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Aug 2025
pmc.ncbi.nlm.nih.gov pmc.ncbi.nlm.nih.gov

RNA polymerase III transcription–associated polyadenylation promotes the accumulation of noncoding retrotransposons during infection

1
1. scibot 21 Aug 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1073/pnas.2507186122
  
  Resource: University of California at Berkeley QB3 Genomics Core Facility (RRID:SCR_022170)
  
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pmc.ncbi.nlm.nih.gov/articles/PMC12358842/
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Sediment and groundwater metagenomes from subsurface microbial communities from the Oak Ridge National Laboratory Oak Ridge Reservation, Oak Ridge, Tennessee, USA

1
1. scibot 16 Aug 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1128/mra.00014-25
  
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pmc.ncbi.nlm.nih.gov/articles/PMC12352057/
www.biorxiv.org www.biorxiv.org

Protein language models reveal evolutionary constraints on synonymous codon choice

1
1. scibot 14 Aug 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1101/2025.08.05.668603
  
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biorxiv.org/content/10.1101/2025.08.05.668603v1
pmc.ncbi.nlm.nih.gov pmc.ncbi.nlm.nih.gov

Deficiency in transmitter release triggers homeostatic transcriptional changes that increase presynaptic excitability

1
1. scibot 13 Aug 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1073/pnas.2322714122
  
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pmc.ncbi.nlm.nih.gov/articles/PMC12337328/
www.biorxiv.org www.biorxiv.org

Cleavage of the RNA polymerase II general transcription factor TFIIB es transcription during stress

1
1. scibot 01 Aug 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1101/2025.07.28.667251
  
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biorxiv.org/content/10.1101/2025.07.28.667251v1
Jul 2025
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Cytoplasmic mRNA decay by the anti-viral nuclease RNase L promotes transcriptional repression

1
1. scibot 23 Jul 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1101/2025.07.08.663778
  
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biorxiv.org/content/10.1101/2025.07.08.663778v1
52.53.155.43 52.53.155.43

A genome assembly for a textbook mammalian study species, the California ground squirrel (Otospermophilus beecheyi).

1
1. scibot 17 Jul 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1093/jhered/esaf045
  
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52.53.155.43/24d8b0cc09ea7caaa6a2e64d2de8b1934e9140a5/esaf045-html.html
journals.asm.org journals.asm.org

Sediment and groundwater metagenomes from subsurface microbial communities from the Oak Ridge National Laboratory Oak Ridge Reservation, Oak Ridge, Tennessee, USA

1
1. scibot 11 Jul 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1128/mra.00014-25
  
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journals.asm.org/doi/10.1128/mra.00014-25
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Intra-Tumoral Treg Ablation Unleashes NK Cell-Mediated Control of CD8 T Cell-Resistant Tumors

1
1. scibot 11 Jul 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1101/2025.06.26.661417
  
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biorxiv.org/content/10.1101/2025.06.26.661417v1
pmc.ncbi.nlm.nih.gov pmc.ncbi.nlm.nih.gov

Exploitable mechanisms of antibody and CAR mediated macrophage cytotoxicity

1
1. scibot 04 Jul 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1038/s41467-025-60745-x
  
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pmc.ncbi.nlm.nih.gov/articles/PMC12216399/
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A subset of conserved phagocytic genes are likely used for the intracellular theft of cnidarian stinging organelles in nudibranch gastropods

1
1. scibot 01 Jul 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1186/s13227-025-00241-x
  
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pmc.ncbi.nlm.nih.gov/articles/PMC12205514/
Jun 2025
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Molecular states underlying neuronal cell type development and plasticity in the postnatal whisker cortex

1
1. scibot 12 Jun 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1371/journal.pbio.3003176
  
  Resource: University of California at Berkeley QB3 Genomics Core Facility (RRID:SCR_022170)
  
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pmc.ncbi.nlm.nih.gov/articles/PMC12119026/
May 2025
pmc.ncbi.nlm.nih.gov pmc.ncbi.nlm.nih.gov

Characterizing the Soil Microbial Community Associated with the Fungal Pathogen Coccidioides immitis

1
1. scibot 21 May 2025
  
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  RRID:SCR_022170
  
  DOI: 10.3390/jof11040309
  
  Resource: University of California at Berkeley QB3 Genomics Core Facility (RRID:SCR_022170)
  
