2024
-
S. Wuchty, A. Olthof, A. White, K.
Drake, A. Augspach, A. Hume, J. Olejnik, V. Aguiar-Pulido, E. Mühlberger and R.
Kanadia, ‘Minor intron genes as a viral Achilles heel?’, PNAS Nexus,
accepted (2024)
- X. Yang,
S.
Wuchty, Z. Liang, L. Ji, B. Wang, J. Zhu, Z. Zhang and Y. Dong, 'Multi-modal features-based
human-herpesvirus protein-protein interaction prediction by using LightGBM', Brief. Bioinformatics, accepted (2024)
- S. Fazal, M.C. Danzi, I. Xu,
S. Nadimpalli Kobren, S. Sunyaev, C. Reuter, S. Marwaha, M. Wheeler, E.
Dolzhenko, F. Lucas, S. Wuchty, M. T
ekin, S. Zuechner and V.
Aguiar-Pulido, ‘RExPRT: a machine learning tool to predict pathogenicity of
tandem repeat loci’, Genome Biol., accepted (2024)
2023
- A.M. Enders,
A. Diekman, C. Klofstad, M. Murthi, D. Verdear,
S. Wuchty and J. Uscinski, ‘
On modeling the correlates of conspiracy thinking
’,
Nature Sci.
Rep., 13, 8325 (2023)
- A.M. Enders, J. Uscinski, M. Seelig, C. Klofstad,
S.
Wuchty, J. Funchion, M. Murthi, K. Premaratne and J. Stoler, ‘The
Relationship Between Social Media Use and Beliefs in Conspiracy Theories and Misinformation
’, Political Behavior, 45(2), 781-804
(2023)
- M. Park, S.K. Mayti,
S. Wuchty and D. Wang, ‘Interdisciplinary
papers supported by disciplinary grants garner deep and broad scientific
impact’,
https://arxiv.org/abs/2303.14732
(2023)
- S. Littrell, C. Klofstad, A.
Diekman, J. Funchion, M. Murthi, K. Premaratne, M. Seelig, D. Verdear,
S.
Wuchty and J.E. Uscinski, ‘Who Knowingly Shares False Information Online?’,
Harvard
Kennedy School Misinformation Review, 4(4) (2023).
- A. Augspach, K.D. Drake, L. Roma, E.
Qian, S.R. Lee, D. Clarke, S. Kumar, M. Jaquet, J. Gallon, M. Bolis,
J. Triscott, J. A. Galván, Y. Chen, G. Thalmann, M. Kruithof-de Julio, J.-P.
Theurillat, S. Wuchty, M. Gerstein, S. Piscuoglio, R. N. Kanadia and M. A. Rubin,
‘Minor intron splicing efficiency increases with the development of lethal prostate
cancer’, Mol. Cell, 83, 1983–2002 (2023)
- Y. Huang, S. Wuchty, Z. Zhang and Y. Zhang, ‘SGPPI:
structure-aware
prediction
of protein-protein interactions in rigorous conditions
with graph convolutional network’, Brief. Bioinformatics, 24(2), 1-10 (2023)
- J. Zheng, X. Yang, Y. Huang, S. Yang, S. Wuchty and Z. Zhang, ‘Deep learning-assisted prediction of
protein-protein interactions in Arabidopsis thaliana’, Plant J., https://doi.org/10.1111/tpj.16188 (2023)
- I. Paul, D. Bolzan, A. Youssef, K.A. Gagnon, H. Hook, G. Karemore, M. Oliphant,
W. Lin, Q. Liu, S. Phanse, C.
White, D.
Padhorny, S.
Kotelnikov, C.S. Chen, P. Hu, G.V. Denis, D. Kozakov, B. Raught, T. Siggers,
S. Wuchty, S.K. Muthuswamy and A. Emili, ‘Parallelized multidimensional analytic
framework applied to mammary epithelial cells uncovers regulatory principles in
EMT, Nature Communications, 14(10),
688 (2023)
- K. Ruan, G. Farinas Perez, M. Kubat, I. Hofacker,
S. Wuchty and R.G. Zhai, ‘MicroRNA-Mediated
Obstruction of Stem-loop Alternative Splicing is a global mechanism for the regulation
of alternative splicing’, https://www.biorxiv.org/content/10.1101/2023.04.14.536877v1
(2023)
- K.A. Wolcott, E.L. Stanley, O.A. Gutierrez,
S. Wuchty and B.A. Whitlock, ‘3D pollination biology
using micro - CT and geometric morphometrics in Theobroma cacao L.’, Appl. Plant Sciences, 11:e11549 (2023)
- A.C. Diaz, A.M. Cirrincione, N.A. Schmidt, M.J. Ugo, M.C. Amaya
Sanchez, C.A. Reimonn,
S. Wuchty, A.D. Pellegrini, L. Rude, L.G. Pappalardo,
D.P. Regan, C. Howell, S. Hrstka, S. Dasari, T.S. Lisse, B.J. Harrison, M.X. Xu,
N.P. Staff and S. Rieger, ‘Epidermal Eg5 promotes X-ROS dependent
paclitaxel neurotoxicity’ https://www.biorxiv.org/content/10.1101/2023.05.22.541784v2
(2023)
2022
- M. Seelig, J. Funchion, R.
