Publications

Articles

Books

Software

Data

Publications (Peer Reviewed)

2022

240. Karve, S., Dasmeh, P., Zheng, J., Wagner, A. (2022) Low protein expression enhances phenotypic evolvability by intensifying selection on folding stability. Nature Ecology and Evolution 6, 1155-1164. [reprint request]

239.  Wagner, A. (2022) AI predicts the effectiveness and evolution of gene promoter sequences. Nature 603, 399-400. [reprint request]

238. Karve, S., Wagner, A. (2022) Environmental complexity is more important than mutation in driving the evolution of latent novel traits in E. coli. Nature Communications 13, 5904. [reprint request]

237. Toll-Riera, M., Olombrada, M., Castro-Giner, F., Wagner, A. (2022) A limit on the evolutionary rescue of an Antarctic bacterium from rising temperatures. Science Advances 8, eabk3511 [reprint request]

236. Wagner, A. (2022) Nutrient competition increases invasion resistance during assembly of microbial communities. Molecular Ecology 31, 4188-4203. [reprint request]

235. Iyengar, B.R., Wagner, A. (2022) Bacterial Hsp90 predominantly buffers but does not potentiate the phenotypic effects of deleterious mutations during fluorescent protein evolution. Genetics 222, iyac154. [reprint request]

234. Iyengar, B.R., Wagner, A. (2022) GroEL/S helps to purge deleterious mutations and reduce genetic diversity during adaptive protein evolution. Molecular Biology and Evolution 39, msac047. [reprint request]

233. Brewer, T.E., Wagner, A. (2022) Translation stalling proline motifs are enriched in slow-growing, thermophilic, and multicellular bacteria. The ISME Journal 16, 1065-1073 [reprint request]

232. Moerman, F., Fronhofer, E.A., Altermatt, F. Wagner, A. (2022) Selection on growth rate and local adaptation drive genomic adaptation during experimental range expansions in the protist Tetrahymena thermophila. Journal of Animal Ecology 91, 1088-1103. [reprint request]

2021

231. Van Gestel, J., Wagner, A. (2021) Cryptic surface-associated multicellularity emerges through cell adhesion and its regulation. PLoS Biology 19(5), e3001250. [reprint request]

230. Wagner, A. (2021) Adaptive gene misregulation. Genetics 217, iyaa044. [reprint request]

229. Dasmeh, P., Wagner, A. (2021) Natural selection on the phase-separation properties of FUS during 160 million years of mammalian evolution. Molecular Biology and Evolution 38, 940-951. [reprint request]

228. Schweizer, G., Wagner, A. (2021) Both binding strength and evolutionary accessibility affet the population frequency of transcription factor binding sequences in Arabidopsis thaliana. Genome Biology and Evolution 13, evab273. [reprint request]

227. Karve, S., Wagner, A. (2021) Multiple novel traits without immediate benefits originate in bacteria evolving on single antibiotics. Molecular Biology and Evolution msab34. [reprint request]

226. San Roman, M., Wagner, A. (2021) Diversity begets diversity during community assembly until ecological limits impose a diversity ceiling. Molecular Ecology 30, 5874-5887 [reprint request]

225. Dasmeh, P., Wagner, A. (2021) Yeast proteins may reversibly aggregate like amphiphilic molecules. Journal of Molecular Biology 434, 167352 [reprint request]

224. Wagner, A. Adaptive evolvability through direct selection instead of indirect, second-order selection. (2021) Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 338: 395–404. [reprint request]

223. Dasmeh, P., Doronin, R., Wagner, A. (2021) The length scale of multivalent interactions is evolutionarily conserved in fungal and vertebrate phase-separating protein. Genetics 220, iyab184. [reprint request]

222. Figueiredo, A.R.T, Wagner, A., Kümmerli, R. (2021) Ecology drives the evolution of diverse social strategies in Pseudomonas aeruginosa. Molecular Ecology 30, 5214-5228. [reprint request]

221. Zheng, J., Bratulic, S., Lischer, H.E.L., Wagner, A. (2021) Mistranslation can promote the exploration of alternative evolutionary trajectories in enzyme evolution. Journal of Evolutionary Biology 34: 1302-1315. [reprint request]

220. Zheng, J., Guo, N., Wagner, A. (2021) Mistranslation reduces mutation load in evolving proteins through negative epistasis with DNA mutations. Molecular Biology and Evolution 38, 4792-4804. [reprint request]

2020

219. Zheng, J., Guo, N., Wagner, A. (2020) Strong selection enhances protein evolvability by increasing mutational robustness and foldability. Science 370, 6521 [reprint request]

218. San Roman, M., Wagner, A. (2020) Acetate and glycerol are not uniquely suited for the evolution of cross-feeding in E. coli. PLoS Computational Biology 16 (11), e1008433 [reprint request]

217. Schweizer, G., Wagner, A. (2020) Genotype networks of 80 quantitative Arabidopsis thaliana phenotypes reveal substantial phenotypic evolvability despite pervasive epistasis. PLoS Computational Biology 16 (8), e1008082. [reprint request]

216. Schmutzer, M., Wagner, A. (2020) Gene expression noise can promote the fixation of beneficial mutations in fluctuating environments. PLoS Computational Biology 16 (10), e1007727. [reprint request]

215. Azpeitia, E., Wagner, A. (2020) Signaling pathways have an inherent need for noise to acquire information. BMC Bioinformatics 21, 1-21. [reprint request]

214. Wagner, A. (2020) Information theory can help quantify the potential of new phenotypes to originate as exaptations. Frontiers of Ecology and Evolution 8: 564071. [reprint request]

213. Azpeitia, E., Wagner, A. (2020) Short residence times of DNA-bound transcription factors can reduce gene expression noise and increase the transmission of information in a gene regulation system. Frontiers in Molecular Biosciences 7: 67 [reprint request]

212. Moerman, F., Fronhofer, E.A., Wagner, A. Altermatt, F. (2020) Gene swamping alters evolution during range expansions in the protist Tetrahymena thermophile. Biology Letters 16, 20200244. [reprint request]

