity’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2021.03.27.437264.

Dölz, M. et al. (2020) ‘The non-coding RNA miR-17~92 is a central mediator of T cell activation’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2020.10.13.336537.

Khan, P. et al. (2020) ‘In vitro culture of aberrant basal-like cells from fibrotic lung tissue’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2020.08.16.247866.

Selmoni, O.M. et al. (2020) ‘Erratum: Sex-specific changes in gene expression in response to estrogen pollution around the onset of sex differentiation in grayling (Salmonidae) (BMC Genomics (2019) 20: 583 DOI: 10.1186/s12864-019-5955-z)’, BMC Genomics, 21(1). Available at: https://doi.org/10.1186/s12864-020-06782-w.

Quero, Lilian et al. (2020) ‘miR-221-3p Drives the Shift of M2-Macrophages to a Pro-Inflammatory Function by Suppressing JAK3/STAT3 Activation’, Frontiers in Immunology, 10. Available at: https://doi.org/10.3389/fimmu.2019.03087.

Bosch, A.J.T. et al. (2019) ‘Air pollution mediates diabetes by disrupting gut innate mucosal immunity’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/827014.

Selmoni, O.M. et al. (2019) ‘Sex-specific changes in gene expression in response to estrogen pollution around the onset of sex differentiation in grayling (Salmonidae)’, BMC Genomics, 20(1). Available at: https://doi.org/10.1186/s12864-019-5955-z.

Blake, L.E. et al. (2018) ‘A comparison of gene expression and DNA methylation patterns across tissues and species’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/487413.

Pavlovic, B.J. et al. (2018) ‘A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues’, Scientific Reports, 8(1). Available at: https://doi.org/10.1038/s41598-018-33478-9.

Križanović, K. et al. (2018) ‘Evaluation of tools for long read RNA-seq splice-aware alignment’, Bioinformatics, 34(5), pp. 748–754. Available at: https://doi.org/10.1093/bioinformatics/btx668.

Komljenovic, A. et al. (2018) ‘BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests’, F1000Research, 5. Available at: https://doi.org/10.12688/f1000research.9973.2.

Börsch, Anastasiya and Schaber, Jörg (2016) ‘How time delay and network design shape response patterns in biochemical negative feedback systems’, BMC Systems Biology, 10. Available at: https://doi.org/10.1186/s12918-016-0325-9.