Publications

2018

  • M. Babu, C. Bundalovic-Torma, C. Calmettes, S. Phanse, Y. Jiang, V. Deineko, J. Mehla, A. Vastermark, O. Kagan, O. Pogoutse, A. Gagarinova, A. Kumar, H. Guo, Z. Minic, H. Aoki, E. Holtzapple, Z. Zhang, Y. Pandya, C.C. Lai, E. Leung, M. El Bakkouri, Y. Hooda, M. Shah, J. Vlasblom, J.F. Greenblatt, S.V. Rajagopala, S. Wuchty, W. Houry, M. Saier, P. Uetz, T. Moraes, J. Parkinson and A. Emili, ‘Global Landscape of Membrane Protein Complexes in Escherichia coli’, Nature Biotechn., 36, 103–112 (2018)

  • H. Feng, L. Wang, S. Wuchty and A.C.C. Wilson, ‘microRNA regulation in an ancient obligate endosymbiosis’, Mol. Ecol., accepted (2018)
  • S. Wuchty, S.A. Mueller, J.H. Caufield, R. Häuser, S.F. Lichtenthaler, M. von Bergen, P. Aloy, S. Kalkhof and P. Uetz, ‘Proteome data improves protein function prediction in the interactome of H. pylori’, Mol. Cell. Prot., accepted (2018)

  • R. Mariano and S. Wuchty, 'Structure-based prediction of host-pathogen protein interactions', Curr. Op. Struct. Biol, 44, 119-124 (2017)
  • J.H. Caufield, C. Wimble, M. Abreu, S. Shary, S. Wuchty and P. Uetz, ‘Bacterial protein meta-interaction networks reveal consistencies among interactomes’, BMC Bioinf., 18, 171 (2017)

  • S. Wuchty, T. Boltz and H. Kücük-McGinty, ‘Links between critical proteins drive the controllability of protein interaction networks’ Proteomics, 17,10, 1700056 (2017)

  • S. Wuchty, S.V. Rajagopala, S.M. Blazie, J.R. Parrish, S. Khuri, R.L. Finley Jr. and P. Uetz, ‘Predicting genome-wide gene functions of S. pneumoniae with a bacterial meta-interactome’, mSystems, 2 (3), e00019-17 (2017)

2017

2016

  • P. Manrique, J. Horgan, P. Gill, H. Qi, D. Johnson, S. Wuchty, C. Song and N. Johnson, ‘Women’s connectivity in extreme networks’, Sci. Adv. 2 (6), e1501742, (2016)

  • N.F. Johnson, M. Zheng, Y. Vorobyeva, A. Gabriel, H. Qi, N. Velasquez, P. Manrique, D. Johnson, E. Restrepo, C. Song and S. Wuchty, ‘New Online Ecology of Adversarial Aggregates: ISIS and beyond ’, Science, 352, 1459-1463 (2016) (in Science News)

  • R. Mariano, S. Khuri, P. Uetz and S. Wuchty, 'Local action with global impact: Infection patters of human viruses and bacteriophages are highly similar’, mSystems, 1(2):e00030-15 (2016) (editor's pick)

  • R. Mariano, S. Wuchty, M. Vizoso-Pinto, R. Haeuser and P. Uetz, ‘The interactome of S. pneumoniae and its bacteriophages show highly specific patterns of interactions among bacteria and their phages ’, Nature Sci. Rep., 6, 24597 (2016) (F1000 recommended)
  • S. L. Keasey, M. Natesan, C. Pugh, T. Kamata, and R.G. Ulrich, ‘Networks of binary protein interactions from the plague bacterium Yersinia pestis’, Mol. Cell. Prot., 15, 3220-3232 (2016) 

     

  • M. Sordo, S. Wuchty and M. Ogihara, ‘An analysis of the evolution of research groups and topics in the ISMIR conference’, 16th Intl. Soc. for Music Information Retrieval Conf. (2015)

  • S.L. Keasey, M. Natesan, C. Pugh, T. Kamata, S. Wuchty and R.G. Ulrich, ‘The road to linking genomics and proteomics of pathogenic bacteria: from binary protein complexes to interaction pathways’, BMC Bioinformatics, 16 (Suppl 2):A9 (2015)

  • S. Khuri and ,'Essentiality and centrality in protein interaction networks revisited’ , BMC Bioinformatics, 16:109 (2015)

