The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics

LK Pino, BC Searle, JG Bollinger… - Mass spectrometry …, 2020 - Wiley Online Library
Skyline is a freely available, open‐source Windows client application for accelerating
targeted proteomics experimentation, with an emphasis on the proteomics and mass …

Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future

SA Huws, CJ Creevey, LB Oyama, I Mizrahi… - Frontiers in …, 2018 - frontiersin.org
The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi,
methanogenic archaea and phages. These microbes interact closely to breakdown plant …

Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex

A Chen, Y Sun, Y Lei, C Li, S Liao, J Meng, Y Bai, Z Liu… - Cell, 2023 - cell.com
Elucidating the cellular organization of the cerebral cortex is critical for understanding brain
structure and function. Using large-scale single-nucleus RNA sequencing and spatial …

Recovering gene interactions from single-cell data using data diffusion

D Van Dijk, R Sharma, J Nainys, K Yim, P Kathail… - Cell, 2018 - cell.com
Single-cell RNA sequencing technologies suffer from many sources of technical noise,
including under-sampling of mRNA molecules, often termed" dropout," which can severely …

A practical guide to linking brain-wide gene expression and neuroimaging data

A Arnatkevic̆iūtė, BD Fulcher, A Fornito - Neuroimage, 2019 - Elsevier
The recent availability of comprehensive, brain-wide gene expression atlases such as the
Allen Human Brain Atlas (AHBA) has opened new opportunities for understanding how …

Chemotherapy resistance in advanced ovarian cancer patients

R Pokhriyal, R Hariprasad, L Kumar… - Biomarkers in …, 2019 - journals.sagepub.com
Ovarian cancer is the seventh most common gynaecologic malignancy seen in women.
Majority of the patients with ovarian cancer are diagnosed at the advanced stage making …

Positive controls in adults and children support that very few, if any, new neurons are born in the adult human hippocampus

SF Sorrells, MF Paredes, Z Zhang, G Kang… - Journal of …, 2021 - Soc Neuroscience
Adult hippocampal neurogenesis was originally discovered in rodents. Subsequent studies
identified the adult neural stem cells and found important links between adult neurogenesis …

Relationship between differentially expressed mRNA and mRNA-protein correlations in a xenograft model system

A Koussounadis, SP Langdon, IH Um, DJ Harrison… - Scientific reports, 2015 - nature.com
Differential mRNA expression studies implicitly assume that changes in mRNA expression
have biological meaning, most likely mediated by corresponding changes in protein levels …

Scaling by shrinking: empowering single-cell'omics' with microfluidic devices

SM Prakadan, AK Shalek, DA Weitz - Nature Reviews Genetics, 2017 - nature.com
Recent advances in cellular profiling have demonstrated substantial heterogeneity in the
behaviour of cells once deemed'identical', challenging fundamental notions of …

[HTML][HTML] Integrative multi-omics approaches in cancer research: from biological networks to clinical subtypes

YJ Heo, C Hwa, GH Lee, JM Park, JY An - Molecules and cells, 2021 - Elsevier
Multi-omics approaches are novel frameworks that integrate multiple omics datasets
generated from the same patients to better understand the molecular and clinical features of …