Simon Cockell @[email protected]

Senior Lecturer in Bioinformatics @UniofNewcastle, Director of Research @NclBNS. #rstats, Python, etc. Gateshead/Newcastle resident. Husband. Dad. Views my own.

[Simon Cockell @[email protected] @sjcockell]

Our Perspective "Mapping the Transcriptome - realising the full potential of spatial data analysis" is out today in @CellCellPress https://t.co/algatKqe0U. A short thread on this work follows...

[Simon Cockell @[email protected] @sjcockell]

Me too :) #UKGS24

[vivienne stern @viviennestern]

So, Conservatives pledge to increase apprenticeships by 100k by cutting 1 in 8 degrees. I feel a little thread is in order.

[Sara Gosline @sargoshoe]

How much more money do we need to dump into automating analysis for non experts until we realize that we need to better train scientists to interpret results!

[Newcastle University IT Service @NU_ITservice]

@TrostLab @NCBI @NLM_NIH @StudentsNCL @NCBI @NLM_NIH we have been in contact with NLM Support (case number #CAS-1234575-J7P7W3) as traffic from our network is being rejected; we’ve chased for updates but had no response since 15th Dec. Can you provide an update on our case please?

[Simon Cockell @[email protected] @sjcockell]

This is a massive problem @NCBI. As @TrostLab mentions, @NU_ITservice maintain this is a server-side problem, some clarity (and a fix!) would be very welcome:

[Matthias Trost 🇪🇺 @TrostLab]

Dear @NCBI @NLM_NIH

in our institution @StudentsNCL in the UK we cannot access Pubmed or any other NIH/NCBI website anymore. this has been intermittently going on for months!

Out IT says it comes from your side.

can you please look into this!

thanks a lot!

[Cell @CellCellPress]

In the latest issue! Mapping the transcriptome: Realizing the full potential of spatial data analysis https://t.co/Qt0GpF37sT

[Jamie Soul @soul_jamie]

A PhD studentship available with me and collaborators
@LabPeffers
and
@IGM_YoungLab
from October 2024.
https://t.co/rnykokm4Ve
Combining omics data to identify regulators of chondrogenesis. Funded via

@NLD_BBSRCDTP

Deadline to apply 15th January
#bioinformatics #PhD

[Simon Cockell @[email protected] @sjcockell]

@ajskelton73 Thanks man :)

[Simon Cockell @[email protected] @sjcockell]

Things you never thought you’d see in your career… featured content in Cell from “Cockell and colleagues”

[Simon Cockell @[email protected] @sjcockell]

Paper now officially published: https://t.co/algatKqe0U

[Cell @CellCellPress]

Bringing 2023 to a close, the new issue features a 3D atlas of the developing human head, how the ineffective control of EBV-induced autoimmunity increases the risk for multiple sclerosis and a machine learning architecture that integrates cell types across single-cell datasets!

To read more of our new issue click👉 https://t.co/DWf0VlDvUt

[Cell @CellCellPress]

Now online! Mapping the transcriptome: Realizing the full potential of spatial data analysis https://t.co/3ZSiCuVCCA

[Simon Cockell @[email protected] @sjcockell]

To quote ourselves, these features mean that the analysis of these types of data should be "spatial by default", and encourage inter-disciplinary collaboration with those in the geographical sciences to help transfer decades of knowledge from that domain

[Simon Cockell @[email protected] @sjcockell]

We demonstrate that key features of spatially-resolved data can be shown in biological data (using Visium data by way of example). 1) The modifiable areal unit problem - that the scale you chose for your analysis can strongly influence the results of that analysis

[Simon Cockell @[email protected] @sjcockell]

3) spatial heterogeneity - the relationships between variables is not static across space, and local relationships rarely look the same as the global picture

[Simon Cockell @[email protected] @sjcockell]

This paper is essentially the manifesto for @LZormpas's PhD work - that the features of spatial data, so well studied in the geographic sciences, manifest themselves in micro-scale spatial molecular biology data.

[Simon Cockell @[email protected] @sjcockell]

So happy, particularly for my student (@LZormpas), that the editors saw the value in this commentary. Thanks also to the helpful reviewers. And of course coauthors @lexcomber and @rachelq_ncl!

[Simon Cockell @[email protected] @sjcockell]

Our Perspective "Mapping the Transcriptome - realising the full potential of spatial data analysis" is out today in @CellCellPress https://t.co/algatKqe0U. A short thread on this work follows...