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Aug 2021
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An essential role for the piRNA pathway in regulating the ribosomal RNA pool in C. elegans

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Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE

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Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures

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The Polycomb-Dependent Epigenome Controls β Cell Dysfunction, Dedifferentiation, and Diabetes

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academic.oup.com/gigascience/article/7/7/giy068/5040257
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Studying immunotherapy resistance in a melanoma autologous humanized mouse xenograft.

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Jul 2021
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Graphical Workflow System for Modification Calling by Machine Learning of Reverse Transcription Signatures

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1. scibot 31 Jul 2021
  
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sciencedirect.com/science/article/pii/S2211124719304553
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Apicomplexan-like parasites are polyphyletic and widely but selectively dependent on cryptic plastid organelles

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1. scibot 30 Jul 2021
  
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CDK12 drives breast tumor initiation and trastuzumab resistance via WNT and IRS1‐ErbB‐PI3K signaling

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1. scibot 30 Jul 2021
  
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embopress.org/doi/10.15252/embr.201948058
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RbFox1 up-regulation impairs BDNF-dependent hippocampal LTP by dysregulating TrkB isoform expression levels

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1. scibot 29 Jul 2021
  
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The Role of m6A/m-RNA Methylation in Stress Response Regulation

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Analysis of the genomic architecture of a complex trait locus in hypertensive rat models links Tmem63c to kidney damage

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Neuroprotective effects of an engineered commensal bacterium in the 1‐methyl‐4‐phenyl‐1, 2, 3, 6‐tetrahydropyridine Parkinson disease mouse model via producing glucagon‐like peptide‐1

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onlinelibrary.wiley.com/doi/full/10.1111/jnc.14694
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Malassezia Is Associated with Crohn’s Disease and Exacerbates Colitis in Mouse Models

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sciencedirect.com/science/article/pii/S1931312819300459
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De novo genome assembly of Camptotheca acuminata, a natural source of the anti-cancer compound camptothecin

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academic.oup.com/gigascience/article/6/9/1/4004835/De-novo-genome-assembly-of-Camptotheca-acuminata-a
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Stem Cell Transcription Factor FoxO Controls Microbiome Resilience in Hydra

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Janus Kinase 1 Plays a Critical Role in Mammary Cancer Progression

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Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence

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A B-Cell-Specific Enhancer Orchestrates Nuclear Architecture to Generate a Diverse Antigen Receptor Repertoire

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Higher-Order Organization Principles of Pre-translational mRNPs

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Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing

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N6-methyladenine DNA Modification in Glioblastoma

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RNA Binding to CBP Stimulates Histone Acetylation and Transcription

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  Cutadapt v1.7.1
  
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sciencedirect.com/science/article/pii/S0092867416317366
May 2021
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Fetal meconium does not have a detectable microbiota before birth

1
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  DOI: 10.1038/s41564-021-00904-0
  
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Morphological and genomic shifts in mole-rat ‘queens’ increase fecundity but reduce skeletal integrity

1
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Loss of Ambra1 promotes melanoma growth and invasion

1
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  DOI: 10.1038/s41467-021-22772-2
  
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Gut vascular barrier impairment leads to intestinal bacteria dissemination and colorectal cancer metastasis to liver

1
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Adult Neural Stem Cells Are Alerted by Systemic Inflammation through TNF-α Receptor Signaling

1
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Developmentally Programmed Tankyrase Activity Upregulates β-Catenin and Licenses Progression of Embryonic Genome Activation

1
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Nested association mapping reveals the genetic architecture of spike emergence and anthesis timing in intermediate wheatgrass

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ncbi.nlm.nih.gov/pmc/articles/PMC8063084/
Apr 2021
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Efficient RNA polymerase II pause release requires U2 snRNP function

1
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Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells

1
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Cellular mRNA triggers structural transformation of Ebola virus matrix protein VP40 to its essential regulatory form

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Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance

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Functional interrogation of DNA damage response variants with base editing screens

