Publications
2023
Epi-Impute: Single-Cell RNA-seq Imputation via Integration with Single-Cell ATAC-seqin International Journal of Molecular Sciences (2023)
2022
ChemPert: mapping between chemical perturbation and transcriptional response for non-cancer cellsin Nucleic Acids Research (2022)
Computational Methods to Identify Cell-Fate Determinants, Identity Transcription Factors, and Niche-Induced Signaling Pathways for Stem Cell Researchin Methods in Molecular Biology (2022)
Fostering experimental and computational synergy to modulate hyperinflammationin Trends in Immunology (2022), 43(1),
Neurodegeneration and neuroinflammation are linked, but independent of a-synuclein inclusions, in a seeding/spreading mouse model of Parkinson's disease; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Glia (2022)
The gut microbiome molecular complex in human health and disease; ; ; ; ; ;
in Cell Host and Microbe (2022), 30(9), 1201-1206
2021
Altered sphingolipid function in Alzheimer's disease; a gene regulatory network approachin Neurobiology of Aging (2021)
A Catalogus Immune Muris of the mouse immune responses to diverse pathogensin Cell Death and Disease (2021)
A computer-guided design tool to increase the efficiency of cellular conversionsin Nature Communications (2021)
Leveraging systems biology for predicting modulators of inflammation in patients with COVID-19in Science Advances (2021)
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Molecular systems biology (2021), 17(10), 10387
2020
FoxO maintains a genuine muscle stem-cell quiescent state until geriatric agein Nature Cell Biology (2020)
FunRes: resolving tissue-specific functional cell states based on a cell-cell communication network modelin Briefings in Bioinformatics (2020)
HuR/ELAVL1 drives malignant peripheral nerve sheath tumour growth and metastasisin Journal of Clinical Investigation (2020)
Multiomics data integration unveils core transcriptional regulatory networks governing cell-type identityin NPJ systems biology and applications (2020)
TransSynW: A single‐cell RNA‐sequencing based web application to guide cell conversion experimentsin Stem Cells Translational Medicine (2020)
Synapse alterations precede neuronal damage and storage pathology in a human cerebral organoid model of CLN3-juvenile neuronal ceroid lipofuscinosis; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Acta Neuropathologica Communications (2020)
Fibroblast mitochondria in idiopathic Parkinson’s disease display morphological changes and enhanced resistance to depolarization; ; ; ; ; ; ; ; ; ; ;
in Scientific Reports (2020)
COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Scientific Data (2020)
TransSynW: A single‐cell RNA‐sequencing based web application to guide cell conversion experiments; ;
in Stem Cells Translational Medicine (2020)
BioKC: a platform for quality controlled curation and annotation of systems biology models; ; ; ;
Scientific Conference (2020, September 04)
BioKC: a collaborative platform for systems biology model curation and annotation; ; ; ;
in bioRxiv (2020)
2019
Optimization ACE inhibition activity in hypertension based on random vector functional link and sine-cosine algorithm; ; ; ;
in Chemometrics and Intelligent Laboratory Systems (2019)
Alzheimer’s disease-associated (hydroxy)methylomic changes in the brain and bloodin Clinical Epigenetics (2019)
Computational Strategies for Niche-Dependent Cell Conversion to Assist Stem Cell Therapyin Trends in Biotechnology (2019)
A general computational approach to predicting synergistic transcriptional cores that determine cellsubpopulation identitiesin Nucleic Acids Research (2019)
Modeling Cellular Differentiation and Reprogramming with Gene Regulatory Networksin Modeling Cellular Differentiation and Reprogramming with Gene Regulatory Networks (2019)
Computational Strategies for Niche-Dependent Cell Conversion to Assist Stem Cell Therapy; ;
in Trends in Biotechnology (2019)
Closing the gap between formats for storing layout information in systems biology.; ; ; ;
in Briefings in bioinformatics (2019)
MINERVA API and plugins: opening molecular network analysis and visualization to the community.; ; ; ;
in Bioinformatics (2019)
Machine Learning to Support the Presentation of Complex Pathway Graphs.; ; ; ;
in IEEE/ACM transactions on computational biology and bioinformatics (2019)
A general computational approach to predicting synergistic transcriptional cores that determine cell subpopulation identities;
in Nucleic Acids Research (2019)
An integrative method to predict signallingperturbations for cellular transitions; ; ;
in Nucleic Acids Research (2019)
2018
Modeling of Cellular Systems: Application in Stem Cell Research and Computational Disease Modeling;
Book published by Springer International Publishing (2018)
Single and Multiobjective Evolutionary Algorithms for Clustering Biomedical Information with Unknown Number of Clusters; ; ; ; ; ;
