Orchestrating high-throughput genomic analysis with Bioconductor

The Sequence Alignment/Map format and SAMtools

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An integrated encyclopedia of DNA elements in the human genome

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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

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Welcome to the tidyverse

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SCANPY: large-scale single-cell gene expression data analysis

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The Perseus computational platform for comprehensive analysis of (prote)omics data

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A survey of best practices for RNA-seq data analysis

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Current best practices in single-cell RNA-seq analysis: a tutorial

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ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization

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Scater: Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R

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ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

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DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA–gene interactions

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Differential abundance testing on single-cell data using k-nearest neighbor graphs

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Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease

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Orchestrating single-cell analysis with Bioconductor

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

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Splatter: simulation of single-cell RNA sequencing data

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Proteogenomic and metabolomic characterization of human glioblastoma

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Neuronal regulation of type 2 innate lymphoid cells via neuromedin U

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Proteogenomic characterization of pancreatic ductal adenocarcinoma

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Rapid non-uniform adaptation to conformation-specific KRAS(G12C) inhibition

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muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data

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Accessible, curated metagenomic data through ExperimentHub

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Single-cell analysis of mixed-lineage states leading to a binary cell fate choice

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Controlling Bias and inflation in epigenome- and transcriptome-wide association studies using the empirical null distribution

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CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data

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Nebulosa recovers single-cell gene expression signals by kernel density estimation

Alquicira-Hernandez, J., & Powell, J. E. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab003 · Cited by 381

Transcriptional signature in microglia associated with Aβ plaque phagocytosis

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The enteric nervous system relays psychological stress to intestinal inflammation

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Peripheral CD8+ T cell characteristics associated with durable responses to immune checkpoint blockade in patients with metastatic melanoma

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PACVr: plastome assembly coverage visualization in R

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Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data

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The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health

De Filippis, F., Pasolli, E., & Ercolini, D. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa015 · Cited by 303

HIF-1α and HIF-2α differently regulate tumour development and inflammation of clear cell renal cell carcinoma in mice

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Genomic atlas of the proteome from brain, CSF and plasma prioritizes proteins implicated in neurological disorders

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Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues

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Lipid abnormalities in atopic skin are driven by type 2 cytokines

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Hierarchy within the mammary STAT5-driven Wap super-enhancer

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PCGF3/5–PRC1 initiates Polycomb recruitment in X chromosome inactivation

Almeida, M., Pintacuda, G., Masui, O., Koseki, Y., Gdula, M., Cerase, A., Brown, D., Mould, A., Innocent, C., Nakayama, M., et al. (2017) · Science · doi:10.1126/science.aal2512 · Cited by 282

Synergy between Variant PRC1 Complexes Defines Polycomb-Mediated Gene Repression

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Neural stem cells traffic functional mitochondria via extracellular vesicles

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The natverse, a versatile toolbox for combining and analysing neuroanatomical data

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Fetuin B is a secreted hepatocyte factor linking steatosis to impaired glucose metabolism

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Evaluation of variability in human kidney organoids

Phipson, B., Er, P. X., Combes, A. N., Forbes, T. A., Howden, S. E., Zappia, L., Yen, H.-J., Lawlor, K. T., Hale, L. J., Sun, J., et al. (2019) · Nature Methods · doi:10.1038/s41592-018-0253-2 · Cited by 253

PRC1 catalytic activity is central to polycomb system function

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Activation of PDGF pathway links LMNA mutation to dilated cardiomyopathy

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Biological plasticity rescues target activity in CRISPR knock outs

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Single-nucleus transcriptome analysis reveals cell-type-specific molecular signatures across reward circuitry in the human brain

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Synthetic Lethal and Convergent Biological Effects of Cancer-Associated Spliceosomal Gene Mutations

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Effect of long-term caloric restriction on DNA methylation measures of biological aging in healthy adults from the CALERIE trial

Waziry, R., Ryan, C. P., Corcoran, D. L., Huffman, K. M., Kobor, M. S., Kothari, M., Graf, G. H., Kraus, V. B., Kraus, W. E., Lin, D. T. S., et al. (2023) · Nature Aging · doi:10.1038/s43587-022-00357-y · Cited by 217

MUON: multimodal omics analysis framework

Bredikhin, D., Kats, I., & Stegle, O. (2022) · Genome Biology · doi:10.1186/s13059-021-02577-8 · Cited by 216

