Blog
Notes on bioinformatics, infrastructure, computer hardware, travel, and whatever else is on my mind.
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Deep learning statistical arbitrage part 1 - replication
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.
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Revisiting VIX Call hedging - 2025 data update and new strategies
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.
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Launching Radical Numerics
Radical Numerics emerges from stealth with $50M of seed funding and state of the art genomic language models.
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Reducing RNA-seq batch effects by re-aligning TCGA and GTEx
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.
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s3stasher simplifies using AWS S3 in python
s3stasher is a python package that transparently handles files in s3. It also maintains a local cache of recent files for offline use.
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Fixing a Milli-q purifier for 99% off
Milli-q water purifiers are too smart for their own good, but splicing in a large resistor can bypass some of the restrictions.
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Does AMD 3D V-Cache help in bioinformatics?
Deciding which server CPUs to buy by giving my 7950X3D split-brain syndrome and running lots of pipelines.
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Tail risk hedging with VIX calls (Stanford MSE448 final)
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. The…
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Cross-account AWS FSx for Lustre and S3 data repository associations
FSx for Lustre and S3 are two complementary methods of storing data in Amazon Web Services (AWS). FSx offers an extremely performant, reliable, true…
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Introducing the ComputeBench: the cloud development environment for bioinformatics
The following is a cross-post from the Deep Origin blog. Today, I’m proud to announce the beta release of Deep Origin’s first product: the ComputeBench. The…
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Accelerated computing is the future of genomics
“We’re out of storage, and we’re out of compute.” I’ll never forget the 2016 Broad Institute Cancer Program meeting where Eric Banks, senior director of the…
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Bioinformatics in the cloud, on a budget
Let’s say you’re a biotech or academic lab that needs to do bioinformatics or computational biology at a reasonably large scale. You have a tight budget and…
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Getting a industry job after grad school
You've decided to move on from the academic career path after finishing your masters or PhD. Congratulations! However, making the transition out of academia…
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Why are bioinformatics workflows different?
Data workflows and pipelines are an integral part of bioinformatics. However, the tools used to write and deploy workflows in bioinformatics are different…
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Deploying redun to AWS Batch - troubleshooting
I recently went down the rabbit hole trying out the newest bioinformatics workflow manager, redun. While installation and running workflows locally went off…
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Trying out redun - the newest workflow manager on the block
Workflow managers form the cornerstone of a modern bioinformatics stack. By enabling data provenance, portability, scalability, and re-entrancy, workflow…
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Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults (2)
When we last left off, I was peering into the -80 freezer at the hundreds of stool samples I would need to analyze. In reality, a lot of experimental design…
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Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults (1)
My final project with the Bhatt Lab is now published! You can find the open access text at Nature Communications. I'm excited to bring this chapter of my…
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Moving into aging research - in dogs!
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…
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Tail risk hedging - replication of the VXTH index
Edit: full writeup on this topic posted here. In my last post about hedging a portfolio with options, I looked at how a complicated 4-option spread could…
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Volatility as an asset class - replication of Doran (2020) and extension to a leveraged risk-parity portfolio
Introduction This post is going to be a departure from the usual genomics tilt of this blog. I've recently been interested in the science (art?) of hedging…
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Large-scale bioinformatics in the cloud with GCP, Kubernetes and Snakemake
I recently finished a large metagenomics sequencing experiment - 96 10X Genomics linked read libraries sequenced across 25 lanes on a HiSeq4000. This was…
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Transmission of crAsspahge in the microbiome
Update! This work has been published in Nature Communications. Siranosian, B.A., Tamburini, F.B., Sherlock, G. et al. Acquisition, transmission and strain…
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What is crAssphage?
