@KaminskiMed @GenomeBiology @YaleIMed @YalePCCSM @yaledatascience @AurelienJustet @ivanorosas @RongFan8 Thank you, Naftali for all the support and inspirations!
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Xiting Yan
18 posts
Xiting Yan
@XitingY
computational biologist, mom of 3 girls, music and sports lover
Connecticut, USA เข้าร่วม Temmuz 2015
90 กำลังติดตาม51 ผู้ติดตาม
Finally out and really great! “SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data”
Kudos Drs Liu, Yan and team!!
genomebiology.biomedcentral.com/articles/10.11…
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Our new method to deconvolve low resolution dpatial data is out! It is the first method to simultaneously consider platform effects, small number of cell types per spot and spatial correlation of the cell type composition across spots. link.springer.com/10.1186/s13059…
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Xiting Yan รีทวีตแล้ว
Important ‼️ This tweak to #CDC policy “Everyone in areas of substantial/high transmission should wear a mask, even if vaccinated”means any place indoors in the US - as cases are increasing EVERYWHERE - back to #MaskUp indoors
CDC@CDCgov
#DeltaVariant surging in U.S. New data show Delta much more contagious than previous versions of #COVID19. Unvaccinated people: get vaccinated & mask until you do. Everyone in areas of substantial/high transmission should wear a mask, even if vaccinated. cdc.gov/coronavirus
New Haven, CT 🇺🇸 English
Our largest EVER transcriptomic study of #sarcoidosis patients is out! We learned so much from this high-quality data but the data is so rich that there is still so much more to do with the data to learn more for better treatment of Sarcoidosis. TBC... #GRADS #CureSarcoidosis
Naftali Kaminski@KaminskiMed
1/n Finally! Biggest ever RNAseq study of #sarcoidosis is out - reveals associations of distinct transcriptional programs with major phenotypic traits ➡️suggests distinct novel Sarcoidosis endotypes #GRADS #CureSarcoidosis #SarcBALRNAseq see thread below erj.ersjournals.com/content/early/…
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Xiting Yan รีทวีตแล้ว
@XitingY @mivukmiro @YaleIMed @YaleMed @ERSpublications @StopSarcoidosis @sarcoid_papers @ATS_AII @HongyuZhao2 @YaleData 🙏 when I wrote the grant, even when we started recruitment, I never expected it to take that long - but when I looked at the data, I said 'it is so complicated, how will we finish?' but we did it #together and ➡️this will accelerate #Sarcoidosis research erj.ersjournals.com/content/early/…
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@KaminskiMed @mivukmiro @YaleIMed @YaleMed @ERSpublications @StopSarcoidosis @sarcoid_papers @ATS_AII @HongyuZhao2 @YaleData Thank you Naftali for all the inspiring suggestions, discussions, patience and leadership! I'm very proud to be part of this study and very thankful for the chance to work with this amazing group of people!
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Xiting Yan รีทวีตแล้ว
9/n The greatest credit for #SarcBALRNAseq goes to shared co-first authors - Drs Vukmirovic & Yan - this was a Herculean effort - I feel fortunate and grateful to have worked (& keep working with both of them) 🙏 #sarcoidosis #teamscience #bigdata erj.ersjournals.com/content/early/…
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1/n Finally! Biggest ever RNAseq study of #sarcoidosis is out - reveals associations of distinct transcriptional programs with major phenotypic traits ➡️suggests distinct novel Sarcoidosis endotypes #GRADS #CureSarcoidosis #SarcBALRNAseq see thread below erj.ersjournals.com/content/early/…
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Xiting Yan รีทวีตแล้ว
8/n # of authors #SarcBALRNAseq does not come close to # people deserving credit - collaborators from Yale, Pitt, Hopkins, Penn, Vanderbilt, NJH, Az, MUSC, UCSF, Hannover, #sarcoidosis patients, @nih_nhlbi - THANKS ALL #PeopleIlookUpTo #TeamScience atsjournals.org/doi/10.1513/An…
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Xiting Yan รีทวีตแล้ว
7/n All #SarcBALRNAseq data available on GEO database - GSE109516 - All analysis codes & results available on GitHub & online supplement #DataSharing #BigData. We hope to generate a #SarcoidAtlas data mining tool soon - stay tuned but for now check out yale-p2med.github.io/SARC_BAL/
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Xiting Yan รีทวีตแล้ว
6/n Sex in #SarcBALRNAseq Results ➡️ while 53% of participants were women - we did NOT find any significant effects of gender on gene expression related to #sarcoidosis traits. Surprising - worth a deeper dive! #NegativeResultsMatter #SABV erj.ersjournals.com/content/early/…
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Xiting Yan รีทวีตแล้ว
5/n #SarcBALRNAseq Results ➡️ further study of gene modules suggested novel molecular endotypes of #sarcoidosis. 2nd cohort validated supervised & unsupervised results - Thanks Dr. Antje Prasse & team 🤝👏 #Collaboration #DataSharing erj.ersjournals.com/content/early/…
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Xiting Yan รีทวีตแล้ว
4/n #SarcBALRNAseq Results ➡️ unsupervised analysis identified distinct modules of gene expression associated with distinct combinations of phenotypic traits, exposures, and geographic location in #Sarcoidosis - I think this is important erj.ersjournals.com/content/early/…
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Xiting Yan รีทวีตแล้ว
4/n #SarcBALRNAseq Results ➡️ genes associated with race & disease severity in #sarcoidosis were enriched for aberrant lipid trafficking,
arachidonic acid production, SCAP/SREBP control of lipid metabolism - need to validate, explore deeper erj.ersjournals.com/content/early/…
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Xiting Yan รีทวีตแล้ว
3/n #SarcBALRNAseq Results ➡️ - In #Sarcoidosis TH1, TH17 transcriptional programs associate with hilar lymphadenopathy, TGFB1, MTOR signaling with parenchymal involvement, IL7 and IL2 airway involvement and so much more erj.ersjournals.com/content/early/…
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Xiting Yan รีทวีตแล้ว
2/n This is the 1st key #Sarcoidosis paper of the @nih_nhlbi funded GRADS multicenter study (atsjournals.org/doi/10.1513/An… >250 research bronchoscopies, extensive phenotyping, RNAseq, microbiome, virome) below are some of the #SarcBALRNAseq insights ➡️ doi.org/10.1183/139930…
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Need to impute your scRNAseq data? Try our method. journals.plos.org/ploscompbiol/a…
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@KaminskiMed @HongyuZhao2 @YalePCCSM @YaleSPH @yaledatascience @PLOSCompBiol @Sc_Ninjas @scell_papers @jonas_schupp @singlecellomics Thank you Natalie for the kudos!
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I love the name! #G2S3 - a novel gene graph-based imputation method for single-cell RNA sequencing data with superior performance in recovering gene expression, identifying cell subtypes. Kudos Dr. Yan & Wang! #scRNASeq journals.plos.org/ploscompbiol/a…
New Haven, CT 🇺🇸 English