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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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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Transcriptional and proteomic insights into the host response in fatal COVID-19 cases

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Distinct Polysaccharide Utilization Determines Interspecies Competition between Intestinal Prevotella spp.

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m 6 A demethylase ALKBH5 controls CD4 + T cell pathogenicity and promotes autoimmunity

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The tumor microenvironment shows a hierarchy of cell-cell interactions dominated by fibroblasts

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Long-term histone lactylation connects metabolic and epigenetic rewiring in innate immune memory

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Ultraconserved Enhancers Are Required for Normal Development

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Small RNA deep sequencing discriminates subsets of extracellular vesicles released by melanoma cells – Evidence of unique microRNA cargos

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RNA Sequence Analysis of Human Huntington Disease Brain Reveals an Extensive Increase in Inflammatory and Developmental Gene Expression

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Enterococcal Metabolite Cues Facilitate Interspecies Niche Modulation and Polymicrobial Infection

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Surveying brain tumor heterogeneity by single-cell RNA-sequencing of multi-sector biopsies

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Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors

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Circulating myeloid-derived MMP8 in stress susceptibility and depression

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CD4+ Th2 cells are directly regulated by IL-10 during allergic airway inflammation

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The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle

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Circadian Entrainment Triggers Maturation of Human In Vitro Islets

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HTR7 Mediates Serotonergic Acute and Chronic Itch

Morita, T., McClain, S. P., Batia, L. M., Pellegrino, M., Wilson, S. R., Kienzler, M. A., Lyman, K. A., Olsen, A. S. B., Wong, J. F., Stucky, C. L., et al. (2015) · Neuron · doi:10.1016/j.neuron.2015.05.044 · Cited by 188

DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development

Kraiczy, J., Nayak, K., Howell, K. J., Ross, A., Forbester, J. L., Salvestrini, C., Mustata, R. C., Perkins, S., Andersson-Rolf, A., Leenen, E., et al. (2017) · Gut · doi:10.1136/gutjnl-2017-314817 · Cited by 189

TFAP2C regulates transcription in human naive pluripotency by opening enhancers

Pastor, W. A., Liu, W., Chen, D., Ho, J., Kim, R., Hunt, T. J., Lukianchikov, A., Liu, X., Polo, J. M., Jacobsen, S. E., et al. (2018) · Nature Cell Biology · doi:10.1038/s41556-018-0089-0 · Cited by 188

Resetting the epigenetic balance of Polycomb and COMPASS function at enhancers for cancer therapy

Wang, L., Zhao, Z., Ozark, P. A., Fantini, D., Marshall, S. A., Rendleman, E. J., Cozzolino, K., Louis, N., He, X., Morgan, M. A., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0034-6 · Cited by 188

Rearrangement bursts generate canonical gene fusions in bone and soft tissue tumors

Anderson, N. D., de Borja, R., Young, M. D., Fuligni, F., Rosic, A., Roberts, N. D., Hajjar, S., Layeghifard, M., Novokmet, A., Kowalski, P. E., et al. (2018) · Science · doi:10.1126/science.aam8419 · Cited by 191

Contribution of plasma cells and B cells to hidradenitis suppurativa pathogenesis

Gudjonsson, J. E., Tsoi, L. C., Ma, F., Billi, A. C., van Straalen, K. R., Vossen, A. R. J. V., van der Zee, H. H., Harms, P. W., Wasikowski, R., Yee, C. M., et al. (2020) · JCI Insight · doi:10.1172/jci.insight.139930 · Cited by 188

Translatome and transcriptome co-profiling reveals a role of TPRXs in human zygotic genome activation

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An Interactive Database for the Assessment of Histone Antibody Specificity

Rothbart, S. B., Dickson, B. M., Raab, J. R., Grzybowski, A. T., Krajewski, K., Guo, A. H., Shanle, E. K., Josefowicz, S. Z., Fuchs, S. M., Allis, C. D., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.06.022 · Cited by 187

Di↵erential analysis of count data - the DESeq2 package

Love, M. I., Anders, S., & Huber, W. (2014) · Cited by 187

Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci

Philippe, C., Vargas-Landín, D. B., Doucet, A. J., van Essen, D., Vera‐Otarola, J., Kuciak, M., Corbin, A., Nigumann, P., & Cristofari, G. (2016) · eLife · doi:10.7554/elife.13926 · Cited by 186

A Lignin Molecular Brace Controls Precision Processing of Cell Walls Critical for Surface Integrity in Arabidopsis

