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Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations.
PMID 24782521 · Nucleic Acids Res · 2014
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Free circular introns with an unusual branchpoint in neuronal projections.
PMID 31697236 · Elife · 2019
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Histone deacetylase SIRT6 regulates tryptophan catabolism and prevents metabolite imbalance associated with neurodegeneration.
PMID 41345108 · Nat Commun · 2025
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Protocol for transcriptomic and epigenomic analysis of JAK inhibitor sensitivity in IFN-γ-primed human macrophages using ATAC-seq and RNA-seq.
PMID 41313685 · STAR Protoc · 2025
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Cell type differences in human cytomegalovirus transcription and epigenetic regulation with insights into major immediate-early enhancer-promoter control.
PMID 40758707 · PLoS Pathog · 2025
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Statistical framework for calling allelic imbalance in high-throughput sequencing data.
PMID 39966391 · Nat Commun · 2025
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Macrophages on the run: Exercise balances macrophage polarization for improved health.
PMID 39476967 · Mol Metab · 2024
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A data-driven estimation of the ribosome drop-off rate in S. cerevisiae reveals a correlation with the genes length.
PMID 38638702 · NAR Genom Bioinform · 2024
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Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-
PMID 38482016 · Front Immunol · 2024
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Transcriptomic and physiological analysis of atractylodes chinensis in response to drought stress reveals the putative genes related to sesquiterpenoid biosynth
PMID 38317086 · BMC Plant Biol · 2024
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Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists.
PMID 37906287 · J Clin Invest · 2024
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Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation.
PMID 37652021 · Immunity · 2023
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Genetics of circulating inflammatory proteins identifies drivers of immune-mediated disease risk and therapeutic targets.
PMID 37563310 · Nat Immunol · 2023
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A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest.
PMID 37277355 · Nat Commun · 2023
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iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltr
PMID 37023414 · Cancer Immunol Res · 2023
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Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart.
PMID 37012284 · Sci Rep · 2023
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In vivo induction of activin A-producing alveolar macrophages supports the progression of lung cell carcinoma.
PMID 36650150 · Nat Commun · 2023
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Critical Role for the Human Cytomegalovirus Major Immediate Early Proteins in Recruitment of RNA Polymerase II and H3K27Ac To an Enhancer-Like Element in Ori
PMID 36645269 · Microbiol Spectr · 2023
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Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance.
PMID 36543858 · Commun Biol · 2022
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Transcriptomic-Based Quantification of the Epithelial-Hybrid-Mesenchymal Spectrum across Biological Contexts.
PMID 35053177 · Biomolecules · 2021
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A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer.
PMID 35047825 · NAR Cancer · 2022
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The butyrophilin 1a1 knockout mouse revisited: Ablation of Btn1a1 leads to concurrent cell death and renewal in the mammary epithelium during lactation.
PMID 34938960 · FASEB Bioadv · 2021
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Reactive astrocytes acquire neuroprotective as well as deleterious signatures in response to Tau and Aß pathology.
PMID 35013236 · Nat Commun · 2022
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An archaeal histone-like protein regulates gene expression in response to salt stress.
PMID 34883507 · Nucleic Acids Res · 2021
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Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.
PMID 34680427 · Biomedicines · 2021
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Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma.
PMID 34654806 · Nat Commun · 2021
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Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development.
PMID 34643182 · Elife · 2021
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miRbiom: Machine-learning on Bayesian causal nets of RBP-miRNA interactions successfully predicts miRNA profiles.
PMID 34637468 · PLoS One · 2021
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DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data.
PMID 34261540 · Genome Med · 2021
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Vaccine-induced ICOS+CD38+ circulating Tfh are sensitive biosensors of age-related changes in inflammatory pathway
PMID 34095875 · Cell Rep Med · 2021
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eVITTA: a web-based visualization and inference toolbox for transcriptome analysis.
PMID 34019643 · Nucleic Acids Res · 2021
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Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer.
PMID 33890574 · Elife · 2021
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Generic injuries are sufficient to induce ectopic Wnt organizers in Hydra.
PMID 33779545 · Elife · 2021
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Topological signatures in regulatory network enable phenotypic heterogeneity in small cell lung cancer.
PMID 33729159 · Elife · 2021
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Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility.
PMID 33707641 · Sci Rep · 2021
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Epigenome screening highlights that JMJD6 confers an epigenetic vulnerability and mediates sunitinib sensitivity in renal cell carcinoma.
PMID 33634984 · Clin Transl Med · 2021
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Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials.
PMID 33558569 · Sci Data · 2021
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Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells.
PMID 33253153 · PLoS Comput Biol · 2020
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Genomic regions and signaling pathways associated with indicator traits for feed efficiency in juvenile Atlantic salmon (Salmo salar).
PMID 33158415 · Genet Sel Evol · 2020
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Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.
PMID 33043022 · Front Med (Lausanne) · 2020
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Synergism between IL7R and CXCR4 drives BCR-ABL induced transformation in Philadelphia chromosome-positive acute lymphoblastic leukemia.
PMID 32581241 · Nat Commun · 2020
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An Erg-driven transcriptional program controls B cell lymphopoiesis.
PMID 32541654 · Nat Commun · 2020
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From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy.
PMID 31830909 · BMC Genomics · 2019
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PDGFRA defines the mesenchymal stem cell Kaposi's sarcoma progenitors by enabling KSHV oncogenesis in an angiogenic environment.
PMID 31881074 · PLoS Pathog · 2019
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mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations.
PMID 31799603 · Nucleic Acids Res · 2020
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Dynamic reversal of random X-Chromosome inactivation during iPSC reprogramming.
PMID 31515287 · Genome Res · 2019
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Spatially clustered loci with multiple enhancers are frequent targets of HIV-1 integration.
PMID 31492853 · Nat Commun · 2019
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Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0.
PMID 31343654 · Invest Ophthalmol Vis Sci · 2019
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Translation affects mRNA stability in a codon-dependent manner in human cells.
PMID 31012849 · Elife · 2019
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Transcriptomic and functional analyses of the piRNA pathway in the Chagas disease vector Rhodnius prolixus.
PMID 30303955 · PLoS Negl Trop Dis · 2018
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