Publications

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.

Publications

1. Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation

2. Exploring the limitations of biophysical propensity scales coupled with machine learning for protein sequence analysis

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

4. 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)

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

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

7. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

8. Computational identification of prion-like RNA-binding proteins that form liquid phase-separated condensates

9. Amphipods in a Greek cave with sulphidic and non-sulphidic water: phylogenetically clustered and ecologically divergent

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

11. 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)

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

13. Predicting disease-causing variant combinations

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

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

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

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

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

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

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

21. Towards a phylogenetic measure to quantify HIV incidence

22. Digenic inheritance of human primary microcephaly delineates centrosomal and non-centrosomal pathways

23. Enhanced processivity of Dnmt1 by monoubiquitinated histone H3

24. An intrinsically disordered proteins community for elixir [version 1; peer review: 2 approved]

25. Global network of computational biology communities: ISCB's regional student groups breaking barriers [version 1; peer review: Not peer reviewed]

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

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

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

4. A global ocean atlas of eukaryotic genes

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

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

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

8. Microbial communities as dynamical systems

9. Signatures of ecological processes in microbial community time series

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

11. Evolutionary dynamics of paroxysmal nocturnal hemoglobinuria

12. Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

13. Comprehensive Characterization of Cancer Driver Genes and Mutations

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

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

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

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

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

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

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

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

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

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

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

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

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

4. Understanding mutational effects in digenic diseases

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

18. Structural characterization of monomeric/dimeric state of p59^fyn SH2 domain