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pmc.ncbi.nlm.nih.gov/articles/PMC12028473/
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Genetic Screen in a Pre-Clinical Model of Sarcoma Development Defines Drivers and Therapeutic Vulnerabilities

1
1. scibot 20 May 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1158/1078-0432.CCR-24-1238
  
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pmc.ncbi.nlm.nih.gov/articles/PMC11530313/
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Calpains orchestrate secretion of annexin-containing microvesicles during membrane repair

1
1. scibot 20 May 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1083/jcb.202408159
  
  Resource: University of California at Berkeley QB3 Genomics Core Facility (RRID:SCR_022170)
  
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pmc.ncbi.nlm.nih.gov/articles/PMC12083247/
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Occurrence of aneuploidy across the range of coast redwood (Sequoia sempervirens)

1
1. scibot 19 May 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1093/g3journal/jkaf063
  
  Resource: University of California at Berkeley QB3 Genomics Core Facility (RRID:SCR_022170)
  
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pmc.ncbi.nlm.nih.gov/articles/PMC12060238/
Apr 2025
pmc.ncbi.nlm.nih.gov pmc.ncbi.nlm.nih.gov

mTORC1 activation drives astrocyte reactivity in cortical tubers and brain organoid models of TSC

1
1. scibot 18 Apr 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1101/2025.02.28.640914
  
  Resource: University of California at Berkeley QB3 Genomics Core Facility (RRID:SCR_022170)
  
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pmc.ncbi.nlm.nih.gov/articles/PMC11908165/
Mar 2025
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Cell differentiation controls iron assimilation in the choanoflagellate Salpingoeca rosetta

1
1. scibot 27 Mar 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1128/msphere.00917-24
  
  Resource: University of California at Berkeley QB3 Genomics Core Facility (RRID:SCR_022170)
  
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pmc.ncbi.nlm.nih.gov/articles/PMC11934334/
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Iguanas rafted more than 8,000 km from North America to Fiji

1
1. scibot 26 Mar 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1073/pnas.2318622122
  
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pnas.org/doi/abs/10.1073/pnas.2318622122
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Honoring the Afro-Colombian musical culture with the naming of Epipedobatescurrulao sp. nov. (Anura, Dendrobatidae), a frog from the Pacific rainforests

1
1. scibot 21 Mar 2025
  
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  RRID:SCR_022170
  
  DOI: 10.3897/zookeys.1226.123803
  
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pmc.ncbi.nlm.nih.gov/articles/PMC11826230/
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Identification of intestinal mediators of Caenorhabditis elegans DBL-1/BMP immune signaling shaping gut microbiome composition

1
1. scibot 14 Mar 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1128/mbio.03703-24
  
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pmc.ncbi.nlm.nih.gov/articles/PMC11898619/
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KLF family members control expression of genes required for tissue macrophage identities

1
1. scibot 14 Mar 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1084/jem.20240379
  
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pmc.ncbi.nlm.nih.gov/articles/PMC11899981/
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A subset of conserved phagocytic genes are likely used for the intracellular theft of cnidarian stinging organelles in nudibranch gastropods

1
1. scibot 13 Mar 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1101/2025.02.13.637864
  
  Resource: University of California at Berkeley QB3 Genomics Core Facility (RRID:SCR_022170)
  
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pmc.ncbi.nlm.nih.gov/articles/PMC11870399/
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Sulfinyl Aziridines as Stereoselective Covalent Destabilizing Degraders of the Oncogenic Transcription Factor MYC

1
1. scibot 07 Mar 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1101/2025.02.24.639755
  
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pmc.ncbi.nlm.nih.gov/articles/PMC11888305/
Feb 2025
pmc.ncbi.nlm.nih.gov pmc.ncbi.nlm.nih.gov

Improved precision, sensitivity, and adaptability of ordered two-template relay cDNA library preparation for RNA sequencing

1
1. scibot 08 Feb 2025
  
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  RRID:SCR_022170
  
  DOI: 10.1261/rna.080318.124
  
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pmc.ncbi.nlm.nih.gov/articles/PMC11789487/
Dec 2024
pmc.ncbi.nlm.nih.gov pmc.ncbi.nlm.nih.gov

Improved precision, sensitivity, and adaptability of Ordered Two-Template Relay cDNA library preparation for RNA sequencing

1
1. scibot 21 Dec 2024
  
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  RRID:SCR_022170
  
  DOI: 10.1101/2024.11.09.622813
  
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pmc.ncbi.nlm.nih.gov/articles/PMC11581009/
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Acetaminophen production in the edible, filamentous cyanobacterium Arthrospira platensis

