Publications

Neuregulin-4 Is Required for Maintaining Soma Size of Pyramidal Neurons in the Motor Cortex

B. Paramo, S. (O.) Bachmann, S. (J.) Baudouin, I. Martinez-Garay, A. (M.) Davies. eNeuro, 8(1):ENEURO.0288-20.2021 (2021)

 

Rescue of oxytocin response and social behaviour in a mouse model of autism

H. Hörnberg, E. Pérez-Garci, D. Schreiner, L. Hatstatt-Burklé, F. Magara, S. Baudouin, A. Matter, K. Nacro, E. Pecho-Vrieseling, P. Scheiffele. Nature, 584(7820):252-256 (2020)

 

Evidence for a Contribution of the Nlgn3/Cyfip1/Fmr1 Pathway in the Pathophysiology of Autism Spectrum Disorders

M. Sledziowska, J. Galloway, S. (J.) Baudouin. Review Neuroscience, 445:31-41 (2020)

 

Complex Interactions between Genes and Social Environment Cause Phenotypes Associated with Autism Spectrum Disorders in Mice

M. Sledziowska, S. Kalbassi, S. (J.) Baudouin. eNeuro, 7(4):ENEURO.0124-20.2020 (2020)

 

Behavioral training rescues motor deficits in Cyfip1 haploinsufficiency mouse model of autism spectrum disorders

S. (O.) Bachmann, M. Sledziowska, E. Cross, S. Kalbassi, S. Waldron, F. Chen, A. Ranson, S. (J.) Baudouin. Transl Psychiatry, 9(1):29 (2019)

 

Explorations and perspectives on the neurobiological bases of autism spectrum disorder

J. (J.) Foxe, S. Molholm, S. (J.) Baudouin, M. (T.) Wallace. Eur J Neurosci, 47(6):488-496 (2018)

 

Male and Female Mice Lacking Neuroligin-3 Modify the Behavior of Their Wild-Type Littermates

S. Kalbassi, S. (O.) Bachmann, E. Cross, V. (H.) Roberton, S. (J.) Baudouin. eNeur, 4(4):ENEURO.0145-17.2017 (2017)

 

Heterogeneity and convergence: the synaptic pathophysiology of autism

S. (J.) Baudouin. Eur J Neurosci, 39(7):1107-13 (2014)

 

Chronic administration of AFQ056/Mavoglurant restores social behaviour in Fmr1 knockout mice

I. Gantois, A. (S.) Pop, C. (E.) F de Esch, R. (A. M.) Buijsen, T. Pooters, B. Gomez-Mancilla, F. Gasparini, B. (A.) Oostra, R. D’Hooge, R. Willemsen. Behav Brain Res, 239:72-9 (2013)

 

Impaired spatial memory in mice lacking CD3ζ is associated with altered NMDA and AMPA receptors signaling independent of T-cell deficiency

A. Louveau, J. Angibaud, F. Haspot, M. (C.) Opazo, R. Thinard, V. Thepenier, S. (J.) Baudouin, L. Lescaudron, P. Hulin, C. (A.) Riedel, H. Boudin. J Neurosci, 33(47):18672-85 (2013)

 

Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling

E. (C.) Budreck, O. Kwon, J. (H.) Jung, S. Baudouin, A. Thommen, H. (S.) Kim, Y. Fukazawa, H. Harada, K. Tabuchi, R. Shigemoto, P. Scheiffele, J. Kim. Proc Natl Acad Sci U S A, 110(2):725-30 (2013)

 

Shared synaptic pathophysiology in syndromic and nonsyndromic rodent models of autism

S. (J.) Baudouin, J. Gaudias, S. Gerharz, L. Hatstatt, K. Zhou, P. Punnakkal, K. (F.) Tanaka, W. Spooren, R. Hen, C. (I.) De Zeeuw, K. Vogt, P. Scheiffele. Science, 338(6103):128-32 (2012)

 

Tweaking the social network

B. Gomez-Mancilla. Sci Transl Med, 25;4(131):131fs9 (2012)

 

The immune molecule CD3zeta and its downstream effectors ZAP-70/Syk mediate ephrin signaling in neurons to regulate early neuritogenesis

J. Angibaud, A. Louveau, S. (J.) Baudouin, V. Nerrière-Daguin, S. Evain, V. Bonnamain, P. Hulin, Z. Csaba, P. Dournaud, R. Thinard, P. Naveilhan, N. Noraz, V. Pellier-Monnin, H. Boudin. J Neurochem, 119(4):708-22 (2011)

 

SnapShot: Neuroligin-neurexin complexes

S. Baudouin, P. Scheiffele. Cell, 141(5):908, 908.e1. (2010)

 

The signaling adaptor protein CD3zeta is a negative regulator of dendrite development in young neurons

S. (J.) Baudouin, J. Angibaud, G. Loussouarn, V. Bonnamain, A. Matsuura, M. Kinebuchi, P. Naveilhan, H. Boudin. Mol Biol Cell 19(6):2444-56 (2008)