211. Moerman, F., Arquint, A., Merkli, S. Wagner, A., Altermatt F., Fronhofer, E.A. (2020) Evolution under pH stress and high population densities leads to increased density‐dependent fitness in the protest Tetrahymena thermophile. Evolution 74, 573-586.   [reprint request]

2019

209. Zheng, J., Payne, J.L., Wagner, A. (2019) Cryptic genetic variation accelerates adaptive evolution by opening alternative paths towards diverse adaptive peaks. Science 365, 347-353. [reprint request]

208. van Gestel, J., Ackermann, M., Wagner, A. (2019) Microbial life cycles link global modularity in regulation to mosaic evolution. Nature Ecology and Evolution 3, 1184-1196. [reprint request]

207. Payne, J.L., Wagner, A. (2019) The causes of evolvability and their evolution. Nature Reviews Genetics 20, 24-38. [reprint request]

206. Libby, E., Hebert-Dufresne, L., Hosseini, S.-R., Wagner, A. (2019) Syntrophy emerges spontaneously in complex metabolic systems. PLoS Computational Biology 15 (7), e1007169. [reprint request]

205. Aguilar-Rodriguez, J., Fares, M.,A., Wagner, A. (2019) Chaperonin overproduction and metabolic erosion caused by mutation accumulation in Escherichia coli. FEMS Microbiology Letters 366 (10), fnz121. [reprint request]

2018

204. Payne, J.L., Khalid, F., Wagner, A. (2018) RNA-mediated gene regulation is less evolvable than transcriptional regulation. Proceedings of the National Academy of Sciences of the U.S.A. 115, E3481-E3490. [reprint request]

203. Hosseini, S.-R., Wagner, A. (2018) Genomic organization underlying deletional robustness in bacterial metabolic systems. Proceedings of the National Academy of Sciences of the U.S.A. 115, 7075-7080. [reprint request]

202. Sprouffske, K., Aguilar-Rodriguez, J., Sniegowski, P., Wagner, A. (2018) High mutation rates limit evolutionary adaptation in Escherichia coli. PLoS Genetics 14, e1007324. [reprint request]

201. Schaerli, Y., Jimenez, A., Duarte, J.M., Mihajlovic, L., Renggli, J., Isalan, M., Sharpe, J., Wagner, A. (2018) Mechanistic causes of constrained phenotypic variation revealed by synthetic gene regulatory circuits. Molecular Systems Biology 14, e8102. [reprint request]

200. San Roman, M., Wagner, A. (2018) An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment. PLoS Computational Biology 14, e1006340. [reprint request]

199. Aguilar Rodriguez, J., Peel, L., Stella, M., Wagner, A. Payne., J.A. (2018) The architecture of an empirical genotype-phenotype map. Evolution 72, 1242-1260. [reprint request]

198. Aguilar-Rodriguez, J., Wagner, A. (2018) Metabolic determinants of enzyme eolution in a genome-scale bacterial metabolic network. Genome Biology and Evolution 10, 3076-3088.[reprint request]

197. Bichsel, M., Barbour, A.D., Wagner, A. (2018) Dynamics of an insertion sequence infection in a spatially structured environment. Journal of Biological Systems 26, 133-166. [reprint request]

196. Chu, H.-Y., Sprouffske, K., Wagner, A. (2018) Assessing the benefits of horizontal gene transfer by laboratory evolution and genome sequencing. BMC evolutionary biology 18, 54. [reprint request]

195. Catalan, P., Wagner, A., Manrubia, S., Cuesta, J.A. (2018) Adding levels of complexity enhances robustness and evolvability in a multi-level genotype-phenotype map. Journal of the Royal Society Interface 15, 20170516. [reprint request]

194. Vahdati, A.R., Wagner, A. (2018) Population size affects adaptation in complex ways: simulations on empirical adaptive landscapes. Evolutionary Biology 45, 156-169. [reprint request]

2017

193. Bratulic, S., Toll-Riera, M., Wagner, A. (2017) Mistranslation benefits adaptive evolution through purging of deleterious mutations. Nature Communications 8, 15410. [reprint request]

192. Aguilar Rodriguez, J., Payne., J.A., Wagner, A. (2017) 1000 empirical adaptive landscapes and their navigability. Nature Ecology and Evolution 1, 0045 (doi: 10.1038/s41559-016-0045). [reprint request]

191. Fortuna, M.A., Zaman, L., Ofria, C., Wagner, A. (2017) The genotype-phenotype map of an evolving digital organism. PLoS Computational Biology13 (2), e1005414. [reprint request]

190. Wagner, A. (2017) The White Knight hypothesis, or does the environment limit evolutionary innovations? Trends in Ecology and Evolution32, 131-140. [reprint request]

189. Hochberg, M. E., Marquet, P.A., Boyd, R., Wagner, A. (2017) Innovation: an emerging focus from cells to societies. Philosophical Transactions of the Royal Society B 372: 20160414. [reprint request]

188. Chu, H.-Y., Sprouffske, K., Wagner, A. (2017) The role of recombination in evolutionary adaptation of Escherichia coli to a novel nutrient. Journal of Evolutionary Biology 30: 1692–1711. [reprint request]

187. Hosseini, S.-R., Wagner, A. (2017) Constraint and contingency pervade the emergence of novel phenotypes in complex metabolic systems. Biophysical Journal 113, 690-701. [reprint request]

186. Wagner, A. (2017) Information theory, evolutionary innovations, and evolvability. Philosophical Transactions of the Royal Society B 372: 20160416. [reprint request]

185. Fortuna, M.A., Zaman, L., Wagner, A., Bascompte, J. (2017) Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms. Philosophical Transactions of the Royal Society B 372: 20160431. [reprint request]

184. Vahdati, A.R., Sprouffske, K., Wagner, A. (2017) Effect of population size and mutation rate on the evolution of RNA sequences on an adaptive landscape determined by RNA folding. International Journal of Biological Sciences 13: 1138. [reprint request]

2016

183. Hosseini, S.-R., Martin, O.C., Wagner, A. (2016) Phenotypic innovation through recombination in genome-scale metabolic networks. Proceedings of the Royal Society B: Biological Sciences283: 20161536. (http://dx.doi.org/10.1098/rspb.2016.1536) [reprint request]

