Computational biologist · Research software engineer

Post-Doctoral Research Fellow
Centre for Regenerative Medicine “Stefano Ferrari”
University of Modena and Reggio Emilia

📫 Email: serena.rosignoli@unimore.it
🔗 LinkedIn: Serena Rosignoli
📚 Publications: Google Scholar

Below is the “shopping-list” style of the things I've worked on, I know you do not really care, just contact me if curious. Random chats are the best.

User-facing platform for protein modelling and structural bioinformatics inside PyMOL.

PyMod integrates sequence analysis, structure prediction, homology modelling, and structural analysis into a graphical molecular-modelling environment.

Through this project, I worked on:

• user-facing workflow design
• integration of external modelling tools
• sequence/structure data handling
• graphical interface logic
• automation of complex modelling protocols
• making structural bioinformatics workflows accessible to non-specialist users

Repository: PyMod

Plugin-based software for molecular docking workflows in PyMOL.

DockingPie was developed to make molecular docking protocols easier to run, compare, and interpret from a unified graphical interface.

Through this project, I worked on:

• plugin architecture
• command-line tool integration
• input/output standardization
• graphical workflow design
• docking protocol automation
• usability-oriented scientific software development

Repository: DockingPie
Publication: Bioinformatics paper

PyMOL plugin for protein contact network analysis.

PyPCN supports the analysis of protein structures as residue-interaction networks, helping users explore structural relationships through graph-based representations.

Through this project, I worked on:

• structural data parsing
• network construction from molecular structures
• PyMOL-integrated visualization
• user-oriented analysis workflows
• scientific plugin development

Repository: PyPCN
Publication: Bioinformatics paper

AlPaCas is a web server and computational pipeline for designing allele-specific CRISPR/Cas strategies.
In practice: start from a mutation, encode the biological constraints, search for usable designs, rank them, and make the result readable enough for people who do not want to inspect every guide by hand.

Publication: Nucleic Acids Research paper

sequence analysis · scoring logic · web server · gene editing

Deep-learning framework for protein classification.

G4REP predicts human RNA G-quadruplex-binding proteins using sequence-based information and deep-learning models.

Publication: Bioinformatics paper

Reproducible pipelines to understand what machine-learning models use when making predictions on molecular systems.
Current focus: attribution methods, stability checks, faithfulness tests, benchmarking, and less hand-wavy ways to decide whether an explanation is actually useful.

Integrated Gradients · model evaluation · benchmarking · reproducibility

Integration of protein design models into practical modelling workflows, including the annoying-but-important details: which residues are designable, which ones must stay fixed, how to run the model, parse the outputs, and bring generated sequences/structures back into the working environment.

ProteinMPNN · LigandMPNN · workflow design · output parsing

Extension of the same logic toward base editing: enumerate guides, map editing windows, check bystander effects, score the designs, and produce outputs that are useful before anyone starts ordering reagents.

CBE/ABE · editing windows · bystander risk · guide ranking

Scripts for molecular dynamics simulations when they need to behave on real systems and real clusters.
Current obsession: checkpointing, clean restarts, SLURM jobs that survive the mood of the node, and analysis scripts that make trajectories easier to inspect.

OpenMM · SLURM · checkpointing · trajectory analysis

Small utilities, examples, and scripts for PyMOL-based development.

Includes:

• PyMOL environment utilities
• plugin-development examples
• threading examples for PyQt/PyMOL plugins
• workflow helpers for structural bioinformatics

Repository: PyMOL toolbox

Slides and teaching material from lectures, workshops, and summer schools.

Topics include:

• molecular docking
• PyMOL and plugin-based modelling
• structural bioinformatics
• protein modelling
• bioinformatics for non-specialists
• data analysis concepts

Repository: Lectures and teaching material

A collection of Python scripts and examples for bioinformatics workflows, data processing, and structural analysis.

Repository: Bioinfo Python toolbox

Programming assignments and algorithmic exercises developed while completing the Stanford Algorithms Specialization.

Repository: Algorithms Specialization