Publications

In press

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See detailAbsence 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
Ashrafi, Amer; Garcia, Pierre; Kollmus, Heike; Schughart, Klaus; del Sol Mesa, Antonio; Buttini, Manuel; Glaab, Enrico

in Neurobiology of Aging (in press)

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2017

See detailBioinformatics Tools for Genome-Wide Epigenetic Research
del Sol Mesa, Antonio

in Neuroepigenomics in Aging and Disease (2017)

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See detailRefBool: a reference-based algorithm for discretizing gene expression data
del Sol Mesa, Antonio; Jung Geb. Zickenrott, Sascha; Hartmann, Andras

in Bioinformatics (2017)

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See detailPrediction of Chromatin Accessibility in Gene-Regulatory Regions from Transcriptomics Data
del Sol Mesa, Antonio; Zickenrott, Sascha

in Scientific Reports (2017)

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2016

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See detailGene Regulatory Network Inference of Immunoresponsive Gene 1 (IRG1) Identifies Interferon Regulatory Factor 1 (IRF1) as Its Transcriptional Regulator in Mammalian Macrophages
Antony, Paul; Tallam, Aravind; Perumal, Thanneer Malai; Jäger, Christian; Fritz, Joëlle; Balling, Rudi; del Sol Mesa, Antonio; Michelucci, Alessandro; Vallar, Laurent

in PLoS ONE (2016)

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See detailProx1 is required for oligodendrocyte cell identity in adult neural stem cells of the subventricular zone
Bunk, Eva; Ertaylan, Goekhan; Ortega, Felipe; Pavlou, Maria; Gonzalez Cano, Laura; Stergiopoulos, Athanasios; Safaiyan, Shima; Voels, Sandra; van Cann, Marianne; Politis, Panagiotis; Berninger, Benedikt; del Sol Mesa, Antonio; Schwamborn, Jens Christian

in Stem Cells (2016)

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See detailMetaheuristic Based Clustering Algorithms for Biological Hypergraphs
Changaival, Boonyarit; Danoy, Grégoire; Ostaszewski, Marek; Lavangnananda, Kittichai; Bouvry, Pascal

in Proceedings of META’2016, 6th International Conference on Metaheuristics and Nature Inspired computing (2016, October 27)

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See detailPrediction of disease-gene-drug relationships following a differential network analysis
del Sol Mesa, Antonio; Zickenrott, Sascha; Espinosa Angarica, Vladimir

in Cell Death & Disease (2016), 7

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See detailMINERVA—a platform for visualization and curation of molecular interaction networks
Gawron, Piotr; Ostaszewski, Marek; Satagopam, Venkata; Gebel, Stephan; Mazein, Alexander; Kuzma, Michael; Zorzan, Simone; McGee, Fintan; Otjacques, Benoit; Balling, Rudi; Schneider, Reinhard

in NPJ Systems Biology and Applications (2016)

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See detailA generalized gene regulatory network model of stem cell differentiation for predicting lineage specifiers
Okawa, Satoshi; Nicklas, Sarah; Zickenrott, Sascha; Schwamborn, Jens Christian; del Sol Mesa, Antonio

in Stem Cell Reports (2016)

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See detailNeurological Diseases from a Systems Medicine Point of View.
Ostaszewski, Marek; Skupin, Alexander; Balling, Rudi

in Methods in molecular biology (Clifton, N.J.) (2016), 1386

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See detailA systems biology approach to identify niche determinants of cellular phenotypes
Ravichandran, Srikanth; Okawa, Satoshi; Martinez Arbas, Susana; del Sol Mesa, Antonio

in Stem Cell Research (2016)

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See detailIntegration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases.
Satagopam, Venkata; Gu, Wei; Eifes, Serge; Gawron, Piotr; Ostaszewski, Marek; Gebel, Stephan; Barbosa-Silva, Adriano; Balling, Rudi; Schneider, Reinhard

in Big data (2016), 4(2), 97-108

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2015

See detailStaining for unphosphorylated alpha-synuclein in the colon mucosa. No difference between patients with Parkinson's disease and healthy controls
Antony, Paul; Antunes, L; Frasquilho, S; Ostaszewski, Marek; Weber, J; Longhino, L; Baumuratov, Aidos; Derkinderen, P; Balling, Rudi; Diederich, Nico

Scientific Conference (2015, June)