182. Toll-Riera, M., San Millan, A., Wagner, A., MacLean, R.C. (2016) The genomic basis of metabolic evolutionary innovation in Pseudomonas aeruginosa. PLoS Genetics12(5), e1006005. [reprint request]

181. Wagner, A., Ortman, S., Maxfield, R. (2016) From the primordial soup to self-driving cars: standards and their role in natural and technological innovation. Journal of the Royal Society Interface13, 20151086. [reprint request]

180. Aguilar-Rodriguez, J., Sabater-Munoz, B., Montagud-Martinez, R. Berlanga, V. Alvarez-Ponce, D., Wagner, A., Fares, M.A. The molecular chaperone DnaK is a source of mutational robustness. (2016) Genome Biology and Evolution 8: 2979-2991. [reprint request]

179. Sprouffske, K., Aguilar-Rodriguez, J., Wagner, A. (2016) How archiving by freezing alters the genome-scale diversity of Escherichia coli populations. Genome Biology and Evolution8 (5), 1290-1298. [reprint request]

178. Hosseini, S.-R., Martin, O.C., Wagner, A. (2016) The potential for non-adaptive origins of evolutionary innovations in central carbon metabolism. BMC Systems Biology 10 (1), 97. [reprint request]

177. Vahdati, A.R., Wagner, A. (2016) Parallel or convergent evolution in human population genomic data revealed by genotype networks. BMC Evolutionary Biology 16, 1. [reprint request]

176. Khalid, F., Aguilar-Rodriguez, J., Wagner, A., Payne, J.L. (2016) Genonets server – A web server for the construction, analysis, and visualization of genotype networks. Nucleic Acids Research, 44: W70-W76. [reprint request]

175. Sprouffske, K., Wagner, A. (2016) Growthcurver: An R package for obtaining interpretable metrics from microbial growth curves. BMC Bioinformatics17, 1. [reprint request]

174. Blattner, A.C., Aguilar-Rodriguez, J., Kranzlin, M., Wagner, A., Lehner, C.F. (2016) Drosophila Nnf1 paralogs are partially redundant for somatic and germ line kinetochore function. Chromosoma., 1-19. doi:10.1007/s00412-016-0579-4. [reprint request]

173. Wagner, A., Payne, J. L. (2016) Robustness and Evolvability in Molecular Evolution. In Encyclopedia of Evolutionary Biology, Elsevier, pp. 484 - 488.

2015

172. Hayden, E., Bendixsen, D.P., Wagner, A. (2015) Intramolecular phenotypic capacitance in a modular RNA molecule. Proceedings of the National Academy of Sciences 112, 12444-12449. [reprint request]

171. Bratulic, S., Gerber, F., Wagner, A. (2015) Mistranslation drives the evolution of robustness but not translational accuracy in TEM-1 beta-lactamase. Proceedings of the National Academy of Sciences 112 , 12758-12763. [reprint request]

170. Hosseini, S.-R., Barve, A., Wagner, A. (2015) Exhaustive analysis of a genotype space comprising 10¹⁵ central carbon metabolisms reveals an organization conducive to metabolic innovation. PLoS Computational Biology 11 (8), e1004329. [reprint request]

169. Bilgin Sonay, T., Carvalho, T., Robinson, M., Greminger, M., Krutzen, M., Comas, D., Highnam, G., Mittelman, D.A., Sharp., A.J., Marques-Bonet, T., Wagner, A. (2015) Tandem repeat variation in human and great ape populations and its impact on gene expression divergence. Genome Research 25, 1591-1599.[reprint request]

168. Sabater-Munoz, B., Prats-Escriche, M., Montagud-Martinez, R., Lopez-Cerdan, A., Toft, C., Aguilar-Rodriguez, J., Wagner, A., Fares, M.A. (2015) Fitness trade-offs determine the role of the molecular chaperonin GroEL in buffering mutations. Molecular Biology and Evolution 32, 2681-2693. [reprint request]

167. Wagner, A. Causal drift, robust signaling, and complex disease. PLoS ONE 10(3), e0118413. [reprint request]

166. Payne, J.L., Wagner, A. (2015) Mechanisms of mutational robustness in transcriptional regulation. Frontiers in Genetics 6, 322, doi: 10.3389/fgene.2015.00322. [reprint request]

165. Payne, J.L., Wagner, A. (2015) Function does not follow form in gene regulatory circuits. Scientific Reports 5, 13015, doi:10.1038/srep13015. [reprint request]

164. Calcott, B., Levy, A., Siegal, M.L., Soyer, O.S., Wagner, A. (2015) Engineering and biology: Counsel for a continued relationship. Biological Theory 10, 50-59. [reprint request]

163. Dall'Olio, G.M., Vahdati, A.R., Bertranpetit, J. Wagner, A. Hafid, L. (2015) VCF2Networks: applying genotype networks to single nucleotide variants data. Bioinformatics 31, 438-439. [reprint request]

162. Bilgin Sonay, T., Koletou, M., Wagner, A. (2015) A survey of tandem repeat instabilities and associated gene expression changes in 35 colorectal cancers. BMC Genomics 16 (1), 702. [reprint request]

2014

161. Payne, J.L., Wagner, A. (2014) The robustness and evolvability of transcription factor binding sites. Science 343, 875-877.[reprint request]

160. Wagner, A. (2014) A genotype network reveals homoplastic cycles of convergent evolution in influenza A (H3N2) evolution. Proceedings of the Royal Society B: Biological Sciences 281, 20132763. [reprint request]

159. Szovenyi, P., Devos, N., Weston, D.J., Yang, X., Hock, Z., Shaw, J.A., Shimizu, K.K., McDaniel, S., Wagner, A. Efficient purging of deleterious mutations in plants with
haploid selfing. Genome Biology and Evolution 6, 1238-1252. [reprint request]

158. Wagner, A., Rosen, W. (2014) Spaces of the possible: universal Darwinism and the wall between technological and biological innovation. Journal of the Royal Society Interface 11, 20131190. [reprint request]

157. Payne, J.L., Wagner, A. Latent phenotypes pervade gene regulatory circuits. BMC Systems Biology 8 (1), 64. [reprint request]