2015

2014

  • S. Wuchty, ‘Controllability of protein interaction networks’, Proc. Natl. Acad. Sci. USA, 111 (19) 7156-7160 (2014)

  • S.V. Rajagopala, P. Sikorski, A. Kumar, R.Mosca, J. Franca-Koh, S. B. Pakala, J. Vlasblom, R. S. Phanse, A. Ceol, R. Häuser, G. Siszler, S. Wuchty, A. Emili, M. Babu, P. Aloy, P. Uetz and R. Pieper, ‘Binary Protein-protein Interaction Landscape of Escherichia coli’, Nature Biotechn., 32, 285–290 (2014)

  • R. Häuser, A. Ceol, S.V. Rajagopala, R. Mosca, G. Siszler, N. Wermke, F. Schwarz, S. Wuchty, P. Aloy and P. Uetz, An extended protein interaction network of H. pylori’, Mol. Cell. Proteomics, 13: 1318-1329 (2014)

  • C. Butler, O. Lucas, S. Wuchty, B. Xue, V. Uversky and M.W. White, ‘Identification of novel pan-picomplexa cell cycle regulated genes’, PLoS One, 9(5), e97625 (2014)

  • S. Wuchty and P. Uetz, ‘Comparative Analysis of protein-protein interactions in E. coli’, Nature Sci. Reports, 4: 7187 (2014)

  • S. Blasche, S. Arens, A. Ceol, G. Siszler, M.A. Schmidt, R. Häuser, F. Schwarz, S. Wuchty, P. Aloy, P. Uetz, T. Stradal and M. Kögl, ‘The EHEC-host interactome reveals novel targets for the translocated intimin receptor’, Nature Sci. Reports, 4: 7531 (2014)

     

2013

  • Y. Huang, S. Wuchty and T. Przytycka, ‘eQTL epistasis – challenges and computational approaches’, Front. Genet. 4, 51, (2013)

  • H. Nishi, M. Tyagi, S. Teng, B. Shoemaker, K. Hashimoto, E. Alexov, S. Wuchty and A. Panchenko, ‘Glioblastoma missense mutations alter binding properties of proteins and their interaction networks’, PLoS One, 8(6): e66273, (2013)

  • S. Blasche, S. Wuchty, S.V. Rajagopala and P. Uetz, The protein interaction network of bacteriophage lambda with its host Escherichia coli’, J. Virol., 87(23), 12745-12755, (2013)

  • Y.-A. Kim, R. Salari, S. Wuchty and T. Przytycka, ‘Module Cover – A New Approach to Genotype-Phenotype Studies’, Pac. Symp. Bioinf., 18:135-146, (2013)

  • B. Shoemaker, S. Wuchty and A. Panchenko, ‘Computational Large-Scale Mapping of Protein-Protein Interactions Using Structural Complexes’, Curr. Protoc. Prot. Sci. 73:3.9.1-3.9.9, (2013)

  • S. Wuchty, D. Arjona and P.O. Bauer, ‘Important miRs of pathways in different tumor types’, PLoS Comp. Biol., 9(1): e1002883, (2013)

  • S. Wuchty, A. Vazquez, S. Bozdag and P.O. Bauer, ‘Genome-wide Associations of Signalling Pathways in Glioma Subtypes’, BMC Med. Genomics, 6:11, (2013)

  • A.L. Vogel, K.L. Hall, S.M. Fiore, J.T. Klein, L.M. Bennett, H. Gadlin, D. Stokols, L.C. Nebeling, S. Wuchty, K. Patrick, E.L. Spotts, C. Pohl, W.T. Riley and H.J. Falk-Krzesinski, ‘The Team Science Toolkit: Enhancing Research Collaboration Through Online Knowledge Sharing’, Am. J. Prev. Med., 45(6), 787-789, (2013)

2012

  • B. Uzzi, S. Wuchty, J. Spiro and B. Jones, ‘Scientific teams and networks change the face of knowledge creation.’ in B. Vedres and M. Scotti (eds.), ‘Networks in Social Policy Problems’, Cambridge University Press, (2012)

  • S. Wuchty, G. Siwo and M.T. Ferdig, ‘Shared molecular strategies of the malaria parasite P. falciparum and the human virus HIV-1 ’, Mol. Cell. Proteomics, 10(10), M111.009035, (2011)

  • M. Tyagi, K. Hashimoto, B. Shoemaker, S. Wuchty and A. Panchenko, ‘A structural network of protein interactions in H. sapiens’, EMBO Reports, 13, 266–271, (2012)