CrAssphage is a like mystery novel full of surprises. First described in 2014 by Dutilh et al., crAssphage acquired it's (rather unfortunate, given that it…
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Metagenome Assembled Genomes enhance short read classification
In the microbiome field we struggle with the fact that reference databases are (sometimes woefully) incomplete. Many gut microbes are difficult to isolate…
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Race report: China Peak Enduro 2019
China Peak was a rocky, rocky race. Photo creadit Scott McClain. I raced the China Peak Enduro mountain bike race last weekend with Nick, Catherine, Peter…
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Short read classification with Kraken2
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…
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Genetic and transcriptional evolution alters cancer cell line drug response
Are your cell lines evolving right under your eyes? Credit : Lauren Solomon and Susanna M. Hamilton, Broad Communications As a scientific researcher, you…
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Joining the Bhatt lab
My third lab rotation in my first year at Stanford took a different path than most of my previous experience. I came to Stanford expecting to research…
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Deep learning to understand and predict single-cell chromatin structure
In my last post, I described how to simulate ensembles of structures representing the 3D conformation of chromatin inside the nucleus. Now, I'm going to…
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Simulating 3D chromatin structure with molecular dynamics and loop extrusion
Much of the current evidence for the loop extrusion hypothesis comes from molecular dynamics simulations. In these simulations, DNA is modeled as a polymer,…
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Is loop extrusion responsible for the 3D structure of the genome?
3D genome organization shapes genetics at all scales. Source: Nature 3D Genome Collection It's generally accepted biological knowledge that chromatin is…
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Down and up the California coast
With 11 days left to go before move-in at Stanford, I had only just made it to California. There was still so much to see! I headed down to the Bay to see…
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Driving West and a Week in Tahoe
After the eclipse, a few friends joined me for the drive West into California. Already four thousand miles of solo driving in, I was grateful for the…
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Jasper, Glacier, Eclipse
After finishing the bikepacking trip and a well-deserved recovery meal, was headed back up North for a few days in Jasper National Park. Situated a few…
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Bikepacking in Banff
The main attraction for this part of the trip was a 3-day bikepacking trip from Banff, south into British Colombia, and back again. This was my first time…
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Getting to know Banff
I was thrilled to finally arrive in Banff. After long days in the car, and hours of cruise-controlled monotony across the plains of Canada, the chilled…
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Moving to California, the long way
I'm starting a PhD in Genetics at Stanford in the fall. The plans are set, I've moved out of my apartment, and thrown away A LOT of clutter from the past…
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Dublin
Another day, another new city and country! I arrived early for a full day in Dublin. The museum highlight of the day was definitely the bog bodies at the…
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Cardiff
After the short time in Lonon, I was on a bus to Cardiff. This was my first time in Wales, and it was nice to be in a calmer place. I was staying with two…
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From simit and kebabs to tea and crumpets
After a tearful goodbye with Lauren and Selen, I hopped on a Turkish Air flight and was headed for London. This was my first time in the city, so I was…
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Doseluna winery
I realized I've been neglecting to talk about the vineyard we were staying on! Doseluna winery is completely owned and operated by Selen's family. They…
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Assos day two - market day
In a nearby town there was a local outdoor market on Fridays. Everyone seemed to show up - buying, selling, exchanging and conversing. You could find…
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Arriving in Assos
How lucky are we? Selen's family runs a vineyard in Assos, on the Turkish coastline near the Greek island Lesvos. We piled in the car -- six hours of…
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Cycling around Büyükada
After so much city time, Lauren and I wanted something more quiet and active for today. Selen recommended Büyükada, the largest of the Princes' Islands in…
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Istanbul's Old City
Monday, Lauren and I were up early the next morning for a full day in Istanbul's old city. We caught a boat from a terminal near Selen's house and rode it…
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Arriving in Istanbul
"Why Turkey?" I was asked this question many times by friends and family as I prepared to travel further East than I've ever been before. Turkey has made…
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ISCB Student Council Symposium 2017
Each year, the International Society for Computational Biology Student Council (ISCB-SC) organizes a conference for students and early career scientists in…
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Cesky Raj (Czech Bohemian Paradise)
Cesky Raj is the first Nature Reserve in the Czech Republic. Two hours North of Prague by train, it's a great day trip to get out of Prague. You'll find…
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Summer travels start NOW!
