Siming Zhao

@samirzaidi @Yale @YaleCancer @ynhhealth Congrats Samir! So happy for you.

Fifteen years ago, my wife, Salimah, and I met as graduate students at @Yale in New Haven. Now, in a full-circle moment, I’m thrilled to share that I’ll be joining the @YaleCancer and @ynhhealth to launch my independent lab in March 2025! @samirzaidi I’ll be based in the Center of Molecular and Cellular Oncology and look forward to collaborating with incredible scientists like @BraunMDPhD, @ishizukalab, @S_J_Aitken, #CarolineMlynarczyk, #FrederickWilson and many others, under the leadership of @MuschenLab. I’m deeply grateful for the invaluable mentorship at @MSKCancerCenter ––from #CharlesSawyers @SawyersLabMSKCC, #MichaelMorris, @DrRosenbergMSK —who have guided me along this path. This transition wouldn’t have been possible without the unwavering support and vision of @DrEricWiner. His leadership made Yale feel not just like an exciting scientific home, but a truly warm and welcoming community—one that I can’t wait to be a part of. Excited to continue seeing patients in my clinic at @YaleCancer, and of course, to introduce our two boys to some legendary New Haven pizza!

My department at Dartmouth is hiring! Senior faculty positions broadly in the field of biostatistics, with a focus on cancer.

Our work led by @liliw_wang on identifying trans genetic effects of gene networks is out in @CellGenomics today!

Our software is available at github.com/xinhe-lab/ctwas. Many thanks to my postdoc advisors @xinhe @mstephens999 co-first author @wescrouse, Sheng Qian and Kevin Luo! Please try our R package and let us know your feedback. Thanks! n/n.

When applying cTWAS on real data, it identified much fewer genes than TWAS, the majority of the TWAS false positive findings were due to confounding by nearby causal variants. 6/n

We then applied our method to a few commonly studied traits (IBD, SBP, schizophrenia) and revealed novel candidate genes. Below is an example of a novel candidate gene (UBE2W) cTWAS identified for IBD, whose association falls below standard TWAS cutoff. 5/n

cTWAS solves this problem by including **all** nearby genes and variants in a Bayesian fine-mapping model, which effectively let gene and variant effects compete to explain the association signal. cTWAS has a well calibrated FPR, without much loss in power. 4/n

Glad to see our paper, with @xinhe2 @mstephens999 @wescrouse Sheng and Kevin, is out today at @NatureGenet! nature.com/articles/s4158…. We developed a new statistical method, causal-TWAS or cTWAS, to reliably identify causal genes in genome-wide association studies (GWAS). 1/n

nearby causal variants or eQTLs of causal genes of the trait can be correlated with the gene under test, thus serving as confounders in the test and resulting in false positives (FP). In simulations, we show previous methods can be severely inflated with FP ( FPR > 50%). 3/n

Many methods have been developed to leverage eQTLs to nominate candidate genes of complex traits, including TWAS, colocalization, mendelian randomization (MR) based methods, etc. However, they all suffer from a key problem: 2/n

@mstephens999 @Sun_Y_Lee It should work, though the current version only takes two groups of variables as covariates, variant genotypes and imputed expression. Wes sheng and me are working to release a new version which can take multiple groups of variables, to include e.g protein expression.

@Sun_Y_Lee yes, should work, although i have to admit I have not used the package myself, so questions on that probably best directed to siming or wes...

I missed tweeting this when posted in Dec. Our attempt to ameliorate some problems with confounding in TWAS. Key idea is to compete (imputed) gene expression and SNPs against one another as explanations for an asssocation. biorxiv.org/content/10.110…

@Wangxf23 @NatureSMB Congratulations Xiaofeng!

Excited to shared our most recent work out today @NatureSMB. We used #TurboID #CUTRUN #HiChIP to study the dynamics of all three #SWISNF subcomplexes targeting and their cooperation with AP1 members in shaping 3D enhancer landscapes #epigenetics #chromatin nature.com/articles/s4159…

@mourisl @GeiselMed Welcome! We are thrilled to have you joining us.

I'm thrilled to announce that I will be joining the Department of Biomedical Data Science @GeiselMed as an assistant professor next month! I will work on algorithms to investigate immune receptors with sequencing data, and develop highly efficient methods for sequence analysis.

Molecular & Systems Biology at the Geisel School of Medicine at Dartmouth is excited to recruit Assistant/Associate Professors to our department. Find information on the breadth of our search and our commitment to faculty diversity at geiselmed.dartmouth.edu/msb/open-facul… @GeiselMed @Dartmouth

The University of Chicago, Department of Human Genetics, is searching for a new computational faculty. apply.interfolio.com/112673 We are a small, friendly department doing top-quality science. Come join us! (Please RT)

Rockefeller's president Richard Lifton, who pioneered the use of genomics to identify the basis for diseases, has been announced as the 2023 recipient of the George M. Kober Medal from the Association of American Physicians. Congratulations! rockefeller.edu/news/32155-ric…

Out now from @Joans and me - (nearly) everything you know about survival analysis in cancer is wrong. cell.com/cell-reports/f…

registration still open for upcoming workshop on eliciting structure in genomics data imsi.institute/eliciting-stru… Aug 30-Sept 3. Great line up of speakers. Come join us by zoom!

@0ussamabatouche I just replied your email

@SimingZhao06 I'm looking for PhD position

I am looking for postdocs !Please RT