 

Dendrite-selective redistribution of the chemokine receptor CXCR4 following agonist stimulation

S. (J.) Baudouin, F. Pujol, A. Nicot, P. Kitabgi, H. Boudin. Mol Cell Neurosci, 33(2):160-9 (2006)

 

A white paper on a neurodevelopmental framework for drug discovery in autism and other neurodevelopmental disorders

C. (M.) Díaz-Caneja, M. (W.) State, R. (J.) Hagerman, S. Jacquemont, O. Marín, C. Bagni, D. Umbricht, E. Simonoff, F. de Andrés-Trelles, A. Kaale, G. Pandina, B. Gómez-Mancilla, P. (P.) Wang, J. Cusak, S. Siafis, S. Leucht, M. Parellada, E. Loth, T. Charman, J. (K.) Buitelaar, D. Murphy, C. Arango. Eur Neuropsychopharmacol, S0924-977X(21)00150-4 (2021)

 

CGG Repeat-Induced FMR1 Silencing Depends on the Expansion Size in Human iPSCs and Neurons Carrying Unmethylated Full Mutations

U. Brykczynska, E. Pecho-Vrieseling, A. Thiemeyer, J. Klein, I. Fruh, T. Doll, C. Manneville, S. Fuchs, M. Iazeolla, M. Beibel, G. Roma, U. Naumann, N. Kelley, E. (J.) Oakeley, M. Mueller, B. Gomez-Mancilla, M. Bühler, E. Tabolacci, P. Chiurazzi, G.Neri, T. Bouwmeester, F. (P.) Di Giorgio, B. (D.) Fodor. Stem Cell Reports, 7(6):1059-1071 (2016)

 

High-Throughput Screening Using iPSC-Derived Neuronal Progenitors to Identify Compounds Counteracting Epigenetic Gene Silencing in Fragile X Syndrome

M. Kaufmann, A. Schuffenhauer, I. Fruh, J. Klein, A. Thiemeyer, P. Rigo, B. Gomez-Mancilla, V. Heidinger-Millot, T. Bouwmeester, U. Schopfer, M. Mueller, B. D. Fodor, A. Cobos-Correa. J Biomol Screen, 20(9):1101-11 (2015)

 

EMMPRIN/CD147 is a novel coreceptor of VEGFR-2 mediating its activation by VEGF

F. Khayati, L. Pérez-Cano, K. Maouche, A. Sadoux, Z. Boutalbi, M. (P.) Podgorniak, U. Maskos, N. Setterblad, A. Janin, F. Calvo, C. Lebbé, S. Menashi, J. Fernandez-Recio, S. Mourah. Oncotarget, 6(12):9766-80 (2015)

 

Obsessive compulsive disorder and the glutamatergic system

C. Kariuki-Nyuthe, B. Gomez-Mancilla, D. (J.) Stein. Curr Opin Psychiatry, 27(1):32-7 (2014)

 

Fragile X syndrome: a preclinical review on metabotropic glutamate receptor 5 (mGluR5) antagonists and drug development

A. (S.) Pop, B. Gomez-Mancilla, G. Neri, R. Willemsen, F. Gasparini. Psychopharmacology (Berl), 231(6):1217-26 (2014)

 

Molecular basis for prospective pharmacological treatment strategies in intellectual disability syndromes

C. Verpelli, I. Galimberti, B. Gomez-Mancilla, C. Sala. Dev Neurobiol, 74(2):197-206 (2014)

 

Heterogeneity and convergence: the synaptic pathophysiology of autism

S. (J.) Baudouin. Eur J Neurosci, 39(7):1107-13 (2014)

 

Translating molecular advances in fragile X syndrome into therapy: a review

R. (J.) Hagerman, V. Des-Portes, F. Gasparini, S. Jacquemont, B. Gomez-Mancilla. J Clin Psychiatry, 75(4):e294-307 (2014)

 

Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling

E. (C.) Budreck, O. Kwon, J. (H.) Jung, S. Baudouin, A. Thommen, H. (S.) Kim, Y. Fukazawa, H. Harada, K. Tabuchi, R. Shigemoto, P. Scheiffele, J. Kim. Proc Natl Acad Sci U S A, 110(2):725-30 (2013)

 

The mGluR5 antagonist AFQ056 does not affect methylation and transcription of the mutant FMR1 gene in vitro

E. Tabolacci, F. Pirozzi, B. Gomez-Mancilla, F. Gasparini, G. Neri. BMC Med Genet, 13:13 (2012)

 

Ectopic expression of the immune adaptor protein CD3zeta in neural stem/progenitor cells disrupts cell-fate specification

J. Angibaud, S. (J.) Baudouin, A. Louveau, V. Nerrière-Daguin, V. Bonnamain, Z. Csaba, P. Dournaud, P. Naveilhan, N. Noraz, V. Pellier-Monnin, H. Boudin. J Mol Neurosci, 46(2):431-41 (2012)

