Publications

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

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

Nucleic Acids Research, 2016 by Moretto M.

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

Nucleic Acids Research, 2016 by Pancsa R.

16. DIDA: A curated and annotated digenic diseases database

Nucleic Acids Research, 2016 by Gazzo A.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. 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.

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

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

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. 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.

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

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

10. Using shRNA experiments to validate gene regulatory networks

Genomics Data, 1 June 2015 by Olsen C.

11. Determinants of community structure in the global plankton interactome

Science, 22 May 2015 by Lima-Mendez G.

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

Bioinformatics, 15 April 2015 by Raimondi D.

13. 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.D.

14. Calibrating probability with undersampling for unbalanced classification

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

15. Cross-biome comparison of microbial association networks

Frontiers in Microbiology, 2015 by Faust K.

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

BioMed Research International, 2015 by Colaprico A.

2. Experimental assessment of static and dynamic algorithms for gene regulation inference from time series expression data

Frontiers in Genetics, 2013 by Lopes M.

3. From protein sequence to dynamics and disorder with DynaMine

Nature Communications, 14 November 2013 by Cilia E.

Publications

1. USP7/Maged1-mediated H2A monoubiquitination in the paraventricular thalamus: an epigenetic mechanism involved in cocaine use disorder

2. A study of deep active learning methods to reduce labelling efforts in biomedical relation extraction

3. Co-targeting HSP90 alpha and CDK7 overcomes resistance against HSP90 inhibitors in BCR-ABL1+ leukemia cells

4. Comprehensive evaluation of the implementation of episignatures for diagnosis of neurodevelopmental disorders (NDDs)

5. Heterotopia of salivary gland tissue in the pancreas

6. A knowledge graph approach to predict and interpret disease-causing gene interactions

7. Faster and more accurate pathogenic combination predictions with VarCoPP2.0

8. Correction: Retinal endothelial cell phenotypic modifications during experimental autoimmune uveitis: a transcriptomic approach (BMC Ophthalmology, (2020), 20, 1, (106), 10.1186/s12886-020-1333-5)

9. Congenital hydrocephalus: new Mendelian mutations and evidence for oligogenic inheritance

10. Author Correction: Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit (Nature Communications, (2021), 12, 1, (6414), 10.1038/s41467-021-26720-y)

11. Author Correction: Deep mutational scanning of essential bacterial proteins can guide antibiotic development (Nature Communications, (2023), 14, 1, (241), 10.1038/s41467-023-35940-3)

12. Deep mutational scanning of essential bacterial proteins can guide antibiotic development

13. Rare variant association on unrelated individuals in case-control studies using aggregation tests: existing methods and current limitations

14. Molecular basis of ClC-6 function and its impairment in human disease

15. Patient-reported outcome measures on mental health and psychosocial factors in patients with Brugada syndrome

16. A workflow to study mechanistic indicators for driver gene prediction with Moonlight

17. Excalibur: A new ensemble method based on an optimal combination of aggregation tests for rare-variant association testing for sequencing data

18. Facing lethal temperatures: Heat-shock response in desert and temperate ants

19. Phylogenetic structure and molecular species delimitation hint a complex evolutionary history in an Alpine endemic Niphargus clade (Crustacea, Amphipoda)

20. Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions

21. CAID prediction portal: A comprehensive service for predicting intrinsic disorder and binding regions in proteins

22. Enzyme Stability-Activity Trade-Off: New Insights from Protein Stability Weaknesses and Evolutionary Conservation

23. Adipose tissue plasticity in pheochromocytoma patients suggests a role of the splicing machinery in human adipose browning

24. The ACPYPE web server for small-molecule MD topology generation

25. Genetic breaks caused by ancient forest fragmentation: phylogeography of Staudtia kamerunensis (Myristicaceae) reveals distinct clusters in the Congo Basin

26. New simulation insights on the structural transition mechanism of bovine rhodopsin activation

27. The sliding motility of the bacilliform virions of Influenza A viruses

28. A pathogenic CTBP1 variant featuring HADDTS with dystrophic myopathology

29. Estimating the Vertical Ionization Potential of Single-Stranded DNA Molecules

30. Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species

31. Clinical and molecular diagnosis of genodermatoses: Review and perspectives

32. RedRibbon: A new rank-rank hypergeometric overlap for gene and transcript expression signatures

33. Model of neural induction in the ascidian embryo

34. Toward reporting standards for the pathogenicity of variant combinations involved in multilocus/oligogenic diseases

35. pyScoMotif: discovery of similar 3D structural motifs across proteins

36. The first record of a stygobiotic form of Garra rufa (Heckel, 1843), sympatric with Garra tashanensis Mousavi-Sabet, Vatandoust, Fatemi & Eagderi, 2016 (Teleostei, Cyprinidae), in Iranian subterranean waters

