TY - JOUR AU - Notley-McRobb, L. AU - Ferenci, T. PY - 1999 DA - 1999// TI - The generation of multiple co-existing mal-regulatory mutations through polygenic evolution in glucose-limited populations of Escherichia coli JO - Environ Microbiol VL - 1 UR - https://doi.org/10.1046/j.1462-2920.1999.00003.x DO - 10.1046/j.1462-2920.1999.00003.x ID - Notley-McRobb1999 ER - TY - JOUR AU - Dunham, M. J. AU - Badrane, H. AU - Ferea, T. AU - Adams, J. AU - Brown, P. O. AU - Rosenzweig, F. PY - 2002 DA - 2002// TI - Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae JO - Proc Natl Acad Sci U S A VL - 99 UR - https://doi.org/10.1073/pnas.242624799 DO - 10.1073/pnas.242624799 ID - Dunham2002 ER - TY - JOUR AU - Araya, C. L. AU - Payen, C. AU - Dunham, M. J. AU - Fields, S. PY - 2010 DA - 2010// TI - Whole-genome sequencing of a laboratory-evolved yeast strain JO - BMC Genomics VL - 11 UR - https://doi.org/10.1186/1471-2164-11-88 DO - 10.1186/1471-2164-11-88 ID - Araya2010 ER - TY - JOUR AU - Yona, A. H. AU - Manor, Y. S. AU - Herbst, R. H. AU - Romano, G. H. AU - Mitchell, A. AU - Kupiec, M. PY - 2012 DA - 2012// TI - Chromosomal duplication is a transient evolutionary solution to stress JO - Proc Natl Acad Sci U S A VL - 109 UR - https://doi.org/10.1073/pnas.1211150109 DO - 10.1073/pnas.1211150109 ID - Yona2012 ER - TY - JOUR AU - Chang, S. -. L. AU - Lai, H. -. Y. AU - Tung, S. -. Y. AU - Leu, J. -. Y. PY - 2013 DA - 2013// TI - Dynamic large-scale chromosomal rearrangements fuel rapid adaptation in yeast populations JO - PLoS Genet VL - 9 UR - https://doi.org/10.1371/journal.pgen.1003232 DO - 10.1371/journal.pgen.1003232 ID - Chang2013 ER - TY - STD TI - Sandberg TE, Salazar MJ, Weng LL, Palsson BO, Feist AM. The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology. Metab Eng. 2019. https://doi.org/10.1016/j.ymben.2019.08.004. ID - ref6 ER - TY - STD TI - Van den Bergh B, Swings T, Fauvart M, Michiels J. Experimental design, population dynamics, and diversity in microbial experimental evolution. Microbiol Mol Biol Rev. 2018;82(3). https://doi.org/10.1128/MMBR.00008-18. ID - ref7 ER - TY - JOUR AU - LaCroix, R. A. AU - Sandberg, T. E. AU - O’Brien, E. J. AU - Utrilla, J. AU - Ebrahim, A. AU - Guzman, G. I. PY - 2015 DA - 2015// TI - Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium JO - Appl Environ Microbiol VL - 81 UR - https://doi.org/10.1128/AEM.02246-14 DO - 10.1128/AEM.02246-14 ID - LaCroix2015 ER - TY - JOUR AU - Barrick, J. E. AU - Lenski, R. E. PY - 2009 DA - 2009// TI - Genome-wide mutational diversity in an evolving population of Escherichia coli JO - Cold Spring Harb Symp Quant Biol VL - 74 UR - https://doi.org/10.1101/sqb.2009.74.018 DO - 10.1101/sqb.2009.74.018 ID - Barrick2009 ER - TY - JOUR AU - Gresham, D. AU - Dunham, M. J. PY - 2014 DA - 2014// TI - The enduring utility of continuous culturing in experimental evolution JO - Genomics VL - 104 UR - https://doi.org/10.1016/j.ygeno.2014.09.015 DO - 10.1016/j.ygeno.2014.09.015 ID - Gresham2014 ER - TY - JOUR AU - Tenaillon, O. AU - Rodríguez-Verdugo, A. AU - Gaut, R. L. AU - McDonald, P. AU - Bennett, A. F. AU - Long, A. D. PY - 2012 DA - 2012// TI - The molecular