 

Dendrite-selective redistribution of the chemokine receptor CXCR4 following agonist stimulation

S. (J.) Baudouin, F. Pujol, A. Nicot, P. Kitabgi, H. Boudin. Mol Cell Neurosci, 33(2):160-9 (2006)

 

Central nervous system drug development: an integrative biomarker approach toward individualized medicine

B. Gomez-Mancilla, E. Marrer, J. Kehren, A. Kinnunen, G. Imbert, R. Hillebrand, M. Bergström, M. (E.) Schmidt. NeuroRx, 2(4):683-95 (2005)

A white paper on a neurodevelopmental framework for drug discovery in autism and other neurodevelopmental disorders

C. (M.) Díaz-Caneja, M. (W.) State, R. (J.) Hagerman, S. Jacquemont, O. Marín, C. Bagni, D. Umbricht, E. Simonoff, F. de Andrés-Trelles, A. Kaale, G. Pandina, B. Gómez-Mancilla, P. (P.) Wang, J. Cusak, S. Siafis, S. Leucht, M. Parellada, E. Loth, T. Charman, J. (K.) Buitelaar, D. Murphy, C. Arango. Eur Neuropsychopharmacol, S0924-977X(21)00150-4 (2021)

 

Explorations and perspectives on the neurobiological bases of autism spectrum disorder

J. (J.) Foxe, S. Molholm, S. (J.) Baudouin, M. (T.) Wallace. Eur J Neurosci, 47(6):488-496 (2018)

 

Protein synthesis levels are increased in a subset of individuals with fragile X syndrome

S. Jacquemont, L. Pacini, A. (E.) Jønch, G. Cencelli, I. Rozenberg, Y. He, L. D’Andrea, G. Pedini, M. Eldeeb, R. Willemsen, F. Gasparini, F. Tassone, R. Hagerman, B. Gomez-Mancilla, C. Bagni. H. (M.). Genet, 27(21):3825 (2018)

 

Drug development for neurodevelopmental disorders: lessons learned from fragile X syndrome

E. (M.) Berry-Kravis, L. Lindemann, A. (E.) Jønch, G. Apostol, M. (F.) Bear, R. (L.) Carpenter, J. (N.) Crawley, A. Curie, V. Des Portes, F. Hossain, F. Gasparini, B. Gomez-Mancilla, D. Hessl, E. Loth, S. (H.) Scharf, P. (P.) Wang, F. Von Raison, R. Hagerman, W. Spooren, S. Jacquemont. Nat Rev Drug Discov, 17(4):280-299 (2018)

 

Reciprocal changes in DNA methylation and hydroxymethylation and a broad repressive epigenetic switch characterize FMR1 transcriptional silencing in fragile X syndrome

S. Brasa, A. Mueller, S. Jacquemont, F. Hahne, I. Rozenberg, T. Peters, Y. He, C. McCormack, F. Gasparini, S. Chibout, O. Grenet, J. Moggs, B. Gomez-Mancilla, R. Terranova. Clin Epigenetics, 8:15 (2016)

 

Assessment of Cognitive Outcome Measures in Teenagers with 15q13.3 Microdeletion Syndrome

E. Crutcher, M. Ali, J. Harrison, J. Sovago, B. Gomez-Mancilla, C. (P.) Schaaf. J Autism Dev Disord, 46(4):1455-63 (2016)

 

High-Throughput Screening Using iPSC-Derived Neuronal Progenitors to Identify Compounds Counteracting Epigenetic Gene Silencing in Fragile X Syndrome

M. Kaufmann, A. Schuffenhauer, I. Fruh, J. Klein, A. Thiemeyer, P. Rigo, B. Gomez-Mancilla, V. Heidinger-Millot, T. Bouwmeester, U. Schopfer, M. Mueller, B. D. Fodor, A. Cobos-Correa. J Biomol Screen, 20(9):1101-11 (2015)

 

Obsessive compulsive disorder and the glutamatergic system

C. Kariuki-Nyuthe, B. Gomez-Mancilla, D. (J.) Stein. Curr Opin Psychiatry, 27(1):32-7 (2014)

 

Development of mavoglurant and its potential for the treatment of fragile X syndrome

B. Gomez-Mancilla, E. Berry-Kravis, R. Hagerman, F. von Raison, G. Apostol, M. Ufer, F. Gasparini, S. Jacquemont. Expert Opin Investig Drugs, 23(1):125-34 (2014)

 

Molecular basis for prospective pharmacological treatment strategies in intellectual disability syndromes

C. Verpelli, I. Galimberti, B. Gomez-Mancilla, C. Sala. Dev Neurobiol, 74(2):197-206 (2014)

 

