Manuela Salvucci

Manuela Salvucci

Computational biologist

Royal College of Surgeons in Ireland (RCSI)

Biography

Driven researcher with 7+ years professional experience in collaborative and international healthcare settings and a strong background in engineering, numerical analysis, data mining, relational databases, modelling, statistics, machine learning and visualization. Experienced with mining multiple high-throughput datasets to develop and validate models to personalize medical recommendations.

Interests

  • machine learning
  • statistics
  • visualization
  • genomics
  • single cell
  • big data

Projects

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CoxVisualizer

CoxVisualizer is a python package to generate tidy Cox hazards regression tables for univariate and multivariate models with support for multiple survival end-points.
Code

PyAnatomogram

PyAnatomogram is a python package to annotate and highlight organs and tissues in figures.
Code

HCP

HCP (HeatmapCovariatePlot) is an open-source Matlab package to generate publication-quality, highly customizable heatmaps annotated with continuous or categorical metadata variables.
PDF Code MATLAB file exchange

ProjectBlack

Root cause analysis for manufacturing defects. Data science project conducted as a part of a (great) team (the ‘black team’, re-baptized the ‘black sybil’) for the ‘Women in Data Science Accelerator’ program (2019) organized by Accenture.
Code

Recent & Upcoming Talks

Python for data analysis and visualization (part 2)

This is the second of two python workshops. This workshop focuses on importing, cleaning and plotting data. It is recommended to attend the “Introduction to Python programming” workshop first for attendees with no previous Python experience.
Dec 4, 2019 12:00 PM — 2:00 PM Royal College of Surgeons in Ireland (RCSI)
PDF Code Slides Binder
Python for data analysis and visualization (part 2)

Version Control with GIT

This workshop is intended for users who are interested in using version control to organize and track history for their files. Version control helps keep track of all the revision of your files, track changes over time and revert unwanted changes without losing track. Version control is commonly used for maintaining programming source code, but can also be used for other types of flat files (csv, txt with data). It can also help with collaboration between multiple authors.
Nov 6, 2019 3:00 PM — 5:00 PM Royal College of Surgeons in Ireland (RCSI)
PDF Code Slides
Version Control with GIT

An introduction to supervised and unsupervised multivariate statistical analysis

Oct 9, 2019 University of Stuttgart
PDF Code Slides Binder

Featured Publications

A machine learning platform to optimize the translation of personalized network models to the clinic

Manuela Salvucci, Arman Rahman, Alexa Resler, Girish Mallya Udupi, Deborah A. McNamara, Elaine W. Kay, Pierre Laurent-Puig, Daniel B. Longley, Patrick G. Johnston, Mark Lawler, Richard Wilson, Manuel Salto-Tellez, Sandra Van Schaeybroeck, Mairin Rafferty, William Gallagher, Markus Rehm, and Jochen H. M. Prehn
PDF Code Dataset Project DOI
A machine learning platform to optimize the translation of personalized network models to the clinic

Simulating and predicting cellular and in vivo responses of colon cancer to combined treatment with chemotherapy and IAP antagonist Birinapant/TL32711

Nyree Crawford, Manuela Salvucci, Christian T Hellwig, Frank A Lincoln, Ruth E Mooney, Carla L O'Connor, Jochen HM Prehn, Daniel B Longley, Markus Rehm
PDF Code Dataset Project DOI
Simulating and predicting cellular and in vivo responses of colon cancer to combined treatment with chemotherapy and IAP antagonist Birinapant/TL32711

System-based Approaches as Prognostic Tools for Glioblastoma

Manuela Salvucci*, Zaitun Zakaria*, Steven Carberry, Amanda Tivnan, Volker Seifert, Donat Kögel, Brona M. Murphy, and Jochen H.M. Prehn
PDF Code Dataset Project DOI
System-based Approaches as Prognostic Tools for Glioblastoma

The apoptosome molecular timer synergises with XIAP to suppress apoptosis execution and contributes to prognosticating survival in colorectal cancer

Gavin Fullstone, Tabea L. Bauer, Cristiano Guttà, Manuela Salvucci, Jochen H. M. Prehn, Markus Rehm
PDF DOI
The apoptosome molecular timer synergises with XIAP to suppress apoptosis execution and contributes to prognosticating survival in colorectal cancer

A stepwise integrated approach to personalized risk predictions in stage III colorectal cancer

Manuela Salvucci, Maximilian L. Würstle, Clare Morgan, Sarah Curry, Mattia Cremona, Andreas U. Lindner, Orna Bacon, Alexa J. Resler, Áine C. Murphy, Robert O'Byrne, Lorna Flanagan, Sonali Dasgupta, Nadege Rice, Camilla Pilati, Elisabeth Zink, Lisa M. Schöller, Sinead Toomey, Mark Lawler, Patrick G. Johnston, Richard Wilson, Sophie Camilleri-Broët, Manuel Salto-Tellez, Deborah A. McNamara, Elaine W. Kay, Pierre Laurent-Puig, Sandra Van Schaeybroeck, Bryan T. Hennessy, Daniel B. Longley, Markus Rehm and Jochen H.M. Prehn
PDF DOI
A stepwise integrated approach to personalized risk predictions in stage III colorectal cancer

BCL-2 system analysis identifies high risk colorectal cancer patients

Andreas U Lindner, Manuela Salvucci, Clare Morgan, Naser Monsefi, Alexa J Resler, Mattia Cremona, Sarah Curry, Sinead Toomey, Robert O’Byrne, Orna Bacon, Michael Stühler, Lorna Flanagan, Richard Wilson, Patrick G Johnston, Manuel Salto-Tellez, Sophie Camilleri-Broët, Deborah A McNamara, Elaine W Kay, Bryan T Hennessy, Pierre Laurent-Puig, Sandra Van Schaeybroeck, Jochen H M Prehn
PDF DOI
BCL-2 system analysis identifies high risk colorectal cancer patients

Accomplish­ments

Databases and SQL for Data Science

Coursera Jun 2020
See certificate

Young Scientist Award (Senior)

European Association Cancer Research Feb 2020
Integrated multi-omics analysis from multi-region resections reveals further fine-grained taxonomies of colorectal cancer (CRC)

Certified Analytics Professional (CAP)

The Analytics Institute of Ireland Mar 2019

Women in Data Science Accelerator Programme

Accenture Mar 2019

Best Scientist Award

Centre for Systems Medicine, RCSI Dec 2016

Young Scientist Award (Junior)

European Association Cancer Research Feb 2016
Translational application of a mathematical model of apoptotic caspase activation provides a prognostic biomarker in stage III colorectal cancer

Programming languages

Python

★★★

matlab

Matlab

★★★

R

★★★

bash

Bash

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c++

C++

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Popular Topics

anatomogram annotated heatmap classification random forest Cox regression model data cleaning data exploration graphics machine learning matlab matplotlib modelling pandas prognostic biomarker python R seaborn statistics survival analysis visualization workshop

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