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See detailPlatelet mitochondrial membrane potential in Parkinson's disease.
Antony, Paul; Boyd, Olga; Trefois, Christophe; Ammerlaan, Wim; Ostaszewski, Marek; Baumuratov, Aidos S.; Longhino, Laura; Antunes, Laurent; Koopman, Werner; Balling, Rudi; Diederich, Nico J.

in Annals of clinical and translational neurology (2015), 2(1), 67-73

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See detailTRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability
Bahnassawy, Lamia’a; Perumal, Thanneer; Gonzalez Cano, Laura; Hillje, Anna-Lena; Taher, Leila; Makalowski, Wojciech; Suzuki, Yutaka; Fuellen, Georg; del Sol Mesa, Antonio; Schwamborn, Jens Christian

in Scientific Reports (2015)

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See detailEnhancement of COPD biological networks using a web-based collaboration interface
Boue, Stephanie; Fields, Brett; Hoeng, Julia; Park, Jennifer; Peitsch, Manuel C.; Schlage, Walter K.; Talikka, Marja; Binenbaum, Ilona; Bondarenko, Vladimir; Bulgakov, Oleg V.; Cherkasova, Vera; Diaz-Diaz, Norberto; Fedorova, Larisa; Guryanova, Svetlana; Guzova, Julia; Igorevna Koroleva, Galina; Kozhemyakina, Elena; Kumar, Rahul; Lavid, Noa; Lu, Qingxian; Menon, Swapna; Ouliel, Yael; Peterson, Samantha C.; Prokhorov, Alexander; Sanders, Edward; Schrier, Sarah; Schwaitzer Neta, Golan; Shvydchenko, Irina; Tallam, Aravind; Villa-Fombuena, Gema; Wu, John; Yudkevich, Ilya; Zelikman, Mariya

in F1000Research (2015), 4(32), 1-22

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See detailTranscriptome of human foetal heart compared with cardiomyocytes from pluripotent stem cells
del Sol Mesa, Antonio; Mummery, Christine

in Development (2015)

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See detailStemness of the hybrid Epithelial/Mesenchymal State in Breast Cancer and Its Association with Poor Survival.
Grosse-Wilde, Anne; Fouquier d'Hérouël, Aymeric; McIntosh, Ellie; Ertaylan, Gökhan; Skupin, Alexander; Kuestner, Rolf E.; del Sol Mesa, Antonio; Walters, Kathie-Anne; Huang, Sui

in PLoS ONE (2015), 10(5), 0126522

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See detailIdentification of large-scale genomic variation in cancer genomes using in silico reference models
Killcoyne, Sarah; del Sol Mesa, Antonio

in Nucleic Acids Research (2015)

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See detailThe RNA helicase DDX6 regulates cell-fate specification in neural stem cells via miRNAs
Nicklas, Sarah; Okawa, Satoshi; Hillje, Anna-Lena; Gonzalez Cano, Laura; del Sol Mesa, Antonio; Schwamborn, Jens Christian

in Nucleic Acids Research (2015)

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See detailA computational strategy for predicting lineage specifiers in stem cell subpopulations
Okawa, Satoshi; del Sol Mesa, Antonio

in Stem Cell Research (2015)

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See detailA differential network analysis approach for lineage specifier prediction in stem cell subpopulations
Okawa, Satoshi; Espinosa Angarica, Vladimir; Lemischka, Ihor; Moore, Kateri; del Sol Mesa, Antonio

in Systems Biology and Applications (2015)

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See detailDiscrete Logic Modelling Optimization to Contextualize Prior Knowledge Networks Using PRUNET
Rodriguez, Ana; Crespo, Isaac; Androsova, Ganna; del Sol Mesa, Antonio

in PLoS ONE (2015), 10(6), 0127216

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See detailTranscriptome of human foetal heart compared with cardiomyocytes from pluripotent stem cells
W. van den Berg, Cathelijne; Okawa, Satoshi; M. Chuva de Sousa Lopes, Susana; van Iperen, Liesbeth; Passier, Robert; R. Braam, Stefan; G. Tertoolen, Leon; del Sol, Antonio; P. Davis, Richard; L. Mummery, Christine

in Development (2015)

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2014

See detailAnalysis of mitochondrial membrane potential in idiopathic Parkinson's disease: A case-control study
Antony, Paul; Boyd, Olga; Trefois, Christophe; Ostaszewski, Marek; Baumuratov, Aidos; Balling, Rudi; Diederich, Nico

Scientific Conference (2014, June 12)

