HTSeq—a Python framework to work with high-throughput sequencing data

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

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Trimmomatic: a flexible trimmer for Illumina sequence data

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The Sequence Alignment/Map format and SAMtools

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<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

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BEDTools: a flexible suite of utilities for comparing genomic features

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featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

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Differential expression analysis for sequence count data

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Bioconductor: open software development for computational biology and bioinformatics

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The NumPy Array: A Structure for Efficient Numerical Computation

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Biopython: freely available python tools for computational molecular biology and bioinformatics

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Epigenetics and energetics in ventral hippocampus mediate rapid antidepressant action: Implications for treatment resistance

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Alternative splicing rewires Hippo signaling pathway in hepatocytes to promote liver regeneration

Bangru, S., Arif, W., Seimetz, J., Bhate, A., Chen, J., Rashan, E. H., Carstens, R. P., Anakk, S., & Kalsotra, A. (2018) · Nature Structural & Molecular Biology · doi:10.1038/s41594-018-0129-2 · Cited by 85

Glial gene networks associated with alcohol dependence

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Neurons burdened by DNA double-strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration

Welch, G. M., Boix, C. A., Schmauch, E., Davila-Velderrain, J., Victor, M. B., Dileep, V., Bozzelli, P. L., Su, Q., Cheng, J. D., Lee, A., et al. (2022) · Science Advances · doi:10.1126/sciadv.abo4662 · Cited by 84

Oligodendroglial α‐synucleinopathy‐driven neuroinflammation in multiple system atrophy

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Transcriptomic and anatomic parcellation of 5-HT3AR expressing cortical interneuron subtypes revealed by single-cell RNA sequencing

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Chromosome contacts in activated T cells identify autoimmune disease candidate genes

Burren, O. S., Rubio García, A., Javierre, B.-M., Rainbow, D. B., Cairns, J., Cooper, N. J., Lambourne, J. J., Schofield, E., Castro Dopico, X., Ferreira, R. C., et al. (2017) · Genome Biology · doi:10.1186/s13059-017-1285-0 · Cited by 80

Acquired resistance to KRAS G12C small-molecule inhibitors via genetic/nongenetic mechanisms in lung cancer

Mohanty, A., Nam, A., Srivastava, S., Jones, J., Lomenick, B., Singhal, S. S., Guo, L., Cho, H., Li, A., Behal, A., et al. (2023) · Science Advances · doi:10.1126/sciadv.ade3816 · Cited by 79

Networks of Cultured iPSC-Derived Neurons Reveal the Human Synaptic Activity-Regulated Adaptive Gene Program

Pruunsild, P., Bengtson, C. P., & Bading, H. (2017) · Cell Reports · doi:10.1016/j.celrep.2016.12.018 · Cited by 78

An Induced Pluripotent Stem Cell Patient Specific Model of Complement Factor H (Y402H) Polymorphism Displays Characteristic Features of Age-Related Macular Degeneration and Indicates a Beneficial Role for UV Light Exposure

Hallam, D., Collin, J., Bojic, S., Chichagova, V., Buskin, A., Xu, Y., Lafage, L., Otten, E. G., Anyfantis, G., Mellough, C., et al. (2017) · Stem Cells · doi:10.1002/stem.2708 · Cited by 75

Global long non-coding RNA expression in the rostral anterior cingulate cortex of depressed suicides

Zhou, Y., Lutz, P.-E., Wang, Y. C., Ragoussis, J., & Turecki, G. (2018) · Translational Psychiatry · doi:10.1038/s41398-018-0267-7 · Cited by 77

Computational design of epitope-specific functional antibodies

Nimrod, G., Fischman, S., Austin, M., Herman, A., Keyes, F., Leiderman, O., Hargreaves, D., Strajbl, M., Breed, J., Klompus, S., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.10.081 · Cited by 77

Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons

Luo, C., Lee, Q. Y., Wapinski, O., Castanon, R., Nery, J. R., Mall, M., Kareta, M. S., Cullen, S. M., Goodell, M. A., Chang, H. Y., et al. (2019) · eLife · doi:10.7554/elife.40197 · Cited by 76

A Cancer-Specific Ubiquitin Ligase Drives mRNA Alternative Polyadenylation by Ubiquitinating the mRNA 3′ End Processing Complex

Yang, S. W., Li, L., Connelly, J. P., Porter, S. N., Kodali, K., Gan, H., Park, J. M., Tacer, K. F., Tillman, H., Peng, J., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2019.12.022 · Cited by 79

Repression of p63 and induction of EMT by mutant Ras in mammary epithelial cells

Yoh, K. E., Regunath, K., Guzman, A., Lee, S.-M., Pfister, N. T., Akanni, O., Kaufman, L. J., Prives, C., & Prywes, R. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1613417113 · Cited by 75

Sustained perfusion of revascularized bioengineered livers heterotopically transplanted into immunosuppressed pigs

Shaheen, M. F., Joo, D. J., Ross, J. J., Anderson, B. D., Chen, H. S., Huebert, R. C., Li, Y., Amiot, B., Young, A., Zlochiver, V., et al. (2019) · Nature Biomedical Engineering · doi:10.1038/s41551-019-0460-x · Cited by 75

Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency

Pękowska, A., Klaus, B., Xiang, W., Severino, J., Daigle, N., Klein, F. A., Oleś, M., Casellas, R., Ellenberg, J., Steinmetz, L. M., et al. (2018) · Cell Systems · doi:10.1016/j.cels.2018.09.003 · Cited by 74

Regulation of early T-lineage gene expression and developmental progression by the progenitor cell transcription factor PU.1

Champhekar, A., Damle, S. S., Freedman, G., Carotta, S., Nutt, S. L., & Rothenberg, E. V. (2015) · Genes & Development · doi:10.1101/gad.259879.115 · Cited by 74

Telomere damage promotes vascular smooth muscle cell senescence and immune cell recruitment after vessel injury

Uryga, A. K., Grootaert, M. O. J., Garrido, A. M., Oc, S., Foote, K., Chappell, J., Finigan, A., Rossiello, F., d’Adda di Fagagna, F., Aravani, D., et al. (2021) · Communications Biology · doi:10.1038/s42003-021-02123-z · Cited by 73

Foxp1 in Forebrain Pyramidal Neurons Controls Gene Expression Required for Spatial Learning and Synaptic Plasticity

Araujo, D. J., Toriumi, K., Escamilla, C. O., Kulkarni, A., Anderson, A. G., Harper, M., Usui, N., Ellegood, J., Lerch, J. P., Birnbaum, S. G., et al. (2017) · The Journal of Neuroscience · doi:10.1523/jneurosci.1005-17.2017 · Cited by 73

Telomerase reverse transcriptase preserves neuron survival and cognition in Alzheimer’s disease models

Shim, H. S., Horner, J. W., Wu, C.-J., Li, J., Lan, Z. D., Jiang, S., Xu, X., Hsu, W.-H., Zal, T., Flores, I. I., et al. (2021) · Nature Aging · doi:10.1038/s43587-021-00146-z · Cited by 73

Impaired plasticity of macrophages in X-linked adrenoleukodystrophy

Weinhofer, I., Zierfuss, B., Hametner, S., Wagner, M., Popitsch, N., Machacek, C., Bartolini, B., Zlabinger, G., Ohradanova-Repic, A., Stockinger, H., et al. (2018) · Brain · doi:10.1093/brain/awy127 · Cited by 72

Tumour gene expression signature in primary melanoma predicts long-term outcomes

Garg, M., Couturier, D.-L., Nsengimana, J., Fonseca, N. A., Wongchenko, M., Yan, Y., Lauss, M., Jönsson, G. B., Newton-Bishop, J., Parkinson, C., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21207-2 · Cited by 70

