MultiQC: summarize analysis results for multiple tools and samples in a single report

Matplotlib: a 2D graphics environment

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Conserved pan-cancer microenvironment subtypes predict response to immunotherapy

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Next-Generation Sequencing Technology: Current Trends and Advancements

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The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight

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RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types

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Bias, robustness and scalability in single-cell differential expression analysis

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Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease

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Biallelic expansion of an intronic repeat in RFC1 is a common cause of late-onset ataxia

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Colorectal Cancer Cells Enter a Diapause-like DTP State to Survive Chemotherapy

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Non-classical Immunity Controls Microbiota Impact on Skin Immunity and Tissue Repair

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Akkermansia muciniphila phospholipid induces homeostatic immune responses

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Global characterization of macrophage polarization mechanisms and identification of M2-type polarization inhibitors

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Acquired Resistance to BET-PROTACs (Proteolysis-Targeting Chimeras) Caused by Genomic Alterations in Core Components of E3 Ligase Complexes

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The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy

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A selective gut bacterial bile salt hydrolase alters host metabolism

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Truncated stathmin-2 is a marker of TDP-43 pathology in frontotemporal dementia

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Tissue damage induces a conserved stress response that initiates quiescent muscle stem cell activation

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Syntrophy via Interspecies H ₂ Transfer between <i>Christensenella</i> and <i>Methanobrevibacter</i> Underlies Their Global Cooccurrence in the Human Gut

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Monocytes re-enter the bone marrow during fasting and alter the host response to infection

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Integrative transcriptomic analysis of the amyotrophic lateral sclerosis spinal cord implicates glial activation and suggests new risk genes

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Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome

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High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development

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Interaction between estrogen receptor-α and PNPLA3 p.I148M variant drives fatty liver disease susceptibility in women

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Micro-environmental sensing by bone marrow stroma identifies IL-6 and TGFβ1 as regulators of hematopoietic ageing

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Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF

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Gut microbiota–driven brain Aβ amyloidosis in mice requires microglia

Dodiya, H. B., Lutz, H. L., Weigle, I. Q., Patel, P., Michalkiewicz, J., Roman-Santiago, C. J., Zhang, C. M., Liang, Y., Srinath, A., Zhang, X., et al. (2022) · Journal of Experimental Medicine · doi:10.1084/jem.20200895 · Cited by 120 · see citing works

Social isolation alters behavior, the gut-immune-brain axis, and neurochemical circuits in male and female prairie voles

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Early-life formula feeding is associated with infant gut microbiota alterations and an increased antibiotic resistance load

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Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes

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Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries

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Candida pathogens induce protective mitochondria-associated type I interferon signalling and a damage-driven response in vaginal epithelial cells

Pekmezovic, M., Hovhannisyan, H., Gresnigt, M. S., Iracane, E., Oliveira-Pacheco, J., Siscar-Lewin, S., Seemann, E., Qualmann, B., Kalkreuter, T., Müller, S., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00875-2 · Cited by 96 · see citing works

Novel insights from a multiomics dissection of the Hayflick limit

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Reduced mitochondrial calcium uptake in macrophages is a major driver of inflammaging

Seegren, P. V., Harper, L. R., Downs, T. K., Zhao, X.-Y., Viswanathan, S. B., Stremska, M. E., Olson, R. J., Kennedy, J., Ewald, S. E., Kumar, P., et al. (2023) · Nature Aging · doi:10.1038/s43587-023-00436-8 · Cited by 88 · see citing works

Genetic, epigenetic, and environmental factors controlling oxytocin receptor gene expression

Danoff, J. S., Wroblewski, K. L., Graves, A. J., Quinn, G. C., Perkeybile, A. M., Kenkel, W. M., Lillard, T. S., Parikh, H. I., Golino, H. F., Gregory, S. G., et al. (2021) · Clinical Epigenetics · doi:10.1186/s13148-021-01017-5 · Cited by 85 · see citing works

