Publications

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

Clinical Epigenetics, December 2022 by Grolaux R.

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

Nature Microbiology, December 2022 by van Spanning R.J.M.

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

BMC Genomics, December 2022 by Rodriguez Jimenez A.

4. Evolutionary adaptation of the protein folding pathway for secretability

EMBO Journal, 1 December 2022 by Smets D.

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

BMC Genomics, December 2022 by Farhat S.

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

Frontiers in Microbiology, 24 November 2022 by Pelicaen R.

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

iScience, 18 November 2022 by Yi X.

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

Experimental Dermatology, November 2022 by Salik D.

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

Plant and Cell Physiology, 1 October 2022 by Riviere Q.

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

Science Advances, September 2022 by Szymczak F.

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

Bioinformatics (Oxford, England), 15 September 2022 by Cia G.

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

Frontiers in Marine Science, 6 September 2022 by Ramírez-Portilla C.

13. Panoramic Perspective on Human Phosphosites

Journal of Proteome Research, 5 August 2022 by Ramasamy P.

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

Frontiers in Molecular Biosciences, 3 August 2022 by Roca-Martinez J.

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

Pediatric Dermatology, July/August 2022 by Salik D.

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

Journal of Molecular Biology, 30 June 2022 by Orlando G.

17. Variable expressivity in Buschke-Ollendorff syndrome

Annales de Dermatologie et de Venereologie, June 2022 by Salik D.

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

Journal of Chemical Physics, 28 April 2022 by Lowensohn J.

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

Human Molecular Genetics, 15 March 2022 by MacHa A.

20. Brownian motion in a growing population of ballistic particles

Physical Review E, March 2022 by Mon Père N.V.

21. Solving the Coral Species Delimitation Conundrum

Systematic Biology, 1 March 2022 by Ramírez-Portilla C.

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

Bioinformatics, 15 February 2022 by Ciortan M.

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

International Journal of Molecular Sciences, February-2 2022 by Cia G.

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

Current Opinion in Structural Biology, February 2022 by Pucci F.

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

ISME Journal, 2022 by Bizic M.

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

Journal of the European Academy of Dermatology and Venereology, 2022 by Salik D.

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

Epigenetics, 2022 by Bizet M.

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

Bioinformatics, 1 January 2022 by Ancien F.

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

Database, 2022 by Nachtegael C.

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

PLoS ONE, January 2022 by Simar C.

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

Computational and Structural Biotechnology Journal, January 2022 by Hou Q.

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

Nature Communications, 1 December 2021 by Boone M.

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

BMC Bioinformatics, December 2021 by Guiglielmoni N.

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

BMC Bioinformatics, December 2021 by Ciortan M.

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

Communications Biology, December 2021 by Acinas S.G.

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

BMC Molecular and Cell Biology, December 2021 by Kagami L.

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

Scientific Reports, December 2021 by Araujo N.d.S.

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

Developmental Cell, 8 November 2021 by Williaume G.

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)

Nature Methods, November 2021 by Walsh I.

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

Molecular Ecology, November 2021 by Perez R.

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

Cell Reports, 12 October 2021 by Alonso L.

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

Cells, October 2021 by Pucci F.

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

Science Advances, October 2021 by Simion P.

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

Molecular Genetics and Genomic Medicine, October 2021 by Sassi A.

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

Nature Methods, October 2021 by Walsh I.

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

Bioinformatics, 1 September 2021 by Hardy A.

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

Physical Review E, September 2021 by Descheemaeker L.

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

Molecular Ecology, August 2021 by Lukicheva S.

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

Bioinformatics, 15 July 2021 by Hou Q.

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

Nucleic Acids Research, 2 July 2021 by Kagami L.P.

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

Genome Biology and Evolution, 1 July 2021 by Lukicheva S.

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

International Journal of Dermatology, July 2021 by Salik D.

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

Journal of the American Chemical Society, 28 June 2021 by Van Puyvelde B.

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

Viruses, May 2021 by Pucci F.

24. Critical assessment of protein intrinsic disorder prediction

Nature Methods, May 2021 by Necci M.

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

International Journal of Molecular Sciences, 1 May 2021 by Ancien F.

26. Multistage feedback-driven compartmental dynamics of hematopoiesis

iScience, 23 April 2021 by Mon Père N.V.

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

Clinical Endocrinology, April 2021 by Laan M.