diversity of adaptive convergence JO - Science. VL - 335 UR - https://doi.org/10.1126/science.1212986 DO - 10.1126/science.1212986 ID - Tenaillon2012 ER - TY - JOUR AU - Huang, D. W. AU - Sherman, B. T. AU - Lempicki, R. A. PY - 2009 DA - 2009// TI - Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn923 DO - 10.1093/nar/gkn923 ID - Huang2009 ER - TY - JOUR AU - Gama-Castro, S. AU - Salgado, H. AU - Santos-Zavaleta, A. AU - Ledezma-Tejeida, D. AU - Muñiz-Rascado, L. AU - García-Sotelo, J. S. PY - 2016 DA - 2016// TI - RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1156 DO - 10.1093/nar/gkv1156 ID - Gama-Castro2016 ER - TY - JOUR AU - Wattam, A. R. AU - Davis, J. J. AU - Assaf, R. AU - Boisvert, S. AU - Brettin, T. AU - Bun, C. PY - 2017 DA - 2017// TI - Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkw1017 DO - 10.1093/nar/gkw1017 ID - Wattam2017 ER - TY - JOUR AU - Tatusov, R. L. AU - Galperin, M. Y. AU - Natale, D. A. AU - Koonin, E. V. PY - 2000 DA - 2000// TI - The COG database: a tool for genome-scale analysis of protein functions and evolution JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.33 DO - 10.1093/nar/28.1.33 ID - Tatusov2000 ER - TY - STD TI - Phaneuf PV, Gosting D, Palsson BO, Feist AM. ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation. Nucleic Acids Res. 2018. https://doi.org/10.1093/nar/gky983. ID - ref16 ER - TY - JOUR AU - Santos-Zavaleta, A. AU - Salgado, H. AU - Gama-Castro, S. AU - Sánchez-Pérez, M. AU - Gómez-Romero, L. AU - Ledezma-Tejeida, D. PY - 2019 DA - 2019// TI - RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12 JO - Nucleic Acids Res VL - 47 UR - https://doi.org/10.1093/nar/gky1077 DO - 10.1093/nar/gky1077 ID - Santos-Zavaleta2019 ER - TY - JOUR AU - Lee, H. AU - Popodi, E. AU - Tang, H. AU - Foster, P. L. PY - 2012 DA - 2012// TI - Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing JO - Proc Natl Acad Sci U S A VL - 109 UR - https://doi.org/10.1073/pnas.1210309109 DO - 10.1073/pnas.1210309109 ID - Lee2012 ER - TY - JOUR AU - Miller, M. L. AU - Reznik, E. AU - Gauthier, N. P. AU - Aksoy, B. A. AU - Korkut, A. AU - Gao, J. PY - 2015 DA - 2015// TI - Pan-cancer analysis of mutation hotspots in protein domains JO - Cell Syst VL - 1 UR - https://doi.org/10.1016/j.cels.2015.08.014 DO - 10.1016/j.cels.2015.08.014 ID - Miller2015 ER - TY - JOUR AU - Tenaillon, O. AU - Barrick, J. E. AU - Ribeck, N. AU - Deatherage, D. E. AU - Blanchard, J. L. AU - Dasgupta, A. PY - 2016 DA - 2016// TI - Tempo and mode of genome evolution in a 50,000-generation experiment JO - Nature. VL - 536 UR - https://doi.org/10.1038/nature18959 DO - 10.1038/nature18959 ID - Tenaillon2016 ER - TY - JOUR AU - Charusanti, P. AU - Conrad, T. M. AU - Knight, E. M. AU - Venkataraman, K. AU - Fong, N. L. AU - Xie, B. PY - 2010 DA - 2010// TI - Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene JO - PLoS Genet VL - 6 UR - https://doi.org/10.1371/journal.pgen.1001186 DO - 10.1371/journal.pgen.1001186 ID - Charusanti2010 ER - TY - JOUR AU - Long, C. P. AU - Gonzalez, J. E. AU - Feist, A. M. AU - Palsson, B. O. AU - Antoniewicz, M. R. PY - 2018 DA - 2018// TI - Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli JO - Proc Natl Acad Sci U S A VL - 115 UR - https://doi.org/10.1073/pnas.1716056115 DO - 10.1073/pnas.1716056115 ID - Long2018 ER - TY - STD TI - LaCroix RA, Palsson BO, Feist AM. A model for designing adaptive laboratory evolution experiments. Appl Environ Microbiol. 