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PUBLICATIONS FROM OUR GROUP

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    2024

  1. Diagnosis and mitigation of the systemic impact of genome reduction in Escherichia coli DGF-298. Antoine Champie, Jean-Christophe Lachance, Anand Sastry, Dominick Matteau, Colton J Lloyd, Frédéric Grenier, Cameron R Lamoureux, Simon Jeanneau, Adam M Feist, Pierre-Étienne Jacques, Bernhard O Palsson, Sébastien Rodrigue. mBio. 2024
  2. Genetic heterogeneity of engineered Escherichia coli Nissle 1917 strains during scale-up simulation. Lara P Munkler, Elsayed T Mohamed, Ruben Vazquez-Uribe, Victoria Visby Nissen, Peter Rugbjerg, Andreas Worberg, John M Woodley, Adam M Feist, Morten O A Sommer. Metabolic engineering. 2024
  3. Evolution and engineering of pathways for aromatic O-demethylation in Pseudomonas putida KT2440. Alissa C Bleem, Eugene Kuatsjah, Josefin Johnsen, Elsayed T Mohamed, William G Alexander, Zoe A Kellermyer, Austin L Carroll, Riccardo Rossi, Ian B Schlander, George L Peabody V, Adam M Guss, Adam M Feist, Gregg T Beckham. Metabolic engineering. 2024
  4. Biocomposite thermoplastic polyurethanes containing evolved bacterial spores as living fillers to facilitate polymer disintegration. Han Sol Kim, Myung Hyun Noh, Evan M White, Michael V Kandefer, Austin F Wright, Debika Datta, Hyun Gyu Lim, Ethan Smiggs, Jason J Locklin, Md Arifur Rahman, Adam M Feist, Jonathan K Pokorski. Nature communications. 2024
  5. Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment. Donghui Choe, Connor A Olson, Richard Szubin, Hannah Yang, Jaemin Sung, Adam M Feist, Bernhard O Palsson. Nature communications. 2024

    6. 2023

  6. TCA cycle tailoring facilitates optimal growth of proton-pumping NADH dehydrogenase-dependent Escherichia coli. Nikita Goel, Stuti Srivastav, Arjun Patel, Akshay Shirsath, Tushar Ranjan Panda, Malay Patra, Adam M Feist, Amitesh Anand. Microbiology spectrum. 2023
  7. Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance. Kevin Rychel, Justin Tan, Arjun Patel, Cameron Lamoureux, Ying Hefner, Richard Szubin, Josefin Johnsen, Elsayed Tharwat Tolba Mohamed, Patrick V Phaneuf, Amitesh Anand, Connor A Olson, Joon Ho Park, Anand V Sastry, Laurence Yang, Adam M Feist, Bernhard O Palsson. Cell reports. 2023
  8. Adaptive evolution of a minimal organism with a synthetic genome. Troy E Sandberg, Kim S Wise, Christopher Dalldorf, Richard Szubin, Adam M Feist, John I Glass, Bernhard O Palsson. iScience. 2023
  9. Have you tried turning it off and on again? Oscillating selection to enhance fitness-landscape traversal in adaptive laboratory evolution experiments. Alexander C Carpenter, Adam M Feist, Fergus S M Harrison, Ian T Paulsen, Thomas C Williams. Metabolic engineering communications. 2023
  10. Adaptive laboratory evolution of Bacillus subtilis to overcome toxicity of lignocellulosic hydrolysate derived from Distiller's dried grains with solubles (DDGS). Jasper L S P Driessen, Josefin Johnsen, Ivan Pogrebnyakov, Elsayed T T Mohamed, Solange I Mussatto, Adam M Feist, Sheila I Jensen, Alex T Nielsen. Metabolic engineering communications. 2023
  11. Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals. Rebecca M Lennen, Hyun Gyu Lim, Kristian Jensen, Elsayed T Mohammed, Patrick V Phaneuf, Myung Hyun Noh, Sailesh Malla, Rosa A Börner, Ksenia Chekina, Emre Özdemir, Ida Bonde, Anna Koza, Jérôme Maury, Lasse E Pedersen, Lars Y Schöning, Nikolaus Sonnenschein, Bernhard O Palsson, Alex T Nielsen, Morten O A Sommer, Markus J Herrgård, Adam M Feist. Metabolic engineering. 2023
  12. Revealing oxidative pentose metabolism in new Pseudomonas putida isolates. Mee-Rye Park, Rahul Gauttam, Bonnie Fong, Yan Chen, Hyun Gyu Lim, Adam M Feist, Aindrila Mukhopadhyay, Christopher J Petzold, Blake A Simmons, Steven W Singer. Environmental microbiology. 2023

