Timothe Rouze
@tmthrz.bsky.social
PhD student in computational biology in Lille.
Just submitted my PhD thesis on algorithms for fast, large-scale k-mer-based sequence analysis. It's now available to read at phd.martayan.org Take a look and feel free to share! #Bioinformatics #PhDone
Algorithm design and implementation for the scale of sequencing data
phd.martayan.org
When utilized in literature review, LLMs consistently 1. fail to mention female authors in female-led literatures, 2. insist that men are more influential or more heavily cited when this is contradicted by objective citation counts, and 3. attribute women’s work to hallucinated male scholars.
one anecdote: I was searching for a link to one of my old papers on Google, and the automated Gemini summary attributed all of my lab's work to my husband
Mel Andrews@bayesianboy.bsky.social · 2mo agoWhen utilized in literature review, LLMs consistently 1. fail to mention female authors in female-led literatures, 2. insist that men are more influential or more heavily cited when this is contradicted by objective citation counts, and 3. attribute women’s work to hallucinated male scholars.
🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12
Fast Set Operations for Compact k-mer Sets https://www.biorxiv.org/content/10.64898/2026.05.24.727514v1
Preprint alert! TLDR: Super Bloom is a Bloom-filter variant for streaming k-mer queries. It uses minimizers to group adjacent k-mers into super-k-mers and map them to the same memory block. Result: much better locality, faster queries, and with the findere trick, dramatically fewer false positives.
doi.org
Super Bloom: Fast and precise filter for streaming k-mer queries https://www.biorxiv.org/content/10.64898/2026.03.17.712354v1
Inverted colored de Bruijn Graph for practical kmer sets storage https://www.biorxiv.org/content/10.64898/2025.12.08.692073v1
Preprint Alert! With @tmthrz.bsky.social and @rayanchikhi.bsky.social we aim to tackle practical unitigs compression! A thread:
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 8mo agoInverted colored de Bruijn Graph for practical kmer sets storage https://www.biorxiv.org/content/10.64898/2025.12.08.692073v1
REINDEER2: practical abundance index at scale https://www.biorxiv.org/content/10.1101/2025.06.16.659990v1
The sequence analysis session of #RECOMB2025 is off to a great start with @jimshaw.bsky.social presenting devider, a new algorithm for haplotyping small sequences from long-read sequencing. www.biorxiv.org/content/10.1...
@camillemrcht.bsky.social is back on stage to present Vizitig, an interactive visualization tool for sequencing datasets developped by @bdegardins.bsky.social
Now our @tmthrz.bsky.social presenting his approach for compressing collections of unitigs - Rayan Chikhi 🤝🏻 @npmalfoy.bsky.social
link.springer.com/article/10.1... our article on large scale comparison of datasets in a Minhash-like setting, but for heterogenous document sizes AND keeping lexicographic information, is out in AMB. By @tmthrz.bsky.social @imartayan.bsky.social @camillemrcht.bsky.social @npmalfoy.bsky.social
Fractional hitting sets for efficient multiset sketching - Algorithms for Molecular Biology
The exponential increase in publicly available sequencing data and genomic resources necessitates the development of highly efficient methods for data processing and analysis. Locality-sensitive hashi...
link.springer.com
