Experiments
Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).
-
Has reproduction · 75
PD-1 and TIGIT coexpression identifies a circulating CD8 T cell subset predictive of response to anti-PD-1 therapy.
PMID 33188038 · PMC7668369 · Journal for immunotherapy of cancer · 2020 · 7 claims · 6 setups
The frequency of circulating PD-1+TIGIT+ (DPOS) CD8+ T cells after 1 month of anti-PD-1 therapy is associated with clinical response and overall survival
-
Has reproduction · 45
Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer.
PMID 33584715 · PMC7873865 · Frontiers in immunology · 2020 · 8 claims · 8 setups
Eight distinct T cell populations can be identified from CRC tumor tissue by unsupervised clustering of scRNA-seq data
-
Has reproduction · 100
Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility.
PMID 33707641 · PMC7970949 · Scientific reports · 2021 · 8 claims · 8 setups
WGCNA on control human cervical spinal cord RNA-seq identifies 13 co-expression modules (SC.M1-M13), each representing distinct biological processes or cell types.
-
Has reproduction · 67
Comprehensive Analysis of Cell Population Dynamics and Related Core Genes During Vitiligo Development.
PMID 33679890 · PMC7933673 · Frontiers in genetics · 2021 · 8 claims · 7 setups
Immune cell infiltration and abnormal gene expression are closely related to vitiligo pathogenesis
-
Has reproduction · 84
Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions.
PMID 33743211 · PMC7951565 · Cell · 2021 · 8 claims · 8 setups
ChIRP-MS of SARS-CoV-2 RNA in infected Huh7.5 and Vero E6 cells identifies a comprehensive set of 309 host proteins that bind the viral RNA during active infection
-
Has reproduction · 86
Development of double-positive thymocytes at single-cell resolution.
PMID 33771202 · PMC8004397 · Genome medicine · 2021 · 7 claims · 8 setups
DP thymocytes can be classified into blast, rearrangement, and selection subtypes, distinguishable by surface markers CD2 and Ly6d
-
Has reproduction · 65
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses.
PMID 33932985 · PMC8088074 · BMC bioinformatics · 2021 · 8 claims · 5 setups
SPEAQeasy is a portable, easy-to-install, Nextflow-powered RNA-seq processing pipeline that lowers the computational entry barrier for biologists/clinicians
-
Has reproduction · 57
Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod.
PMID 33782539 · PMC8007741 · Communications biology · 2021 · 8 claims · 7 setups
t-SNE clustering of all-gene expression data groups field-collected (diapause program) samples into one cluster while early and late culture (reproductive program) samples separate into two distinct phenotypes
-
Has reproduction · 74
MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction.
PMID 34172000 · PMC8235852 · BMC genomics · 2021 · 8 claims · 8 setups
MicroPIPE, an end-to-end Nextflow/Singularity-based pipeline built from systematically validated tool choices, produces high-quality complete bacterial genome assemblies without manual intervention.
-
Has reproduction · 60
TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes.
PMID 34197621 · PMC8464036 · Nucleic acids research · 2021 · 8 claims · 8 setups
TRAPID 2.0 is a web application performing global characterization of de novo transcriptomes via structural, functional, and taxonomic annotation in an initial processing phase, followed by an exploratory phase of downstream analyses.
-
Has reproduction · 50
Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing.
PMID 34244540 · PMC8270970 · Scientific reports · 2021 · 8 claims · 5 setups
BoHV-1 infection causes substantial up- and down-regulation of host gene networks, including antiviral response and viral transcription/translation-associated genes
-
Has reproduction · 58
Phosphorylation of ribosomal protein S6 differentially affects mRNA translation based on ORF length.
PMID 34871442 · PMC8682771 · Nucleic acids research · 2021 · 8 claims · 8 setups
RPS6 becomes progressively dephosphorylated on ribosomes as they translate along an mRNA CDS
-
Has reproduction · 50
GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring.
PMID 35087491 · PMC8787282 · Frontiers in microbiology · 2021 · 8 claims · 8 setups
GAL08 is a dominant bacterial clade in Dewar Creek hot spring sediment, comprising up to 29.2% of the microbial community by relative read abundance
-
Has reproduction · 84
Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells.
PMID 35177610 · PMC8854666 · Nature communications · 2022 · 8 claims · 7 setups
SHARC uses chemical crosslinkers of defined lengths to measure distances between nucleotides in cellular RNA
-
Has reproduction · 90
Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.
PMID 35464437 · PMC9019466 · Frontiers in immunology · 2022 · 8 claims · 8 setups
Differential polyadenylation occurs in infected Calu-3 and Vero cells at a late time point (48 hpi)
-
Has reproduction · 73
A transcriptomic atlas of Aedes aegypti reveals detailed functional organization of major body parts and gut regional specializations in sugar-fed and blood-fed adult females.
PMID 35471187 · PMC9113746 · eLife · 2022 · 8 claims · 5 setups
Created Aegypti-Atlas, an online RNAseq resource covering Ae. aegypti body parts, gut regions, and a blood meal digestion time course
-
Has reproduction · 95
Utility of Triti-Map for bulk-segregated mapping of causal genes and regulatory elements in Triticeae.
PMID 35605195 · PMC9284283 · Plant communications · 2022 · 8 claims · 4 setups
Triti-Map is a computational package suite plus web interface specifically optimized for bulk-segregated gene mapping in Triticeae, accepting DNA-seq, RNA-seq/ChIP-seq, and traditional QTL data as input
-
Has reproduction · 81
Transcriptional regulation and chromatin architecture maintenance are decoupled functions at the Sox2 locus.
PMID 35710138 · PMC9296009 · Genes & development · 2022 · 8 claims · 7 setups
Sox2 transcriptional activation is traced almost entirely to two key transcription factor-bound regions (SRR107 and SRR111) within the SCR
-
Has reproduction · 100
Sox8 remodels the cranial ectoderm to generate the ear.
PMID 35867760 · PMC9282420 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 8 claims · 8 setups
Sox8 sits at the top of a core transcriptional circuit (Sox8, Pax2, Lmx1a, Zbtb16) that determines otic identity
-
Has reproduction · 100
Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics.
PMID 35910650 · PMC9326479 · Frontiers in microbiology · 2022 · 8 claims · 8 setups
The causal agent of konjac soft rot in China is Pectobacterium aroidearum, confirmed via in vitro/in vivo pathogenicity tests, ANI, dDDH, and phylogenomic analysis.