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BET Inhibition Blocks Inflammation-Induced Cardiac Dysfunction and SARS-CoV-2 Infection

1
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The SMC5/6 complex compacts and silences unintegrated HIV-1 DNA and is antagonized by Vpr

1
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  DOI: 10.1016/j.chom.2021.03.001
  
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Evidence for additive and synergistic action of mammalian enhancers during cell fate determination

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ncbi.nlm.nih.gov/pmc/articles/PMC8004103/
Mar 2021
faseb.onlinelibrary.wiley.com faseb.onlinelibrary.wiley.com

Genomic exploration of the targets of FOXL2 and ESR2 unveils their implication in cell migration, invasion, and adhesion

1
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  DOI: 10.1096/fj.202002444R
  
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faseb.onlinelibrary.wiley.com/doi/10.1096/fj.202002444R
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The case for using mapped exonic non-duplicate reads when reporting RNA-sequencing depth: examples from pediatric cancer datasets

1
1. scibot 18 Mar 2021
  
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  DOI: 10.1093/gigascience/giab011
  
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academic.oup.com/gigascience/article/10/3/giab011/6169410
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Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis

1
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ncbi.nlm.nih.gov/pmc/articles/PMC7920552/
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Post-transcriptional regulation of antiviral gene expression by N6-methyladenosine

1
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sciencedirect.com/science/article/pii/S2211124721001121
Feb 2021
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Comparison of long-read methods for sequencing and assembly of a plant genome

1
1. scibot 27 Feb 2021
  
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  DOI: 10.1093/gigascience/giaa146
  
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academic.oup.com/gigascience/article/9/12/giaa146/6042729
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Interferon-λ Mediates Non-redundant Front-Line Antiviral Protection against Influenza Virus Infection without Compromising Host Fitness

1
1. scibot 26 Feb 2021
  
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cell.com/immunity/abstract/S1074-7613(17)30190-5
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Osteoclasts recycle via osteomorphs during RANKL-stimulated bone resorption

1
1. scibot 26 Feb 2021
  
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Whole‐Genome Sequence of Synthesized Allopolyploids in Cucumis Reveals Insights into the Genome Evolution of Allopolyploidization

1
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onlinelibrary.wiley.com/doi/10.1002/advs.202004222
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Development of antibody-dependent cell cytotoxicity function in HIV-1 antibodies

1
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ncbi.nlm.nih.gov/pmc/articles/PMC7884072/
Jan 2021
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Manipulation of the human tRNA pool reveals distinct tRNA sets that act in cellular proliferation or cell cycle arrest

1
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ncbi.nlm.nih.gov/pmc/articles/PMC7781600/
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Charting Extracellular Transcriptomes in The Human Biofluid RNA Atlas

1
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sciencedirect.com/science/article/pii/S2211124720315412
Dec 2020
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The Neuroanatomical Ultrastructure and Function of a Biological Ring Attractor

1
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  DOI: 10.1016/j.neuron.2020.08.006
  
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cell.com/neuron/abstract/S0896-6273(20)30613-9
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Turnip mosaic virus in oilseed rape activates networks of sRNA-mediated interactions between viral and host genomes

1
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  DOI: 10.1038/s42003-020-01425-y
  
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High neural activity accelerates the decline of cognitive plasticity with age in Caenorhabditis elegans

1
1. scibot 07 Dec 2020
  
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ncbi.nlm.nih.gov/pmc/articles/PMC7685709/
Nov 2020
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Mycobacterium bovis genomics reveals transmission of infection between cattle and deer in Ireland

1
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ncbi.nlm.nih.gov/pmc/articles/PMC7641417/
Oct 2020
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A novel role for the pineal gland: Regulating seasonal shifts in the gut microbiota of Siberian hamsters

1
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onlinelibrary.wiley.com/doi/10.1111/jpi.12696
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The visual pigment xenopsin is widespread in protostome eyes and impacts the view on eye evolution