Colibactin-driven colon cancer requires adhesin-mediated epithelial binding

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Regionally Distinct Astrocytes Display Unique Transcription Factor Profiles in the Adult Brain

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Intrinsic IL-2 production by effector CD8 T cells affects IL-2 signaling and promotes fate decisions, stemness, and protection

Kahan, S. M., Bakshi, R. K., Ingram, J. T., Hendrickson, R. C., Lefkowitz, E. J., Crossman, D. K., Harrington, L. E., Weaver, C. T., & Zajac, A. J. (2022) · Science Immunology · doi:10.1126/sciimmunol.abl6322 · Cited by 67 · see citing works

The Epigenetic Evolution of Glioma Is Determined by the <i>IDH1</i> Mutation Status and Treatment Regimen

Malta, T. M., Sabedot, T. S., Morosini, N. S., Datta, I., Garofano, L., Vallentgoed, W., Varn, F. S., Aldape, K., D'Angelo, F., Bakas, S., et al. (2024) · Cancer Research · doi:10.1158/0008-5472.can-23-2093 · Cited by 68 · see citing works

The Oral Microbiome and Inflammation in Mild Cognitive Impairment

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Aducanumab anti-amyloid immunotherapy induces sustained microglial and immune alterations

Cadiz, M. P., Gibson, K. A., Todd, K. T., Nascari, D. G., Massa, N., Lilley, M. T., Olney, K. C., Al-Amin, M. M., Jiang, H., Holtzman, D. M., et al. (2024) · Journal of Experimental Medicine · doi:10.1084/jem.20231363 · Cited by 55 · see citing works

Revealing the microbial heritage of traditional Brazilian cheeses through metagenomics

Kothe, C. I., Mohellibi, N., & Renault, P. (2022) · Food Research International · doi:10.1016/j.foodres.2022.111265 · Cited by 51 · see citing works

The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Rocafort, M., Bowen, J. K., Hassing, B., Cox, M. P., McGreal, B., de la Rosa, S., Plummer, K. M., Bradshaw, R. E., & Mesarich, C. H. (2022) · BMC Biology · doi:10.1186/s12915-022-01442-9 · Cited by 52 · see citing works

Integrative genomic analyses identify candidate causal genes for calcific aortic valve stenosis involving tissue-specific regulation

Thériault, S., Li, Z., Abner, E., Luan, J., Manikpurage, H. D., Houessou, U., Zamani, P., Briend, M., Estonian Biobank Research Team, Boudreau, D. K., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-46639-4 · Cited by 49 · see citing works

Identification of Hypoxia-Specific Biomarkers in Salmonids Using RNA-Sequencing and Validation Using High-Throughput qPCR

Akbarzadeh, A., Houde, A. L. S., Sutherland, B. J. G., Günther, O. P., & Miller, K. M. (2020) · G3 Genes|Genomes|Genetics · doi:10.1534/g3.120.401487 · Cited by 40 · see citing works

Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes

Proctor, D. M., Sansom, S. E., Deming, C., Conlan, S., Blaustein, R. A., Atkins, T. K., Program, N. C. S., Mullikin, J., Thomas, J., Young, A., et al. (2025) · Nature · doi:10.1038/s41586-025-08608-9 · Cited by 37 · see citing works

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

Narayanan, A., Kumar, P., Chauhan, A., Kumar, M., Yadav, K., Banerjee, A., Sharma, R. D., Rudramurthy, S. M., Chakrabarti, A., Sanyal, K., et al. (2022) · mBio · doi:10.1128/mbio.03052-22 · Cited by 35 · see citing works

Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome

Samarra, A., Alcañiz, A. J., Martínez-Costa, C., Marina, A., Comas, I., Segata, N., Quijada, N. M., & Collado, M. C. (2025) · Nature Communications · doi:10.1038/s41467-025-61154-w · Cited by 32 · see citing works