Mutational signatures reveal the role of RAD52 in p53-independent p21-driven genomic instability

Galanos, P., Pappas, G., Polyzos, A., Kotsinas, A., Svolaki, I., Giakoumakis, N. N., Glytsou, C., Pateras, I. S., Swain, U., Souliotis, V. L., et al. (2018) · Genome Biology · doi:10.1186/s13059-018-1401-9 · Cited by 67

Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition

Bues, J., Biočanin, M., Pezoldt, J., Dainese, R., Chrisnandy, A., Rezakhani, S., Saelens, W., Gardeux, V., Gupta, R., Sarkis, R., et al. (2022) · Nature Methods · doi:10.1038/s41592-021-01391-1 · Cited by 71

Berberine reverses multidrug resistance in Candida albicans by hijacking the drug efflux pump Mdr1p

Tong, Y., Zhang, J., Sun, N., Wang, X.-M., Wei, Q., Zhang, Y., Huang, R., Pu, Y., Dai, H., Ren, B., et al. (2021) · Science Bulletin · doi:10.1016/j.scib.2020.12.035 · Cited by 70

HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy

Jiang, Q., Braun, D. A., Clauser, K. R., Ramesh, V., Shirole, N. H., Duke-Cohan, J. E., Nabilsi, N., Kramer, N. J., Forman, C., Lippincott, I. E., et al. (2025) · Cell · doi:10.1016/j.cell.2025.01.046 · Cited by 68

High‐throughput sequencing identifies aetiology‐dependent differences in ductular reaction in human chronic liver disease

Govaere, O., Cockell, S., Van Haele, M., Wouters, J., Van Delm, W., Van den Eynde, K., Bianchi, A., van Eijsden, R., Van Steenbergen, W., Monbaliu, D., et al. (2019) · The Journal of Pathology · doi:10.1002/path.5228 · Cited by 61

Novel atherogenic pathways from the differential transcriptome analysis of diabetic epicardial adipose, tissue

Camarena, V., Sant, D., Mohseni, M., Salerno, T., Zaleski, M. L., Wang, G., & Iacobellis, G. (2017) · Nutrition Metabolism and Cardiovascular Diseases · doi:10.1016/j.numecd.2017.05.010 · Cited by 67

The genomic landscape of 8-oxodG reveals enrichment at specific inherently fragile promoters

Gorini, F., Scala, G., Di Palo, G., Dellino, G. I., Cocozza, S., Pelicci, P. G., Lania, L., Majello, B., & Amente, S. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa175 · Cited by 67

Transcriptome sequencing implicates dorsal striatum-specific gene network, immune response and energy metabolism pathways in bipolar disorder

Pacifico, R., & Davis, R. L. (2017) · Molecular Psychiatry · doi:10.1038/mp.2016.94 · Cited by 61

Negative autoregulation mitigates collateral RNase activity of repeat-targeting CRISPR-Cas13d in mammalian cells

Kelley, C. P., Haerle, M. C., & Wang, E. T. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111226 · Cited by 61

Sodium oligomannate alters gut microbiota, reduces cerebral amyloidosis and reactive microglia in a sex-specific manner

Bosch, M. E., Dodiya, H. B., Michalkiewicz, J., Lee, C., Shaik, S. M., Weigle, I. Q., Zhang, C., Osborn, J., Nambiar, A., Patel, P., et al. (2024) · Molecular Neurodegeneration · doi:10.1186/s13024-023-00700-w · Cited by 70

USP7 deubiquitinates and stabilizes NOTCH1 in T-cell acute lymphoblastic leukemia

Shan, H., Li, X., Xiao, X., Dai, Y., Huang, J., Song, J., Liu, M., Yang, L., Lei, H., Tong, Y., et al. (2018) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-018-0028-3 · Cited by 66

An LaeA- and BrlA-Dependent Cellular Network Governs Tissue-Specific Secondary Metabolism in the Human Pathogen Aspergillus fumigatus