2017; 83(8). https://doi.org/10.1128/AEM.03115-16. ID - ref23 ER - TY - JOUR AU - Mundhada, H. AU - Seoane, J. M. AU - Schneider, K. AU - Koza, A. AU - Christensen, H. B. AU - Klein, T. PY - 2017 DA - 2017// TI - Increased production of L-serine in Escherichia coli through adaptive laboratory evolution JO - Metab Eng VL - 39 UR - https://doi.org/10.1016/j.ymben.2016.11.008 DO - 10.1016/j.ymben.2016.11.008 ID - Mundhada2017 ER - TY - JOUR AU - Conrad, T. M. AU - Joyce, A. R. AU - Applebee, M. K. AU - Barrett, C. L. AU - Xie, B. AU - Gao, Y. PY - 2009 DA - 2009// TI - Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-10-r118 DO - 10.1186/gb-2009-10-10-r118 ID - Conrad2009 ER - TY - JOUR AU - McCloskey, D. AU - Xu, S. AU - Sandberg, T. E. AU - Brunk, E. AU - Hefner, Y. AU - Szubin, R. PY - 2018 DA - 2018// TI - Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase system JO - Metab Eng VL - 48 UR - https://doi.org/10.1016/j.ymben.2018.06.005 DO - 10.1016/j.ymben.2018.06.005 ID - McCloskey2018 ER - TY - BOOK AU - Phaneuf, P. PY - 2019 DA - 2019// TI - SBRG/bop27refseq: Zenodo DOI release (Version v1.4.1) [Internet] UR - https://doi.org/10.5281/zenodo.3590393 DO - 10.5281/zenodo.3590393 ID - Phaneuf2019 ER - TY - JOUR AU - Herring, C. D. AU - Raghunathan, A. AU - Honisch, C. AU - Patel, T. AU - Applebee, M. K. AU - Joyce, A. R. PY - 2006 DA - 2006// TI - Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale JO - Nat Genet VL - 38 UR - https://doi.org/10.1038/ng1906 DO - 10.1038/ng1906 ID - Herring2006 ER - TY - JOUR AU - Deutscher, J. PY - 2008 DA - 2008// TI - The mechanisms of carbon catabolite repression in bacteria JO - Curr Opin Microbiol VL - 11 UR - https://doi.org/10.1016/j.mib.2008.02.007 DO - 10.1016/j.mib.2008.02.007 ID - Deutscher2008 ER - TY - JOUR AU - Görke, B. AU - Stülke, J. PY - 2008 DA - 2008// TI - Carbon catabolite repression in bacteria: many ways to make the most out of nutrients JO - Nat Rev Microbiol VL - 6 UR - https://doi.org/10.1038/nrmicro1932 DO - 10.1038/nrmicro1932 ID - Görke2008 ER - TY - JOUR AU - Larson, T. J. AU - Cantwell, J. S. AU - Loo-Bhattacharya, A. T. PY - 1992 DA - 1992// TI - Interaction at a distance between multiple operators controls the adjacent, divergently transcribed glpTQ-glpACB operons of Escherichia coli K-12 JO - J Biol Chem VL - 267 ID - Larson1992 ER - TY - JOUR AU - Freddolino, P. L. AU - Amini, S. AU - Tavazoie, S. PY - 2012 DA - 2012// TI - Newly identified genetic variations in common Escherichia coli MG1655 stock cultures JO - J Bacteriol VL - 194 UR - https://doi.org/10.1128/JB.06087-11 DO - 10.1128/JB.06087-11 ID - Freddolino2012 ER - TY - JOUR AU - Zwaig, N. AU - Lin, E. C. PY - 1966 DA - 1966// TI - Feedback inhibition of glycerol kinase, a catabolic enzyme in Escherichia coli JO - Science. VL - 153 UR - https://doi.org/10.1126/science.153.3737.755 DO - 10.1126/science.153.3737.755 ID - Zwaig1966 