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

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The Sequence Alignment/Map format and SAMtools

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Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers

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Expression of the MHC Class II Pathway in Triple-Negative Breast Cancer Tumor Cells Is Associated with a Good Prognosis and Infiltrating Lymphocytes

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Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria

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Low TREM1 expression in whole blood predicts anti-TNF response in inflammatory bowel disease

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Detecting and correcting systematic variation in large-scale RNA sequencing data

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Antifungal drug resistance evoked via RNAi-dependent epimutations

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Metatranscriptome analyses indicate resource partitioning between diatoms in the field

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Autism-like phenotype and risk gene mRNA deadenylation by CPEB4 mis-splicing

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De novo annotation and characterization of the translatome with ribosome profiling data

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Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation

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Increased lipid metabolism impairs NK cell function and mediates adaptation to the lymphoma environment

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SIRT3 consolidates heterochromatin and counteracts senescence

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Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine

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Mismatch repair deficiency is not sufficient to elicit tumor immunogenicity

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Human 3D cellular model of hypoxic brain injury of prematurity

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Loss of 5-hydroxymethylcytosine is linked to gene body hypermethylation in kidney cancer

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Meta-analysis of Icelandic and UK data sets identifies missense variants in SMO, IL11, COL11A1 and 13 more new loci associated with osteoarthritis

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Cyclin A2/E1 activation defines a hepatocellular carcinoma subclass with a rearrangement signature of replication stress

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Transcriptome networks identify mechanisms of viral and nonviral asthma exacerbations in children

Altman, M. C., Gill, M. A., Whalen, E., Babineau, D. C., Shao, B., Liu, A. H., Jepson, B. M., Gruchalla, R. S., O’Connor, G. T., Pongracic, J. A., et al. (2019) · Nature Immunology · doi:10.1038/s41590-019-0347-8 · Cited by 174

Tumor cell plasticity, heterogeneity, and resistance in crucial microenvironmental niches in glioma

Jung, E., Osswald, M., Ratliff, M., Dogan, H., Xie, R., Heuer, S., Hoffmann, D. C., Kurz, F. T., Keßler, T., Heiland, S., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21117-3 · Cited by 175

E. coli enhance colonization resistance against Salmonella Typhimurium by competing for galactitol, a context-dependent limiting carbon source

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The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencingPreprint

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Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

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Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq

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Autologous iPSC-Based Vaccines Elicit Anti-tumor Responses In Vivo

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Co-targeting RNA Polymerases IV and V Promotes Efficient De Novo DNA Methylation in Arabidopsis

Gallego‐Bartolomé, J., Liu, W., Kuo, P. H., Feng, S., Ghoshal, B., Gardiner, J., Zhao, J. M.-C., Park, S. Y., Chory, J., & Jacobsen, S. E. (2019) · Cell · doi:10.1016/j.cell.2019.01.029 · Cited by 173

Mammalian oocytes store mRNAs in a mitochondria-associated membraneless compartment

Cheng, S., Altmeppen, G., So, C., Welp, L. M., Penir, S. M. U., Ruhwedel, T., Menelaou, K., Harasimov, K., Stützer, A., Blayney, M. L., et al. (2022) · Science · doi:10.1126/science.abq4835 · Cited by 173

Precise genomic editing of pathogenic mutations in RBM20 rescues dilated cardiomyopathy

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Cohesin loss alters adult hematopoietic stem cell homeostasis, leading to myeloproliferative neoplasms

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AXL promotes Zika virus infection in astrocytes by antagonizing type I interferon signalling

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Large-Scale Human Dendritic Cell Differentiation Revealing Notch-Dependent Lineage Bifurcation and Heterogeneity

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The IRE1 endoplasmic reticulum stress sensor activates natural killer cell immunity in part by regulating c-Myc

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The G-Box Transcriptional Regulatory Code in Arabidopsis

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Gut microbiota remodeling reverses aging-associated inflammation and dysregulation of systemic bile acid homeostasis in mice sex-specifically

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Short-Term Fasting Reveals Amino Acid Metabolism as a Major Sex-Discriminating Factor in the Liver