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

Annals of Applied Biology, March 2021 by Rivière Q.

29. MobiDB: Intrinsically disordered proteins in 2021

Nucleic Acids Research, 8 January 2021 by Piovesan D.

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

Science Advances, 6 January 2021 by Szymczak F.

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

Belgian Journal of Zoology, 2021 by Weber D.

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

Computational and Structural Biotechnology Journal, January 2021 by Grau I.

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

Pediatric Reports, 2021 by D’Amico G.

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

Nature Methods, January 2021 by Uchański T.

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

European Journal of Medical Genetics, January 2021 by Dontaine P.

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

Nucleic Acids Research, 2021 by Orlando G.

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

BMC Biology, 1 December 2020 by Schwersensky M.

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

Organisms Diversity and Evolution, 1 December 2020 by Stoch F.

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

Food Microbiology, December 2020 by Pelicaen R.

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

Scientific Reports, 1 December 2020 by Rocha L.E.C.

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

Scientific Reports, 1 December 2020 by Vet S.

6. Interpreting pathways to discover cancer driver genes with Moonlight

Nature Communications, 1 December 2020 by Colaprico A.

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

Frontiers in Physiology, 17 November 2020 by González-Vélez V.

8. HaplowebMaker and CoMa: Two web tools to delimit species using haplowebs and conspecificity matrices

Methods in Ecology and Evolution, 1 November 2020 by Spöri Y.

9. Novel homozygous variant of carbonic anhydrase 8 gene expanding the phenotype of cerebellar ataxia, mental retardation, and disequilibrium syndrome subtype 3

American Journal of Medical Genetics, Part A, 1 November 2020 by Paternoster L.

10. How did subterranean amphipods cross the Adriatic Sea? Phylogenetic evidence for dispersal–vicariance interplay mediated by marine regression–transgression cycles

Journal of Biogeography, 1 September 2020 by Delić T.

11. Scop3P: A Comprehensive Resource of Human Phosphosites within Their Full Context

Journal of Proteome Research, 7 August 2020 by Ramasamy P.

12. Combining single-cell RNA-sequencing with a molecular atlas unveils new markers for Caenorhabditis elegans neuron classes

Nucleic Acids Research, 27 July 2020 by Lorenzo R.

13. Infiltrative tumour growth pattern correlates with poor outcome in oesophageal cancer

BMJ Open Gastroenterology, 15 July 2020 by Anciaux M.

14. Stochastic logistic models reproduce experimental time series of microbial communities

eLife, July 2020 by Descheemaeker L.

15. Distance-Based Metrics for Comparing Conformational Ensembles of Intrinsically Disordered Proteins

Biophysical Journal, 16 June 2020 by Lazar T.

16. Demographic history, range size and habitat preferences of the groundwater amphipod Niphargus puteanus (C.L. Koch in Panzer, 1836)

Limnologica, May 2020 by Weber D.

17. Accurate prediction of protein beta-aggregation with generalized statistical potentials

Bioinformatics, 1 April 2020 by Orlando G.

18. Retinal endothelial cell phenotypic modifications during experimental autoimmune uveitis: A transcriptomic approach

BMC Ophthalmology, 17 March 2020 by Lipski D.A.

19. Unraveling heteroplasmy patterns with NOVOPlasty

NAR Genomics and Bioinformatics, 1 March 2020 by Dierckxsens N.

20. Toward perfect reads: Self-correction of short reads via mapping on de Bruijn graphs

Bioinformatics, 1 March 2020 by Limasset A.

21. SOLart: A structure-based method to predict protein solubility and aggregation

Bioinformatics, 1 March 2020 by Hou Q.

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

Human Mutation, 1 February 2020 by Duerinckx S.

23. Towards a Phylogenetic Measure to Quantify HIV Incidence

Communications in Computer and Information Science, 2020 by Libin P.

24. DisProt: Intrinsic protein disorder annotation in 2020

Nucleic Acids Research, 1 January 2020 by Hatos A.

25. Enhanced processivity of Dnmt1 by monoubiquitinated histone H3

Genes to Cells, 1 January 2020 by Mishima Y.

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

Frontiers in Microbiology, 5 December 2019 by Pelicaen R.

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

Scientific Reports, 1 December 2019 by Raimondi D.

3. 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.

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

Nature Communications, 1 December 2019 by Istaces N.