ER - TY - JOUR AU - Novotny, M. J. AU - Frederickson, W. L. AU - Waygood, E. B. AU - Saier, M. H. PY - 1985 DA - 1985// TI - Allosteric regulation of glycerol kinase by enzyme IIIglc of the phosphotransferase system in Escherichia coli and Salmonella typhimurium JO - J Bacteriol VL - 162 UR - https://doi.org/10.1128/JB.162.2.810-816.1985 DO - 10.1128/JB.162.2.810-816.1985 ID - Novotny1985 ER - TY - JOUR AU - Applebee, M. K. AU - Joyce, A. R. AU - Conrad, T. M. AU - Pettigrew, D. W. AU - Palsson, B. Ø. PY - 2011 DA - 2011// TI - Functional and metabolic effects of adaptive glycerol kinase (GLPK) mutants in Escherichia coli JO - J Biol Chem VL - 286 UR - https://doi.org/10.1074/jbc.M110.195305 DO - 10.1074/jbc.M110.195305 ID - Applebee2011 ER - TY - JOUR AU - Saier, M. H. AU - Kukita, C. AU - Zhang, Z. PY - 2017 DA - 2017// TI - Transposon-mediated directed mutation in bacteria and eukaryotes JO - Front Biosci VL - 22 UR - https://doi.org/10.2741/4553 DO - 10.2741/4553 ID - Saier2017 ER - TY - JOUR AU - Roy, A. AU - Danchin, A. AU - Joseph, E. AU - Ullmann, A. PY - 1983 DA - 1983// TI - Two functional domains in adenylate cyclase of Escherichia coli JO - J Mol Biol VL - 165 UR - https://doi.org/10.1016/S0022-2836(83)80251-4 DO - 10.1016/S0022-2836(83)80251-4 ID - Roy1983 ER - TY - JOUR AU - Eppler, T. AU - Postma, P. AU - Schütz, A. AU - Völker, U. AU - Boos, W. PY - 2002 DA - 2002// TI - Glycerol-3-phosphate-induced catabolite repression in Escherichia coli JO - J Bacteriol VL - 184 UR - https://doi.org/10.1128/JB.184.11.3044-3052.2002 DO - 10.1128/JB.184.11.3044-3052.2002 ID - Eppler2002 ER - TY - JOUR AU - Stauffer, L. T. AU - Stauffer, G. V. PY - 2005 DA - 2005// TI - GcvA interacts with both the alpha and sigma subunits of RNA polymerase to activate the Escherichia coli gcvB gene and the gcvTHP operon JO - FEMS Microbiol Lett VL - 242 UR - https://doi.org/10.1016/j.femsle.2004.11.027 DO - 10.1016/j.femsle.2004.11.027 ID - Stauffer2005 ER - TY - JOUR AU - Ghrist, A. C. AU - Heil, G. AU - Stauffer, G. V. PY - 2001 DA - 2001// TI - GcvR interacts with GcvA to inhibit activation of the Escherichia coli glycine cleavage operon JO - Microbiology. VL - 147 UR - https://doi.org/10.1099/00221287-147-8-2215 DO - 10.1099/00221287-147-8-2215 ID - Ghrist2001 ER - TY - JOUR AU - Heil, G. AU - Stauffer, L. T. AU - Stauffer, G. V. PY - 2002 DA - 2002// TI - Glycine binds the transcriptional accessory protein GcvR to disrupt a GcvA/GcvR interaction and allow GcvA-mediated activation of the Escherichia coli gcvTHP operon JO - Microbiology. VL - 148 UR - https://doi.org/10.1099/00221287-148-7-2203 DO - 10.1099/00221287-148-7-2203 ID - Heil2002 ER - TY - JOUR AU - Pulvermacher, S. C. AU - Stauffer, L. T. AU - Stauffer, G. V. PY - 2009 DA - 2009// TI - Role of the sRNA GcvB in regulation of cycA in Escherichia coli JO - Microbiology. VL - 155 UR - https://doi.org/10.1099/mic.0.023598-0 DO - 10.1099/mic.0.023598-0 ID - Pulvermacher2009 ER - TY - JOUR AU - Ghrist, A. C. AU - Stauffer, G. V. PY - 1995 DA - 1995// TI - The Escherichia coli glycine transport system and its role in the regulation of the glycine cleavage enzyme system JO - Microbiology. VL - 141 UR - https://doi.org/10.1099/00221287-141-1-133 DO - 10.1099/00221287-141-1-133 ID - Ghrist1995 ER - TY - JOUR AU - Berman, H. M. AU - Westbrook, J. AU - Feng, Z. AU - Gilliland, G. AU - Bhat, T. N. AU - Weissig, H. PY - 2000 DA - 2000// TI - The Protein Data Bank JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.235 DO - 10.1093/nar/28.1.235 ID - Berman2000 ER - TY - JOUR PY - 2017 DA - 2017// TI - UniProt: the universal protein knowledgebase JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkw1099 DO - 10.1093/nar/gkw1099 ID - ref45 ER - TY - JOUR AU - Keseler, I. M. AU - Mackie, A. AU - Santos-Zavaleta, A. AU - Billington, R. AU - Bonavides-Martínez, C. AU - Caspi, R. PY - 2017 DA - 2017// TI - The EcoCyc database: reflecting new knowledge about Escherichia coli K-12 JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkw1003 DO - 10.1093/nar/gkw1003 ID - Keseler2017 ER - TY - JOUR AU - Ashburner, M. AU - Ball, C. A. AU - Blake, J. A. AU - Botstein, D. AU - Butler, H. AU - Cherry, J. M. PY - 2000 DA - 2000// TI - Gene ontology: tool for the unification of biology. The Gene Ontology Consortium JO - Nat Genet VL - 25 UR - https://doi.org/10.1038/75556 DO - 10.1038/75556 ID - Ashburner2000 ER - TY - JOUR PY - 2019 DA - 2019// TI - The gene ontology resource: 20 years and still GOing strong JO - Nucleic Acids Res VL - 47 UR - https://doi.org/10.1093/nar/gky1055 DO - 10.1093/nar/gky1055 ID - ref48 ER - TY - JOUR AU - Sandberg, T. E. AU - Pedersen, M. AU - LaCroix, R. A. AU - Ebrahim, A. AU - Bonde, M. AU - Herrgard, M. J. PY - 2014 DA - 2014// TI - Evolution of Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations JO - Mol Biol Evol VL - 31 UR - https://doi.org/10.1093/molbev/msu209 DO - 10.1093/molbev/msu209 ID - Sandberg2014 ER - TY - STD TI - Sandberg TE, Long CP, Gonzalez JE, Feist AM. Evolution of E. coli on [U-13C] glucose reveals a negligible isotopic influence on metabolism and physiology. PLoS One. 2016. https://doi.org/10.1371/journal.pone.0151130. ID - ref50 ER - TY - STD TI - Sandberg TE, Lloyd CJ, Palsson BO, Feist AM. Laboratory evolution to alternating substrate environments yields distinct phenotypic and genetic adaptive strategies. Appl Environ Microbiol. 2017;83(13). https://doi.org/10.1128/AEM.00410-17. ID - ref51 ER - TY - STD TI - McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, et al. Multiple optimal phenotypes overcome redox and glycolytic intermediate metabolite imbalances in Escherichia coli pgi knockout evolutions. Appl Environ Microbiol. 2018;84(19). https://doi.org/10.1128/AEM.00823-18. ID - ref52 ER - TY - JOUR AU - McCloskey, D. AU - Xu, S. AU - Sandberg, T. E. AU - Brunk, E. AU - Hefner, Y. AU - Szubin, R. PY - 2018 DA - 2018// TI - Growth adaptation of gnd and sdhCB Escherichia coli deletion strains diverges from a similar initial perturbation of the Transcriptome JO - Front Microbiol VL - 9 UR - https://doi.org/10.3389/fmicb.2018.01793 DO - 10.3389/fmicb.2018.01793 ID - McCloskey2018 ER - TY - JOUR AU - McCloskey, D. AU - Xu, S. AU - Sandberg, T. E. AU - Brunk, E. AU - Hefner, Y. AU - Szubin, R. PY - 2018 DA - 2018// TI - Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes