Computational Biology | Dipartimento di Biologia – Università degli Studi di Napoli Federico II

Computational Biology Core

Coordinator: Prof. Marco Salvemini

The Computational Biology Core at the Department of Biology, University of Naples Federico II, serves as a pivotal resource for advancing biological research through computational methodologies. This core facility provides, to internal and external researchers, expertise and support in bioinformatics, data analysis, and computational modeling to enhance the understanding of complex biological systems. By integrating cutting-edge computational tools with experimental biology, the core aims to foster interdisciplinary collaborations, drive innovative research projects, and equip researchers with the necessary skills to tackle modern biological challenges.

Computational infrastructure

The Bioinformatics Core features the following computational infrastructure:

BioServer1 Hypatia

2 AMD EPYC 7552 “Zen 2” processors, 2.20 Ghz, featuring 48 cores, 96 threads
1024 Gb DDR4 RAM memory
3 Intel SSD DC P4510 Series NVMe 4Tb physical memory
1 SATA HD 2Tb physical memory

Coordinator: Dr. Giovanni Scala – giovanni.scala@unina.it

ACTIVITIES

Epigenomics Core

Epigenomics core

Coordinator: Prof. Dario Antonini

email: dario.antonini@unina.it

The epigenomics core aims to define and to identify the chromatin status and histone marks on the genome through ChIP-seq and ATAC-seq analysis.

Core activities:

Consultation on experimental design
Genome binding/occupancy profiling (ChIP-seq) analysis
Genome chromatin states/accessibility profiling (ATAC-seq) analysis
Integration, and interpretation of expression profiling (RNA-seq) using statistical models
Assistance with the preparation of manuscripts and grant proposals

Genomics Core

Genomics core

Coordinator: Prof. Marco Salvemini

email: marco.salvemini@unina.it

The genomics core at the Department of Biology at the University of Naples Federico II supports researchers and Ph.D students in the design and execution of genomic analyses in both model and non model organisms.

In particular the core provides expertise on the following analyses:

Genomic analyses on non model organisms:

Genomics analysis in new experimental models
Genomic assembly with data from long-read sequencing
Annotation of genomes
Database development for data mining of genomics and transcriptomics data

Genomic analyses on model organisms:

DNA methylation analysis
DNA variants analysis
DNA oxidation analisys

Structural Biology

Structural Biology Core

Coordinator: Dr. Bruno Hay Mele

email: bruno.haymele@unina.it

The Structural Bioinformatics Core supports the description, analysis, and prediction of protein structures, focusing on function and evolution. The core also offers expertise in modelling protein-protein interactions and evaluating _in silico_ structural and functional effects missense mutations.

The core covers:

protein structural prediction, assessment, and analysis
molecular docking (PPI and ligand)
Molecular dynamics simulations
Protein Variant effect prediction
Biochemical modelling

Systems Biology Core

Systems Biology Core

Coordinator: Dr. Giovanni Scala

email: giovanni.scala@unina.it

The Systems Biology Core at the Department of Biology at University of Naples Federico II offers researchers and Ph.D students expertise and software infrastructures for research projects and teaching classes for Ph.D and ungraduated students involving the design and validation of Systems Biology models, starting from public and in house generated data.

In particular, the core provides expertise and tools for the following activities:

Multi-omics data integration
Network biology
Development of Systems Biology models
AI based biological models

Transcriptomics Core

Transcriptomics core

Coordinator: Prof. Serena Aceto

email: serena.aceto@unina.it

The transcriptomics core at the Department of Biology at the University of Naples Federico II supports researchers and Ph.D students in the design and execution of Transcriptomics analyses in both model and non model organisms.

In particular the core provides expertise on the following analyses:

Transcriptomics analyses in non model organisms:

Analysis of RNA-seq data
De novo assembly of transcriptomes of non-model species
Transcriptome annotation and differential expression analysis
Analysis of long non-coding RNA from RNA-seq data
Variant calling analysis on RNA-seq data
Metatranscriptomics and metagenomics analysis

Transcriptomics analyses in model organisms:

Analysis of RNA-seq data
Analysis of RNA-seq single cell data

ACKNOWLEDGEMENTS

All the users and collaborators of the IMGF Facility are obligated to acknowledge it in publications as it follows: “The authors acknowledge the Computational Biology Core at the Department of Biology of University of Naples Federico II for their scientific support”.