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- April 2025 Understanding GreedyMini
- March 2025 Path Pruning Revisited
- March 2025 Beyond Global Alignment
- March 2025 SimdSketch: a fast bucket sketch
- March 2025 Types of tigs
- February 2025 Thesis: Optimal Throughput Bioinformatics
- February 2025 A History of Pairwise Alignment
- February 2025 Low Density Minimizers
- February 2025 High Throughput Bioinformatics
- February 2025 Minimizer papers
- February 2025 Binary search variants and the effects of batching
- February 2025 Thoughts on Consensus MPHF and tiny pointers
- February 2025 PtrHash: Minimal Perfect Hashing at RAM Throughput
- January 2025 Code snippets for Latex, Rust, and Python
- January 2025 Setting up traffic monitoring using GoAccess
- December 2024 Static search trees: 40x faster than binary search
- November 2024 Comments on Brisk
- November 2024 Comments on GreedyMini
- October 2024 Comments on 'When Less is More' minimizer review
- October 2024 A lemma on suffix array searching
- October 2024 FM-index implementations
- September 2024 Practical minimizers
- September 2024 Calling Rust from Python
- September 2024 AI reading list
- September 2024 PACE 24
- August 2024 [WIP] Feynman problems
- July 2024 SimdMinimizers: Computing random minimizers, fast
- July 2024 Links for talks & posters
- June 2024 A near-tight lower bound on minimizer density
- June 2024 CPU performance
- June 2024 Tools for suffix array searching
- June 2024 Crates for suffix array construction
- May 2024 Thoughts on POASTA
- March 2024 A*PA2: Up to 19x faster exact global alignment
- January 2024 Review of refined minimizes
- January 2024 Mod-minimizers and other minimizers
- January 2024 Intro to Rust
- January 2024 Notes on bidirectional anchors
- January 2024 Notes on SsHash
- January 2024 One Billion Row Challenge
- December 2023 Perfect NtHash for Robust Minimizers
- December 2023 A*PA talk @ CWI
- December 2023 Notes on implementing Longest Common Repeat (LCR)
- November 2023 ALPACA/PANGAIA winter workshop notes
- November 2023 Notes on writing course
- October 2023 BAPCtools instruction
- September 2023 PTRHash: Notes on adapting PTHash in Rust
- September 2023 BBHash: some ideas
- September 2023 BitPAl bitpacking algorithm
- August 2023 [WIP] Bitpacking and string searching
- July 2023 Shortest paths, bucket queues, and A* on the edit graph
- July 2023 Research proposal: subquadratic string graph construction
- July 2023 Loukides, Pissis, Thankachan, Zuba :: Suffix-Prefix Queries on a Dictionary
- March 2023 DSB 2023
- December 2022 Doctoral plan
- November 2022 One Year Of Rust
- November 2022 The complexity and performance of WFA and band doubling
- November 2022 String algorithm visualizations
- November 2022 Thoughts on linear programming
- October 2022 Local Doubling
- October 2022 BWT and FM-index
- October 2022 A Combinatorial Identity
- October 2022 Tensor embedding preserves Hamming distance
- October 2022 Linear-time suffix array construction
- September 2022 Competitive Programming Lecture
- September 2022 Reducing A* memory usage using fronts
- September 2022 Speeding up A*: computational volumes and path-pruning
- September 2022 Revised Oxford Bioinformatics latex template
- August 2022 Linear memory WFA?
- August 2022 Transforming match bonus into cost
- August 2022 Paper styleguide
- August 2022 Diamond optimisation for diagonal transition
- July 2022 Bidirectional A*
- July 2022 The BiWFA meeting condition
- June 2022 A* variants
- June 2022 IGGSY 22 Slides
- April 2022 Benchmark attention points
- April 2022 Motivation
- April 2022 Proof sketch for linear time seed heuristic alignment
- April 2022 Variations on the WFA recursion
- April 2022 Glossary
- April 2022 A survey of exact global pairwise alignment
- December 2021 Pruning for A* heuristics
- November 2021 AStarix
- November 2021 Neighbour joining
- October 2021 UPGMA
- October 2021 RTFE
- October 2021 1st law of Procrastination
- October 2021 Data should be reviewed
- October 2021 Spaced K-mer Seeded Distance
- October 2021 Open Science
- October 2021 Hugo and ox-hugo
- October 2021 Hello, World!
- July 2021 Spaced k-mer and assembler methods
- July 2021 Ideas for assembling [long] reads
- July 2021 Hamming Similarity Search
- July 2021 Detached fullscreen in Sway
- July 2021 Open source contributions
- July 2021 Powersearch with Vimium
- July 2021 Wayland utilities
- July 2021 Browsing in the dark with Vimium and Dark Reader
- July 2021 Window switching in Sway
- June 2021 Clean your homedir with XDG Base Dir
- June 2021 Emacs Doom
- June 2021 Environment variables done once
- May 2021 28000x speedup with Numba.CUDA
- May 2021 X1 Extreme Gen 3 - Migrating to Wayland
- April 2021 SE Endurance: Early game
- April 2021 Hashcode 2021 Finals
- March 2021 Hashcode 2021: A lucky ride