Publications

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

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

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

The hitchhiker's guide to single-locus species delimitation

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

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

Microbial communities as dynamical systems

Signatures of ecological processes in microbial community time series

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

Evolutionary dynamics of paroxysmal nocturnal hemoglobinuria

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

Comprehensive Characterization of Cancer Driver Genes and Mutations

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

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

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

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

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

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

AmyPro: A database of proteins with validated amyloidogenic regions

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

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

Correction to: IQSEC2-related encephalopathy in males and females: a comparative study including 37 novel patients (Genetics in Medicine, (2018), 10.1038/s41436-018-0268-1)

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

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

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

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

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

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

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

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

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

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

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

Physical and molecular bases of protein thermal stability and cold adaptation

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

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

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

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

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

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

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

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

How interacting pathways are regulated by miRNAs in breast cancer subtypes

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

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

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

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

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

PharmacoGx: An R package for analysis of large pharmacogenomic datasets

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

A blocking strategy for ranking features according to probabilistic relevance

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

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

DIDA: A curated and annotated digenic diseases database

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