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The green peach aphid gut contains host plant microRNAs identified by comprehensive annotation of Brassica oleracea small RNA data.

Thompson MC, Feng H, Wuchty S, Wilson ACC.

Sci Rep. 2019 Dec 11;9(1):18904. doi: 10.1038/s41598-019-54488-1.


Epigenomic signatures underpin the axonal regenerative ability of dorsal root ganglia sensory neurons.

Palmisano I, Danzi MC, Hutson TH, Zhou L, McLachlan E, Serger E, Shkura K, Srivastava PK, Hervera A, Neill NO, Liu T, Dhrif H, Wang Z, Kubat M, Wuchty S, Merkenschlager M, Levi L, Elliott E, Bixby JL, Lemmon VP, Di Giovanni S.

Nat Neurosci. 2019 Nov;22(11):1913-1924. doi: 10.1038/s41593-019-0490-4. Epub 2019 Oct 7.


MicroRNA miR-1002 Enhances NMNAT-Mediated Stress Response by Modulating Alternative Splicing.

Park J, Zhu Y, Tao X, Brazill JM, Li C, Wuchty S, Zhai RG.

iScience. 2019 Sep 27;19:1048-1064. doi: 10.1016/j.isci.2019.08.052. Epub 2019 Aug 30.


Hidden resilience and adaptive dynamics of the global online hate ecology.

Johnson NF, Leahy R, Restrepo NJ, Velasquez N, Zheng M, Manrique P, Devkota P, Wuchty S.

Nature. 2019 Sep;573(7773):261-265. doi: 10.1038/s41586-019-1494-7. Epub 2019 Aug 21.


Promoter conservation in HDACs points to functional implications.

Boltz TA, Khuri S, Wuchty S.

BMC Genomics. 2019 Jul 27;20(1):613. doi: 10.1186/s12864-019-5973-x.


Collective influencers in protein interaction networks.

Boltz TA, Devkota P, Wuchty S.

Sci Rep. 2019 Mar 8;9(1):3948. doi: 10.1038/s41598-019-40410-2.


A network biology approach to unraveling inherited axonopathies.

Bis-Brewer DM, Danzi MC, Wuchty S, Züchner S.

Sci Rep. 2019 Feb 8;9(1):1692. doi: 10.1038/s41598-018-37119-z.


Protein-protein interactions of human viruses.

Goodacre N, Devkota P, Bae E, Wuchty S, Uetz P.

Semin Cell Dev Biol. 2018 Jul 26. pii: S1084-9521(17)30499-8. doi: 10.1016/j.semcdb.2018.07.018. [Epub ahead of print] Review.


Beyond degree and betweenness centrality: Alternative topological measures to predict viral targets.

Devkota P, Danzi MC, Wuchty S.

PLoS One. 2018 May 24;13(5):e0197595. doi: 10.1371/journal.pone.0197595. eCollection 2018.


Proteome Data Improves Protein Function Prediction in the Interactome of Helicobacter pylori.

Wuchty S, Müller SA, Caufield JH, Häuser R, Aloy P, Kalkhof S, Uetz P.

Mol Cell Proteomics. 2018 May;17(5):961-973. doi: 10.1074/mcp.RA117.000474. Epub 2018 Feb 1.


microRNA regulation in an ancient obligate endosymbiosis.

Feng H, Wang L, Wuchty S, Wilson ACC.

Mol Ecol. 2018 Apr;27(8):1777-1793. doi: 10.1111/mec.14464. Epub 2018 Jan 22.


Global landscape of cell envelope protein complexes in Escherichia coli.

Babu M, Bundalovic-Torma C, Calmettes C, Phanse S, Zhang Q, Jiang Y, Minic Z, Kim S, Mehla J, Gagarinova A, Rodionova I, Kumar A, Guo H, Kagan O, Pogoutse O, Aoki H, Deineko V, Caufield JH, Holtzapple E, Zhang Z, Vastermark A, Pandya Y, Lai CC, El Bakkouri M, Hooda Y, Shah M, Burnside D, Hooshyar M, Vlasblom J, Rajagopala SV, Golshani A, Wuchty S, F Greenblatt J, Saier M, Uetz P, F Moraes T, Parkinson J, Emili A.

Nat Biotechnol. 2018 Jan;36(1):103-112. doi: 10.1038/nbt.4024. Epub 2017 Nov 27.


The Protein Interactome of Streptococcus pneumoniae and Bacterial Meta-interactomes Improve Function Predictions.

Wuchty S, Rajagopala SV, Blazie SM, Parrish JR, Khuri S, Finley RL Jr, Uetz P.

mSystems. 2017 Jun 6;2(3). pii: e00019-17. doi: 10.1128/mSystems.00019-17. eCollection 2017 May-Jun.


Links between critical proteins drive the controllability of protein interaction networks.

Wuchty S, Boltz T, Küçük-McGinty H.

Proteomics. 2017 May;17(10):e1700056. doi: 10.1002/pmic.201700056. Epub 2017 May 2.


Structure-based prediction of host-pathogen protein interactions.