The past few weeks have been a whirlwind. Since the end of June, I have: Quit my job at the Broad Institute (yet somehow I'm still working) Moved out of my…
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What's next: Stanford Genetics!
After a long process of PhD applications, interviews and waiting for results, I'm happy to announce that I've settled on a home for the next 5 years.…
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Vineyard 70.3 - 4th place!
After months of training for the Vineyard 70.3 triathlon, the weekend of the race was finally here! I was slightly nervous, but mostly excited to test my…
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4 things I learned from keynote lectures at SCS2016
SCS2016 featured keynote lectures by two senior scientists in computational biology. John Quackenbush and Janet Thornton each shared scientific findings and…
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How do you organize an international symposium?
One word: communication. I was approached by the ISCB Student Council leadership almost a year ago with an invitation to work as the co-chair for SCS2016.…
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Use your computational skills to advance biomedical research and win cash by competing in the CMap Inference Challenge
The Connectivity Map team at the Broad Institute is crowdsourcing solutions to a computational problem in our line of work. Can you build a predictive model…
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Cotopaxi Questival
A 24 hour adventure race through Boston! Involving lots of biking and pretzels.
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Martha's Vineyard 70.3 triathlon
I've been interested in doing a triathlon for a while now - the combination of swim, bike and run is an excellent test of fitness, endurance and skill. Last…
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Road Trip: Final Numbers and Thoughts
Back home on the East Coast, I started to reflect on the trip that had occupied the past month of my life. There were so many things I learned about…
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Road Trip: Shenandoah NP to Boston, MA
I had to include a trip on Skyline Drive through Shenandoah on my route back. I visited once on a backpacking trip with the Brown Outing Club 3 years ago…
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Road Trip: Nashville to Atlanta
Next stop: Nashville. The city of Country Music and BBQ was alive to welcome me when I arrived in the early afternoon. I tried to stop at the famous Cafe…
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Road Trip: Utah, Dever, Missouri
The next stop on the trip was Denver, Colorado. Colorado has been calling to me for a while now, so I was excited to have the chance to visit. The drive…
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Road Trip: Southern Utah
After a long, hot day of driving (high temperature of 114˚F!), I made it to the dessert outside of Zion NP. My plan for the night was to pitch a tent on…
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Road Trip: Turning back east
Lizzy left from LAX, and I'm on my own for the next week and a half until I get back to the East Coast. Just my luck, because soon after leaving California,…
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Road Trip: Santa Cruz, CA
After our time roughing it in Yosemite, Lizzy and I were looking forward to the comfort of staying at her brother's house in Santa Cruz, California.…
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Road Trip: Santa Cruz to LA
We made our way down the Pacific Coast Highway again to stay with Lizzy's other brother in LA. It was a beautiful sunny day and perfect for a drive. We…
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Road Trip: Yosemite National Park
I've been attached to Yosemite since I got into climbing freshman year at Brown, and I was thrilled I finally had a chance to visit the park. Lizzy and I…
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Road Trip: California Coast
We were headed south, down to Yosemite National Park. The best way to drive in California (okay, maybe I'm a bit biased) is along the coast. The Pacific…
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Road Trip: Oregon
Lizzy and I spent two days exploring different sections of Oregon. The first night we camped at Columbia River Gorge and explored the surrounding area. We…
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Road Trip: Seattle, Washington
My girlfriend Lizzy flew out to Seattle to join me for the next section of the trip - a tour down the West Coast. Our first day in the city was packed with…
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Road Trip: Grand Teton National Park
We wanted to spend a night in the backcountry in Grand Teton National Park, but all backcountry stays require a permit. The park saves a portion of the…
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Road Trip: Yellowstone National Park
We spent Thursday exploring Yellowstone. My first impression driving into the park: this place is big. Hundreds of miles of road link the different sections…
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Road Trip: Backcountry in the Badlands 2
I woke up to sunrise in the Badlands. The landscape here is amazing - rolling prairie fields, towering mesas and sedimentary mountain peaks surround you. I…
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Road Trip: Backcountry in the Badlands
We arrived at Badlands National Park later in the day on Monday. We planned to spend Monday and Tuesday night out in the backcountry, and stopped by the…
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Road Trip: Badlands to Yellowstone + Devil's Tower
We drove the 500 miles from Badlands to Yellowstone over two days, stopping for a night at the Prune Creek Campground in the Bighorn National Forest,…
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Road Trip: Michigan to the Badlands
The next part of the trip had a ton of driving. It was a 9 hour trip from Michigan to my friend's house in Ames, Iowa where we spent Sunday night. Thanks,…
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Day 2: Rockwood, NY to Lake Orion, MI (and Niagara Falls)
Early start this morning! Which would have been great, had I not forgotten a part of my Aeropress coffee maker at home... If you know me, you know I need…
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Road Trip: Day 1
The trip is off to a good start! Today, I packed up the Saab with camping gear, some leftover food from my apartment, and my hammock. I left Cape Cod and…
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Start of a road trip
I have a lot to update on this site... my last post is a year old! Well, those updates will come. Most recently, I'm starting on a one month road trip of…
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What's in the portion of reads that don't map to a reference?
