Tag e_coli [185 articles] Export

Recent papers classified by the tag e_coli.

	The transcription unit architecture of the Escherichia coli genome [My Copy] Nature Biotechnology, Vol. 27, No. 11. (01 November 2009), pp. 1043-1049. by Byung-Kwan Cho, Karsten Zengler, Yu Qiu, et al.Young S. Park, Eric M. Knight, Christian L. Barrett, Yuan Gao, Bernhard O. Palsson posted to transcription mrna genome gene_regulation e_coli dna_binding chromosome_organization bacteria by jjray on 2009-11-09 03:49:20 as along with 1 person rsaito
	Compensatory Evolution of Gene Regulation in Response to Stress by Escherichia coli Lacking RpoS [My Copy] PLoS Genet, Vol. 5, No. 10. (2 October 2009), e1000671. by Daniel M. Stoebel, Karsten Hokamp, Michael S. Last, Charles J. Dorman posted to stress_response sigma_factor evolution e_coli bacteria by jjray on 2009-11-03 23:33:51 as
	Invariant Distribution of Promoter Activities in Escherichia coli [My Copy] PLoS Comput Biol, Vol. 5, No. 10. (23 October 2009), e1000545. by Alon Zaslaver, Shai Kaplan, Anat Bren, et al.Adrian Jinich, Avi Mayo, Erez Dekel, Uri Alon, Shalev Itzkovitz posted to promoter gene_expression e_coli distribution bacteria by jjray on 2009-11-03 23:28:45 as along with 1 person dbikard
	Genome evolution and adaptation in a long-term experiment with Escherichia coli [My Copy] Nature, Vol. 461, No. 7268. (18 October 2009), pp. 1243-1247. by Jeffrey E. Barrick, Dong S. Yu, Sung H. Yoon, et al.Haeyoung Jeong, Tae K. Oh, Dominique Schneider, Richard E. Lenski, Jihyun F. Kim posted to population_genetics evolution e_coli bacteria adaptation by jjray on 2009-10-21 19:27:03 as along with 24 people and 4 groups jasontsai aaltenburger sawasthi nurban josepe tjandra venancio maren qayub Garamonfok yyfwuhan Asclepius dbikard nzm djkt treangen lp2 codonusage operon diamantis michaelbarton druvus DrRichardBadge richardfranzese Pedro Martinez EvoDevo lab Barcelona iSEEM Journal picks BergmanLab
	The Modular Organization of Protein Interactions in Escherichia coli [My Copy] PLoS Comput Biol, Vol. 5, No. 10. (2 October 2009), e1000523. by José M. Peregrín-Alvarez, Xuejian Xiong, Chong Su, John Parkinson posted to protein_complex protein-protein_interaction network_evolution module modularity e_coli by biomcgary on 2009-10-13 22:47:39 as along with 6 people and 2 groups venancio CorinYeats grahamc kiekyon poirel dswan Orengo Group Journal Picks Bioinformatics
	Optimal cytoplasmatic density and flux balance model under macromolecular crowding effects [My Copy] (11 Oct 2009) by Alexei Vazquez posted to optimization metabolism e_coli diffusion cytoplasm bacteria by jjray on 2009-10-13 16:45:07 as along with 1 person apocapoc
	Induction Kinetics of a Conditional pH Stress Response System in Escherichia coli [My Copy] Journal of Molecular Biology (21 August 2009) by Georg Fritz, Christiane Koller, Korinna Burdack, et al.Larissa Tetsch, Ina Haneburger, Kirsten Jung, Ulrich Gerland posted to stress_response quantitative_data mathematical_model kinetics gene_expression e_coli bacteria by jjray on 2009-10-01 15:34:58 as
	Global Analysis of Extracytoplasmic Stress Signaling in Escherichia coli [My Copy] PLoS Genet, Vol. 5, No. 9. (18 September 2009), e1000651. by Stéphanie Bury-Moné, Yanoura Nomane, Nancie Reymond, et al.Romain Barbet, Eric Jacquet, Sandrine Imbeaud, Annick Jacq, Philippe Bouloc posted to stress_response signaling e_coli bacteria by jjray on 2009-09-26 23:21:21 as
