Publications

Year

Paper

2023

Low-dose Bisphenol A exposure alters the functionality and cellular environment in a human cardiomyocyte model
Federica Lamberto, Bachuki Shashikadze, Radwa Elkhateib, Salvo Danilo Lombardo, Alex Horánszky, Andrea Balogh, Kornél Kistamás, Melinda Zana, Jörg Menche, Thomas Fröhlich, András Dinnyés.
Environ Pollut. 2023 Aug 9;335:122359. doi: 10.1016/j.envpol.2023.122359. Online ahead of print.
Abstract: https://pubmed.ncbi.nlm.nih.gov/37567409/

2023

Maternal hyperglycemia induces alterations in hepatic amino acid, glucose and lipid metabolism of neonatal offspring: Multi-omics insights from a diabetic pig model
Bachuki Shashikadze, Libera Valla, Salvo Danilo Lombardo, Cornelia Prehn, Mark Haid, Fabien Riols, Jan Bernd Stöckl, Radwa Elkhateib, Simone Renner, Birgit Rathkolb, Jörg Menche, Martin Hrabĕ de Angelis, Eckhard Wolf, Elisabeth Kemter, Thomas Fröhlich.
Mol Metab. 2023 Sep;75:101768. doi: 10.1016/j.molmet.2023.101768. Epub 2023 Jul 4.
Abstract: https://pubmed.ncbi.nlm.nih.gov/37414142/

2023

Assessment of community efforts to advance network-based prediction of protein-protein interactions
Xu-Wen Wang, Lorenzo Madeddu, Kerstin Spirohn, Leonardo Martini, Adriano Fazzone, Luca Becchetti, Thomas P Wytock, István A Kovács, Olivér M Balogh, Bettina Benczik, Mátyás Pétervári, Bence Ágg, Péter Ferdinandy, Loan Vulliard, Jörg Menche, Stefania Colonnese, Manuela Petti, Gaetano Scarano, Francesca Cuomo, Tong Hao, Florent Laval, Luc Willems, Jean-Claude Twizere, Marc Vidal, Michael A Calderwood, Enrico Petrillo, Albert-László Barabási, Edwin K Silverman, Joseph Loscalzo, Paola Velardi, Yang-Yu Liu.
Nat Commun. 2023 Mar 22;14(1):1582. doi: 10.1038/s41467-023-37079-7.
Abstract: https://pubmed.ncbi.nlm.nih.gov/36949045/

2023

Proline and glucose metabolic reprogramming supports vascular endothelial and medial biomass in pulmonary arterial hypertension
Bradley M Wertheim, Rui-Sheng Wang, Christelle Guillermier, Christiane Vr Hütter, William M Oldham, Jörg Menche, Matthew L Steinhauser, Bradley A Maron.
JCI Insight. 2023 Feb 22;8(4):e163932. doi: 10.1172/jci.insight.163932.
Abstract: https://pubmed.ncbi.nlm.nih.gov/36626231/

2022

Network Approaches for Charting the Transcriptomic and Epigenetic Landscape of the Developmental Origins of Health and Disease
Salvo Danilo Lombardo, Ivan Fernando Wangsaputra, Jörg Menche, Adam Stevens.
Genes (Basel). 2022 Apr 26;13(5):764. doi: 10.3390/genes13050764.
Abstract: https://pubmed.ncbi.nlm.nih.gov/35627149/

2022

The regulatory network architecture of cardiometabolic diseases
Harald H H W Schmidt, Jörg Menche.
Nat Genet. 2022 Jan;54(1):2-3. doi: 10.1038/s41588-021-00994-w.
Abstract: https://pubmed.ncbi.nlm.nih.gov/35022603/

2022

Year

Paper

2021

Lahnsteiner M, Caldera M, Moura HM, Cerrón-Infantes DA, Roeser J, Konegger T, Thomas A, Menche J, Unterlass MM. Hydrothermal polymerization of porous aromatic polyimide networks and machine learning-assisted computational morphology evolution interpretation. J Mater Chem A Mater. 2021 Sep 8;9(35):19754-19769. doi: 10.1039/d1ta01253c. eCollection 2021 Sep 14.
Abstract: https://pubmed.ncbi.nlm.nih.gov/34589226/

2021

Vulliard L, Hancock J, Kamnev A, Fell CW, Ferreira da Silva J, Loizou JI, Nagy V, Dupré L, Menche J. BioProfiling.jl: Profiling biological perturbations with high-content imaging in single cells and heterogeneous populations. Bioinformatics. 2021 Dec 22;38(6):1692-9. doi: 10.1093/bioinformatics/btab853. Online ahead of print.
Abstract: https://pubmed.ncbi.nlm.nih.gov/34935929/

2021

Rahman MR, Islam T, Shahjaman M, Islam MR, Lombardo SD, Bramanti P, Ciurleo R, Bramanti A, Tchorbanov A, Fisicaro F, Fagone P, Nicoletti F, Pennisi M. Discovering common pathogenetic processes between COVID-19 and diabetes mellitus by differential gene expression pattern analysis. Brief Bioinform. 2021 Nov 5;22(6):bbab262. doi: 10.1093/bib/bbab262.
Abstract: https://pubmed.ncbi.nlm.nih.gov/34260684/

2021

German Y, Vulliard L, Kamnev A, Pfajfer L, Huemer J, Mautner AK, Rubio A, Kalinichenko A, Boztug K, Ferrand A, Menche J, Dupré L. Morphological profiling of human T and NK lymphocytes by high-content cell imaging. Cell Rep. 2021 Jul 6;36(1):109318. doi: 10.1016/j.celrep.2021.109318.
Abstract: https://pubmed.ncbi.nlm.nih.gov/34233185/

2021

Buphamalai P, Kokotovic T, Nagy V, Menche J. Network analysis reveals rare disease signatures across multiple levels of biological organization. Nat Commun. 2021 Nov 9;12(1):6306. doi: 10.1038/s41467-021-26674-1.
Abstract: https://pubmed.ncbi.nlm.nih.gov/34753928/

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/ _blank

2021

Lahnsteiner M, Caldera M, Moura HM, Cerrón-Infantes DA, Roeser J, Konegger T, Thomas A, Menche J, Unterlass MM. Hydrothermal polymerization of porous aromatic polyimide networks and machine learning-assisted computational morphology evolution interpretation. J Mater Chem A Mater. 2021 Sep 8;9(35):19754-19769. doi: 10.1039/d1ta01253c.
Abstract: https://pubmed.ncbi.nlm.nih.gov/34589226/ _blank

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.
Abstract: https://pubmed.ncbi.nlm.nih.gov/33855809/ _blank

2021

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