The challenges of clinical trials in fragile X syndrome

S. Jacquemont, E. Berry-Kravis, R. Hagerman, F. von Raison, F. Gasparini, G. Apostol, M. Ufer, V. Des Portes, B. Gomez-Mancilla. Psychopharmacology (Berl), 231(6):1237-50 (2014)

 

Translating molecular advances in fragile X syndrome into therapy: a review

R. (J.) Hagerman, V. Des-Portes, F. Gasparini, S. Jacquemont, B. Gomez-Mancilla. J Clin Psychiatry, 75(4):e294-307 (2014)

 

Epigenetic modification of the FMR1 gene in fragile X syndrome is associated with differential response to the mGluR5 antagonist AFQ056

S. Jacquemont, A. Curie, V. des Portes, M. (G.) Torrioli, E. Berry-Kravis, R. (J.) Hagerman, F. (J.) Ramos, K. Cornish, Y. He, C. Paulding, G. Neri, F. Chen, N. Hadjikhani, D. Martinet, J. Meyer, J. (S.) Beckmann, K. Delange, A. Brun, G. Bussy, F. Gasparini, T. Hilse, A. Floesser, J. Branson, G. Bilbe, D. Johns, B. Gomez-Mancilla. Sci Transl Med, 3(64):64ra1 (2011)

 

Central nervous system drug development: an integrative biomarker approach toward individualized medicine

B. Gomez-Mancilla, E. Marrer, J. Kehren, A. Kinnunen, G. Imbert, R. Hillebrand, M. Bergström, M. (E.) Schmidt. NeuroRx, 2(4):683-95 (2005)

 

Pharmacogenetics and pharmacogenomics in drug development and regulatory decision making: report of the first FDA-PWG-PhRMA-DruSafe Workshop

L. (J.) Lesko, R. (A.) Salerno, B. (B.) Spear, D. (C.) Anderson, T. Anderson, C. Brazell, J. Collins, A. Dorner, D. Essayan, B. Gomez-Mancilla, J. Hackett, S. Huang, S. Ide, J. Killinger, J. Leighton, E. Mansfield, R. Meyer, S. (G.) Ryan, V. Schmith, P. Shaw, F. Sistare, M. Watson, A. Worobec. J Clin Pharmacol, 43(4):342-58 (2003)

 

Elements of informed consent for pharmacogenetic research; perspective of the pharmacogenetics working group

D. (C.) Anderson, B. Gomez-Mancilla, B. (B.) Spear, D. (M.) Barnes, K. Cheeseman, P. (M.) Shaw, J. Friedman, A. McCarthy, C. Brazell, S. (C.) Ray, D. McHale, L. Hashimoto, R. Sandbrink, M. (L.) Watson, R. (A.) Salerno, N. Cohen, C. (E.) Lister, Pharmacogenetics Working Group. Pharmacogenomics J, 2(5):284-92 (2002)

Brain gene co-expression networks link complement signaling with convergent synaptic pathology in schizophrenia

M. Kim, J. (R.) Haney, P. Zhang, L. (M.) Hernandez, L. (K.) Wang, L. Perez-Cano, L. (M. O.) Loohuis, L. de la Torre-Ubieta, M. (J.) Gandal. Nat Neurosci, PMID: 33958802 (2021)

 

Impairment of the mitochondrial one-carbon metabolism enzyme SHMT2 causes a novel brain and heart developmental syndrome

À. García-Cazorla, E. Verdura, N. Juliá-Palacios, E. (N.) Anderson, L. Goicoechea, L. Planas-Serra, E. Tsogtbaatar, N. (R.) Dsouza, A. Schlüter, R. Urreizti, J. (M.) Tarnowski, R. (H.) Gavrilova, SHMT2 Working Group; M. Ruiz, A. Rodríguez-Palmero, S. Fourcade, B. Cogné, T. Besnard, M. Vincent, S. Bézieau, C. (D.) Folmes, M. (T.) Zimmermann, E. (W.) Klee, U. (B.) Pandey, R. Artuch, M. (A.) Cousin, A. Pujol. Acta Neuropathol, 140(6):971-975 (2020)

 

Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks

E. (K.) Ruzzo#, L. Pérez-Cano#, J. Jung, L. Wang, D. Kashef-Haghighi, C. Hartl, C. Singh, J. Xu, J. (N.) Hoekstra, O. Leventhal, V. (M.) Leppä, M. (J.) Gandal, K. Paskov, N. Stockham, D. Polioudakis, J. (K.) Lowe, D. (A.) Prober, D. (H.) Geschwind, D. (P.) Wall. Cell, 178(4):850-866 (2019) [# Contributed equally]

 

Improving pharmacogenetic prediction of extrapyramidal symptoms induced by antipsychotics

D. Boloc, A. Gortat, J. (Q.) Cheng-Zhang, S. García-Cerro, N. Rodríguez, M. Parellada, J. Saiz-Ruiz, M. (J.) Cuesta, P. Gassó, A. Lafuente, M. Bernardo, S. Mas. Translational Psychiatry, 8(1):276 (2018)

