A Galaxy of informatics resources for MS-based proteomics

S Mehta, M Bernt, M Chambers, M Fahrner… - Expert Review of …, 2023 - Taylor & Francis
Introduction Continuous advances in mass spectrometry (MS) technologies have enabled
deeper and more reproducible proteome characterization and a better understanding of …

Comparative Genomics and Epigenomics of Transcriptional Regulation

H Zhou, E Clark, D Guan, S Lagarrigue… - Annual review of …, 2024 - annualreviews.org
Transcriptional regulation in response to diverse physiological cues involves complicated
biological processes. Recent initiatives that leverage whole genome sequencing and …

Galaxy Training: A powerful framework for teaching!

S Hiltemann, H Rasche, S Gladman… - PLoS computational …, 2023 - journals.plos.org
There is an ongoing explosion of scientific datasets being generated, brought on by recent
technological advances in many areas of the natural sciences. As a result, the life sciences …

[HTML][HTML] Delayed boosting improves human antigen-specific Ig and B cell responses to the RH5. 1/AS01B malaria vaccine

CM Nielsen, JR Barrett, C Davis, JK Fallon, C Goh… - JCI insight, 2023 - ncbi.nlm.nih.gov
Modifications to vaccine delivery that increase serum antibody longevity are of great interest
for maximizing efficacy. We have previously shown that a delayed fractional (DFx) dosing …

User-friendly, scalable tools and workflows for single-cell RNA-seq analysis

P Moreno, N Huang, JR Manning, S Mohammed… - Nature …, 2021 - nature.com
To the Editor—As single-cell RNA sequencing (scRNA-seq) becomes widespread,
accessible and scalable computational pipelines for data analysis are needed. We introduce …

scFlow: a scalable and reproducible analysis pipeline for single-cell RNA sequencing data

C Khozoie, N Fancy, MM Marjaneh, AE Murphy… - bioRxiv, 2021 - biorxiv.org
Advances in single-cell RNA-sequencing technology over the last decade have enabled
exponential increases in throughput: datasets with over a million cells are becoming …

Toward a data infrastructure for the Plant Cell Atlas

N Fahlgren, M Kapoor, G Yordanova… - Plant …, 2023 - academic.oup.com
We review how a data infrastructure for the Plant Cell Atlas might be built using existing
infrastructure and platforms. The Human Cell Atlas has developed an extensive …

Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research

M Kapoor, ES Ventura, A Walsh, A Sokolov… - Frontiers in …, 2024 - frontiersin.org
Introduction The agriculture genomics community has numerous data submission standards
available, but the standards for describing and storing single-cell (SC, eg, scRNA-seq) data …

A Web-based Software Resource for Interactive Analysis of Multiplex Tissue Imaging Datasets

A Creason, C Watson, Q Gu, D Persson, L Sargent… - BioRxiv, 2022 - biorxiv.org
Highly multiplexed tissue imaging (MTI) is accomplished by applying powerful antibody-
based spatial proteomics technologies that characterize tissues in situ at single-cell and …

[HTML][HTML] scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparison

A Ferrena, XY Zheng, K Jackson, B Hoang, B Morrow… - bioRxiv, 2024 - ncbi.nlm.nih.gov
Single-cell transcriptomics profiling has increasingly been used to evaluate cross-group
differences in cell population and cell-type gene expression. This often leads to large …