Trego, S. Kuebler, D. Verdear, J. Uscinski, C. Klofstad, M. Murthi, S. Wuchty
and K. Premaratne,‘The Dark Side of Twitter: A Framing Analysis of Conspiratorial
Rhetoric Stoking Fear’, 72nd Annual Intl. Communication
Association (ICA) (2022)
- J.
Uscinski, A. Enders, M. Seelig, C. Klofstad, J. Funchion, C. Everett, S. Wuchty,
K. Premaratne and M. Murthi, ‘Who Supports QAnon? A Case
Study in Political Extremism’, J.
of Politics, 84(3), 1844-1849, (2022)
-
Uscinski, A. Enders, A.
Diekman, J. Funchion, C. Klofstad, S. Kuebler, M. Murthi, K. Premaratne, M. Seelig,
D. Verdear and S. Wuchty, ‘The Psychological and Political Correlates
of Conspiracy Theory Beliefs’, Nature Sci. Rep., accepted (2022)
-
I. Paul, D. Bolzan, A.
Youssef,
K.A. Gagnon,
H. Hook,
G. Karemore, M. Oliphant, W.
Lin, Q. Liu, S. Phanse,
C.
White,
D. Padhorny,
S. Kotelnikov,
G.P.
Andrieu,
C.S.
Chen
,
P. Hu,
G.V.
Denis,
D. Kozakov,
B. Raught, T. Siggers,
S. Wuchty,
S.K.
Muthuswamy, A. Emili
, ‘A multi-tiered map of EMT defines major transition points and
identifies vulnerabilities’, Nature Communications, accepted, (2022)
- X. Yang, S. Yang, P. Ren, S. Wuchty and Z. Zhang, ‘Deep
learning-powered prediction of human-virus protein-protein interactions’,
Frontiers in Microbiol., 13, 842976 (2022)
- A. Augspach,
K.D. Drake, L. Roma, E.
Qian, S.R. Lee,
D. Clarke, S. Kumar, M. Jaquet, J. Gallon, M. Bolis,
J. Triscott, J. A. Galván, Y. Chen, G. Thalmann, M. Kruithof-de Julio, J.-P.
Theurillat, S. Wuchty, M. Gerstein,
S. Piscuoglio, R. N. Kanadia and
M. A. Rubin, ‘Minor intron splicing efficiency increases with the development
of lethal prostate cancer’, https://www.biorxiv.org/content/10.1101/2021.12.09.471104v1
(2022)
- S. Wuchty, A. Olthof, A. White, K. Drake, A.
Augspach, A. Hume, J. Olejnik, E. Muehlberger, M. Rubin, V. Aguiar-Pulido and
R. Kanadia, ‘Minor intron genes as a viral Achilles heel?’, https://www.biorxiv.org/content/10.1101/2022.09.30.510319v1
(2022)
2021
-
X. Yang, X. Lian, C.
Fu, S. Yang, S. Wuchty and Z. Zhang, 'HVIDB: a comprehensive database resource associated with human-virus
protein-protein interactions’, Briefings in Bioinformatics, 22 (2), 832-844, (2021)
- X. Yang, Z. Zhang and S. Wuchty, ‘Transfer learning via multi-scale convolutional neural layers
for the prediction of human-virus protein interactions’, Proceedings of the 13th Intl. Conference on Agents and Artificial Intelligence, 41-48 (2021)
- S. Wuchty, A.J. Myers, M. Ramirez-Restrepo,
M. Huentelman, R. Richolt, F. Gould, P.D. Harvey, V. Michopolous, J. Steven,
A. Wingo, A. Lori, J. Maples-Keller, A. Rothbaum, T. Jovanovic, B. Rothbaum, K.J.
Ressler and C.B. Nemeroff, ‘Integration of peripheral Transcriptomics, Genomics
and Interactomics Following Trauma Identifies Genes for Post-Traumatic Stress
Disorder and Major Depression’, Mol. Psychiatry, 26(7), 3077-3092 (2021)
- A. Lori, K.
Schultebraucks, I. Galatzer-Levy, N. Daskalakis, S. Katrinli, A.K. Smith, A.J. Myers, R.
Richholt, M. Huentelman, G. Guffanti, S. Wuchty, F. Gould, C.B. Nemeroff, T.
