Advertisement ยท 728 ร— 90

Posts by Nick Riley

I don't remember seeing an image of Earth before that captures the (thin, fragile, tiny layer of) atmosphere so clearly. I mean, look at that.

2 weeks ago 5373 1665 35 69
Preview
DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci DNA O-MAP enables proximity labeling at specific genomic loci in fixed cells using programmable oligonucleotides, revealing locus-proximal proteomes and chromatin interactions without genetic modifica...

The next iteration of O-MAP targeting genomic loci is now at eLife!!

DNA O-MAP enables proximity labeling at specific DNA loci took a ton of work from many lab members and collaborators, so it's really exciting to wrap up this paper with @oligopain.bsky.social!

elifesciences.org/articles/102...

1 week ago 31 12 1 2
Post image
1 week ago 61 10 1 2
Preview
N. G. BOECK HELLO! (Are you looking for M. Nicole Nazzaro? You found me! My professional byline changed in April 2025, but everything else is staying the same: email, phone, website URL, etc. Welcome!) WHAT I...

Check out her other work here: www.impactmedianw.com

2 weeks ago 0 0 0 0

(Disclaimer: I was not involved with this article, but Nicole and I have had a lot of great conversations since she took my Quantitative Analysis course, so I am a bit biased!)

2 weeks ago 0 0 1 0

Her background as a bona fide journalist w/ career pivot back into science and research makes her writing on science/the scientific enterprise particularly interesting.

This topic about managing failure and fostering perseverance is evergreen in science. Thanks for adding to this dialogue, Nicole!

2 weeks ago 0 0 1 0
My PhD student is stuck. How do I teach them perseverance and problem solving? A new principal investigator wants to help PhD students to develop resilience and creativity in the laboratory without hovering or doing the work for them.

It is very cool to see this piece from a former student of mine, @mnicolen.bsky.social, in Nature's Career Feature section:

www.nature.com/articles/d41...

2 weeks ago 4 1 1 0
Preview
2026 I. M. Kolthoff Award Winners The I.M. Kolthoff Award is given annually to deserving undergraduates who have done undergraduate research in the field of analytical chemistry, broadly defined, in celebration of the life and accompl...

A big congratulations to the 2026 I. M. Kolthoff Award Winners! acsanalytical.org/2026/03/12/2...

This @acs.org award for undergraduate researchers supported 4 outstanding students (Damon Chan, Alex Szczepankiewicz, Katelyn Barnes, & Zane Alsebai) attending @pittcon.bsky.social and #ACSspring 2026

3 weeks ago 4 2 0 0
Preview
Meet an Analytical Chemist Suggestion Form American Chemical Society Division of Analytical Chemistry Education Committee is sponsoring a new initiative called "Meet an Analytical Chemist" where we highlight a scientist from our community once...

We plan to highlight a new analytical chemist each quarter in the Division Newsletter. If you are interested in nominating someone to be highlighted, please enter their information here:
docs.google.com/forms/d/e/1F...

3 weeks ago 0 0 0 0
Preview
Meet an Analytical Chemist โ€“ February 2026 Christina Jones, Ph.D.National Institute of Standards and Technology, Office of Advanced Manufacturing, Partnerships and Outreach Strategist How did you get started in the field of Analytical Chemistr...

Check out the newest entry in the ACS Div. of Analytical Chem. Education Committee's "Meet an Analytical Chemist" initiative.

This quarter we highlight Dr. Christina Jones, Partnerships and Outreach Strategist at NIST: acsanalytical.org/2026/02/26/m...

3 weeks ago 6 3 1 0
Advertisement
Preview
2026 I. M. Kolthoff Award Winners The I.M. Kolthoff Award is given annually to deserving undergraduates who have done undergraduate research in the field of analytical chemistry, broadly defined, in celebration of the life and accompl...

A big congratulations to the 2026 I. M. Kolthoff Award Winners! acsanalytical.org/2026/03/12/2...

This @acs.org award for undergraduate researchers supported 4 outstanding students (Damon Chan, Alex Szczepankiewicz, Katelyn Barnes, & Zane Alsebai) attending @pittcon.bsky.social and #ACSspring 2026

3 weeks ago 4 2 0 0

Fantastic new resource for glycoproteomics from @nmriley.bsky.social and coworkers #glycotime

3 weeks ago 10 3 0 0

As always, we appreciate authors like Rebeca and Morten (and many in our field) who make raw data publicly available.

Data sharing streamlines #glycotime tool building and helps us advance together as a field.

3 weeks ago 6 0 0 0

Mucin-binding protein shuttles enable delivery of brain-targeted therapeutics www.biorxiv.org/content/10.64898/2026.03...

3 weeks ago 1 1 0 0
Preview
GitHub - riley-research/GlycoDiveR Contribute to riley-research/GlycoDiveR development by creating an account on GitHub.

In all, GlycoDiveR is meant to improve accessibility of glycoproteomic-specific analyses and lower the barrier to exploring biological narratives embedded in rich glycoproteomic datasets.

We hope it can be useful for your #glycotime work. Try it out here: github.com/riley-resear...