  • Y. Huang, G. Siwo, S. Wuchty, M.T. Ferdig and T. Przytycka,, ‘The linkage disequilibrium and epistatic interactions between genomic loci in Plasmodium falciparum’, Mol. Biosys., 8 (5), 1544–1552, (2012)

  • S. Wuchty, D. Arjona, S. Bozdag and P.O. Bauer, ‘Involvement of miR families in cancer’, Nucl. Acids Res., 40 (17), 8219-8226, (2012)

2011

  • Y.-A. Kim, S. Wuchty, J. Przytycki and T. Przytycka, ‘Modeling information flow in biological networks’, Phys. Biol., 8(3), 035012, (2011)

  • Y.-A. Kim, S. Wuchty and T. Przytycka, ‘Identifying Causal Genes and Dysregulated Pathways in Complex Diseases’, PLoS Comp. Biol., 7(3): e1001095, (2011)

  • S. Wuchty, D. Arjona, A. Li, Y. Kotliarov, A. Zhang, J. Walling, S. Ahn, A. Zhang, D. Maric, R. Anolik, J.-C. Zenklusen and H.A. Fine, ‘Prediction of associations between microRNAs and gene expression in gliomas’, PLoS One, 6(2): e14681, (2011)

  • S. Wuchty, ‘Computational prediction of protein interactions between the malaria parasite P. falciparum and H. sapiens’, PLoS One, 6(11): e26960, (2011)

  • S. Wuchty, G. Siwo and M.T. Ferdig, ‘Shared molecular strategies of the malaria parasite P. falciparum and the human virus HIV-1 ’, Mol. Cell. Proteomics, 10(10), M111.009035, (2011)

  • S. Wuchty and B. Uzzi, ‘Detecting Real Social Attachments in Electronic Footstep Data’, PLoS One, 6(11): e26972, (2011)

2010

  • Y. Kotliarov, S. Bozdag, S. Wuchty, J.-C. Zenklusen and H.A. Fine, ‘CNAReporter: A computational tool for the generation of clinical reports of genomic alterations’, BMC Med. Genomics, 3: 11, (2010)

  • S. Bozdag, A. Li, S. Wuchty and H.A Fine, ‘FastMedusa: A parallelized tool to infer gene

    regulatory networks’, Bioinformatics, 26, 1792-1793, (2010)

  • S. Wuchty, G. Siwo and M.T. Ferdig, ‘Viral organization of human proteins’, PLoS One, 5(8): e11796, (2010)

  • Y. Kim, S. Wuchty and T. Przytycka, ‘Simultaneous identification of causal genes and dysregulated pathways in complex diseases’, RECOMB 2010, 263-280, (2010)

  • S. Wuchty, A. Zhang, J. Walling, S. Ahn, A. Li, J.-C. Zenklusen and H.A. Fine, ‘Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology’, J. Biomed. Inf., 43, 945-952, (2010)

     

2009

  • S. Wuchty, ‘What is a social tie?’, Proc. Natl. Acad. Sci. USA,  106 (36), 15099-15100, (2009)

  • S. Kanaan, C. Huang, S. Wuchty, D. Cheng and J. Izaguirre, ‘Inferring Protein-Protein Interactions from multiple domain interactions’, Methods Mol. Biol., 541, 43-59, (2009)

  • S. Wuchty, J.H. Adams and M.T. Ferdig, ‘A comprehensive Plasmodium falciparum protein interaction map reveals a distinct architecture of a core interactome’, Proteomics, 9(7), 1841-1849, (2009)

  • Y. Huang, S. Wuchty, M.T. Ferdig and T. Przytycka, ‘Graph theoretical approach to study eQTL: A case study of Plasmodium falciparum’, Bioinformatics, 25(12), i15-i20, (2009)

2008

  • J.M. Gonzales, J.J. Patel, N. Ponmee, L. Jiang, A. Tan, S.P. Maher, S. Wuchty, P.K. Rathod and M.T. Ferdig, ‘Regulatory Hotspots in the Malaria Parasite Genome Dictate Transcriptional Variation’, PLoS Biol., 6(9): e238, (2008)

  • B. Jones, S. Wuchty and B. Uzzi, ‘Multi-University Research Teams: Shifting Impact, Geography, and Stratification in Science’, Science, 322, 1259-1262, (2008)

2007

  • S. Wuchty, B. Jones and B. Uzzi, ‘The Increasing Dominance of Teams in the Production of Knowledge’, Science, 316, 1036-1039, (2007)