	Design Parameters to Control Synthetic Gene Expression in Escherichia coli [My Copy] PLoS ONE, Vol. 4, No. 9. (14 September 2009), e7002. by Mark Welch, Sridhar Govindarajan, Jon E. Ness, et al.Alan Villalobos, Austin Gurney, Jeremy Minshull, Claes Gustafsson posted to synthetic_biology gene_expression e_coli bacteria by jjray to the group Synthetic Biology on 2009-09-26 15:41:38 as along with 6 people dbikard RasmusJensen pala0088 Vincent_Rouilly michaelbarton bmduggan
	Network motifs in the transcriptional regulation network of Escherichia coli [My Copy] Nature Genetics, Vol. 31, No. 1. (22 April 2002), pp. 64-68. by Shai S. Shen-Orr, Ron Milo, Shmoolik Mangan, Uri Alon posted to network_motifs genetic gene_regulation e_coli biology by vtraag on 2009-09-25 13:02:22 as along with 18 people and 1 group sergiun mtagaya kaarsinogen cswinburne jstajic jjray ssb nickluscombe gurkanbebek jtaylor jayster4 karfunkel blobbybirdman zibuyu maralena hannahrajasingh Borelli ethkim EBI-regulation
	Systematic identification and sequence analysis of the genomic islands of the enteropathogenic Escherichia coli strain B171-8 by the combined use of whole-genome PCR scanning and fosmid mapping. [My Copy] Journal of bacteriology, Vol. 190, No. 21. (November 2008), pp. 6948-6960. by Yoshitoshi Ogura, Hiroyuki Abe, Keisuke Katsura, et al.Ken Kurokawa, Md Asadulghani, Atsushi Iguchi, Tadasuke Ooka, Keisuke Nakayama, Atsushi Yamashita, Masahira Hattori, Toru Tobe, Tetsuya Hayashi posted to e_coli by jewel6621 on 2009-09-23 05:44:39 as
	Correlation between gene expression profiles and protein-protein interactions within and across genomes [My Copy] Bioinformatics, Vol. 21, No. 11. (1 June 2005), pp. 2730-2738. by Nitin Bhardwaj, Hui Lu posted to yeast protein_interactions gene_expression e_coli by jjray on 2009-09-10 19:44:28 as along with 2 people and 1 group jperkins lfriedl kdl
	Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli [My Copy] Genome Biology, Vol. 5, No. 11. (2004), R87. by Brian Peter, Javier Arsuaga, Adam Breier, Arkady Khodursky, Patrick Brown, Nicholas Cozzarelli posted to transcription supercoiling gene_expression e_coli bacteria by jjray on 2009-09-10 17:07:30 as along with 2 people comb supercoiling
	Metabolic engineering of Escherichia coli for the production of putrescine, a four carbon diamine [My Copy] Biotechnology and Bioengineering (2009), pp. n/a-n/a. by Zhi-Gang Qian, Xiao-Xia Xia, Sang Y. Lee posted to synthetic_biology gmos e_coli by chriswillmott on 2009-09-03 15:26:06 as
	Recombination Speeds Adaptation by Reducing Competition between Beneficial Mutations in Populations of Escherichia coli [My Copy] PLoS Biol, Vol. 5, No. 9. (21 August 2007), e225. by Tim F. Cooper posted to recombination population_genetics evolution e_coli bacteria by jjray on 2009-08-31 18:42:53 as along with 1 person yuhc
	Autogenous and nonautogenous control of response in a genetic network [My Copy] Proceedings of the National Academy of Sciences, Vol. 103, No. 34. (22 August 2006), pp. 12718-12723. by Francisco M. Camas, Jesús Blázquez, Juan F. Poyatos posted to sos response_time gene_regulation feedback e_coli bacteria by jjray on 2009-08-29 06:21:22 as along with 1 person aalibes
	Genome-scale thermodynamic analysis of Escherichia coli metabolism. [My Copy] Biophysical journal, Vol. 90, No. 4. (15 February 2006), pp. 1453-1461. by Christopher S. Henry, Matthew D. Jankowski, Linda J. Broadbelt, Vassily Hatzimanikatis posted to thermodynamic stoichiometry flux fba e_coli by winterstream on 2009-08-24 13:19:36 as along with 4 people schwartzjmc csanford lylu JeremyZucker