 

Disruption of a miR-29 binding site leading to COL4A1 upregulation causes pontine autosomal dominant microangiopathy with leukoencephalopathy

E. Verdura, D. Hervé, F. Bergametti, C. Jacquet, T. Morvan, C. Prieto-Morin, A. Mackowiak, E. Manchon, H. Hosseini, C. Cordonnier, I. Girard-Buttaz, S. Rosenstingl, C. Hagel, G. Kuhlenbaümer, E. Leca-Radu, D. Goux, L. Fleming, T. Van Agtmael, H. Chabriat, F. Chapon, E. Tournier-Lasserve. A. Neurol, 80(5):741-753 (2016)

 

High-Throughput Screening Using iPSC-Derived Neuronal Progenitors to Identify Compounds Counteracting Epigenetic Gene Silencing in Fragile X Syndrome

M. Kaufmann, A. Schuffenhauer, I. Fruh, J. Klein, A. Thiemeyer, P. Rigo, B. Gomez-Mancilla, V. Heidinger-Millot, T. Bouwmeester, U. Schopfer, M. Mueller, B. D. Fodor, A. Cobos-Correa. J Biomol Screen, 20(9):1101-11 (2015)

Brain gene co-expression networks link complement signaling with convergent synaptic pathology in schizophrenia

M. Kim, J. (R.) Haney, P. Zhang, L. (M.) Hernandez, L. (K.) Wang, L. Pérez-Cano, L. (M. O.) Loohuis, L. de la Torre-Ubieta, M. (J.) Gandal. Nat Neurosci, PMID: 33958802 (2021)

 

Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks

E. (K.) Ruzzo#, L. Pérez-Cano#, J. Jung, L. Wang, D. Kashef-Haghighi, C. Hartl, C. Singh, J. Xu, J. (N.) Hoekstra, O. Leventhal, V. (M.) Leppä, M. (J.) Gandal, K. Paskov, N. Stockham, D. Polioudakis, J. (K.) Lowe, D. (A.) Prober, D. (H.) Geschwind, D. (P.) Wall. Cell, 178(4):850-866 (2019) [# Contributed equally]

 

M. Bosio, O. Drechsel, R. Rahman, F. Muyas, R. Rabionet, D. Bezdan, L. (S.) Domenech, H. Hor, J. (J.) Schott, F. Munell, R. Colobran, A. Macaya, X. Estivill, S. Ossowski. Human mutation, 40(7):865-878 (2019)

 

GUILDify v2. 0: a tool to identify molecular networks underlying human diseases, their comorbidities and their druggable targets

J. Aguirre-Plans, J. Piñero, F. Sanz, L. (I.) Furlong, N. Fernandez-Fuentes, B. Oliva, E. Guney. Journal of molecular biology, 431 (13), 2477-2484 (2019)

 

A diseasome cluster-based drug repurposing of soluble guanylate cyclase activators from smooth muscle relaxation to direct neuroprotection

F. Langhauser, A. (I.) Casas, E. Guney, J. Menche, E. Geuss, P. (W.M.) Kleikers, M. (G.) López, A. (L.) Barabási, C. Kleinschnitz, H. (H.H.W.) Schmidt. NPJ systems biology and applications 4 (1), 1-13 (2018)

 

Proximal pathway enrichment analysis for targeting comorbid diseases via network endopharmacology

J. Aguirre-Plans, J. Piñero, J. Menche, F. Sanz, L. (I.) Furlong, H. (H.H.W.) Schmidt, B. Oliva, E. Guney. Pharmaceuticals 11 (3), 61 (2018)

 

Improving pharmacogenetic prediction of extrapyramidal symptoms induced by antipsychotics

D. Boloc, A. Gortat, J. (Q.) Cheng-Zhang, S. García-Cerro, N. Rodríguez, M. Parellada, J. Saiz-Ruiz, M. (J.) Cuesta, P. Gassó, A. Lafuente, M. Bernardo, S. Mas. Translational Psychiatry, 8(1):276 (2018)

 

Transcription Factor NRF2 as a Therapeutic Target for Chronic Diseases: A Systems Medicine Approach

A. Cuadrado, G. Manda, A. Hassan, M. (J.) Alcaraz, C. Barbas, A. Daiber, P. Ghezzi, R. León, M. (G.) López, B. Oliva, M. Pajares, A. (I.) Rojo, N. Robledinos-Antón, A. (M.) Valverde, E. Guney, H. (H.) (H.) (W.) Schmidt. Pharmacol Rev, 70(2):348-383 (2018)

 

Comparing structural and transcriptional drug networks reveals signatures of drug activity and toxicity in transcriptional responses

F. Sirci, F. Napolitano, S. Pisonero-Vaquero, D. Carrella, D. (L.) Medina, D. di Bernardo. NPJ Systems Biology and Applications, 3 1 23 (2017)