Jovanovic, J.L. Maples-Keller, J.S. Stevens, V. Michopolous, B.O. Rothbaum, A.P.
Wingo, and K.J. Ressler, ‘Transcriptome-wide association study of post-trauma symptom
trajectories identified GRIN3B as a potential biomarker for PTSD development’, Neuropsychopharmacology,
46, 1811–1820, (2021)
- X. Yang, S. Yang, X. Lian, S. Wuchty and Z. Zhang, ‘TransPPI: transfer
learning via multi-scale convolutional neural layers for human-virus PPI
prediction’, Bioinformatics, 37(24), 4771-4778 (2021)
- J. Uscinski, A.
Enders, M. Seelig, C. Klofstad, J. Funchion, C. Everett, S. Wuchty, K.
Premaratne and M. Murthi, ‘American Politics in Two Dimensions: Partisan and Ideological
Identities versus Anti-Establishment Orientations’, Am. J. Pol. Science, 65(4),
877-895 (2021)
- A.M.
Enders, J. Uscinski, M. Seelig, C. Klofstad, S. Wuchty, J. Funchion, M. Murthi
and K. Premaratne, ‘Do Conspiracy Beliefs form a Belief System? Examining the
Structure and Organization of Conspiracy Beliefs’, J. Soc. Pol. Psych., 9(1),
255-271 (2021)
- A.
Enders, J. Uscinski, C. Klofstad, K. Premaratne, M. Seelig, S. Wuchty, M.
Murthi and J. Funchion, ‘The 2020 presidential election and beliefs about
fraud: Continuity or change?’, Electoral Studies, 72, 102366, (2021)
- A.M.
Enders, J. Uscinski, M. Seelig, C. Klofstad, S. Wuchty, J. Funchion, M. Murthi,
K. Premaratne and J. Stoler, ‘The Relationship Between Social Media Use and
Beliefs in Conspiracy Theories and Misinformation’, Political Behavior, (2021)
2020
- J. Uscinski, A.
Enders, M. Seelig, C. Klofstad, J. Funchion, C. Everett, S. Wuchty, K.
Premaratne and
M. Murthi, ‘Conspiracy Thinking, Denialism,
and Partisanship Promote COVID-19 Conspiracy Theories’, Harvard
Kennedy School Misinformation Review (2020)
- N.F. Johnson,
N. Velasquez, N. Johnson Restrepo, R. Leahy, N. Gabriel, S. El Oud, M. Zheng,
P. Manrique, S. Wuchty and Y. Lupu, ‘Mapping the online ecology and
interactions of vaccine views’, Nature, 582, 230–233 (2020)
- X. Yang, S. Yang, Q. Li, S. Wuchty and Z. Zhang, ‘Prediction of
human-virus protein-protein interactions through a sequence embedding-based
machine learning method’, Comp. Struct. Biotech. J., 18, 153-161, (2020)
- P. Devkota and S. Wuchty, ‘Controllability of
molecular pathways’, Nature Sci. Reports, 10:
2943,
(2020)
- H. Dhrif, L.
Sanchez-Giraldo, M. Kubat and S. Wuchty, ‘Stable Feature Selection for Gene
Expression using enhanced Binary Particle Swarm Optimization’, Proc. of the 12th
Intl. Conference on Agents and Artificial Intelligence, 437-444, (2020)
- P. Devkota, M.C. Danzi, V.P.
Lemmon, J.L. Bixby and S. Wuchty, ‘Computational Determination
of Genes to control Axon Growth’, SLAS Discov. 25(7), 792-800 (2020)
- H. Dhrif, V. Bolon and S. Wuchty, ‘Feature Selection
for Transfer Learning using Bilevel Multi-objective Particle Swarm Optimization’, 19TH
IEEE
Intl. Conf. on Machine Learning & Applications,
1317-1323 (2020)
- R.M. Hekman,
A.J. Hume, R. Kumar Goel, K.M. Abo, J. Huang, B. Blum, R. Bree Werder, E.L.
Suder, I. Paul, S. Phanse, A. Youssef, K.D. Alysandratos, D. Padhorny, S. Ojha,
A. Mora-Martin, D. Kretov, P. Ash, M. Varma, J. Zhao, J.J. Patten, C.
Villacorta-Martin, D. Bolzan, C. Perea-Resa, E. Bullitt, A. Hinds, S. Farhangmehr,
