2021

The VRNetzer Platform Enables Interactive Network Analysis in Virtual Reality. S. Pirch, F. Müller, E. Iofinova, J. Pazmandi, C. V.R. Hütter, M. Chiettini, C. Sin, K. Boztug, I. Podkosova, H. Kaufmann & J. Menche. Nature Communications Commun (in press); 2021

Green hydrothermal synthesis of fluorescent 2, 3-diarylquinoxalines and large-scale computational comparison to existing alternatives. F.A. Amaya-García, M. Caldera, A. Koren, S. Kubicek, J. Menche, M.M. Unterlass. ChemSusChem ; 2021

Beneficial Metabolic Effects of TREM2 in Obesity are Uncoupled from its Expression on Macrophages. O. Sharif, J.S. Brunner, A. Korosec, R. Martins, A. Jais, B. Snijder, A. Vogel, M. Caldera, A. Hladik, K. Lakovits, S. Saluzzo, B. Boehm, A-D. Gorki, I. Mesteri, J. Lindroos-Christensen, K. Tillmann, D. Stoiber, J. Menche, G. Schabbauer, M. Bilban, G. Superti-Furga, H. Esterbauer, S. Knapp. Diabetes ; 2021

Structure and Function in Complex Biological Networks. J. Hancock & J. Menche. Systems Medicine 26; 2021

Complex Networks in Health and Disease. L. Vulliard & J. Menche. Systems Medicine 26; 2021

2020

The PI3K pathway preserves metabolic health through MARCO-dependent lipid uptake by adipose tissue macrophages. J.S. Brunner, A. Vogel, A. Lercher, M. Caldera, A. Korosec, M. Pühringer, M. Hofmann, A. Hajto, M. Kieler, L. Quemada Garrido, M. Kerndl, M. Kuttke, I. Mesteri, M.W. Górna, M. Kulik, P.M. Dominiak, A.E. Brandon, E. Estevez, C.L. Egan, F. Gruber, M. Schweiger, J. Menche, A. Bergthaler, T. Weichhart, K. Klavins, M.A. Febbraio, O. Sharif, G. Schabbauer. Nature Metab 2, 1427–1442; 2020

The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. E Salzer, S Zoghi, MG Kiss, F Kage, C Rashkova, S Stahnke, M Haimel, R Platzer, M Caldera, RC Ardy, B Hoeger, J Block, D Medgyesi, C Sin, S Shahkarami, R Kain, V Ziaee, P Hammerl, C Bock, J Menche, L Dupré, JB Huppa, M Sixt, A Lomakin, K Rottner, CJ Binder, TEB Stradal, N Rezaei, K Boztug. Science Immunology 5(49); 2020 

Germline Biallelic PIK3CG Mutations In A Multifaceted Immunodeficiency With Immune Dysregulation. M Thian, B Hoeger, A Kamnev, F Poyer, S Köstel Bal, M Caldera, R Jiménez-Heredia, J Huemer, WF Pickl, M Groß, S Ehl, CL Lucas, J Menche, C Hutter, A Attarbaschi, L Dupré, K Boztug. Haematologica (in press); 2020 

Environmental arginine controls multinuclear giant cell metabolism and formation. JS Brunner, L Vulliard, M Hofmann, M Kieler, A Lercher, A Vogel, M. Russier. JB Brüggenthies, M Kerndl, V Saferding, B Niederreiter, A Junza, A Frauenstein, C Scholtysek, Y Mikami, K Klavins, G Krönke, A Bergthaler, JJ O’Shea, T Weichhart, F Meissner, JS Smolen, P Cheng, O Yanes, J Menche, PJ Murray, O Sharif, S Blüml, G Schabbauer. Nature Communications 11(1), 1-15; 2020 

Complex Networks in Health and Disease. L Vulliard, J Menche. Reference Module in Biomedical Sciences 2020

Morphological profiling of human T and NK lymphocytes identifies actin-mediated control of the immunological synapse
Authors. Y German, L Vulliard, A Rubio, K Boztug, A Ferrand, J Menche, L Dupre. bioRxiv 2020

 