Lind, A. L., Lim, F. Y., Soukup, A. A., Keller, N. P., & Rokas, A. (2018) · mSphere · doi:10.1128/msphere.00050-18 · Cited by 64

Neoantigen-specific immunity in low mutation burden colorectal cancers of the consensus molecular subtype 4

van den Bulk, J., Verdegaal, E. M. E., Ruano, D., Ijsselsteijn, M. E., Visser, M., van der Breggen, R., Duhen, T., van der Ploeg, M., de Vries, N. L., Oosting, J., et al. (2019) · Genome Medicine · doi:10.1186/s13073-019-0697-8 · Cited by 63

2-Deoxyglucose drives plasticity via an adaptive ER stress-ATF4 pathway and elicits stroke recovery and Alzheimer’s resilience

Kumar, A., Karuppagounder, S. S., Chen, Y., Corona, C., Kawaguchi, R., Cheng, Y., Balkaya, M., Sagdullaev, B. T., Wen, Z., Stuart, C., et al. (2023) · Neuron · doi:10.1016/j.neuron.2023.06.013 · Cited by 64

Deep immune phenotyping reveals similarities between aging, Down syndrome, and autoimmunity

Lambert, K., Moo, K. G., Arnett, A., Goel, G., Hu, A., Flynn, K. J., Speake, C., Wiedeman, A. E., Gersuk, V. H., Linsley, P. S., et al. (2022) · Science Translational Medicine · doi:10.1126/scitranslmed.abi4888 · Cited by 64

Multi-omics analysis reveals contextual tumor suppressive and oncogenic gene modules within the acute hypoxic response

Andrysik, Z., Bender, H., Galbraith, M. D., & Espinosa, J. M. (2021) · Nature Communications · doi:10.1038/s41467-021-21687-2 · Cited by 63

IRX3 and IRX5 Inhibit Adipogenic Differentiation of Hypertrophic Chondrocytes and Promote Osteogenesis

Tan, Z., Kong, M., Wen, S., Tsang, K. Y., Niu, B., Hartmann, C., Chan, D., Hui, C.-C., & Cheah, K. S. E. (2020) · Journal of Bone and Mineral Research · doi:10.1002/jbmr.4132 · Cited by 52

Single-cell multi-omics sequencing of human spermatogenesis reveals a DNA demethylation event associated with male meiotic recombination

Huang, Y., Li, L., An, G., Yang, X., Cui, M., Song, X., Lin, J., Zhang, X., Yao, Z., Wan, C., et al. (2023) · Nature Cell Biology · doi:10.1038/s41556-023-01232-7 · Cited by 59

Aster-dependent nonvesicular transport facilitates dietary cholesterol uptake

Ferrari, A., Whang, E., Xiao, X., Kennelly, J. P., Romartinez-Alonso, B., Mack, J. J., Weston, T., Chen, K., Kim, Y., Tol, M. J., et al. (2023) · Science · doi:10.1126/science.adf0966 · Cited by 61

Bone morphogenetic protein 8B promotes the progression of non-alcoholic steatohepatitis

Vacca, M., Leslie, J., Virtue, S., Lam, B. Y. H., Govaere, O., Tiniakos, D., Snow, S., Davies, S., Petkevicius, K., Tong, Z., et al. (2020) · Nature Metabolism · doi:10.1038/s42255-020-0214-9 · Cited by 60

Blocking siglec-10hi tumor-associated macrophages improves anti-tumor immunity and enhances immunotherapy for hepatocellular carcinoma

Xiao, N., Zhu, X., Li, K., Chen, Y., Liu, X., Xu, B., Lei, M., Xu, J., & Sun, H.-C. (2021) · Experimental Hematology & Oncology · doi:10.1186/s40164-021-00230-5 · Cited by 61

The MazF-regulon: a toolbox for the post-transcriptional stress response in Escherichia coli