See detailCuration of complex molecular pathways of Parkinson's disease as a collaborative scientific community effort
Antony, Paul; Ostaszewski, Marek; Gawron, P; Trefois, Christophe; Fujita, K.A.; Mosch, Sabine; Balling, Rudi

Scientific Conference (2014, June 12)

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See detailA population shift view of cellular reprogramming
del Sol Mesa, Antonio

in Stem Cells (2014)

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See detailGene regulatory network analysis reveals differences in site-specific cell fate determination in mammalian brain
Ertaylan, Gökhan; Okawa, Satoshi; Schwamborn, Jens Christian; del Sol Mesa, Antonio

in Frontiers in Cellular Neuroscience (2014)

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See detailIntegrating Pathways of Parkinson's Disease in a Molecular Interaction Map
Fujita, Kazuhiro A.; Ostaszewski, Marek; Matsuoka, Yukiko; Ghosh, Samik; Glaab, Enrico; Trefois, Christophe; Crespo, Isaac; Perumal, Thanneer Malai; Jurkowski, Wiktor; Antony, Paul; Diederich, Nico; Buttini, Manuel; Kodama, Akihiko; Satagopam, Venkata; Eifes, Serge; del Sol Mesa, Antonio; Schneider, Reinhard; Kitano, Hiroaki; Balling, Rudi

in Molecular Neurobiology (2014)

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See detailVisualization and Classification of Protein Secondary Structures using Self-Organizing Maps
Grevisse, Christian; Muller, Ian William; Jimenez Laredo, Juan Luis; Ostaszewski, Marek; Danoy, Grégoire; Bouvry, Pascal

in IEEE Symposium Series on Computational Intelligence (IEEE SSCI 2014) (2014, December)

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See detailFIGG: Simulating populations of whole genome sequences for heterogeneous data analyses.
Killcoyne, Sarah; del Sol Mesa, Antonio

in BMC Bioinformatics (2014), 15(1),

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See detailModelling Fanconi anemia pathogenesis and therapeutics using integration-free patient-derived iPSCs.
Liu, Guang-Hui; Suzuki, Keiichiro; Li, Mo; Qu, Jing; Montserrat, Nuria; Tarantino, Carolina; Gu, Ying; Yi, Fei; Xu, Xiuling; Zhang, Weiqi; Ruiz, Sergio; Plongthongkum, Nongluk; Zhang, Kun; Masuda, Shigeo; Nivet, Emmanuel; Tsunekawa, Yuji; Soligalla, Rupa Devi; Goebl, April; Aizawa, Emi; Kim, Na Young; Kim, Jessica; Dubova, Ilir; Li, Ying; Ren, Ruotong; Benner, Chris; del Sol Mesa, Antonio; Bueren, Juan; Trujillo, Juan Pablo; Surralles, Jordi; Cappelli, Enrico; Dufour, Carlo; Esteban, Concepcion Rodriguez; Izpisua Belmonte, Juan Carlos

in Nature communications (2014), 5

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See detailpathPSA: A Dynamical Pathway-Based Parametric Sensitivity
Perumal, Thanneer Malai; Gunawan, Rudiyanto

in Industrial and Engineering Chemistry (2014)

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See detailHippocampal extracellular matrix levels and stochasticity in synaptic protein expression increase with age and are associated with age-dependent cognitive decline.
Vegh, Marlene J.; Rausell, Antonio; Loos, Maarten; Heldring, Celine M.; Jurkowski, Wiktor; van Nierop, Pim; Paliukovich, Iryna; Li, Ka Wan; del Sol Mesa, Antonio; Smit, August B.; Spijker, Sabine; van Kesteren, Ronald E.

in Molecular & cellular proteomics : MCP (2014)

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2013

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See detailPredicting missing expression values in gene regulatory networks using a discrete logic modeling optimization guided by network stable states
Crespo, Isaac; Krishna, Abhimanyu; Le Béchec, Antony; del Sol Mesa, Antonio; *Co-first-authors

in Nucleic Acids Research (2013), 41(1), 8

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See detailImmune-responsive gene 1 protein links metabolism to immunity by catalyzing itaconic acid production
Michelucci, Alessandro; Cordes, Thekla; Ghelfi, Jenny; Pailot, Arnaud; Reiling, Norbert; Goldmann, Oliver; Binz, Tina; Wegner, André; Tallam, Aravind; Rausell, Antonio; Buttini, Manuel; Linster, Carole; Medina, Eva; Balling, Rudi; Hiller, Karsten

in Proceedings of the National Academy of Sciences of the United States of America (2013)