2019

Mapping the perturbome network of cellular perturbations. M Caldera, F Müller, I Kaltenbrunner, M Licciardello, C-Hugues Lardeau, S Kubicek, J Menche. Nature Communications 10(1), 1-14; 2019

Type I Interferon Signaling Disrupts the Hepatic Urea Cycle and Alters Systemic Metabolism to Suppress T Cell Function. A Lercher, A Bhattacharya, AM Popa, M Caldera, MF Schlapansky, H Baazim, P Majek, JS Brunner, LJ Kosack, D Vitko, T Pinter, B Guertl, D Reil, U Kalinke, KL Bennett, J Menche, PN Cheng, G Schabbauer, M Trauner, K Klavins, A Bergthaler. Immunity 51, 1-14; 2019

Assessment of network module identification across complex diseases. S Choobdar, ME Ahsen, J Crawford, M Tomasoni, T Fang, D Lamparter, J Lin, B Hescott, X Hu, J Mercer, T Natoli, R Narayan, The DREAM Module Identification Challenge Consortium (incl. J Menche), A Subramanian, JD Zhang, G Stolovitzky, Z Kutalik, K Lage, DK Slonim, J Saez-Rodriguez, LJ Cowen, S Bergmann, D Marbach, Nature Methods 16 (9), 843-852; 2019

Plasticity of the Cullin-RING Ligase Repertoire Shapes Sensitivity to Ligand-Induced Protein Degradation. C Mayor-Ruiz, MG Jaeger, S Bauer, M Brand, C Sin, A Hanzl, AC Mueller, J Menche, GE Winter, Molecular Cell 75 (4), 849-858. E8; 2019

Mutational landscape of the transcriptome offers putative targets for immunotherapy of myeloproliferative neoplasms. F Schischlik, R Jäger, F Rosebrock, E Hug, M Schuster, R Holly, E Fuchs, JD Milosevic Feenstra, E Bogner, B Gisslinger, M Schalling, E Rumi, D Pietra, G Fischer, I Faé, L Vulliard, J Menche, T Haferlach, M Meggendorfer, A Stengel, C Bock, M Cazzola, H Gisslinger & R Kralovics. Blood  134 (2), 199-210; 2019

Systematic characterization of BAF mutations explains intra-complex synthetic lethalities. S Schick, A Rendeiro, B Boidol, K Runggatscher, M Hinkel, P Májek, L Vulliard, T Penz, K Parapatics, C Schmidl, A Ringler, J Menche, G Boehmelt, M Petronczki, A Müller, C Bock & S Kubicek. Nature Genetics 51 (9), 1399-1410; 2019

HACE1 Deficiency Leads to Structural and Functional Neurodevelopmental Defects. V Nagy, R Hollstein, T-P Pai, MK Herde, P Buphamalai, P Moeseneder, E Lenartowicz, A Kavirayani, GC Korenke, I Kozieradzki, R Nitsch, A Cicvaric, FJ Monje Quiroga, MA Deardorff, EC Bedoukian, Y Li, G Yigit, J Menche, EF Perçin, B Wollnik, C Henneberger, FJ Kaiser, JM Penninger. Neurol Genet 5 (3): e330. 2019

MTHFD1 interaction with BRD4 links folate metabolism to transcriptional regulation. S Sdelci, AF Rendeiro, P Rathert, W You, JM Lin, A Ringler, G Hofstaetter, HP Moll, B Gürtl, M Farlik, S Schick, F Klepsch, M Oldach, P Buphamalai, F Schischlik, P Májek, K Parapatics, C Schmidl, M Schuster, T Penz, DL Buckley, O Hudecz, R Imre, S-Y Wang, HM Maric, R Kralovics, KL Bennett, AC Müller, K Mechtler, J Menche, JE Bradner, GE Winter, K Klavins, E Casanova, C Bock, J Zuber & Stefan Kubicek. Nature Genetics 6;51(6):990; 2019

Mapping the human kinome in response to DNA damage. M Owusu, P Bannauer, J Ferreira da Silva, TP Mourikis, A Jones, P Májek, M Caldera, M Wiedner, C-H Lardeau, AC Mueller, J Menche, S Kubicek, F Ciccarelli & JI Loizou. Cell Reports 26(3), 555-563; 2019; 2019