in Bioinspired Optimization Methods and Their Applications (2018)
Transcriptional synergy as an emergent property defining cell subpopulation identity enables population shiftin Nature Communications (2018)
Integrative Computational Network Analysis Reveals Site-Specific Mediators of Inflammation in Alzheimer's Disease; ;
in Frontiers in Physiology (2018)
SeesawPred: A Web Application for Predicting Cell-fate Determinants in Cell Differentiation; ; ;
in Scientific Reports (2018)
Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms.; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in NPJ systems biology and applications (2018), 4
Signaling-Dependent Control of Apical Membrane Size and Self-Renewal in Rosette-Stage Human Neuroepithelial Stem Cells; ; ; ; ; ;
in Stem Cell Reports (2018)
A complex of the ubiquitin ligase TRIM32 and the deubiquitinase USP7 balances the level of c-Myc ubiquitination and thereby determines neural stem cell fate specification; ; ; ; ; ; ;
in Cell Death and Differentiation (2018)
Transcriptional synergy as an emergent property defining cell subpopulation identity enables population shift; ; ; ; ; ;
in Nature Communications (2018)
Community-driven roadmap for integrated disease maps.; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Briefings in bioinformatics (2018)
Clustering approaches for visual knowledge exploration in molecular interaction networks.; ; ; ;
in BMC bioinformatics (2018), 19(1), 308
2017
Absence of regulator of G-protein signaling 4 does not protect against dopamine neuron dysfunction and injury in the mouse 6-hydroxydopamine lesion model of Parkinson's disease; ; ; ; ; ;
in Neurobiology of Aging (2017), 58
Big-data-driven stem cell science and tissue engineering: vision and unique opportunitiesin Cell Stem Cell (2017)
Bioinformatics Tools for Genome-Wide Epigenetic Researchin Neuroepigenomics in Aging and Disease (2017)
RefBool: a reference-based algorithm for discretizing gene expression data; ;
in Bioinformatics (2017)
Prediction of Chromatin Accessibility in Gene-Regulatory Regions from Transcriptomics Data;
in Scientific Reports (2017)
Regulation of Fn14 Receptor and NF-κB Underlies Inflammation in Meniere’s Disease; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Frontiers in Immunology (2017)
Computational Systems Biology Approach for the Study of Rheumatoid Arthritis: From a Molecular Map to a Dynamical Model; ; ; ; ; ; ;
in Genomics and Computational Biology (2017)
2016
Exploring therapeutic viability of a non-dopaminergic target for Parkinson’s disease; ; ; ;
in Movement Disorders (2016), 31(2), 630
Enteric neurons from Parkinson's disease patients display ex vivo aberrations in mitochondrial structure.; ; ; ; ; ; ; ; ; ;
in Scientific reports (2016), 6
Prox1 is required for oligodendrocyte cell identity in adult neural stem cells of the subventricular zone; ; ; ; ; ; ; ; ; ; ; ;
in Stem Cells (2016)
Metaheuristic Based Clustering Algorithms for Biological Hypergraphs; ; ; ;
in Proceedings of META’2016, 6th International Conference on Metaheuristics and Nature Inspired computing (2016, October 27)
Prediction of disease-gene-drug relationships following a differential network analysis; ;
in Cell Death and Disease (2016), 7
MINERVA—a platform for visualization and curation of molecular interaction networks; ; ; ; ; ; ; ; ; ;
in NPJ Systems Biology and Applications (2016)
A generalized gene regulatory network model of stem cell differentiation for predicting lineage specifiers; ; ; ;
in Stem Cell Reports (2016)
Neurological Diseases from a Systems Medicine Point of View.; ;
in Methods in Molecular Biology (2016), 1386
A systems biology approach to identify niche determinants of cellular phenotypes; ; ;
in Stem Cell Research (2016)
Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases.; ; ; ; ; ; ; ;
in Big data (2016), 4(2), 97-108
2015
Staining for unphosphorylated alpha-synuclein in the colon mucosa. No difference between patients with Parkinson's disease and healthy controls; ; ; ; ; ; ; ; ;
Scientific Conference (2015, June)
Platelet mitochondrial membrane potential in Parkinson's disease.; ; ; ; ; ; ; ; ; ;
in Annals of clinical and translational neurology (2015), 2(1), 67-73
TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability; ; ; ; ; ; ; ; ;
in Scientific Reports (2015)
Enhancement of COPD biological networks using a web-based collaboration interface; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in F1000Research (2015), 4(32), 1-22
The RNA helicase DDX6 regulates cell-fate specification in neural stem cells via miRNAsin Nucleic Acids Research (2015)
Transcriptome of human foetal heart compared with cardiomyocytes from pluripotent stem cells;
in Development (2015)
Stemness of the hybrid Epithelial/Mesenchymal State in Breast Cancer and Its Association with Poor Survival.; ; ; ; ; ; ; ;
in PLoS ONE (2015), 10(5), 0126522
