Ben Siranosian — genomic language models at Radical Numerics. Computational biology, bioinformatics, infrastructure, quant finance, and travel.https://bsiranosian.com/https://bsiranosian.com/blog/reducing-rna-seq-batch-effects-by-re-aligning-tcga-and-gtex/https://bsiranosian.com/blog/reducing-rna-seq-batch-effects-by-re-aligning-tcga-and-gtex/I want to be able to compare RNA-seq data between several public sources and internal datasets. I care a lot about the differential expression of certain…Tue, 11 Nov 2025 00:00:00 GMThttps://bsiranosian.com/blog/s3stasher-simplifies-using-aws-s3-in-python/https://bsiranosian.com/blog/s3stasher-simplifies-using-aws-s3-in-python/Working with cloud files in python is a necessary pain at any biotech organization. While packages like pandas transparently handle S3 URIs, I still found…Sun, 09 Nov 2025 00:00:00 GMThttps://bsiranosian.com/blog/fixing-a-milli-q-purifier-for-99-off/https://bsiranosian.com/blog/fixing-a-milli-q-purifier-for-99-off/We bought a used Milli-q 7005 ultrapure water purifier from an auction for a great price. It came with most of what we need, but was missing the external…Tue, 05 Aug 2025 00:00:00 GMThttps://bsiranosian.com/blog/does-amd-3d-v-cache-help-in-bioinformatics/https://bsiranosian.com/blog/does-amd-3d-v-cache-help-in-bioinformatics/Introduction In our new office at Pattern, I have 42U of server rack space to play with, so I want to get an AMD EPYC server for some long-running…Mon, 26 May 2025 00:00:00 GMThttps://bsiranosian.com/blog/tail-risk-hedging-with-vix-calls-stanford-mse448-final/https://bsiranosian.com/blog/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…Sun, 25 May 2025 00:00:00 GMThttps://bsiranosian.com/blog/cross-account-aws-fsx-for-lustre-and-s3-data-repository-associations/https://bsiranosian.com/blog/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…Wed, 06 Dec 2023 00:00:00 GMThttps://bsiranosian.com/blog/introducing-the-computebench/https://bsiranosian.com/blog/introducing-the-computebench/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…Tue, 21 Nov 2023 00:00:00 GMThttps://bsiranosian.com/blog/accelerated-computing-is-the-future-of-genomics/https://bsiranosian.com/blog/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…Tue, 10 Jan 2023 00:00:00 GMThttps://bsiranosian.com/blog/bioinformatics-in-the-cloud-on-a-budget/https://bsiranosian.com/blog/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…Sat, 22 Oct 2022 00:00:00 GMThttps://bsiranosian.com/blog/getting-a-industry-job-after-grad-school/https://bsiranosian.com/blog/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…Sun, 02 Oct 2022 00:00:00 GMThttps://bsiranosian.com/blog/why-are-bioinformatics-workflows-different/https://bsiranosian.com/blog/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…Sun, 14 Aug 2022 00:00:00 GMThttps://bsiranosian.com/blog/deploying-redun-to-aws-batch-troubleshooting/https://bsiranosian.com/blog/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…Tue, 05 Jul 2022 00:00:00 GMThttps://bsiranosian.com/blog/trying-out-redun-the-newest-workflow-manager-on-the-block/https://bsiranosian.com/blog/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…Tue, 05 Jul 2022 00:00:00 GMThttps://bsiranosian.com/blog/rare-transmission-of-commensal-and-pathogenic-bacteria-in-the-gut-microbiome-of-hospitalized-adults-2/https://bsiranosian.com/blog/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…Wed, 02 Feb 2022 00:00:00 GMThttps://bsiranosian.com/blog/rare-transmission-of-commensal-and-pathogenic-bacteria-in-the-gut-microbiome-of-hospitalized-adults-1/https://bsiranosian.com/blog/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…Tue, 01 Feb 2022 00:00:00 GMThttps://bsiranosian.com/blog/moving-into-aging-research-in-dogs/https://bsiranosian.com/blog/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…Mon, 01 Nov 2021 00:00:00 GMThttps://bsiranosian.com/blog/tail-risk-hedging-replication-of-the-vxth-index/https://bsiranosian.com/blog/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…Tue, 12 Jan 2021 00:00:00 GMThttps://bsiranosian.com/blog/volatility-as-an-asset-class/https://bsiranosian.com/blog/volatility-as-an-asset-class/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…Tue, 05 Jan 2021 00:00:00 GMThttps://bsiranosian.com/blog/large-scale-bioinformatics-in-the-cloud-with-gcp-kubernetes-and-snakemake/https://bsiranosian.com/blog/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…Wed, 