Mariano R, Wuchty S.

Curr Opin Struct Biol. 2017 Jun;44:119-124. doi: 10.1016/ Epub 2017 Mar 17. Review.


Bacterial protein meta-interactomes predict cross-species interactions and protein function.

Caufield JH, Wimble C, Shary S, Wuchty S, Uetz P.

BMC Bioinformatics. 2017 Mar 16;18(1):171. doi: 10.1186/s12859-017-1585-0.


Local Action with Global Impact: Highly Similar Infection Patterns of Human Viruses and Bacteriophages.

Mariano R, Khuri S, Uetz P, Wuchty S.

mSystems. 2016 Mar 8;1(2). pii: e00030-15. eCollection 2016 Mar-Apr.


Cell-free Determination of Binary Complexes That Comprise Extended Protein-Protein Interaction Networks of Yersinia pestis.

Keasey SL, Natesan M, Pugh C, Kamata T, Wuchty S, Ulrich RG.

Mol Cell Proteomics. 2016 Oct;15(10):3220-3232. Epub 2016 Aug 3.


Women's connectivity in extreme networks.

Manrique P, Cao Z, Gabriel A, Horgan J, Gill P, Qi H, Restrepo EM, Johnson D, Wuchty S, Song C, Johnson N.

Sci Adv. 2016 Jun 10;2(6):e1501742. doi: 10.1126/sciadv.1501742. eCollection 2016 Jun.


New online ecology of adversarial aggregates: ISIS and beyond.

Johnson NF, Zheng M, Vorobyeva Y, Gabriel A, Qi H, Velasquez N, Manrique P, Johnson D, Restrepo E, Song C, Wuchty S.

Science. 2016 Jun 17;352(6292):1459-63. doi: 10.1126/science.aaf0675. Epub 2016 Jun 16.


The interactome of Streptococcus pneumoniae and its bacteriophages show highly specific patterns of interactions among bacteria and their phages.

Mariano R, Wuchty S, Vizoso-Pinto MG, Häuser R, Uetz P.

Sci Rep. 2016 Apr 22;6:24597. doi: 10.1038/srep24597.


Essentiality and centrality in protein interaction networks revisited.

Khuri S, Wuchty S.

BMC Bioinformatics. 2015 Apr 1;16:109. doi: 10.1186/s12859-015-0536-x.


The EHEC-host interactome reveals novel targets for the translocated intimin receptor.

Blasche S, Arens S, Ceol A, Siszler G, Schmidt MA, Häuser R, Schwarz F, Wuchty S, Aloy P, Uetz P, Stradal T, Koegl M.

Sci Rep. 2014 Dec 18;4:7531. doi: 10.1038/srep07531.


Protein-protein Interaction Networks of E. coli and S. cerevisiae are similar.

Wuchty S, Uetz P.

Sci Rep. 2014 Nov 28;4:7187. doi: 10.1038/srep07187.


Identifying novel cell cycle proteins in Apicomplexa parasites through co-expression decision analysis.

Butler CL, Lucas O, Wuchty S, Xue B, Uversky VN, White M.

PLoS One. 2014 May 19;9(5):e97625. doi: 10.1371/journal.pone.0097625. eCollection 2014.


Controllability in protein interaction networks.

Wuchty S.

Proc Natl Acad Sci U S A. 2014 May 13;111(19):7156-60. doi: 10.1073/pnas.1311231111. Epub 2014 Apr 28.


A second-generation protein-protein interaction network of Helicobacter pylori.

Häuser R, Ceol A, Rajagopala SV, Mosca R, Siszler G, Wermke N, Sikorski P, Schwarz F, Schick M, Wuchty S, Aloy P, Uetz P.

Mol Cell Proteomics. 2014 May;13(5):1318-29. doi: 10.1074/mcp.O113.033571. Epub 2014 Mar 13.


The binary protein-protein interaction landscape of Escherichia coli.

Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Häuser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P.

Nat Biotechnol. 2014 Mar;32(3):285-290. doi: 10.1038/nbt.2831. Epub 2014 Feb 23.


Computational large-scale mapping of protein-protein interactions using structural complexes.

Shoemaker B, Wuchty S, Panchenko AR.

Curr Protoc Protein Sci. 2013 Sep 24;73:3.9.1-3.9.9. doi: 10.1002/0471140864.ps0309s73.


The Team Science Toolkit: enhancing research collaboration through online knowledge sharing.

Vogel AL, Hall KL, Fiore SM, Klein JT, Bennett LM, Gadlin H, Stokols D, Nebeling LC, Wuchty S, Patrick K, Spotts EL, Pohl C, Riley WT, Falk-Krzesinski HJ.

Am J Prev Med. 2013 Dec;45(6):787-9. doi: 10.1016/j.amepre.2013.09.001. No abstract available.


The protein interaction network of bacteriophage lambda with its host, Escherichia coli.

Blasche S, Wuchty S, Rajagopala SV, Uetz P.

J Virol. 2013 Dec;87(23):12745-55. doi: 10.1128/JVI.02495-13. Epub 2013 Sep 18.