    13. 2022

  13. Understanding Functional Redundancy and Promiscuity of Multidrug Transporters in E. coli under Lipophilic Cation Stress. Mohammad S Radi, Lachlan J Munro, Jesus E Salcedo-Sora, Se Hyeuk Kim, Adam M Feist, Douglas B Kell. Membranes. 2022
  14. Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes. Erol S Kavvas, Christopher P Long, Anand Sastry, Saugat Poudel, Maciek R Antoniewicz, Yang Ding, Elsayed T Mohamed, Richard Szubin, Jonathan M Monk, Adam M Feist, Bernhard O Palsson. mSystems. 2022
  15. Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity. Amitesh Anand, Arjun Patel, Ke Chen, Connor A Olson, Patrick V Phaneuf, Cameron Lamoureux, Ying Hefner, Richard Szubin, Adam M Feist, Bernhard O Palsson. Nature communications. 2022
  16. Membrane transporter identification and modulation via adaptive laboratory evolution. Mohammad S Radi, Jesus E SalcedoSora, Se Hyeuk Kim, Suresh Sudarsan, Anand V Sastry, Douglas B Kell, Markus J Herrgård, Adam M Feist. Metabolic engineering. 2022
  17. Engineering Pseudomonas putida for improved utilization of syringyl aromatics. Joshua Mueller, Howard Willett, Adam M Feist, Wei Niu. Biotechnology and bioengineering. 2022
  18. Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network. Hyun Gyu Lim, Kevin Rychel, Anand V Sastry, Gayle J Bentley, Joshua Mueller, Heidi S Schindel, Peter E Larsen, Philip D Laible, Adam M Guss, Wei Niu, Christopher W Johnson, Gregg T Beckham, Adam M Feist, Bernhard O Palsson. Metabolic engineering. 2022
  19. Selection for Cell Yield Does Not Reduce Overflow Metabolism in Escherichia coli. Iraes Rabbers, Willi Gottstein, Adam M Feist, Bas Teusink, Frank J Bruggeman, Herwig Bachmann. Molecular biology and evolution. 2022

    20. 2021

  20. Escherichia coli Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data. Patrick V Phaneuf, Daniel C Zielinski, James T Yurkovich, Josefin Johnsen, Richard Szubin, Lei Yang, Se Hyeuk Kim, Sebastian Schulz, Muyao Wu, Christopher Dalldorf, Emre Ozdemir, Rebecca M Lennen, Bernhard O Palsson, Adam M Feist. ACS synthetic biology. 2021
  21. Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility. Anand V Sastry, Nicholas Dillon, Amitesh Anand, Saugat Poudel, Ying Hefner, Sibei Xu, Richard Szubin, Adam M Feist, Victor Nizet, Bernhard Palsson. mSphere. 2021
  22. Genome-scale metabolic modeling reveals key features of a minimal gene set. Jean-Christophe Lachance, Dominick Matteau, Joëlle Brodeur, Colton J Lloyd, Nathan Mih, Zachary A King, Thomas F Knight, Adam M Feist, Jonathan M Monk, Bernhard O Palsson, Pierre-Étienne Jacques, Sébastien Rodrigue. Molecular systems biology. 2021
  23. Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus. Henrique Machado, Yara Seif, George Sakoulas, Connor A Olson, Ying Hefner, Amitesh Anand, Ying Z Jones, Richard Szubin, Bernhard O Palsson, Victor Nizet, Adam M Feist. Communications biology. 2021
  24. Compensatory evolution of Pseudomonas aeruginosa's slow growth phenotype suggests mechanisms of adaptation in cystic fibrosis. Ruggero La Rosa, Elio Rossi, Adam M Feist, Helle Krogh Johansen, Søren Molin. Nature communications. 2021
  25. Adaptive laboratory evolution of Rhodosporidium toruloides to inhibitors derived from lignocellulosic biomass and genetic variations behind evolution. Zhijia Liu, Mohammad Radi, Elsayed T T Mohamed, Adam M Feist, Giuliano Dragone, Solange I Mussatto. Bioresource technology. 2021
  26. Restoration of fitness lost due to dysregulation of the pyruvate dehydrogenase complex is triggered by ribosomal binding site modifications. Amitesh Anand, Connor A Olson, Anand V Sastry, Arjun Patel, Richard Szubin, Laurence Yang, Adam M Feist, Bernhard O Palsson. Cell reports. 2021
  27. Identifying the effect of vancomycin on health care-associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media. Akanksha Rajput, Saugat Poudel, Hannah Tsunemoto, Michael Meehan, Richard Szubin, Connor A Olson, Yara Seif, Anne Lamsa, Nicholas Dillon, Alison Vrbanac, Joseph Sugie, Samira Dahesh, Jonathan M Monk, Pieter C Dorrestein, Rob Knight, Joe Pogliano, Victor Nizet, Adam M Feist, Bernhard O Palsson. GigaScience. 2021