	A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. [My Copy] Molecular systems biology, Vol. 3 (26 June 2007) by Adam M. Feist, Christopher S. Henry, Jennifer L. Reed, et al.Markus Krummenacker, Andrew R. Joyce, Peter D. Karp, Linda J. Broadbelt, Vassily Hatzimanikatis, Bernhard Ø. Palsson posted to thermodynamic stoichiometry in_silico flux fba e_coli by winterstream on 2009-08-24 13:18:08 as along with 7 people aheilbut schwartzjmc alexg cjeans hryk michaelbarton JeremyZucker
	Genome-scale gene/reaction essentiality and synthetic lethality analysis [My Copy] Molecular Systems Biology, Vol. 5 (18 August 2009) by Patrick F. Suthers, Alireza Zomorrodi, Costas D. Maranas posted to systems_biology synthetic_rescue synthetic_lethal network metabolism flux_balance essentiality_conditional essentiality e_coli by biomcgary on 2009-08-18 22:57:41 as along with 2 people and 1 group robertrentzsch pinney Orengo Group Journal Picks
	Role of Translational Coupling in Robustness of Bacterial Chemotaxis Pathway [My Copy] PLoS Biol, Vol. 7, No. 8. (18 August 2009), e1000171. by Linda Løvdok, Kajetan Bentele, Nikita Vladimirov, et al.Anette Müller, Ferencz S. Pop, Dirk Lebiedz, Markus Kollmann, Victor Sourjik posted to systems_biology stochastic_variation signalling_cascade selection_positive robustness protein_translation pathway noise e_coli chemotaxis bacteria by biomcgary on 2009-08-18 20:18:21 as along with 2 people vladimirov jjray
	On the accessibility of adaptive phenotypes of a bacterial metabolic network [My Copy] (14 Aug 2009) by Wilfred Ndifon, Joshua B. Plotkin, Jonathan Dushoff posted to simulation network metabolism evolutionary_dynamics evolution e_coli bacteria adaptation by jjray on 2009-08-17 17:45:02 as along with 1 person apocapoc
	Programming cells by multiplex genome engineering and accelerated evolution [My Copy] Nature, Vol. 460, No. 7257. (26 July 2009), pp. 894-898. by Harris H. Wang, Farren J. Isaacs, Peter A. Carr, et al.Zachary Z. Sun, George Xu, Craig R. Forest, George M. Church posted to systems_engineering systems_biology synthetic_biology protein_engineering mutation metabolism homologous_recombination genome evolution e_coli directional_selection designed_mutations cellular_reprogramming by biomcgary on 2009-08-12 21:38:51 as along with 13 people and 2 groups abhishek_tiwari TorstenWaldminghaus jdoconnell dswan Annab badi druvus dayjm pkonings zwang phoenixzxl djkt dbikard Journal picks Synthetic Biology
	Relation of Intracellular Signal Levels and Promoter Activities in the gal Regulon of Escherichia coli [My Copy] Journal of Molecular Biology (23 June 2009) by Sandeep Krishna, László Orosz, Kim Sneppen, Sankar Adhya, Szabolcs Semsey posted to bacteria e_coli gene_regulation mathematical_model metabolism operon signaling by jjray on 2009-08-10 17:36:51 as
	Stabilized gene duplication enables long-term selection-free heterologous pathway expression [My Copy] Nat Biotech, Vol. 27, No. 8. (August 2009), pp. 760-765. by Keith E. J. Tyo, Parayil K. Ajikumar, Gregory Stephanopoulos posted to e_coli gene_duplication homologous_recombination selection systems_engineering by biomcgary on 2009-08-07 17:36:03 as along with 1 person abhishek_tiwari
	Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli [My Copy] Genome Biology, Vol. 9, No. 1. (07 January 2008), R4. by Morgan Price, Paramvir Dehal, Adam Arkin posted to convergent_evolution e_coli gene_duplication horizontal_gene_transfer operon parallel_evolution paralog transcription_factor transcription_factor_binding_site by biomcgary on 2009-08-03 21:49:27 as along with 1 person erel10
	Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli [My Copy] Biophysical Journal, Vol. 83, No. 3. (September 2002), pp. 1331-1340. by R. Mahadevan, J. Edwards, F. Doyleiii posted to balance dynamics e_coli fba flux growth in_silico network networks stoichiometry by winterstream on 2009-07-28 15:13:54 as along with 1 person yujiangwang
	Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions [My Copy] BMC Bioinformatics, Vol. 1, No. 1. (2000), pp. 1-1. by Jeremy S. Edwards, Bernhard O. Palsson posted to balance e_coli fba flux graph growth metabolic network networks by winterstream on 2009-07-23 20:12:49 as along with 2 people and 2 groups icases raiyar steinmetzlab TNT
	Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. [My Copy] Applied and environmental microbiology, Vol. 60, No. 10. (1 October 1994), pp. 3724-3731. by A. Varma, B. O. Palsson posted to e_coli fba flux growth metabolic stoichiometry by winterstream on 2009-07-20 11:07:47 as along with 2 people JeremyZucker madhadron
	Adaptive prediction of environmental changes by microorganisms [My Copy] Nature, Vol. 460, No. 7252. (17 June 2009), pp. 220-224. by Amir Mitchell, Gal H. Romano, Bella Groisman, et al.Avihu Yona, Erez Dekel, Martin Kupiec, Orna Dahan, Yitzhak Pilpel posted to adaptation e_coli environmental_sensing evolution learning by biomcgary on 2009-07-16 21:46:40 as along with 8 people and 1 group yyfwuhan kinestetika sriesenfeld timotay izuleta djkt jjray michaelbarton iSEEM
	High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 30. (15 July 2009), pp. 12412-12417. by Sujay Chattopadhyay, Scott J. Weissman, Vladimir N. Minin, Thomas A. Russo, Daniel E. Dykhuizen, Evgeni V. Sokurenko posted to bacteria e_coli evolution mutation by jjray on 2009-07-16 16:50:55 as along with 2 people jasontsai zwang
	Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy [My Copy] PLoS Biol, Vol. 7, No. 6. (23 June 2009), e1000137. by Derek Greenfield, Ann L. McEvoy, Hari Shroff, et al.Gavin E. Crooks, Ned S. Wingreen, Eric Betzig, Jan Liphardt posted to bacteria chemotaxis e_coli protein_interactions signaling by jjray on 2009-07-01 17:10:58 as along with 4 people tomd66 schmidtm robfsouza dbikard
	Functional Characterization in Vitro of All Two-component Signal Transduction Systems from Escherichia coli [My Copy] J. Biol. Chem., Vol. 280, No. 2. (14 January 2005), pp. 1448-1456. by Kaneyoshi Yamamoto, Kiyo Hirao, Taku Oshima, Hirofumi Aiba, Ryutaro Utsumi, Akira Ishihama posted to bacteria crosstalk e_coli phobr phopq two-component_system by jjray on 2009-06-15 18:47:26 as
	Chaperonin overexpression promotes genetic variation and enzyme evolution. [My Copy] Nature, Vol. 459, No. 7247. (4 June 2009), pp. 668-673. by Nobuhiko Tokuriki, Dan S. Tawfik posted to bacteria e_coli evolution protein_folding stability by jjray on 2009-06-03 21:33:24 as along with 3 people yyfwuhan absterga zwang
	Mutual Information between Input and Output Trajectories of Biochemical Networks [My Copy] Physical Review Letters, Vol. 102, No. 21. (2009), 218101. by Filipe Tostevin, Pieter R. ten Wolde posted to bacteria biochemistry chemotaxis e_coli information network signaling by jjray on 2009-05-29 20:33:51 as
	Differential Affinity and Catalytic Activity of CheZ in <italic>E. coli</italic> Chemotaxis [My Copy] PLoS Comput Biol, Vol. 5, No. 5. (8 May 2009), e1000378. by Siebe B. van Albada, Pieter R. ten Wolde edited by Christopher Rao posted to bacteria chemotaxis e_coli phosphorylation signaling two-component_system by jjray on 2009-05-29 16:44:25 as
