Personal details

AndreaGuarracinoPhoto

Computer engineer working on pangenomics.

Guarracino et al., 2023, Nature
Guarracino et al., 2022, Bioinformatics

Current position

1 Nov. 2022 to Present
Postdoctoral Scholar at the University of Tennessee Health and Science Center (Memphis, USA).
Reporting to Prof. Erik Garrison.

Collaborations

1 Nov. 2023 to Present
Honorary contract holder at the Princess Máxima Center for Pediatric Oncology (Utrecht, Netherlands).
Reporting to Dr. Ruben van Boxtel and Prof. Pjotr Prins.

  • Personalized pangenome references for improved cancer genomics

1 Nov. 2022 to Present
E-Visitor at the Human Technopole (Milan, Italy).
Reporting to Prof. Nicole Soranzo and Prof. Erik Garrison.

1 Nov. 2019 to Present
Italian Institute for Genomic Medicine (Candiolo, Italy) and the Candiolo Cancer Institute (Candiolo, Italy).
Reporting to Dr. Ilio Vitale.

  • Spindle Assembly Checkpoint functionality in colon-rectal cancer stem cell

  • Exploiting karyotypic aberrations and chromosomal instability in cancer stem cells for precision immunotherapy

Employment

1 Nov. 2021 to 31 Oct. 2022 (1 year)
Postdoctoral Associate at the Human Technopole (Milan, Italy).
Reporting to Prof. Nicole Soranzo and Prof. Erik Garrison.

4 Mar. 2013 to 31 Oct. 2018 (5 years, 7 months, 28 days)
Computer engineer for multiplatform firmware/software development, GISA (Salerno, Italy).
Reporting to Eng. Gaetano Giordano.

  • Firmware development in STMicroelectronics microcontrollers for high-efficiency embedded systems

  • Firmware and library development in open-source hardware and software platforms (Arduino/Genuino)

  • Development of multi-management software and desktop applications for embedded systems programming

  • Mobile applications development for programming and the control of multi-service machines via Bluetooth

  • Implementation of proprietary communication protocols and contact/contactless (RFID) interfaces

  • Development and maintenance of websites and an e-commerce

  • Remote assistance to customers for the usage and programming of multi-service machines

  • Patent application on a universal system for services fruition (ITUA20165252, A1) (Patent)

  • Basic design of simple electrical circuits for controlling actuators and reading analog/digital signals

4 Oct. 2012 to 20 Jan. 2013 (3 months, 17 days)
Salesman, L’Erborista S.A.S. di Sarno Adele & C (Salerno, Italy).

  • Selling products, warehouse management and cleaning

1 Nov. 2010 to 3 Mar. 2013 (2 years, 4 months, 3 days)
Web Developer, Virtual (Salerno, Italy).

  • Development of dynamic websites using Java Server Page, JavaScript, ASP.NET, PHP, MySQL

Education

1 Nov. 2018 to 8 Feb. 2022
Ph.D. in Cellular and Molecular Biology (Bioinformatics), University of Rome Tor Vergata (Rome, Italy).
Supervisors: Prof. Manuela Helmer-Citterich and Dr. Ilio Vitale.
Thesis: "Investigating chromosomal instability in cancer stem cells".
Evaluation: excellent quality.

3 Oct. 2016 to 25 Oct. 2018
Master’s degree in Bioinformatics (LM-6), University of Rome Tor Vergata (Rome, Italy).
Thesis: "Energetic and functional characterization of phosphorylations involved in the co-regulation of protein interaction".
Evaluation: 110/110 cum laude; GPA: 4.00, A+.

1 Oct. 2007 to 29 Oct. 2010
Bachelor’s degree in Computer Engineering (L-8), University of Salerno (Salerno, Italy).
Thesis: "Energetic and functional characterization of phosphorylations involved in the co-regulation of protein interaction".
Evaluation: 110/110 cum laude; GPA: 4.00, A+.

