Mehrdad Bakhtiari

Awesome work by @mdbakhtiari in Vineet Bafna's group to rapidly and accurately genotype variable number tandem repeats (VNTRs). Enables the discovery of eQTL elements based on those previously difficult to quantify VNTR expansion loci.

A neural network method for rapid and accurate genotyping of variable number tandem repeats from large whole genome sequencing datasets. @mdbakhtiari @mgymrek @bvhalldorsson @ucsd_cse @UCSDJacobs nature.com/articles/s4146…

When a cancer genome carries focally amplified oncogenes, what genomic structures permit them? Can we reconstruct the amplified rearrangements, like #ecDNA and #BFB? Oftentimes yes, we can! Out today in @NatureComms is our paper on AmpliconReconstructor. nature.com/articles/s4146…

New online work by our lab: Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs biorxiv.org/content/10.110…

Our @biorxivpreprint on VNTRs impact on gene expression regulation in GTEx is out now! We show VNTRs are likely eQTL causal variants in many cases. Thanks to @mgymrek @bvhalldorsson @KariStefans Vineet Bafna and many others! biorxiv.org/content/10.110…

@niemasd @sdrnoise that's the answer to every linux question as far as one can tell

Check out our paper about assembling centromeres from long error-prone reads! We present the first automated assembly of human centromere X. biorxiv.org/content/10.110…

Our SV caller SVIM 🐟 for long reads detects 5 SV classes, distinguishes between novel insertions and interspersed duplications and links source and destination region of duplications. Available via bioconda or pip: github.com/eldariont/svim

Our new pre-print is out now!

Contribution of structural variation to genome structure: TAD fusion discovery and ranking biorxiv.org/cgi/content/sh… #bioRxiv

Check out our lab's @biorxivpreprint: A reference haplotype panel for genome-wide imputation of short tandem repeats bit.ly/str-imputation awesome work by @shubsaini and @ileena_mitra #genomics #bioinformatics

"#AI can have extremely high accuracy and efficiency in distinguishing between cancer types and subtypes" @hajirasouliha news.weill.cornell.edu/news/2018/02/a…

ClusterPicker-II: Massively scalable transmission clustering using phylogenetic trees dlvr.it/QFNk8J #bioinformatics

iSAFE (integrated Selection of Allele Favored by Evolution) for identifying the target mutation in a selective sweep, Akbari et al. w/ Vineet Bafna of @UCSanDiego @UCSDJacobs Compare & contrast with SWIF(r) coming soon to a tweet near you. @naturemethods nature.com/articles/nmeth…

Our new preprint on "Inferring Cancer Progression from Single Cell Sequencing while allowing loss of mutations" biorxiv.org/content/early/…