37. Experiences with a training DSW knowledge model for early-stage researchers

38. DNA Modification Patterns Filtering and Analysis Using DNAModAnnot

39. Critical review of conformational B-cell epitope prediction methods

40. Deciphering the RRM-RNA recognition code: A computational analysis

41. Evolution of CRISPR-associated endonucleases as inferred from resurrected proteins

42. EDIR: exome database of interspersed repeats

43. Co-Occurrence of Hypohidrotic Ectodermal Dysplasia and Food Protein-Induced Enterocolitis Syndrome: A Report of a New Ectodysplasin A Variant

1. Molecular analyses of groundwater amphipods (Crustacea: Niphargidae) from Luxembourg: new species reveal limitations of morphology-based checklists

2. Identification of differentially methylated regions in rare diseases from a single-patient perspective

3. Methanotrophy by a Mycobacterium species that dominates a cave microbial ecosystem

4. Comparative genome analysis of Vagococcus fluvialis reveals abundance of mobile genetic elements in sponge-isolated strains

5. Evolutionary adaptation of the protein folding pathway for secretability

6. Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks

7. Application of comparative genomics of Acetobacter species facilitates genome-scale metabolic reconstruction of the Acetobacter ghanensis LMG 23848T and Acetobacter senegalensis 108B cocoa strains

8. Mining the transcriptome of target tissues of autoimmune and degenerative pancreatic β-cell and brain diseases to discover therapies

9. Comparative study of keratinocyte primary culture methods from paediatric skin biopsies for RNA-sequencing

10. Exploiting Genomic Features to Improve the Prediction of Transcription Factor-Binding Sites in Plants

11. Transcription and splicing regulation by NLRC5 shape the interferon response in human pancreatic β cells

12. SpikePro: a webserver to predict the fitness of SARS-CoV-2 variants

13. Quantitative three-dimensional morphological analysis supports species discrimination in complex-shaped and taxonomically challenging corals

14. Panoramic Perspective on Human Phosphosites

15. Challenges in describing the conformation and dynamics of proteins with ambiguous behavior

16. Evaluation of neurodevelopmental symptoms in 10 cases of neonatal ichthyosis and sclerosing cholangitis syndrome

17. Prediction of Disordered Regions in Proteins with Recurrent Neural Networks and Protein Dynamics

18. Variable expressivity in Buschke-Ollendorff syndrome

19. Sliding across a surface: Particles with fixed and mobile ligands

20. Biallelic gephyrin variants lead to impaired GABAergic inhibition in a patient with developmental and epileptic encephalopathy

21. Brownian motion in a growing population of ballistic particles

22. Solving the Coral Species Delimitation Conundrum

23. GNN-based embedding for clustering scRNA-seq data

24. Analysis of the Neutralizing Activity of Antibodies Targeting Open or Closed SARS-CoV-2 Spike Protein Conformations

25. Artificial intelligence challenges for predicting the impact of mutations on protein stability

26. A deep dive into genome assemblies of non-vertebrate animals

27. Ēngines of Ēternity: An Artistic Inquiry into Space Settlement Ideology Using Rotifer Experiments on Board the ISS

28. An exome-wide study of renal operational tolerance

29. Chromosome-level genome assembly and annotation of two lineages of the ant Cataglyphis hispanica: stepping stones towards genomic studies of hybridogenesis and thermal adaptation in desert ants

30. Substantial genetic mixing among sexual and androgenetic lineages within the clam genus Corbicula

31. Improving Infinium MethylationEPIC data processing: re-annotation of enhancers and long noncoding RNA genes and benchmarking of normalization methods

32. MutaFrame - an interpretative visualization framework for deleteriousness prediction of missense variants in the human exome

33. Scaling up oligogenic diseases research with OLIDA: The Oligogenic Diseases Database

34. Riemannian classification of single-trial surface EEG and sources during checkerboard and navigational images in humans

35. Using metagenomic data to boost protein structure prediction and discovery

1. Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit

7. Application of comparative genomics of Acetobacter species facilitates genome-scale metabolic reconstruction of the Acetobacter ghanensis LMG 23848^T and Acetobacter senegalensis 108B cocoa strains