156. Dhar, R., Bergmiller, T., Wagner, A. (2014) Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Evolution 68, 1775-1791. [reprint request]

155. Hayden, E., Bratulic, S., Konig, I., Ferrada, E., Wagner, A. (2014) The effects of stabilizing and directional selection on phenotypic and genotypic variation in a population of RNA enzymes. Journal of Molecular Evolution 78, 101-108. [reprint request]

154. Barve, A., Hosseini, S.-R., Martin, O.C., Wagner, A. Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms. BMC Systems Biology 2014, 8:48. [reprint request]

153. Wagner, A. (2014) Mutational robustness accelerates the origin of novel RNA phenotypes through phenotypic plasticity. Biophysical Journal 106, 955-965. [reprint request]

152. Sunnaker, M., Zamora-Sillero, E., Garcia de Lomana, A.L., Rudroff, F., Sauer, U., Stelling, J., Wagner, A. (2014) Topological augmentation to infer hidden processes in biological systems. Bioinformatics 30, 221-227. [reprint request]

151. Dall'Olio, G.M., Bertranpetit, J. Wagner, A. Hafid, L. (2014) Human genome variation and the concept of genotype networks. PLoS ONE 9(6), e99424. doi:10.1371/journal.pone.0099424. [reprint request]

150. Wagner, A., Andriasyan, V., Barve, A. (2014) The organization of metabolic genotype space facilitates adaptive evolution in nitrogen metabolism. Journal of Molecular Biochemistry 3: 2-13. [reprint request]

149. Payne, J.L., Moore, J.H., Wagner, A. (2014) Robustness, evolvability, and the
logic of genetic regulation. Artificial Life 20, 111-126. [reprint request]

2013

148. Barve, A., Wagner, A. (2013) A latent capacity for evolutionary innovation through exaptation in metabolic systems. Nature 500, 203-206. [reprint request]

147. Sunnaker, M., Zamora-Sillero, E., Dechant, R., Ludwig, C., Busetto, A.G., Wagner, A., Stelling, J. (2013) Automatic generation of predictive dynamic models reveals nuclear phosphorylation as the key Msn2 control mechanism. Science Signaling 6, ra41. [reprint request]

146. Szovenyi, P., Ricca, M., Hock, Z., Shaw, J.A., Shimizu, K.K., Wagner, A. (2013) Selection is no more efficient in haploid than in diploid life stages of an angiosperm and a moss. Molecular Biology and Evolution 30: 1929-1939. [reprint request]

145. Payne, J.A., Wagner, A. (2013) Constraint and contingency in multifunctional gene regulatory circuits. PLoS Computational Biology 9 (6), e1003071. [reprint request]

144. Dhar, R., Saegesser, R., Weikert, C., Wagner, A. (2013) Yeast adapts to a changing stressful environment by evolving cross-protection and anticipatory gene regulation. Molecular Biology and Evolution 30, 573-588. [reprint request]

143. Sabath, N., Ferrada, E., Barve, A., Wagner, A., (2013) Growth temperature and genome size in bacteria are negatively correlated, suggesting genomic streamlining during thermal adaptation. Genome Biology and Evolution 5, 966-977. [reprint request] .

142. Bilgin, T., Kurnaz, I.A., Wagner, A. (2013) Selection shapes the robustness of ligand-binding amino acids. Journal of Molecular Evolution 76, 343-349. [reprint request] .

141. Bichsel, M., Barbour, A.D., Wagner, A. (2013) Estimating the fitness effect of insertion sequences. Journal of Mathematical Biology 66, 95-114. [reprint request]

140. Wagner, A. (2013) Genotype networks and evolutionary innovations in biological systems. In Handbook of Systems Biology. Eds: Walhout, A.J.M., Vidal, M., Dekker, J., Academic Press, London, p 251-264. [reprint request]

139. Wagner, A. (2013) Metabolic networks and their evolution. In Encyclopedia of Systems Biology; p 1256-1259; Dubitzky, W., Wolkenhauer, O., Yokota, H., Cho, K.-H. (eds) Springer, New York.

2012

138. Barve, A., Rodrigues, J.F.M., Wagner, A. (2012) Superessential reactions in metabolic networks. Proceedings of the National Academy of Sciences of the U.S.A. 109 (18), E1121-E1130. [reprint request]

137. Wagner, A. (2012) The role of robustness in phenotypic adaptation and innovation. Proceedings of the Royal Society B: Biological Sciences 279, 1249-1258.[reprint request]

136. Hayden, E.J., Wagner, A. (2012) Environmental change exposes beneficial epistatic interactions in a catalytic RNA. Proceedings of the Royal Society B: Biological Sciences 279, 3418-3425.    

135. Chen, B., Wagner, A. (2012) Hsp90 is important for fecundity, longevity, and buffering of cryptic deleterious variation in wild fly populations. BMC Evolutionary Biology 12, 25. [reprint request]

134. Wagner, A. (2012) The role of randomness in Darwinian evolution. Philosophy of Science 79, 95-119. [reprint request]

133. Sabath, N., Wagner, A., Karlin, D. (2012) Evolution of viral proteins originated de novo by overprinting. Molecular Biology and Evoluion 29, 3767-3780.