  • S. Wuchty, B. Jones and B. Uzzi, ‘Science Commentary: Why do Team-Authored Papers get cited more?’, Science, 317, 1496-1498, (2007)

  • C. Huang, F.M. Gonzalez, S. Kanaan, S. Wuchty, D. Cheng and J. Izaguirre, ‘Predicting Protein-Protein Interactions from Protein Domains Using A Set Cover Approach’, IEEE Trans. Comp. Biol. Bioinf., 4 (1), 78-87, (2007)

  • S. Wuchty and J. Ipsaro, ‘A draft of the interactome of the human malaria parasite P. falciparum’, J. Proteome Res., 6 (4), 1461-1470, (2007)

  • S. Wuchty, ‘Rich club phenomenon in the interactome of P. falciparum – Signature of a parasitic life style?’, PLoS One, 2(3): e335, (2007)

2006

  • S. Wuchty, A.-L. Barabasi and M.T. Ferdig, ‘Stable evolutionary signal in a Yeast protein interaction network ‘, BMC Evol. Biol. 6:8, (2006)

  • S. Wuchty, ‘Topology and weights in a protein domain interaction network - A novel way to infer protein interactions’, BMC Genomics, 7: 122, (2006)

before 2006

  • S. Wuchty, A.-L. Barabasi and M.T. Ferdig, ‘Stable evolutionary signal in a Yeast protein interaction network ‘, BMC Evol. Biol. 6:8, (2006)

  • S. Wuchty, ‘Topology and weights in a protein domain interaction network - A novel way to infer protein interactions’, BMC Genomics, 7: 122, (2006)

  • A.-L. Barabasi, Z.N. Oltvai and S. Wuchty, ‘Characteristics of Biological Networks’,  in E. Ben-Naim, H. Frauenfelder and Z. Toroczkai (eds.),  ‘Complex Networks’, Lect. Notes Phys., 650, (2004)

  • S. Wuchty and E. Almaas, ‘Peeling the Yeast Proteome’, Proteomics, 5, 445-449, (2005)

  • S. Wuchty and E. Almaas, ‘Evolutionary cores of domain co-occurrence networks’, BMC Evol. Biol., 5:24, (2005)

  • K. Wegner, S. Jansen, R. Gauges, S. Wuchty and U. Kummer, ‘CombAlign: A Protein Sequence Alignment Algorithm Considering Recombinations’, InSilico Biol., 4, 0021, (2004)

  • S. Wuchty, ‘Evolution and topology in the yeast protein interaction network’, Genome Res., 14, 1310-1314, (2004)

  • S. Wuchty, E. Ravasz and A.-L. Barabasi, ‘The Architecture of Biological Networks’,  in T.S. Deisboeck, J. Yasha Kresh and T. B. Kepler (eds.), ‘Complex Systems Science in  Biomedicine’, Kluwer Academic Publishing, (2004)

  • S. Wuchty, ‘Small-Worlds in RNA’, Nucl. Acids Res., 31, 1108 - 1117, (2003)

  • S. Wuchty and P.F. Stadler, ‘Centers of Large Networks’, J. Theoret. Biol., 223, 45-53, (2003)

  • S. Wuchty, Z.N. Oltvai and A.-L. Barabasi, ‘Evolutionary conservation of motif constituents within the yeast protein interaction network’, Nature Genetics, 35, 176-179, (2003)

  • S. Wuchty, ‘Interaction and Domain Networks of Yeast’, Proteomics, 2 (12), 1715-1723, (2002)

  • S. Wuchty, ‘Scale-free Behavior in Protein Domain Networks’, Mol. Biol. Evol., 18 (9), 1694-1702, (2001)

  • S. Wuchty, W. Fontana, I. Hofacker and P. Schuster, ‘Complete Suboptimal Folding of RNA and the Stability of Secondary Structures’, Biopolymers, 49, 145-165, (1999)

  • Schober, G. Schlingloff, D. Tomandl, J.M. Köhler, G. Mayer, A. Gross, S. Wuchty, H. Deppe,  B. Diefenbach and H. Wurziger, ’Chemical and Biochemical Synthesis and Screening in Silico’,  In  H. Reichl, E. Obermaier (eds.), Microsystem Technologies 98, 6th Internat. Conf. on Micro-, Electro-, Opto- and Mechanical Systems and Components, 451-456, Potsdam, (1998)

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