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1

Fecal Aliquot Straw Technique (FAST) allows for easy and reproducible subsampling: assessing interpersonal variation in trimethylamine-N-oxide (TMAO) accumulation

Romano, Kymberleigh A., Dill-McFarland, Kimberly A., Kasahara, Kazuyuki, Kerby, Robert L., Vivas, Eugenio I., Amador-Noguez, Daniel, Herd, Pamela, Rey, Federico E.

Journal:

Year:

2018

Language:

english

File:

PDF, 1.10 MB

english, 2018

2

Deletion of Type I glutamine synthetase deregulates nitrogen metabolism and increases ethanol production in Clostridium thermocellum

Rydzak, Thomas, Garcia, David, Stevenson, David M., Sladek, Margaret, Klingeman, Dawn M., Holwerda, Evert K., Amador-Noguez, Daniel, Brown, Steven D., Guss, Adam M.

Journal:

Metabolic Engineering

Year:

2017

Language:

english

File:

PDF, 1.00 MB

english, 2017

3

Gender-specific alterations in gene expression and loss of liver sexual dimorphism in the long-lived Ames dwarf mice

Daniel Amador-Noguez, John Zimmerman, Susan Venable, Gretchen Darlington

Journal:

Biochemical and Biophysical Research Communications

Year:

2005

Language:

english

File:

PDF, 944 KB

english, 2005

4

Recent applications of metabolomics to advance microbial biofuel production

Martien, Julia I, Amador-Noguez, Daniel

Journal:

Current Opinion in Biotechnology

Year:

2017

Language:

english

File:

PDF, 680 KB

english, 2017

5

Systems-Level Analysis of Oxygen Exposure in Zymomonas mobilis : Implications for Isoprenoid Production

Martien, Julia I., Hebert, Alexander S., Stevenson, David M., Regner, Matthew R., Khana, Daven B., Coon, Joshua J., Amador-Noguez, Daniel, Vickers, Claudia

Journal:

Year:

2019

File:

PDF, 5.30 MB

2019

6

Cardiac function in growth hormone receptor knockout mice

Reddy, A.K., Hartley, C.J., Huq, F., Pham, T.T., Amador-Noguez, D., Entman, M.L., Darlington, G.J., Taffet, G.E.

Journal:

Journal of Biomechanics

Year:

2006

Language:

english

File:

PDF, 161 KB

english, 2006

7

Metabolic flux analysis and fluxomics-driven determination of reaction free energy using multiple isotopes

Xu, Jimmy, Martien, Julia, Gilbertson, Cole, Ma, Junyu, Amador-Noguez, Daniel, Park, Junyoung O

Journal:

Current Opinion in Biotechnology

Year:

2020

File:

PDF, 1.06 MB

2020

8

Different Functions of Phylogenetically Distinct Bacterial Complex I Isozymes

Spero, Melanie A., Brickner, Joshua R., Mollet, Jordan T., Pisithkul, Tippapha, Amador-Noguez, Daniel, Donohue, Timothy J., Metcalf, W. W.

Journal:

Journal of Bacteriology

Year:

2016

Language:

english

File:

PDF, 3.21 MB

english, 2016

9

Systems-Level Metabolic Flux Profiling Elucidates a Complete, Bifurcated Tricarboxylic Acid Cycle in Clostridium acetobutylicum

Amador-Noguez, D., Feng, X.-J., Fan, J., Roquet, N., Rabitz, H., Rabinowitz, J. D.

Journal:

Journal of Bacteriology

Year:

2010

Language:

english

File:

PDF, 1.57 MB

english, 2010

10

Metabolic Remodeling during Biofilm Development of Bacillus subtilis

Pisithkul, Tippapha, Schroeder, Jeremy W., Trujillo, Edna A., Yeesin, Ponlkrit, Stevenson, David M., Chaiamarit, Tai, Coon, Joshua J., Wang, Jue D., Amador-Noguez, Daniel, Ghigo, Jean-Marc, Greenberg,

Journal:

Year:

2019

Language:

english

File:

PDF, 7.24 MB

english, 2019

11

Metabolic and evolutionary responses of Clostridium thermocellum to genetic interventions aimed at improving ethanol production

Holwerda, Evert K., Olson, Daniel G., Ruppertsberger, Natalie M., Stevenson, David M., Murphy, Sean J. L., Maloney, Marybeth I., Lanahan, Anthony A., Amador-Noguez, Daniel, Lynd, Lee R.