1
1. scibot 13 Dec 2024
  
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  RRID:SCR_022170
  
  DOI: 10.1002/bit.28858
  
  Resource: University of California at Berkeley QB3 Genomics Core Facility (RRID:SCR_022170)
  
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pmc.ncbi.nlm.nih.gov/articles/PMC11632167/
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Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in zebrafish

1
1. scibot 11 Dec 2024
  
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  DOI: 10.1371/journal.pbio.3002887
  
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pmc.ncbi.nlm.nih.gov/articles/PMC11620358/
Nov 2024
pubs.acs.org pubs.acs.org

Evaluation of the Impact of Concentration and Extraction Methods on the Targeted Sequencing of Human Viruses from Wastewater

2
1. scibot 29 Nov 2024
  
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  RRID: SCR_022170
  
  DOI: 10.1021/acs.est.4c00580
  
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2. scibot 29 Nov 2024
  
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  RRID:SCR_022170
  
  DOI: 10.1021/acs.est.4c00580
  
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pubs.acs.org/doi/10.1021/acs.est.4c00580
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Regulation of disease-associated microglia in the optic nerve by lipoxin B4 and ocular hypertension

1
1. scibot 26 Nov 2024
  
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  RRID:SCR_022170
  
  DOI: 10.1186/s13024-024-00775-z
  
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pmc.ncbi.nlm.nih.gov/articles/PMC11580672/
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High-throughput protein characterization by complementation using DNA barcoded fragment libraries

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1. scibot 08 Nov 2024
  
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  RRID:SCR_022170
  
  DOI: 10.1038/s44320-024-00068-z
  
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pmc.ncbi.nlm.nih.gov/articles/PMC11535334/
Sep 2024
www.sciencedirect.com www.sciencedirect.com

A developmental gradient reveals biosynthetic pathways to eukaryotic toxins in monocot geophytes

1
1. scibot 17 Sep 2024
  
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  DOI: 10.1016/j.cell.2024.08.027
  
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sciencedirect.com/science/article/pii/S0092867424009188
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Pervasive heteroplasmy in an invasive ambrosia beetle (Scolytinae) in southern California

1
1. scibot 16 Sep 2024
  
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  RRID:SCR_022170
  
  DOI: 10.1038/s41437-024-00722-0
  
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nature.com/articles/s41437-024-00722-0
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Oligodendroglioma patient survival is associated with circulating B-cells and age

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1. scibot 12 Sep 2024
  
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  RRID:SCR_022170
  
  DOI: 10.1093/noajnl/vdae143
  
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ncbi.nlm.nih.gov/pmc/articles/PMC11379917/
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DMDA-PatA mediates RNA sequence-selective translation repression by anchoring eIF4A and DDX3 to GNG motifs

1
1. scibot 05 Sep 2024
  
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  DOI: 10.1038/s41467-024-51635-9
  
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Aug 2024
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Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts

1
1. scibot 29 Aug 2024
  
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  DOI: 10.1038/s41467-024-51258-0
  
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RAF inhibitors activate the integrated stress response by direct activation of GCN2

1
1. scibot 22 Aug 2024
  
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  DOI: 10.1101/2024.08.15.607884
  
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Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance

1
1. scibot 20 Aug 2024
  
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  DOI: 10.1038/s41467-024-50124-3
  
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ncbi.nlm.nih.gov/pmc/articles/PMC11300592/
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Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates

1
1. scibot 01 Aug 2024
  
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ncbi.nlm.nih.gov/pmc/articles/PMC11287214/
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Cortical plasticity is associated with blood–brain barrier modulation

1
1. scibot 20 Jul 2024
  
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  DOI: 10.7554/eLife.89611
  
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ncbi.nlm.nih.gov/pmc/articles/PMC11257677/
Jun 2024
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Multiplexed CRISPR-Cas9 mutagenesis of rice PSBS1 noncoding sequences for transgene-free overexpression

1
1. scibot 09 Jun 2024
  
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  DOI: 10.1126/sciadv.adm7452
  
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ncbi.nlm.nih.gov/pmc/articles/PMC11160471/
May 2024
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Cell-type-specific expression of a DCYTB ortholog enables the choanoflagellate Salpingoeca rosetta to utilize ferric colloids

1
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  DOI: 10.1101/2024.05.25.595918
  
