Filip Nemčko

A reasoning LLM combining ESM3 embeddings with GO-GPT term predictions produces protein function annotations that experts rated tie-or-better than UniProt in 79% of cases (SFT model).

The paper identifies Hcfc1 as a CGI-specific co-activator that bridges transcription factors to TFIID, revealing a promoter-class-specific activation mechanism for CGI promoters.

The paper shows that the Drosophila Piwi-piRNA pathway silences transposons by degrading their RNA via the nuclear exosome, with TEsup proteins facilitating this process.

ORFtag enables proteome-scale tagging and functional screening in mammalian cells, identifying known and novel regulators of transcription and post-transcriptional processes.

The paper shows that different promoter classes use distinct PIC compositions and mechanisms, leading to focused or dispersed transcription initiation patterns in Drosophila.

The paper identifies and characterizes repressive domains in Drosophila transcription factors using a new high-throughput method, revealing conserved motifs and co-repressor interactions.