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Year
Paper
2021
Amaya-García F, Caldera M, Koren A, Kubicek S, Menche J, Unterlass MM. Green Hydrothermal Synthesis of Fluorescent 2,3-Diarylquinoxalines and Large-Scale Computational Comparison to Existing Alternatives. ChemSusChem. 2021 Apr 22;14(8):1853-1863. doi: 10.1002/cssc.202100433. Epub 2021 Mar 26.
Abstract: https://pubmed.ncbi.nlm.nih.gov/33662183/
2021
Amaya-García F, Caldera M, Koren A, Kubicek S, Menche J, Unterlass MM. Green Hydrothermal Synthesis of Fluorescent 2,3-Diarylquinoxalines and Large-Scale Computational Comparison to Existing Alternatives. ChemSusChem. 2021 Apr 22;14(8):1780. doi: 10.1002/cssc.202100607. Epub 2021 Apr 14.
Abstract: https://pubmed.ncbi.nlm.nih.gov/33855809/
2021
Pirch S, Müller F, Iofinova E, Pazmandi J, Hütter CVR, Chiettini M, Sin C, Boztug K, Podkosova I, Kaufmann H, Menche J. The VRNetzer platform enables interactive network analysis in Virtual Reality. Nat Commun. 2021 Apr 23;12(1):2432. doi: 10.1038/s41467-021-22570-w.
Abstract: https://pubmed.ncbi.nlm.nih.gov/33893283/
2020
Fagone P, Ciurleo R, Lombardo SD, Iacobello C, Palermo CI, Shoenfeld Y, Bendtzen K, Bramanti P, Nicoletti F. Transcriptional landscape of SARS-CoV-2 infection dismantles pathogenic pathways activated by the virus, proposes unique sex-specific differences and predicts tailored therapeutic strategies. Autoimmun Rev. 2020 Jul;19(7):102571. doi: 10.1016/j.autrev.2020.102571. Epub 2020 May 3.
Abstract: https://pubmed.ncbi.nlm.nih.gov/32376402/
2020
Salzer E, Zoghi S, Kiss MG, Kage F, Rashkova C, Stahnke S, Haimel M, Platzer R, Caldera M, Ardy RC, Hoeger B, Block J, Medgyesi D, Sin C, Shahkarami S, Kain R, Ziaee V, Hammerl P, Bock C, Menche J, Dupré L, Huppa JB, Sixt M, Lomakin A, Rottner K, Binder CJ, Stradal TEB, Rezaei N, Boztug K. The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. Sci Immunol. 2020 Jul 10;5(49):eabc3979. doi: 10.1126/sciimmunol.abc3979.
Abstract: https://pubmed.ncbi.nlm.nih.gov/32646852/
2020
Thian M, Hoeger B, Kamnev A, Poyer F, Köstel Bal S, Caldera M, Jiménez-Heredia R, Huemer J, Pickl WF, Groß M, Ehl S, Lucas CL, Menche J, Hutter C, Attarbaschi A, Dupré L, Boztug K. Germline biallelic PIK3CG mutations in a multifaceted immunodeficiency with immune dysregulation. Haematologica. 2020 Oct 1;105(10):e488. doi: 10.3324/haematol.2019.231399.
Abstract: https://pubmed.ncbi.nlm.nih.gov/33054089/
2020
Lombardo SD, Bramanti A, Ciurleo R, Basile MS, Pennisi M, Bella R, Mangano K, Bramanti P, Nicoletti F, Fagone P. Profiling of inhibitory immune checkpoints in glioblastoma: Potential pathogenetic players. Oncol Lett. 2020 Dec;20(6):332. doi: 10.3892/ol.2020.12195. Epub 2020 Oct 7.
Abstract: https://pubmed.ncbi.nlm.nih.gov/33123243/
2020
Brunner JS, Vogel A, Lercher A, Caldera M, Korosec A, Pühringer M, Hofmann M, Hajto A, Kieler M, Garrido LQ, Kerndl M, Kuttke M, Mesteri I, Górna MW, Kulik M, Dominiak PM, Brandon AE, Estevez E, Egan CL, Gruber F, Schweiger M, Menche J, Bergthaler A, Weichhart T, Klavins K, Febbraio MA, Sharif O, Schabbauer G. The PI3K pathway preserves metabolic health through MARCO-dependent lipid uptake by adipose tissue macrophages. Nat Metab. 2020 Dec;2(12):1427-1442. doi: 10.1038/s42255-020-00311-5. Epub 2020 Nov 16.
