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).

• A comparative analysis of blastoid models through single-cell transcriptomics.

  PMID 39524369 · PMC11543915 · iScience · 2024 · 8 claims · 7 setups

  Has reproduction · 60

  EPSC-derived blastoids are transcriptomically distinct from nPSC-derived blastoids, with nPSC-blastoids clustering closer to natural blastocysts.

  blastoid natural combined integrated scrnaseq lineage kolmogorov-smirnov

• Genetic architecture of natural variation of cardiac performance from flies to humans.

  PMID 36383075 · PMC9668334 · eLife · 2022 · 8 claims · 7 setups

  Has reproduction · 74

  Natural genetic variation significantly influences cardiac performance traits (rhythmicity and contractility) across 167 DGRP lines

  drosophila dgrp gene induced high-speed genome-wide epistasis

• Expression analysis of candidate breast tumour suppressor genes on chromosome 16q.

  PMID 16280054 · PMC1410740 · Breast cancer research : BCR · 2005 · 8 claims · 7 setups

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  None of the six candidate genes (CBFA2T3, TERF2, TERF2IP, FBXL8, LRRC29, FANCA) showed inactivating mutations or expression differences clearly associated with 16q LOH status

  breast quantitative fragment gene-expression

• Multilocus analysis of SNP and metabolic data within a given pathway.

  PMID 16412218 · PMC1382210 · BMC genomics · 2006 · 8 claims · 7 setups

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  The combinatorial partitioning method (CPM) with optimal thresholds can identify SNPs associated with quantitative metabolite levels rather than only categorical traits.

  healthy plasma genomic chi-square combinatorial leave-one-out

• Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia.

  PMID 19039135 · PMC2746051 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

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  Diagnosis and relapse ALL samples show different patterns of CNAs, with relapse-acquired abnormalities preferentially affecting cell cycle regulation and B-cell development genes

  matched bone leukemia diagnosis snp flow quantitative

• Systems analysis of bone.

  PMID 20046860 · PMC2790199 · Wiley interdisciplinary reviews. Systems biology and medicine · 2009 · 8 claims · 7 setups

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  Fracture risk and skeletal traits are highly heritable, with over 350 QTLs mapped across the mouse genome and genes such as LRP5, Alox15, and Darc identified as regulators of bone mass.

  intercross long tibiae mandible qtl dual-energy whole-bone

• Epigenetics and phenotypic variation in mammals.

  PMID 16688527 · PMC3906716 · Mammalian genome : official journal of the International Mammalian Genome Society · 2006 · 8 claims · 8 setups

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  Epigenetic modifications are mitotically heritable, but the fidelity of meiotic/transgenerational inheritance in mammals is poorly understood and evidence in mammals is scanty.

  mammalian mhc chromosomes embryonic methylation high-throughput chip

• A proteomic analysis of IVF follicular fluid in women

  PMID 18980758 · PMC3916005 · Fertility and sterility · 2009 · 8 claims · 4 setups

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  2D-PAGE proteomic evaluation of follicular fluid can identify potential biomarkers distinguishing good versus poor IVF responders in matched patient pairs

  follicular excised clinical polyacrylamide liquid direct

• Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia.

  PMID 18248679 · PMC2277413 · BMC genomics · 2008 · 8 claims · 4 setups

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  Chromatin remodelling-associated genes SMARCC1, NCOR1, MRFAP1 and MORF4L2 are upregulated during progression of cervical intraepithelial neoplasia

  cervical independent computational long real-time gene

• PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype.

  PMID 19969003 · PMC2822003 · Journal of molecular biology · 2010 · 7 claims · 7 setups

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  PCP-consensus sequences of E protein show insertions/deletions that distinguish tick-borne, mosquito-borne, no-known-vector (NKV), and yellow fever virus (YFV) Flaviviruses

  natural aligned ns3 denv sequence pcp-consensus physicochemical

• Identification and characterization of HLA-A*0301 epitopes in HIV-1 gag proteins using a novel approach.

  PMID 19903485 · PMC2836169 · Journal of immunological methods · 2010 · 7 claims · 7 setups

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  PS mutations V7I and I34L (p17) and K403R (p7) in HIV-1 gag significantly correlate with HLA-A*0301

  hiv-1-infected genomic hiv-1 hla-a*0301 statistical pcr gag

• Mutation spectrum of homogentisic acid oxidase (HGD) in alkaptonuria.

  PMID 19862842 · PMC2830005 · Human mutation · 2009 · 8 claims · 6 setups

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  Mutations in HGD, which encodes homogentisate dioxygenase, cause AKU by blocking conversion of homogentisic acid to maleylacetoacetic acid in the tyrosine catabolic pathway

  aku hgd recombinant hgd missense splice

• Genomic views of distant-acting enhancers.

  PMID 19741700 · PMC2923221 · Nature · 2009 · 8 claims · 8 setups

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  Meta-analysis of ~1200 top GWAS SNPs found that in 40% of cases (472/1170) no known exons overlap the linked SNP or its haplotype block, implying noncoding variation causally contributes to many traits.

  genome patients embryos ret gwas targeted transgenic

• The gentle art of gene arrangement: the meaning of gene clusters.

  PMID 11897017 · PMC139018 · Genome biology · 2002 · 8 claims · 7 setups

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  Gene order in eukaryotic genomes is likely optimized by natural selection rather than arising purely by chance reshuffling.

  populations mhc interphase cartilaginous sequence codon comparative

• Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays.

  PMID 15722479 · PMC549431 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  Two base deletion probes display the highest average hybridization specificity, followed by single base substitution, single base deletion, and single base insertion probes.

  atm hybridized probe oligonucleotide transcription microarray

• Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

  PMID 16672049 · PMC1464126 · BMC genomics · 2006 · 8 claims · 7 setups

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  Seven genomic islands (VPaI-1 to VPaI-7, 10-81 kb) were identified in V. parahaemolyticus RIMD2210633 by aberrant GC content, presence of integrases/transposases, flanking direct repeats, and absence from related Vibrionaceae genomes.

  parahaemolyticus vulnificus clinical ecori-digested bioinformatic comparative pcr

• Analysis of sequence conservation at nucleotide resolution.

  PMID 18166073 · PMC2230682 · PLoS computational biology · 2007 · 8 claims · 4 setups

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  SCONE (Sequence CONservation Evaluation) is a novel method that estimates evolutionary rate and a neutrality p-value for individual nucleotide positions in a multiple sequence alignment.

  encode population comparative snp functional

• Does distance matter? Variations in alternative 3' splicing regulation.

  PMID 17704130 · PMC2018619 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Alternative 3' splice sites can be distinguished from constitutive splice sites by a combination of sequence/conservation properties that vary depending on the distance between the splice sites.

  intronic human-mouse same comparative polypyrimidine branch

• Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.

  PMID 18953408 · PMC2568805 · PloS one · 2008 · 8 claims · 8 setups

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  Re-sequencing and genotyping across a 28.5 kb region delineates the prostate cancer risk association within FHIT intron 5 to a 15 kb LD block in European-Americans.

  european-american yoruban japanese case sanger snp linkage

• Biomarkers of lupus nephritis determined by serial urine proteomics.

  PMID 18596723 · PMC2614389 · Kidney international · 2008 · 7 claims · 6 setups

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  SELDI-TOF-MS screening of the LMW urine proteome identifies protein ions that are differentially expressed across phases of the lupus nephritis flare cycle (baseline, pre-flare, flare, post-flare)

  low-molecular-weight lmw urine kidney seldi-tof-ms on-chip capillary