akraemer's library 72 articles Export

	On schemes of combinatorial transcription logic [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 9. (29 April 2003), pp. 5136-5141. by Nicolas E. Buchler, Ulrich Gerland, Terence Hwa posted to transcriptional_regulation combinatorial_regulation by akraemer on 2009-10-10 00:41:25 as along with 6 people and 1 group dbikard jjray siebert balajis olympos discreteonyxorb Synthetic Biology
	Information flow and optimization in transcriptional regulation [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 34. (26 August 2008), pp. 12265-12270. by Gašper Tkačik, Curtis G. Callan, William Bialek posted to aps2009 information transcriptional_regulation by akraemer on 2009-03-31 19:35:38 as along with 5 people TRHvidsten bshkspr vkwn jjray roys
	Reverse engineering of regulatory networks in human B cells. [My Copy] Nat Genet (20 March 2005) by Katia Basso, Adam A A. Margolin, Gustavo Stolovitzky, Ulf Klein, Riccardo Dalla-Favera, Andrea Califano posted to b_cells immune_system by akraemer on 2009-03-23 16:48:26 as along with 12 people Neeperando verdicchio ggallone snuppepuppan kentsis dragonrez jfr wnpx raiyar naegele heliopais lylu
	ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. [My Copy] BMC Bioinformatics, Vol. 7 Suppl 1 (2006) by A. A. Margolin, I. Nemenman, K. Basso, et al.C. Wiggins, G. Stolovitzky, R. Dalla Favera, A. Califano posted to biological_network information by akraemer on 2009-03-23 16:33:14 as along with 18 people frohike dolchan tonamswish Neeperando APRegier verdicchio behindtherabbit kaarsinogen mbehbah1 druvus giovenko ptrobajo kentsis tmmurali jfr shigepong natstreet heliopais
	Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size [My Copy] Mol Syst Biol, Vol. 4 (2008) by Jingshan Zhang, Sergei Maslov, Eugene I. Shakhnovich posted to aps2009 protein_binding by akraemer on 2009-03-22 03:56:40 as along with 7 people kiekyon TRHvidsten jjray grahamc Ema zwang biehl
	Simple probabilistic algorithm for detecting community structure [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 3. (2009), 036111. by Wei Ren, Guiying Yan, Xiaoping Liao, Lan Xiao posted to network_modularity networks by akraemer on 2009-03-22 03:49:26 as along with 1 person deanmalmgren
	Nucleocytoplasmic transport: a thermodynamic mechanism [My Copy] (15 Mar 2009) by R. B. Kopito, M. Elbaum posted to cellular_transport by akraemer on 2009-03-22 03:47:35 as
	A logical analysis of T cell activation and anergy [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 7. (30 March 1999), pp. 3894-3899. by Marcelle Kaufman, Fabienne Andris, Oberdan Leo posted to aps2009 boolean_networks t_cells by akraemer on 2009-03-22 03:28:45 as
	Network model of survival signaling in large granular lymphocyte leukemia [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 42. (21 October 2008), pp. 16308-16313. by Ranran Zhang, Mithun V. Shah, Jun Yang, et al.Susan B. Nyland, Xin Liu, Jong K. Yun, Réka Albert, Thomas P. Loughran posted to aps2009 boolean_networks t_cells by akraemer on 2009-03-22 02:53:55 as along with 1 person vvoorr
	Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli [My Copy] PLoS Comput Biol, Vol. 3, No. 10. (5 October 2007), e192. by Osbaldo Resendis-Antonio, Jennifer L. Reed, Sergio Encarnación, Julio Collado-Vides, Bernhard Palsson posted to aps2009 flux_balance_analysis metabolic_network by akraemer on 2009-03-22 02:47:39 as along with 1 person schwartzjmc
