Evaluating molecular representations in machine learning models for drug response prediction and interpretability

JOURNAL ARTICLE published 30 September 2022 in Journal of Integrative Bioinformatics

Research funded by Fundação para a Ciência e a Tecnologia (SFRH/BD/130913/2017,UIDB/04469/2020) | European Regional Development Fund (NORTE-01-0247-FEDER- 039831)

Authors: Delora Baptista | João Correia | Bruno Pereira | Miguel Rocha

Classification of Breast Cancer Subtypes by combining Gene Expression and DNA Methylation Data

JOURNAL ARTICLE published 1 June 2014 in Journal of Integrative Bioinformatics

Authors: Markus List | Anne-Christin Hauschild | Qihua Tan | Torben A. Kruse | Jan Baumbach | Richa Batra

Integrative Systems Biology Visualization with MAYDAY

JOURNAL ARTICLE published 1 December 2010 in Journal of Integrative Bioinformatics

Authors: Stephan Symonsy | Christian Zipplies | Florian Battke | Kay Nieselt

Systematic assessment of template-based genome-scale metabolic models created with the BiGG Integration Tool

JOURNAL ARTICLE published 30 September 2022 in Journal of Integrative Bioinformatics

Research funded by Fundação para a Ciência e a Tecnologia (DFA/BD/10205/2020,DFA/BD/8076/2020,SFRH/BD/139198/2018,SFRH/BD/144643/2019,SFRH/BD/147271/2019,UIDB/04469/2020) | Universidade do Minho (UMI-NHO/BIM/2020/68)

Authors: Alexandre Oliveira | Emanuel Cunha | Fernando Cruz | João Capela | João C. Sequeira | Marta Sampaio | Cláudia Sampaio | Oscar Dias

A Methodology for Comparative Functional Genomics

JOURNAL ARTICLE published 1 December 2007 in Journal of Integrative Bioinformatics

Authors: Intikhab Alam | Mike Cornell | Darren M. Soanes | Cornelia Hedeler | Han Min Wong | Magnus Rattray | Simon J. Hubbard | Nicholas J. Talbot | Stephen G. Oliver | Norman W. Paton

Mining Protein Databases using Machine Learning Techniques

JOURNAL ARTICLE published 1 June 2008 in Journal of Integrative Bioinformatics

Authors: Renata da Silva Camargo | Mahesan Niranjan

On the identification of potential novel therapeutic targets for spinocerebellar ataxia type 1 (SCA1) neurodegenerative disease using EvoPPI3

JOURNAL ARTICLE published 31 July 2023 in Journal of Integrative Bioinformatics

Research funded by Ministerio de Universidades (“María Zambrano” contract (Hugo López-Fernández)) | Conselleria de Cultura, Educación e Universidade (ED431C 2022/03-GRC) | Fundação para a Ciência e a Tecnologia (UIDB/04293/2020)

Authors: André Sousa | Sara Rocha | Jorge Vieira | Miguel Reboiro-Jato | Hugo López-Fernández | Cristina P. Vieira

Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays

JOURNAL ARTICLE published 1 June 2012 in Journal of Integrative Bioinformatics

Authors: Xiaogang Wu | Christoph Reinhard | Shuyu D. Li | Hui Huang | Tao Wei | Ragini Pandey | Jake Y. Chen

Identifying Transcription Regulatory Elements in the Human and Mouse Genomes Using Tissue-specific Gene Expression Profiles

JOURNAL ARTICLE published 1 June 2007 in Journal of Integrative Bioinformatics

Authors: Amitava Karmaker | Kihoon Yoon | Mark Doderer | Russell Kruzelock | Stephen Kwek

DBE2 – Management of experimental data for the VANTED system

JOURNAL ARTICLE published 1 June 2011 in Journal of Integrative Bioinformatics

Authors: Hendrik Mehlhorn | Falk Schreiber

Integration of Data in Pathogenomics: Three Layers of cellular complexity and an XML-based Framework

JOURNAL ARTICLE published 1 December 2004 in Journal of Integrative Bioinformatics

Authors: M. Dünßer | R. Lampidis | S. Schmidt | D. Seipel | T. Dandekar

ExPlanes: Exploring Planes in Triplet Data

JOURNAL ARTICLE published 1 December 2010 in Journal of Integrative Bioinformatics

Authors: Bruno Schwenk | Joachim Selbig | Yehuda Ben-Zion | Matthias Holschneider

From Binary to Multivalued to Continuous Models: The lac Operon as a Case Study

JOURNAL ARTICLE published 1 March 2010 in Journal of Integrative Bioinformatics

Authors: Raimo Franke | Fabian J. Theis | Steffen Klamt

Discovery and Annotation of Plant Endogenous Target Mimicry Sequences from Public Transcriptome Libraries: A Case Study of Prunus persica

JOURNAL ARTICLE published 28 June 2017 in Journal of Integrative Bioinformatics

Authors: Gökhan Karakülah

Bioinformatic tools help molecular characterization of Perkinsus olseni differentially expressed genes

JOURNAL ARTICLE published 1 December 2011 in Journal of Integrative Bioinformatics

Authors: Rita M. T. Ascenso

The implications for Bioinformatics of integration across physical scales

JOURNAL ARTICLE published 1 December 2006 in Journal of Integrative Bioinformatics

Authors: T.C. Hodgman | Y. Ugartechea-Chirino | G. Tansley | I. Dryden

Assembling cell context-specific gene sets: a case in cardiomyopathy

JOURNAL ARTICLE published 1 March 2013 in Journal of Integrative Bioinformatics

Authors: Mingming Liu | Vanessa King | Wei Keat Lim

Protein analysis tools and services at IBIVU

JOURNAL ARTICLE published 1 June 2011 in Journal of Integrative Bioinformatics

Authors: Bernd W. Brandt | Jaap Heringa

Efficient mapping of genomic sequences to optimize multiple pairwise alignment in hybrid cluster platforms

JOURNAL ARTICLE published 1 December 2014 in Journal of Integrative Bioinformatics

Authors: Alberto Montañola | Concepció Roig | Porfidio Hernández

The LAILAPS Search Engine: A Feature Model for Relevance Ranking in Life Science Databases

JOURNAL ARTICLE published 1 December 2010 in Journal of Integrative Bioinformatics

Authors: Matthias Lange | Karl Spies | Christian Colmsee | Steffen Flemming | Matthias Klapperstück | Uwe Scholz