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KDM: embedding DNA/RNA motifs and sequences in a shared k-mer space for unified discovery, analysis and binding prediction
Motif discovery and binding-site prediction in DNA and RNA sequences are central tasks in regulatory genomics, yet the methodological landscape is split between interpretable but rigid position weight matrices (PWMs) and high-performing but opaque machine-learning models. We present KDM, a unifying framework in which both motifs and sequences are represented as probability distributions over a shared k-mer dictionary, embedded via the Hellinger transformation. This common geometry enables...
The anti-lexicographic SUS-anchor: a near-optimal k=1 sampling scheme
Announce Type: new Abstract: In recent years, there has been a renewed interest in the search for low density minimizer schemes. These schemes take a window of $w$ consecutive $k$-mers, and sample one of them: the smallest under some specific order. Schemes such as the mod-minimizer provide a low density (fraction of sampled $k$-mers) when $k \gg w$, while schemes such as the greedy minimizer work well for explicit small parameters roughly in the regime $k \leq 2w$, for $k$ and $w$ up to...
The anti-lexicographic SUS-anchor: a near-optimal k=1 sampling scheme
arXiv:2606.01190v2 Announce Type: replace Abstract: In recent years, there has been a renewed interest in the search for low density minimizer schemes. These schemes take a window of $w$ consecutive $k$-mers, and sample one of them: the smallest under some specific order. Schemes such as the mod-minimizer provide a low density (fraction of sampled $k$-mers) when $k \gg w$, while schemes such as the greedy minimizer work well for explicit small parameters roughly in the regime $k \leq 2w$,...
Fragmentation Patterns of Human Telomeric Chromatin in Plasma cfDNA
The unique chromatin structure at telomeres protects the linear ends of chromosomes from DNA surveillance machineries. Here, we demonstrate that circulating cell-free DNA (cfDNA) from plasma can map chromatin structure at telomeres. We find that the telomeric 6-mer repeats (TTAGGG/CCCTAA) are the most abundant circulating 6-mers in cfDNA.
D-Day 82nd anniversary honoured in France
World leaders and the last remaining veterans gathered in Normandy on Saturday to mark the 82nd anniversary of the D-Day landings. Commemorations in Langrune-sur-Mer and Colleville-sur-Mer paid tribute to the 160,000 Allied troops who launched the liberation of Europe in 1944.
$p$-adic Bi-Filtrations for Topological Machine Learning on Genomic Sequences
arXiv:2606.06117v1 Announce Type: cross Abstract: We introduce pVR, a topological machine learning framework for alignment-free genomic sequence classification that combines $p$-adic numbers with topological data analysis. Each DNA sequence is encoded along two complementary axes: a $p$-adic distance on $k$-mer prefixes, which captures hierarchical positional structure, and a compositional $L_1$ distance on $k$-mer frequencies, which captures local sequence content. The two distances jointly...
Residents of French village say US Defense Secretary Hegseth not welcome for D-Day visit
Residents of French village say US Defense Secretary Hegseth not welcome for D-Day visit US Defense Secretary Pete Hegseth on Saturday marked the 82nd anniversary of the World War II D-Day landings with a visit to Normandy, but did not attend the international ceremony hosted in Langrune-sur-Mer. Residents said his "warlike views" were unwelcome in their village and questioned his commitment to "democratic values". US Defense Secretary Pete Hegseth on Saturday travelled to Normandy to...
First AI-designed ‘universal vaccine’ tested in humans
First AI-designed ‘universal vaccine’ tested in humans The experimental jab is intended to target a wide range of viruses, including those behind deadly outbreaks like Sars, Mers and Covid-19 A vaccine targeting a broad range of viruses that was designed using artificial intelligence had a “modest” effect on immune systems in a small, early trial, according to a new study. The trial marks the first time a vaccine whose active ingredient was entirely designed by AI has been tested in humans,...
Bullion movement: Gold prices to track US–Iran peace talks, Fed signals and key data releases this week
In the upcoming week, gold prices will be shaped by developments in US–Iran peace negotiations, movements in crude oil rates and a series of macroeconomic data releases. Analysts have said that speeches by officials of the US Federal Reserve could also play a key role in shaping interest rate expectations, which in turn may guide the near-term direction of bullion prices. "Momentum for precious metals such as gold and silver still looks sideways to corrective," Pranav Mer, Vice President,...
In D-Day speech, Hegseth urges Europe to counter ‘invasion’ of migrants
US Defence Secretary Pete Hegseth on Saturday urged Europe to counter what he termed an “invasion” of its coastline by migration, as he marked the 82nd anniversary of the World War II D-Day landings in northern France. Hegseth also called on European countries to do more to contribute to their defence, in a speech at the American military cemetery in Colleville-sur-mer in Normandy. He was however conspicuously set to skip the main international ceremony marking the anniversary of the...