    28. 2020

  28. Elucidating aromatic acid tolerance at low pH in Saccharomyces cerevisiae using adaptive laboratory evolution. Rui Pereira, Elsayed T Mohamed, Mohammad S Radi, Markus J Herrgård, Adam M Feist, Jens Nielsen, Yun Chen. Proceedings of the National Academy of Sciences of the United States of America. 2020
  29. Adaptive laboratory evolution of Pseudomonas putida KT2440 improves p-coumaric and ferulic acid catabolism and tolerance. Elsayed T Mohamed, Allison Z Werner, Davinia Salvachúa, Christine A Singer, Kiki Szostkiewicz, Manuel Rafael Jiménez-Díaz, Thomas Eng, Mohammad S Radi, Blake A Simmons, Aindrila Mukhopadhyay, Markus J Herrgård, Steven W Singer, Gregg T Beckham, Adam M Feist. Metabolic engineering communications. 2020
  30. Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers. David Heckmann, Anaamika Campeau, Colton J Lloyd, Patrick V Phaneuf, Ying Hefner, Marvic Carrillo-Terrazas, Adam M Feist, David J Gonzalez, Bernhard O Palsson. Proceedings of the National Academy of Sciences of the United States of America. 2020
  31. Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity. Patrick V Phaneuf, James T Yurkovich, David Heckmann, Muyao Wu, Troy E Sandberg, Zachary A King, Justin Tan, Bernhard O Palsson, Adam M Feist. BMC genomics. 2020
  32. Genetic Determinants Enabling Medium-Dependent Adaptation to Nafcillin in Methicillin-Resistant Staphylococcus aureus. Michael J Salazar, Henrique Machado, Nicholas A Dillon, Hannah Tsunemoto, Richard Szubin, Samira Dahesh, Joseph Pogliano, George Sakoulas, Bernhard O Palsson, Victor Nizet, Adam M Feist. mSystems. 2020
  33. Directed Metabolic Pathway Evolution Enables Functional Pterin-Dependent Aromatic-Amino-Acid Hydroxylation in Escherichia coli. Hao Luo, Lei Yang, Se Hyeuk Kim, Tune Wulff, Adam M Feist, Markus Herrgard, Bernhard Ø Palsson. ACS synthetic biology. 2020
  34. MEMOTE for standardized genome-scale metabolic model testing. Christian Lieven, Moritz E Beber, Brett G Olivier, Frank T Bergmann, Meric Ataman, Parizad Babaei, Jennifer A Bartell, Lars M Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E Ebert, Janaka N Edirisinghe, José P Faria, Adam M Feist, Georgios Fengos, Ronan M T Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, Wout van Helvoirt, Christopher S Henry, Henning Hermjakob, Markus J Herrgård, Ali Kaafarani, Hyun Uk Kim, Zachary King, Steffen Klamt, Edda Klipp, Jasper J Koehorst, Matthias König, Meiyappan Lakshmanan, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory L Medlock, Jonathan M Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Bernhard O Palsson, Jason A Papin, Kiran R Patil, Mark Poolman, Nathan D Price, Osbaldo Resendis-Antonio, Anne Richelle, Isabel Rocha, Benjamín J Sánchez, Peter J Schaap, Rahuman S Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A H Wodke, Joana C Xavier, Qianqian Yuan, Maksim Zakhartsev, Cheng Zhang. Nature biotechnology. 2020
  35. High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities. Juan Nogales, Joshua Mueller, Steinn Gudmundsson, Francisco J Canalejo, Estrella Duque, Jonathan Monk, Adam M Feist, Juan Luis Ramos, Wei Niu, Bernhard O Palsson. Environmental microbiology. 2020
  36. OxyR Is a Convergent Target for Mutations Acquired during Adaptation to Oxidative Stress-Prone Metabolic States. Amitesh Anand, Ke Chen, Edward Catoiu, Anand V Sastry, Connor A Olson, Troy E Sandberg, Yara Seif, Sibei Xu, Richard Szubin, Laurence Yang, Adam M Feist, Bernhard O Palsson. Molecular biology and evolution. 2020
  37. Adaptive laboratory evolution of Escherichia coli under acid stress. Bin Du, Connor A Olson, Anand V Sastry, Xin Fang, Patrick V Phaneuf, Ke Chen, Muyao Wu, Richard Szubin, Sibei Xu, Ye Gao, Ying Hefner, Adam M Feist, Bernhard O Palsson. Microbiology (Reading, England). 2020