08 Jan 2020 00:00:00 GMThttps://bsiranosian.com/blog/transmission-of-crasspahge-in-the-microbiome/https://bsiranosian.com/blog/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…Wed, 24 Jul 2019 00:00:00 GMThttps://bsiranosian.com/blog/what-is-crassphage/https://bsiranosian.com/blog/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…Wed, 24 Jul 2019 00:00:00 GMThttps://bsiranosian.com/blog/metagenome-assembled-genomes-enhance-short-read-classification/https://bsiranosian.com/blog/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…Mon, 22 Jul 2019 00:00:00 GMThttps://bsiranosian.com/blog/race-report-china-peak-enduro-2019/https://bsiranosian.com/blog/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…Tue, 02 Jul 2019 00:00:00 GMThttps://bsiranosian.com/blog/short-read-classification-with-kraken2/https://bsiranosian.com/blog/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…Thu, 20 Jun 2019 00:00:00 GMThttps://bsiranosian.com/blog/genetic-and-transcriptional-evolution-alters-cancer-cell-line-drug-response/https://bsiranosian.com/blog/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…Thu, 09 Aug 2018 00:00:00 GMThttps://bsiranosian.com/blog/joining-the-bhatt-lab/https://bsiranosian.com/blog/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…Sun, 24 Jun 2018 00:00:00 GMThttps://bsiranosian.com/blog/deep-learning-to-understand-and-predict-single-cell-chromatin-structure/https://bsiranosian.com/blog/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…Thu, 29 Mar 2018 00:00:00 GMThttps://bsiranosian.com/blog/simulating-chromatin-structure-with-loop-extrusion/https://bsiranosian.com/blog/simulating-chromatin-structure-with-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,…Sun, 25 Mar 2018 00:00:00 GMThttps://bsiranosian.com/blog/is-loop-extrusion-responsible-for-the-3d-structure-of-the-genome/https://bsiranosian.com/blog/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…Sat, 24 Mar 2018 00:00:00 GMThttps://bsiranosian.com/blog/down-and-up-the-california-coast/https://bsiranosian.com/blog/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…Fri, 20 Oct 2017 00:00:00 GMThttps://bsiranosian.com/blog/driving-west-and-a-week-in-tahoe/https://bsiranosian.com/blog/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…Thu, 19 Oct 2017 00:00:00 GMThttps://bsiranosian.com/blog/jasper-glacier-eclipse/https://bsiranosian.com/blog/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…Tue, 17 Oct 2017 00:00:00 GMThttps://bsiranosian.com/blog/bikepacking-in-banff/https://bsiranosian.com/blog/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…Thu, 05 Oct 2017 00:00:00 GMThttps://bsiranosian.com/blog/getting-to-know-banff/https://bsiranosian.com/blog/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…Wed, 04 Oct 2017 00:00:00 GMThttps://bsiranosian.com/blog/moving-to-california-the-long-way/https://bsiranosian.com/blog/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…Wed, 04 Oct 2017 00:00:00 GMThttps://bsiranosian.com/blog/dublin/https://bsiranosian.com/blog/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…Fri, 04 Aug 2017 00:00:00 GMThttps://bsiranosian.com/blog/cardiff/https://bsiranosian.com/blog/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…Thu, 03 Aug 2017 00:00:00 GMThttps://bsiranosian.com/blog/onward-to-london/https://bsiranosian.com/blog/onward-to-london/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…Wed, 02 Aug 2017 00:00:00 GMThttps://bsiranosian.com/blog/doseluna-winery/https://bsiranosian.com/blog/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…Mon, 31 Jul 2017 00:00:00 GMThttps://bsiranosian.com/blog/assos-day-two-market-day/https://bsiranosian.com/blog/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…Sun, 30 Jul 2017 00:00:00 GMThttps://bsiranosian.com/blog/arriving-in-assos/https://bsiranosian.com/blog/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…Sat, 29 Jul 2017 00:00:00 GMThttps://bsiranosian.com/blog/cycling-around-buyukada/https://bsiranosian.com/blog/cycling-around-buyukada/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…Thu, 27 Jul 2017 00:00:00 GMThttps://bsiranosian.com/blog/istanbuls-old-city/https://bsiranosian.com/blog/istanbuls-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…Wed, 26 Jul 2017 00:00:00 