Research experience

1 Nov. 2018 to 8 Nov. 2022
Bioinformatic analyses of multiomics data, University of Rome Tor Vergata (Rome, Italy).

  • Germline and somatic variants analyses on Whole-Exome sequencing (WES) data: quality control, sample matching, rRNA contamination, read trimming and mapping, variant calling, and functional prediction

  • Microsatellite instability (MSI) status on paired tumor-normal and tumor-only WES data

  • Variant calling and differential expression analyses on RNA-seq data

  • Neoantigen prediction and prioritization by integrating WES data and RNA-seq data

  • Analysis of Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data

  • Normalization and correlation analysis of transcriptomic microarray data (Affymetrix)

  • Proteomic and phosphoproteomic analyses of Reverse Phase Protein microarray (RPPA) data

  • RNA structural characterization and conservation research (Pietrosanto, Adinolfi, Guarracino et al., 2021)

  • Web server development for RNA sequence and structure motif scan (Guarracino et al., 2021)

  • Energetic and functional analyses of phosphorylations applied in silico on 3D structures of protein complexes

  • Cox modeling and survival analysis on patient cohorts (from TCGA and cBioPortal platforms)

  • Basic procedures on High Performance Computing (HPC) machines

5 Apr. 2020 to 21 Sept. 2022
Previous software development for pangenomics.

  • Workflow development of a public sequence resource for on-the-fly analyses ( bh20-seq-resource)

  • Development of a pangenome graph browser ( Pantograph)

Teaching

Time Course Role Links

26 Oct. 2020 to Present

Data Structures for Bioinformatics (2 CFU/ECTS), Master’s degree in Bioinformatics, University of Rome Tor Vergata (Rome, Italy)

Teacher, created new material, held all the lessons, assisted the students, did final exams

Material

13 Nov. 2023 to 17 Nov. 2023

Pangenome & RefGraph Workshop by H3ABioNet (Cape Town, South Africa)

Instructor, created new material and analyzed new human genome assemblies

Material
Invitation

8 Oct. 2023 to 12 Oct. 2023

Complex Trait Community & Rat Genome CTC-RG2023 (Memphis, USA)

Organizer and instructor, created new material for the Pangenome workshop

Website

30 May 2023 to 2 June 2023

MemPanG23 Pangenomics, University of Tennessee Health and Science Center (Memphis, USA)

Organizer, instructor and chair, created new material and tutorials, held some lessons, assisted the participants, configured the virtual machines

Website
Material
Certificate

28 Feb. 2023 to 28 Feb. 2023

Advanced Bioinformatics: Data Mining and Data Integration for Life Science (1.5 CFU/ECTS), Master’s degree, Utrecht Bioinformatics Center (Utrecht, Netherlands)

Teacher, introducing pangenomics and PGGB (PanGenome Graph Builder)

Website

23 May 2022 to 27 May 2022

CPANG22 Computational PANGenomics, Instituto Gulbenkian de Ciência (Oeiras, Portugal)

Instructor, created new material and tutorials, held some lessons, assisted the participants

Website
Material
Poster
Certificate

2018 to 2021

Bioinformatics (6 CFU/ECTS), Bachelor’s degree in Biological Science, University of Rome Tor Vergata (Rome, Italy)

Tutor, reviewed the practical lessons, assisted the students

Certificate

16 Dec. 2019 to 29 Mar. 2021

Computational Proteogenomics (2 CFU/ECTS), Master’s degree in Bioinformatics, University of Rome Tor Vergata (Rome, Italy)

Exam assistant

Page 1

7 June 2019 to 21 July 2021

Molecular Biology (8 CFU/ECTS), Bachelor’s degree in Biological Science, University of Rome Tor Vergata (Rome, Italy)

Exam assistant

Page 1

7 June 2019 to 21 July 2021

Bioinformatics (6 CFU/ECTS), Bachelor’s degree in Biological Science, University of Rome Tor Vergata (Rome, Italy)

Exam assistant

Page 1

Mentoring

Time University Thesis Links

2 Sept. 2021 to 20 Apr. 2022

Master’s degree in Bioinformatics, University of Rome Tor Vergata (Rome, Italy)

Machine learning to automatically detect the C. elegans bodies from microscope images and measure their growth over time

Page 3

20 Apr. 2021 to 02 Nov. 2021

Bachelor’s degree in Biological Science, University of Rome Tor Vergata (Rome, Italy)

Analysis of the effect of SARS-CoV-2 mutations on the pairing between the viral genome and human miRNAs

Page 3

28 Apr. 2020 to 5 Nov. 2020

Bachelor’s degree in Biological Science, University of Rome Tor Vergata (Rome, Italy)

Analysis of repeated sequences in lincRNA candidates for exon shuffling

Page 3

9 Mar. 2020 to 12 Mar. 2021

Master’s degree in Bioinformatics, University of Rome Tor Vergata (Rome, Italy)

Machine Learning methods applied to kinase-substrate interaction prediction

Page 3

2 Mar. 2020 to 17 Dec. 2020

Master’s degree in Bioinformatics, University of Rome Tor Vergata (Rome, Italy)

