Zobrazeno 1 - 10
of 10
pro vyhledávání: '"Stephen Federowicz"'
Autor:
Haythem Latif, Stephen Federowicz, Ali Ebrahim, Janna Tarasova, Richard Szubin, Jose Utrilla, Karsten Zengler, Bernhard O Palsson
Publikováno v:
PLoS ONE, Vol 13, Iss 5, p e0197272 (2018)
Numerous in vitro studies have yielded a refined picture of the structural and molecular associations between Cyclic-AMP receptor protein (Crp), the DNA motif, and RNA polymerase (RNAP) holoenzyme. In this study, high-resolution ChIP-exonuclease (ChI
Externí odkaz:
https://doaj.org/article/edd8d9883a85420a971a6a07b4a2a415
Autor:
Stephen Federowicz, Donghyuk Kim, Ali Ebrahim, Joshua Lerman, Harish Nagarajan, Byung-kwan Cho, Karsten Zengler, Bernhard Palsson
Publikováno v:
PLoS Genetics, Vol 10, Iss 4, p e1004264 (2014)
Determining how facultative anaerobic organisms sense and direct cellular responses to electron acceptor availability has been a subject of intense study. However, even in the model organism Escherichia coli, established mechanisms only explain a sma
Externí odkaz:
https://doaj.org/article/153a087e12cb4160b8fe3205ad081a5c
Autor:
Kimberline Y. Gerrick, Jenny Laraio, Kelsey Annen, Hoang Tran, Marcus M. Fischer, Yevgeniy Freyman, Geeta Sharma, Isaac Bishof, Stephen Federowicz, Divya Pankajakshan, Claire L. Neilan, Biju Mangatt, Anthony Mazurek, Mark R. Lackner, Michael White, Zineb Mounir
Publikováno v:
Cancer Research. 83:1637-1637
Methylthioadenosine phosphorylase (MTAP) is co-deleted with the tumor suppressor CDKN2A in approximately 15% of solid tumors and can elicit dependency on methionine adenosyltransferase 2A (MAT2A) production of S-adenosyl methionine (SAM), the major m
Autor:
Tyson R. Shepherd, Clint Davis, Charles D. Johnson, Stephen Tanner, Jocelyne Bruand, Thomas Hraha, Tian Tian, Steven Alvarez, Eric Abbate, Shea Lambert, Timothy M. Shaver, Bryan A Leland, Paul Hardenbol, Michael Graige, Stephen Federowicz, Mathew Barber, Scott Bolte, Christopher G. Abraham, Miles Gander, Simon Cawley, Gozde Gencer, J. Christian J. Ray, Andrew D. Garst, Richard Fox, Maciej Swat, Surbhi Jain, Matthew Estes, Kara Juneau, Craig A. Struble, Ken Wishart, Andrea L. Halweg-Edwards, Deanna M. Church, Francesca Pearson, Eileen Colie Spindler, Nandini Krishnamurthy, Chad Sanada, Joshua Shorenstein
Genome engineering methodologies are transforming biological research and discovery. Approaches based on CRISPR technology have been broadly adopted and there is growing interest in the generation of massively parallel edited cell libraries. Comparin
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::3fe0e8bc1ff7b70e400f9a7f173cf58a
https://doi.org/10.1101/2021.09.23.458228
https://doi.org/10.1101/2021.09.23.458228
Autor:
Philip C. Miller, Andreas Dräger, Justin S. Lu, Zachary A. King, Ali Ebrahim, Nathan E. Lewis, Bernhard O. Palsson, Joshua A. Lerman, Stephen Federowicz
Publikováno v:
Nucleic Acids Research
King, Z A, Lu, J, Dräger, A, Miller, P, Federowicz, S, Lerman, J A, Ebrahim, A, Palsson, B & Lewis, N 2016, ' BiGG Models: A platform for integrating, standardizing and sharing genome-scale models ', Nucleic Acids Research, vol. 44, gkv1049, pp. D515-D522 . https://doi.org/10.1093/nar/gkv1049
Nucleic acids research, vol 44, iss D1
King, Z A, Lu, J, Dräger, A, Miller, P, Federowicz, S, Lerman, J A, Ebrahim, A, Palsson, B & Lewis, N 2016, ' BiGG Models: A platform for integrating, standardizing and sharing genome-scale models ', Nucleic Acids Research, vol. 44, gkv1049, pp. D515-D522 . https://doi.org/10.1093/nar/gkv1049