Journal:

Biotechnology for Biofuels

Year:

2020

Language:

english

File:

PDF, 3.47 MB

english, 2020

12

Post-translational modifications as key regulators of bacterial metabolic fluxes

Pisithkul, Tippapha, Patel, Nishaben M, Amador-Noguez, Daniel

Journal:

Current Opinion in Microbiology

Year:

2015

Language:

english

File:

PDF, 605 KB

english, 2015

13

Steady-State Metabolite Concentrations Reflect a Balance between Maximizing Enzyme Efficiency and Minimizing Total Metabolite Load

Tepper, Naama, Noor, Elad, Amador-Noguez, Daniel, Haraldsdóttir, Hulda S., Milo, Ron, Rabinowitz, Josh, Liebermeister, Wolfram, Shlomi, Tomer, Thattai, Mukund

Journal:

Year:

2013

Language:

english

File:

PDF, 2.14 MB

english, 2013

14

Metabolic Remodeling during Biofilm Development of Bacillus subtilis

Pisithkul, Tippapha, Schroeder, Jeremy W., Trujillo, Edna A., Yeesin, Ponlkrit, Stevenson, David M., Chaiamarit, Tai, Coon, Joshua J., Wang, Jue D., Amador-Noguez, Daniel, Ghigo, Jean-Marc, Greenberg,

Journal:

Year:

2019

File:

PDF, 7.24 MB

2019

15

Metabolomic Analysis via Reversed-Phase Ion-Pairing Liquid Chromatography Coupled to a Stand Alone Orbitrap Mass Spectrometer

Lu, Wenyun, Clasquin, Michelle F., Melamud, Eugene, Amador-Noguez, Daniel, Caudy, Amy A., Rabinowitz, Joshua D.

Journal:

Analytical Chemistry

Year:

2010

Language:

english

File:

PDF, 262 KB

english, 2010

16

INCREASED PLASMA TRIMETHYLAMINE-N-OXIDE (TMAO) IS ASSOCIATED WITH LOWER HIPPOCAMPAL BLOOD FLOW

Beilfuss, Matthew A., Vogt, Nicholas M., Romano, Kymberleigh, Oh, Jennifer M., Amador-Noguez, Daniel, Johnson, Sterling C., Asthana, Sanjay, Rey, Federico E., Bendlin, Barbara B.

Journal:

Alzheimer's & Dementia

Year:

2018

Language:

english

File:

PDF, 308 KB

english, 2018

17

Gene expression profile of long-lived Ames dwarf mice and Little mice

Daniel Amador-Noguez, Kazuo Yagi, Susan Venable, Gretchen Darlington

Journal:

Year:

2004

Language:

english

File:

PDF, 660 KB

english, 2004

18

Evidence for an Alternative Glycolytic Pathway in Rapidly Proliferating Cells

Vander Heiden, M. G., Locasale, J. W., Swanson, K. D., Sharfi, H., Heffron, G. J., Amador-Noguez, D., Christofk, H. R., Wagner, G., Rabinowitz, J. D., Asara, J. M., Cantley, L. C.

Journal:

Year:

2010

Language:

english

File:

PDF, 728 KB

english, 2010

19

Metabolic, Epigenetic, and Transgenerational Effects of Gut Bacterial Choline Consumption

Romano, Kymberleigh A., Martinez-del Campo, Ana, Kasahara, Kazuyuki, Chittim, Carina L., Vivas, Eugenio I., Amador-Noguez, Daniel, Balskus, Emily P., Rey, Federico E.

Journal:

Cell Host & Microbe

Year:

2017

Language:

english

File:

PDF, 1.90 MB

english, 2017

20

Few Differences in Metabolic Network Use Found Between Salmonella enterica Colonization of Plants and Typhoidal Mice

Kwan, Grace, Plagenz, Brett, Cowles, Kimberly, Pisithkul, Tippapha, Amador-Noguez, Daniel, Barak, Jeri D.

