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gfold specifications

Information


Unique identifier OMICS_09264
Name gfold
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No

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Publication for gfold

gfold in publications

 (29)
PMCID: 5945637
PMID: 29749372
DOI: 10.1038/s41467-018-04274-w

[…] administration but not in the pbs-treated group, indicating defective expansion in the absence of txnrd1 (fig.  and supplementary fig. ).fig. 6, among the top differentially expressed gene sets (|gfold| > 1.5; false discovery rate [fdr] < 0.2) between seb-stimulated txnrd1-deficient and control t cell groups, the cell cycle inhibitor cdkn1a (the gene encoding p21; fdr = 0.05) […]

PMCID: 5831843
PMID: 29507608
DOI: 10.1186/s13068-018-1051-x

[…] point mutations were modeled (excluding residues that are within 5 å from the fad cofactor) and their respective values in free energy of folding were compared with that of the wild-type enzyme (∆∆gfold). by omitting the residues that are close to the active site, the risk of creating a mutant with lower or no activity is limited. the first in silico step consisted of a selection based on free […]

PMCID: 5591532
PMID: 28886694
DOI: 10.1186/s12864-017-4077-8

[…] formation, multiple comparisons among the rna-seq data from different fiber developing stages of the three materials (two cssls and ccri36) were performed. plenty of degs were identified based on gfold analysis. the degs were then underwent go functional enrichment and kegg metabolic pathway analysis followed by accuracy validation using quantitative real-time pcr (qrt-pcr). the results […]

PMCID: 5633395
PMID: 28874383
DOI: 10.1534/g3.117.300108

[…] at 25 dpa, 615 significant degs were identified in mbi7747 and 543 were identified in mbi7561, many more than were identified in mbi7285 (). the common degs that were significantly upregulated (gfold > 0.5) were associated with polysaccharide metabolic processes, regulation of hormone levels, and regulation of transcription (). the common degs that were significantly downregulated (gfold […]

PMCID: 5573122
PMID: 28846714
DOI: 10.1371/journal.pone.0183567

[…] the fusarium species., the rna-seq data was primarily used to support the annotation of protein coding genes and to get a glimpse of the differential gene expression at various developmental stages. gfold, which is one of the best available algorithms for differential expression analysis from single samples without biological replicates, was used to analyse rna-seq data. more fungal genes […]


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gfold institution(s)
Department of Mathematics, Center for Combinatorics, Key Laboratory of Pure Mathematics and Combinatorics - TianJin key Laboratory of Combinatorics; Department of Biology, College of Life Science, Nankai University Tianjin, China; Department of Mathematics, Center for Quantum Geometry of Moduli Spaces, Aarhus University, Århus C, Denmark; Department of Mathematics and Physics, California Institute of Technology, Pasadena, CA, USA; Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig; Max Planck Institute for Mathematics in the Sciences; RNomics Group, Fraunhofer IZI, Leipzig, Germany; Institut fur Theoretical Chemistry, University of Vienna, Vienna, Austria; Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej, Frederiksberg, Denmark; The Santa Fe Institute, Santa Fe, NM, USA; Department of Computer Science, University of Kaiserslautern, Kaiserslautern, Germany

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