Leeds Institute of Cancer and Pathology

Pre-Cancer Genomics

Stefano Berri – postdoctoral scientist


Contact information

Dr. Stefano Berri
Section of Pre-Cancer Genomics
Leeds Institute of Molecular Medicine
Wellcome Trust Brenner Building
St James’s University Hospital
LS9 7TF, Leeds
United Kingdom

tel: +44 (0) 113 2064070
email: s.berri@leeds.ac.uk

UPDATE: I am now working at Illumina. Please visit my new up to date webpage

I am a postdoctoral scientist working in the bioinformatic unit of the Precancer group together with Dr Henry Wood and Dr Lucy Stead.

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 take advantage of the linearity between depth of coverage and CNA to estimate ploidy and tumour content in clinical samples. Such information will allow a better understanding of CNA in hundreds of clinical samples. We have produced a Bioconductor package.

More recently, we have started to compare several cancer samples from the same patient using an integrated approach and different technologies: low and high coverage genomic data (Illumina) high coverage data from Complete Genomics and ultra deep sequencing of targeted regions with Haloplex technology.

I also take care of the general task of storing, tracking and retrieving all sequencing data. I developed a pipeline to automatically convert, detag and align the fastq files we receive from both the in-house as well as external sequencing facility. All metadata, such as file names, location, parameters used, description of biological samples and libraries is stored in a MySQL database accessible by the group.

Brief resume

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.

Publications in peer reviewed journals

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, Volume 14, Issue 11

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

Boyle JH, Berri S, Cohen N. “Gait modulation in C. elegans: an integrated neuromechanical model” Frontiers in Computational Neuroscience 2012, vol 6
PMID: 22408616, DOI: 10.3389/fncom.2012.00010

Boyle JH, Berri S, Tassieri M, Hope IA and Cohen N. “Gait Modulation in C. elegans: It’s Not a Choice, It’s a Reflex!” Front Behav Neurosci 2011 Mar 7;5:10.
PMID: 21430792, DOI: 10.3389/fnbeh.2011.00010

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

van Enckevort LJ, Droc G, Piffanelli P, Greco R, Gagneur C, Weber C, González VM, Cabot P, Fornara F, Berri S, Miro B, Lan P, Rafel M, Capell T, Puigdomènech P, Ouwerkerk PB, Meijer AH, Pe’ E, Colombo L, Christou P, Guiderdoni E and Pereira A. “EU-OSTID: a collection of transposon insertional mutants for functional genomics in rice.” Plant Mol Biol. 2005 Sep;59(1):99-110
PMID: 16217605, DOI: 10.1007/s11103-005-8532-6

 A full list of all publications can be found here

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