Identification of large-scale genomic variation in cancer genomes using in silico reference models;
in Nucleic Acids Research (2015)
The RNA helicase DDX6 regulates cell-fate specification in neural stem cells via miRNAs; ; ; ; ;
in Nucleic Acids Research (2015)
A computational strategy for predicting lineage specifiers in stem cell subpopulations;
in Stem Cell Research (2015)
A differential network analysis approach for lineage specifier prediction in stem cell subpopulations; ; ; ;
in NPJ Systems Biology and Applications (2015)
Discrete Logic Modelling Optimization to Contextualize Prior Knowledge Networks Using PRUNET; ; ;
in PLoS ONE (2015), 10(6), 0127216
Transcriptome of human foetal heart compared with cardiomyocytes from pluripotent stem cells; ; ; ; ; ; ; ; ;
in Development (2015)
2014
Analysis of mitochondrial membrane potential in idiopathic Parkinson's disease: A case-control study; ; ; ; ; ;
Scientific Conference (2014, June 12)
Curation of complex molecular pathways of Parkinson's disease as a collaborative scientific community effort; ; ; ; ; ;
Scientific Conference (2014, June 12)
Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytesin Protein and Cell (2014)
Gene regulatory network analysis reveals differences in site-specific cell fate determination in mammalian brain; ; ;
in Frontiers in Cellular Neuroscience (2014)
Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Molecular Neurobiology (2014)
Visualization and Classification of Protein Secondary Structures using Self-Organizing Maps; ; ; ; ;
in IEEE Symposium Series on Computational Intelligence (IEEE SSCI 2014) (2014, December)
FIGG: Simulating populations of whole genome sequences for heterogeneous data analyses.;
in BMC Bioinformatics (2014), 15(1),
Modelling Fanconi anemia pathogenesis and therapeutics using integration-free patient-derived iPSCs.; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Nature communications (2014), 5
pathPSA: A Dynamical Pathway-Based Parametric Sensitivity;
in Industrial and Engineering Chemistry (2014)
Hippocampal extracellular matrix levels and stochasticity in synaptic protein expression increase with age and are associated with age-dependent cognitive decline.; ; ; ; ; ; ; ; ; ; ;
in Molecular and Cellular Proteomics (2014)
2013
Predicting missing expression values in gene regulatory networks using a discrete logic modeling optimization guided by network stable states; ; ; ;
in Nucleic Acids Research (2013), 41(1), 8
Detecting cellular reprogramming determinants by differential stability analysis of gene regulatory networksin BMC Systems Biology (2013)
Immune-responsive gene 1 protein links metabolism to immunity by catalyzing itaconic acid production; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Proceedings of the National Academy of Sciences of the United States of America (2013)
The Parkinson's Disease Map: A Framework for Integration, Curation and Exploration of Disease-related Pathways; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Poster (2013, March 09)
2012
Gene regulatory network analysis supports inflammation as a key neurodegeneration process in prion disease.; ; ; ;
in BMC Systems Biology (2012), 6(132),
PLAU inferred from a correlation network is critical for suppressor function of regulatory T cellsin Molecular Systems Biology (2012)
Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.; ; ; ; ; ; ;
in BMC Bioinformatics (2012), 13
A Novel Network Integrating a miRNA-203/SNAI1 Feedback Loop which Regulates Epithelial to Mesenchymal Transition.; ; ; ; ; ; ;
in PLoS ONE (2012), 7(4), 35440
Evolutionary conservation and network structure characterize genes of phenotypic relevance for mitosis in human; ;
in PLoS ONE (2012), 7(5), 36488
Constructing a comprehensive map of Parkinson’s disease to elucidate underlying mechanisms of its multifaceted molecular pathology; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Poster (2012, August)
2011
PPARγ population shift produces disease-related changes in molecular networks associated with metabolic syndrome; ; ; ;
in Cell Death and Disease (2011), 2(8), 192
2010
2009
Methyl side-chain dynamics prediction based on protein structure;
in Bioinformatics (2009), 25(19), 2552-8
Energetic determinants of protein binding specificity: insights into protein interaction networks; ;
in Proteomics (2009), 9(7), 1744-53
Residues crucial for maintaining short paths in network communication mediate signaling in proteins; ; ;
in Molecular Systems Biology (2009), 2
The origin of Allosteric Modulation: Multiple Pre-existing Pathways Selection; ; ;
in Structure (2009), 17(8), 1042-1050
Multiobjective Classification with moGEP: An Application in the Network Traffic Domain; ;
in GECCO '09: Proceedings of the 11th Annual conference on Genetic and evolutionary computation (2009)
Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms; ;
in Molecular Biosystems (2009), 5(3), 207-16
