Ilya E. Vorontsov

Inferring binding specificities of human transcription factors with the wisdom of crowds

The paper benchmarks methods for inferring transcription factor binding specificities using a large community challenge and finds deep learning models outperform traditional methods, though positional weight matrices are competitive.

EPIC: An open community challenge for sequence-based prediction of transcription initiation in five non-model metazoans

EPIC challenges teams to predict transcription initiation from DNA sequence in non-model metazoans, aiming to assess generalizability beyond human and model species.

Identification of methylation-sensitive human transcription factors using meSMiLE-seq

This study identifies DNA binding motifs for 98 human transcription factors using meSMiLE-seq, revealing methylation-sensitive binding preferences for some TFs.

GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors

The paper uses GHT-SELEX to show many human TFs have high intrinsic sequence specificity and complex DNA binding, often matching in vivo ChIP-seq results.

Classic machine learning on top of multiple position weight matrices improves genomic prediction of transcription factor binding sites

ArChIPelago combines multiple PWMs using classic machine learning to improve TFBS prediction, outperforming individual PWMs and other models across species.

Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors

The paper evaluates cross-platform DNA motif discovery tools using 4,237 experiments to identify reliable transcription factor binding motifs and highlights challenges in motif detection.

GAME: Genomic API for Model Evaluation

GAME provides a standardized framework for benchmarking genomics models across tasks, enabling consistent evaluation and community contributions.

Extensive binding of nebulous human transcription factors to genomic dark matter

The paper identifies genomic binding sites of 166 poorly characterized human transcription factors, revealing that some bind to dark matter DNA and others to regulatory regions.

Codebook: sequence specificity and genomic binding of poorly-characterized human transcription factors

The paper systematically determines the sequence specificity of 332 poorly characterized human transcription factors, identifying over 4,000 experiments and revealing tens of thousands of new TF binding sites.

Landscape of allele-specific transcription factor binding in the human genome

The paper identifies allele-specific transcription factor binding events across the human genome using ChIP-Seq data, revealing regulatory variants linked to disease and molecular mechanisms.

Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping

The paper functionally annotates human long non-coding RNAs by systematically knocking down 285 lncRNAs and analyzing molecular phenotypes using CAGE sequencing.

Enhanced C/EBPs binding to C>T mismatches facilitates fixation of CpG mutations

The paper identifies enhanced C/EBP binding to C>T mismatches as a mechanism for selective accumulation of [C>T]G mutations in transcription factor binding sites.