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List of works by Susana Vinga

A Combinatorial Algorithm for Microbial Consortia Synthetic Design

scientific article published on 4 July 2016

A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog

scientific article published on 01 March 2021

A model for bone remodeling: Cellular dynamics and mechanical loading

article

A survey on methods for modeling and analyzing integrated biological networks

scientific article published on July 2011

Adenoma incidence decreases under the effect of polypectomy

scientific article published in March 2012

AliClu - Temporal sequence alignment for clustering longitudinal clinical data

scientific article published on 30 December 2019

Alignment-free sequence comparison-a review

scientific article

An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance

scientific article

An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2,3-butanediol production

scientific article published on 13 January 2014

Analysis of the genetic variability of virulence-related loci in epidemic clones of methicillin-resistant Staphylococcus aureus.

scientific article

Assessment of allelic variation in the ccrAB locus in methicillin-resistant Staphylococcus aureus clones

scientific article published on 30 May 2006

Automated smoother for the numerical decoupling of dynamics models

scientific article

BGFit: management and automated fitting of biological growth curves

scientific article

Biological sequences as pictures: a generic two dimensional solution for iterated maps

scientific article

CcrB typing tool: an online resource for staphylococci ccrB sequence typing

scientific article published on 27 January 2008

Comparative evaluation of word composition distances for the recognition of SCOP relationships.

scientific article

Computing distribution of scale independent motifs in biological sequences

scientific article

Consensus outlier detection in survival analysis using the rank product test

article published in 2018

Control analysis of the impact of allosteric regulation mechanism in a Escherichia coli kinetic model: Application to serine production

DegreeCox - a network-based regularization method for survival analysis

scientific article

Dynamic modeling of bone metastasis, microenvironment and therapy: Integrating parathyroid hormone (PTH) effect, anti-resorptive and anti-cancer therapy

scientific article published on 4 December 2015

Dynamic modeling of bone remodeling, osteolytic metastasis and PK/PD therapy: introducing variable order derivatives as a simplification technique

scientific article published in 2021

Editorial: Alignment-free methods in computational biology

scientific article published on 01 May 2014

Entropic Profiler - detection of conservation in genomes using information theory

scientific article

Fractal MapReduce decomposition of sequence alignment

scientific article

From physiology to systems metabolic engineering for the production of biochemicals by lactic acid bacteria

scientific article published on 06 April 2013

Fuzzy Clustering for Incomplete Short Time Series Data

Global meta-analysis of transcriptomics studies

scientific article

Host glycan sugar-specific pathways in Streptococcus pneumoniae: galactose as a key sugar in colonisation and infection [corrected]

scientific article (publication date: 2015)

Hybrid identification of time-varying parameter with particle filtering and expectation maximization

Identification and automatic segmentation of multiphasic cell growth using a linear hybrid model

scientific article published on 14 July 2016

Identification of neutral biochemical network models from time series data

scientific article

Identification of switched ARX models via convex optimization and expectation maximization

Identifying IIR filter coefficients using particle swarm optimization with application to reconstruction of missing cardiovascular signals

Improving Protein Expression Prediction Using Extra Features and Ensemble Averaging

scientific article

Information theory applications for biological sequence analysis

scientific article

Interplay Between Capsule Expression and Uracil Metabolism in Streptococcus pneumoniae D39.

scientific article published on 6 March 2018

KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems

scientific article

Kinetic modeling of cell metabolism for microbial production

scientific article published on 24 December 2015

Local Renyi entropic profiles of DNA sequences

scientific article

MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering

scientific article published on 24 February 2020

MassBlast: A workflow to accelerate RNA-seq and DNA database analysis

article

Modeling multiple experiments using regularized optimization: A case study on bacterial glucose utilization dynamics.

scientific article published on 15 September 2014

Modelling cancer outcomes of bone metastatic patients: combining survival data with N-Telopeptide of type I collagen (NTX) dynamics through joint models

scientific article published on 17 January 2019

Nonlinear MPC of HIV-1 infection with periodic inputs

article

Online Bayesian Time-varying Parameter Estimation of HIV-1 Time-series*

article

OptPipe - a pipeline for optimizing metabolic engineering targets

scientific article published on 21 December 2017

Optimal and receding horizon control of tumor growth in myeloma bone disease

scholarly article by João M. Lemos et al published February 2016 in Biomedical Signal Processing and Control

Optimization strategies for metabolic networks

scientific article

Outlier Detection in Cox Proportional Hazards Models Based on the Concordance c-Index

Parameter estimation and identifiability of a HIV-1 model

article

Parameter optimization in S-system models

scientific article

Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis

scientific article

Quantitative Modeling the Saccharomyces cerevisiae FLR1 Regulatory Network Using an S-System Formalism

Quantitative modeling of the Saccharomyces cerevisiae FLR1 regulatory network using an S-system formalism

scientific article published in October 2011

Robust identification of target genes and outliers in triple-negative breast cancer data

article

Rényi continuous entropy of DNA sequences

scientific article published on 01 December 2004

Sparse network-based regularization for the analysis of patientomics high-dimensional survival data

article

Subcellular metabolic organization in the context of dynamic energy budget and biochemical systems theories

scientific article

TCox: Correlation-Based Regularization Applied to Colorectal Cancer Survival Data

scientific article published on 10 November 2020

Transcriptional and metabolic effects of glucose on Streptococcus pneumoniae sugar metabolism

scientific article

Universal sequence map (USM) of arbitrary discrete sequences

scientific article

Unsupervised learning of pharmacokinetic responses

article

Using information interaction to discover epistatic effects in complex diseases

scientific article

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