YearPaper
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
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 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 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 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
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 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 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 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 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 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 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
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
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
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 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 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 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
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 tostructural 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
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 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 totranscriptional 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