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Evaluation of the Impact of Concentration and Extraction Methods on the Targeted Sequencing of Human Viruses from Wastewater

1
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  DOI: 10.1021/acs.est.4c00580
  
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Synchronization between chloroplastic and cytosolic protein synthesis for photosynthesis complex assembly

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  DOI: 10.1101/2024.05.03.592458
  
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High-throughput protein characterization by complementation using DNA barcoded fragment libraries

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  DOI: 10.1101/2024.05.08.593210
  
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Improving rice drought tolerance through host-mediated microbiome selection

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  DOI: 10.1101/2024.02.03.578672
  
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Evaluation of the impact of concentration and extraction methods on the targeted sequencing of human viruses from wastewater

2
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The RNA polymerase II general transcription factor TFIIB is a target for transcriptome control during cellular stress and viral infection

2
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  DOI: 10.1101/2024.01.16.575933
  
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Apr 2024
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Hypoxia exposure blunts angiogenic signaling and upregulates the antioxidant system in endothelial cells derived from elephant seals

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  DOI: 10.1186/s12915-024-01892-3
  
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Dysregulation of neuroprotective lipoxin pathway in astrocytes in response to cytokines and ocular hypertension

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  DOI: 10.1186/s40478-024-01767-2
  
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Regulation of Diseases-Associated Microglia in the Optic Nerve by Lipoxin B4 and Ocular Hypertension

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Spatial co-transcriptomics reveals discrete stages of the arbuscular mycorrhizal symbiosis

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  DOI: 10.1038/s41477-024-01666-3
  
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nature.com/articles/s41477-024-01666-3
Mar 2024
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Krüppel-like Factor (KLF) family members control expression of genes required for serous cavity and alveolar macrophage identities

1
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biorxiv.org/content/10.1101/2024.02.28.582578v1
Feb 2024
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Defining the mechanisms and properties of post-transcriptional regulatory disordered regions by high-throughput functional profiling

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Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates

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  DOI: 10.1101/2023.12.21.572947
  
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Jan 2024
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Perfluorooctanoic acid induces transcriptomic alterations in second trimester human cytotrophoblasts

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  DOI: 10.1093/toxsci/kfad097
  
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dx.doi.org/10.1093/toxsci/kfad097
Dec 2023
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Modulation of tooth regeneration through opposing responses to Wnt and BMP signals in teleosts

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  DOI: 10.1242/dev.202168
  
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ncbi.nlm.nih.gov/pmc/articles/PMC10730089/
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Codon optimality modulates protein output by tuning translation initiation

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  DOI: 10.1101/2023.11.27.568910
  
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Identification of intestinal mediators of Caenorhabditis elegans DBL-1/BMP immune signaling shaping gut microbiome composition

1
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  DOI: 10.1101/2023.10.26.564221
  
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biorxiv.org/content/10.1101/2023.10.26.564221v1
Nov 2023
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Determinants of genetic diversity in Neotropical salamanders (Plethodontidae: Bolitoglossini)

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  DOI: 10.1002/ece3.10707
  
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ncbi.nlm.nih.gov/pmc/articles/PMC10654480/
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Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth

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  DOI: 10.1016/j.cell.2023.10.026
  
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sciencedirect.com/science/article/pii/S0092867423011777
Oct 2023
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Multiplexed CRISPR/Cas9 mutagenesis of rice PSBS1 non-coding sequences for transgene-free overexpression

1
1. scibot 27 Oct 2023
  
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  DOI: 10.1101/2023.10.20.563333
  
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An RFX transcription factor regulates ciliogenesis in the closest living relatives of animals

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  DOI: 10.1016/j.cub.2023.07.022
  
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ncbi.nlm.nih.gov/pmc/articles/PMC10530576/
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Streamlined and sensitive mono- and di-ribosome profiling in yeast and human cells

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  DOI: 10.1038/s41592-023-02028-1
  
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nature.com/articles/s41592-023-02028-1
Sep 2023
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Pateamine A mediates RNA sequence-selective translation repression by anchoring eIF4A and DDX3 to GNG motifs

1
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  DOI: 10.1101/2023.09.21.558742
  
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Modular pooled discovery of synthetic knockin sequences to program durable cell therapies

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  DOI: 10.1016/j.cell.2023.08.013
  
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sciencedirect.com/science/article/pii/S0092867423009029
Aug 2023
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Geochemical constraints on bacteriophage infectivity in terrestrial environments

