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

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

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

4. EDIR: exome database of interspersed repeats

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

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

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

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

4. Evolutionary adaptation of the protein folding pathway for secretability

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

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

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

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

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

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

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

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

13. Panoramic Perspective on Human Phosphosites

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

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

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

17. Variable expressivity in Buschke-Ollendorff syndrome

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

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

20. Brownian motion in a growing population of ballistic particles

21. Solving the Coral Species Delimitation Conundrum

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

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

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

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

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

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

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

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

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

31. 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

2. Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms

3. Contrastive self-supervised clustering of scRNA-seq data

4. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

5. Online biophysical predictions for SARS-CoV-2 proteins

6. Gene expression and epigenetics reveal species-specific mechanisms acting upon common molecular pathways in the evolution of task division in bees

7. Cell geometry, signal dampening, and a bimodal transcriptional response underlie the spatial precision of an ERK-mediated embryonic induction

8. Author Correction: DOME: recommendations for supervised machine learning validation in biology (Nature Methods, (2021), 18, 10, (1122-1127), 10.1038/s41592-021-01205-4)

9. Molecular adaptations to heat stress in the thermophilic ant genus Cataglyphis

10. TIGER: The gene expression regulatory variation landscape of human pancreatic islets

11. Quantifying renin-angiotensin-system alterations in covid-19

12. Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga

13. Compound heterozygous null mutations of NOBOX in sisters with delayed puberty and primary amenorrhea

14. DOME: recommendations for supervised machine learning validation in biology

15. DNAModAnnot: A R toolbox for DNA modification filtering and annotation

16. Heavy-tailed abundance distributions from stochastic Lotka-Volterra models

17. Whole-genome sequencing reveals asymmetric introgression between two sister species of cold-resistant leaf beetles

18. SWOTein: A structure-based approach to predict stability Strengths and Weaknesses of prOTEINs

19. B2bTools: Online predictions for protein biophysical features and their conservation

20. Genome Assembly of the Cold-Tolerant Leaf Beetle Gonioctena quinquepunctata, an Important Resource for Studying Its Evolution and Reproductive Barriers between Species

21. New variant in deficiency of interleukin-36 receptor antagonist syndrome (DITRA)

22. Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients

23. Prediction and evolution of the molecular fitness of sars-cov-2 variants: Introducing spikepro

24. Critical assessment of protein intrinsic disorder prediction

25. In silico analysis of the molecular-level impact of smpd1 variants on niemann-pick disease severity

26. Multistage feedback-driven compartmental dynamics of hematopoiesis

27. NR5A1 c.991-1G > C splice-site variant causes familial 46,XY partial gonadal dysgenesis with incomplete penetrance

28. Mg deficiency interacts with the circadian clock and phytochromes pathways in Arabidopsis

29. MobiDB: Intrinsically disordered proteins in 2021

30. Gene expression signatures of target tissues in type 1 diabetes, lupus erythematosus, multiple sclerosis, and rheumatoid arthritis

31. The genus Microniphargus (Crustacea, Amphipoda): evidence for three lineages distributed across northwestern Europe and transfer from Niphargidae to Pseudoniphargidae

32. Interpreting a black box predictor to gain insights into early folding mechanisms

33. Acquired zinc deficiency mimicking acrodermatitis enteropathica in a breast-fed Premature Infant

34. Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM

35. Digestive involvement in a severe form of Snyder-Robinson syndrome: Possible expansion of the phenotype

36. ShiftCrypt: A web server to understand and biophysically align proteins through their NMR chemical shift values

1. Large-scale in silico mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness

2. Molecular taxonomy, phylogeny and biogeography of the Niphargus tatrensis species complex (Amphipoda, Niphargidae) in Austria

3. Genome-scale metabolic modeling of Acetobacter pasteurianus 386B reveals its metabolic adaptation to cocoa fermentation conditions

4. Dynamic contact networks of patients and MRSA spread in hospitals

5. Mutualistic cross-feeding in microbial systems generates bistability via an Allee effect

6. Interpreting pathways to discover cancer driver genes with Moonlight

7. Calcium Oscillations in Pancreatic α-cells Rely on Noise and ATP-Driven Changes in Membrane Electrical Activity

6. 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