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).

Publications 1.3k Datasets 392.5k Experiments 26

System / cell line: sequence ✕ Assay: time-course ✕ Clear

Environmental genome project: a positive sequence of events.

PMID 11171540 · PMC1242069 · Environmental health perspectives · 2001 · 8 claims · 5 setups

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Exposure to alkylating agents evokes at least threefold expression changes in about one-third of the yeast genome (~2,000 genes), far beyond DNA repair genes alone

yeast genes population microarray time-course resequencing
A Novel Algicidal Bacterium, Microbulbifer sp. YX04, Triggered Oxidative Damage and Autophagic Cell Death in Phaeocystis globosa, Which Causes Harmful Algal Blooms.

PMID 35019679 · PMC8754136 · Microbiology spectrum · 2022 · 8 claims · 9 setups

Has reproduction · 36

Microbulbifer sp. YX04 shows high algicidal activity against P. globosa, peaking at 93.2% in the declining growth phase

phaeocystis strain yx04 globosa algicidal 16s scanning
In silico segmentations of lentivirus envelope sequences.

PMID 17376229 · PMC1847453 · BMC bioinformatics · 2007 · 8 claims · 8 setups

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C and V regions of lentivirus SU sequences have distinct statistical (oligonucleotide/amino-acid) compositions that HMMs can learn and use to delimit them.

eiav hiv hmm-based hmm artificial
Novel point mutation in the extracellular domain of the granulocyte colony-stimulating factor (G-CSF) receptor in a case of severe congenital neutropenia hyporesponsive to G-CSF treatment.

PMID 10449521 · PMC2195597 · The Journal of experimental medicine · 1999 · 7 claims · 8 setups

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A novel C→A point mutation at nucleotide 850 of GCSFR cDNA causes a Pro→His substitution at position 206 (P206H) in the proline-rich hinge of the CRH domain of the G-CSF receptor extracellular domain in an SCN patient hyporesponsive to G-CSF.

bone fibroblast 32d.cl8.6 32d rt-pcr genomic flow
Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes.

PMID 18775783 · PMC2729512 · Molecular and cellular neurosciences · 2008 · 8 claims · 8 setups

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Six 22q11 genes (Mrpl40, Prodh, Slc25a1, Txnrd2, T10, Zdhhc8) encode proteins that localize to mitochondria, including neuronal/synaptic mitochondria.

orthologues nih-3t3 3t3 mefs bioinformatic egfp co-transfection
Similarities and differences in genome-wide expression data of six organisms.

PMID 14737187 · PMC300882 · PLoS biology · 2004 · 8 claims · 8 setups

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Coexpression of functionally related genes is frequently conserved across evolutionarily distant organisms

saccharomyces caenorhabditis escherichia arabidopsis genome-wide large-scale developmental
Global mapping of the topography and magnitude of proteolytic events in apoptosis.

PMID 18724940 · PMC2597167 · Cell · 2008 · 7 claims · 6 setups

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PROTOMAP, a method combining 1D SDS-PAGE fractionation with LC-MS/MS-derived sequence coverage and spectral counting visualized as 'peptographs', enables global mapping of proteolytic topography and magnitude

jurkat sds-page fragmentation caspase-3
GOLD.db: genomics of lipid-associated disorders database.

PMID 15588328 · PMC544894 · BMC genomics · 2004 · 8 claims · 4 setups

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GOLD.db integrates annotated pathways, gene/protein reference information, and curated gene expression datasets for lipid-associated disorders research

adipocyte adipose-specific 3t3-l1 gene curated whole-body insulin
Reconstructing transcriptional regulatory networks through genomics data.

PMID 20048387 · PMC3666560 · Statistical methods in medical research · 2009 · 7 claims · 5 setups

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Location data (ChIP-chip/ChIP-seq) alone is insufficient for TRN inference because binding does not imply regulation, TF binding is dynamic across conditions/time, and TRNs involve combinatorial effects of multiple TFs not captured by single-TF ChIP experiments.

yeast generic perturbations followed chip-chip chip-seq gene
Meeting highlights: beyond the genome 2000: the 18th International Congress of Biochemistry and Molecular Biology.

PMID 11119309 · PMC2448388 · Yeast (Chichester, England) · 2000 · 8 claims · 8 setups

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Celera sequenced a human genome to ~45-fold coverage from one donor and used high-quality sequence stretches to define ~6 million SNPs

homo saccharomyces nicotiana arabidopsis whole-genome oligonucleotide molecular
Harnessing the HGP of public health.