A Game Changer for Bipolar Disorder Diagnosis Using RNA Editing-Based Biomarkers

Salvetat, N., Checa-Robles, F. J., Patel, V., Cayzac, C., Dubuc, B., Chimienti, F., Abraham, J.-D., Dupré, P., Vetter, D., Méreuze, S., et al. (2022) · Translational Psychiatry · doi:10.1038/s41398-022-01938-6 · Cited by 31 · see citing works

The dynamics of adaptation to stress from standing genetic variation and de novo mutations

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B cell-derived acetylcholine promotes liver regeneration by regulating Kupffer cell and hepatic CD8+ T cell function

Modares, N. F., Hendrikse, L. D., Smith, L. K., Paul, M. S., Haight, J., Luo, P., Liu, S., Fortin, J., Tong, F. K., Wakeham, A. C., et al. (2025) · Immunity · doi:10.1016/j.immuni.2025.04.002 · Cited by 29 · see citing works

Transcriptomic and genomic studies classify NKL54 as a histone deacetylase inhibitor with indirect influence on MEF2-dependent transcription

Minisini, M., Di Giorgio, E., Kerschbamer, E., Dalla, E., Faggiani, M., Franforte, E., Meyer-Almes, F.-J., Ragno, R., Antonini, L., Mai, A., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac081 · Cited by 28 · see citing works

Overlooked <i>Candida glabrata</i> petites are echinocandin tolerant, induce host inflammatory responses, and display poor <i>in vivo</i> fitness

Arastehfar, A., Daneshnia, F., Hovhannisyan, H., Fuentes, D., Cabrera, N., Quinteros, C., Ilkit, M., Ünal, N., Hilmioğlu-Polat, S., Jabeen, K., et al. (2023) · mBio · doi:10.1128/mbio.01180-23 · Cited by 27 · see citing works

Whole Blood Transcriptome Analysis Reveals Footprints of Cattle Adaptation to Sub-Arctic Conditions

Pokharel, K., Weldenegodguad, M., Popov, R., Honkatukia, M., Huuki, H., Lindeberg, H., Peippo, J., Reilas, T., Zarovnyaev, S., & Kantanen, J. (2019) · Animal Genetics · doi:10.1111/age.12783 · Cited by 23 · see citing works

Population genomics of the muskox' resilience in the near absence of genetic variation

Pečnerová, P., Lord, E., Garcia‐Erill, G., Hanghøj, K., Rasmussen, M. S., Meisner, J., Liu, X., van der Valk, T., Santander, C. G., Quinn, L., et al. (2024) · Molecular Ecology · doi:10.1111/mec.17205 · Cited by 19 · see citing works

The small CRL4CSA ubiquitin ligase component DDA1 regulates transcription-coupled repair dynamics

Llerena Schiffmacher, D. A., Lee, S.-H., Kliza, K. W., Theil, A. F., Akita, M., Helfricht, A., Bezstarosti, K., Gonzalo-Hansen, C., van Attikum, H., Verlaan-de Vries, M., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-50584-7 · Cited by 19 · see citing works

Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

Viner, C., Ishak, C. A., Johnson, J., Walker, N. J., Shi, H., Sjöberg-Herrera, M. K., Shen, S. Y., Lardo, S. M., Adams, D. J., Ferguson-Smith, A. C., et al. (2016) · doi:10.1101/043794 · Cited by 18 · see citing works

Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis

Lim, B., Kamal, A., Gomez Ramos, B., Adrian Segarra, J. M., Ibarra, I. L., Dignas, L., Kindinger, T., Volz, K., Rahbari, M., Rahbari, N., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02081-w · Cited by 17 · see citing works

Long-term stability of acquired drug resistance and resistance associated mutations in the fungal pathogen Nakaseomyces glabratus (Candida glabrata)

Ksiezopolska, E., Schikora-Tamarit, M. À., Carlos Nunez-Rodriguez, J., & Gabaldón, T. (2024) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2024.1416509 · Cited by 15 · see citing works

Apolipoprotein E2 Stimulates Protein Synthesis and Promotes Melanoma Progression and Metastasis

