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Rapid and pervasive development- and tissue-specific homeolog expression partitioning in newly formed inter-subspecific rice segmental allotetraploids.
Publication Type: Academic Journal
Source(s): BMC genomics [BMC Genomics] 2018 Oct 19; Vol. 19 (1), pp. 756. Date of Electronic Publication: 2018 Oct 19.
Abstract: Background: In diverse plant taxa, whole-genome duplication (WGD) events are major sources of phenotypic novelty. Studies of gene expression in synthetic polyploids have shown immediate expression and functional partitioning of duplicated genes among d...
Inter-individual variation in genes governing human hippocampal progenitor differentiation in vitro is associated with hippocampal volume in adulthood.
Publication Type: Academic Journal
Source(s): Scientific reports [Sci Rep] 2017 Nov 08; Vol. 7 (1), pp. 15112. Date of Electronic Publication: 2017 Nov 08.
Abstract: Hippocampal volumes are smaller in psychiatric disorder patients and lower levels of hippocampal neurogenesis are the hypothesized cause. Understanding which molecular processes regulate hippocampal progenitor differentiation might aid in the identific...
Applications of single-cell RNA sequencing in drug discovery and development.
Publication Type: Academic Journal
Source(s): Nature reviews. Drug discovery [Nat Rev Drug Discov] 2023 Jun; Vol. 22 (6), pp. 496-520. Date of Electronic Publication: 2023 Apr 28.
Abstract: Single-cell technologies, particularly single-cell RNA sequencing (scRNA-seq) methods, together with associated computational tools and the growing availability of public data resources, are transforming drug discovery and development. New opportunitie...
Tackling intra- and inter-tumor heterogeneity to combat triple negative breast cancer.
Publication Type: Academic Journal
Source(s): Frontiers in bioscience (Landmark edition) [Front Biosci (Landmark Ed)] 2017 Jun 01; Vol. 22 (9), pp. 1549-1580. Date of Electronic Publication: 2017 Jun 01.
Abstract: Rampant inter-patient and intra-tumor heterogeneity present formidable challenges in the clinical management of triple-negative breast cancer (TNBC) and mandate a "divide-and-conquer" approach wherein deep biomarker profiling drives patient segmentatio...
Inter- and intra-species variation in genome-wide gene expression of Drosophila in response to parasitoid wasp attack.
Publication Type: Academic Journal
Source(s): BMC genomics [BMC Genomics] 2017 Apr 27; Vol. 18 (1), pp. 331. Date of Electronic Publication: 2017 Apr 27.
Abstract: Background: Parasitoid resistance in Drosophila varies considerably, among and within species. An immune response, lamellocyte-mediated encapsulation, evolved in a subclade of Drosophila and was subsequently lost in at least one species within this sub...
Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing.
Publication Type: Academic Journal
Source(s): Nature biotechnology [Nat Biotechnol] 2023 Feb; Vol. 41 (2), pp. 204-211. Date of Electronic Publication: 2022 Sep 15.
Abstract: Here we introduce a mostly natural sequencing-by-synthesis (mnSBS) method for single-cell RNA sequencing (scRNA-seq), adapted to the Ultima genomics platform, and systematically benchmark it against current scRNA-seq technology. mnSBS uses mostly natur...
Hidden patterns of gene expression provide prognostic insight for colorectal cancer.
Publication Type: Academic Journal
Source(s): Cancer gene therapy [Cancer Gene Ther] 2023 Jan; Vol. 30 (1), pp. 11-21. Date of Electronic Publication: 2022 Aug 18.
Abstract: Cancer tissue samples contain cancer cells and non-cancer cells with each biopsied site containing distinct proportions of these populations. Consequently, assigning useful tumor subtypes based on gene expression measurements from clinical samples is c...
Beyond Transcript Concentrations: Quantifying Polyploid Expression Responses per Biomass, per Genome, and per Cell with RNA-Seq.
Publication Type: Academic Journal
Source(s): Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2023; Vol. 2545, pp. 227-250.
Abstract: RNA-seq has been used extensively to study expression responses to polyploidy. Most current methods for normalizing RNA-seq data yield estimates of transcript concentrations (transcripts per transcriptome). The implicit assumption of these normalizatio...
Inter-laboratory study of human in vitro toxicogenomics-based tests as alternative methods for evaluating chemical carcinogenicity: a bioinformatics perspective.
Publication Type: Academic Journal
Source(s): Archives of toxicology [Arch Toxicol] 2016 Sep; Vol. 90 (9), pp. 2215-2229. Date of Electronic Publication: 2015 Nov 02.
Abstract: The assessment of the carcinogenic potential of chemicals with alternative, human-based in vitro systems has become a major goal of toxicogenomics. The central read-out of these assays is the transcriptome, and while many studies exist that explored th...
Investigating inter-chromosomal regulatory relationships through a comprehensive meta-analysis of matched copy number and transcriptomics data sets.
Publication Type: Academic Journal
Source(s): BMC genomics [BMC Genomics] 2015 Nov 18; Vol. 16, pp. 967. Date of Electronic Publication: 2015 Nov 18.
Abstract: Background: Gene regulatory relationships can be inferred using matched array comparative genomics and transcriptomics data sets from cancer samples. The way in which copy numbers of genes in cancer samples are often greatly disrupted works like a natu...