Vera Pancaldi

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Biography

NEWS: Try our new software!
A webtool and an R package to integrate chromatin contacts with other (epi)genomic data.
 
Call for abstracts closing 31st September 2019 Free registration for ICSB attendees on eventbrite
As of September 2018 I have started a new group at the Cancer Research Centre of Toulouse, as the recipient of the joint Fondation Toulouse Cancer Santé / Pierre Fabre Research institute Chair of Bio-Informatics in Oncology of the CRCT.
I will maintain an affiliation within BSC and will focus on themes including cellular heterogeneity and 3D genome architecture. 
Contact me for details of open positions.

Since 2017 I have been a senior researcher in the Life Science department and I was previously a FEBS fellow in the Structural Biology and Biocomputing group at the CNIO (Spanish National Cancer Research Centre) in Madrid, Spain from 2012 to 2017. Before that I have held post-doctoral research positions at Cambridge University working on epigenetics and hybrid vigour in plants, and at the Sanger Institute and University College London working on fission yeast functional genomics. I hold a degree in Physics and PhD in engineering from Imperial College London.
 

You can find all my publications here(pdfs available on arXiv if not open access)

I'm also a cofounder of Cambridge Networks Network

Recent publications:
Paper on chromatin assortativity (2016) What does happiness on twitter have in common with Polycomb proteins binding DNA?
 

Some of my past projects:

  • Epigenomics (BLUEPRINTEpiGeneSys)
  • Evolutionary Boolean models of hybrid vigour (paper)
  • Opinion piece on noise in chemotaxis and stress response (paper)
  • Boolean models of cancer networks, embryonal tumours (ASSET project)
  • An online tool for prediction of protein-protein interactions in fission yeast (PInt) 
  • Effect of stress on yeast interaction networks (paper)
  • Meta-analysis of microarray data for fission yeast in different genetic and environmental conditions
  • Characterisation and prediction of protein-mRNA interactions in budding yeast
  • The role of epigenetic effects and siRNAs in the formation of inter-specific hybrids in tomato
  • Boolean models of stress response in fission yeast
Collaborations:
Alfonso Valencia, BSC
Emanuele Raineri, CNAG-CRG Barcelona
Juan Mendez, CNIO, Madrid
Peter Fraser, Mikhail Spivakov, the Babraham Institute, Cambridge (3D Chromatin contact maps).
Simone Ecker, University College London
José-Ignacio Martin-Subero, Elias Campo, University of Barcelona (Spanish CLL project).
Branka Radic, Superti-Furga lab at CeMM, Vienna (on cell line models for predicting drug synergies).
Zachary Gurard-Levin, Almouzni Lab at Insitut Curie, Paris (on models for predicting breast cancer drug sensitivities)
Meetings organized:
NetMed19: Getting connected: Systems medicine and networks, 28th May 2019, A NetSci2019 Satellite, Organized with Amitabh Sharma and Abhijeet Sonawane (Channing Division of Network Medicine at Harvard Medical School).

NetMed18: Personalized Medicine in the Era of Big Data, Paris, 11th June 2018, A NetSci2018 Satellite, Organized with Amitabh Sharma, Marc Santolini (Northwestern University) and Thomas Rolland (Institut Pasteur, Paris).

NetSciReg'15 Network Models in Cellular Regulation, Zaragoza, Spain, 1 June 2015 (a NetSci2015 Satellite)

Modelling Approaches in Epigenetics, 20-21 March 2014, Cambridge, UK

Keywords

  • Nucleome
  • Biological Networks
  • Cell biology
  • Cancer
  • Functional Genomics
  • Promoter Capture HiC
  • Hybrid vigour and evolution
  • Biological noise
  • Chromatin Interaction Networks
  • HiC
  • Complexity
  • Computational Biology
  • Epigenomics
  • Yeast
  • Gene Regulatory Networks

Educación

PhD Flow in Porous Media, Imperial College London (Physics/Earth Science Engineering, advisors Peter R. King and Kim Christensen) (2004-2008)

Thesis

MSci Physics Imperial College London (2000-2004)

Main Research Lines