Natural Language Processing techniques for protein encoding applied to phosphorylation prediction

Page 3

13 Dec. 2019 to 11 June 2020

Bachelor’s degree in Biological Science, University of Rome Tor Vergata (Rome, Italy)

Study of normalization techniques' effects in gene expression correlation analyses

Page 3

Invitations

Time Place Description Links

14 Sept. 2023 to 16 Sept. 2023

Joint Meeting AGI-SIMAG, Cortona, Italy

Invited speaker on "Heterologous recombination in the human pangenome"

Invitation
Brochure

13 Sept. 2023

University of Salerno

Seminar on "Heterologous recombination in the human pangenome"

Invitation

Publications

*first authorship

Journal Title Contribution Links

bioRxiv, In review

*Building pangenome graphs

Software development, experiments, paper writing, documentation, testing

Preprint

bioRxiv, Submitted

*Pangenome graph layout by Path-Guided Stochastic Gradient Descent

Algorithm implementation and evaluation, paper writing

Preprint

None, Submitted

Global diversity, recurrent evolution, and recent selection on amylase structural haplotypes in humans

Pangenome graph analsysis, genome assembly, manuscript writing and editing

None

Genome Biology, Accepted

A reference-unbiased super-pangenome of the North American wild grape species (Vitis spp.) reveals genus-wide association with adaptive traits

Support for pangenome graph building and read mapping against the graph

Preprint

bioRxiv, Submitted

The complete human diploid reference genome of RPE-1 identifies the phased epigenetic landscapes from multi-omics data

Support for the analyses and figures, Figure 2, paper writing

Preprint

Nature, 2023

The complete sequence of a human Y chromosome

Variants and Liftover

Paper

Frontiers in Genetics, 2023

Pangenome Graphs in Infectious Disease: A Comprehensive Genetic Variation Analysis of Neisseria Meningitidis leveraging Oxford Nanopore long reads

Pangenomic analyses and support, paper editing

Paper

Nature, 2023

*Recombination between heterologous human acrocentric chromosomes

Pangenomic analyses, Figures from 1 to 5, paper writing

Paper

Nature, 2023

A draft human pangenome reference

Paper editing, pangenome graph creation and visualization, population genetic analysis

Paper

Bioinformatics, 2023

Optimal gap-affine alignment in O(s) space

Testing, evaluation, Figure 2

Paper

Bioinformatics, 2022

Unbiased pangenome graphs

Parallelization of a bottleneck, bug fixings, experiments in multiple species

Paper

Nature, 2022

Semi-automated assembly of high-quality diploid human reference genomes

Pangenome alignments, Jaccard, PCA and MHC analyses, Figure 2

Paper

Nature Immunology, 2022

Type I IFNs promote cancer cell stemness by triggering the epigenetic regulator KDM1B

Figure 6.a, 7.a, and 7.b, contributed for Figure 6.c, 6.e, performed RNA-seq, ATAC-seq, microarray data analysis, correlation analyses, TF-binding motif enrichment, survival analyses

Paper

Bioinformatics, 2022

*ODGI: understanding pangenome graphs

Paper and documentation writing, figures and table, implemented several tools

Paper

Non-coding RNA Research, 2022

Evaluation of potential miRNA sponge effects of SARS genomes in human

Genome sequences collection, filtering, deduplication, alignment, variant calling

Paper

Nucleic Acids Research, 2021

*BRIO: a web server for RNA sequence and structure motif scan

Paper writing, figures and table, refactored and completed the webserver, datasets refinement

Paper
Webserver
Repository

Communications Biology, 2021

Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis

Differential expression analyses, including batch effects exploration, GO/pathway enrichment analyses

Paper
Repository

Cancers, 2021

The Targeting of MRE11 or RAD51 Sensitizes Colorectal Cancer Stem Cells to CHK1 Inhibition

Figure 1.A, helped in analyzing survival data

Paper

Cell Death & Disease, 2021

Inhibition of HECT E3 ligases as potential therapy for COVID-19

Figure 4, in silico 3D structures analysis

Paper

NAR Genomics & Bioinformatics, 2021

*Relative Information Gain: Shannon entropy-based measure of the relative structural conservation in RNA alignments

Paper writing, contributed to Figure 2, made Figure 3, 4, and 5, and fixed, refactored and completed the framework

Paper
Repository

Cell Death & Disease, 2021

Control of replication stress and mitosis in colorectal cancer stem cells through the interplay of PARP1, MRE11 and RAD51