132. Guo, B., Zuo, M., Wagner, A. (2012) Pervasive indels and their evolutionary dynamics after the fish-specific genome duplication. Molecular Biology and Evolution. doi: 10.1093/molbev/mss108. [reprint request]

131. Bragg, J.G., Quigg, A., Raven, J.A., Wagner, A. (2012) Protein elemental sparing and codon usage bias are correlated among bacteria. Molecular Ecology 21, 2480–248. [reprint request]

130. Ferrada, E., Wagner, A. (2012) A comparison of genotype-phenotype maps for RNA and proteins. Biophysical Journal 102, 1916-1925. [reprint request]

129. Matias Rodrigues, J.F., Rankin, D., Rossetti, V., Wagner, A., Bagheri, H.C. (2012) Differences in cell division rates drive the evolution of terminal and differentiation in microbes. PLoS Computational Biology 8 (4), e1002468. [reprint request]

128. De la Chaux, N., Tsuchimatsu, T., Shimizu, K.K., Wagner, A. (2012) The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata. Mobile DNA 3, 2. [reprint request]

127. Bilgin, T., Wagner, A. (2012) Design constraints on a synthetic metabolism. PLoS ONE 7(6): e39903. [reprint request]

126. Wagner, A. (2012) Metabolic networks and their evolution. Evolutionary Systems Biology/Advances in Experimental Medicine and Biology 751: 29-52. [reprint request]

125. Wagner, A. (2012) High dimensional adaptive landscapes facilitate evolutionary innovation p271-282 in Svensson, E.I., Calsbeek, R. (eds) The adaptive landscape in evolutionary biology. Oxford University Press, Oxford, UK. [reprint request]

124. Wagner, A., Weikert, C. (2012) Phenotypic constraints and phenotypic hitchhiking in a promiscuous enzyme. The Open Evolution Journal 6, 14-28. [reprint request]

123. Hayden, E., Wagner, A. (2012) Directional selection causes decanalization in a catalytic RNA. PLoS ONE 7(9), e45351. [reprint request]

2011

122. Hayden, E.J., Ferrada, E., Wagner, A. (2011) Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme. Nature 474, 92-95.[reprint request]

121. Wagner, A. (2011) The molecular origins of evolutionary innovations. Trends in Genetics 27, 397-410. [reprint request]

120. Wagner, A. (2011) Genotype networks shed light on evolutionary constraints. Trends in Ecology and Evolution 26, 577-584. [reprint request]

119. Dhar, R., Sägesser, R., Weikert, C., Yuan, J., Wagner, A. (2011) Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution. Journal of Evolutionary Biology 5, 1135-1153. [reprint request]

118. Wagner, A. (2011) The low cost of recombination in creating novel phenotypes. Bioessays 33, 636-646. [reprint request]

117. Zamora-Sillero, E. Hafner, M., Ibig, A., Stelling, J., Wagner, A. (2011) Efficient characterization of high-dimensional parameter spaces for systems biology. BMC Systems Biology 5, 142. [reprint request]

116. Samal, A., Wagner, A., Martin, O.C. (2011) Environmental versatility promotes modularity in large scale metabolic networks. BMC Systems Biology 5,135.[reprint request]

115. Espinosa-Soto, C. Martin, O.C., Wagner, A. (2011) Phenotypic plasticity can facilitate adaptive evolution in gene regulatory circuits. BMC Evolutionary Biology 11:5, doi:10.1186/1471-2148-11-5. [reprint request]

114. Rodrigues, J.F.M., Wagner, A. (2011) Genotype networks, innovation, and robustness in sulfur metabolism. BMC Systems Biology 5:39. [reprint request]

113. Raman, K., Wagner, A. (2011) The evolvability of programmable hardware. Journal of the Royal Society Interface 8: 269-281. [reprint request]

112. Raman, K., Wagner, A. (2011) Evolvability and robustness in a complex signaling circuit. Molecular BioSystems 7, 1081-1092. [reprint request]

111. De la Chaux, N., Wagner, A. (2011) BEL/Pao retrotransposons in metazoan genomes. BMC Evolutionary Biology 11 :154. [reprint request]

110. Wright, J., Bellissimi, E., de Hulster, E., Wagner, A., Pronk, J.T., van Maris, A.J.A. (2011) Batch and continuous culture-based selection strategies for acetic acid tolerance in xylose-fermenting Saccharomyces cerevisiae. FEMS Yeast Research 11,299–306. [reprint request]

109. Espinosa-Soto, C., Martin, O.C., Wagner, A. (2011) Phenotypic plasticity can increase phenotypic variability after non-genetic perturbations in gene regulatory circuits. Journal of Evolutionary Biology 24, 1284-1297. [reprint request]

108. Guo, B., Wagner, A., He, S. (2011) Duplicated gene evolution following whole-genome duplication in teleost fish. pp. 27-36. In: Friedberg, F. (ed.), Gene duplication. InTech, Rijeka, Croatia. [reprint request]

2010

107. Espinosa-Soto, C., Wagner, A. (2010) Specialization can drive the evolution of modularity. PloS Computational Biology 6: e1000719. [reprint request]

106. Samal, A., Matias Rodrigues, J.F.., Jost, J., Martin, O.C., Wagner, A. (2010) Genotype networks in metabolic reaction spaces. BMC Systems Biology 4:30. [reprint request]

105. Rankin, D.J., Bichsel, M. Wagner, A. (2010) Mobile DNA can drive lineage extinction in bacterial populations. Journal of Evolutionary Biology 23, 2422-2431. [reprint request]

104. Raman, K., Wagner, A. (2010) The evolvability of programmable hardware. Journal of the Royal Society, Interface. June 9, doi: 10.1098/rsif.2010.0212. [reprint request]

103. Ferrada, E., Wagner, A. (2010) Evolutionary innovations and the organization of protein functions in genotype space. PLoS ONE 5(11): e14172. doi:10.1371/journal.pone.0014172. [reprint request]

102. Bichsel, M., Barbour, A.D., Wagner, A. (2010) The early phase of an insertion sequence infection. Theoretical Population Biology 78, 278-288. [reprint request]

101. Sulc, P., Wagner, A., Martin, O.C. (2010) Quantifying slow evolutionary dynamics in RNA fitness landscapes. Journal of Bioinformatics and Computational Biology 8, 1027-1040. [reprint request]

100. Wagner, A. (2010) On the energy and material cost of gene duplication. In: Dittmar, K., Liberles, D. Evolution after gene duplication. Wiley-Blackwell, Hoboken, NJ, p 207-214. [reprint request]

99. Bragg, JG, Wagner, A. (2010) The evolution of protein material costs. In: Evolutionary genomics and systems biology, Caetano-Anolles, G., Ed., Wiley, NY, pp. 203-211. [reprint request]

2009

98. Bragg, J.G., Wagner, A. (2009) Protein material costs: single atoms can make an evolutionary difference. Trends in Genetics 25, 5-8. [reprint request]