 

Structural and energy determinants in protein-RNA docking

L. Pérez-Cano, M. Romero-Durana, J. Fernández-Recio. Methods, 118-119:163-170 (2017)

 

Genetic and functional characterization of disease associations explains comorbidity

C. Rubio-Perez#, E. Guney#, D. Aguilar, J. Piñero, J. Garcia-Garcia, B. Iadarola, F. Sanz, N. Fernandez-Fuentes, L. (I.) Furlong, B. Oliva. Scientific reports, 7 (1), 1-14 (2017) [# Contributed equally]

 

Integrating personalized gene expression profiles into predictive disease-associated gene pools

J. Menche#, E. Guney#, A. Sharma, P. (J.) Branigan, M. (J.) Loza, F. Baribaud, R. Dobrin, A. (L.) Barabási. NPJ systems biology and applications, 3 (1), 1-10 (2017) [# Contributed equally]

 

SiNoPsis: Single Nucleotide Polymorphisms selection and promoter profiling

D. Boloc, N. Rodríguez, P. Gassó, J. (F.) Abril, M. Bernardo, A. Lafuente, S. Mas. Bioinformatics, btx570 (2017)

 

Potential of Mean Force Calculations of Solute Permeation Across UT-B and AQP1: A Comparison between Molecular Dynamics and 3D-RISM

I. Ariz-Extreme, J. (S.) Hub. The Journal of Physical Chemistry B, 121(7), 1506-1519 (2017)

 

Dimensionality reduction methods for molecular simulations

S. Doerr, I. Ariz-Extreme, M. (J.) Harvey, G. De Fabritiis. arXiv:1710.10629 (2017)

 

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

S. (K.) Sieberts, F. Zhu, J. García-García, E. Stahl, A. Pratap, G. Pandey, D. Pappas, D. Aguilar, B. Anton, J. Bonet, R. Eksi, O. Fornés, E. Guney, H. Li, M. (A.) Marín, B. Panwar, J. Planas-Iglesias, D. Poglayen, J. Cui, A. (O.) Falcao, C. Suver, B. Hoff, V. (S.K.) Balagurusamy, D. Dillenberger, E. (C.) Neto, T. Norman, T. Aittokallio, C. (A.) Azencott, V. Bellón, V. Boeva, K. Bunte, H. Chheda, L. Cheng, J. Corander, M. Dumontier, A. Goldenberg, P.i Gopalacharyulu, M. Hajiloo, D. Hidru, A. Jaiswal, S. Kaski, B. Khalfaoui, S. (A.) Khan, E. (R.) Kramer, P. Marttinen, A. (M.) Mezlini, B. Molparia, M.Pirinen, J. Saarela, M. Samwald, V. Stoven, H. Tang, J. Tang, A. Torkamani, J. (P.) Vert, B. Wang, T. Wang, K. Wennerberg, N. (E.) Wineinger, G. Xiao, Y. Xie, R. Yeung, X. Zhan, C. Zhao, J.Greenberg, J. Kremer, K. Michaud, A. Barton, M. Coenen, X. Mariette, C. Miceli, N. Shadick, M. Weinblatt, N. De Vries, P. (P.) Tak, D. Gerlag, T. (W.J.) Huizinga, F. Kurreeman, C. (F.) Allaart, S. (L.) Bridges Jr, L. Criswell, L. Moreland, L. Klareskog, S. Saevarsdottir, L. Padyukov, P. (K.) Gregersen, S. Friend, R. Plenge, G. Stolovitzky, B. Oliva, Y. Guan, L. (M.) Mangravite. Nature communications 7 (1), 1-10 (2016)

 

Network-based in silico drug efficacy screening

E. Guney, J. Menche, M. Vidal, A. (L.) Barábasi. Nature Communications volume 7, Article number: 10331 (2016)

 

Computational Drug Networks: a computational approach to elucidate drug mode of action and to facilitate drug repositioning for neurodegenerative diseases

F. Sirci, F. Napolitano, D. Bernardo. Drug Discovery Today: Disease Models 19 11-17 (2016)

 

Blind prediction of interfacial water positions in CAPRI

M. (F.) Lensink, I. (H.) Moal, P. (A.) Bates, P. (L.) Kastritis, A. (S. J.) Melquiond, E. Karaca, C. Schmitz, M. van Dijk, A. (M. J. J.) Bonvin, M. Eisenstein, B. Jiménez-García, S. Grosdidier, A. Solernou, L. Pérez-Cano, C. Pallara, J. Fernández-Recio, J. Xu, P. Muthu, K. (P.) Kilambi, J. (J.) Gray, S. Grudinin, G. Derevyanko, J. (C.) Mitchell, J. Wieting, E. Kanamori, Y. Tsuchiya, Y. Murakami, J. Sarmiento, D. (M.) Standley, M. Shirota, K. Kinoshita, H. Nakamura, M. Chavent, D. (W.) Ritchie, H. Park, J. Ko, H. Lee, C. Seok, Y. Shen, D. Kozakov, S. Vajda, P. (J.) Kundrotas, I. (A.) Vakser, B. (G.) Pierce, H. Hwang, T. Vreven, Z. Weng, I. Buch, E. Farkash, H. (J.) Wolfson, M. Zacharias, S. Qin, H. (X.) Zhou, S. Y. Huang, X. Zou, J. (A.) Wojdyla, C. Kleanthous, S. (J.) Wodak. Proteins, 82(4):620-32 (2014)

