Stefano Berri, Ph.D.
Software engineer

I have developed Pelops, a dedicated caller for DUX4 rearrangements from whole genome sequencing data, published as a Python package.

My interests are in extreme programming, genomics, molecular biology, tumour evolution and reproducible science.

Brief resume

2022-present: Software engineer at Illumina.

2013-2022: Bioinformatics scientists at Illumina.
My role bridged between software development and data analysis. I wrote tools and apps to analyse and visualise genomic data from tumour samples as well as track associated metadata.

2009-2013: Post-doc position at Leeds institute of Molecular Medicine, University of Leeds.
In collaboration with Dr Arief Gusnanto and Dr Henry Wood, I have developed a method, CNAnorm, to use very low coverage high throughput sequencing data (Illumina) to estimate Copy Number Alterations (CNA) in patients’ tumour. In particular, we took advantage of the linearity between depth of coverage and CNA to estimate ploidy and tumour content in clinical samples. We have produced a Bioconductor package.

2006-2009: Post-doc position at School of Computing, University of Leeds.
I was involved in a multidisciplinary project aiming at modeling the locomotion of the nematode worm Caenorhabditis elegans. My role was both experimental and computational. Here I acquired most of my computational skills.

2002-2006: Ph.D in Genetics and Biomolecular sciences at the Department of Biomolecular Sciences and Biotechnology, University of Milan. I performed a phylogenetic and functional characterization of a family of plant transcription factors (WRKY) in rice using custom oligo microarrays.

Selected publications in peer reviewed journals

Samman M, Wood HM, Berri S, Pentenero M, High A, Rabbitts P. “PP066: No association between human papillomavirus infection and oral verrucous lesions”. Oral Oncology 2013 49, S116
DOI: 10.1016/j.oraloncology.2013.03.309

Hayes JL, Tzika A, Thygesen H, Berri S, Wood HM, Hewitt S, Pendlebury M, Coates A, Willoughby L, Watson CM, Rabbitts P, Roberts P, Taylor GR. “Diagnosis of copy number variation by Illumina next generation sequencing is comparable in performance to oligonucleotide array comparative genomic hybridisation”. Genomics. 2013 Apr 15
PMID: 23598253, DOI: 10.1016/j.ygeno.2013.04.006

Stead LF, Berri S, Wood HM, Egan P, Conway C, Daly C, Papagiannopoulos K, Rabbitts P. “The transcriptional consequences of somatic amplifications, deletions and rearrangements in a human lung squamous cell carcinoma”. Neoplasia. 2012; 14(11):1075-86.
PMID: 23226101

Conway C, Chalkley R, High A, Maclennan K, Berri S, Chengot P, Alsop M, Egan P, Morgan J, Taylor GR, Chester J, Sen M, Rabbitts P, Wood HM. “Next generation sequencing for simultaneous determination of HPV load, subtype and associated genomic copy number changes in tumors”. Journal of Molecular Diagnostics. 2012
PMID: 22240447, DOI: 10.1016/j.jmoldx.2011.10.003

Belvedere O, Berri S, Chalkley R, Conway C, Barbone F, Pisa F, Maclennan K, Daly C, Alsop M, Morgan J, Menis J, Tcherveniakov P, Papagiannopoulos K, Rabbitts P and Wood HM. “A computational index derived from whole-genome copy number analysis is a novel tool for prognosis in early stage lung squamous cell carcinoma.” Genomics. 2012; 99(1):18-24
PMID: 22050995, DOI: 10.1016/j.bbr.2011.03.031

Gusnanto A, Wood HM, Pawitan Y, Rabbitts P and Berri S. “Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next generation sequence data.” Bioinformatics 2012, 28(1):40-47
PMID: 22039209, DOI: 10.1093/bioinformatics/btr593

Berri S, Boyle JH, Tassieri M, Hope IA and Cohen N. “Forward locomotion of the nematode C. elegans is achieved through modulation of a single gait.” HFSP J. 2009 Jun;3(3):186-93.
PMID: 19639043, DOI: 10.2976/1.3082260

Berri S, Abbruscato P, Faivre-Rampant O, Brasileiro AC, Fumasoni I, Satoh K, Kikuchi S, Mizzi L, Morandini P, Pe ME and Piffanelli P. “Characterization of WRKY co-regulatory networks in rice and Arabidopsis.” BMC Plant Biol. 2009 Sep 22;9(1):120.
PMID: 19772648, DOI: 10.1186/1471-2229-9-120

A full list of all publications can be found here