GMThttps://bsiranosian.com/blog/arriving-in-istanbul/https://bsiranosian.com/blog/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…Mon, 24 Jul 2017 00:00:00 GMThttps://bsiranosian.com/blog/iscb-student-council-symposium-2017/https://bsiranosian.com/blog/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…Sun, 23 Jul 2017 00:00:00 GMThttps://bsiranosian.com/blog/cesky-raj-czech-bohemian-paradise/https://bsiranosian.com/blog/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…Thu, 20 Jul 2017 00:00:00 GMThttps://bsiranosian.com/blog/summer-travels-start-now/https://bsiranosian.com/blog/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…Sun, 16 Jul 2017 00:00:00 GMThttps://bsiranosian.com/blog/whats-next-stanford-genetics/https://bsiranosian.com/blog/whats-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.…Tue, 09 May 2017 00:00:00 GMThttps://bsiranosian.com/blog/vineyard-70-3-4th-place/https://bsiranosian.com/blog/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…Mon, 12 Sep 2016 00:00:00 GMThttps://bsiranosian.com/blog/4-things-i-learned-from-keynote-lectures-at-scs2016/https://bsiranosian.com/blog/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…Mon, 25 Jul 2016 00:00:00 GMThttps://bsiranosian.com/blog/how-do-you-organize-an-international-symposium/https://bsiranosian.com/blog/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.…Wed, 20 Jul 2016 00:00:00 GMThttps://bsiranosian.com/blog/use-your-computational-skills-to-advance-biomedical-research-and-win-cash-by-competing-in-the-cmap-inference-challenge/https://bsiranosian.com/blog/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…Wed, 29 Jun 2016 00:00:00 GMThttps://bsiranosian.com/blog/cotopaxi-questival/https://bsiranosian.com/blog/cotopaxi-questival/A 24 hour adventure race through Boston! Involving lots of biking and pretzels.Sat, 28 May 2016 00:00:00 GMThttps://bsiranosian.com/blog/marthas-vineyard-70-3-triathlon/https://bsiranosian.com/blog/marthas-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…Fri, 04 Mar 2016 00:00:00 GMThttps://bsiranosian.com/blog/road-trip-final-numbers-and-thoughts/https://bsiranosian.com/blog/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…Sat, 04 Jul 2015 00:00:00 GMThttps://bsiranosian.com/blog/road-trip-shenandoah-np-to-boston-ma/https://bsiranosian.com/blog/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…Fri, 03 Jul 2015 00:00:00 GMThttps://bsiranosian.com/blog/road-trip-nashville-to-atlanta/https://bsiranosian.com/blog/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…Thu, 02 Jul 2015 00:00:00 GMThttps://bsiranosian.com/blog/road-trip-utah-dever-missouri/https://bsiranosian.com/blog/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…Thu, 02 Jul 2015 00:00:00 GMThttps://bsiranosian.com/blog/road-trip-southern-utah/https://bsiranosian.com/blog/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…Wed, 01 Jul 2015 00:00:00 GMThttps://bsiranosian.com/blog/road-trip-turning-back-east/https://bsiranosian.com/blog/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,…Tue, 30 Jun 2015 00:00:00 GMThttps://bsiranosian.com/blog/road-trip-santa-cruz-ca/https://bsiranosian.com/blog/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.…Mon, 29 Jun 2015 00:00:00 GMThttps://bsiranosian.com/blog/road-trip-santa-cruz-to-la/https://bsiranosian.com/blog/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…Mon, 29 Jun 2015 00:00:00 GMThttps://bsiranosian.com/blog/road-trip-yosemite-national-park/https://bsiranosian.com/blog/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…Mon, 29 Jun 2015 00:00:00 GMThttps://bsiranosian.com/blog/road-trip-california-coast/https://bsiranosian.com/blog/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…Wed, 24 Jun 2015 00:00:00 GMThttps://bsiranosian.com/blog/road-trip-oregon/https://bsiranosian.com/blog/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…Wed, 24 Jun 2015 00:00:00 GMThttps://bsiranosian.com/blog/road-trip-seattle-washington/https://bsiranosian.com/blog/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…Sun, 21 Jun 2015 00:00:00 GMThttps://bsiranosian.com/blog/road-trip-grand-teton-national-park/https://bsiranosian.com/blog/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…Sun, 07 Jun 2015 00:00:00 GMThttps://bsiranosian.com/blog/road-trip-yellowstone-national-park/https://bsiranosian.com/blog/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…Sun, 07 Jun 2015 00:00:00 