Journal:

Frontiers in Microbiology

Year:

2018

Language:

english

File:

PDF, 1.94 MB

english, 2018

21

Cytochrome P450 Monooxygenase-Mediated Metabolic Utilization of Benzo[ a ]Pyrene by Aspergillus Species

Ostrem Loss, Erin M., Lee, Mi-Kyung, Wu, Ming-Yueh, Martien, Julia, Chen, Wanping, Amador-Noguez, Daniel, Jefcoate, Colin, Remucal, Christina, Jung, Seunho, Kim, Sun-Chang, Yu, Jae-Hyuk, Fischer, Rein

Journal:

Year:

2019

File:

PDF, 1.61 MB

2019

22

acI Actinobacteria Assemble a Functional Actinorhodopsin with Natively-synthesized Retinal

Dwulit-Smith, Jeffrey R., Hamilton, Joshua J., Stevenson, David M., He, Shaomei, Oyserman, Ben O., Moya-Flores, Francisco, Garcia, Sarahi L., Amador-Noguez, Daniel, McMahon, Katherine D., Forest, Katr

Journal:

Applied and Environmental Microbiology

Year:

2018

Language:

english

File:

PDF, 2.32 MB

english, 2018

23

Systems-Level Analysis of Oxygen Exposure in Zymomonas mobilis : Implications for Isoprenoid Production

Martien, Julia I., Hebert, Alexander S., Stevenson, David M., Regner, Matthew R., Khana, Daven B., Coon, Joshua J., Amador-Noguez, Daniel, Vickers, Claudia

Journal:

Year:

2019

Language:

english

File:

PDF, 5.30 MB

english, 2019

24

Expression of Phosphofructokinase Is Not Sufficient to Enable Embden-Meyerhof-Parnas Glycolysis in Zymomonas mobilis ZM4

Felczak, Magdalena M., Jacobson, Tyler B., Ong, Wai Kit, Amador-Noguez, Daniel, TerAvest, Michaela A.

Journal:

Frontiers in Microbiology

Year:

2019

File:

PDF, 6.78 MB

2019

25

Expression of Phosphofructokinase Is Not Sufficient to Enable Embden-Meyerhof-Parnas Glycolysis in Zymomonas mobilis ZM4

Felczak, Magdalena M., Jacobson, Tyler B., Ong, Wai Kit, Amador-Noguez, Daniel, TerAvest, Michaela A.

Journal:

Frontiers in Microbiology

Year:

2019

Language:

english

File:

PDF, 6.78 MB

english, 2019

26

Cytochrome P450 Monooxygenase-Mediated Metabolic Utilization of Benzo[ a ]Pyrene by Aspergillus Species

Ostrem Loss, Erin M., Lee, Mi-Kyung, Wu, Ming-Yueh, Martien, Julia, Chen, Wanping, Amador-Noguez, Daniel, Jefcoate, Colin, Remucal, Christina, Jung, Seunho, Kim, Sun-Chang, Yu, Jae-Hyuk, Fischer, Rein

Journal:

Year:

2019

Language:

english

File:

PDF, 1.61 MB

english, 2019

27

Alterations in xenobiotic metabolism in the long-lived Little mice

Daniel Amador-Noguez, Adam Dean, Wendong Huang, Kenneth Setchell, David Moore, Gretchen Darlington

Journal:

Year:

2007

Language:

english

File:

PDF, 637 KB

english, 2007

28

Cyclooxygenase-1 and -2 Play Contrasting Roles in Listeria -Stimulated Immunity

Theisen, Erin, McDougal, Courtney E., Nakanishi, Masako, Stevenson, David M., Amador-Noguez, Daniel, Rosenberg, Daniel W., Knoll, Laura J., Sauer, John-Demian

Journal:

The Journal of Immunology

Year:

2018

Language:

english

File:

PDF, 1.19 MB

english, 2018

29

Regulated redirection of central carbon flux enhances anaerobic production of bioproducts in Zymomonas mobilis

Liu, Yang, Ghosh, Indro Neil, Martien, Julia, Zhang, Yaoping, Amador-Noguez, Daniel, Landick, Robert

Journal:

Metabolic Engineering

Year:

2020

File:

PDF, 7.13 MB

2020

30

The exometabolome ofClostridium thermocellumreveals overflow metabolism at high cellulose loading

Holwerda, Evert K, Thorne, Philip G, Olson, Daniel G, Amador-Noguez, Daniel, Engle, Nancy L, Tschaplinski, Timothy J, van Dijken, Johannes P, Lynd, Lee R

Journal:

Biotechnology for Biofuels

Year:

2014

Language:

english

File:

PDF, 1.29 MB

english, 2014

31

Systems-Level Metabolic Flux Profiling Elucidates a Complete, Bifurcated Tricarboxylic Acid Cycle in Clostridium acetobutylicum

Amador-Noguez, D., Feng, X.-J., Fan, J., Roquet, N., Rabitz, H., Rabinowitz, J. D.