Lee, Y., Yoon, T. H., Lee, J., Jeon, S. Y., Lee, J. H., Lee, M. K., Chen, H., Yun, J., Oh, S. Y., Wen, X., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.060 · Cited by 187

Spatiotemporal expansion of primary progenitor zones in the developing human cerebellum

Haldipur, P., Aldinger, K. A., Bernardo, S., Deng, M., Timms, A. E., Overman, L. M., Winter, C., Lisgo, S., Razavi, Silvestri, E., et al. (2019) · Science · doi:10.1126/science.aax7526 · Cited by 187

Membrane Tension Gates ERK-Mediated Regulation of Pluripotent Cell Fate

Belly, H. D., Stubb, A., Yanagida, A., Labouesse, C., Jones, P. H., Paluch, E. K., & Chalut, K. J. (2020) · Cell stem cell · doi:10.1016/j.stem.2020.10.018 · Cited by 187

Transferrin receptor 1 ablation in satellite cells impedes skeletal muscle regeneration through activation of ferroptosis

Ding, H., Chen, S., Pan, X., Dai, X., Pan, G., Li, Z., Mai, X., Tian, Y., Zhang, S., Liu, B., et al. (2021) · Journal of Cachexia Sarcopenia and Muscle · doi:10.1002/jcsm.12700 · Cited by 187

Phenotypic plasticity and genetic control in colorectal cancer evolution

Househam, J., Heide, T., Cresswell, G. D., Spiteri, I., Kimberley, C., Zapata, L., Lynn, C., James, C. T., Mossner, M., Fernández-Mateos, J., et al. (2022) · Nature · doi:10.1038/s41586-022-05311-x · Cited by 187

Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis

Dong, J., Hu, Y., Fan, X., Wu, X., Mao, Y., Hu, B., Guo, H., Wen, L., & Tang, F. (2018) · Genome Biology · doi:10.1186/s13059-018-1416-2 · Cited by 187

Heat stress yields a unique MADS box transcription factor in determining seed size and thermal sensitivity

Chen, C., Begcy, K., Liu, K., Folsom, J. J., Wang, Z., Zhang, C., & Walia, H. (2016) · PLANT PHYSIOLOGY · doi:10.1104/pp.15.01992 · Cited by 186

Differential bacterial capture and transport preferences facilitate co-growth on dietary xylan in the human gut

Leth, M. L., Ejby, M., Workman, C., Ewald, D. A., Pedersen, S. S., Sternberg, C., Bahl, M. I., Licht, T. R., Aachmann, F. L., Westereng, B., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0132-8 · Cited by 167

Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia

Bell, C. C., Fennell, K. A., Chan, Y.-C., Rambow, F., Yeung, M. M., Vassiliadis, D., Gonzalez, L. E. L., Yeh, P. S.-H., Martelotto, L. G., Rogiers, A., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10652-9 · Cited by 186

A Pathogen-Responsive Gene Cluster for Highly Modified Fatty Acids in Tomato

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Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem

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GDSL-domain proteins have key roles in suberin polymerization and degradation

Ursache, R., Teixeira, C. D. J. V., Tendon, V. D., Gully, K., Bellis, D. D., Schmid‐Siegert, E., Andersen, T. G., Shekhar, V., Calderon, S., Pradervand, S., et al. (2021) · Nature Plants · doi:10.1038/s41477-021-00862-9 · Cited by 186

ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration

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Digital image analysis outperforms manual biomarker assessment in breast cancer

Stålhammar, G., Martínez, N. F., Lippert, M. F., Tobin, N. P., Mølholm, I., Kis, L. L., Rosin, G., Rantalainen, M., Pedersen, L., Bergh, J. C. S., et al. (2016) · Modern Pathology · doi:10.1038/modpathol.2016.34 · Cited by 185

RNA-dependent RNA targeting by CRISPR-Cas9

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Reversible De-differentiation of Mature White Adipocytes into Preadipocyte-like Precursors during Lactation

Wang, Q. A., Song, A., Chen, W., Schwalie, P. C., Zhang, F., Vishvanath, L., Jiang, L., Ye, R., Shao, M., Tao, C., et al. (2018) · Cell Metabolism · doi:10.1016/j.cmet.2018.05.022 · Cited by 185