    38. 2019

  38. Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media. Akanksha Rajput, Saugat Poudel, Hannah Tsunemoto, Michael Meehan, Richard Szubin, Connor A Olson, Anne Lamsa, Yara Seif, Nicholas Dillon, Alison Vrbanac, Joseph Sugie, Samira Dahesh, Jonathan M Monk, Pieter C Dorrestein, Rob Knight, Victor Nizet, Bernhard O Palsson, Adam M Feist, Joe Pogliano. Scientific data. 2019
  39. Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration. Amitesh Anand, Ke Chen, Laurence Yang, Anand V Sastry, Connor A Olson, Saugat Poudel, Yara Seif, Ying Hefner, Patrick V Phaneuf, Sibei Xu, Richard Szubin, Adam M Feist, Bernhard O Palsson. Proceedings of the National Academy of Sciences of the United States of America. 2019
  40. Adaptive laboratory evolution of tolerance to dicarboxylic acids in Saccharomyces cerevisiae. Rui Pereira, Yongjun Wei, Elsayed Mohamed, Mohammad Radi, Carl Malina, Markus J Herrgård, Adam M Feist, Jens Nielsen, Yun Chen. Metabolic engineering. 2019
  41. Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus. Henrique Machado, Liam L Weng, Nicholas Dillon, Yara Seif, Michelle Holland, Jonathan E Pekar, Jonathan M Monk, Victor Nizet, Bernhard O Palsson, Adam M Feist. Applied and environmental microbiology. 2019
  42. The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology. Troy E Sandberg, Michael J Salazar, Liam L Weng, Bernhard O Palsson, Adam M Feist. Metabolic engineering. 2019
  43. Cellular responses to reactive oxygen species are predicted from molecular mechanisms. Laurence Yang, Nathan Mih, Amitesh Anand, Joon Ho Park, Justin Tan, James T Yurkovich, Jonathan M Monk, Colton J Lloyd, Troy E Sandberg, Sang Woo Seo, Donghyuk Kim, Anand V Sastry, Patrick Phaneuf, Ye Gao, Jared T Broddrick, Ke Chen, David Heckmann, Richard Szubin, Ying Hefner, Adam M Feist, Bernhard O Palsson. Proceedings of the National Academy of Sciences of the United States of America. 2019
  44. Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution. Elsayed T Mohamed, Hemanshu Mundhada, Jenny Landberg, Isaac Cann, Roderick I Mackie, Alex Toftgaard Nielsen, Markus J Herrgård, Adam M Feist. Microbial cell factories. 2019
  45. Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism. Chuankai Cheng, Edward J O'Brien, Douglas McCloskey, Jose Utrilla, Connor Olson, Ryan A LaCroix, Troy E Sandberg, Adam M Feist, Bernhard O Palsson, Zachary A King. PLoS computational biology. 2019
  46. Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media. Saugat Poudel, Hannah Tsunemoto, Michael Meehan, Richard Szubin, Connor A Olson, Anne Lamsa, Yara Seif, Nicholas Dillon, Alison Vrbanac, Joseph Sugie, Samira Dahesh, Jonathan M Monk, Pieter C Dorrestein, Joseph Pogliano, Rob Knight, Victor Nizet, Bernhard O Palsson, Adam M Feist. Scientific data. 2019
  47. BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. Jean-Christophe Lachance, Colton J Lloyd, Jonathan M Monk, Laurence Yang, Anand V Sastry, Yara Seif, Bernhard O Palsson, Sébastien Rodrigue, Adam M Feist, Zachary A King, Pierre-Étienne Jacques. PLoS computational biology. 2019
  48. Enzyme promiscuity shapes adaptation to novel growth substrates. Gabriela I Guzmán, Troy E Sandberg, Ryan A LaCroix, Ákos Nyerges, Henrietta Papp, Markus de Raad, Zachary A King, Ying Hefner, Trent R Northen, Richard A Notebaart, Csaba Pál, Bernhard O Palsson, Balázs Papp, Adam M Feist. Molecular systems biology. 2019
  49. Coupling S-adenosylmethionine-dependent methylation to growth: Design and uses. Hao Luo, Anne Sofie L Hansen, Lei Yang, Konstantin Schneider, Mette Kristensen, Ulla Christensen, Hanne B Christensen, Bin Du, Emre Özdemir, Adam M Feist, Jay D Keasling, Michael K Jensen, Markus J Herrgård, Bernhard O Palsson. PLoS biology. 2019
  50. The genetic basis for adaptation of model-designed syntrophic co-cultures. Colton J Lloyd, Zachary A King, Troy E Sandberg, Ying Hefner, Connor A Olson, Patrick V Phaneuf, Edward J O'Brien, Jon G Sanders, Rodolfo A Salido, Karenina Sanders, Caitriona Brennan, Gregory Humphrey, Rob Knight, Adam M Feist. PLoS computational biology. 2019
  51. Pseudogene repair driven by selection pressure applied in experimental evolution. Amitesh Anand, Connor A Olson, Laurence Yang, Anand V Sastry, Edward Catoiu, Kumari Sonal Choudhary, Patrick V Phaneuf, Troy E Sandberg, Sibei Xu, Ying Hefner, Richard Szubin, Adam M Feist, Bernhard O Palsson. Nature microbiology. 2019
  52. ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation. Patrick V Phaneuf, Dennis Gosting, Bernhard O Palsson, Adam M Feist. Nucleic acids research. 2019