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

Nature Communications, 1 December 2019 by Menden M.P.

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

Nature Communications, 1 December 2019 by Orlando G.

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

Genome Biology, 19 November 2019 by Zhou N.

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

Bioinformatics, 1 November 2019 by Orlando G.

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

Systematics and Biodiversity, 18 August 2019 by Borko Š.

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

Artificial Intelligence in Medicine, August 2019 by Versbraegen N.

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)

Genetics in Medicine, 1 August 2019 by Mignot C.

12. Structural basis of the subcellular topology landscape of Escherichia coli

Frontiers in Microbiology, July 2019 by Loos M.S.

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

Nucleic Acids Research, 1 July 2019 by Renaux A.

14. Predicting disease-causing variant combinations

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

15. 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.

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

PLoS ONE, May 2019 by Descheemaeker L.

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

Genetics in Medicine, 1 April 2019 by Mignot C.

18. 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.

19. 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.

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

PLoS ONE, February 2019 by Vet S.

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

F1000Research, 2019 by Davey N.E.

22. Towards a phylogenetic measure to quantify HIV incidence

CEUR Workshop Proceedings, 2019 by Libin P.

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

F1000Research, 2019 by Shome S.

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

eLife, 2019 by Saykali B.

1. 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.

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

Scientific Reports, 1 December 2018 by Willot Q.

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

Scientific Reports, 1 December 2018 by Ancien F.

4. A global ocean atlas of eukaryotic genes

Nature Communications, 1 December 2018 by Carradec Q.

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

Brain, 1 November 2018 by Marini C.

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

Molecular Ecology Resources, November 2018 by Dellicour S.

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

Bioinformatics, 15 September 2018 by Raimondi D.

9. Microbial communities as dynamical systems

Current Opinion in Microbiology, August 2018 by Gonze D.

10. Signatures of ecological processes in microbial community time series

Microbiome, 28 June 2018 by Faust K.

11. Evolutionary dynamics of paroxysmal nocturnal hemoglobinuria

PLoS Computational Biology, June 2018 by Mon Père N.

12. 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.

13. Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

Cell, 5 April 2018 by Malta T.M.

14. Comprehensive Characterization of Cancer Driver Genes and Mutations

Cell, 5 April 2018 by Bailey M.H.

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

Biomolecular NMR Assignments, 1 April 2018 by Kieken F.

16. 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.

17. 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.

18. 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.

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

Bioinformatics, 15 January 2018 by Brysbaert G.

20. TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data [version 1; peer review: 1 approved, 1 approved with reservations]

F1000Research, 2018 by Silva T.C.

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

BMC Genomics, 2018 by Cava C.

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.

24. 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.

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

Bioinformatics, 1 October 2017 by Xu T.

5. Understanding mutational effects in digenic diseases

Nucleic Acids Research, 1 September 2017 by Gazzo A.

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

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

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

Genome Medicine, 19 July 2017 by Reggiani C.

8. 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.A.

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

Nucleic Acids Research, 3 July 2017 by Raimondi D.

11. 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.

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

BioData Mining, 6 May 2017 by Pham N.C.

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

BMC Bioinformatics, 10 February 2017 by Dalkas G.A.

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

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

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

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

16. 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.C.

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

Nucleic acids research, 4 January 2017 by Piovesan D.

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

Nucleic Acids Research, 1 January 2017 by Piovesan D.

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

Methods in Molecular Biology, 2017 by Huculeci R.

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

Nucleic Acids Research, 2017 by Dierckxsens N.

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

Human Mutation, 1 January 2017 by Raimondi 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. TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

F1000Research, 2016 by Silva T.C.

13. 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.

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.

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

PLoS Computational Biology, 1 November 2014 by Skwark M.J.

2. Predicting virus mutations through statistical relational learning

BMC Bioinformatics, September 19, 2014 by Cilia E.

3. The DynaMine webserver: Predicting protein dynamics from sequence

Nucleic Acids Research, 1 July 2014 by Cilia E.

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

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

5. 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.

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

Frontiers in Genetics, 2014 by Olsen C.

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

Genomics, 2014 by Olsen C.

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

Genomics, April 2014 by Lopes M.

1. Stability of feature selection algorithms for classification in high-throughput genomics datasets

13th IEEE International Conference on BioInformatics and BioEngineering, IEEE BIBE 2013, 2013 by Moulos P.

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.