High-throughput identification of human SNPs affecting regulatory element activity

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Orai1-Mediated Antimicrobial Secretion from Pancreatic Acini Shapes the Gut Microbiome and Regulates Gut Innate Immunity

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DUX4 recruits p300/CBP through its C-terminus and induces global H3K27 acetylation changes

Choi, S. H., Gearhart, M. D., Cui, Z., Bosnakovski, D., Kim, M., Schennum, N., & Kyba, M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw141 · Cited by 196

Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation

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Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem Cells

Rhodes, J. D. P., Feldmann, A., Hernández-Rodríguez, B., Díaz, N., Brown, J. M., Fursova, N. A., Blackledge, N. P., Prathapan, P., Dobrinic, P., Huseyin, M. K., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2019.12.057 · Cited by 187

Dynamic Chromatin Targeting of BRD4 Stimulates Cardiac Fibroblast Activation

Stratton, M. S., Bagchi, R. A., Felisbino, M. B., Hirsch, R. A., Smith, H. E., Riching, A. S., Enyart, B. Y., Koch, K. A., Cavasin, M. A., Alexanian, M., et al. (2019) · Circulation Research · doi:10.1161/circresaha.119.315125 · Cited by 179

Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq

Cole, M. B., Risso, D., Wagner, A., DeTomaso, D., Ngai, J., Purdom, E., Dudoit, S., & Yosef, N. (2019) · Cell Systems · doi:10.1016/j.cels.2019.03.010 · Cited by 173

Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability

Rizzardi, L. F., Hickey, P. F., Rodriguez DiBlasi, V., Tryggvadóttir, R., Callahan, C. M., Idrizi, A., Hansen, K. D., & Feinberg, A. P. (2019) · Nature Neuroscience · doi:10.1038/s41593-018-0297-8 · Cited by 146

Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

Ma, S., Shungin, D., Mallick, H., Schirmer, M., Nguyen, L. H., Kolde, R., Franzosa, E., Vlamakis, H., Xavier, R., & Huttenhower, C. (2022) · Genome biology · doi:10.1186/s13059-022-02753-4 · Cited by 164

A multiregional proteomic survey of the postnatal human brain

Carlyle, B. C., Kitchen, R. R., Kanyo, J. E., Voss, E. Z., Pletikos, M., Sousa, A. M. M., Lam, T. T., Gerstein, M. B., Sestan, N., & Nairn, A. C. (2017) · Nature Neuroscience · doi:10.1038/s41593-017-0011-2 · Cited by 143

Individual and additive effects of vitamin D, omega-3 and exercise on DNA methylation clocks of biological aging in older adults from the DO-HEALTH trial

Bischoff-Ferrari, H. A., Gängler, S., Wieczorek, M., Belsky, D. W., Ryan, J., Kressig, R. W., Stähelin, H. B., Theiler, R., Dawson-Hughes, B., Rizzoli, R., et al. (2025) · Nature Aging · doi:10.1038/s43587-024-00793-y · Cited by 140

Genome-wide mapping of autonomous promoter activity in human cells

van Arensbergen, J., FitzPatrick, V. D., de Haas, M., Pagie, L., Sluimer, J., Bussemaker, H. J., & van Steensel, B. (2017) · Nature Biotechnology · doi:10.1038/nbt.3754 · Cited by 140

Loss of microRNA-128 promotes cardiomyocyte proliferation and heart regeneration

Huang, W., Feng, Y., Liang, J., Yu, H., Wang, C., Wang, B., Wang, M., Jiang, L., Meng, W., Cai, W., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03019-z · Cited by 139

Single-cell RNA-seq of mouse dopaminergic neurons informs candidate gene selection for sporadic Parkinson disease

Hook, P. W., McClymont, S. A., Cannon, G. H., Law, W. D., Morton, A. J., Goff, L. A., & McCallion, A. S. (2018) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2018.02.001 · Cited by 136

The RNA Binding Protein IMP2 Preserves Glioblastoma Stem Cells by Preventing let-7 Target Gene Silencing

Degrauwe, N., Schlumpf, T. B., Janiszewska, M., Martin, P., Cauderay, A., Provero, P., Riggi, N., Suvà, M.-L., Paro, R., & Stamenkovic, I. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.086 · Cited by 136