Bioinformatics support

Paper

Awards

Time Place Description Amount Links

5 July 2022

International Genome Graph Symposium 2022

Student Travel Grant

600 CHF (632.36 EUR)

Certificate

Talks & Posters

Time Conference Title Links

23 July 2023 to 27 July 2023

Society for Molecular Biology & Evolution 2023 (SMBE23)

Recombination between heterologous human acrocentric chromosomes

Poster
Certificate

23 July 2023 to 27 July 2023

Society for Molecular Biology & Evolution 2023 (SMBE23)

Building a Pangenome Graph for the HXB/BXH Recombinant Inbred Rat Strain Family: Enhanced Discovery of Complex Variants and Validation with Sanger Sequencing

Poster
Certificate

29 Sept. 2022 to 30 Sept. 2022

Complex Trait Community and the Rat Genomics 2022

Initial effort in generating a rat pangenome

Abstract

4 July 2022 to 7 July 2022

International Genome Graph Symposium 2022

Chromosome communities in the human pangenome

Presentation

2 Nov. 2021 to 4 Nov. 2022

3D-BioInfo 2021

RNA secondary structure motifs involved in the interaction with RNA binding proteins

Abstract

27 Sept. 2021 to 1 Oct. 2021

Biodiversity Genomics 2021

Chromosome communities in the human pangenome

Abstract
Presentation

21 Sept. 2021 to 24 Sept. 2021

AGI2021 Congress

A pangenome for the expanded BXD family of mice

Abstract
Poster

6 Sept. 2021 to 8 Sept. 2021

German Conference on Bioinformatics 2021

ODGI: scalable tools for pangenome graphs

Abstract
Presentation

9 June 2021 to 12 June 2021

EACR 2021

Control of replication stress and mitosis in cancer stem cells

Abstract
Poster

20 May 2021 to 21 May 2021

EMBL in Italy 2021

Identification of RNA sequence and structure motifs for protein interaction

Poster

11 May 2021 to 14 May 2021

The Biology of Genomes 2021

Identification of RNA sequence and structure motifs for protein interaction

Abstract
Poster

11 May 2021 to 14 May 2021

BBCC2021

Population genomics analyses on pangenome graphs

Abstract
Presentation (f1000research link)

28 Sept. 2020 to 1 Oct. 2020

EG VCBM 2020

Graph Layout by Path-Guided Stochastic Gradient

Abstract
Presentation

21 Sept. 2020 to 23 Sept. 2020

T2T-HPRC-Virtual Conference 2020

Graph Layout by Path-Guided Stochastic Gradient

Abstract
Presentation

21 Sept. 2020 to 23 Sept. 2020

T2T-HPRC-Virtual Conference 2020

Scalable Variant Detection In Pangenome Models

Abstract
Presentation
Blog

17 July 2020 to 25 July 2020

BCC 2020

COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource

Abstract
Poster
Presentation

13 July 2020 to 16 July 2020

ISMB 2020

Pantograph: Scalable Interactive Graph Genome Visualization

Abstract
Poster

13 July 2020 to 16 July 2020

ISMB 2020

Semantic Variation Graphs - A Pangenome Ontology

Abstract
Poster
Best Poster Prize
Citation

13 July 2020 to 16 July 2020

ISMB 2020

Comprehensive analysis of human SARS-CoV-2 infection and host-virus interaction

Abstract
Poster

Courses

Time Place Title Links

17 July 2023 to 21 July 2023

Lorentz Center, Leiden, Netherlands

A multidisciplinary approach to epistasis detection

Poster

08 July 2020

Enago academy, Virtual

Overcoming Challenges in Academic Writing: Tips for Writing Articles and Grant Applications

Certificate

21 Apr. 2018

English language certification

English Speaking Board (ESB) Level 1 (B2 CEFR), Pass with distinction

Certificate

27 Sept. 2017 to 29 Sept. 2017

University of Salerno

Best practices for RNA-Seq data analysis - ELIXIR-IIB

Website
Certificate
Repository

Misc

Time Info What Links

20 Oct. 2020 to Present

Human Pangenome Reference Consortium

Associate Member of the Human Pangenome Reference Consortium

Collection

09 July 2021

University of Rome Tor Vergata

Chair at the "Deciphering the complexity in neurodegeneration and cancer" workshop

Poster

07 June 2020 to 30 Aug. 2020

Google Summer of Code (GSOC)

Helper for the "Parallel Graph Traversal for Variation Graphs" project

Blog

20 June 2020

Lemonde/binaire

Quote in the newspaper Le Monde: SARS-CoV-2 et Covid-19

Blog