Adaku, N., Ostendorf, B. N., Mei, W., & Tavazoie, S. F. (2023) · Cancer Research · doi:10.1158/0008-5472.can-23-1252 · Cited by 15 · see citing works

Differences in peripheral immune system gene expression in frontotemporal degeneration

Sawyer, R. P., Hill, E. J., Yokoyama, J., Medvedovic, M., Ren, Y., Zhang, X., Choubey, D., Shatz, R. S., Miller, B., & Woo, D. (2022) · Medicine · doi:10.1097/md.0000000000028645 · Cited by 9 · see citing works

Profiling the resistome and virulome of Bacillus strains used for probiotic-based sanitation: a multicenter WGS analysis

Bini, F., Soffritti, I., D’Accolti, M., Mazziga, E., Caballero, J. D., David, S., Argimon, S., Aanensen, D. M., Volta, A., Bisi, M., et al. (2025) · BMC Genomics · doi:10.1186/s12864-025-11582-1 · Cited by 11 · see citing works

Transcriptomic signatures of calcific aortic valve stenosis severity in human tricuspid and bicuspid aortic valves

Houessou, U., Zamani, P., Manikpurage, H. D., Li, Z., Gaudreault, N., Dahmene, M., Dagenais, F., Couture, C., Clavel, M.-A., Pibarot, P., et al. (2025) · JACC: Basic to Translational Science · doi:10.1016/j.jacbts.2025.01.018 · Cited by 11 · see citing works

Neural precursor cells rescue symptoms of Rett syndrome by activation of the Interferon γ pathway

Frasca, A., Miramondi, F., Butti, E., Indrigo, M., Balbontin Arenas, M., Postogna, F. M., Piffer, A., Bedogni, F., Pizzamiglio, L., Cambria, C., et al. (2024) · EMBO Molecular Medicine · doi:10.1038/s44321-024-00144-9 · Cited by 9 · see citing works

Effects of Resistant Starch on Symptoms, Fecal Markers and Gut Microbiota in Parkinson’s Disease – The RESISTA-PD Trial

Becker, A., Schmartz, G. P., Gröger, L., Grammes, N., Galata, V., Philippeit, H., Weiland, J., Ludwig, N., Meese, E., Tierling, S., et al. (2021) · doi:10.1101/2021.02.07.21251098 · Cited by 102 · see citing works

Role of natural transformation in the evolution of small cryptic plasmids in <i>Synechocystis</i> sp. <scp>PCC</scp> 6803

Nies, F., Wein, T., Hanke, D. M., Springstein, B. L., Alcorta, J., Taubenheim, C., & Dagan, T. (2023) · Environmental Microbiology Reports · doi:10.1111/1758-2229.13203 · Cited by 5 · see citing works

<i>TDP1</i> splice-site mutation causes HAP1 cell hypersensitivity to topoisomerase I inhibition

Goh, C. G., Bader, A. S., Tran, T.-A., Belotserkovskaya, R., D’Alessandro, G., & Jackson, S. P. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkae1163 · Cited by 5 · see citing works

Aortic valve-specific genes dysregulated in calcific aortic valve stenosis as potential biomarkers and therapeutic targets

Zamani, P., Houessou, U., Manikpurage, H. D., Li, Z., Dahmene, M., Gaudreault, N., Dagenais, F., Clavel, M.-A., Pibarot, P., Arsenault, B. J., et al. (2025) · Human Genetics and Genomics Advances · doi:10.1016/j.xhgg.2025.100448 · Cited by 3 · see citing works

Community‐Onset Fungemias: Epidemiology and Genomic Characterization at a Tertiary‐Care Hospital in Barcelona, Spain

Batista, C. S. P., Rivera, A., Alvarez Albarran, M. T., Rubio, M., Belen-Figas, I., Lopez-Querol, C., Miró, E., Navarro, F., & Sanchez-Reus, F. (2025) · Journal of Fungi · doi:10.3390/jof11110808 · Cited by 2 · see citing works

Connecting proteomics and genomics to identify causal biomarkers specific for aortic valve stenosis

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