Author Archives: Gabe Rudy

Gabe Rudy

About Gabe Rudy

Meet Gabe Rudy, GHI’s Vice President of Product and Engineering and team member since 2002. Gabe thrives in the dynamic and fast-changing field of bioinformatics and genetic analysis. Leading a killer team of Computer Scientists and Statisticians in building powerful products and providing world-class support, Gabe puts his passion into enabling Golden Helix’s customers to accelerate their research. When not reading or blogging, Gabe enjoys the outdoor Montana lifestyle. But most importantly, Gabe truly loves spending time with his sons, daughter, and wife. Follow Gabe on Twitter @gabeinformatics.
Gabe Rudy

Supercentenarian Variant Annotation: Complex to Primitive

In a previous blog post, I demonstrated using VarSeq to directly analyze the whole genomes of 17 supercentenarians. Since then, I have been working with the variant set from these long-lived genomes to prepare a public data track useful for … Continue reading

Posted in Public data & annotations | Leave a comment
Gabe Rudy

What TriCon 2015 Foreshadows for Clinical Genomics

I spent a very eventful week at the Molecular TriCon in downtown San Francisco, and have been pondering the very clear trends that emerged by attending the clinical and NGS focused talks. Cancer gene panels make sense economically and as … Continue reading

Posted in Big picture, News, events, & announcements | Tagged , , , , , , | 2 Comments
Gabe Rudy

In Pursuit of Longevity: Analyzing the Supercentenarian Whole Genomes with VarSeq

If you haven’t been closely watching the twittersphere or other headline sources of the genetics community, you may have missed the recent chatter about the whole genome sequencing of 17 supercentenarians (people who live beyond 110 years). While genetics only … Continue reading

Posted in Best practices in genetic analysis, Big picture, Clinical genetics | Tagged , | 33 Comments
Gabe Rudy

6 Population Catalogs Compared with the ExAC 61,486 Exomes

To say the announcement of Dan MacArthur’s group’s release of the Exome Aggregation Consortium (ExAC) data was highly anticipated at ASHG 2014 would be an understatement. Basically, there were two types of talks at ASHG. Those that proceeded the official … Continue reading

Posted in Big picture, Bioinformatic support, Clinical genetics, Uncategorized | Tagged , , , , | 5 Comments
Gabe Rudy

VarSeq: Making Variant Discovery and Gene Panels Easy

Last week, our CEO Andreas Scherer announced our entrance into the clinical testing market with VarSeq. This week, I will be giving a webcast on Wednesday introducing this new tool and demonstrating its capabilities. (Register for the webcast) VarSeq’s focused purpose is making NGS gene testing and variant discovery efficient, scalable and … Continue reading

Posted in Big picture, News, events, & announcements | Tagged , , , , | 2 Comments
Gabe Rudy

Updates to ClinVar and dbSNPs: Fresh charts for Cromonaughts!

I’m sitting in the Smithsonian Air and Space Museum basking in the incredible product of human innovation and the hard work of countless engineers. My volunteer tour guide started us off at the Wright brother’s fliers and made a point of saying … Continue reading

Posted in Technology review | Tagged , , , , , , | 2 Comments
Gabe Rudy

RefSeq Genes: Updated to NCBI Provided Alignments and Why You Care

You probably haven’t spent much time thinking about how we represent genes in a genomic reference sequence context. And by genes, I really mean transcripts since genes are just a collection of transcripts that produce the same product. But in … Continue reading

Posted in Best practices in genetic analysis, Big picture, Bioinformatic support, General statistical genetics principles, Technology review, Uncategorized | Tagged , , , | 5 Comments
Gabe Rudy

The New Human Genome Reference and Clinical Grade Annotations: It’s All About the Coordinates

On my flight back from this year’s Molecular Tri-Conference in San Francisco, I couldn’t help but ruminate over the intriguing talks, engaging round table discussions, and fabulous dinners with fellow speakers. And I kept returning to the topic of how … Continue reading

Posted in Best practices in genetic analysis, Clinical genetics, Personal genomics | 2 Comments
Gabe Rudy

All I Want for Christmas Is a New File Format for Genomics

Tis the season of quiet, productive hours. I’ve been spending a lot of mine thinking about file formats. Actually I’ve been spending mine implementing a new one, but more on that later. File formats are amazingly important in big data … Continue reading

Posted in Technology review | 15 Comments
Gabe Rudy

The State of NGS Variant Calling: DON’T PANIC!!

I’m a believer in the signal. Whole genomes and exomes have lots of signal. Man, is it cool to look at a pile-up and see a mutation as clear as day that you arrived at after filtering through hundreds of … Continue reading

Posted in Assessment of new methods, Technology review | 6 Comments