    53. 2018

  53. Reframing gene essentiality in terms of adaptive flexibility. Gabriela I Guzmán, Connor A Olson, Ying Hefner, Patrick V Phaneuf, Edward Catoiu, Lais B Crepaldi, Lucas Goldschmidt Micas, Bernhard O Palsson, Adam M Feist. BMC systems biology. 2018
  54. Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology. Jonathan E Pekar, Patrick Phaneuf, Richard Szubin, Bernhard Palsson, Adam Feist, Jonathan M Monk. Microbiology resource announcements. 2018
  55. Enhanced Metabolite Productivity of Escherichia coli Adapted to Glucose M9 Minimal Medium. Peter Rugbjerg, Adam M Feist, Morten Otto Alexander Sommer. Frontiers in bioengineering and biotechnology. 2018
  56. Identification of growth-coupled production strains considering protein costs and kinetic variability. Hoang V Dinh, Zachary A King, Bernhard O Palsson, Adam M Feist. Metabolic engineering communications. 2018
  57. Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. Douglas McCloskey, Sibei Xu, Troy E Sandberg, Elizabeth Brunk, Ying Hefner, Richard Szubin, Adam M Feist, Bernhard O Palsson. Nature communications. 2018
  58. Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome. Douglas McCloskey, Sibei Xu, Troy E Sandberg, Elizabeth Brunk, Ying Hefner, Richard Szubin, Adam M Feist, Bernhard O Palsson. Frontiers in microbiology. 2018
  59. Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions. Douglas McCloskey, Sibei Xu, Troy E Sandberg, Elizabeth Brunk, Ying Hefner, Richard Szubin, Adam M Feist, Bernhard O Palsson. Applied and environmental microbiology. 2018
  60. Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System. Douglas McCloskey, Sibei Xu, Troy E Sandberg, Elizabeth Brunk, Ying Hefner, Richard Szubin, Adam M Feist, Bernhard O Palsson. Metabolic engineering. 2018
  61. Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes. Douglas McCloskey, Sibei Xu, Troy E Sandberg, Elizabeth Brunk, Ying Hefner, Richard Szubin, Adam M Feist, Bernhard O Palsson. Metabolic engineering. 2018
  62. Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae. Tomas Strucko, Katharina Zirngibl, Filipa Pereira, Eleni Kafkia, Elsayed T Mohamed, Mandy Rettel, Frank Stein, Adam M Feist, Paula Jouhten, Kiran Raosaheb Patil, Jochen Forster. Metabolic engineering. 2018
  63. Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli. Christopher P Long, Jacqueline E Gonzalez, Adam M Feist, Bernhard O Palsson, Maciek R Antoniewicz. Proceedings of the National Academy of Sciences of the United States of America. 2018
  64. Computational Methods to Assess the Production Potential of Bio-Based Chemicals. Miguel A Campodonico, Sumesh Sukumara, Adam M Feist, Markus J Herrgård. Methods in molecular biology (Clifton, N.J.). 2018
  65. Underground metabolism: network-level perspective and biotechnological potential. Richard A Notebaart, Bálint Kintses, Adam M Feist, Balázs Papp. Current opinion in biotechnology. 2018