U. Braunschweig, A. Tilston-Lunel, X. Varelas, J.H. Kwan, M. McComb, A. Basu,
M. Saeed, V. Perrissi, E.J. Burks, M.D. Layne, J.H. Connor, R. Davey, J.-X.
Cheng, B.L. Wolozon, B.J. Blencowe, S. Wuchty, S.M. Lyons, D. Kozakov, D. Cifuentes,
M. Blower, D.N. Kotton, A.A. Wilson, E. Mühlberger and A. Emili, ‘Systems Level
Survey of Actionable Cytopathogenic Host Responses of Human Lung Alveolar Type
2 Cells to SARS-CoV-2 Infection ’, Mol. Cell, 80, 1104-1122 (2020)
2019
- Palmisano, M.C. Danzi, E. McLachlan, K. Shkura,
S. Prashant, A. Hervera, M. Johnson, B. Lenhard, N. O’Neill, T. Liu, H. Dhrif,
Z. Wang, S. Wuchty, J.L. Bixby, V.P. Lemmon and S. Di Giovanni, ‘Epigenomic
signatures in dorsal root ganglia underlie differential injury responses
between regeneration-competent versus regeneration-incompetent axonal injury’,
Nature Neuroscience, 22, 1913-1924 (2019)
- M.C. Thompson, H. Feng, S. Wuchty and A.C. C. Wilson, ‘
The green peach aphid gut contains host plant microRNAs
identified by comprehensive annotation of Brassica oleracea small RNA data’,
Nature Sci. Reports, 9:18904 (2019)
- J. Park, Y. Zhu,
X. Tao,
J.M. Brazill,
C. Li,
S. Wuchty, R.G. Zhai, ‘MicroRNA
miR-1002 enhances
NMNAT-mediated stress response
by
modulating
alternative splicing’, iScience, 19,
1048-1064 (2019)
- H. Dhrif, L. Sanchez-Giraldo, M.
Kubat and S. Wuchty, ‘A Consistent Hybrid Method for Feature Subset Selection using Particle
Swarm Optimization with Local Search’, Proceedings of the Genetic and Evolutionary Computation
Conference (GECCO 2019), 13-21 (2019)
- D. Bis, M.
Danzi, S. Wuchty and S. Zuechner, ‘A network biology approach to unraveling
inherited axonopathies’, Nature Sci. Rep., 9:1692 (2019)
- T. Boltz, P. Devkota and S. Wuchty, ‘Collective
influencers in protein interaction networks’, Nature Sci. Rep.,
9:3948, (2019)
- T. Boltz, S. Khuri and S. Wuchty, ‘Promoter conservation in HDACs point to functiona implications’, BMC Genomics
, 20, 613 (2019)
- N.F. Johnson,
R. Leahy, N. Johnson Restrepo, N. Velasquez, M. Zheng, P. Manrique, P. Devkota and
S. Wuchty, ‘Hidden global resilience and adaptive dynamics of online hate’, Nature, 573, 261-265 (2019)
2018
-
H. Feng, L. Wang,
S. Wuchtyand A.C.C. Wilson,
‘
microRNA regulation in an ancient obligate endosymbiosis
’, Mol. Ecol., 27, 1777–1793 (2018)
- P. Devkota, M. Danzi and S. Wuchty,
‘Beyond degree and betweeness centrality: Novel network measures to predict
viral targets’, PLoS One, 13(5), e0197595 (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., 17 (5) 961-973 (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, 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)
- N. Goodacre, P. Devkota, S. Wuchty and
P. Uetz, ‘Virus genomes and virus-host interactions in human disease’, Semin. Cell. Dev. Biol., S1084-9521 (17) 30499-8
(2018)
2017
- R.
Mariano and S. Wuchty, ‘Structure-based prediction of host-pathogen protein interactions’,
Curr. Opin. 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)
2016
- P. Manrique, J. Horgan, P. Gill, H. Qi, D. Johnson, S. Wuchty,
C. Song and N. Johnson, ‘Women’s
connectivity in extreme networks’, Science 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)
- R.
Mariano, S. Khuri, P. Uetz and S. Wuchty, ‘Local action with global impact:
infection patternsof
human viruses and bacteriophages are highly similar’, mSystems, 1(2):e00030-15
(2016)
- 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)
- S. L. Keasey, M. Natesan, C. Pugh, T.
Kamata, S. Wuchty and R.G. Ulrich, ‘Networks of binary protein interactions
from the plague bacterium Yersinia pestis’, Mol. Cell. Prot., 15, 3220-3232
(2016)
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 S. Wuchty, ‘Essentiality and centrality in protein interaction networks
revisited’, BMC Bioinformatics, 16:109 (2015)
- 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)
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. Arnold, 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-apicomplexa 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. Rep., 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. Rep., 4, 7531 (2014)
before 2014
- 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)
- 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)
- 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)
- 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)
- 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)
- 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)
- 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)
- 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)
- 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)
- S. Wuchty, ‘What is a social
tie?’, Proc. Natl. Acad. Sci. USA, 106 (36), 15099-15100, (2009)
- 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)
- 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)
- 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)
- 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)