	Synthetic Gene Networks That Count [My Copy] Science, Vol. 324, No. 5931. (29 May 2009), pp. 1199-1202. by Ari E. Friedland, Timothy K. Lu, Xiao Wang, David Shi, George Church, James J. Collins posted to bacteria e_coli gene_network mathematical_model synthetic_biology by jjray on 2009-05-29 16:01:17 as along with 14 people pyjamashark abhishek_tiwari mjoach myzhang reyez austin alexknight twatanab kshundyak phoenixzxl sen_cheng leliavski jbhiatt dswan
	Stochasticity in Protein Levels Drives Colinearity of Gene Order in Metabolic Operons of Escherichia coli [My Copy] PLoS Biol, Vol. 7, No. 5. (26 May 2009), e1000115. by Károly Kovács, Laurence D. Hurst, Balázs Papp posted to bacteria chromosome_organization e_coli gene_order metabolism stochastic by jjray on 2009-05-27 17:52:56 as along with 6 people elifsu emptyhb trfield dipenps pinney kentsis
	A coordinated network of transporters with overlapping specificities provides a robust survival strategy [My Copy] Proceedings of the National Academy of Sciences (18 May 2009) by Nir Tal, Shimon Schuldiner posted to antibiotics bacteria crosstalk e_coli robustness by jjray on 2009-05-22 23:20:11 as along with 2 people viktor21614 trfield
	Probing the Roles of the Two Different Dimers Mediated by the Receiver Domain of the Response Regulator PhoB [My Copy] Journal of Molecular Biology (14 April 2009) by Timothy R. Mack, Rong Gao, Ann M. Stock posted to bacteria e_coli gene_regulation phobr phosphorylation protein_binding two-component_system by jjray on 2009-05-18 20:11:39 as
	Synthesis of orthogonal transcription-translation networks [My Copy] Proceedings of the National Academy of Sciences (14 May 2009) by Wenlin An, Jason W. Chin posted to bacteria e_coli feedforward network synthetic_biology translation by jjray on 2009-05-15 17:37:24 as
	On finding minimal absent words [My Copy] BMC Bioinformatics, Vol. 10 (08 May 2009), 137. by Armando, Joao M. O. S. Rodrigues posted to dna e_coli electrostatics text_mining by lptolik on 2009-05-15 10:09:50 as along with 1 person and 1 group stajich Mycology
	Predictions from a stochastic polymer model for the MinDE dynamics in E.coli [My Copy] (13 May 2009) by Peter Borowski, Eric N. Cytrynbaum posted to bacteria biophysics e_coli oscillation polymer spatial stochastic by jjray on 2009-05-14 17:10:34 as
	Stochastic Analysis of the SOS Response in Escherichia coli [My Copy] PloS one, Vol. 4, No. 5. (8 May 2009), e5363. by Yishai Shimoni, Shoshy Altuvia, Hanah Margalit, Ofer Biham posted to stochastic sos network mixed_feedback mathematical_model gillespie_algorithm gene_regulation feedback e_coli bacteria by jjray on 2009-05-13 21:51:38 as
	Mutual information between in- and output trajectories of biochemical networks [My Copy] (4 Jan 2009) by Filipe Tostevin, Pieter posted to bacteria biochemistry e_coli information mutual_information network signaling by jjray on 2009-05-07 16:22:56 as along with 1 person akraemer
	Modeling DNA-binding of Escherichia coli sigma70 exhibits a characteristic energy landscape around strong promoters [My Copy] Nucl. Acids Res. (16 October 2007), gkm720. by Johanna Weindl, Pavol Hanus, Zaher Dawy, Juergen Zech, Joachim Hagenauer, Jakob C. Mueller posted to bacteria dna e_coli energy gene_regulation promoter sigma_factor by jjray on 2009-04-28 19:05:32 as along with 3 people and 1 group operon dpollard maximilianh EisenLab
