Saikat Banerjee

Postdoc @UChicago @HGEN_UChicago. Physicist turned bioinformatician. Current interests #eQTL, #GWAS, #genomics, #ai, #PrecisonMedicine, #ML

[Saikat Banerjee @banskt]

Happy to see our method for predicting trans-eQTLs published at @GenomeBiology. Demonstrated on #eQTL data from @GTExPortal. Fun working with @francosimonetti, @SoedingL, @Raktim7879, @KaphleAnubhav and others. Thread for a quick overview. \1

[Genome Biology @GenomeBiology]

Tejaas, from @banskt, @francosimonetti, @SoedingL and co, is a method for predicting trans-eQTLs. Rather than regressing expression level on SNP minor allele count, it performs multiple regression of the SNP on all genes jointly. Demonstrated on GTEx data https://t.co/qhCmUYLt7k

[Jonathan Pritchard @jkpritch]

Sharing this in case it's useful: I find that students often have a hard time conceptualizing quantitative parameters in genomics and popgen

Here's a cheat-sheet I put together for teaching. It's also part of a textbook I have been writing on human genetics (more on that below)

[Human Genetics @ UChicago @HGEN_UChicago]

A successful conference for UChicago Human Genetics at #probgen23 💻🧬 Thanks for having us @cshlmeetings @CSHL

[Rikhia Ghosh @rikhiag]

Excited to share our latest work on membrane endocytosis of molecular condensates formed by liquid liquid phase separation, out now in @NatureComms @SpringerNature! We determine the mechanical behavior of membrane that control the endocytic pathway 1/n
https://t.co/uRxX2xdAeC

[Fabian Theis @fabian_theis]

Beautiful perspective @NatureMedicine about the impact of the Human Cell Atlas on medicine by @jennyErood with Sarah @teichlab and Aviv Regev. Great summary of resources as well as open challenges!
https://t.co/13koEIZQzk

[Saikat Banerjee @banskt]

@slmsoh @croth44 @IMPRS_GS @SoedingL @mpi_bpc @uniGoettingen @Rosy_Zh @vikhuryn @milot_mirdita Congratulations @croth

[Sek Kathiresan MD @skathire]

Does chronic disease need to equal chronic care? No

👇in @Nature from @VerveTx

One-time base editing Rx (in vivo liver),
durable⬇️LDL-C

In monkeys:

*⬇️90% PCSK9,⬇️60% LDL-C, now out to 10 mos

* VERVE-101: efficacy at LNP doses as low as 0.5 mg/kg

https://t.co/rimsHKld8c

[Joanna Howson @joannahowson]

Ever wondered if the mitochondrial DNA affects common disease risk? Well take a look at our work out @NatureGenet We re-called & analyse mtDNA SNPs in 100s of traits in @uk_biobank found assoc of mtDNA SNPs with T2D MS liver&kidney fct & blood cell params. https://t.co/slWslDMyXe

[Cell @CellCellPress]

In the latest issue! Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease
@sbmontgom @StanfordMed
https://t.co/m8ou8L6c22

[Saikat Banerjee @banskt]

@GalenWright @francosimonetti @SoedingL @Raktim7879 @KaphleAnubhav Results also available at https://t.co/pD5KeKwJPy

Sorry for the inconvenience. And thanks for reporting.

[Saikat Banerjee @banskt]

Happy to see our method for predicting trans-eQTLs published at @GenomeBiology. Demonstrated on #eQTL data from @GTExPortal. Fun working with @francosimonetti, @SoedingL, @Raktim7879, @KaphleAnubhav and others. Thread for a quick overview. \1

[Genome Biology @GenomeBiology]

Tejaas, from @banskt, @francosimonetti, @SoedingL and co, is a method for predicting trans-eQTLs. Rather than regressing expression level on SNP minor allele count, it performs multiple regression of the SNP on all genes jointly. Demonstrated on GTEx data https://t.co/qhCmUYLt7k

[Saikat Banerjee @banskt]

Project funded by @medicine_e, @MBExC_de, @mpi_bpc. #GWAS data from @hakyim lab. And finally, for all the thoughtful suggestions and critiques which significantly improved the manuscript, a huge Thank You to the unknown reviewer! \10

[Saikat Banerjee @banskt]

There are some major limitations of our method, including (i) choice of the L2 prior, and (ii) inability to use standard confounder correction (we proposed an alternate non-linear, unsupervised, hidden confounder correction method using k-nearest neighbors). \9

[IISc Bangalore @iiscbangalore]

The last date for international students to apply for the UG programme 2021-22 at IISc has been extended to May 30, 2021. More details at:
https://t.co/b6fVeljuxs