Refined RIP-seq protocol for epitranscriptome analysis with low input materials

Zeng, Y., Wang, S., Gao, S., Soares, F., Ahmed, M., Guo, H., Wang, M., Hua, J. T., Guan, J., Moran, M. F., et al. (2018) · PLoS Biology · doi:10.1371/journal.pbio.2006092 · Cited by 185

Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design

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Specific molecular signatures predict decitabine response in chronic myelomonocytic leukemia

Meldi, K. M., Qin, T., Buchi, F., Droin, N. M., Sotzen, J. R., Micol, J., Selimoglu‐Buet, D., Masala, E., Allione, B., Gioia, D. M., et al. (2015) · Journal of Clinical Investigation · doi:10.1172/jci78752 · Cited by 184

Interactions between horizontally acquired genes create a fitness cost in Pseudomonas aeruginosa

Millán, Á. S., Toll‐Riera, M., Qi, Q., & MacLean, R. C. (2015) · Nature Communications · doi:10.1038/ncomms7845 · Cited by 184

Dynamic regulation of RNA editing in human brain development and disease

Hwang, T., Park, C., Leung, A. K. L., Gao, Y., Hyde, T. M., Kleinman, J. E., Rajpurohit, A., Tao, R., Shin, J. H., & Weinberger, D. R. (2016) · Nature Neuroscience · doi:10.1038/nn.4337 · Cited by 184

Histone H3 lysine 36 methylation affects temperature-induced alternative splicing and flowering in plants

Pajoro, A., Severing, E. I., Angenent, G. C., & Immink, R. G. H. (2017) · Genome biology · doi:10.1186/s13059-017-1235-x · Cited by 184

Ploidy and Size at Multiple Scales in the Arabidopsis Sepal

Robinson, D., Coate, J. E., Singh, A., Hong, L., Bush, M., Doyle, J. J., & Roeder, A. (2018) · The Plant Cell · doi:10.1105/tpc.18.00344 · Cited by 184

Mesenchymal Niche-Specific Expression of Cxcl12 Controls Quiescence of Treatment-Resistant Leukemia Stem Cells

Agarwal, P., Isringhausen, S., Li, H., Paterson, A. J., He, J., Gomariz, Á., Nagasawa, T., Nombela‐Arrieta, C., & Bhatia, R. (2019) · Cell stem cell · doi:10.1016/j.stem.2019.02.018 · Cited by 184

Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data

Gao, G. F., Parker, J. S., Reynolds, S. M., Silva, T. C., Wang, L.-B., Zhou, W., Akbani, R., Bailey, M. H., Balu, S., Berman, B. P., et al. (2019) · Cell Systems · doi:10.1016/j.cels.2019.06.006 · Cited by 184

Fatty acid overproduction by gut commensal microbiota exacerbates obesity

Takeuchi, T., Kameyama, K., Miyauchi, E., Nakanishi, Y., Kanaya, T., Fujii, T., Kato, T., Sasaki, T., Tachibana, N., Negishi, H., et al. (2023) · Cell Metabolism · doi:10.1016/j.cmet.2022.12.013 · Cited by 186

A comprehensive analysis of breast cancer microbiota and host gene expression

Thompson, K. J., Ingle, J. N., Tang, X., Chia, N., Jeraldo, P. R., Walther-Antonio, M. R., Kandimalla, K. K., Johnson, S., Yao, J. Z., Harrington, S. C., et al. (2017) · PLOS ONE · doi:10.1371/journal.pone.0188873 · Cited by 183

Global role of the bacterial post-transcriptional regulator CsrA revealed by integrated transcriptomics

Potts, A. H., Vakulskas, C. A., Pannuri, A., Yakhnin, H., Babitzke, P., & Romeo, T. (2017) · Nature Communications · doi:10.1038/s41467-017-01613-1 · Cited by 183

The Arabidopsis Transcriptome Responds Specifically and Dynamically to High Light Stress

Huang, J., Zhao, X., & Chory, J. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.11.051 · Cited by 183

Systematic identification of silencers in human cells

Pang, B., & Snyder, M. P. (2020) · Nature Genetics · doi:10.1038/s41588-020-0578-5 · Cited by 183

Two interacting ethylene response factors regulate heat stress response

Huang, J., Zhao, X., Bürger, M., Wang, Y., & Chory, J. (2020) · The Plant Cell · doi:10.1093/plcell/koaa026 · Cited by 183

Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses

Mancabelli, L., Milani, C., Lugli, G. A., Turroni, F., Mangifesta, M., Viappiani, A., Ticinesi, A., Nouvenne, A., Meschi, T., van Sinderen, D., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-10663-w · Cited by 182

