Publications

1. EOMES interacts with RUNX3 and BRG1 to promote innate memory cell formation through epigenetic reprogramming

Nature Communications, 1 December 2019 by Istaces N.

2. Author Correction: Exploring the Sequence-based Prediction of Folding Initiation Sites in Proteins (Scientific Reports, (2017), 7, 1, (8826), 10.1038/s41598-017-08366-3)

Scientific Reports, 1 December 2019 by Raimondi D.

3. Auto-encoding NMR chemical shifts from their native vector space to a residue-level biophysical index

Nature Communications, 1 December 2019 by Orlando G.

4. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

Nature Communications, 1 December 2019 by Menden M.

5. Using game theory and decision decomposition to effectively discern and characterise bi-locus diseases

Artificial Intelligence in Medicine, August 2019 by Versbraegen N.

6. Correction: IQSEC2-related encephalopathy in males and females: a comparative study including 37 novel patients (Genetics in Medicine, (2019), 21, 4, (837-849), 10.1038/s41436-018-0268-1)

Genetics in Medicine, 1 August 2019 by Mignot C.

7. ORVAL: a novel platform for the prediction and exploration of disease-causing oligogenic variant combinations

Nucleic acids research, 2 July 2019 by Renaux A.

8. Predicting disease-causing variant combinations

Proceedings of the National Academy of Sciences of the United States of America, 11 June 2019 by Papadimitriou S.

9. Non-monotonic auto-regulation in single gene circuits

PLoS ONE, May 2019 by Descheemaeker L.

10. Computational characterization of the mtORF of Pocilloporid Corals: Insights into protein structure and function in Stylophora lineages from contrasting Environments

Genes, May 2019 by Banguera-Hinestroza E.

11. Distinct mesoderm migration phenotypes in extra-embryonic and embryonic regions of the early mouse embryo

eLife, 5 April 2019 by Saykali B.

12. IQSEC2-related encephalopathy in males and females: a comparative study including 37 novel patients

Genetics in Medicine, 1 April 2019 by Mignot C.

13. Truncating RAX Mutations: Anophthalmia, Hypopituitarism, Diabetes Insipidus, and Cleft Palate in Mice and Men

Journal of Clinical Endocrinology and Metabolism, 21 March 2019 by Brachet C.

14. New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEX

PLoS Computational Biology, March 2019 by Mounir M.

15. Excitable dynamics through toxin-induced mRNA cleavage in bacteria

PLoS ONE, February 2019 by Vet S.

1. Molecular chaperoning helps safeguarding mitochondrial integrity and motor functions in the Sahara silver ant Cataglyphis bombycina

Scientific Reports, 1 December 2018 by Willot Q.

2. Prediction and interpretation of deleterious coding variants in terms of protein structural stability

Scientific Reports, 1 December 2018 by Ancien F.

3. Large-scale in-silico statistical mutagenesis analysis sheds light on the deleteriousness landscape of the human proteome

Scientific Reports, 1 December 2018 by Raimondi D.

4. A global ocean atlas of eukaryotic genes

Nature Communications, 1 December 2018 by Carradec Q.

5. The hitchhiker's guide to single-locus species delimitation

Molecular Ecology Resources, November 2018 by Dellicour S.

6. HCN1 mutation spectrum: From neonatal epileptic encephalopathy to benign generalized epilepsy and beyond

Brain, 1 November 2018 by Marini C.

7. Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community

eLife, October 2018 by D’hoe K.

8. Microbial communities as dynamical systems

Current Opinion in Microbiology, August 2018 by Gonze D.

9. Signatures of ecological processes in microbial community time series

Microbiome, 28 June 2018 by Faust K.

10. Bistability in a system of two species interacting through mutualism as well as competition: Chemostat vs. Lotka-Volterra equations

PLoS ONE, June 2018 by Vet S.

11. Evolutionary dynamics of paroxysmal nocturnal hemoglobinuria

PLoS Computational Biology, June 2018 by Mon Père N.

12. Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

Cell, 5 April 2018 by Malta T.

13. Comprehensive Characterization of Cancer Driver Genes and Mutations

Cell, 5 April 2018 by Bailey M.

14. Chemical shift assignments of the partially deuterated Fyn SH2–SH3 domain

Biomolecular NMR Assignments, 1 April 2018 by Kieken F.

15. In-silico integration approach to identify a key miRNA regulating a gene network in aggressive prostate cancer

International Journal of Molecular Sciences, 19 March 2018 by Cava C.

16. Combination of Gene Expression Signature and Model for End-Stage Liver Disease Score Predicts Survival of Patients With Severe Alcoholic Hepatitis

Gastroenterology, March 2018 by Trépo E.

17. Changes in chromatin state reveal ARNT2 at a node of a tumorigenic transcription factor signature driving glioblastoma cell aggressiveness

Acta Neuropathologica, 1 February 2018 by Bogeas A.

