- Rapid re-identification of human samples using portable DNA sequencing -- Using Nanopore Sequencers to identify individuals from whom DNA was taken. With Sophie Zaaijer, Assaf Gordon, Robert Piccone, Simon Cornelis Groen, and Yaniv Erlich. I devised the core algorithm and did the first test; the coauthors took it from there. Published in eLife. Previously prepublished as Democratizing dna fingerprinting
- DNA.Land -- A framework to collect genomes and phenomes in the era of abundant genetic information. With Jie Yuan, Assaf Gordon, Richard Aufrichtig, Dina Zielinski, Joseph Pickrell and Yaniv Erlich. I contributed various features to the DNA.Land project. Published in Nature Genetics.
- Using mobile sequencers in an academic classroom -- A case study of using nanopore sequencers in class. I was a student in the class, so this is more research on me than by me, but I'm technically on the coauthor list, and my code is offered as an example of student work in such a class. Since I was the only one to solve the second "hackathon", my code probably qualifies as a cherry-picked example, but what can you do? Published in eLife.
- Is there a Firefox Gene? Short answer: no. Long answer: searching for one reveals a lot about what genetic research is like
- CNN Trojan Defense -- Inserting Trojan Horses into Convolutional Neural Nets, and then detecting them.
- Causal Inference -- Inferring Causality from Finite Data using Conditional Independence, with special interest in microbiome disruption and Ileal Crohn's Disease.
- Recursive Systemic Profiler -- Profiling systems which spread across many processes
- SpatialTable -- A Bigtable-style distributed database for spatial information and rectangle queries. Faster than geohashing at the 99th percentile.
- Semi-Byzantine Reputation Networks -- In a world with many bad agents who are willing to lie in a reputation system, can MCMC techniques estimate whom we should trust?. The approach looks promising, but impractical without extensive training data that includes ground truth.
- Alignments -- A way of computing [DNA] sequence alignments more efficiently than the normal dynamic programming approach, for sequences that are pretty similar to begin with. The raw source code is also available.
- ForNet -- This is a distributed logging system for large IP
networks. I worked on it along with Professor Nasir Memon, Kulesh
Shanmugasundaram, Amos Wetherbee and Radion Khait. Others have
worked on the project at other times as well. The project has its own
webpage and we wrote
a report about it.
- Semi-Automated Refactoring -- This was a project I did as
part of a class, and as such is not entirely complete. The idea was
to detect sections of code that can and should be combined into single
functions to decrease bloat. The software succeeded in finding some
such code, but it is not really ready for practical use. You can read
my report or you can
download the software.
- Email: email@example.com
- GPG Public Key: as text, as binary GPG keyring. (Please do not encrypt email to me by default. To keep my private key safe, I keep it in a place that's somewhat inconvenient for me to get at.)
- Phone: 646-506-5378 (I usually don't answer for unfamiliar numbers, but I do read texts and Signal messages)
- Facebook Messenger: daniel.speyer
In case you want to know what I look like
- Harbor Town -- The board game Le Havre, online for social distancing.
- Antepenultimate Minesweeper -- Minesweeper has been around for a long time, and nobody actually added features to it. Now I have. A silly little game. Not as silly as all the "ultimate" games out there which are really the same old games with eye candy, though.