1
1. scibot 07 Oct 2020
  
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  DOI: 10.7554/eLife.55193
  
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elifesciences.org/articles/55193
Sep 2020
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Construction of a chromosome-scale long-read reference genome assembly for potato

1
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  DOI: 10.1093/gigascience/giaa100
  
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pubmed.ncbi.nlm.nih.gov/32964225/
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Maturational Changes in Mouse Cutaneous Touch and Piezo2-Mediated Mechanotransduction

1
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Interleukin-33 Signaling Controls the Development of Iron-Recycling Macrophages

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  DOI: 10.1016/j.immuni.2020.03.006
  
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Senescence-Induced Vascular Remodeling Creates Therapeutic Vulnerabilities in Pancreas Cancer

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Bacterial Nucleoside Catabolism Controls Quorum Sensing and Commensal-to-Pathogen Transition in the Drosophila Gut

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Generation of a chromosome-scale genome assembly of the insect-repellent terpenoid-producing Lamiaceae species, Callicarpa americana

1
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Investigating Human Mitochondrial Genomes in Single Cells

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A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

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Imprinted Maternally Expressed microRNAs Antagonize Paternally Driven Gene Programs in Neurons

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DAZL mediates a broad translational program regulating expansion and differentiation of spermatogonial progenitors

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Umbilical cord blood-derived ILC1-like cells constitute a novel precursor for mature KIR+NKG2A- NK cells

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Novel and de novo point and large microdeletion mutation in PRRT2‐related epilepsy

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Selective 40S Footprinting Reveals Cap-Tethered Ribosome Scanning in Human Cells

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A haplotype-resolved draft genome of the European sardine (Sardina pilchardus)

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Adipocyte Hypoxia-Inducible Factor 2α Suppresses Atherosclerosis by Promoting Adipose Ceramide Catabolism

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Liver Is a Generative Site for the B Cell Response to Ehrlichia muris

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Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation

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Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures

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The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs

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P Granules Protect RNA Interference Genes from Silencing by piRNAs

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Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity

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The piRNA Response to Retroviral Invasion of the Koala Genome

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Phenotypic effects of dietary stress in combination with a respiratory chain bypass in mice

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Genetic, epigenetic and genomic effects on variation of gene expression among grape varieties

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Untitled document

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  DOI: 10.1016/j.immuni.2018.12.021
  
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  DOI: 10.1038/s41586-018-0845-0
  
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Untitled document

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An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies

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  DOI: 10.1093/gigascience/giz029
  
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High‐fat diet intake modulates maternal intestinal adaptations to pregnancy and results in placental hypoxia, as well as altered fetal gut barrier proteins and immune markers

1
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Untitled document

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Untitled document

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Maternal Ribosomes Are Sufficient for Tissue Diversification during Embryonic Development in C. elegans

1
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  DOI: 10.1016/j.devcel.2019.01.019
  
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Nov 2018
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RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing

1
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Targeting Processive Transcription Elongation via SEC Disruption for MYC-Induced Cancer Therapy

1
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HOXA9 Reprograms the Enhancer Landscape to Promote Leukemogenesis

1
1. scibot 05 Nov 2018
  
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Phosphorylation of the Ribosomal Protein RPL12/uL11 Affects Translation during Mitosis

1
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An Atypical Parvovirus Drives Chronic Tubulointerstitial Nephropathy and Kidney Fibrosis

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Disruption of the β1L Isoform of GABP Reverses Glioblastoma Replicative Immortality in a TERT Promoter Mutation-Dependent Manner

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A Map of Toll-like Receptor Expression in the Intestinal Epithelium Reveals Distinct Spatial, Cell Type-Specific, and Temporal Patterns

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Hoxc-Dependent Mesenchymal Niche Heterogeneity Drives Regional Hair Follicle Regeneration

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Decoupling the impact of microRNAs on translational repression versus RNA degradation in embryonic stem cells

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Biology and Clinical Implications of the 19q13 Aggressive Prostate Cancer Susceptibility Locus