 

2018

Mutational Landscape of the Transcriptome Offers a Rich Neoantigen Resource for Immunotherapy of Myeloproliferative Neoplasms. F Schischlik, R Jäger, F Rosebrock, E Hug, M Schuster, R Holly, E Fuchs, JD Milosevic Feenstra, E Bogner, B Gisslinger, M Schalling, E Rumi, D Pietra, G Fischer, I Faé, L Vulliard, J Menche, T Haferlach, M Meggendorfer, A Stengel, C Bock, M Cazzola, H Gisslinger & R Kralovics. Blood132 (Suppl 1), 3058-3058; 2018

Non-classical monocytes as mediators of tissue destruction in arthritis. A Puchner, V Saferding, M Bonelli, Y Mikami, M Hofmann, JS Brunner, M Caldera, E Goncalves-Alves, NB Binder, A Fischer, E Simader, C-W Steiner, H Leiss, S Hayer, B Niederreiter, T Karonitsch, MI Koenders, BK Podesser, JJ O’Shea, J Menche, JS Smolen, K Redlich & S Blüml. Annals of the Rheumatic Diseases 77 (10), 1490-1497; 2018

Integration of Molecular Interactome and Targeted Interaction Analysis to Identify a COPD Disease Network Module. A Sharma, M Kitsak, MH Cho, A Ameli, X Zhou, Z Jiang, JD Crapo, TH Beaty, J Menche, PS Bakke, M Santolini & EK Silverman. Scientific Reports 8 (1), 14439; 2018

Proximal pathway enrichment analysis for targeting comorbid diseases via network endopharmacology. J Aguirre-Plans, J Piñero, J Menche, F Sanz, L Furlong, HHHW Schmidt, B Oliva & E Guney; Pharmaceuticals 11 (3), 61 2018

Controllability in an islet specific regulatory network identifies the transcriptional factor NFATC4, which regulates Type 2 Diabetes associated genes. A Sharma, A Halu, JL Decano, M Padi, Y-Y Liu, RB Prasad, J Fadista, M Santolini, J Menche, ST Weiss, M Vidal, EK Silverman, M Aikawa, A-L Barabási, L Groop & J Loscalzo. npj Systems Biology & Applications 4 (1), 25; 2018

Map of synthetic rescue interactions for the Fanconi anemia DNA repair pathway identifies USP48. G Velimezi, L Robinson-Garcia, F Muñoz-Martínez, WW Wiegant, J Ferreira da Silva, M Owusu, M Moder, M Wiedner, S Brin Rosenthal, KM Fisch, J Moffat, J Menche, H van Attikum, SP Jackson & JI Loizou. Nature Communications 9:2280; 2018

BAFF Neutralization Aggravates Atherosclerosis. D Tsiantoulas, AP Sage, L Göderle, M Ozsvar-Kozma, D Murphy, F Porsch, G Pasterkamp, J Menche, P Schneider, Z Mallat, CJ Binder. Circulation 117.032790; 2018 [link]

A diseasome cluster-based drug repurposing of soluble guanylate cyclase activators from smooth muscle relaxation to direct neuroprotection. F Langhauser, AI Casas, VTV Dao, E Guney, J Menche, E Geuss, PWM Kleikers MG Lopez, AL, Barabási, C Kleinschnitz, HHHW Schmidt. npj Systems Biology & Applications 4:8; 2018 [link]

Open community challenge reveals molecular network modules with key roles in diseases. S Choobdar, ME Ahsen, J Crawford, M Tomasoni, D Lamparter, J Lin, B Hescott, X Hu, J Mercer, T Natoli, R Narayan, A Subramanian, G Stolovitzky, Z Kutalik, K Lage, DK Slonim, J Saez-Rodriguez, LJ Cowen, S Bergmann, D Marbach, DREAM Module Identification Challenge Consortium. bioRxiv 265553; 2018 [link]

 

