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Items: 35

1.

Plasticity of the Cullin-RING Ligase Repertoire Shapes Sensitivity to Ligand-Induced Protein Degradation.

Mayor-Ruiz C, Jaeger MG, Bauer S, Brand M, Sin C, Hanzl A, Mueller AC, Menche J, Winter GE.

Mol Cell. 2019 Aug 22;75(4):849-858.e8. doi: 10.1016/j.molcel.2019.07.013.

PMID:
31442425
2.

Systematic characterization of BAF mutations provides insights into intracomplex synthetic lethalities in human cancers.

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.

Nat Genet. 2019 Sep;51(9):1399-1410. doi: 10.1038/s41588-019-0477-9. Epub 2019 Aug 19.

PMID:
31427792
3.

HACE1 deficiency leads to structural and functional neurodevelopmental defects.

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.

Neurol Genet. 2019 Apr 29;5(3):e330. doi: 10.1212/NXG.0000000000000330. eCollection 2019 Jun.

4.

MTHFD1 interaction with BRD4 links folate metabolism to transcriptional regulation.

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, Mechtler K, Menche J, Bradner JE, Winter GE, Klavins K, Casanova E, Bock C, Zuber J, Kubicek S.

Nat Genet. 2019 Jun;51(6):990-998. doi: 10.1038/s41588-019-0413-z. Epub 2019 May 27.

PMID:
31133746
5.

Mutational landscape of the transcriptome offers putative targets for immunotherapy of myeloproliferative neoplasms.

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.

Blood. 2019 Jul 11;134(2):199-210. doi: 10.1182/blood.2019000519. Epub 2019 May 7.

6.

Mapping the Human Kinome in Response to DNA Damage.

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.

Cell Rep. 2019 Jan 15;26(3):555-563.e6. doi: 10.1016/j.celrep.2018.12.087.

7.

Integration of Molecular Interactome and Targeted Interaction Analysis to Identify a COPD Disease Network Module.

Sharma A, Kitsak M, Cho MH, Ameli A, Zhou X, Jiang Z, Crapo JD, Beaty TH, Menche J, Bakke PS, Santolini M, Silverman EK.

Sci Rep. 2018 Sep 27;8(1):14439. doi: 10.1038/s41598-018-32173-z.

8.

Controllability in an islet specific regulatory network identifies the transcriptional factor NFATC4, which regulates Type 2 Diabetes associated genes.

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.

NPJ Syst Biol Appl. 2018 Jul 3;4:25. doi: 10.1038/s41540-018-0057-0. eCollection 2018.

9.

Non-classical monocytes as mediators of tissue destruction in arthritis.

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.

Ann Rheum Dis. 2018 Oct;77(10):1490-1497. doi: 10.1136/annrheumdis-2018-213250. Epub 2018 Jun 29.

10.

Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology.

Aguirre-Plans J, Piñero J, Menche J, Sanz F, Furlong LI, Schmidt HHHW, Oliva B, Guney E.

Pharmaceuticals (Basel). 2018 Jun 22;11(3). pii: E61. doi: 10.3390/ph11030061.

11.

Map of synthetic rescue interactions for the Fanconi anemia DNA repair pathway identifies USP48.

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.

Nat Commun. 2018 Jun 11;9(1):2280. doi: 10.1038/s41467-018-04649-z.

12.

B Cell-Activating Factor Neutralization Aggravates Atherosclerosis.

Tsiantoulas D, Sage AP, Göderle L, Ozsvar-Kozma M, Murphy D, Porsch F, Pasterkamp G, Menche J, Schneider P, Mallat Z, Binder CJ.

Circulation. 2018 Nov 13;138(20):2263-2273. doi: 10.1161/CIRCULATIONAHA.117.032790.

13.

A diseasome cluster-based drug repurposing of soluble guanylate cyclase activators from smooth muscle relaxation to direct neuroprotection.

Langhauser F, Casas AI, Dao VT, Guney E, Menche J, Geuss E, Kleikers PWM, López MG, Barabási AL, Kleinschnitz C, Schmidt HHHW.