 

Structural bases for the interaction and stabilization of the human amino acid transporter LAT2 with its ancillary protein 4F2hc

A. Rosell, M. Meury, E. Álvarez-Marimon, M. Costa, L. Pérez-Cano, A. Zorzano, J. Fernández-Recio, M. Palacín, D. Fotiadis. Proc Natl Acad Sci U S A, 111(8):2966-71 (2014)

 

Conformational transitions in human translin enable nucleic acid binding

L. Pérez-Cano, E. Eliahoo, K. Lasker, H. (J.) Wolfson, F. Glaser, H. Manor, P. Bernadó, J. Fernández-Recio.Nucleic Acids Res, 41(21):9956-66 (2013)

 

Expanding the frontiers of protein-protein modeling: from docking and scoring to binding affinity predictions and other challenges

C. Pallara, B. Jiménez-García, L. Pérez-Cano, M. Romero-Durana, A. Solernou, S. Grosdidier, C. Pons, I. (H.) Moal, J. Fernandez-Recio. Proteins, 81(12):2192-200 (2013)

 

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

R. Moretti, S. (J.) Fleishman, R. Agius, M. Torchala, P. (A.) Bates, P. (L.) Kastritis, J. (P. G. L. M.) Rodrigues, M. Trellet, A. (M. J. J.) Bonvin, M. Cui, M. Rooman, D. Gillis, Y. Dehouck, I. Moal, M. Romero-Durana, L. Pérez-Cano, C. Pallara, B. Jimenez, J. Fernandez-Recio, S. Flores, M. Pacella, K. (P.) Kilambi, J. (J.) Gray, P. Popov, S. Grudinin, J. Esquivel-Rodríguez, D. Kihara, N. Zhao, D. Korkin, X. Zhu, O. (N. A.) Demerdash, J. (C.) Mitchell, E. Kanamori, Y. Tsuchiya, H. Nakamura, H. Lee, H. Park, C. Seok, J. Sarmiento, S. Liang, S. Teraguchi, D. (M.) Standley, H. Shimoyama, G. Terashi, M. Takeda-Shitaka, M. Iwadate, H. Umeyama, D. Beglov, D. (R.) Hall, D. Kozakov, S. Vajda, B. (G.) Pierce, H. Hwang, T. Vreven, Z. Weng, Y. Huang, H. Li, X. Yang, X. Ji, S. Liu, Y. Xiao, M. Zacharias, S. Qin, H. (X.) Zhou, S. (Y.) Huang, X. Zou, S. Velankar, J. Janin, S. (J.) Wodak, D. Baker. Proteins, 81(11):1980-7 (2013)

 

Gene expression data classification combining hierarchical representation and efficient feature selection

M. Bosio, P. Bellot, P. Salembier, A. Oliveras-Vergés. Journal of Biological Systems, 20 (04), 349-375,9 (2012)

 

A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data

L. Pérez-Cano, B. Jiménez-García, J. Fernández-Recio. Proteins, 80(7):1872-82 (2012)

 

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

S. (J.) Fleishman, T. (A.) Whitehead, E. (M.) Strauch, J. (E.) Corn, S. Qin, H. (X.) Zhou, J. (C.) Mitchell, O. (N. A.) Demerdash, M. Takeda-Shitaka, G. Terashi, I. (H.) Moal, X. Li, P. (A.) Bates, M. Zacharias, H. Park, J. Ko, H. Lee, C. Seok, T. Bourquard, J. Bernauer, A. Poupon, J. Azé, S. Soner, S. K. Ovali, P. Ozbek, N. (B.) Tal, T. Haliloglu, H. Hwang, T. Vreven, B. (G.) Pierce, Z. Weng, L. Pérez-Cano, C. Pons, J. Fernández-Recio, F. Jiang, F. Yang, X. Gong, L. Cao, X. Xu, B. Liu, P. Wang, C. Li, C. Wang, C. (H.) Robert, M. Guharoy, S. Liu, Y. Huang, L. Li, D. Guo, Y. Chen, Y. Xiao, N. London, Z. Itzhaki, O. Schueler-Furman, Y. Inbar, V. Potapov, M. Cohen, G. Schreiber, Y. Tsuchiya, E. Kanamori, D. (M.) Standley, H. Nakamura, K. Kinoshita, C. (M.) Driggers, R. (G.) Hall, J. (L.) Morgan, V. (L.) Hsu, J. Zhan, Y. Yang, Y. Zhou, P. (L.) Kastritis, A. (M. J. J.) Bonvin, W. Zhang, C. (J.) Camacho, K. (P.) Kilambi, A. Sircar, J. (J.) Gray, M. Ohue, N. Uchikoga, Y. Matsuzaki, T. Ishida, Y. Akiyama, R. Khashan, S. Bush, D. Fouches, A. Tropsha, J. Esquivel-Rodríguez, D. Kihara, P. (B.) Stranges, R. Jacak, B. Kuhlman, S. (Y.) Huang, X. Zou, S. (J.) Wodak, J. Janin, D. Baker. J Mol Biol, 414(2):289-302 (2011)

