Published Articles

2022

Network Approaches for Charting the Transcriptomic and Epigenetic Landscape of the Developmental Origins of Health and Disease.
SD Lombardo, IF Wangsaputra, J Menche, and A Stevens.
Genes 13, no. 5: 764; 2022 [pdf]

BioProfiling. jl: Profiling biological perturbations with high-content imaging in single cells and heterogeneous populations.
L Vulliard, J Hancock, A Kamnev, CW Fell, J Ferreira da Silva, JI Loizou, V Nagy, L Dupré, and J Menche.
Bioinformatics 38, no. 6: 1692-1699; 2022 [pdf]

Cartographs enable interpretation of complex network visualizations.
CVR Hütter, and J Menche.
Nature Research Briefing 2, no. 2: 76-77; 2022 [pdf]

Network cartographs for interpretable visualizations.
CVR Hütter, C Sin, F Müller, and J Menche.
Nature Computational Science 2, no. 2: 84-89; 2022 [pdf]

Large neutral amino acid levels tune perinatal neuronal excitability and survival.
LS Knaus, B Basilico, D Malzl, MG Bujalkova, M Smogavec, LA Schwarz, S Gorkiewicz, N Amberg, F Pauler, T Rülicke, J Menche, S Hippenmeyer, and G Novarino.
bioRxiv; 2022 [pdf]

The regulatory network architecture of cardiometabolic diseases.
HHHW Schmidt, and J Menche.
Nature Genetics 54, no. 1: 2-3; 2022 [pdf]

2021

Network analysis reveals rare disease signatures across multiple levels of biological organization.
P Buphamalai, T Kokotovic, V Nagy, and J Menche.
Nature Communications 12, no. 1: 1-15; 2021 [pdf]

Morphological profiling of human T and NK lymphocytes by high-content cell imaging.
Y German, L Vulliard, A Kamnev, L Pfajfer, J Huemer, AK Mautner, A Rubio, A Kalinichenko, K Boztug, A Ferrand, J Menche and L Dupré.
Cell Reports 36, no. 1: 109318; 2021 [pdf]

The VRNetzer Platform Enables Interactive Network Analysis in Virtual Reality.
S Pirch, F Müller, E Iofinova, J Pazmandi, CVR Hütter, M Chiettini, C Sin, K Boztug, I Podkosova, H Kaufmann & J Menche.
Nature Communications 12 (1), 1-14; 2021 2021 [pdf]

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

Hydrothermal polymerization of porous aromatic polyimide networks and machine learning-assisted computational morphology evolution interpretation.
M Lahnsteiner, M Caldera, HM Moura, DA Cerrón-Infantes, J Roeser, T Konegger, A Thomas, J Menche, and MM Unterlass.
Journal of Materials Chemistry A 9, no. 35: 19754-19769; 2021 [pdf]

Beneficial Metabolic Effects of TREM2 in Obesity are Uncoupled from its Expression on Macrophages.
O Sharif, JS Brunner, A Korosec, R Martins, A Jais, B Snijder, A Vogel, M Caldera, A Hladik, K Lakovits, S Saluzzo, B Boehm, AD 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 [pdf]

Structure and Function in Complex Biological Networks.
J Hancock, and J Menche.
Systems Medicine 26; 2021 [pdf]

Complex Networks in Health and Disease.
L Vulliard, and J Menche.
Systems Medicine 26; 2021 [pdf]

2020

The PI3K pathway preserves metabolic health through MARCO-dependent lipid uptake by adipose tissue macrophages.
JS 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, MW Górna, M Kulik, PM Dominiak, AE Brandon, E Estevez, CL Egan, F Gruber, M Schweiger, J Menche, A Bergthaler, T Weichhart, K Klavins, MA Febbraio, O Sharif, G Schabbauer.
Nature Metabolism 2, 1427–1442; 2020 [pdf]

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 [pdf]

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 105 (10), e448; 2020 [pdf]

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 [pdf]

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

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 [pdf]

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 [pdf]

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 [pdf]

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 [pdf]

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 [pdf]

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 [pdf]

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.
Neurology: Genetics 5 (3): e330. 2019 [pdf]

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 [pdf]

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 [pdf]

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 [pdf]

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 [pdf]

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 [pdf]

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 [pdf]

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 [pdf]

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 [pdf]

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 [pdf]

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 [pdf]

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 [pdf]

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 Menche.
Cardiovascular 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 Menche.
Current Opinions in Systems Biology3:88; 2017 [pdf]

The immune system as a social network.
A Bergthaler. J Menche.
Nature 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 Menche.
arXiv preprint cond-mat/0312139; 2003

Quantifying a certain ''advantage law'': minority game with above the rules agents.
JRL de Almeida, J Menche.
Brazilian 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

Book Chapters

Network Medicine
P Buphamalai, M Caldera, F Müller & J Menche.
In “Analyzing Network Data in Biology and Medicine” edited by N Pržulj.
Cambridge University Press (2019)
[pdf]

The Network of Networks involved in Human Disease
C Sin & J Menche,
In “Molecular networks, the rise of networks of networks” edited by N Kiani, D Gomez-Cabrero & G Bianconi.
Springer (2019)
[pdf]

Introduction to Network Analysis
J Menche & A-L Barabási
In “Network Medicine. Complex Systems in Human Disease and Therapeutics” edited by J Loscalzo, A-L Barabási and EK Silverman. Harvard University Press (2017)
[pdf]