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edyeet is a fork of Chirag Jain's mashmap2 focused on obtaining base-level alignment using edlib. It's faster than minimap2 for variation graph induction, sensitive to repeats, and provides mashmap's probabilistic guarantees of alignment length and quality github.com/ekg/edyeet

Many assume all patients with high-risk DNA mutations — such as familial hyperchol mutations for heart attack — will develop disease But some remain healthy ‘Polygenic background’ one important reason why Press release: bit.ly/2EkAqDI Paper: go.nature.com/3hePocV

Clear Demonstration of Reinforcement Learning Relevant to #AI and #MachineLearning Students by - #BigData #ML #ArtificialIntelligence #DeepLearning #MI #DataScience #DL #MachineIntelligence Cc: Dr Maggie Lieu Mike Gualtieri Jennifer Stirrup #MBA Topics: #AI #Data #Strategy Shannon Platz

Newest results from me and all my colleagues at Deciphering Developmental Disorders Wellcome Sanger Institute. We designed a new tool (InDelible) that uses split reads from exome sequencing to identify breakpoints of structural variants missed by other approaches: medrxiv.org/content/10.110…

Come work with me! Sema4 has -lots- of job openings, listed here. sema4.com/careers/ We're committed to equity, inclusion, and access, and I'm committed to casting a wide net. Please reach out even if you don't match every single requirement.

When developing methods, it is good to know the variability in user data. It was hard to find varied data from many GIAB samples, so we sequenced HG001-7+NA12891/2 on NovaSeq and HiSeqX/4000 in both WGS 50x PCR-Free and PCR+ runs and 3 WES capture kits. biorxiv.org/content/10.110…

High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios biorxiv.org/cgi/content/sh… #biorxiv_genomic

Ever wondered if mapping to the GRCh37 or GRCh38 reference significantly changes your exome variant calls? We did! So we wrote a paper (authors.elsevier.com/c/1dEncgeW~iVa) about DISCREPs (DISCordant REference Patches) that is published today in AJHG ! (1/9)

Wait - this is bizarre and fascinating, as FTO is the top GWAS hit for body size and obesity. Carrying a SNP in FTO can change one's weight 6.6lbs on average. Expressing human FTO in plants makes them huge? I had always assumed it had some weird hypothalamic role in satiety...

My team NY Genome Center is growing. Looking for a highly motivated, detail-oriented Bioinformatics Programmer to help us develop novel tools for whole-genome sequencing data analysis. Please spread the word: nygenome-openhire.silkroad.com/epostings/inde…

If you could read the DNA of half a million people, would you do it and why? Would it work? What would you learn? To answer this and several related questions, let me walk you through the work my Regeneron Genetics Center colleagues just published in Nature. 1/24 nature.com/articles/s4158…

2022: A Wild Year for Short Reads?omicsomics.blogspot.com/2022/01/2022-w…

So incredibly proud to introduce our new liquid biopsy platform MRD-EDGE on bioRxiv! MRD-EDGE is a crucial next step in our lab’s effort to capitalize on the breadth of signal available from plasma whole genome sequencing (WGS). THREAD doi.org/10.1101/2022.0…

I am excited about our (Genome in a Bottle Jason Chin Heng Li &many more) paper today in Nature Biotechnology to characterize 395 challenging medically relevant genes& errors in GRCH37&GRCH38 that impact analysis nature.com/articles/s4158… BCM HGSC #Bioinformatics DNAnexus, Inc. From the Labs at Baylor College of Medicine

Cost-efficient whole genome-sequencing using novel mostly natural sequencing-by-synthesis chemistry and open fluidics platform | bioRxiv biorxiv.org/content/10.110…

Very happy to officially share the high-coverage 1000 Genomes Project (1kGP) whole-genome sequencing (WGS) resource, out today in Cell! cell.com/cell/fulltext/… (1/7)

Very excited to see our paper on the high-coverage sequencing and analysis of the samples from the 1000 Genomes project come out. It was a wonderful collaboration with Marta Byrska-Bishop @AniaOkulaBasile and Xuefang Zhao from Talkowski Lab. Please check out this awesome thread!

PSA, since I've now seen problems arising from this: As of Sept 2023, GATK no longer makes missing genotypes explicit in VCFs (i.e. "./." as in the VCF spec). Missing genotypes are instead coded as "0/0" with a DP=0 format field. See attached for examples.

Tandem repeat Genome in a Bottle benchmark Nature Biotechnology out today: rdcu.be/dFQNN . Characterization of 1.7 million TR + benchmark variants + new method to overcome var. representation issues! Great work lead by Adam E. BCM HGSC & great collab. from so many! (1/4)

AlphaQubit draws on Transformers to decode quantum computers, leading to a new state of the art in quantum error correction accuracy. An exciting intersection of AI + quantum computing - we’re sharing more in nature today. blog.google/technology/goo…