Abstract: https://pubmed.ncbi.nlm.nih.gov/33199895/
2020
Brunner JS, Vulliard L, Hofmann M, Kieler M, Lercher A, Vogel A, Russier M, Brüggenthies JB, Kerndl M, Saferding V, Niederreiter B, Junza A, Frauenstein A, Scholtysek C, Mikami Y, Klavins K, Krönke G, Bergthaler A, O'Shea JJ, Weichhart T, Meissner F, Smolen JS, Cheng P, Yanes O, Menche J, Murray PJ, Sharif O, Blüml S, Schabbauer G. Environmental arginine controls multinuclear giant cell metabolism and formation. Nat Commun. 2020 Jan 22;11(1):431. doi: 10.1038/s41467-020-14285-1.
Abstract: https://pubmed.ncbi.nlm.nih.gov/31969567/
2019
Schick S, Rendeiro AF, Runggatscher K, Ringler A, Boidol B, Hinkel M, Májek P, Vulliard L, Penz T, Parapatics K, Schmidl C, Menche J, Boehmelt G, Petronczki M, Müller AC, Bock C, Kubicek S. Systematic characterization of BAF mutations provides insights into intracomplex synthetic lethalities in human cancers. Nat Genet. 2019;51(9):1399–1410. doi:10.1038/s41588-019-0477-9
Abstract: https://pubmed.ncbi.nlm.nih.gov/31427792/
2019
Mayor-Ruiz C, Jaeger MG, Bauer S, Brand M, Sin C, Hanzl A, Mueller AC, Menche J, Winter GE. Plasticity of the Cullin-RING Ligase Repertoire Shapes Sensitivity to Ligand-Induced Protein Degradation. Mol Cell. 2019 Aug 22;75(4):849-858.e8. doi: 10.1016/j.molcel.2019.07.013.
Abstract: https://pubmed.ncbi.nlm.nih.gov/31442425/
2019
Lercher A, Bhattacharya A, Popa AM, Caldera M, Schlapansky MF, Baazim H, Agerer B, Gürtl B, Kosack L, Májek P, Brunner JS, Vitko D, Pinter T, Genger JW, Orlova A, Pikor N, Reil D, Ozsvár-Kozma M, Kalinke U, Ludewig B, Moriggl R, Bennett KL, Menche J, Cheng PN, Schabbauer G, Trauner M, Klavins K, Bergthaler A. Type I Interferon Signaling Disrupts the Hepatic Urea Cycle and Alters Systemic Metabolism to Suppress T Cell Function. Immunity. 2019;51(6):1074–1087.e9. doi:10.1016/j.immuni.2019.10.014
Abstract: https://pubmed.ncbi.nlm.nih.gov/31784108/
2019
Caldera M, Müller F, Kaltenbrunner I, Licciardello MP, Lardeau CH, Kubicek S, Menche J. Mapping the perturbome network of cellular perturbations. Nat Commun. 2019 Nov 13;10(1):5140. doi: 10.1038/s41467-019-13058-9.
