Diego di Bernardo

Carbon-A annotates protein-coding genes across eukaryotic genomes using a large encoder model, achieving high accuracy and enabling the creation of a comprehensive annotation database.

The paper introduces CO_SCPLOWARBONC_SCPLOW, a family of efficient DNA language models that address challenges in genomic sequence modeling by adapting LLM techniques to DNA's unique properties.

The paper introduces CRISPRaTOR, a biomolecular circuit that maintains constant gene expression across varying conditions using CRISPR technology and synthetic domains.

This paper introduces a method to design high-performance mammalian whole-cell biosensors by integrating synthetic biology and control engineering, resulting in a versatile biosensor named CASense.

The paper introduces the CASwitch, a synthetic gene circuit that reduces leakiness while maintaining high inducible gene expression using mathematical modeling and experimental validation.

The paper evaluates deconvolution methods for bulk RNA-Seq using scnRNA-Seq data, identifies biases, and introduces SQUID, a method that outperforms others in predicting cell mixtures and identifying cancer subclones.

The paper identifies RNA editing sites in human retinal transcriptomes and links editing QTLs to retinal diseases.

The paper creates a breast cancer cell line atlas to study tumour heterogeneity and drug response by integrating single-cell data with bulk gene expression and drug screening results.

The paper identifies widespread transcription initiation at microsatellites across species and develops deep learning models to predict STR-associated transcription and its impact on disease variants.

This paper develops a cyber-genetic system to achieve long-term cell cycle synchronization in yeast using closed-loop feedback control.

DECCODE identifies small molecules that enhance cell reprogramming and conversion using transcriptional data and drug profiles.

ChipSeg segments bacterial and mammalian cells in microfluidic devices using thresholding, enabling fluorescence quantification and cell tracking in time-lapse experiments.

This paper proposes a strategy to synchronize yeast cell cycles using quorum sensing, modeled with ordinary differential equations.

The paper designs control strategies to synchronize yeast cell cycles using methionine levels, validated both in silico and experimentally.

The paper develops a dual-input system to dynamically regulate gene expression and protein stability in mouse embryonic stem cells, enabling precise control of protein levels and faster response times.

This paper develops and evaluates feedback control strategies to synchronize the cell cycle in yeast populations while minimizing volume growth.

gene2drug prioritizes drugs based on their impact on transcriptional pathways of target genes, validated both computationally and experimentally for two drug repositioning cases.

The paper integrates drug chemical structures with transcriptional responses to identify noisy responses and a transcriptional signature for phospholipidosis.