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  DOI: 10.1038/s43705-023-00297-7
  
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Spatial Co-transcriptomics Reveals Discrete Stages of the Arbuscular Mycorrhizal Symbiosis

1
1. scibot 12 Aug 2023
  
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  DOI: 10.1101/2023.08.02.551648
  
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Jul 2023
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov

Coding and non-coding elements comprise a regulatory network controlling transcription in Kaposi’s sarcoma-associated herpesvirus

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1. scibot 25 Jul 2023
  
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  RRID:SCR_022170
  
  DOI: 10.1101/2023.07.08.548212
  
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ncbi.nlm.nih.gov/pmc/articles/PMC10350069/
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Dysregulation of Neuroprotective Lipoxin Pathway in Astrocytes in Response to Cytokines and Ocular Hypertension

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1. scibot 18 Jul 2023
  
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  RRID:SCR_022170
  
  DOI: 10.1101/2023.06.22.546157
  
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ncbi.nlm.nih.gov/pmc/articles/PMC10327029/
Jun 2023
www.nature.com www.nature.com

A convolutional neural network STIFMap reveals associations between stromal stiffness and EMT in breast cancer

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1. scibot 17 Jun 2023
  
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  DOI: 10.1038/s41467-023-39085-1
  
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nature.com/articles/s41467-023-39085-1
May 2023
www.biorxiv.org www.biorxiv.org

Cortical Plasticity is associated with Blood-Brain-Barrier Modulation

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1. scibot 18 May 2023
  
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  DOI: 10.1101/2023.04.23.537964
  
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biorxiv.org/content/10.1101/2023.04.23.537964v2
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A developmental gradient reveals biosynthetic pathways to eukaryotic toxins in monocot geophytes

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1. scibot 18 May 2023
  
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  RRID:SCR_022170
  
  DOI: 10.1101/2023.05.12.540595
  
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biorxiv.org/content/10.1101/2023.05.12.540595v1
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Highly-multiplexed and efficient long-amplicon PacBio and Nanopore sequencing of hundreds of full mitochondrial genomes

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1. scibot 04 May 2023
  
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  RRID:SCR_022170
  
  DOI: 10.1186/s12864-023-09277-6
  
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link.springer.com/article/10.1186/s12864-023-09277-6
Apr 2023
www.biorxiv.org www.biorxiv.org

Geochemical constraints on bacteriophage infectivity in terrestrial environments

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1. scibot 20 Apr 2023
  
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  RRID:SCR_022170
  
  DOI: 10.1101/2023.04.10.536276
  
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biorxiv.org/content/10.1101/2023.04.10.536276v1
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Engineering osmolysis susceptibility in Cupriavidus necator and Escherichia coli for recovery of intracellular products

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1. scibot 13 Apr 2023
  
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  DOI: 10.1186/s12934-023-02064-8
  
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link.springer.com/article/10.1186/s12934-023-02064-8
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X-chromosome target specificity diverged between dosage compensation mechanisms of two closely related Caenorhabditis species

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1. scibot 07 Apr 2023
  
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  DOI: 10.7554/eLife.85413
  
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ncbi.nlm.nih.gov/pmc/articles/PMC10076027/
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Intracellular replication of Pseudomonas aeruginosa in epithelial cells requires suppression of the caspase-4 inflammasome

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1. scibot 05 Apr 2023
  
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  RRID:SCR_022170
  
  DOI: 10.1101/2023.02.13.528260
  
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biorxiv.org/content/10.1101/2023.02.13.528260v1
Mar 2023
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Streamlined and sensitive mono- and diribosome profiling in yeast and human cells

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1. scibot 03 Mar 2023
  
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  DOI: 10.1101/2023.02.01.526718
  
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biorxiv.org/content/10.1101/2023.02.01.526718v1
Dec 2022
www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov

Comprehensive molecular and morphological resolution of blubber stratification in a deep-diving, fasting-adapted seal

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1. scibot 30 Dec 2022
  
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  DOI: 10.3389/fphys.2022.1057721
  
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ncbi.nlm.nih.gov/pmc/articles/PMC9795062/
Sep 2022
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Combinatorial clustering of distinct DNA motifs directs synergistic binding of <i>Caenorhabditis elegans</i> dosage compensation complex to X chromosomes

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1. scibot 10 Sep 2022
  
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  DOI: 10.1073/pnas.2211642119
  
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pnas.org/doi/abs/10.1073/pnas.2211642119

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