Cancer missense mutations alter binding properties of proteins and their interaction networks.

Nishi H, Tyagi M, Teng S, Shoemaker BA, Hashimoto K, Alexov E, Wuchty S, Panchenko AR.

PLoS One. 2013 Jun 14;8(6):e66273. doi: 10.1371/journal.pone.0066273. Print 2013.


eQTL Epistasis - Challenges and Computational Approaches.

Huang Y, Wuchty S, Przytycka TM.

Front Genet. 2013 May 31;4:51. doi: 10.3389/fgene.2013.00051. eCollection 2013.


Genome-wide associations of signaling pathways in glioblastoma multiforme.

Wuchty S, Vazquez A, Bozdag S, Bauer PO.

BMC Med Genomics. 2013 Mar 28;6:11. doi: 10.1186/1755-8794-6-11.


Module cover - a new approach to genotype-phenotype studies.

Kim YA, Salari R, Wuchty S, Przytycka TM.

Pac Symp Biocomput. 2013:135-46.


Important miRs of pathways in different tumor types.

Wuchty S, Arjona D, Bauer PO.

PLoS Comput Biol. 2013;9(1):e1002883. doi: 10.1371/journal.pcbi.1002883. Epub 2013 Jan 24.


Involvement of microRNA families in cancer.

Wuchty S, Arjona D, Bozdag S, Bauer PO.

Nucleic Acids Res. 2012 Sep 1;40(17):8219-26. Epub 2012 Jun 28.


Symmetric Epistasis Estimation (SEE) and its application to dissecting interaction map of Plasmodium falciparum.

Huang Y, Siwo G, Wuchty S, Ferdig MT, Przytycka TM.

Mol Biosyst. 2012 Apr;8(5):1544-52. doi: 10.1039/c2mb05333k. Epub 2012 Mar 15.


Large-scale mapping of human protein interactome using structural complexes.

Tyagi M, Hashimoto K, Shoemaker BA, Wuchty S, Panchenko AR.

EMBO Rep. 2012 Mar 1;13(3):266-71. doi: 10.1038/embor.2011.261.


Human communication dynamics in digital footsteps: a study of the agreement between self-reported ties and email networks.

Wuchty S, Uzzi B.

PLoS One. 2011;6(11):e26972. doi: 10.1371/journal.pone.0026972. Epub 2011 Nov 17.


Computational prediction of host-parasite protein interactions between P. falciparum and H. sapiens.

Wuchty S.

PLoS One. 2011;6(11):e26960. doi: 10.1371/journal.pone.0026960. Epub 2011 Nov 17.


Shared molecular strategies of the malaria parasite P. falciparum and the human virus HIV-1.

Wuchty S, Siwo GH, Ferdig MT.

Mol Cell Proteomics. 2011 Oct;10(10):M111.009035. doi: 10.1074/mcp.M111.009035. Epub 2011 May 17.


Modeling information flow in biological networks.

Kim YA, Przytycki JH, Wuchty S, Przytycka TM.

Phys Biol. 2011 Jun;8(3):035012. doi: 10.1088/1478-3975/8/3/035012. Epub 2011 May 13. Review.


Identifying causal genes and dysregulated pathways in complex diseases.

Kim YA, Wuchty S, Przytycka TM.

PLoS Comput Biol. 2011 Mar;7(3):e1001095. doi: 10.1371/journal.pcbi.1001095. Epub 2011 Mar 3.


Prediction of Associations between microRNAs and Gene Expression in Glioma Biology.

Wuchty S, Arjona D, Li A, Kotliarov Y, Walling J, Ahn S, Zhang A, Maric D, Anolik R, Zenklusen JC, Fine HA.

PLoS One. 2011 Feb 16;6(2):e14681. doi: 10.1371/journal.pone.0014681.


Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology.

Wuchty S, Zhang A, Walling J, Ahn S, Li A, Quezado M, Oberholtzer C, Zenklusen JC, Fine HA.

J Biomed Inform. 2010 Dec;43(6):945-52. doi: 10.1016/j.jbi.2010.08.011. Epub 2010 Sep 7.


Viral organization of human proteins.

Wuchty S, Siwo G, Ferdig MT.

PLoS One. 2010 Aug 25;5(8):e11796. doi: 10.1371/journal.pone.0011796.


FastMEDUSA: a parallelized tool to infer gene regulatory networks.

Bozdag S, Li A, Wuchty S, Fine HA.

Bioinformatics. 2010 Jul 15;26(14):1792-3. doi: 10.1093/bioinformatics/btq275. Epub 2010 May 30.


CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations.

Kotliarov Y, Bozdag S, Cheng H, Wuchty S, Zenklusen JC, Fine HA.

BMC Med Genomics. 2010 Apr 9;3:11. doi: 10.1186/1755-8794-3-11.


What is a social tie?

Wuchty S.

Proc Natl Acad Sci U S A. 2009 Sep 8;106(36):15099-100. doi: 10.1073/pnas.0907905106. Epub 2009 Sep 1. No abstract available.

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