Sauert, M., Wolfinger, M. T., Vesper, O., Müller, C., Byrgazov, K., & Moll, I. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw115 · Cited by 57

Primate innate immune responses to bacterial and viral pathogens reveals an evolutionary trade-off between strength and specificity

Hawash, M. B. F., Sanz-Remón, J., Grenier, J.-C., Kohn, J., Yotova, V., Johnson, Z., Lanford, R. E., Brinkworth, J. F., & Barreiro, L. B. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2015855118 · Cited by 56

A fluorophore-conjugated reagent enabling rapid detection, isolation and live tracking of senescent cells

Magkouta, S., Veroutis, D., Pousias, A., Papaspyropoulos, A., Pippa, N., Lougiakis, N., Kambas, K., Lagopati, N., Polyzou, A., Georgiou, M., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.09.006 · Cited by 59

The statistical geometry of transcriptome divergence in cell-type evolution and cancer

Liang, C., the FANTOM Consortium, Forrest, A. R. R., & Wagner, G. P. (2015) · Nature Communications · doi:10.1038/ncomms7066 · Cited by 59

In vivo CRISPR screening identifies BAZ2 chromatin remodelers as druggable regulators of mammalian liver regeneration

Jia, Y., Li, L., Lin, Y.-H., Gopal, P., Shen, S., Zhou, K., Yu, X., Sharma, T., Zhang, Y., Siegwart, D. J., et al. (2022) · Cell Stem Cell · doi:10.1016/j.stem.2022.01.001 · Cited by 59

Honokiol induces superoxide production by targeting mitochondrial respiratory chain complex I in Candida albicans

Sun, L., Liao, K., & Wang, D. (2017) · PLOS ONE · doi:10.1371/journal.pone.0184003 · Cited by 57

Deletion of Abi3 gene locus exacerbates neuropathological features of Alzheimer’s disease in a mouse model of Aβ amyloidosis

Karahan, H., Smith, D. C., Kim, B., Dabin, L. C., Al-Amin, M. M., Wijeratne, H. R. S., Pennington, T., Viana di Prisco, G., McCord, B., Lin, P. B.-C., et al. (2021) · Science Advances · doi:10.1126/sciadv.abe3954 · Cited by 53

The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways

Tscherner, M., Zwolanek, F., Jenull, S., Sedlazeck, F. J., Petryshyn, A., Frohner, I. E., Mavrianos, J., Chauhan, N., von Haeseler, A., & Kuchler, K. (2015) · PLOS Pathogens · doi:10.1371/journal.ppat.1005218 · Cited by 57

The Fungal Histone Acetyl Transferase Gcn5 Controls Virulence of the Human Pathogen Candida albicans through Multiple Pathways

Shivarathri, R., Tscherner, M., Zwolanek, F., Singh, N. K., Chauhan, N., & Kuchler, K. (2019) · Scientific Reports · doi:10.1038/s41598-019-45817-5 · Cited by 58

Astrocyte-specific transcriptome responses to chronic ethanol consumption

Erickson, E. K., Farris, S. P., Blednov, Y. A., Mayfield, R. D., & Harris, R. A. (2018) · The Pharmacogenomics Journal · doi:10.1038/s41397-017-0012-2 · Cited by 56

Zinc finger protein SALL4 functions through an AT-rich motif to regulate gene expression

Kong, N. R., Bassal, M. A., Tan, H. K., Kurland, J. V., Yong, K. J., Young, J. J., Yang, Y., Li, F., Lee, J. D., Liu, Y., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2020.108574 · Cited by 56

Reversal of liver failure using a bioartificial liver device implanted with clinical-grade human-induced hepatocytes

Wang, Y., Zheng, Q., Sun, Z., Wang, C., Cen, J., Zhang, X., Jin, Y., Wu, B., Yan, T., Wang, Z., et al. (2023) · Cell Stem Cell · doi:10.1016/j.stem.2023.03.013 · Cited by 55