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Translational Control through Differential Ribosome Pausing during Amino Acid Limitation in Mammalian Cells

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The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes

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Iron Drives T Helper Cell Pathogenicity by Promoting RNA-Binding Protein PCBP1-Mediated Proinflammatory Cytokine Production

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Genome of an allotetraploid wild peanut Arachis monticola: a de novo assembly

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Developmental Origin Governs CD8+ T Cell Fate Decisions during Infection

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BRG1 governs glucocorticoid receptor interactions with chromatin and pioneer factors across the genome

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The Polycomb-Dependent Epigenome Controls β Cell Dysfunction, Dedifferentiation, and Diabetes

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Spliceosome Profiling Visualizes Operations of a Dynamic RNP at Nucleotide Resolution

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Inflammation-Modulated Metabolic Reprogramming Is Required for DUOX-Dependent Gut Immunity in Drosophila

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Systematic Discovery of RNA Binding Proteins that Regulate MicroRNA Levels

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Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building

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Insm1 Induces Neural Progenitor Delamination in Developing Neocortex via Downregulation of the Adherens Junction Belt-Specific Protein Plekha7

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Comparative analysis of the transcriptome of injured nerve segments reveals spatiotemporal responses to neural damage in mice

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Nov 2017
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The DREAM complex through its subunit Lin37 cooperates with Rb to initiate quiescence

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Ribosome Collision Is Critical for Quality Control during No-Go Decay

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Deciphering the Origin and Evolution of Hepatitis B Viruses by Means of a Family of Non-enveloped Fish Viruses - ScienceDirect

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Muscle Stem Cells Undergo Extensive Clonal Drift during Tissue Growth via Meox1-Mediated Induction of G2 Cell-Cycle Arrest

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LTR-Retrotransposon Control by tRNA-Derived Small RNAs

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Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide

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Distinct Roles of RNA Helicases MVH and TDRD9 in PIWI Slicing-Triggered Mammalian piRNA Biogenesis and Function

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Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity

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elifesciences.org/articles/22194v2
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov

Mice deficient of Myc super-enhancer region reveal differential control mechanism between normal and pathological growth

1
1. scibot 08 Nov 2017
  
  in Public
  
  SCR_011841
  
  Curator: @gabimpine
  
  Resource used:
  
  (cutadapt, RRID:SCR_011841)
  
  SciCrunch record: RRID:SCR_011841
  
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ncbi.nlm.nih.gov/pmc/articles/PMC5461110/
www.sciencedirect.com www.sciencedirect.com

Interferon-λ Mediates Non-redundant Front-Line Antiviral Protection against Influenza Virus Infection without Compromising Host Fitness

1
1. scibot 08 Nov 2017
  
  in Public
  
  SCR_011841
  
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sciencedirect.com/science/article/pii/S1074761317301905
www.sciencedirect.com www.sciencedirect.com

The RNA Exosome Syncs IAV-RNAPII Transcription to Promote Viral Ribogenesis and Infectivity

1
1. scibot 08 Nov 2017
  
  in Public
  
  Cutadapt
  
  Curator: @kaitlinsung
  
  Resource used:
  
  (cutadapt, RRID:SCR_011841)
  
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sciencedirect.com/science/article/pii/S0092867417304725
www.sciencedirect.com www.sciencedirect.com

Hybrid Cellular Metabolism Coordinated by Zic3 and Esrrb Synergistically Enhances Induction of Naive Pluripotency

1
1. scibot 08 Nov 2017
  
  in Public
  
  cutadapt-1.3
  
  Curator: @Zeljana_Babic
  
  Resource used:
  
  (cutadapt, RRID:SCR_011841)
  
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sciencedirect.com/science/article/pii/S155041311730222X
www.sciencedirect.com www.sciencedirect.com

The Emergence of Directional Selectivity in the Visual Motion Pathway of Drosophila

1
1. scibot 08 Nov 2017
  
  in Public
  
  cutadapt
  
  Curator: @kaitlinsung
  
  Resource used:
  
