Publications

Clinical Research (1)

Safety, Tolerability, and EEG-Based Target Engagement of STP1 (PDE3,4 Inhibitor and NKCC1 Antagonist) in a Randomized Clinical Trial in a Subgroup of Patients with ASD

C. A. Erickson, L. Pérez-Cano, E. V. Pedapati, E. Painbeni, G. Bonfils, L. M. Schmitt, H. Sachs, M. Nelson, L. De Stefano, G. Westerkamp, A. L. S. de Souza, O. Pohl, O. Laufer, G. Issachar, T. Blaettler, J.M. Hyvelin, L. Durham. Biomedicines , https://doi.org/10.3390/biomedicines12071430 (2024)

Computational/Systems Biology (29)

Identification of novel driver risk genes in CNV loci associated with neurodevelopmental disorders

S. Azidane, X. Gallego, L .Durham, M. Cáceres, E. Guney, L. Pérez-Cano. HGG Advances , https://doi.org/10.1016/j.xhgg.2024.100316 (2024)

The human hepatocyte TXG-MAPr: gene co-expression network modules to support mechanism-based risk assessment

G. Callegaro, S. (J.) Kunnen, P. Trairatphisan, S. Grosdidier, M. Niemeijer, W. den Hollander, E. Guney, J. (P.) Gonzalez, L. Furlong, Y. (W.) Webster, J. Saez-Rodriguez, J. (J.) Sutherland, J. Mollon, J. (L.) Stevens, B. van de Water. Springer Link , 3745–3775 (2021)

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 , 865-878 (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. PNAS , 116 (14) 7129-7136 (2019)

Network, Transcriptomic and Genomic Features Differentiate Genes Relevant for Drug Response

J. Piñero, A. Gonzalez-Perez, E. Guney, J. Aguirre-Plans, F. Sanz, B. Oliva, L. (I.) Furlong. Frontiers in Genetics , 10.3389 (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 , 4 (1), 1-13 (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 , 8(1):276 (2018)

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 , 431 (13), 2477-2484 (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 , 70(2):348-383 (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 , 118-119:163-170 (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 , 10331 (2017)

Structural and energy determinants in protein-RNA docking

L. Pérez-Cano, M. Romero-Durana, J. Fernández-Recio. Methods , 3 1 23 (2017)

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 , 7 (1), 1-14 (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 , 1710.10629 (2016)

Network-based in silico drug efficacy screening

E. Guney, J. Menche, M. Vidal, A. (L.) Barábasi. Nature Communications volume , 7 (1), 1-10 (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 , 19 11-17 (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 , 82(4):620-32 (2014)

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 , 41(21):9956-66 (2013)

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 , 111(8):2966-71 (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(12):2192-200 (2013)

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

L. Pérez-Cano, B. Jiménez-García, J. Fernández-Recio. Proteins , 20 (04), 349-375,9 (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 , 80(7):1872-82 (2011)

Dissection and prediction of RNA-binding sites on proteins

L. Pérez-Cano, J. Fernández-Recio. Biomol Concepts , 414(2):289-302 (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 , 38(9):2975-89 (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 , 78(1):25-35 (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 , 1(5-6):345-55 (2010)

Present and future challenges and limitations in protein-protein docking

C. Pons, S. Grosdidier, A. Solernou, L. Pérez-Cano, J. Fernández-Recio. Proteins , 293-301 (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):95-108 (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)

NDD Genomics (2)

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: , 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)

Preclinical Research (2)

Characterization of a Clinically and Biologically Defined Subgroup of Patients with Autism Spectrum Disorder and Identification of a Tailored Combination Treatment

L. Pérez-Cano, L. Boccuto, F. Sirci, J.M. Hidalgo, S. Valentini, M. Bosio, X. Liogier D’Ardhuy, C. Skinner, L. Cascio, S. Srikanth, K. Jones, C. Buchanan, S.A. Skinner, B. Gomez-Mancilla, J.M. Hyvelin, E. Guney, L. Durham. Biomedicines , https://doi.org/10.3390/biomedicines12050991 (registering DOI) (2024)

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)

Review (6)

Re-Addressing Dementia by Network Medicine and Mechanism-Based Molecular Endotypes

M. Pacheco Pachado, A. I. Casas, M. H. Elbatreek, C. Nogales, E. Guney, A. J. Espay, H. H. H. W. Schmidt. IOS Press , 10.3233/JAD-230694 (2023)

The contributions of rare inherited and polygenic risk to ASD in multiplex families

M. Cirnigliaro, T. S. Chang, S. A. Arteaga, L. Pérez-Cano, E. K. Ruzzo, A. Gordon, L. K. Bicks, J.-Y. Jung, J. K. Lowe, D. P. Wall, D. H. Geschwind. PNAS , 2215632120 (2023)

Translating precision medicine for autism spectrum disorder: A pressing need

L. Pérez-Cano, S. Azidane Chenlo, R. Sabido-Vera, F. Sirci, L. Durham, E. Guney. ScienceDirect , 2023.103486 (2023)

Implications of sex-specific differences on clinical studies of human health

J. Piñero, F.-C. Quevenco, L. I. Furlong, E. Guney. ScienceDirect , B978-0-12-821392-6.00011-X (2022)

A needle for Alzheimer’s in a haystack of claims data

E. Guney, A. Athie. Nature Aging , 10.1038/s43587-021-00139y (2021)

Heterogeneity in Fragile X Syndrome Highlights the Need for Precision Medicine-Based Treatments

E. Verdura, L. Pérez-Cano, R. Sabido-Vera, E. Guney, J.M. Hyvelin, L. Durham, B. Gomez-Mancilla. Frontiers in Psychiatry , 10.3389/fpsyt.2021.722378 (2021)