Abstract: https://pubmed.ncbi.nlm.nih.gov/31723137/
2019
Sdelci S, Rendeiro AF, Rathert P, You W, Lin JG, Ringler A, Hofstätter G,Moll HP, Gürtl B, Farlik M, Schick S, Klepsch F, Oldach M, Buphamalai P,Schischlik F, Májek P, Parapatics K, Schmidl C, Schuster M, Penz T, Buckley DL,Hudecz O, Imre R, Wang SY, Maric HM, Kralovics R, Bennett KL, Müller AC, MechtlerK, Menche J, Bradner JE, Winter GE, Klavins K, Casanova E, Bock C, Zuber J,Kubicek S. MTHFD1 interaction with BRD4 links folate metabolism to transcriptional regulation. Nat Genet. 2019 Jun;51(6):990-998. doi:10.1038/s41588-019-0413-z. Epub 2019 May 27.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/31133746
2019
Schischlik F, Jäger R, Rosebrock F, Hug E, Schuster M, Holly R, Fuchs E,Milosevic Feenstra JD, Bogner E, Gisslinger B, Schalling M, Rumi E, Pietra D,Fischer G, Faé I, Vulliard L, Menche J, Haferlach T, Meggendorfer M, Stengel A,Bock C, Cazzola M, Gisslinger H, Kralovics R. Mutational landscape of the transcriptome offers putative targets for immunotherapy of myeloproliferative neoplasms. Blood. 2019 Jul 11;134(2):199-210. doi: 10.1182/blood.2019000519. Epub2019 May 7.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/31064751
2019
Owusu M, Bannauer P, Ferreira da Silva J, Mourikis TP, Jones A, Májek P,Caldera M, Wiedner M, Lardeau CH, Mueller AC, Menche J, Kubicek S, Ciccarelli FD,Loizou JI. Mapping the Human Kinome in Response to DNA Damage. Cell Rep. 2019 Jan15;26(3):555-563.e6. doi: 10.1016/j.celrep.2018.12.087.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/30650350
2019
Nagy V, Hollstein R, Pai TP, Herde MK, Buphamalai P, Moeseneder P,Lenartowicz E, Kavirayani A, Korenke GC, Kozieradzki I, Nitsch R, Cicvaric A,Monje Quiroga FJ, Deardorff MA, Bedoukian EC, Li Y, Yigit G, Menche J, Perçin EF,Wollnik B, Henneberger C, Kaiser FJ, Penninger JM. HACE1 deficiency leads to structural and functional neurodevelopmental defects. Neurol Genet. 2019 Apr29;5(3):e330. doi: 10.1212/NXG.0000000000000330. eCollection 2019 Jun. PubMedPMID: 31321300;
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/6561753
2018
Sharma A, Kitsak M, Cho MH, Ameli A, Zhou X, Jiang Z, Crapo JD, Beaty TH, Menche J, Bakke PS, Santolini M, Silverman EK. Integration of Molecular Interactome and Targeted Interaction Analysis to Identify a COPD Disease Network Module. Sci Rep. 2018 Sep 27;8(1):14439. doi: 10.1038/s41598-018-32173-z.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/30262855
2018
Sharma A, Halu A, Decano JL, Padi M, Liu YY, Prasad RB, Fadista J, Santolini M, Menche J, Weiss ST, Vidal M, Silverman EK, Aikawa M, Barabási AL, Groop L, Loscalzo J. Controllability in an islet specific regulatory network identifies the transcriptional factor NFATC4, which regulates Type 2 Diabetes associated genes. NPJ Syst Biol Appl. 2018 Jul 3;4:25. doi: 10.1038/s41540-018-0057-0. eCollection 2018.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/29977601
2018
Puchner A, Saferding V, Bonelli M, Mikami Y, Hofmann M, Brunner JS, Caldera M, Goncalves-Alves E, Binder NB, Fischer A, Simader E, Steiner CW, Leiss H, Hayer S, Niederreiter B, Karonitsch T, Koenders MI, Podesser BK, O'Shea JJ, Menche J, Smolen JS, Redlich K, Blüml S. Non-classical monocytes as mediators of tissue destruction in arthritis. Ann Rheum Dis. 2018 Oct;77(10):1490-1497. doi: 10.1136/annrheumdis-2018-213250. Epub 2018 Jun 29.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/29959183
2018
Aguirre-Plans J, Piñero J, Menche J, Sanz F, Furlong LI, Schmidt HHHW, Oliva B, Guney E. Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology. Pharmaceuticals (Basel). 2018 Jun 22;11(3). pii: E61. doi: 10.3390/ph11030061.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/29932108
2018
Velimezi G, Robinson-Garcia L, Muñoz-Martínez F, Wiegant WW, Ferreira da Silva J, Owusu M, Moder M, Wiedner M, Rosenthal SB, Fisch KM, Moffat J, Menche J, van Attikum H, Jackson SP, Loizou JI. Map of synthetic rescue interactions for the Fanconi anemia DNA repair pathway identifies USP48. Nat Commun. 2018 Jun 11;9(1):2280. doi: 10.1038/s41467-018-04649-z.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/29891926
2017
M Caldera*, P Buphamalai*, F Müller, J Menche. Interactome-based approaches to human disease. Current Opinions in Systems Biology 3:88; 2017.
Abstract: https://doi.org/10.1016/j.coisb.2017.04.015
2017
Khamina K , Lercher  A , Caldera M, Schliehe C , Vilagos B , Sahin M, Kosack L, Bhattacharya A, Májek P, Stukalov A, Sacco R, James LC, Pinschewer DD, Bennett KL, Menche J, Bergthaler A. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens 13(12): e1006758; 2017.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/29261807
2017
J Menche*, E Guney*, A. Sharma, P.J. Branigan, M.J. Loza, F. Baribaud, R. Dobrin, A.-L. Barabási. Integrating personalized gene expression profiles into predictive disease-associated gene pool. npj Systems Biology & Applications 3:10; 2017. doi:10.1038/s41540-017-0009-0.