	Does replication-induced transcription regulate synthesis of the myriad low copy number proteins of <I>Escherichia coli</I>? [My Copy] BioEssays, Vol. 17, No. 11. (1995), pp. 987-997. by Purnananda Guptasarma posted to bacteria copy_number e_coli stochastic transcription by jjray on 2009-04-27 23:17:26 as
	Coding-sequence determinants of gene expression in Escherichia coli. [My Copy] Science (New York, N.Y.), Vol. 324, No. 5924. (10 April 2009), pp. 255-258. by Grzegorz Kudla, Andrew W. Murray, David Tollervey, Joshua B. Plotkin posted to e_coli mutation transcription by absterga on 2009-04-12 19:04:46 as along with 32 people and 1 group balabu yyfwuhan dbikard kinestetika samgj dswan bpcusack emptyhb sameersoi dpsuslo8 anwazo Vincent_Rouilly kintoki erel10 michaelbarton fenghezi VGreiff ramanuja austin twatanab coela polivares rpatward lizbiogen jdbowes operon jasontsai jbhiatt jjray kshundyak zwang friendpine BergmanLab
	Phosphorylation of nitrogen regulator I (NRI) of Escherichia coli. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 85, No. 23. (December 1988), pp. 8919-8923. by V. Weiss, B. Magasanik posted to bacteria e_coli phosphorylation signaling two-component_system by jjray on 2009-03-18 20:26:17 as
	DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli [My Copy] Genome Biology, Vol. 10, No. 3. (06 March 2009), R27. by Karen Lemmens, Tijl De Bie, Thomas Dhollander, et al.Sigrid De Keersmaecker, Inge Thijs, Geert Schoofs, Ami De Weerdt, Bart De Moor, Jos Vanderleyden, Julio C. Vides, Kristof Engelen, Kathleen Marchal posted to complexity e_coli modularity regulatory_network systems_biology by biomcgary on 2009-03-17 16:57:50 as along with 5 people frohike druvus natstreet tvdbulck dolchan
	Metabolic switching in the sugar phosphotransferase system of Escherichia coli. [My Copy] Biophys J, Vol. 85, No. 2. (August 2003), pp. 744-754. by M. Thattai, B. I. Shraiman posted to bacteria bistability e_coli mathematical_model metabolism by jjray on 2009-03-03 20:51:47 as along with 1 person Norlins

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bacteria	98
two-component_system	39
gene_regulation	31
signaling	29
evolution	22
metabolism	16
network	16
feedback	13
mathematical_model	12
transcription	12
gene_expression	11
bara	10
dna_binding	10
stochastic	10
transcription_factor	10
phopq	8
synthetic_biology	8
adaptation	7
campylobacter_jejuni	7
chemotaxis	7
csra	7
enterotoxin	7
bacterial_infections	6
electrostatics	6
genome	6
phosphorylation	6
probiotics	6
transcriptional_regulation	6
atp	5
crosstalk	5
fba	5
flux	5
stress_response	5
systems_approach	5
tor	5
biophysics	4
ibd	4
mutation	4
network_motifs	4
noise	4
operon	4
promoter	4
protein-dna_interaction	4
quantitative_data	4
review	4
sigma_factor	4
stoichiometry	4
systems_biology	4
biochemistry	3
biofilm	3
dna	3
feedforward	3
gene_order	3
growth	3
kinetics	3
metabolic	3
mrna	3
persister	3
phenotypic_heterogeneity	3
positive_feedback	3
receptor	3
robustness	3
thermodynamics	3
yeast	3
bacillus_subtilis	2
balance	2
bistability	2
chromosome_organization	2
convergent_evolution	2
demand_theory	2
dna_looping	2
eucariotic_transcription_regulation	2
evolutionary_dynamics	2
gene_duplication	2
gillespie_algorithm	2
glt-1	2
hela	2
homologous_recombination	2
in_silico	2
information	2
kinematics	2
microarray	2
modularity	2
networks	2
palsson	2
phobr	2
population_genetics	2
protein_binding	2
protein_interactions	2
selection	2
simulation	2
sos	2
supercoiling	2
systems_engineering	2
thermodynamic	2
tk2420	2
transcriptional_regulatory_complex	2
translation	2
gltph	1
multiscale	1

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