	Self-Assembly and Evolution of Homomeric Protein Complexes [My Copy] Physical Review Letters, Vol. 102, No. 11. (2009), 118106. by Gabriel Villar, Alex W. Wilber, Alex J. Williamson, et al.Parvinder Thiara, Jonathan P. K. Doye, Ard A. Louis, Mara N. Jochum, Anna C. F. Lewis, Emmanuel D. Levy posted to self_assembly by akraemer on 2009-03-22 02:33:58 as along with 2 people robfsouza kshundyak
	Elongation dynamics shape bursty transcription and translation [My Copy] Proceedings of the National Academy of Sciences (5 February 2009) by Maciej Dobrzyński, Frank J. Bruggeman posted to transcriptional_regulation by akraemer on 2009-03-14 00:08:44 as along with 2 people ocs jjray
	Random hypergraphs and their applications [My Copy] (3 Mar 2009) by Gourab Ghoshal, Vinko Zlatic, Guido Caldarelli, M. E. J. Newman posted to network by akraemer on 2009-03-14 00:06:24 as along with 3 people Borelli striborcumez Bolozna
	Communities in Networks [My Copy] (9 Sep 2009) by Mason A. Porter, Jukka-Pekka Onnela, Peter J. Mucha posted to network by akraemer on 2009-03-14 00:04:44 as along with 11 people acrmartins apocapoc Borelli rst macc lawraga dpf Bolozna deanmalmgren rrbarb vtraag
	Symbolic Dynamics of Biological Feedback Networks [My Copy] Physical Review Letters, Vol. 102, No. 8. (2009) by Simone Pigolotti, Sandeep Krishna, Mogens H. Jensen posted to biological_network by akraemer on 2009-02-26 19:31:35 as
	Quantitative analysis of virus and plasmid trafficking in cells [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 1. (2009) by Thibault Lagache, Emmanuel Dauty, David Holcman posted to virus by akraemer on 2009-01-30 00:08:49 as along with 2 people usschwarz kshundyak
	Computational Modeling of the Hematopoietic Erythroid-Myeloid Switch Reveals Insights into Cooperativity, Priming, and Irreversibility [My Copy] PLoS Comput Biol, Vol. 5, No. 1. (23 January 2009), e1000268. by Vijay Chickarmane, Tariq Enver, Carsten Peterson posted to cell_fate development by akraemer on 2009-01-24 03:08:41 as along with 2 people balabu samubernard
	Replicator equations and the principle of minimal production of information [My Copy] (16 Jan 2009) by Georgiy P. Karev posted to information by akraemer on 2009-01-22 00:44:47 as
	Nucleosome-mediated cooperativity between transcription factors [My Copy] (19 Jan 2009) by Leonid A. Mirny posted to transcriptional_regulation by akraemer on 2009-01-22 00:34:19 as along with 1 person emptyhb
	Adaptively inferring human transcriptional subnetworks [My Copy] Mol Syst Biol, Vol. 2 (6 June 2006) by Debopriya Das, Zaher Nahle, Michael Q. Zhang posted to transcriptional_regulation by akraemer on 2009-01-16 22:57:13 as along with 5 people tmmurali wnpx Ao_Li2007 kmdaily heliopais
	Rare event simulation for T-cell activation [My Copy] (15 Jan 2009) by Florian Lipsmeier, Ellen Baake posted to immune_system by akraemer on 2009-01-16 17:53:23 as
	Genetic reconstruction of a functional transcriptional regulatory network. [My Copy] Nat Genet (8 April 2007) by Zhanzhi Hu, Patrick J J. Killion, Vishwanath R R. Iyer posted to transcriptional_regulation by akraemer on 2009-01-07 23:17:53 as along with 15 people and 6 groups sergiun TheresaNiederberger behindtherabbit ptrobajo dpollard xico nickluscombe zwang lizabeth dejori xingxu naegele czeller mapplab siebert Bioinformatics EisenLab WetBiology EBI-regulation ic4 generif_paper
	Spin glasses and fragile glasses: Statics, dynamics, and complexity [My Copy] Vol. 103, No. 21. (23 May 2006), pp. 7948-7955. by Giorgio Parisi posted to spin_glasses by akraemer on 2009-01-07 21:38:24 as