Abstract: http://www.nature.com/articles/s41540-017-0009-0
2017
Bergthaler A, Menche J. The immune system as a social network. Nat Immunol. 2017 Apr 18;18(5):481-482. doi: 10.1038/ni.3727. No abstract available.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/28418389
2017
Licciardello MP, Ringler A, Markt P, Klepsch F, Lardeau CH, Sdelci S, Schirghuber E, Müller AC, Caldera M, Wagner A, Herzog R, Penz T, Schuster M, Boidol B, Dürnberger G, Folkvaljon Y, Stattin P, Ivanov V, Colinge J, Bock C, Kratochwill K, Menche J, Bennett KL, Kubicek S. A combinatorial screen of the CLOUD uncovers a synergy targeting the androgen receptor. Nat Chem Biol. 2017 Jul;13(7):771-778. doi: 10.1038/nchembio.2382. Epub 2017 May 22.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/28530711
2017
Menche J. Network medicine: a new paradigm for cardiovascular disease research and beyond. Cardiovasc Res. 2017 Aug 1;113(10):e29-e30. doi: 10.1093/cvr/cvx129. No abstract available.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/28899006
2017
Moder M, Velimezi G, Owusu M, Mazouzi A, Wiedner M, Ferreira da Silva J, Robinson-Garcia L, Schischlik F, Slavkovsky R, Kralovics R, Schuster M, Bock C, Ideker T, Jackson SP, Menche J, Loizou JI. Parallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex and Fanconi anemia. Nat Commun. 2017 Nov 1;8(1):1238. doi: 10.1038/s41467-017-01439-x.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/29089570
2017
J Menche*, E Guney*, A. Sharma, P.J. Branigan, M.J. Loza, F. Baribaud, R. Dobrin, A.-L. Barabási. Integrating personalized gene expression profiles into predictive disease-associated gene pool. npj Systems Biology & Applications 3:10; 2017. doi:10.1038/s41540-017-0009-0
Abstract: http://www.nature.com/articles/s41540-017-0009-0
2016
E Guney, J Menche, M Vidal, AL Barabási. Network-based in silico drug efficacy screening. Nature Communications 7:10331, 2016. doi: 10.1038/ncomms10331.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/26831545
2016
Q Zhong, S J Pevzner, T Hao, Y Wang, R Mosca, J Menche, M Taipale, M Tasan, C Fan, X Yang, P Haley, R R Murray, F Mer, F Gebreab, S Tam, A MacWilliams, A Dricot, P Reichert, B Santhanam, L Ghamsari, M A Calderwood, T Rolland, B Charloteaux, S Lindquist, A-L Barabási, D E Hill, P Aloy, M E Cusick, Y Xia, F P Roth & M Vidal. An inter-species protein–protein interaction network across vast evolutionary distance Molecular Systems Biology 12:865; 2016. doi: 10.15252/msb.20156484.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/27107014
2016
SD Ghiassian, J Menche, DI Chasman, F Giulianini, R Wang, P Ricchiuto, M Aikawa, H Iwata, C Müller, T Zeller, A Sharma, P Wild, K Lackner, S Singh, PM Ridker, S Blankenberg, A-L Barabási, J Loscalzo. Endophenotype Network Models: Common Core of Complex Diseases. Scientific Reports 6:27414; 2016. doi: 10.1038/srep27414.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/27278246
2016
D Gomez-Cabrero, J Menche, C Vargas, I Cano, D Maier, A-L Barabási, J Tegnér, J Roca and on behalf of Synergy-COPD Consortia. From comorbidities of chronic obstructive pulmonary disease to identification of shared molecular mechanisms by data integration. BMC Bioinformatics 17:1291; 2016. doi: 10.1186/s12859-016-1291-3.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/28185567
2016
M Kitsak, A Sharma, J Menche, E Guney, SD Ghiassian, J Loscalzo, A-L Barabási, J Loscalzo. Tissue Specificity of Human Disease Module . Scientific Reports 6:35241; 2016. doi: 10.1038/srep35241.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/27748412