2017

Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. K Khamina, A Lercher, M Caldera, C Schliehe, B Vilagos, M Sahin, L Kosack, A Bhattacharya, P Májek, A Stukalov, R Sacco, LC James, DD Pinschewer, KL Bennett, J Menche, A Bergthaler. PLoS Pathogens 13(12): e1006758; 2017 [link]

Parallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex and Fanconi anemia. M Moder, G Velimezi, M Owusu, A Mazouzi, M Wiedner, J Ferreira da Silva, L Robinson-Garcia, F Schischlik, R Slavkovsky, R Kralovics, M Schuster, C Bock, T Ideker, SP Jackson, J Menche & JI Loizou Nature Communications 8:1238; 2017 [link]

Network medicine: a new paradigm for cardiovascular disease research and beyond. J MencheCardiovascular Research 113 (10): e29-e30; 2017 [link]

A combinatorial screen of the CLOUD uncovers a synergy targeting the androgen receptor MP Licciardello, A Ringler, P Markt, F Klepsch, C-H Lardeau, S Sdelci, E Schirghuber, AC Müller, M Caldera, A Wagner, R Herzog, T Penz, M Schuster, B Boidol, G Dürnberger, Y Folkvaljon, P Stattin, V Ivanov, J Colinge, C Bock, K Kratochwill, J Menche, KL Bennett, S Kubicek. Nature Chemical Biology; 2017 [pdf]

Interactome-based approaches to human disease M Caldera*, P Buphamalai*, F Müller, J MencheCurrent Opinions in Systems Biology3:88; 2017 [pdf]

The immune system as a social network A BergthalerJ MencheNature Immunology 5:18; 2017 [pdf]

Integrating personalized gene expression profiles into predictive disease-associated gene pool. J Menche*, E Guney*, A Sharma, PJ Branigan, MJ Loza, F Baribaud, R Dobrin, A-L Barabási. npj Systems Biology & Applications 3:10; 2017 [pdf]

 

2016

From comorbidities of chronic obstructive pulmonary disease to identification of shared molecular mechanisms by data integration. 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. BMC Bioinformatics 17:1291; 2016 [pdf]

Tissue Specificity of Human Disease Module. M Kitsak, A Sharma, J Menche, E Guney, SD Ghiassian, J Loscalzo, A-L Barabási, J Loscalzo. Scientific Reports 6:35241; 2016 [pdf]

Endophenotype Network Models: Common Core of Complex Diseases 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. Scientific Reports 6:27414; 2016 [pdf]

An inter-species protein–protein interaction network across vast evolutionary distance. 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. Molecular Systems Biology 12:865; 2016 [pdf]

Network-based in silico drug efficacy screening. E Guney, J Menche, M Vidal, AL Barabási. Nature Communications 7:10331, 2016 [pdf]

 

2015

Canonical Genetic Signatures of the Adult Human Brain. M Hawrylycz, J Miller, V Menon, D Feng, T Dolbeare, A Guillozet-Bongaarts, A Jegga, BJ Aronow, Chang-Kyu Lee, A Bernard, M Glasser, D Dierker, J Menche, F Collman, P Grange, K Berman, S Mihalas, Z Yao, L Stewart, AL Barabási, J Schulkin, J Phillips, L Ng, C Dang, D Haynor, A Jones, D Van Essen, C Koch, E Lein. Nature Neuroscience 18: 1832–1844; 2015 [pdf]

Uncovering disease-disease relationships through the incomplete interactome J Menche, A Sharma, M Kitsak, SD Ghiassian, M Vidal, J Loscalzo, AL Barabási; Science 347 (6224), 1257601; 2015 [pdf]

A DiseAse MOdule Detection (DIAMOnD) algorithm derived from a systematic analysis of connectivity patterns of disease proteins in the human Interactome SD Ghiassian*, J Menche*, AL Barabási; PLoS Comput Biol 11(4): e1004120; 2015 [pdf]

A disease module in the interactome explains disease heterogeneity, drug response and captures novel pathways and genes in asthma A Sharma*, J Menche*, C Huang, T Ort, X Zhou, M Kitsak, N Sahni, D Thibault, L Voung, F Guo, N Gulbahce, F Baribaud, J Tocker, R Dobrin, E Barnathan, H Liu, RA Panettieri, KG Tantisira, W Qiu, BA Raby, EK Silverman, M Vidal, ST Weiss, AL Barabási; Human Molecular Genetics, ddv001; 2015 [pdf]

