Hong Zheng

PhD|Bioinformatics|Cancer genomics|Genetics|Machine learning

[Hong Zheng @bitsoftime]

A good source for annotating CD4+ T cell subsets
https://t.co/JeGBrse6G9

[Hong Zheng @bitsoftime]

@shazanfar @accidental__aRt My data sends its love to me

[Purvesh Khatri @purveshkhatri]

Thrilled to see our pan-virus conserved host response signature paper finally out https://t.co/UxUYmNSESj. More in the thread below https://t.co/OnV7hKI7A2

[Shirley B. Wang @ShirleyBWang]

Not even 24 hours later and the gaslighting and denying of anti-Asian racism is already flooding in. This is the reality of being Asian in America. Never belonging, never fully American, and even when the racism is so blindingly obvious - people are so quick to ignore and deny.

[Hong Zheng @bitsoftime]

#SpuriousCorrelations
Spice use (mean number of spice ingredients per recipe) is correlated with road traffic fatalities
(Reproduced from https://t.co/ElYB5MOvjc)

[Hong Zheng @bitsoftime]

What is the best Python tool to look at 2.5 million single cell transcriptome data? Scanpy?

[Hong Zheng @bitsoftime]

I've been using alevin for scRNA-seq analysis. Quite happy about it. The only issue is CITE-seq analysis: it takes long time to do antibody sequence mapping in some samples. @k3yavi @nomad421 is alevin-fry better than alevin, and is there a tutorial for CITE-seq processing?

[bioRxiv Bioinfo @biorxiv_bioinfo]

A like-for-like comparison of lightweight-mapping pipelines for single-cell RNA-seq data pre-processing https://t.co/NkmmdtBy2v #biorxiv_bioinfo

[Nature Communications @NatureComms]

@ogevaert @ArnoutDevos @linayqiu and @bitsoftime and colleague use meta-learning to predict cancer patient survival using genomic data

https://t.co/ZmmkCusiy1

@NatResCancer #CancerResearch

[Purvesh Khatri @purveshkhatri]

We recently showed that conserved host response to viral infection can predict outcome of viral infection. Our follow up pre-print describing a 6-gene signature and validation in prospective cohort with a qRT-LAMP assay
https://t.co/SG4O8UKePh

[Hong Zheng @bitsoftime]

Timeline of FDA-approved PD-1/PD-L1 checkpoint inhibitor drugs for lung cancer

[Hong Zheng @bitsoftime]

50 shades of blue😉

[Hong Zheng @bitsoftime]

My visit notes from the doctor stated that :
"Patient is otherwise a healthy, pleasant cancer researcher who voices no pain or discomfort."😂

[Hong Zheng @bitsoftime]

Adding to the list
6) log normalization vs. sctransform
7) MAGIC imputation vs. no imputation

[Hong Zheng @bitsoftime]

Things I tried to find the optimal clusters for scRNAseq:
1) Number of variable features
2) Number of PCs
3) Number of neighbors in KNN
4) Different cluster resolutions
5) Different tools (Seurat vs. Monocle3)

Still can't find a nice and stable solution...

[Hong Zheng @bitsoftime]

For the cells that can't be consistently clustered and classified, I might as well just name them "Schrödinger's cells"

[Hong Zheng @bitsoftime]

Things I tried to find the optimal clusters for scRNAseq:
1) Number of variable features
2) Number of PCs
3) Number of neighbors in KNN
4) Different cluster resolutions
5) Different tools (Seurat vs. Monocle3)

Still can't find a nice and stable solution...

[Hong Zheng @bitsoftime]

Things I tried to find the optimal clusters for scRNAseq:
1) Number of variable features
2) Number of PCs
3) Number of neighbors in KNN
4) Different cluster resolutions
5) Different tools (Seurat vs. Monocle3)

Still can't find a nice and stable solution...

[Purvesh Khatri @purveshkhatri]

Adding our latest work to this growing list https://t.co/NPy2qz3FHo. In patients with severe viral infection, we see decoupling between IFN response and protective host response module.

[Hong Zheng @bitsoftime]

So proud to work on this fantastic project with the amazing team!

[Purvesh Khatri @purveshkhatri]

[Thread] 1/22 Check out our pan-virus analysis! Tremendous teamwork by @bitsoftime @adityarao95 Denis Dermadi, @jiaying_toh, @ladoctorajones @mdonato1138 and @yemlooo with our collaborators @LabHeath @isbsci and @yehudithasin and Yudong He @inflammatix_inc https://t.co/tDIo9FOqcA

[Hong Zheng @bitsoftime]

#colorpalette

[BuzzFeed News @BuzzFeedNews]

Humanity has “entered a pandemic era,” with the coronavirus outbreak likely the first of accelerating epidemics to come, public health experts warn https://t.co/9udmSoPtDl