Jarning Gau (@GauJarning) profile picture

Jarning Gau

@GauJarning

PhD candidate major in bioinformatics, good at #singlecell transcriptome analysis.

 Hefei, Anhui, China
jarninggau.github.io
Joined July 2021
  • Tweets27
  • Following71
  • Followers13
ProjectSVR: Mapping single-cell RNA-seq data to reference atlases by supported vector regression biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
1
2
901
Models that matter dlvr.it/Sj47nP
Models that matter

Models that matter

Models, like the Central Dogma, are a core feature of many papers we publish, yet their utility can be undermined when they are either overly simplistic or overly complicated, and it can contribute...

cell.com
6
19
5,881
Jarning Gau retweeted
antisense. (@razoralign) profile picture
antisense.@razoralign8 Feb 2023
CellOracle: Dissecting cell identity via network inference and in silico gene perturbation nature.com/articles/s41586-0…
Image from antisense. (@razoralign)
17
58
4,515
Jarning Gau retweeted
evo-devo (@Xiaojie_Qiu) profile picture
evo-devo
@Xiaojie_Qiu25 Oct 2022
Building Transformers from Neurons and Astrocytes biorxiv.org/content/10.1101/…
Building Transformers from Neurons and Astrocytes

Building Transformers from Neurons and Astrocytes

Glial cells account for roughly 90% of all human brain cells, and serve a variety of important developmental, structural, and metabolic functions. Recent experimental efforts suggest that astrocytes,...

biorxiv.org
2
3
Right on target: Chromatin jets arise from targeted cohesin loading in wild-type cells dlvr.it/SbfFXC
Right on target: Chromatin jets arise from targeted cohesin loading in wild-type cells

Right on target: Chromatin jets arise from targeted cohesin loading in wild-type cells

Uncovering an informative feature of 3D genome structure, Guo et al. (2022) describe chromatin jets in quiescent murine thymocytes: 1–2 Mb structures formed by targeted cohesin loading at narrow...

cell.com
1
9
Introducing STELLAR: a geometric deep learning method for cell type discovery and identification in spatially resolved single-cell datasets. @jure @GarryPNolan @SnyderShot nature.com/articles/s41592-0…
Image from Nature Methods (@naturemethods)
48
5
184
Jarning Gau retweeted
antisense. (@razoralign) profile picture
antisense.@razoralign22 Oct 2022
Census: accurate, automated, deep, fast, and hierarchical scRNA-seq cell-type annotation biorxiv.org/content/10.1101/…
Image from antisense. (@razoralign)
3
45
2
209
Tumor microbiome links cellular programs and immunity in pancreatic cancer dlvr.it/SbHkjn
Tumor microbiome links cellular programs and immunity in pancreatic cancer

Tumor microbiome links cellular programs and immunity in pancreatic cancer

Ghaddar et al. use the computational pipeline SAHMI (single-cell analysis of host-microbiome interactions) to probe the microbiome in pancreatic cancer. They identify a subset of tumors with bacteria...

cell.com
27
1
66
Out today and freely available, a tool many in the image analysis community have been waiting for! PyImageJ: A library for integrating ImageJ and Python @EliceiriK @UWMadisonLOCI @ctrueden @CiminiLab @DrAnneCarpenter nature.com/articles/s41592-0…
11
302
35
1,081
(1/n) This thread will describe recent advances in life-long learning (LL) as an essential player in the current single-cell atlases. LL in this context means building a map, and iteratively updating it with new data.blob,
Image from Mo Lotfollahi (@mo_lotfollahi)
3
66
2
208
Jarning Gau retweeted
Jimmie Ye (@yimmieg) profile picture
Jimmie Ye@yimmieg7 Apr 2022
In 2018, we developed mux-seq and demuxlet to enable population-scale single-cell sequencing. Today, excited to share our paper in @ScienceMagazine where we deployed mux-seq to profile 1.2M immune cells from 162 lupus patients and 99 healthy controls: science.org/doi/full/10.1126…. 1/n
Image from Jimmie Ye (@yimmieg)
18
203
14
848
Single-celled Lacrymaria olor attacks another cell: #biology
137
1,349
306
7,769
ZFP541 maintains the repression of pre-pachytene transcriptional programs and promotes male meiosis progression dlvr.it/SMBGML
ZFP541 maintains the repression of pre-pachytene transcriptional programs and promotes male meiosis...

ZFP541 maintains the repression of pre-pachytene transcriptional programs and promotes male meiosis...

Xu et al. demonstrate that ZFP541 predominantly maintains the repression of pre-pachytene transcriptional programs, including meiotic DSB formation genes, in pachytene spermatocytes and suppresses...

cell.com
3
6
If Darwin went on his voyage of the Beagle today his research would've ended with a t-SNE of the bird specimens that he collected instead of a theory of evolution
22
162
30
1,540
Review on zero-inflation of single-cell RNA-seq data, from @Ruochen_Jiang, @jsb_ucla & co. They discuss the sources of biological and non-biological zeroes, methods to address them, and how they influence analysis. genomebiology.biomedcentral.…
Table illustrating the different sources of technical and biological zeroes

ALT Table illustrating the different sources of technical and biological zeroes

17
2
73
Our fingerprint patterns—whether they are circular, wavy, or winding —are influenced by genes controlling limb development and not skin patterning, finds a comprehensive analysis. Learn more in @CellCellPress: cell.com/cell/fulltext/S0092…
Image from Cell Press (@CellPressNews)
3
64
12
347
Gene expression units explained: RPM, RPKM, FPKM, TPM, <i>DESeq</i>, TMM, SCnorm, GeTMM, and ComBat-Seq reneshbedre.com/blog/express… via @renbedre

Gene expression units explained: RPM, RPKM, FPKM, TPM, DESeq, TMM, SCnorm, GeTMM, and ComBat-Seq

bulk and single-cell RNA-seq expression units, count normalization, formula, examples in Python, gene quantification, batch effects, and between-sample and within-sample normalization

reneshbedre.com
Two websites for search helpful code snippet: programcreek.com/ codegetter.io/
Jarning Gau retweeted
gerry melino (@melino_G) profile picture
gerry melino@melino_G16 Sep 2021
Natural selection at the cellular level: insights from male germ cell #differentiation #CellDeathDifferentiation go.nature.com/3zLJgCV
Image from gerry melino (@melino_G)
2
4
Mark
Volker Bergen (@VolkerBergen) profile pictureVolker Bergen@VolkerBergen26 Aug 2021
Perspectives in RNA velocity! Great insights on this intriguing concept from most fruitful discussions wrapped into a manuscript on **current challenges and future perspectives**, with @_ruslansoldatov, @KharchenkoLab and @fabian_theis. Check out doi.org/10.15252/msb.2021102….
Load more