PMID 15176090 · PMC1241998 · Environmental health perspectives · 2004 · 8 claims · 7 setups

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The tombusvirus p19 protein selectively recognizes and sequesters short (21-22 nucleotide) silencing siRNAs, discriminating them from longer siRNAs by measuring siRNA length via tryptophan-mediated end-stacking interactions

carnation cirv blood rice x-ray site-directed mass
The SARS-CoV-2 subgenome landscape and its novel regulatory features.

PMID 33713597 · PMC7927579 · Molecular cell · 2021 · 8 claims · 6 setups

Has reproduction · 84

Template switching in SARS-CoV-2 can occur bidirectionally, generating diverse subgenomes through successive template-switching events

vero caco-2 sars-cov-2 ngs nanopore northern
Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider.

PMID 36203191 · PMC9535882 · BMC biology · 2022 · 8 claims · 8 setups

Has reproduction · 65

Comparative RNA-seq of cells isolated from central, intermediate, and peripheral regions of stage-3 embryos identifies genes with locally restricted expression genome-wide

tepidariorum drosophila rna-seq whole-mount parental
Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat.

PMID 35857869 · PMC9335242 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 6 claims · 8 setups

Has reproduction · 80

AvrPm17 is encoded by a paralogous, tandemly duplicated effector gene pair located in a pericentromeric, mildew sublineage-specific effector cluster (family E003) showing signs of recurring gene conversion.

b.g parental nicotiana benthamiana qtl comparative rna-sequencing
Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups

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XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray

hct116 macaque cos-7 genomic cdna est molecular
A well-conserved Plasmodium falciparum var gene shows an unusual stage-specific transcript pattern.

PMID 12787360 · PMC2869446 · Molecular microbiology · 2003 · 8 claims · 8 setups

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Full-length var transcripts (detected by the complex var exon 2 probe) are present only in ring stages, not in pigmented trophozoites, across multiple parasite lines

falciparum red northern static rt-pcr
Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.

PMID 15230980 · PMC459218 · BMC molecular biology · 2004 · 8 claims · 8 setups

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P. falciparum produces full-length PfCnA/PfCnB (calcineurin) and PP7 as well as proteolytically processed catalytic cores in vivo, likely as intermediates of a degradation pathway

falciparum coli native falciparum-infected rt-pcr recombinant peptide
A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein.

PMID 17183673 · PMC1762436 · PloS one · 2006 · 8 claims · 7 setups

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HCNCp is a novel invariant (non-variant) cyst protein belonging to a new family of high-cysteine membrane proteins (HCMp) abundant in the Giardia genome

giardia serial northern western
Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.

PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups

Has reproduction · 27

A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.

radish assembled rna-seq novo functional
Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.

PMID 18831773 · PMC3226104 · BMC genomics · 2008 · 8 claims · 8 setups

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Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare

mcf7 arabidopsis specified different chip-seq microarray array-based

Experiments

Environmental genome project: a positive sequence of events.

A Novel Algicidal Bacterium, Microbulbifer sp. YX04, Triggered Oxidative Damage and Autophagic Cell Death in Phaeocystis globosa, Which Causes Harmful Algal Blooms.

In silico segmentations of lentivirus envelope sequences.

Novel point mutation in the extracellular domain of the granulocyte colony-stimulating factor (G-CSF) receptor in a case of severe congenital neutropenia hyporesponsive to G-CSF treatment.

Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes.

Similarities and differences in genome-wide expression data of six organisms.

Global mapping of the topography and magnitude of proteolytic events in apoptosis.

GOLD.db: genomics of lipid-associated disorders database.

Reconstructing transcriptional regulatory networks through genomics data.

Meeting highlights: beyond the genome 2000: the 18th International Congress of Biochemistry and Molecular Biology.

Harnessing the HGP of public health.

The SARS-CoV-2 subgenome landscape and its novel regulatory features.

Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider.

Ancient variation of the AvrPm17 gene in powdery mildew limits the effectiveness of the introgressed rye Pm17 resistance gene in wheat.

Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

A well-conserved Plasmodium falciparum var gene shows an unusual stage-specific transcript pattern.

Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.

A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein.

Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.

Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.