NPJ Syst Biol Appl. 2018 Feb 5;4:8. doi: 10.1038/s41540-017-0039-7. eCollection 2018.

14.

Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein.

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.

PLoS Pathog. 2017 Dec 20;13(12):e1006758. doi: 10.1371/journal.ppat.1006758. eCollection 2017 Dec.

15.

Parallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex and Fanconi anemia.

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.

Nat Commun. 2017 Nov 1;8(1):1238. doi: 10.1038/s41467-017-01439-x.

16.

Network medicine: a new paradigm for cardiovascular disease research and beyond.

Menche J.

Cardiovasc Res. 2017 Aug 1;113(10):e29-e30. doi: 10.1093/cvr/cvx129. No abstract available.

PMID:
28899006
17.

Integrating personalized gene expression profiles into predictive disease-associated gene pools.

Menche J, Guney E, Sharma A, Branigan PJ, Loza MJ, Baribaud F, Dobrin R, Barabási AL.

NPJ Syst Biol Appl. 2017 Mar 13;3:10. doi: 10.1038/s41540-017-0009-0. eCollection 2017.

18.

A combinatorial screen of the CLOUD uncovers a synergy targeting the androgen receptor.

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.

Nat Chem Biol. 2017 Jul;13(7):771-778. doi: 10.1038/nchembio.2382. Epub 2017 May 22.

PMID:
28530711
19.

The immune system as a social network.

Bergthaler A, Menche J.

Nat Immunol. 2017 Apr 18;18(5):481-482. doi: 10.1038/ni.3727. No abstract available.

PMID:
28418389
20.

From comorbidities of chronic obstructive pulmonary disease to identification of shared molecular mechanisms by data integration.

Gomez-Cabrero D, Menche J, Vargas C, Cano I, Maier D, Barabási AL, Tegnér J, Roca J; Synergy-COPD Consortia.

BMC Bioinformatics. 2016 Nov 22;17(Suppl 15):441. doi: 10.1186/s12859-016-1291-3.

21.

Tissue Specificity of Human Disease Module.

Kitsak M, Sharma A, Menche J, Guney E, Ghiassian SD, Loscalzo J, Barabási AL.

Sci Rep. 2016 Oct 17;6:35241. doi: 10.1038/srep35241.

22.

Endophenotype Network Models: Common Core of Complex Diseases.

Ghiassian SD, Menche J, Chasman DI, Giulianini F, Wang R, Ricchiuto P, Aikawa M, Iwata H, Müller C, Zeller T, Sharma A, Wild P, Lackner K, Singh S, Ridker PM, Blankenberg S, Barabási AL, Loscalzo J.

Sci Rep. 2016 Jun 9;6:27414. doi: 10.1038/srep27414.

23.

An inter-species protein-protein interaction network across vast evolutionary distance.

Zhong Q, Pevzner SJ, Hao T, Wang Y, Mosca R, Menche J, Taipale M, Taşan M, Fan C, Yang X, Haley P, Murray RR, Mer F, Gebreab F, Tam S, MacWilliams A, Dricot A, Reichert P, Santhanam B, Ghamsari L, Calderwood MA, Rolland T, Charloteaux B, Lindquist S, Barabási AL, Hill DE, Aloy P, Cusick ME, Xia Y, Roth FP, Vidal M.

Mol Syst Biol. 2016 Apr 22;12(4):865. doi: 10.15252/msb.20156484.

24.

Network-based in silico drug efficacy screening.

Guney E, Menche J, Vidal M, Barábasi AL.

Nat Commun. 2016 Feb 1;7:10331. doi: 10.1038/ncomms10331.

25.

Canonical genetic signatures of the adult human brain.

Hawrylycz M, Miller JA, Menon V, Feng D, Dolbeare T, Guillozet-Bongaarts AL, Jegga AG, Aronow BJ, Lee CK, Bernard A, Glasser MF, Dierker DL, Menche J, Szafer A, Collman F, Grange P, Berman KA, Mihalas S, Yao Z, Stewart L, Barabási AL, Schulkin J, Phillips J, Ng L, Dang C, Haynor DR, Jones A, Van Essen DC, Koch C, Lein E.