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See detailThe Parkinson's Disease Map: A Framework for Integration, Curation and Exploration of Disease-related Pathways
Ostaszewski, Marek; Fujita, Kazuhiro; Matsuoka, Yukiko; Ghosh, Samik; Glaab, Enrico; Trefois, Christophe; Crespo, Isaac; Perumal, Thanneer Malai; Jurkowski, Wiktor; Antony, Paul; Diederich, Nico; Buttini, Manuel; Kolodkin, Alexey; Kodama, Akihiko; Satagopam, Venkata; Biryukov, Maria; Eifes, Serge; del Sol Mesa, Antonio; Schneider, Reinhard; Kitano, Hiroaki; Balling, Rudi

Poster (2013, March 09)

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2012

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See detailGene regulatory network analysis supports inflammation as a key neurodegeneration process in prion disease.
Crespo, Isaac; Rump, Kirsten; Jurkowski, Wiktor; Kitano, H.; del Sol Mesa, Antonio

in BMC Systems Biology (2012), 6(132),

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See detailHydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.
Lewis, Steven; Csordas, Attila; Killcoyne, Sarah; Hermjakob, Henning; Hoopmann, Michael R.; Moritz, Robert L.; Deutsch, Eric W.; Boyle, John

in BMC Bioinformatics (2012), 13

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See detailA Novel Network Integrating a miRNA-203/SNAI1 Feedback Loop which Regulates Epithelial to Mesenchymal Transition.
Moes, Michèle; Le Béchec, Antony; Crespo, Isaac; Laurini, Christina; Halavatyi, Aliaksandr; Vetter, G.; del Sol Mesa, Antonio; Friederich, A.

in PLoS ONE (2012), 7(4), 35440

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See detailEvolutionary conservation and network structure characterize genes of phenotypic relevance for mitosis in human
Ostaszewski, Marek; Eifes, Serge; del Sol Mesa, Antonio

in PLoS ONE (2012), 7(5), 36488

See detailConstructing a comprehensive map of Parkinson’s disease to elucidate underlying mechanisms of its multifaceted molecular pathology
Trefois, Christophe; Fujita, A. K.; Ostaszewski, Marek; Matsuoka, Yukiko; Ghosh, Samic; Glaab, Enrico; Crespo, Isaac; Perumal, T. M.; Jurkowski, Wiktor; Antony, Paul; Diederich, Nico; Buttini, Manuel; Kodama, Akihiko; Satagopam, Venkata; Eifes, Serge; del Sol Mesa, Antonio; Schneider, Reinhard; Kitano, Hiroaki; Balling, Rudi

Poster (2012, August)

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2011

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See detailPPARγ population shift produces disease-related changes in molecular networks associated with metabolic syndrome
Jurkowski, Wiktor; Roomp, Kirsten; Crespo, Isaac; Schneider, Jochen; del Sol Mesa, Antonio

in Cell Death & Disease (2011), 2(8), 192

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2010

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See detailDiseases as network perturbations
del Sol Mesa, Antonio; Balling, Rudi; Hood, Leroy; Galas, David J.

in Current Opinion in Biotechnology (2010), 21(4), 566-571

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2009

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See detailMethyl side-chain dynamics prediction based on protein structure
Carbonell, P.; del Sol Mesa, Antonio

in Bioinformatics (2009), 25(19), 2552-8

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See detailEnergetic determinants of protein binding specificity: insights into protein interaction networks
Carbonell, P.; Nussinov, R.; del Sol Mesa, Antonio

in Proteomics (2009), 9(7), 1744-53

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See detailResidues crucial for maintaining short paths in network communication mediate signaling in proteins
del Sol Mesa, Antonio; Fujihashi, Hirotomo; Amoros, Dolors; Nussinov, Ruth

in Molecular Systems Biology (2009), 2

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See detailThe origin of Allosteric Modulation: Multiple Pre-existing Pathways Selection
del Sol Mesa, Antonio; Tsai, Chung-Jung; Ma, Buyong; Nussinov, Ruth

in Structure (2009), 17(8), 1042-1050

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See detailMultiobjective Classification with moGEP: An Application in the Network Traffic Domain
Ostaszewski, Marek; Bouvry, Pascal; Seredynski, Franciszek

in GECCO '09: Proceedings of the 11th Annual conference on Genetic and evolutionary computation (2009)

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See detailProtein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms
Tsai, C. J.; del Sol Mesa, Antonio; Nussinov, R.

in Molecular Biosystems (2009), 5(3), 207-16

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