JO - Metab Eng VL - 48 UR - https://doi.org/10.1016/j.ymben.2018.05.012 DO - 10.1016/j.ymben.2018.05.012 ID - McCloskey2018 ER - TY - STD TI - Anand A, Chen K, Catoiu E, Sastry AV, Olson CA, Sandberg TE, et al. OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states. Mol Biol Evol. 2019. https://doi.org/10.1093/molbev/msz251. ID - ref55 ER - TY - STD TI - Lennen RM, Jensen K, Mohammed ET, Malla S, Börner RA, Chekina K, et al. Adaptive laboratory evolution reveals general and specific chemical tolerance mechanisms and enhances biochemical production [Internet]. bioRxiv. 2019:634105. https://doi.org/10.1101/634105v1. ID - ref56 ER - TY - JOUR AU - Guzmán, G. I. AU - Sandberg, T. E. AU - LaCroix, R. A. AU - Nyerges, Á. AU - Papp, H. AU - Raad, M. PY - 2019 DA - 2019// TI - Enzyme promiscuity shapes adaptation to novel growth substrates JO - Mol Syst Biol VL - 15 UR - https://doi.org/10.15252/msb.20188462 DO - 10.15252/msb.20188462 ID - Guzmán2019 ER - TY - JOUR AU - Hunter, J. D. PY - 2007 DA - 2007// TI - Matplotlib: a 2D graphics environment JO - Comput Sci Eng VL - 9 UR - https://doi.org/10.1109/MCSE.2007.55 DO - 10.1109/MCSE.2007.55 ID - Hunter2007 ER - TY - STD TI - Waskom M, Botvinnik O, O’Kane D, Hobson P, Ostblom J, Lukauskas S, et al. mwaskom/seaborn: v0.9.0 (July 2018) [Internet]. 2018. Available from: https://zenodo.org/record/1313201. UR - https://zenodo.org/record/1313201 ID - ref59 ER - TY - JOUR AU - Lupton, R. C. AU - Allwood, J. M. PY - 2017 DA - 2017// TI - Hybrid Sankey diagrams: visual analysis of multidimensional data for understanding resource use JO - Resour Conserv Recycl VL - 124 UR - https://doi.org/10.1016/j.resconrec.2017.05.002 DO - 10.1016/j.resconrec.2017.05.002 ID - Lupton2017 ER - TY - BOOK AU - Schroeder, M. P. AU - Lopez-Bigas, N. PY - 2015 DA - 2015// TI - muts-needle-plot: mutations needle plot v0.8.0 [Internet] ID - Schroeder2015 ER - TY - JOUR AU - Deatherage, D. E. AU - Barrick, J. E. PY - 2014 DA - 2014// TI - Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq JO - Methods Mol Biol VL - 1151 UR - https://doi.org/10.1007/978-1-4939-0554-6_12 DO - 10.1007/978-1-4939-0554-6_12 ID - Deatherage2014 ER - TY - BOOK AU - Phaneuf, P. PY - 2018 DA - 2018// TI - SBRG/bop27refseq: Zenodo DOI release [Internet] ID - Phaneuf2018 ER - TY - JOUR AU - Chen, S. AU - Huang, T. AU - Zhou, Y. AU - Han, Y. AU - Xu, M. AU - Gu, J. PY - 2017 DA - 2017// TI - AfterQC: automatic filtering, trimming, error removing and quality control for fastq data JO - BMC Bioinformatics VL - 18 UR - https://doi.org/10.1186/s12859-017-1469-3 DO - 10.1186/s12859-017-1469-3 ID - Chen2017 ER - TY - JOUR AU - Wagih, O. AU - Galardini, M. AU - Busby, B. P. AU - Memon, D. AU - Typas, A. AU - Beltrao, P. PY - 2018 DA - 2018// TI - A resource of variant effect predictions of single nucleotide variants in model organisms JO - Mol Syst Biol VL - 14 UR - https://doi.org/10.15252/msb.20188430 DO - 10.15252/msb.20188430 ID - Wagih2018 ER - TY - BOOK AU - Phaneuf, P. PY - 2020 DA - 2020// TI - ALE variant analysis scripts and data v0.1.0 [Internet] UR - https://doi.org/10.5281/zenodo.3766454 DO - 10.5281/zenodo.3766454 ID - Phaneuf2020 ER -