Dan Skelly

Data science, systems genetics/genomics, statgen, QTL, single-cell gene expression. I work @jacksonlab but views are my own.

[Dan Skelly @genomequant]

Our diverse ESC work is out! Amazing collaboration with generous colleagues esp @Laura_Reinholdt C Baker @stevemunger G Churchill + more.

https://t.co/kZuhbn2bU8

1/3

[Cell Stem Cell @CellStemCell]

New Short Article online now CellStemCell: Mapping the Effects of Genetic Variation on Chromatin State and Gene Expression Reveals Loci That Control Ground State Pluripotency https://t.co/jAqEb69I9o

[Greg Keele @grkeele]

Interested in doing an genetic experiment with a cutting-edge mouse multiparental population (MPP), but don't know which best suits your needs (e.g., inbred vs outbred)?

Using simulations from real genetic data, I sought to provide some answers and guidelines.

[. @PoliticsVerse]

BREAKING via Washington Post:

The FBI found documents in Trump's bedroom, office, and the first-floor storage room at Mar-a-Lago during the Aug. 8 search.

[UW Genome Sciences @uwgenome]

Genome Sciences mourns the loss of our colleague, Dr. Deborah Nickerson.
https://t.co/Eo0XNgMWTw

[Pinto Lab @pinto_lab]

See our latest officially out in circulation now!

[KB Choi @kwangbom]

GBRS manuscript is up on bioRxiv. We show how we apply an allele-specific expression (ASE) algorithm to reconstructing individual imputed genomes/transcriptome, and then, to quantifying gene expression.

[Dan Skelly @genomequant]

My very favorite visualization -- RNA-Seq of 185 genetically diverse ESC lines:
pluripotency genes = highly expressed (as expected)
lineage markers = lowly expressed
… but check out that variation 🤩!

3/3

[Dan Skelly @genomequant]

Our diverse ESC work is out! Amazing collaboration with generous colleagues esp @Laura_Reinholdt C Baker @stevemunger G Churchill + more.

https://t.co/kZuhbn2bU8

1/3

[Cell Stem Cell @CellStemCell]

New Short Article online now CellStemCell: Mapping the Effects of Genetic Variation on Chromatin State and Gene Expression Reveals Loci That Control Ground State Pluripotency https://t.co/jAqEb69I9o

[Dan Skelly @genomequant]

@selcan_t has a great explainer that weaves together this paper with our companion work led by @OrtmannDaniel and @VallierLab

https://t.co/IQ0Vl4FxAv

2/3

[Dan Skelly @genomequant]

This was a fun one. Congrats @kwangbom!

[KB Choi @kwangbom]

Finally out in Genome Biology https://t.co/6cI5ITagai

[Dan Skelly @genomequant]

Really fun collab. I think in the future we will see much more integrating #singlecell across genetic backgrounds ... Congrats @ElviraForte1!

[Elvira Forte @ElviraForte1]

Our paper is officially out! @CellReports Dynamic Interstitial Cell Response during Myocardial Infarction Predicts Resilience to Rupture in Genetically Diverse Mice https://t.co/VKR7HUFuTU @jacksonlab,@genomequant, @nadia_rosenthal, @vivekepsilon, #SingleCell

[Dan Skelly @genomequant]

very nice paper showing multiple tissue integration of gene expr/ATAC QTL with identification of candidate causal models. Congrats!

[Greg Keele @grkeele]

Excited to see (and share) the final version of this work with @bryancquach! From the labs of @WilliamValdar, Ivan Rusyn, and Terry Furey.

#PLOSGenetics: Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissu ... https://t.co/kueJ1NHsFO

[Dan Skelly @genomequant]

New tools for integrating GWAS and scRNA-Seq. Really looking forward to diving in and giving them a try!

[Pascal N. Timshel @ptimshel]

THRILLED to share our two NEW computational toolkits called CELLEX and CELLECT for integrating GWAS and scRNA-seq to prioritize etiologic cell-types underlying traits and diseases. Tweetorial 1/12
https://t.co/zL3Xt6lpDW

[Dan Skelly @genomequant]

Really interesting paper on microbiome genetics in diverse mice. Congrats @ElissaJChesler @jbubier!

[Dan Skelly @genomequant]

Our attempt at scRNA-Seq profiling of the heart maximizing both data quality and cellular diversity. Homeostasis and AngII model. Really fun study and collaboration between nearly opposite sides of the globe!

[Alex Pinto @Alex_R_Pinto]

Our latest work to help better understand cellular drivers of cardiac fibrosis and hypertrophy. A fantastic team effort by an excellent group of people from @BakerResearchAu @PAM_latrobe @jacksonlab @genomequant.

https://t.co/ZgjLLgfKDR

[Dan Skelly @genomequant]

Congratulations @kwangbom ... This work is a tour de force and worth a read for anyone interested in ASE!

[KB Choi @kwangbom]

[1/n] Multiple bulk RNA-seq studies showed that allelic imbalance (AI) is pretty common. It is subtle in many genes, but sometimes it is extreme as in imprinted or X-inactivated genes. We are curious to see what AI would look like at single-cell resolution.

[Dan Skelly @genomequant]

@fabian_theis @VolkerBergen @falexwolf Fantastic work and really grateful that you have made the code and clear docs easily available -- I have already been using the software pre-preprint!

[Dan Skelly @genomequant]

TT requirement arguably has merit as a shortcut to filtering out unqualified PIs, but I'd push CZI to take the risk of a few unqualified apps in return for engaging with a pool of dynamic pre-TT applicants (assess qualifications using preprints, github, etc). 4/4

[Dan Skelly @genomequant]

Dear @cziscience: love the new #inflammation in disease https://t.co/PgKOV49X6t and other RFAs. But I have to gripe about eligibility criteria (only PIs with TT position). 1/4

[biohub @biohub]

The role of #inflammation in health and disease is not well understood. @ChanZuckerberg’s new call for applications will support science teams to collaborate + apply new tools to gain greater insight into inflammatory diseases https://t.co/b33FYpbMEf

[Dan Skelly @genomequant]

Non-TT can be doing great science in an independent capacity (e.g. advanced postdoc or research scientist), may have awesome ideas but lack the resources to bring them to fruition. 3/4