Nat Neurosci. 2015 Dec;18(12):1832-44. doi: 10.1038/nn.4171. Epub 2015 Nov 16.

26.

A DIseAse MOdule Detection (DIAMOnD) algorithm derived from a systematic analysis of connectivity patterns of disease proteins in the human interactome.

Ghiassian SD, Menche J, Barabási AL.

PLoS Comput Biol. 2015 Apr 8;11(4):e1004120. doi: 10.1371/journal.pcbi.1004120. eCollection 2015 Apr.

27.

Disease networks. Uncovering disease-disease relationships through the incomplete interactome.

Menche J, Sharma A, Kitsak M, Ghiassian SD, Vidal M, Loscalzo J, Barabási AL.

Science. 2015 Feb 20;347(6224):1257601. doi: 10.1126/science.1257601.

28.

A disease module in the interactome explains disease heterogeneity, drug response and captures novel pathways and genes in asthma.

Sharma A, Menche J, Huang CC, Ort T, Zhou X, Kitsak M, Sahni N, Thibault D, Voung L, Guo F, Ghiassian SD, Gulbahce N, Baribaud F, Tocker J, Dobrin R, Barnathan E, Liu H, Panettieri RA Jr, Tantisira KG, Qiu W, Raby BA, Silverman EK, Vidal M, Weiss ST, Barabási AL.

Hum Mol Genet. 2015 Jun 1;24(11):3005-20. doi: 10.1093/hmg/ddv001. Epub 2015 Jan 12.

29.

Systems Medicine: from molecular features and models to the clinic in COPD.

Gomez-Cabrero D, Menche J, Cano I, Abugessaisa I, Huertas-Migueláñez M, Tenyi A, Marin de Mas I, Kiani NA, Marabita F, Falciani F, Burrowes K, Maier D, Wagner P, Selivanov V, Cascante M, Roca J, Barabási AL, Tegnér J.

J Transl Med. 2014 Nov 28;12 Suppl 2:S4. doi: 10.1186/1479-5876-12-S2-S4. Epub 2014 Nov 28.

30.

A proteome-scale map of the human interactome network.

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

Cell. 2014 Nov 20;159(5):1212-1226. doi: 10.1016/j.cell.2014.10.050.

31.

A diVIsive Shuffling Approach (VIStA) for gene expression analysis to identify subtypes in Chronic Obstructive Pulmonary Disease.

Menche J, Sharma A, Cho MH, Mayer RJ, Rennard SI, Celli B, Miller BE, Locantore N, Tal-Singer R, Ghosh S, Larminie C, Bradley G, Riley JH, Agusti A, Silverman EK, Barabási AL.

BMC Syst Biol. 2014;8 Suppl 2:S8. doi: 10.1186/1752-0509-8-S2-S8. Epub 2014 Mar 13.

32.

Human symptoms-disease network.

Zhou X, Menche J, Barabási AL, Sharma A.

Nat Commun. 2014 Jun 26;5:4212. doi: 10.1038/ncomms5212.

PMID:
24967666
33.

Network-based analysis of genome wide association data provides novel candidate genes for lipid and lipoprotein traits.

Sharma A, Gulbahce N, Pevzner SJ, Menche J, Ladenvall C, Folkersen L, Eriksson P, Orho-Melander M, Barabási AL.

Mol Cell Proteomics. 2013 Nov;12(11):3398-408. doi: 10.1074/mcp.M112.024851. Epub 2013 Jul 23.

34.

Sequences of phase transitions in Ising models on correlated networks.

Menche J, Valleriani A, Lipowsky R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Jun;83(6 Pt 1):061129. Epub 2011 Jun 20.

PMID:
21797324
35.

Asymptotic properties of degree-correlated scale-free networks.

Menche J, Valleriani A, Lipowsky R.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Apr;81(4 Pt 2):046103. Epub 2010 Apr 9.

PMID:
20481782

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