GMThttps://bsiranosian.com/blog/road-trip-backcountry-in-the-badlands-2/https://bsiranosian.com/blog/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…Sat, 06 Jun 2015 00:00:00 GMThttps://bsiranosian.com/blog/road-trip-backcountry-in-the-badlands/https://bsiranosian.com/blog/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…Sat, 06 Jun 2015 00:00:00 GMThttps://bsiranosian.com/blog/road-trip-badlands-to-yellowstone-devils-tower/https://bsiranosian.com/blog/road-trip-badlands-to-yellowstone-devils-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,…Sat, 06 Jun 2015 00:00:00 GMThttps://bsiranosian.com/blog/road-trip-michigan-to-the-badlands/https://bsiranosian.com/blog/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,…Sat, 06 Jun 2015 00:00:00 GMThttps://bsiranosian.com/blog/day-2-rockwood-ny-to-lake-orion-mi-and-niagara-falls/https://bsiranosian.com/blog/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…Sun, 31 May 2015 00:00:00 GMThttps://bsiranosian.com/blog/road-trip-day-1/https://bsiranosian.com/blog/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…Sun, 31 May 2015 00:00:00 GMThttps://bsiranosian.com/blog/start-of-a-road-trip/https://bsiranosian.com/blog/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…Fri, 29 May 2015 00:00:00 GMThttps://bsiranosian.com/blog/whats-in-the-portion-of-reads-that-dont-map-to-a-reference/https://bsiranosian.com/blog/whats-in-the-portion-of-reads-that-dont-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…Wed, 30 Jul 2014 00:00:00 GMThttps://bsiranosian.com/blog/biotech-at-ismb-2014/https://bsiranosian.com/blog/biotech-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…Mon, 21 Jul 2014 00:00:00 GMThttps://bsiranosian.com/blog/highlights-from-ismb-day-3/https://bsiranosian.com/blog/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…Tue, 15 Jul 2014 00:00:00 GMThttps://bsiranosian.com/blog/highlights-from-ismb-day-2/https://bsiranosian.com/blog/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…Mon, 14 Jul 2014 00:00:00 GMThttps://bsiranosian.com/blog/highlights-from-ismb-day-1/https://bsiranosian.com/blog/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…Sun, 13 Jul 2014 00:00:00 GMThttps://bsiranosian.com/blog/iscb-student-council-symposium-2014/https://bsiranosian.com/blog/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…Fri, 11 Jul 2014 00:00:00 GMThttps://bsiranosian.com/blog/thoughts-from-the-sea-phages-symposium/https://bsiranosian.com/blog/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…Sun, 15 Jun 2014 00:00:00 GMThttps://bsiranosian.com/blog/sea-phages-symposium-2014/https://bsiranosian.com/blog/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…Sat, 14 Jun 2014 00:00:00 GMThttps://bsiranosian.com/blog/counting-tetranucleotides-in-mycobacteriophages/https://bsiranosian.com/blog/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…Tue, 10 Jun 2014 00:00:00 GMThttps://bsiranosian.com/blog/iscb-student-council-2014/https://bsiranosian.com/blog/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…Sat, 17 May 2014 00:00:00 GMThttps://bsiranosian.com/blog/finished-with-junior-year/https://bsiranosian.com/blog/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…Wed, 14 May 2014 00:00:00 GMThttps://bsiranosian.com/blog/blogs-i-follow/https://bsiranosian.com/blog/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.…Sun, 11 May 2014 00:00:00 GMThttps://bsiranosian.com/blog/husband-and-wife-phd/https://bsiranosian.com/blog/husband-and-wife-phd/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…Mon, 05 May 2014 00:00:00 GMThttps://bsiranosian.com/blog/publishing-code-on-github/https://bsiranosian.com/blog/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…Fri, 02 May 2014 00:00:00 GMThttps://bsiranosian.com/blog/k-mers-are-everywhere/https://bsiranosian.com/blog/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…Thu, 24 Apr 2014 00:00:00 GMThttps://bsiranosian.com/blog/academia-or-industry/https://bsiranosian.com/blog/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…Thu, 17 Apr 2014 00:00:00 GMThttps://bsiranosian.com/blog/books-on-graduate-school/https://bsiranosian.com/blog/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…Fri, 11 Apr 2014 00:00:00 GMThttps://bsiranosian.com/blog/brown-club-of-boston-biotech-conference/https://bsiranosian.com/blog/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…Tue, 08 Apr 2014 00:00:00 GMT