18. RINspector: A Cytoscape app for centrality analyses and DynaMine flexibility prediction

Bioinformatics, 15 January 2018 by Brysbaert G.

19. Integration of multiple networks and pathways identifies cancer driver genes in pan-cancer analysis

BMC Genomics, 2018 by Cava C.

20. BCL11A frameshift mutation associated with dyspraxia and hypotonia affecting the fine, gross, oral, and speech motor systems

American Journal of Medical Genetics, Part A, January 2018 by Soblet J.

21. Ultra-fast global homology detection with Discrete Cosine Transform and Dynamic Time Warping

Bioinformatics, 2018 by Raimondi D.

22. AmyPro: A database of proteins with validated amyloidogenic regions

Nucleic Acids Research, 1 January 2018 by Varadi M.

23. MobiDB 3.0: More annotations for intrinsic disorder, conformational diversity and interactions in proteins

Nucleic Acids Research, 1 January 2018 by Piovesan D.

1. SVM-dependent pairwise HMM: An application to protein pairwise alignments

Bioinformatics, 15 December 2017 by Orlando G.

2. Exploring the Sequence-based Prediction of Folding Initiation Sites in Proteins

Scientific Reports, 1 December 2017 by Raimondi D.

3. SCooP: an accurate and fast predictor of protein stability curves as a function of temperature

Bioinformatics (Oxford, England), 1 November 2017 by Pucci F.

4. Understanding mutational effects in digenic diseases

Nucleic Acids Research, 1 September 2017 by Gazzo A.

5. DNA methylation-based immune response signature improves patient diagnosis in multiple cancers

Journal of Clinical Investigation, 1 August 2017 by Jeschke J.

6. Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability

Genome Medicine, 19 July 2017 by Reggiani C.

7. MHC class II expression and potential antigen-presenting cells in the retina during experimental autoimmune uveitis

Journal of Neuroinflammation, 18 July 2017 by Lipski D.

8. DEOGEN2: Prediction and interactive visualization of single amino acid variant deleteriousness in human proteins

Nucleic Acids Research, 3 July 2017 by Raimondi D.

9. PMut: A web-based tool for the annotation of pathological variants on proteins, 2017 update

Nucleic Acids Research, 3 July 2017 by López-Ferrando V.

10. Seeing the trees through the forest: Sequencebased homo- and heteromeric protein-protein interaction sites prediction using random forest

Bioinformatics, 15 May 2017 by Hou Q.

11. Study of Meta-analysis strategies for network inference using information-theoretic approaches

BioData Mining, 6 May 2017 by Pham N.

12. SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence

BMC Bioinformatics, 10 February 2017 by Dalkas G.

13. Physical and molecular bases of protein thermal stability and cold adaptation

Current Opinion in Structural Biology, 1 February 2017 by Pucci F.

14. SpidermiR: An R/bioconductor package for integrative analysis with miRNA data

International Journal of Molecular Sciences, February 2017 by Cava C.

15. Study of Meta-analysis Strategies for Network Inference Using Information-Theoretic Approaches

Proceedings - International Workshop on Database and Expert Systems Applications, DEXA, 12 January 2017 by Pham N.

16. Corrigendum: DisProt 7.0: a major update of the database of disordered proteins

Nucleic acids research, 4 January 2017 by Piovesan D.

17. Investigating the Molecular Mechanisms Behind Uncharacterized Cysteine Losses from Prediction of Their Oxidation State

Human Mutation, 1 January 2017 by Raimondi D.

18. Structural characterization of monomeric/dimeric state of p59fyn SH2 domain

Methods in Molecular Biology, 2017 by Huculeci R.

19. NOVOPlasty: De novo assembly of organelle genomes from whole genome data

Nucleic Acids Research, 2017 by Dierckxsens N.

20. CancerSubtypes: An R/Bioconductor package for molecular cancer subtype identification, validation and visualization

Bioinformatics, 2017 by Xu T.

21. DisProt 7.0: A major update of the database of disordered proteins

Nucleic Acids Research, 1 January 2017 by Piovesan D.

1. Observation selection bias in contact prediction and its implications for structural bioinformatics

Scientific Reports, 18 November 2016 by Orlando G.

2. Improved insights into protein thermal stability: From the molecular to the structurome scale

Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 13 November 2016 by Pucci F.

3. How interacting pathways are regulated by miRNAs in breast cancer subtypes

BMC Bioinformatics, 8 November 2016 by Cava C.

4. Dynamically Coupled Residues within the SH2 Domain of FYN Are Key to Unlocking Its Activity

Structure, 1 November 2016 by Huculeci R.

5. Multilevel biological characterization of exomic variants at the protein level significantly improves the identification of their deleterious effects

Bioinformatics, 15 June 2016 by Raimondi D.