Molecular analysis of aggressive renal cell carcinoma with unclassified histology reveals distinct subsets

Chen, Y., Xu, J., Skanderup, A. J., Dong, Y., Brannon, A. R., Wang, L., Won, H. H., Wang, P. I., Nanjangud, G. J., Jungbluth, A. A., et al. (2016) · Nature Communications · doi:10.1038/ncomms13131 · Cited by 184

Integrating Omics and Alternative Splicing Reveals Insights into Grape Response to High Temperature

Jiang, J., Liu, X., Liu, C., Liu, G., Li, S., & Wang, L. (2017) · PLANT PHYSIOLOGY · doi:10.1104/pp.16.01305 · Cited by 182

Host blood RNA signatures predict the outcome of tuberculosis treatment

Thompson, E. G., Du, Y., Malherbe, S. T., Shankar, S., Braun, J., Valvo, J., Ronacher, K., Tromp, G., Tabb, D. L., Alland, D., et al. (2017) · Tuberculosis · doi:10.1016/j.tube.2017.08.004 · Cited by 182

Telobox motifs recruit CLF/SWN–PRC2 for H3K27me3 deposition via TRB factors in Arabidopsis

Zhou, Y., Wang, Y. J., Krause, K., Yang, T., Dongus, J. A., Zhang, Y., & Turck, F. (2018) · Nature Genetics · doi:10.1038/s41588-018-0109-9 · Cited by 182

Combining multiple tools outperforms individual methods in gene set enrichment analyses

Alhamdoosh, M., Ng, M., Wilson, N. J., Sheridan, J. M., Huynh, H., Wilson, M. J., & Ritchie, M. E. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw623 · Cited by 182

Analysis of wild tomato introgression lines elucidates the genetic basis of transcriptome and metabolome variation underlying fruit traits and pathogen response

Szymański, J., Bocobza, S. E., Panda, S., Sonawane, P. D., Cárdenas, P. D., Lashbrooke, J., Kamble, A. C., Shahaf, N., Meir, S., Bovy, A. G., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0690-6 · Cited by 182

Fusobacterium nucleatum aggravates rheumatoid arthritis through FadA-containing outer membrane vesicles

Hong, M., Li, Z., Liu, H., Zheng, S., Zhang, F., Zhu, J., Shi, H., Ye, H., Chou, Z., Gao, L., et al. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.03.018 · Cited by 182

Sex bias in CNS autoimmune disease mediated by androgen control of autoimmune regulator

Zhu, M., Bakhru, P., Conley, B. E., Nelson, J. S., Free, M. E., Martin, A. J., Starmer, J., Wilson, E. M., & Su, M. A. (2016) · Nature Communications · doi:10.1038/ncomms11350 · Cited by 181

Phosphorylation of histone H3.3 at serine 31 promotes p300 activity and enhancer acetylation

Martire, S., Gogate, A. A., Whitmill, A., Tafessu, A., Nguyen, J., Teng, Y., Tastemel, M., & Banaszynski, L. A. (2019) · Nature Genetics · doi:10.1038/s41588-019-0428-5 · Cited by 183

CDK4/6 Inhibitors Impair Recovery from Cytotoxic Chemotherapy in Pancreatic Adenocarcinoma

Salvador-Barberó, B., Álvarez‐Fernández, M., Zapatero‐Solana, E., Bakkali, A. E., Menéndez, C., Lopez-Casas, P. P., Domenico, T. D., Xie, T., VanArsdale, T. L., Shields, D. J., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.01.007 · Cited by 181

OsNSUN2-Mediated 5-Methylcytosine mRNA Modification Enhances Rice Adaptation to High Temperature

Tang, Y., Gao, C., Gao, Y., Yang, Y., Shi, B., Yu, J.-L., Lyu, C., Sun, B., Wang, H.-L., Xu, Y., et al. (2020) · Developmental Cell · doi:10.1016/j.devcel.2020.03.009 · Cited by 181

Reference genome assemblies reveal the origin and evolution of allohexaploid oat

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Selective Neuronal Vulnerability in Alzheimer’s Disease: A Network-Based Analysis

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Co-evolution of Hormone Metabolism and Signaling Networks Expands Plant Adaptive Plasticity

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Tissue-Specific Transcriptomics Reveals an Important Role of the Unfolded Protein Response in Maintaining Fertility upon Heat Stress in Arabidopsis

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