Nucleic acids research, vol 44, iss D1
Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maxim
Autor:
Bernhard O. Palsson, Richard Szubin, Haythem Latif, Janna Tarasova, Karsten Zengler, Stephen Federowicz, Ali Ebrahim, José Utrilla
Publikováno v:
Latif, H, Federowicz, S, Ebrahim, A, Tarasova, J, Szubin, R, Utrilla, J, Zengler, K & Palsson, B O 2018, ' ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions ', P L o S One, vol. 13, no. 5, e0197272 . https://doi.org/10.1371/journal.pone.0197272
PloS one, vol 13, iss 5
PLoS ONE
PLoS ONE, Vol 13, Iss 5, p e0197272 (2018)
PloS one, vol 13, iss 5
PLoS ONE
PLoS ONE, Vol 13, Iss 5, p e0197272 (2018)
Numerousin vitrostudies have yielded a refined picture of the structural and molecular associations between Cyclic-AMP receptor protein (Crp), the DNA motif, and RNA polymerase (RNAP) holoenzyme. In this study, high-resolution ChIP-exonuclease (ChIP-
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f6bf6ac3af0ce08721d665308653386b
Autor:
Mallory Embree, Bernhard O. Palsson, Young-Seoub Park, Byung-Kwan Cho, Stephen Federowicz, Donghyuk Kim
Publikováno v:
Nucleic Acids Research
The PurR transcription factor plays a critical role in transcriptional regulation of purine metabolism in enterobacteria. Here, we elucidate the role of PurR under exogenous adenine stimulation at the genome-scale using high-resolution chromatin immu
Autor:
Bernhard O. Palsson, Stephen Federowicz, Haythem Latif, Ali Ebrahim, Harish Nagarajan, Jan Schellenberger, Nathan E. Lewis, Aarash Bordbar
Publikováno v:
Molecular Systems Biology
Pathways are a universal paradigm for functionally describing cellular processes. Even though advances in high-throughput data generation have transformed biology, the core of our biological understanding, and hence data interpretation, is still pred
Autor:
Harish Nagarajan, Bernhard O. Palsson, Joshua A. Lerman, Stephen Federowicz, Byung-Kwan Cho, Ali Ebrahim, Donghyuk Kim, Karsten Zengler
Publikováno v:
Federowicz, S, Kim, D, Ebrahim, A, Lerman, J, Nagarajan, H, Cho, B, Zengler, K & Palsson, B 2014, ' Determining the Control Circuitry of Redox Metabolism at the Genome-Scale ', P L o S Genetics, vol. 10, no. 4, e1004264 . https://doi.org/10.1371/journal.pgen.1004264
PLoS Genetics
PLoS genetics, vol 10, iss 4
PLoS Genetics, Vol 10, Iss 4, p e1004264 (2014)
PLoS Genetics
PLoS genetics, vol 10, iss 4
PLoS Genetics, Vol 10, Iss 4, p e1004264 (2014)
Determining how facultative anaerobic organisms sense and direct cellular responses to electron acceptor availability has been a subject of intense study. However, even in the model organism Escherichia coli, established mechanisms only explain a sma
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::13377dcd9e4427b1562091155771c113
https://orbit.dtu.dk/en/publications/423d44f5-d407-46f7-a3a9-a39f7a28fe85
https://orbit.dtu.dk/en/publications/423d44f5-d407-46f7-a3a9-a39f7a28fe85
Although metabolic networks have been reconstructed on a genome-scale, the corresponding reconstruction and integration of governing transcriptional regulatory networks has not been fully achieved. Here we reconstruct such an integrated network for a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e44bea58e96d14a61a18f47d05aa16ce
https://europepmc.org/articles/PMC3777760/
https://europepmc.org/articles/PMC3777760/