 

2014

Systems Medicine: from molecular features and models to the clinic in COPD. D Gomez-Cabrero*, J Menche*, I Cano, I Abugessaisa, M Huertas-Migueláñez, A Tenyi, I Marin de Mas, N Kiani, F Marabita, F Falciani, K Burrowes, D Maier, P Wagner, V Selivanov, M Cascante, J Roca, AL Barabási, J Tegnér; Journal of Translational Medicine 12 (Suppl 2), S4; 2014 [pdf]

A proteome-scale map of the human interactome network. T Rolland, M Taşan, B Charloteaux, SJ Pevzner, Q Zhong, N Sahni, S Yi, I Lemmens, C Fontanillo, R Mosca, A Kamburov, SD Ghiassian, X Yang, L Ghamsari, D Balcha, BE Begg, P Braun, M Brehme, MP Broly, AR Carvunis, D Convery-Zupan, R Corominas, J Coulombe-Huntington, E Dann, M Dreze, A Dricot, C Fan, E Franzosa, F Gebreab, BJ Gutierrez, MF Hardy, M Jin, S Kang, R Kiros, GN Lin, K Luck, A MacWilliams, J Menche, RR Murray, A Palagi, MM Poulin, X Rambout, J Rasla, P Reichert, V Romero, E Ruyssinck, JM Sahalie, A Scholz, AA Shah, A Sharma, Y Shen, K Spirohn, S Tam, AO Tejeda, SA Trigg, JC Twizere, K Vega, J Walsh, ME Cusick, Y Xia, AL Barabási, LM Iakoucheva, P Aloy, J De Las Rivas, J Tavernier, MA Calderwood, DE Hill, T Hao, FP Roth, M Vidal; Cell 159 (5), 1212-1226; 2014 [pdf]

Human symptoms–disease network XZ Zhou*, J Menche*, AL Barabási, A Sharma; Nature Communications 5; 2014 [pdf]

A diVIsive Shuffling Approach (VIStA) for gene expression analysis to identify subtypes in Chronic Obstructive Pulmonary. Disease J Menche*, A Sharma*, MH Cho, RJ Mayer, SI Rennard, B Celli, BE Miller, N Locantore, R Tal-Singer, S Ghosh, C Larminie, G Bradley, JH Riley, A Agusti, EK Silverman, AL Barabási; BMC Systems Biology 8 (Suppl 2), S8; 2014 [pdf]

 

Before 2014

Network-based analysis of genome wide association data provides novel candidate genes for lipid and lipoprotein traits. A Sharma, N Gulbahce, SJ Pevzner, J Menche, C Ladenvall, L Folkersen, P Eriksson, M Orho-Melander, AL Barabási; Molecular & Cellular Proteomics 12 (11), 3398-3408; 2013 [pdf]

Sequences of phase transitions in Ising models on correlated networks J Menche, A Valleriani, R Lipowsky; Physical Review E 83 (6), 061129; 2011 [pdf]

Asymptotic properties of degree-correlated scale-free networks J Menche, A Valleriani, R Lipowsky; Physical Review E 81 (4), 046103; 2010 [pdf]

Dynamical processes on dissortative scale-free networks J Menche, A Valleriani, R Lipowsky; Europhysics Letters 89 (1), 18002; 2010 [pdf]

Two particles with bistable coupling on a ratchet J Menche, L Schimansky-Geier; Physics Letters A 359 (2), 90-98; 2006 [pdf]

Crab effect, advantage law, silver medal and other applications of the minority game JRL de Almeida, J MenchearXiv preprint cond-mat/0312139; 2003

Quantifying a certain ''advantage law'': minority game with above the rules agents JRL de Almeida, J MencheBrazilian Journal of Physics33 (4), 895-898; 2003 [pdf]

It is worth thinking twice or Improving the performance of minority games J Menche, JRL de Almeida; arXiv preprint cond-mat/0308181; 2003