3 weeks ago 2 0 0 0

These figures are a sampling of GlycoDiveR's >25 customizable functions & publication-quality visualizations, each accessible with a single line of code.

Its modular architecture can accommodate new analyses from us and others, and we plan to update it with new visualizations regularly.

3 weeks ago 2 0 1 0
Post image Post image Post image

Once glycoproteins of interest are pinpointed via glycoproteome-scale analyses, GlycoDiveR also generates glycosite-level analyses for indiv proteins. This includes site maps w/ heterogeneity differences b/t conditions, a quant heat map for all glycosites, and glycan comparisons for indiv glycosites

3 weeks ago 1 0 1 0
Post image

Importing data w/ GlycoDiveR automatically connects to the @glycosmos.bsky.social API to provide GlyTouCan accession numbers for glycopeptides, and it connects to the #uniprot API to pull in associated protein annotations to assess, for example, which BP, CC, or MF are associated with glycopeptides.

3 weeks ago 3 1 1 0
Advertisement
Post image

Glycoprotein-Glycan (GPG) bipartite networks have been adopted by several groups as way to "fingerprint" the glycoproteome when viewing an entire dataset.

They can also be filtered to show how specific glycan features are distributed across the glycoproteome or differ between conditions.

3 weeks ago 0 0 1 0
Post image Post image

Classic visualizations for differential expression, like volcano plots, are available, and subsets of glycopeptides can be further processed to look for trends, such as glycan categories more represented in up- or down-regulated species.

Glycoprotein rank plots can also show abundance shifts.

3 weeks ago 1 0 1 0
Post image Post image

GlycoDiveR generates Venn digrams and UpSet plots to compare overlap in glycopeptides, glycoproteins, glycosites, and glycans between two groups or large sets of groups.

Glycan vs. Glycosite scatter plots can identify potentially interesting glycoproteins with high or low glycan microheterogeneity.

3 weeks ago 1 0 1 0
Post image Post image

For glycoproteome-scale analyses, visualizing data completeness and filtering for desired numbers of quantitated species per condition are functions our group uses often.

Look at where in the LC-MS/MS gradient glycopeptides eluted can help with data assessment and experiment iterations, too.

3 weeks ago 1 0 1 0
Post image Post image Post image Post image

GlycoDiveR makes data normalization easy to perform and assess, including loadings plots for PCA. A single line of code generates other data quality assessments (w filtering capabilities), too, including identification bar graphs, peptide length distributions, m/z error trends, and CV distributions.

3 weeks ago 1 0 1 0
Preview
HEXB Drives Raised Paucimannosylation in Colorectal Cancer and Stratifies Patient Risk In BriefAiming to find glyco-markers against colorectal cancer (CRC), we applied systems glycobiology to CRC patient specimens. Multiomics data revealed that noncanonical paucimannosidic proteins form...

GlycoDiveR is an open-source, modular R framework with >25 customizable glycoproteome- and glycosite-scale visualizations that can be generated with minimal programming expertise.

We reanalyzed data from Kawahara et al. to demonstrate GlycoDiveR's features: www.mcponline.org/article/S153...

3 weeks ago 2 0 1 1

The complexity of glycoproteomics data creates a bottleneck in data interpretation and communication.

We (@timveth.bsky.social, @riley-research.bsky.social) built GlycoDiveR as a step toward bridging gaps between search-engine output and biological interpretation through #glycotime visualizations.

3 weeks ago 15 5 2 1
Post image

GlycoDiveR: a modular R framework to analyze and visualize highly dimensional glycoproteomics data www.biorxiv.org/cont...
---
#proteomics #prot-preprint

3 weeks ago 4 1 0 0
Advertisement

Exciting new discovery from @jimwellsucsf.bsky.social and coworkers, a new class of potential cancer antigens flipped onto the cell surface via autophagy-associated exocytosis, featuring first author and former PhD student Corleone Delaveris! #proudofalumni

1 month ago 29 11 0 0

We are generally limited by long accumulation times, so we try to keep it to as few scans per precursor as possible. But sometimes multiple scans can be the only answer, depending on what you need!

1 month ago 1 0 0 0

Wee thread ๐Ÿงตโฌ‡๏ธ on our new #glycotime with @siglecdude.bsky.social John Klassen and @glycocode.bsky.social ๐Ÿฅณ where we show Siglecs as molecular precision tools, able to recognise sialylated glycans with surgical precision in their natural environment, not bad for a lectin! ๐Ÿ˜Ž

doi.org/10.1038/s420...

1 month ago 39 13 0 2
Preview
Understanding m/z Range Settings for MS/MS Scans: A Case Study with Intact Glycopeptides Effective glycopeptide identification with tandem mass spectrometry (MS/MS) often relies on both low mass-to-charge (m/z) ions derived from glycan-specific oxonium ions and higher m/z peptide fragment...

This was a relatively straightforward set of experiments we approached from a tutorial-like perspective.

Hopefully it can be useful for folks interested in #glycotime that have not thought much about MS/MS scan ranges before.

Check out the publication here:
pubs.acs.org/doi/10.1021/...

10/10

1 month ago 2 0 0 0