Journal:

Journal of Bacteriology

Year:

2011

File:

PDF, 17 KB

2011

32

Metabolome analysis reveals a role for glyceraldehyde 3-phosphate dehydrogenase in the inhibition of C. thermocellum by ethanol

Tian, Liang, Perot, Skyler J., Stevenson, David, Jacobson, Tyler, Lanahan, Anthony A., Amador-Noguez, Daniel, Olson, Daniel G., Lynd, Lee R.

Journal:

Biotechnology for Biofuels

Year:

2017

Language:

english

File:

PDF, 1.91 MB

english, 2017

33

Glycolysis without pyruvate kinase in Clostridium thermocellum

Olson, Daniel G., Hörl, Manuel, Fuhrer, Tobias, Cui, Jingxuan, Zhou, Jilai, Maloney, Marybeth I., Amador-Noguez, Daniel, Tian, Liang, Sauer, Uwe, Lynd, Lee R.

Journal:

Metabolic Engineering

Year:

2016

Language:

english

File:

PDF, 1.54 MB

english, 2016

34

Developing a Cell-Free Extract Reaction (CFER) System in Clostridium thermocellum to Identify Metabolic Limitations to Ethanol Production

Cui, Jingxuan, Stevenson, David, Korosh, Travis, Amador-Noguez, Daniel, Olson, Daniel G., Lynd, Lee R.

Journal:

Frontiers in Energy Research

Year:

2020

File:

PDF, 3.39 MB

2020

35

Small Alarmone Synthetase SasA Expression Leads to Concomitant Accumulation of pGpp, ppApp, and AppppA in Bacillus subtilis

Fung, Danny K., Yang, Jin, Stevenson, David M., Amador-Noguez, Daniel, Wang, Jue D.

Journal:

Frontiers in Microbiology

Year:

2020

File:

PDF, 2.68 MB

2020

36

In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13 C and 2 H Tracers

Jacobson, Tyler B., Korosh, Travis K., Stevenson, David M., Foster, Charles, Maranas, Costas, Olson, Daniel G., Lynd, Lee R., Amador-Noguez, Daniel, Porto, Carla

Journal:

Year:

2020

File:

PDF, 804 KB

2020

37

TrpE feedback mutants reveal roadblocks and conduits toward increasing secondary metabolism in Aspergillus fumigatus

Wang, Pin-Mei, Choera, Tsokyi, Wiemann, Philipp, Pisithkul, Tippapha, Amador-Noguez, Daniel, Keller, Nancy P.

Journal:

Fungal Genetics and Biology

Year:

2015

Language:

english

File:

PDF, 2.51 MB

english, 2015

38

Cardiac Function in Young and Old Little Mice

Reddy, A. K., Amador-Noguez, D., Darlington, G. J., Scholz, B. A., Michael, L. H., Hartley, C. J., Entman, M. L., Taffet, G. E.

Journal:

The Journals of Gerontology Series A Biological Sciences and Medical Sciences

Year:

2007

Language:

english

File:

PDF, 225 KB

english, 2007

39

The nucleotide pGpp acts as a third alarmone in Bacillus, with functions distinct from those of (p) ppGpp

Yang, Jin, Anderson, Brent W., Turdiev, Asan, Turdiev, Husan, Stevenson, David M., Amador-Noguez, Daniel, Lee, Vincent T., Wang, Jue D.

Journal:

Nature Communications

Year:

2020

File:

PDF, 917 KB

2020

40

INCREASED PLASMA TRIMETHYLAMINE-N-OXIDE (TMAO) IS ASSOCIATED WITH LOWER HIPPOCAMPAL BLOOD FLOW

Beilfuss, Matthew A., Vogt, Nicholas M., Romano, Kymberleigh, Oh, Jennifer M., Amador-Noguez, Daniel, Johnson, Sterling C., Asthana, Sanjay, Rey, Federico E., Bendlin, Barbara B.

