Danny A. Bitton

Ovo, an Open-Source Ecosystem for De Novo Protein Design

Ovo provides an open-source platform for de novo protein design, integrating tools, workflows, and visualization to simplify and scale the design process.

InCytokine, an open-source software, reveals a TREM2 variant specific cytokine signature

InCytokine is an open-source tool for analyzing cytokine and chemokine data from protein arrays, revealing genotype-specific signatures in TREM2 variants.

SPACE: multimodal spatial CRISPR screening with whole-transcriptome readout at subcellular resolution in 3D models

SPACE enables spatial CRISPR screening with whole-transcriptome and protein readouts at subcellular resolution, revealing novel regulatory mechanisms in tumor microenvironments.

AnNoBrainer, an Automated Annotation of Mouse Brain Images using Deep Learning

AnNoBrainer automates mouse brain image annotation using deep learning, improving accuracy, reproducibility, and efficiency compared to manual methods.

mRNAid, an Open-Source Platform for Therapeutic mRNA Design and Optimization Strategies

mRNAid is an open-source software that optimizes mRNA sequences to reduce immunogenicity, improve stability, and enhance protein output.

TraceTrack, an Open-Source Software for Batch Processing, Alignment and Visualization of Sanger Sequencing Chromatograms

TraceTrack is an open-source tool for batch processing, aligning, and visualizing Sanger sequencing chromatograms, offering improved functionality over existing software.

PepSeA: Peptide Sequence Alignment and Visualization Tools to Enable Lead Optimization

PepSeA provides tools for peptide sequence alignment and visualization to support lead optimization in drug discovery.

BioPhi: A platform for antibody design, humanization and humanness evaluation based on natural antibody repertoires and deep learning

BioPhi provides automated tools for antibody humanization and humanness evaluation using deep learning and natural antibody repertoires, achieving results comparable to human experts.

BioCompute Objects to communicate a viral detection pipeline with potential for use in a regulatory environment

The paper presents BioCompute Objects (BCOs) as a standardized framework for communicating computational analyses, demonstrating their use in a viral detection pipeline for regulatory environments.

Mutation Maker, An Open Source Oligo Design Platform for Protein Engineering

Mutation Maker is an open-source tool for designing mutagenic oligos in protein engineering, enabling efficient and accurate library creation for both random and directed mutagenesis.

A Deep Learning Genome-Mining Strategy Improves Biosynthetic Gene Cluster Prediction

This paper introduces DeepBGC, a deep learning method for improved biosynthetic gene cluster prediction, uncovering previously undetectable clusters with potential novel biological activities.

Fitness Landscape of the Fission Yeast Genome

The paper uses transposon mutagenesis and a hidden Markov model to identify functional elements in the fission yeast genome, finding that 90% of the genome has fitness consequences.

Long non-coding RNA repertoire and regulation by nuclear exosome, cytoplasmic exonuclease and RNAi in fission yeast

The paper identifies 5775 novel lncRNAs in fission yeast and characterizes their regulation by RNA-processing pathways.

Cdk9, Spt5 and histone H2B mono-ubiquitylation cooperate to ensure antisense suppression by the Clr6-CII/Rpd3S HDAC complex

The paper investigates the interaction between Cdk9, H2Bub1, and the Clr6-CII HDAC complex in regulating antisense and sense transcription in fission yeast.