Benjamin Siranosian

Reproducing the headline results from "Deep learning statistical arbitrage" (Guijarro-Ordonez et al. 2022) on my own data, with a python implementation you can use.

Five years on: revisiting OTM VIX-call tail hedges with a 2025 data extension - equity curves, risk/return frontier, and timing luck reduction, reproduced in Python.

Radical Numerics emerges from stealth with $50M of seed funding and state of the art genomic language models.

Batch effects are a constant pain when comparing RNA-seq data from different sources, but re-processing with consistent bioinformatics tools can reduce much of the effect.

s3stasher is a python package that transparently handles files in s3.

Milli-q water purifiers are too smart for their own good, but splicing in a large resistor can bypass some of the restrictions.

Deciding which server CPUs to buy by giving my 7950X3D split-brain syndrome and running lots of pipelines.

A few years ago, while in the last year of my PhD at Stanford, I published this blog post on using VIX calls to hedge against severe market downturns.

FSx for Lustre and S3 are two complementary methods of storing data in Amazon Web Services (AWS).

The following is a cross-post from the Deep Origin blog.

“We’re out of storage, and we’re out of compute.”

Let’s say you’re a biotech or academic lab that needs to do bioinformatics or computational biology at a reasonably large scale.

You've decided to move on from the academic career path after finishing your masters or PhD.

Data workflows and pipelines are an integral part of bioinformatics.

Workflow managers form the cornerstone of a modern bioinformatics stack.

I recently went down the rabbit hole trying out the newest bioinformatics workflow manager, redun.

When we last left off, I was peering into the -80 freezer at the hundreds of stool samples I would need to analyze.

My final project with the Bhatt Lab is now published!

P - H - Done As I finish up my PhD at Stanford and consider my next career moves, I'm positive I want to work at a small and rapidly growing biotech…

Edit: full writeup on this topic posted here.

Introduction This post is going to be a departure from the usual genomics tilt of this blog.

I recently finished a large metagenomics sequencing experiment - 96 10X Genomics linked read libraries sequenced across 25 lanes on a HiSeq4000.

CrAssphage is a like mystery novel full of surprises.

Update!

In the microbiome field we struggle with the fact that reference databases are (sometimes woefully) incomplete.

China Peak was a rocky, rocky race.

After sequencing a community of bacteria, phages, fungi and other organisms in a microbiome experiment, the first question we tend to ask is "What's in my…

Are your cell lines evolving right under your eyes?

My third lab rotation in my first year at Stanford took a different path than most of my previous experience.

In my last post, I described how to simulate ensembles of structures representing the 3D conformation of chromatin inside the nucleus.

Much of the current evidence for the loop extrusion hypothesis comes from molecular dynamics simulations.

3D genome organization shapes genetics at all scales.

With 11 days left to go before move-in at Stanford, I had only just made it to California.

After the eclipse, a few friends joined me for the drive West into California.

After finishing the bikepacking trip and a well-deserved recovery meal, was headed back up North for a few days in Jasper National Park.

The main attraction for this part of the trip was a 3-day bikepacking trip from Banff, south into British Colombia, and back again.

I'm starting a PhD in Genetics at Stanford in the fall.

I was thrilled to finally arrive in Banff.

Another day, another new city and country!

After the short time in Lonon, I was on a bus to Cardiff.

After a tearful goodbye with Lauren and Selen, I hopped on a Turkish Air flight and was headed for London.

I realized I've been neglecting to talk about the vineyard we were staying on!

In a nearby town there was a local outdoor market on Fridays.

How lucky are we?

After so much city time, Lauren and I wanted something more quiet and active for today.

Monday, Lauren and I were up early the next morning for a full day in Istanbul's old city.

"Why Turkey?"

Each year, the International Society for Computational Biology Student Council (ISCB-SC) organizes a conference for students and early career scientists in…

Cesky Raj is the first Nature Reserve in the Czech Republic.

The past few weeks have been a whirlwind.