Journal:

Alzheimer's & Dementia

Year:

2018

Language:

english

File:

PDF, 158 KB

english, 2018

41

Corrigendum to “Gender-specific alterations in gene expression and loss of liver sexual dimorphism in the long-lived Ames dwarf mice” [Biochem. Biophys. Res. Commun. 332 (2005) 1086–1100]

Daniel Amador-Noguez, John Zimmerman, Susan Venable, Gretchen Darlington

Journal:

Biochemical and Biophysical Research Communications

Year:

2005

Language:

english

File:

PDF, 81 KB

english, 2005

42

Metabolome Remodeling during the Acidogenic-Solventogenic Transition in Clostridium acetobutylicum

Amador-Noguez, D., Brasg, I. A., Feng, X.-J., Roquet, N., Rabinowitz, J. D.

Journal:

Applied and Environmental Microbiology

Year:

2011

Language:

english

File:

PDF, 3.01 MB

english, 2011

43

OptSSeq explores enzyme expression and function landscapes to maximize isobutanol production rate

Ghosh, Indro N., Martien, Julia, Hebert, Alexander S., Zhang, Yaoping, Coon, Joshua J., Amador-Noguez, Daniel, Landick, Robert

Journal:

Metabolic Engineering

Year:

2018

Language:

english

File:

PDF, 1.86 MB

english, 2018

44

The thermophilic biomass-degrading bacterium Caldicellulosiruptor bescii utilizes two enzymes to oxidize glyceraldehyde-3-phosphate during glycolysis

Scott, Israel M., Rubinstein, Gabriel M., Poole, Farris L., Lipscomb, Gina L., Schut, Gerrit J., Williams-Rhaesa, Amanda M, Stevenson, David M., Amador-Noguez, Daniel, Kelly, Robert M, Adams, Michael

Journal:

Journal of Biological Chemistry

Year:

2019

Language:

english

File:

PDF, 936 KB

english, 2019

45

Near-equilibrium glycolysis supports metabolic homeostasis and energy yield

Park, Junyoung O., Tanner, Lukas B., Wei, Monica H., Khana, Daven B., Jacobson, Tyler B., Zhang, Zheyun, Rubin, Sara A., Li, Sophia Hsin-Jung, Higgins, Meytal B., Stevenson, David M., Amador-Noguez, D

Journal:

Nature Chemical Biology

Year:

2019

Language:

english

File:

PDF, 2.01 MB

english, 2019

46

Dual metabolomic profiling uncovers Toxoplasma manipulation of the host metabolome and the discovery of a novel parasite metabolic capability

Olson, William J., Martorelli Di Genova, Bruno, Gallego-Lopez, Gina, Dawson, Anthony R., Stevenson, David, Amador-Noguez, Daniel, Knoll, Laura J., Soldati-Favre, Dominique

Journal:

Year:

2020

File:

PDF, 7.94 MB

2020

47

Metabolic Fluxes of Nitrogen and Pyrophosphate in Chemostat Cultures of Clostridium thermocellum and Thermoanaerobacterium saccharolyticum

Holwerda, Evert K., Zhou, Jilai, Hon, Shuen, Stevenson, David M., Amador-Noguez, Daniel, Lynd, Lee R., van Dijken, Johannes P., Semrau, Jeremy D.

Journal:

Applied and Environmental Microbiology

Year:

2020

File:

PDF, 1.36 MB

2020

48

Comprehensive quantitation of metabolite concentrations, gross reaction fluxes, and reaction free energies across cells from four organisms

Park, Junyoung, Rubin, Sara, Xu, Yi-Fan, Amador-Noguez, Daniel, Fan, Jing, Rabinowitz, Joshua

Journal:

Cancer & Metabolism

Year:

2014

Language:

english

File:

PDF, 98 KB

english, 2014

49

2H and 13C metabolic flux analysis elucidates in vivo thermodynamics of the ED pathway in Zymomonas mobilis

Jacobson, Tyler B., Adamczyk, Paul A., Stevenson, David M., Regner, Matthew, Ralph, John, Reed, Jennifer, Amador-Noguez, Daniel

Journal:

Metabolic Engineering

Year:

2019

Language:

english

File:

PDF, 1.21 MB

english, 2019

50

De Novo Amino Acid Biosynthesis Contributes to Salmonella enterica Growth in Alfalfa Seedling Exudates

Kwan, Grace, Pisithkul, Tippapha, Amador-Noguez, Daniel, Barak, Jeri, Schottel, J. L.

Journal:

Applied and Environmental Microbiology

Year:

2015

Language:

english

File:

PDF, 797 KB

english, 2015

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