  (cutadapt, RRID:SCR_011841)
  
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sciencedirect.com/science/article/pii/S0896627317301939
www.sciencedirect.com www.sciencedirect.com

H3K4 Methylation-Dependent Memory of Somatic Cell Identity Inhibits Reprogramming and Development of Nuclear Transfer Embryos

1
1. scibot 08 Nov 2017
  
  in Public
  
  cutadapt 1.0
  
  Curator: @Zeljana_Babic
  
  Resource used:
  
  (cutadapt, RRID:SCR_011841)
  
  SciCrunch record: RRID:SCR_011841
  
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sciencedirect.com/science/article/pii/S1934590917300747
www.sciencedirect.com www.sciencedirect.com

Gene Resistance to Transcriptional Reprogramming following Nuclear Transfer Is Directly Mediated by Multiple Chromatin-Repressive Pathways

1
1. scibot 08 Nov 2017
  
  in Public
  
  cutadapt 1.0
  
  Curator: @Zeljana_Babic
  
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  (cutadapt, RRID:SCR_011841)
  
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sciencedirect.com/science/article/pii/S1097276517300564
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Destabilization of B2 RNA by EZH2 Activates the Stress Response

1
1. scibot 08 Nov 2017
  
  in Public
  
  Cutadapt
  
  Curator: @chewbeccax
  
  Resource used:
  
  (cutadapt, RRID:SCR_011841)
  
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sciencedirect.com/science/article/pii/S0092867416316518
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov

Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex

1
1. scibot 08 Nov 2017
  
  in Public
  
  SCR_011841
  
  Curator: @kaitlinsung
  
  Resource used:
  
  (cutadapt, RRID:SCR_011841)
  
  SciCrunch record: RRID:SCR_011841
  
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ncbi.nlm.nih.gov/pmc/articles/PMC5325622/
www.sciencedirect.com www.sciencedirect.com

The DEAD-Box Protein Dhh1p Couples mRNA Decay and Translation by Monitoring Codon Optimality

1
1. scibot 08 Nov 2017
  
  in Public
  
  CutAdapt
  
  Curator: @gabimpine
  
  Resource used:
  
  (cutadapt, RRID:SCR_011841)
  
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sciencedirect.com/science/article/pii/S0092867416311503
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov

A molecular portrait of maternal sepsis from Byzantine Troy

1
1. scibot 08 Nov 2017
  
  in Public
  
  SCR_011841
  
  Curator: @gabimpine
  
  Resource used:
  
  (cutadapt, RRID:SCR_011841)
  
  SciCrunch record: RRID:SCR_011841
  
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ncbi.nlm.nih.gov/pmc/articles/PMC5224923/
onlinelibrary.wiley.com onlinelibrary.wiley.com

Gene expression profiling of granule cells and Purkinje cells in the zebrafish cerebellum

1
1. scibot 08 Nov 2017
  
  in Public
  
  Cutadapt
  
  Curator: @gabimpine
  
  Resource used:
  
  (cutadapt, RRID:SCR_011841)
  
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onlinelibrary.wiley.com/doi/10.1002/cne.24114/full
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov

Oral transfer of chemical cues, growth proteins and hormones in social insects

1
1. scibot 08 Nov 2017
  
  in Public
  
  SCR_011841
  
  Curator: @chewbeccax
  
  Resource used:
  
  (cutadapt, RRID:SCR_011841)
  
  SciCrunch record: RRID:SCR_011841
  
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ncbi.nlm.nih.gov/pmc/articles/PMC5153251/
elifesciences.org elifesciences.org

Cell culture-based profiling across mammals reveals DNA repair and metabolism as determinants of species longevity

1
1. scibot 08 Nov 2017
  
  in Public
  
  SCR_011841
  
  Curator: @chewbeccax
  
  Resource used:
  
  (cutadapt, RRID:SCR_011841)
  
  SciCrunch record: RRID:SCR_011841
  
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elifesciences.org/articles/19130

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