Quantitative challenges and their bioinformatic solutions in mass spectrometry-based metabolomics
Improving the quantitative performance of mass spectrometry (MS)-based metabolomics is
the key to its successful application in a broad range of research questions. Like other …
the key to its successful application in a broad range of research questions. Like other …
Design, execution, and interpretation of plant RNA-seq analyses
Genomics has transformed our understanding of the genetic architecture of traits and the
genetic variation present in plants. Here, we present a review of how RNA-seq can be …
genetic variation present in plants. Here, we present a review of how RNA-seq can be …
Early immune pressure initiated by tissue-resident memory T cells sculpts tumor evolution in non-small cell lung cancer
CE Weeden, V Gayevskiy, C Marceaux, D Batey, T Tan… - Cancer Cell, 2023 - cell.com
Tissue-resident memory T (T RM) cells provide immune defense against local infection and
can inhibit cancer progression. However, it is unclear to what extent chronic inflammation …
can inhibit cancer progression. However, it is unclear to what extent chronic inflammation …
Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
Background Batch effects are notoriously common technical variations in multiomics data
and may result in misleading outcomes if uncorrected or over-corrected. A plethora of batch …
and may result in misleading outcomes if uncorrected or over-corrected. A plethora of batch …
Computational textural mapping harmonises sampling variation and reveals multidimensional histopathological fingerprints
Background Technical factors can bias H&E digital slides potentially compromising
computational histopathology studies. Here, we hypothesised that sample quality and …
computational histopathology studies. Here, we hypothesised that sample quality and …
SuperCellCyto: enabling efficient analysis of large scale cytometry datasets
Advancements in cytometry technologies have enabled quantification of up to 50 proteins
across millions of cells at single cell resolution. Analysis of cytometry data routinely involves …
across millions of cells at single cell resolution. Analysis of cytometry data routinely involves …
The circadian clock is disrupted in pancreatic cancer
PB Schwartz, M Nukaya, ME Berres… - PLoS …, 2023 - journals.plos.org
Disruption of the circadian clock is linked to cancer development and progression.
Establishing this connection has proven beneficial for understanding cancer pathogenesis …
Establishing this connection has proven beneficial for understanding cancer pathogenesis …
Easy NanoString nCounter data analysis with the NanoTube
The NanoTube is an open-source pipeline that simplifies the processing, quality control,
normalization and analysis of NanoString nCounter gene expression data. It is implemented …
normalization and analysis of NanoString nCounter gene expression data. It is implemented …
Cardiac substrate utilization and relationship to invasive exercise hemodynamic parameters in HFpEF
The authors conducted transcardiac blood sampling in healthy subjects and subjects with
heart failure with preserved ejection fraction (HFpEF) to compare cardiac metabolite and …
heart failure with preserved ejection fraction (HFpEF) to compare cardiac metabolite and …
ahctf1 and kras mutations combine to amplify oncogenic stress and restrict liver overgrowth in a zebrafish model of hepatocellular carcinoma
KJ Morgan, K Doggett, F Geng, S Mieruszynski… - Elife, 2023 - elifesciences.org
The nucleoporin (NUP) ELYS, encoded by AHCTF1, is a large multifunctional protein with
essential roles in nuclear pore assembly and mitosis. Using both larval and adult zebrafish …
essential roles in nuclear pore assembly and mitosis. Using both larval and adult zebrafish …