TFEB Transcriptional Responses Reveal Negative Feedback by BHLHE40 and BHLHE41

Carey, K. L., Paulus, G. L. C., Wang, L., Balce, D. R., Luo, J. W., Bergman, P., Ferder, I. C., Kong, L., Renaud, N., Singh, S., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108371 · Cited by 55

Differences in DNA repair capacity, cell death and transcriptional response after irradiation between a radiosensitive and a radioresistant cell line

Borràs-Fresneda, M., Barquinero, J.-F., Gomolka, M., Hornhardt, S., Rössler, U., Armengol, G., & Barrios, L. (2016) · Scientific Reports · doi:10.1038/srep27043 · Cited by 54

Functional identity of hypothalamic melanocortin neurons depends on Tbx3

Quarta, C., Fisette, A., Xu, Y., Colldén, G., Legutko, B., Tseng, Y.-T., Reim, A., Wierer, M., De Rosa, M. C., Klaus, V., et al. (2019) · Nature Metabolism · doi:10.1038/s42255-018-0028-1 · Cited by 54

Small‐molecule‐mediated chemical knock‐down of MuRF1/MuRF2 and attenuation of diaphragm dysfunction in chronic heart failure

Adams, V., Bowen, T. S., Werner, S., Barthel, P., Amberger, C., Konzer, A., Graumann, J., Sehr, P., Lewis, J., Provaznik, J., et al. (2019) · Journal of Cachexia, Sarcopenia and Muscle · doi:10.1002/jcsm.12448 · Cited by 51

Regulation of angiopoietin-like protein 4 production during and after exercise

Norheim, F., Hjorth, M., Langleite, T. M., Lee, S., Holen, T., Bindesbøll, C., Stadheim, H. K., Gulseth, H. L., Birkeland, K. I., Kielland, A., et al. (2014) · Physiological Reports · doi:10.14814/phy2.12109 · Cited by 53

Telomere shortening leads to an acceleration of synucleinopathy and impaired microglia response in a genetic mouse model

Scheffold, A., Holtman, I. R., Dieni, S., Brouwer, N., Katz, S.-F., Jebaraj, B. M. C., Kahle, P. J., Hengerer, B., Lechel, A., Stilgenbauer, S., et al. (2016) · Acta Neuropathologica Communications · doi:10.1186/s40478-016-0364-x · Cited by 53

A bio-functional polymer that prevents retinal scarring through modulation of NRF2 signalling pathway

Parikh, B. H., Liu, Z., Blakeley, P., Lin, Q., Singh, M., Ong, J. Y., Ho, K. H., Lai, J. W., Bogireddi, H., Tran, K. C., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30474-6 · Cited by 54

Arid1a restrains Kras-dependent changes in acinar cell identity

Livshits, G., Alonso-Curbelo, D., Morris, J. P., Koche, R., Saborowski, M., Wilkinson, J. E., & Lowe, S. W. (2018) · eLife · doi:10.7554/elife.35216 · Cited by 48

Histone Lysine Methylation Dynamics Control EGFR DNA Copy-Number Amplification

Clarke, T. L., Tang, R., Chakraborty, D., Van Rechem, C., Ji, F., Mishra, S., Ma, A., Kaniskan, H. Ü., Jin, J., Lawrence, M. S., et al. (2020) · Cancer Discovery · doi:10.1158/2159-8290.cd-19-0463 · Cited by 50

Mesenchymal stromal cell activation by breast cancer secretomes in bioengineered 3D microenvironments

Blache, U., Horton, E. R., Xia, T., Schoof, E. M., Blicher, L. H., Schönenberger, A., Snedeker, J. G., Martin, I., Erler, J. T., & Ehrbar, M. (2019) · Life Science Alliance · doi:10.26508/lsa.201900304 · Cited by 49

Human iPSC-derived Down syndrome astrocytes display genome-wide perturbations in gene expression, an altered adhesion profile, and increased cellular dynamics

