Past, ongoing, and future research plans

Some lists of ongoing work to keep things organised for myself.

Upcoming journal papers Link to heading

• Sassy (Beeloo and Groot Koerkamp 2025): submitted to bioinformatics
• Deacon (Constantinides, Lees, and Crook 2025): to be submitted
• Barbell (Beeloo et al. 2025): to be submitted
• Mim (Patro et al. 2025): to be submitted
• Sassy v2: to be finished and submitted (maybe WABI/Recomb-seq?)

Upcoming conference papers Link to heading

• QuadRank: SEA (Jan 23)
• QuickHeap: SEA (Jan 23)? ESA B (April)?
• Chaining: WABI (May)? Recomb-Seq (March)?
• SimdSketch: WABI (May)? Recomb-Seq (March)?
• Small-k minimizers: WABI (May)?
• k-PHF hashmap: ESA B (April)

Upcoming conference dates & deadlines Link to heading

Sorted by CfP deadline.

• Recomb:
  • CfP: Nov 7 2025 (full paper: Nov 14)
  • May 26-29 2026, Thessaloniki, Greece
• DSB:
  • CfP: Jan 9 2026
  • Feb 18-19 2026, Venice, Italy
• HiTSeq:
  • CfP: proceedings: Jan 20, 2026, abstract: April 9, 2026, poster: May 7, 2026
  • ISMB: July 12-16, Washington DC
• SEA:
  • CfP: January 23, 2026
  • June 22-24 2026, Copenhagen, Denmark
  • papers: QuadRank, (QuickHeap)
• Recomb-Seq:
  • CfP: Proceedings: March 12 2026, Short talks / posters: ~March 2026
  • May 24-25 2026, Thessaloniki, Greece
• ESA:
  • CfP: ~April
  • September 0-4 2026, L’Aquila, Italy
• WABI:
  • CfP: ~May
  • September 0-4 2026, L’Aquila, Italy

Dormant Link to heading

• Minimizers:
  • publish the anti-lex scheme?
  • continue investigation of greedymini to develop ‘understandable’ equivalent schemes.
  • Find exact optimal schemes for all \(k\equiv 1\pmod w\)
  • lower bound for local schemes

Code:

• sshash-rs (gh)
• suffix array searching (gh, post) (Bahne et al. 2019)

Long term plans Link to heading

If anything here interests you, feel free to reach out for collaborations.

• engineer STPD (Becker et al. 2025): write a highly optimized implementation.
  • minimizer space?
  • fuzzy version by only using minimizer start positions?
• Optimal CPU/memory performance given 3D latency and cooling constraints.
• Pairwise alignment review paper based on thesis chapter 2 (this post).
  • Review on approximate string matching, this post (will never happen).
• Minimizers review paper based on thesis part 2 (this post).

Abandoned Link to heading

• Affine A*PA2: too much of an overhaul.
• Spaced $k$-mer similarity: see this post.
• Expected linear time A*PA: see a draft in this post.
• Linear memory WFA: Instead of storing furthest reaching points for all wavefronts, it is sufficient to only store critical points where paths split/merge. This should lower memory usage of WFA to close to linear, without needing BiWFA. See this post. This has similar vibes to TALCO (Walia et al. 2024).
• Local doubling: see this post.

References Link to heading