    66. 2017

  66. Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution. Elsayed T Mohamed, Shizeng Wang, Rebecca M Lennen, Markus J Herrgård, Blake A Simmons, Steven W Singer, Adam M Feist. Microbial cell factories. 2017
  67. iML1515, a knowledgebase that computes Escherichia coli traits. Jonathan M Monk, Colton J Lloyd, Elizabeth Brunk, Nathan Mih, Anand Sastry, Zachary King, Rikiya Takeuchi, Wataru Nomura, Zhen Zhang, Hirotada Mori, Adam M Feist, Bernhard O Palsson. Nature biotechnology. 2017
  68. Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring. Christopher P Long, Jacqueline E Gonzalez, Adam M Feist, Bernhard O Palsson, Maciek R Antoniewicz. Metabolic engineering. 2017
  69. Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies. Troy E Sandberg, Colton J Lloyd, Bernhard O Palsson, Adam M Feist. Applied and environmental microbiology. 2017
  70. A Model for Designing Adaptive Laboratory Evolution Experiments. Ryan A LaCroix, Bernhard O Palsson, Adam M Feist. Applied and environmental microbiology. 2017
  71. Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion. Zachary A King, Edward J O'Brien, Adam M Feist, Bernhard O Palsson. Metabolic engineering. 2017
  72. Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution. Hemanshu Mundhada, Jose M Seoane, Konstantin Schneider, Anna Koza, Hanne B Christensen, Tobias Klein, Patrick V Phaneuf, Markus Herrgard, Adam M Feist, Alex T Nielsen. Metabolic engineering. 2017

    73. 2016

  73. Acidithiobacillus ferrooxidans's comprehensive model driven analysis of the electron transfer metabolism and synthetic strain design for biomining applications. Miguel A Campodonico, Daniela Vaisman, Jean F Castro, Valeria Razmilic, Francesca Mercado, Barbara A Andrews, Adam M Feist, Juan A Asenjo. Metabolic engineering communications. 2016
  74. Multi-omic data integration enables discovery of hidden biological regularities. Ali Ebrahim, Elizabeth Brunk, Justin Tan, Edward J O'Brien, Donghyuk Kim, Richard Szubin, Joshua A Lerman, Anna Lechner, Anand Sastry, Aarash Bordbar, Adam M Feist, Bernhard O Palsson. Nature communications. 2016
  75. Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes. Jonathan M Monk, Anna Koza, Miguel A Campodonico, Daniel Machado, Jose Miguel Seoane, Bernhard O Palsson, Markus J Herrgård, Adam M Feist. Cell systems. 2016
  76. What do cells actually want? Adam M Feist, Bernhard O Palsson. Genome biology. 2016
  77. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. Elizabeth Brunk, Kevin W George, Jorge Alonso-Gutierrez, Mitchell Thompson, Edward Baidoo, George Wang, Christopher J Petzold, Douglas McCloskey, Jonathan Monk, Laurence Yang, Edward J O'Brien, Tanveer S Batth, Hector Garcia Martin, Adam Feist, Paul D Adams, Jay D Keasling, Bernhard O Palsson, Taek Soon Lee. Cell systems. 2016
  78. Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution. Jose Utrilla, Edward J O'Brien, Ke Chen, Douglas McCloskey, Jacky Cheung, Harris Wang, Dagoberto Armenta-Medina, Adam M Feist, Bernhard O Palsson. Cell systems. 2016
  79. Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale. Douglas McCloskey, Jamey D Young, Sibei Xu, Bernhard O Palsson, Adam M Feist. Analytical chemistry. 2016
  80. Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology. Troy E Sandberg, Christopher P Long, Jacqueline E Gonzalez, Adam M Feist, Maciek R Antoniewicz, Bernhard O Palsson. PloS one. 2016
  81. MID Max: LC-MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications. Douglas McCloskey, Jamey D Young, Sibei Xu, Bernhard O Palsson, Adam M Feist. Analytical chemistry. 2016