97. Martin, O.C.M., Wagner, A. (2009) Effects of recombination on complex regulatory circuits. Genetics 183, 673-684. [reprint request]

96. Wagner, A. (2009) Evolutionary constraints permeate large metabolic networks. BMC Evolutionary Biology  9:231 [reprint request]

95. Rodrigues, J., Wagner, A. (2009) Evolutionary plasticity and innovations in complex metabolic reaction networks. PloS Computational Biology 5(12): e1000613. [reprint request]

94. Hafner, M., Koeppl, H., Hasler, M., Wagner, A. (2009) “Glocal” robustness analysis and model discrimination for circadian oscillators. PloS Computational Biology 5(10): e1000534. [reprint request]

93. de la Chaux, N., Wagner, A. (2009) Evolutionary dynamics of the LTR retrotransposon roo inferred from twelve complete Drosophila genomes. BMC Evolutionary Biology 9:205. [reprint request]

92. Wagner, A. (2009) Transposable elements as genomic diseases. Molecular Biosystems, 5 32. [reprint request]

91. Wagner, A. (2009) Networks in molecular evolution. In: Meyers, R.A. (ed.) Encyclopedia of Complexity and System Science. Springer, Heidelberg. [reprint request]

90. Hafner, M., Koeppl, H., Wagner, A. (2009) Evolution of feedback loops in oscillatory systems.  Proceedings of the Third International Conference on Foundations of Systems Biology in Engineering (FOSBE 2009), Denver, CO, August 9-12, 2009. [reprint request]

2008

89. Wagner, A. (2008) Neutralism and selectionism: A network-based reconciliation. Nature Reviews Genetics 9, 965-974. [reprint request]

88. Wagner, A. (2008) Robustness and evolvability: A paradox resolved. Proc. Roy. Soc. London Series. B 275, 91-100. [reprint request]

87. Ferrada, E., Wagner, A. (2008) Protein robustness promotes evolutionary innovations on large evolutionary time scales Proc. Roy. Soc. London Series. B 275:1595-602.
[reprint request]

86. Wright, J., Wagner, A. (2008) The systems biology research tool: Evolvable open-source software. BMC Systems Biology 2:55. [request reprint]

85. Martin, OC, Wagner, A. (2008) Multifunctionality and robustness tradeoffs in model genetic circuits. Biophysical Journal  94, 2927-2937. [request reprint]

84. Wagner, A. (2008) Gene duplications, robustness, and evolutionary innovations. Bioessays 30, 367-373. [reprint request]

83. Felix, M-A, Wagner, A. (2008) Robustness and evolution: concepts, insights, and challenges from a developmental model system. Heredity 100, 132-140. [reprint request]

82. Jörg, T., Martin, OC, Wagner, A. (2008) Neutral network sizes of biological RNA molecules can be computed and are atypically large. BMC Bioinformatics 9:464. [reprint request]

81. Wagner, A., de la Chaux, N. (2008) Distant horizontal gene transfer is rare for mobile prokaryotic DNA. Molecular Genetics and Genomics 280, 397-408. [reprint request]

80. Wright, J., Wagner, A. (2008) Exhaustive identification of steady state cycles in large stoichiometric networks. BMC Systems Biology, 2:61. [reprint request]

79. Fuller, M., Wagner, A. , Enquist, J. (2008) Using network analysis to characterize forest structure. Natural Resources Modeling 21, 225-247. [reprint request]

2007

78. Ciliberti, S., Martin, OC, Wagner, A. (2007) Innovation and robustness in complex regulatory gene networks. Proc. Natl. Acad. Sci. U.S.A. 104, 13591-13596. [reprint request]

77. Ciliberti, S, Martin, OC, Wagner, A. (2007) Robustness can evolve gradually in complex regulatory networks with varying topology. PLoS Computational Biology 3(2): e15. [reprint request]

76. Wagner, A., Lewis, C., Bichsel, M. (2007) A survey of transposable elements using IScan. Nucleic Acids Research 35, 5284-5293. [reprint request]

75. Wagner, A. (2007) Rapid detection of positive selection in genes and genomes through variation clusters. Genetics 176: 2451–2463. [reprint request]

74. Bragg, JG, Wagner, A. (2007) Protein carbon content evolves in response to carbon availability and may influence the fate of duplicated genes. Proc. Roy. Soc. London Series. B 274, 1063-1070. [reprint request]

73. Wagner, A. (2007) From bit to it: The transformation of information into living matter by metabolic networks. BMC Systems Biology 1: 33. [reprint request]

72. Wagner, A. (2007) Energy costs constrain the evolution of gene expression. Journal of Experimental Zoology (Molecular and Developmental Evolution) 308B:322–324 [reprint request]

71. Wagner, A., Wright, J. (2007) Alternative routes and mutational robustness in complex
regulatory networks. Biosystems 88, 163-172. [reprint request]

70. Wagner, A. (2007) Gene networks and natural selection: Is there a network biology? In Pagel, M. Pomiankowski, A. (eds.) Evolutionary Genomics and Proteomics, Sinauer Associates, Sunderland, MA, USA. [Abstract]

69. Sumedha, Martin, OC, Wagner, A. (2007) New structural variation in evolutionary searches of RNA neutral networks. Biosystems 90: 475-485. [reprint request]

2006

68. Wagner, A. (2006) Cooperation is Fleeting in the World of Transposable Elements. PLoS Computational Biology 2(12): e162. [reprint request]

67. Wagner, A . (2006) Periodic extinctions of transposable elements in bacterial lineages: Evidence from intragenomic variation in multiple genomes. Molecular Biology and Evolution 23, 723-733. [reprint request]

66. Vitkup, D, Kharchenko, P., Wagner, A. (2006) Influence of metabolic network structure and function on enzyme evolution. Genome Biology 7 (5):R39. [reprint request] 

65. Gilchrist, MA, Wagner, A. (2006) A model of protein translation including codon bias, nonsense errors,and ribosome recycling. Journal of Theoretical Biology239, 417-434. [reprint request]

2005

64. Wagner, A. (2005) Circuit topology and the evolution of robustness in two-gene circadian oscillators. Proc. Natl. Acad. Sci. U.S.A. 102, 11775-11780 [reprint request]