Rapamycin transiently induces mitochondrial remodeling to reprogram energy metabolism in old hearts

Chiao, Y. A., Kolwicz, S. C., Basisty, N., Gagnidze, A., Zhang, J., Gu, H., Djukovic, D., Beyer, R. P., Raftery, D., MacCoss, M., et al. (2016) · Aging · doi:10.18632/aging.100881 · Cited by 128

Novel App knock-in mouse model shows key features of amyloid pathology and reveals profound metabolic dysregulation of microglia

Xia, D., Lianoglou, S., Sandmann, T., Calvert, M., Suh, J. H., Thomsen, E., Dugas, J., Pizzo, M. E., DeVos, S. L., Earr, T. K., et al. (2022) · Molecular Neurodegeneration · doi:10.1186/s13024-022-00547-7 · Cited by 124

Incorporation of a nucleoside analog maps genome repair sites in postmitotic human neurons

Reid, D. A., Reed, P. J., Schlachetzki, J. C. M., Nitulescu, I. I., Chou, G., Tsui, E. C., Jones, J. R., Chandran, S., Lu, A. T., McClain, C. A., et al. (2021) · Science · doi:10.1126/science.abb9032 · Cited by 121

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

Berest, I., Arnold, C., Reyes-Palomares, A., Palla, G., Rasmussen, K. D., Giles, H., Bruch, P.-M., Huber, W., Dietrich, S., Helin, K., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.10.106 · Cited by 119

MafB-restricted local monocyte proliferation precedes lung interstitial macrophage differentiation

Vanneste, D., Bai, Q., Hasan, S., Peng, W., Pirottin, D., Schyns, J., Maréchal, P., Ruscitti, C., Meunier, M., Liu, Z., et al. (2023) · Nature Immunology · doi:10.1038/s41590-023-01468-3 · Cited by 111

Cerebrospinal fluid microRNAs are potential biomarkers of temporal lobe epilepsy and status epilepticus

Raoof, R., Jimenez-Mateos, E. M., Bauer, S., Tackenberg, B., Rosenow, F., Lang, J., Onugoren, M. D., Hamer, H., Huchtemann, T., Körtvélyessy, P., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-02969-6 · Cited by 109

A catalog of single nucleotide changes distinguishing modern humans from archaic hominins

Kuhlwilm, M., & Boeckx, C. (2019) · Scientific Reports · doi:10.1038/s41598-019-44877-x · Cited by 108

Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition

Inoue, D., Polaski, J. T., Taylor, J., Castel, P., Chen, S., Kobayashi, S., Hogg, S. J., Hayashi, Y., Pineda, J. M. B., El Marabti, E., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00828-9 · Cited by 108

Small-Molecule PAPD5 Inhibitors Restore Telomerase Activity in Patient Stem Cells

Nagpal, N., Wang, J., Zeng, J., Lo, E., Moon, D. H., Luk, K., Braun, R. O., Burroughs, L. M., Keel, S. B., Reilly, C., et al. (2020) · Cell Stem Cell · doi:10.1016/j.stem.2020.03.016 · Cited by 105

Dual-center, dual-platform microRNA profiling identifies potential plasma biomarkers of adult temporal lobe epilepsy

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Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin

Liang, W.-W., Lu, R. J.-H., Jayasinghe, R. G., Foltz, S. M., Porta-Pardo, E., Geffen, Y., Wendl, M. C., Lazcano, R., Kolodziejczak, I., Song, Y., et al. (2023) · Cancer Cell · doi:10.1016/j.ccell.2023.07.013 · Cited by 105

microRNA targeting of the P2X7 purinoceptor opposes a contralateral epileptogenic focus in the hippocampus

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The Transcriptionally Permissive Chromatin State of Embryonic Stem Cells Is Acutely Tuned to Translational Output

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A molecular glue degrader of the WIZ transcription factor for fetal hemoglobin induction

Ting, P. Y., Borikar, S., Kerrigan, J. R., Thomsen, N. M., Aghania, E., Hinman, A. E., Reyes, A., Pizzato, N., Fodor, B. D., Wu, F., et al. (2024) · Science · doi:10.1126/science.adk6129 · Cited by 97

Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer’s disease-specific cis-regulatory elements

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Isoform- and cell-state-specific lipidation of ApoE in astrocytes

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