    82. 2015

  82. Do genome-scale models need exact solvers or clearer standards? Ali Ebrahim, Eivind Almaas, Eugen Bauer, Aarash Bordbar, Anthony P Burgard, Roger L Chang, Andreas Dräger, Iman Famili, Adam M Feist, Ronan Mt Fleming, Stephen S Fong, Vassily Hatzimanikatis, Markus J Herrgård, Allen Holder, Michael Hucka, Daniel Hyduke, Neema Jamshidi, Sang Yup Lee, Nicolas Le Novère, Joshua A Lerman, Nathan E Lewis, Ding Ma, Radhakrishnan Mahadevan, Costas Maranas, Harish Nagarajan, Ali Navid, Jens Nielsen, Lars K Nielsen, Juan Nogales, Alberto Noronha, Csaba Pal, Bernhard O Palsson, Jason A Papin, Kiran R Patil, Nathan D Price, Jennifer L Reed, Michael Saunders, Ryan S Senger, Nikolaus Sonnenschein, Yuekai Sun, Ines Thiele. Molecular systems biology. 2015
  83. Next-generation genome-scale models for metabolic engineering. Zachary A King, Colton J Lloyd, Adam M Feist, Bernhard O Palsson. Current opinion in biotechnology. 2015
  84. Model-driven discovery of underground metabolic functions in Escherichia coli. Gabriela I Guzmán, José Utrilla, Sergey Nurk, Elizabeth Brunk, Jonathan M Monk, Ali Ebrahim, Bernhard O Palsson, Adam M Feist. Proceedings of the National Academy of Sciences of the United States of America. 2015
  85. Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium. Ryan A LaCroix, Troy E Sandberg, Edward J O'Brien, Jose Utrilla, Ali Ebrahim, Gabriela I Guzman, Richard Szubin, Bernhard O Palsson, Adam M Feist. Applied and environmental microbiology. 2015

    86. 2014

  86. Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. Joanne K Liu, Edward J O'Brien, Joshua A Lerman, Karsten Zengler, Bernhard O Palsson, Adam M Feist. BMC systems biology. 2014
  87. Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path. Miguel A Campodonico, Barbara A Andrews, Juan A Asenjo, Bernhard O Palsson, Adam M Feist. Metabolic engineering. 2014
  88. Evolution of Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel mutations. Troy E Sandberg, Margit Pedersen, Ryan A LaCroix, Ali Ebrahim, Mads Bonde, Markus J Herrgard, Bernhard O Palsson, Morten Sommer, Adam M Feist. Molecular biology and evolution. 2014
  89. Tracing compartmentalized NADPH metabolism in the cytosol and mitochondria of mammalian cells. Caroline A Lewis, Seth J Parker, Brian P Fiske, Douglas McCloskey, Dan Y Gui, Courtney R Green, Natalie I Vokes, Adam M Feist, Matthew G Vander Heiden, Christian M Metallo. Molecular cell. 2014
  90. Optimal cofactor swapping can increase the theoretical yield for chemical production in Escherichia coli and Saccharomyces cerevisiae. Zachary A King, Adam M Feist. Metabolic engineering. 2014
  91. Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens. Adam M Feist, Harish Nagarajan, Amelia-Elena Rotaru, Pier-Luc Tremblay, Tian Zhang, Kelly P Nevin, Derek R Lovley, Karsten Zengler. PLoS computational biology. 2014
  92. Cofactory: sequence-based prediction of cofactor specificity of Rossmann folds. Henrik Marcus Geertz-Hansen, Nikolaj Blom, Adam M Feist, Søren Brunak, Thomas Nordahl Petersen. Proteins. 2014
  93. A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent. Douglas McCloskey, Jon A Gangoiti, Zachary A King, Robert K Naviaux, Bruce A Barshop, Bernhard O Palsson, Adam M Feist. Biotechnology and bioengineering. 2014