63. Wagner, A. (2005) Robustness, Neutrality, and Evolvability. FEBS Letters 579: 1772–1778. [reprint request]

62. Wagner, A. (2005) Distributed robustness versus redundancy as causes of mutational robustness. Bioessays 27,176–188. [reprint request]

61. Wagner, A. (2005) Energy constraints on the evolution of gene expression. Molecular Biology and Evolution 22:1365–1374. [reprint request]

60. Conant, GC, Wagner, A. (2005) The rarity of gene shuffling in conserved genes. Genome Biology 6(6), R50 [reprint request]

59. Wagner, A., Wright, J (2005). Compactness and cycles in signal transduction and transcriptional regulation networks: a signature of natural selection? Advances in Complex Systems 7, 419-432. [reprint request]

58. Wagner, A. (2005) Lessons from a genetic network about the evolution of dominance. In: Veitia R. (ed.) The biology of genetic dominance. Landes Bioscience, Georgetown, TX. [Preprint request]

57. Wagner, A. (2005) The structure of large genetic networks: design, history, or (mere) chemistry? In: Koonin, EV (ed.)  Power laws, scale-free networks and genome biology. Landes Bioscience, Georgetown, TX. [Preprint request]

2004

56. Evangelisti, A, Wagner, A. (2004) Molecular evolution in the transcriptional regulation network of yeast. Journal of Experimental Zoology Part B – Molecular and Developmental Evolution 302B, 392-411. [reprint request]

55. Conant, G.C., Wagner, A. (2004) Duplicate genes and robustness to transient gene knockouts in Caenorhabditis elegans. Proc. Roy. Soc. London Series. B 271, 89-96. [reprint request]

54. Hahn, M., Conant, G.C., Wagner, A. (2004) Evolution in large genetic networks: does connectivity equal importance? Journal of Molecular Evolution 58, 203-211. [reprint request]

53. Berg, J. Lässig, M., Wagner, A., (2004) Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplication. BMC Evolutionary Biology 2004, 4:51. [reprint request]

52. Tringe, SG, Wagner, A., Ruby, S.W. (2004) Enriching for direct regulatory targets in perturbed gene expression profiles. Genome Biology 5, 109 [reprint request]

51. Wagner, A. (2004) Reconstructing pathways in large genetic networks from genetic perturbations. Journal of Computational Biology 11, 53-60. [reprint request]

50. Gilchrist, M.A., Salter, L.A., Wagner, A. Gilchrist, MA, Salter, L., Wagner, A. (2004) A statistical framework for combining and interpreting proteomic datasets. Bioinformatics 20, 689-700. [reprint request]

49. Conant, G.C., Wagner, A. (2004) A fast algorithm for determining the longest combination of local alignments to a query sequence. BMC Bioinformatics 5, 62 [reprint request]

2003

48. Conant, G.C. Wagner, A. (2003) Convergent evolution in gene circuits. Nature Genetics 34, 264-266 [reprint request]

47. Wagner, A. Does natural selection mold molecular networks? (2003) Science STKE, pe 41-43. [reprint request]

46. Wagner, A. (2003) How large protein interaction networks evolve. Proc. R. Soc. Lond. B 270, 457-466 [reprint request]

45. Conant, G.C., Wagner, A. (2003) Asymmetric sequence divergence of duplicate genes. Genome Research 13, 2052-2058 [reprint request]

44. Wagner, A. (2003) Risk management in biological evolution. Journal of Theoretical Biology 225, 45-47. [reprint request]

43. de Visser,  J.A.G.M, Hermisson, J., Wagner, G.P., Ancel, L.W.,  Bagheri, H.,  Blanchard, J.L., Chao, L., Cheverud, J.M., Elena, S.F., Fontana, W., Gibson, G., Hansen, T., Krakauer, D., Lewontin, R.C., Ofria, C., Rice, S.H., von Dassow, G., Wagner, A., and Whitlock, M.C. Evolution and detection of genetic robustness. (2003) Evolution 57, 1959-1972. [reprint request]

42. Conant, G.C., Plimpton, S.J. Old, W., Wagner, A., Fain, P.R., Pacheco, T.R. and Heffelfinger, G. (2003) Parallel Genehunter: Implementation of a Linkage Analysis Package for Distributed-Memory Architectures, Journal of Parallel and Distributed Computing 63, 674-682. [reprint request]

41. Wagner, A. (2003) Protein networks. In Complex Systems Science in Biomedicine. Deisboeck, TS, Kresh, JY, Kepler, TB (eds.) Kluwer, New York.

2002

40. Wagner, A. (2002) Asymmetric functional divergence of duplicate genes. Mol. Biol. Evol. 19, 1760-1768. [reprint request]

39. Conant, G.C., Wagner, A. (2002) GenomeHistory: a software tool and its application to fully sequenced genomes. Nucleic Acids Research  30, 1-10. [reprint request] [Supplement]

38. Wagner, A. (2002) Estimating coarse gene network structure from large-scale gene perturbation data. Genome Research 12, 309-315. [reprint request]

37. Wagner, A. (2002) Selection after gene duplication: a view from the genome. Genome Biology 3, reviews 1012.1-1012.3 [reprint request]

36. Wagner, A. (2002) The large-scale structure of metabolic networks: a glimpse at life's origin? Complexity  8, 15-19. [reprint request]

35. Wagner, A. (2002) Gene duplications and gene redundancy. In: Encyclopedia of Life Sciences. Nature Publishing Group: London, UK. (http://www.els.net/). [reprint request]

2001

34. Wagner, A., Fell, D. (2001) The small world inside large metabolic networks. Proc. Roy. Soc. London Series B, 268, 1803-1810. [reprint request]

33. Wagner, A. (2001) The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Molecular Biology and Evolution 18, 1283-1292. [reprint request]

32. Wagner, A. (2001) How to reconstruct a large genetic network from n gene perturbation in n^2 easy steps. Bioinformatics 17, 1183-1197. [reprint request]

31. Wagner, A. (2001) Birth and death of redundant duplicate genes. Trends in Genetics 17, 237-239.  [reprint request]

30. Gleiss, P.M., Stadler, P.F., Wagner, A., Fell, D.A. (2001) Relevant cycles in chemical reaction networks. Advances in Complex Systems 4, 207-226.  [reprint request]