One of the first steps in the analysis of most next generation sequencing datasets (unless you're doing a novel genome or transcript assembly) is mapping to…
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Biotech and software companies at ISMB 2014
In my past three posts I talked about the highlights of the 2014 Intelligent Systems for Molecular Biology conference in Boston, MA. In addition to all the…
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Highlights from ISMB - Day 3
Today was the third and final day of the main ISMB conference! I slept in until noon (attending these things is surprisingly tiring) so I missed some of the…
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Highlights from ISMB - Day 2
I'll be continuing my updates on the Intelligent Systems for Molecular Biology (ISMB) conference with some of the research that I saw today. Tracking Cells…
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Highlights from ISMB - Day 1
Today was the first day of the main ISMB conference in Boston. Between volunteering duties I had a chance to catch a few interesting talks. Here's what I…
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ISCB Student Council Symposium 2014
I had an excellent opportunity to present my mycobacteriophage kmer usage research at the ISCB Student Council Symposium earlier today. I was one of 12…
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Thoughts from the SEA-PHAGES symposium
What a weekend! The past two days have been filled with excellent student presentations, ample opportunities for networking and fruitful conversations about…
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SEA-PHAGES symposium 2014
This weekend I'm down at HHMI's Janelia Farm Research Campus at the SEA-PHAGES undergraduate research symposium. The phage hunters class I TA is…
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Counting tetranucleotides in mycobacteriophages
As a teaching assistant in Brown's first year seminar "Phage Hunters" I lead several freshman biology and computer science students in an independent…
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ISCB student council 2014
I submitted some research I've been working on (as a byproduct of TAing a first year seminar and leading some students in an independent bioinformatics…
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Finished with junior year!
I handed in the final assignment of the semester yesterday, which marked the end of my Junior year at Brown. I can safely say it was the best year I've had…
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Blogs I follow
I don't know how they find the time to do it, but many of today's top bioinformatics and computational biology researchers have a regularly updated blog.…
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Husband and wife start PhD after learning of disease
Eric Minikel and Sonia Vallabh were working as an urban planner and a lawyer until 2011, when they learned Sonia has a rare heritable disease - Fatal…
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Publishing code on GitHub
This semester, I've made an effort to get all the code I write under version control. In the past I simply maintained my codebase in Dropbox. This worked…
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k-mers are everywhere!
Many problems in bioinformatics involve working with short pieces of DNA sequence. We call these short words k-mers, where k is an integer usually less than…
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Academia or Industry?
That question seems to be on the mind of a lot of the people around me lately. Junior year of my undergrad studies at Brown is almost over, and my…
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Books on Graduate School
Students are pretty much on their own for figuring things out after undergrad (I definitely don't miss high school guidance counselors, though). Grad school…
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Brown Club of Boston Biotech Conference
I just returned from an excellent conference sponsored by the Brown Club of Boston. The conference was designed to facilitate networking between Brown…