    94. 2013

  94. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Jonathan M Monk, Pep Charusanti, Ramy K Aziz, Joshua A Lerman, Ned Premyodhin, Jeffrey D Orth, Adam M Feist, Bernhard Ø Palsson. Proceedings of the National Academy of Sciences of the United States of America. 2013
  95. Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association. Harish Nagarajan, Mallory Embree, Amelia-Elena Rotaru, Pravin M Shrestha, Adam M Feist, Bernhard Ø Palsson, Derek R Lovley, Karsten Zengler. Nature communications. 2013
  96. Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Douglas McCloskey, Bernhard Ø Palsson, Adam M Feist. Molecular systems biology. 2013
  97. Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746. Matthew C Gonnerman, Matthew N Benedict, Adam M Feist, William W Metcalf, Nathan D Price. Biotechnology journal. 2013
  98. Sulfide-driven microbial electrosynthesis. Yanming Gong, Ali Ebrahim, Adam M Feist, Mallory Embree, Tian Zhang, Derek Lovley, Karsten Zengler. Environmental science & technology. 2013

    99. 2012

  99. Maximizing biomass productivity and cell density of Chlorella vulgaris by using light-emitting diode-based photobioreactor. Weiqi Fu, Olafur Gudmundsson, Adam M Feist, Gisli Herjolfsson, Sigurdur Brynjolfsson, Bernhard Ø Palsson. Journal of biotechnology. 2012

    100. 2011

  100. A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. Aarash Bordbar, Adam M Feist, Renata Usaite-Black, Joseph Woodcock, Bernhard O Palsson, Iman Famili. BMC systems biology. 2011
  101. Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli. Dae-Hee Lee, Adam M Feist, Christian L Barrett, Bernhard Ø Palsson. PloS one. 2011
  102. A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011. Jeffrey D Orth, Tom M Conrad, Jessica Na, Joshua A Lerman, Hojung Nam, Adam M Feist, Bernhard Ø Palsson. Molecular systems biology. 2011
  103. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Jan Schellenberger, Richard Que, Ronan M T Fleming, Ines Thiele, Jeffrey D Orth, Adam M Feist, Daniel C Zielinski, Aarash Bordbar, Nathan E Lewis, Sorena Rahmanian, Joseph Kang, Daniel R Hyduke, Bernhard Ø Palsson. Nature protocols. 2011

    104. 2010

  104. The biomass objective function. Adam M Feist, Bernhard O Palsson. Current opinion in microbiology. 2010
  105. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Adam M Feist, Daniel C Zielinski, Jeffrey D Orth, Jan Schellenberger, Markus J Herrgard, Bernhard Ø Palsson. Metabolic engineering. 2010

    106. 2009

  106. Reconstruction of biochemical networks in microorganisms. Adam M Feist, Markus J Herrgård, Ines Thiele, Jennie L Reed, Bernhard Ø Palsson. Nature reviews. Microbiology. 2009

    107. 2008

  107. Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network. Joungmin Lee, Hongseok Yun, Adam M Feist, Bernhard Ø Palsson, Sang Yup Lee. Applied microbiology and biotechnology. 2008
  108. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Adam M Feist, Bernhard Ø Palsson. Nature biotechnology. 2008

    109. 2007

  109. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Adam M Feist, Christopher S Henry, Jennifer L Reed, Markus Krummenacker, Andrew R Joyce, Peter D Karp, Linda J Broadbelt, Vassily Hatzimanikatis, Bernhard Ø Palsson. Molecular systems biology. 2007
  110. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Scott A Becker, Adam M Feist, Monica L Mo, Gregory Hannum, Bernhard Ø Palsson, Markus J Herrgard. Nature protocols. 2007

    111. 2006

  111. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Adam M Feist, Johannes C M Scholten, Bernhard Ø Palsson, Fred J Brockman, Trey Ideker. Molecular systems biology. 2006