 

Dissection and prediction of RNA-binding sites on proteins

L. Pérez-Cano, J. Fernández-Recio. Biomol Concepts, 1(5-6):345-55 (2010)

 

Structural prediction of protein-RNA interaction by computational docking with propensity-based statistical potentials

L. Pérez-Cano, A. Solernou, C. Pons, J. Fernández-Recio. Pac Symp Biocomput, 293-301 (2010)

 

Present and future challenges and limitations in protein-protein docking

C. Pons, S. Grosdidier, A. Solernou, L. Pérez-Cano, J. Fernández-Recio. Proteins, 78(1):95-108 (2010)

 

Optimal protein-RNA area, OPRA: a propensity-based method to identify RNA-binding sites on proteins

L. Pérez-Cano, J. Fernández-Recio. Proteins, 78(1):25-35 (2010)

 

Mapping of interaction sites of the Schizosaccharomyces pombe protein Translin with nucleic acids and proteins: a combined molecular genetics and bioinformatics study

E. Eliahoo, R. (B.) Yosef, L. Pérez-Cano, J. Fernández-Recio, F. Glaser, H. Manor. Nucleic Acids Res, 38(9):2975-89 (2010)

 

Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding

C. Pons, A. Solernou, L. Pérez-Cano, S. Grosdidier, J. Fernandez-Recio. Proteins, 78(15):3182-8 (2010)

 

Assembly and channel opening in a bacterial drug efflux machine

V. (N.) Bavro, Z. Pietras, N. Furnham, L. Pérez-Cano, J. Fernández-Recio, X. (Y.) Pei, R. Misra, B. Luisi. Mol Cell, 30(1):114-21 (2008)

 

 

GUILDify v2. 0: a tool to identify molecular networks underlying human diseases, their comorbidities and their druggable targets

J. Aguirre-Plans, J. Piñero, F. Sanz, L. (I.) Furlong, N. Fernandez-Fuentes, B. Oliva, E. Guney. Journal of molecular biology, 431 (13), 2477-2484 (2019)

 

From single drug targets to synergistic network pharmacology in ischemic stroke

A. (I.) Casas, A. (A.) Hassan, S. (J.) Larsen, V. Gomez-Rangel, M. Elbatreek, P. (W.M.) Kleikers, E. Guney, J. Egea, M. (G.) López, J. Baumbach, H. (H.H.W.) Schmidt. Proceedings of the National Academy of Sciences 116 (14), 7129-7136 (2019)

 

A diseasome cluster-based drug repurposing of soluble guanylate cyclase activators from smooth muscle relaxation to direct neuroprotection

F. Langhauser, A. (I.) Casas, E. Guney, J. Menche, E. Geuss, P. (W.M.) Kleikers, M. (G.) López, A. (L.) Barabási, C. Kleinschnitz, H. (H.H.W.) Schmidt. NPJ systems biology and applications 4 (1), 1-13 (2018)

 

Proximal pathway enrichment analysis for targeting comorbid diseases via network endopharmacology

J. Aguirre-Plans, J. Piñero, J. Menche, F. Sanz, L. (I.) Furlong, H. (H.H.W.) Schmidt, B. Oliva, E. Guney. Pharmaceuticals 11 (3), 61 (2018)

 

Comparing structural and transcriptional drug networks reveals signatures of drug activity and toxicity in transcriptional responses

F. Sirci, F. Napolitano, S. Pisonero-Vaquero, D. Carrella, D. (L.) Medina, D. di Bernardo. NPJ Systems Biology and Applications, 3 1 23 (2017)

 

Reproducible drug repurposing: When similarity does not suffice

E. Guney. Pacific Symposium on Biocomputing 132-143 (2017)

 

Computational Drug Networks: a computational approach to elucidate drug mode of action and to facilitate drug repositioning for neurodegenerative diseases

F. Sirci, F. Napolitano, D. Bernardo. Drug Discovery Today: Disease Models 19 11-17 (2016)

 

Network-based in silico drug efficacy screening

E. Guney, J. Menche, M. Vidal, A. (L.) Barábasi. Nature Communications volume 7, Article number: 10331 (2016)

 

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