Ponroy Bally, B., Farmer, W. T., Jones, E. V., Jessa, S., Kacerovsky, J. B., Mayran, A., Peng, H., Lefebvre, J. L., Drouin, J., Hayer, A., et al. (2020) · Human Molecular Genetics · doi:10.1093/hmg/ddaa003 · Cited by 49

A nonredundant role for T cell-derived interleukin 22 in antibacterial defense of colonic crypts

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Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice

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Cooperation of Nutlin-3a and a Wip1 inhibitor to induce p53 activity

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The Rim pathway mediates antifungal tolerance in Candida albicans through newly identified Rim101 transcriptional targets, including Hsp90 and Ipt1

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Increased Type I interferon signaling and brain endothelial barrier dysfunction in an experimental model of Alzheimer’s disease

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Genetic perturbations of disease risk genes in mice capture transcriptomic signatures of late-onset Alzheimer’s disease

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Identification and Characterization of Oncogenic SOS1 Mutations in Lung Adenocarcinoma

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The RUNX1/IL-34/CSF-1R axis is an autocrinally regulated modulator of resistance to BRAF-V600E inhibition in melanoma

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Comparative Transcriptomics Reveal Possible Mechanisms of Amphotericin B Resistance in Candida auris

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Transcriptome Analysis Uncovers a Link Between Copper Metabolism, and Both Fungal Fitness and Antifungal Sensitivity in the Opportunistic Yeast Candida albicans

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CDK4 inhibition diminishes p53 activation by MDM2 antagonists

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Resveratrol improves muscle regeneration in obese mice through enhancing mitochondrial biogenesis

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Lung endothelium exploits susceptible tumor cell states to instruct metastatic latency

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Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria

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Comparative MRNA-Seq Analysis Reveals the Improved EPS Production Machinery in Streptococcus Thermophilus ASCC 1275 during Optimized Milk Fermentation

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Genetic interaction mapping informs integrative structure determination of protein complexes

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Aging is associated with an expansion of CD49fhi mammary stem cells that show a decline in function and increased transformation potential

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Nicotinamide mononucleotide reduces melanin production in aged melanocytes by inhibiting cAMP/Wnt signaling

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Loss of FOXA2 induces ER stress and hepatic steatosis and alters developmental gene expression in human iPSC-derived hepatocytes

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Semaglutide ameliorates Alzheimer's disease and restores oxytocin in APP/PS1 mice and human brain organoid models

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Stimulation of superoxide production increases fungicidal action of miconazole against Candida albicans biofilms

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Directed Evolution Detects Supernumerary Centric Chromosomes Conferring Resistance to Azoles in Candida auris

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Transcriptomics and Phenotyping Define Genetic Signatures Associated with Echinocandin Resistance in Candida auris

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Hepatic SREBP signaling requires SPRING to govern systemic lipid metabolism in mice and humans

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Nonredundant, isoform-specific roles of HDAC1 in glioma stem cells

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Yap1 Mediates Trametinib Resistance in Head and Neck Squamous Cell Carcinomas

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Transcriptome Signatures Predict Phenotypic Variations of Candida auris

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The R136S mutation in the APOE3 gene confers resilience against tau pathology via inhibition of the cGAS-STING-IFN pathway

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Transcriptional profiling of normal, stenotic, and regurgitant human aortic valves

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Short and dysfunctional telomeres sensitize the kidneys to develop fibrosis

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The Set1 Histone H3K4 Methyltransferase Contributes to Azole Susceptibility in a Species-Specific Manner by Differentially Altering the Expression of Drug Efflux Pumps and the Ergosterol Gene Pathway

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New Cell Adhesion Molecules in Human Ischemic Cardiomyopathy. PCDHGA3 Implications in Decreased Stroke Volume and Ventricular Dysfunction

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Analysing high-throughput sequencing data in Python with HTSeq 2.0

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A Simple Process of RNA-Sequence Analyses by Hisat2, Htseq and DESeq2

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