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Social regulation of insulin signaling and the evolution of eusociality in ants

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PIWI-interacting RNA-54265 is oncogenic and a potential therapeutic target in colorectal adenocarcinoma

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Defining the Transcriptional Landscape during Cytomegalovirus Latency with Single-Cell RNA Sequencing

Shnayder, M., Nachshon, A., Krishna, B. A., Poole, E. L., Boshkov, A., Binyamin, A., Maza, I., Sinclair, J. H., Schwartz, M., & Stern‐Ginossar, N. (2018) · mBio · doi:10.1128/mbio.00013-18 · Cited by 171

Catecholamines Induce Trained Immunity in Monocytes In Vitro and In Vivo

van der Heijden, C. D. C. C., Groh, L. A., Keating, S. T., Kaffa, C., Noz, M. P., Kersten, S., van Herwaarden, A. E., Hoischen, A., Joosten, L. A. B., Timmers, H. J. L. M., et al. (2020) · Circulation Research · doi:10.1161/circresaha.119.315800 · Cited by 171

Expression of SARS-CoV-2 Entry Molecules ACE2 and TMPRSS2 in the Gut of Patients With IBD

Burgueño, J. F., Reich, A. M., Hazime, H., Quintero, M. A., Fernández, I., Fritsch, J., Santander, A. M., Brito, N., Damas, O. M., Deshpande, A. R., et al. (2020) · Inflammatory Bowel Diseases · doi:10.1093/ibd/izaa085 · Cited by 171

Metabolite signatures of diverse Camellia sinensis tea populations

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Gut microbiota exaggerates triclosan-induced liver injury via gut-liver axis

Zhang, P., Zheng, L., Duan, Y., Gao, Y., Gao, H., Mao, D., & Luo, Y. (2021) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2021.126707 · Cited by 171

Spatial metatranscriptomics resolves host–bacteria–fungi interactomes

Saarenpää, S., Shalev, O., Ashkenazy, H., Carlos, V., Lundberg, D. S., Weigel, D., & Giacomello, S. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01979-2 · Cited by 171

Single-cell genomics and regulatory networks for 388 human brains

Emani, P. S., Liu, J. J., Clarke, D., Jensen, M., Warrell, J., Gupta, C., Meng, R., Lee, C.-Y., Xu, S., Dursun, C., et al. (2024) · Science · doi:10.1126/science.adi5199 · Cited by 188

mTAIL-seq reveals dynamic poly(A) tail regulation in oocyte-to-embryo developmentPreprint

Lim, J., Lee, M., Son, A., Chang, H., & Kim, V. N. (2016) · Genes & Development · doi:10.1101/gad.284802.116 · Cited by 171

The RNA-Binding Protein PUM2 Impairs Mitochondrial Dynamics and Mitophagy During Aging

D’Amico, D., Mottis, A., Potenza, F., Sorrentino, V., Li, H., Romani, M., Lemos, V., Schoonjans, K., Zamboni, N., Knott, G., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2018.11.034 · Cited by 159

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

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Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq

Macaulay, I. C., Teng, M. J., Haerty, W., Kumar, P., Ponting, C. P., & Voet, T. (2016) · Nature Protocols · doi:10.1038/nprot.2016.138 · Cited by 170

Anti-tumour immunity induces aberrant peptide presentation in melanoma

Bartok, O., Pataskar, A., Nagel, R., Laos, M., Goldfarb, E., Hayoun, D., Levy, R., Körner, P.-R., Kreuger, I. Z. M., Champagne, J., et al. (2020) · Nature · doi:10.1038/s41586-020-03054-1 · Cited by 170

Characterization of a common progenitor pool of the epicardium and myocardium

Tyser, R. C. V., Ibarra-Soria, X., McDole, K., Jayaram, S. A., Godwin, J., van den Brand, T., Miranda, A. M. A., Scialdone, A., Keller, P., Marioni, J. C., et al. (2021) · Science · doi:10.1126/science.abb2986 · Cited by 170

Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination

Tamiru, M., Natsume, S., Takagi, H., White, B., Yaegashi, H., Shimizu, M., Yoshida, K., Uemura, A., Oikawa, K., Abe, A., et al. (2017) · BMC Biology · doi:10.1186/s12915-017-0419-x · Cited by 169

Dynamic expression of tRNA‐derived small RNAs define cellular states

Yim, D. G., Gopinath, S. K., Lakshmanan, V., Koh, J. L., Park, J. E., Cheong, J. K., Low, J. L., Lim, M. J., Junyu, I., Nah, J. M., et al. (2019) · EMBO Reports · doi:10.15252/embr.201947789 · Cited by 170

The U1 spliceosomal RNA is recurrently mutated in multiple cancers

Shuai, S., Suzuki, H., Díaz‐Navarro, A., Nadeu, F., Kumar, S. A., Gutiérrez‐Fernández, A., Delgado, J., Pinyol, M., López-Otı́n, C., Puente, X. S., et al. (2019) · Nature · doi:10.1038/s41586-019-1651-z · Cited by 169

A phase-separated nuclear GBPL circuit controls immunity in plants

Huang, S., Zhu, S., Kumar, P., & MacMicking, J. D. (2021) · Nature · doi:10.1038/s41586-021-03572-6 · Cited by 169

Targeting Aurora B kinase prevents and overcomes resistance to EGFR inhibitors in lung cancer by enhancing BIM- and PUMA-mediated apoptosis

Tanaka, K., Yu, H. A., Yang, S., Han, S., Selçuklu, S. D., Kim, K., Ramani, S., Ganesan, Y. T., Moyer, A. F., Sinha, S., et al. (2021) · Cancer Cell · doi:10.1016/j.ccell.2021.07.006 · Cited by 169

Transcriptome Analysis of Individual Stromal Cell Populations Identifies Stroma-Tumor Crosstalk in Mouse Lung Cancer Model

Choi, H., Sheng, J., Gao, D., Li, F., Durrans, A., Ryu, S., Lee, S. B., Narula, N., Rafii, S., Elemento, O., et al. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.01.040 · Cited by 168

In situ expansion of engineered human liver tissue in a mouse model of chronic liver disease

Stevens, K. R., Scull, M. A., Ramanan, V., Fortin, C. L., Chaturvedi, R. R., Knouse, K. A., Xiao, J., Fung, C., Mirabella, T., Chen, A. X., et al. (2017) · Science Translational Medicine · doi:10.1126/scitranslmed.aah5505 · Cited by 168

Targeting Multiple Effector Pathways in Pancreatic Ductal Adenocarcinoma with a G-Quadruplex-Binding Small Molecule

Marchetti, C., Zyner, K. G., Ohnmacht, S. A., Robson, M. P., Haider, S. M., Morton, J. P., Marsico, G., Vo, T. D., Laughlin, S., Ahmed, A. A., et al. (2018) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.7b01781 · Cited by 168

Compressive force induces reversible chromatin condensation and cell geometry–dependent transcriptional response

Damodaran, K., Venkatachalapathy, S., Alisafaei, F., Radhakrishnan, A., Jokhun, D. S., Shenoy, V. B., & Shivashankar, G. V. (2018) · Molecular Biology of the Cell · doi:10.1091/mbc.e18-04-0256 · Cited by 168

Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory

Bertero, A., Fields, P., Ramani, V., Bonora, G., Yardımcı, G. G., Reinecke, H., Pabon, L., Noble, W. S., Shendure, J., & Murry, C. E. (2019) · Nature Communications · doi:10.1038/s41467-019-09483-5 · Cited by 168

A mutation-independent approach for muscular dystrophy via upregulation of a modifier gene

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Clonally Expanded T Cells Reveal Immunogenicity of Rhabdoid Tumors

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The Parkinson’s disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability

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ATG16L1 orchestrates interleukin-22 signaling in the intestinal epithelium via cGAS–STING

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Functional convergence of histone methyltransferases EHMT1 and KMT2C involved in intellectual disability and autism spectrum disorder

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Expansion and differentiation of human hepatocyte-derived liver progenitor-like cells and their use for the study of hepatotropic pathogens

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