29. Wagner, A. (2001) Neutralist view. In Encyclopedia of the Human Genome. David Cooper (ed.) Nature Publishing Group, London. In press.   [reprint request]

28. Wagner, A. (2001) Selectionist view. In Encyclopedia of the Human Genome. David Cooper (ed.) Nature Publishing Group, London. In press.   [reprint request]

2000

27. Wagner, A. (2000) Mutational robustness in genetic networks of yeast. Nature Genetics 24, 355 - 361.  [reprint request]

26. Fell, D., Wagner, A. (2000) The small world of metabolism. Nature Biotechnology 18, 1121-1122.  [reprint request]

25. Wagner, A. (2000) The role of pleiotropy, population size fluctuations, and fitness effects of mutations in the evolution of redundant gene functions. Genetics 154, 1389-1401 [reprint request]

24. Wagner, A. (2000) Decoupled evolution of coding region and expression patterns after gene duplications: implications for the neutralist-selectionist debate. Proc. Natl. Acad. Sci. U.S.A.97, 6579-6584.  [reprint request]

23. Wagner, A. (2000) Inferring life style from gene expression patterns. Molecular Biology and Evolution 17, 1985-1987  [reprint request]

22. Fell, D.A. and Wagner, A. (2000) Structural properties of metabolic networks: implications for evolution and modelling of metabolism. In: J.-H. S. Hofmeyr, J. M. Rohwer and J. L. Snoep (eds) Animating the cellular map. Stellenbosch University Press, Stellenbosch. pp. 79-85. [reprint request]

1991-1999

21. Wagner, A., Stadler, P. (1999) Viral RNA and evolved mutational robustness. Journal of Experimental Zoology 285, 119-127 [reprint request]

20. Wagner, A. (1999) Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes. Bioinformatics 15, 776-784   [reprint request]

19. Wagner, A.  (1999) Redundant gene functions and natural selection.  Journal of Evolutionary Biology 12, 1-16 [reprint request]

18. Wagner, A.  (1999) Causality in complex systems. Biology and Philosophy 14, 83-101 [reprint request]

17. Dudgeon, S., Wagner, A., Vaisnys, J.R., Buss,  L.W. (1999) Dynamics of gastrovascular circulation in the hydrozoan Podocoryne carnea: the one-polyp case. Biological Bulletin  196, 1-17   [reprint request]

16. Wagner, A. (1998) Distribution of transcription factor binding sites in the yeast genome suggests abundance of coordinately regulated genes. Genomics 50, 293-295   [reprint request]

15. Wagner, A. (1998) The fate of duplicated genes: loss or new function? BioEssays 20, 785-788   [reprint request]

14. Lavorgna, G., Boncinelli, E., Wagner, A. and T. Werner (1998) Detection of potential target genes in silico? Trends in Genetics 14, 375-376   [reprint request]

13. Wagner, A. (1998) A computational "genome walk" technique to identify regulatory interactions in gene networks. In: Altman, R.B., Dunker, K.A., Hunter, L., Klein, T.E. (eds.), Proceedings of the Pacific Symposium on Biocomputing 1998,  264-278.   [reprint request]

12. Wagner, A., Dudgeon, S., Vaisnys, R., and L.W. Buss. (1998) Non-linear oscillations in polyps of the colonial hydroid Podocoryne carnea. Naturwissenschaften 85, 117-120.   [reprint request]

11. Wagner, A. (1997) A computational genomics approach to the identification of gene networks. Nucleic Acids Research 25, 3594-3604. [reprint request]

10. Wagner, A. (1997) Models in the biological sciences. In: Dialektik 1997 (1) Falkenburg, B.; Hauser, S. (Eds.),  43-57. Felix Meiner, Hamburg. [reprint request]

9. Wagner, A. (1996) Does evolutionary plasticity evolve? Evolution 50, 1008-1023.  [reprint request]

8. Wagner, A. (1996) Can nonlinear epigenetic interactions obscure causal relations between genotype and phenotype? Nonlinearity 9, 607-629.   [reprint request]

7. Wagner, A. (1996) Genetic redundancy caused by gene duplications and its evolution in networks of transcriptional regulators. Biological Cybernetics 74, 557-567.   [reprint request]

6. Wagner, A. (1995) Reductionism in Evolutionary Biology: A Perceptional Artifact? in 1993 Lectures in Complex Systems, eds. D. Stein and L. Nadel, Santa Fe Institute Studies in the Sciences of Complexity, Lect. Vol. VI, Reading, MA:Addison-Wesley, 603-611.  [reprint request]

5. Wagner, A., Blackstone, N., Cartwright, P., Dick, M., Misof, B., Snow, P., Wagner, G.P., Bartels, J., Murtha, M. and J. Pendleton. (1994) Surveys of gene families using polymerase chain reaction: PCR selection and PCR drift. Syst. Biol. 43, 250-261. [reprint request]

4. Wagner, A. (1994) Evolution of gene networks by gene duplications: a mathematical model and its implications on genome organization. Proc. Natl. Acad. Sci. USA. 91, 4387-4391.  [reprint request]

3. Wagner, A., Wagner, G.P. and P. Similon. (1994) Epistasis can facilitate the evolution of reproductive isolation by peak shifts: a two-locus two-allele model. Genetics 138, 533-545.  [reprint request]

2. Belazzi, T., Wagner, A., Wieser, R., Schanz, M., Adam, G., Hartig, A. and H. Ruis. (1991) Negative regulation of transcription of the Saccharomyces cerevisiae catalase T (CTT1) gene by cAMP is mediated by a positive control element. EMBO J. 10, 585-592.  [reprint request]

1. Wieser, R., Adam, G., Wagner, A., Schueller, C., Marchler, G., Ruis, H., Krawiec, Z. and T. Bilinski. (1991) Heat shock factor-independent heat control of transcription of the CTT1 gene encoding the cytosolic catalase T of Saccharomyces cerevisiae. J. Biol. Chem., 19, 12406-12411.  [reprint request]