6. High-quality thermodynamic data on the stability changes of proteins upon single-site mutations

Journal of Physical and Chemical Reference Data, 1 June 2016 by Pucci F.

7. Strategies for structuring interdisciplinary education in systems biology: An European perspective

npj Systems Biology and Applications, 26 May 2016 by Cvijovic M.

8. TCGAbiolinks: An R/Bioconductor package for integrative analysis of TCGA data

Nucleic Acids Research, 5 May 2016 by Colaprico A.

9. From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors

PLoS Computational Biology, May 2016 by Zafra Ruano A.

10. PharmacoGx: An R package for analysis of large pharmacogenomic datasets

Bioinformatics, 15 April 2016 by Smirnov P.

11. Predicting protein thermal stability changes upon point mutations using statistical potentials: Introducing HoTMuSiC

Scientific Reports, 18 March 2016 by Pucci F.

12. A blocking strategy for ranking features according to probabilistic relevance

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2016 by Bontempi G.

13. Start2Fold: A database of hydrogen/deuterium exchange data on protein folding and stability

Nucleic Acids Research, 2016 by Pancsa R.

14. DIDA: A curated and annotated digenic diseases database

Nucleic Acids Research, 2016 by Gazzo A.

15. TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 1; referees: 1 approved, 1 approved with reservations]

F1000Research, 2016 by Silva T.

16. TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

F1000Research, 2016 by Silva T.

17. COLOMBOS v3.0: Leveraging gene expression compendia for cross-species analyses

Nucleic Acids Research, 2016 by Moretto M.

1. From dependency to causality: A machine learning approach

Journal of Machine Learning Research, December 2015 by Bontempi G.

2. Structural insights into the intertwined dimer of fyn SH2

Protein Science, 1 December 2015 by Huculeci R.

3. NetBenchmark: A bioconductor package for reproducible benchmarks of gene regulatory network inference

BMC Bioinformatics, September 29, 2015 by Bellot P.

4. Analysis of the structural quality of the CASD-NMR 2013 entries

Journal of Biomolecular NMR, 22 August 2015 by Ragan T.

5. The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013

Journal of Biomolecular NMR, 22 August 2015 by Rosato A.

6. Computational approaches for inferring the functions of intrinsically disordered proteins

Frontiers in Molecular Biosciences, 5 August 2015 by Varadi M.

7. An evolutionary view on Disulfide bond connectivities prediction using phylogenetic trees and a simple cysteine mutation model

PLoS ONE, 10 July 2015 by Raimondi D.

8. Metagenomics meets time series analysis: Unraveling microbial community dynamics

Current Opinion in Microbiology, June 01, 2015 by Faust K.

9. Determinants of community structure in the global plankton interactome

Science, 22 May 2015 by Lima-Mendez G.

10. Clustering-based model of cysteine co-evolution improves disulfide bond connectivity prediction and reduces homologous sequence requirements

Bioinformatics, 15 April 2015 by Raimondi D.

11. When is undersampling effective in unbalanced classification tasks?

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2015 by Pozzolo A.

12. Integrative Analysis with Monte Carlo Cross-Validation Reveals miRNAs Regulating Pathways Cross-Talk in Aggressive Breast Cancer

BioMed Research International, 2015 by Colaprico A.

13. Calibrating probability with undersampling for unbalanced classification

Proceedings - 2015 IEEE Symposium Series on Computational Intelligence, SSCI 2015, 2015 by Pozzolo A.

14. Cross-biome comparison of microbial association networks

Frontiers in Microbiology, 2015 by Faust K.

15. Using shRNA experiments to validate gene regulatory networks

Genomics Data, 1 June 2015 by Olsen C.

16. NMR Exchange Format: A unified and open standard for representation of NMR restraint data

Nature Structural and Molecular Biology, 3 June 2015 by Gutmanas A.

1. Predicting virus mutations through statistical relational learning

BMC Bioinformatics, September 19, 2014 by Cilia E.

2. The DynaMine webserver: Predicting protein dynamics from sequence

Nucleic Acids Research, 1 July 2014 by Cilia E.

3. On the null distribution of the precision and recall curve

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2014 by Lopes M.

4. Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns

PLoS Computational Biology, 1 November 2014 by Skwark M.

5. NMR structure validation in relation to dynamics and structure determination

Progress in Nuclear Magnetic Resonance Spectroscopy, October 2014 by Vranken W.

6. Temporal profiling of cytokine-induced genes in pancreatic β-cells by meta-analysis and network inference

Genomics, April 2014 by Lopes M.

7. Inference and validation of predictive gene networks from biomedical literature and gene expression data

Genomics, 2014 by Olsen C.

8. Relevance of different prior knowledge sources for inferring gene interaction networks

Frontiers in Genetics, 2014 by Olsen C.