	Information-theoretic approach to the study of control systems [My Copy] Physica A: Statistical Mechanics and its Applications, Vol. 331, No. 1-2. (01 January 2004), pp. 140-172. by H. Touchette, S. Lloyd posted to information by akraemer on 2009-01-07 21:30:39 as
	How mammalian transcriptional repressors work. [My Copy] European journal of biochemistry / FEBS, Vol. 271, No. 14. (July 2004), pp. 2855-2862. by G. Thiel, M. Lietz, M. Hohl posted to transcriptional_regulation by akraemer on 2009-01-07 21:27:42 as
	Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis [My Copy] Physical Review Letters, Vol. 77, No. 9. (1996), 1905. by Monique M. Tirion posted to gaussian_network_model by akraemer on 2009-01-07 21:25:10 as along with 4 people and 1 group abovell joseph_x_zhou aqeel Diego_Prada protein_Dyn
	Role of Reversibility in Viral Capsid Growth: A Paradigm for Self-Assembly [My Copy] Physical Review Letters, Vol. 101, No. 18. (2008) by D. C. Rapaport posted to self_assembly by akraemer on 2009-01-07 19:50:45 as along with 3 people kshundyak janwedekind paulschlesinger
	Physical Limits on Computation by Assemblies of Allosteric Proteins [My Copy] Physical Review Letters, Vol. 101, No. 17. (2008) by John M. Robinson posted to protein_binding by akraemer on 2009-01-07 19:24:27 as
	Likelihood method and Fisher information in construction of physical models [My Copy] (21 Nov 2008) by E. W. Piotrowski, J. Sladkowski, J. Syska, S. Zajac posted to information by akraemer on 2009-01-07 19:21:50 as along with 1 person jarekadam
	Temporal Analysis of Active and Passive Transport in Living Cells [My Copy] Physical Review Letters, Vol. 101, No. 24. (2008) by Delphine Arcizet, Börn Meier, Erich Sackmann, Joachim O. Rädler, Doris Heinrich posted to cellular_transport by akraemer on 2009-01-07 19:17:54 as along with 1 person kshundyak
	Extinction and resurrection in gene networks [My Copy] Proceedings of the National Academy of Sciences (25 November 2008) by Daniel Schultz, Aleksandra M. Walczak, José N. Onuchic, Peter G. Wolynes posted to networks transcriptional_regulation by akraemer on 2009-01-07 19:11:56 as along with 3 people jjray kshundyak stk
	Malleable machines in transcription regulation: the mediator complex. [My Copy] PLoS computational biology, Vol. 4, No. 12. (December 2008) by A. Tóth-Petróczy, C. J. Oldfield, I. Simon, et al.Y. Takagi, A. K. Dunker, V. N. Uversky, M. Fuxreiter posted to transcriptional_regulation combinatorial_regulation by akraemer on 2009-01-07 19:03:45 as along with 2 people siebert chad_davis
	Fundamentally different strategies for transcriptional regulation are revealed by information-theoretical analysis of binding motifs [My Copy] (21 Jan 2009) by Leonid A. Mirny, Zeba Wunderlich posted to transcriptional_regulation combinatorial_regulation by akraemer on 2009-01-07 18:57:42 as along with 3 people emptyhb chrn jjray
	Dynamics and Modular Structure in Networks [My Copy] (9 Dec 2008) by R. Lambiotte, J. C. Delvenne, M. Barahona posted to network_modularity by akraemer on 2009-01-07 18:54:45 as along with 2 people vtraag spool
	Mutual information between in- and output trajectories of biochemical networks [My Copy] (4 Jan 2009) by Filipe Tostevin, Pieter posted to information network by akraemer on 2009-01-07 17:48:10 as along with 1 person jjray
	Identification of direct residue contacts in protein–protein interaction by message passing [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 1. (6 January 2009), pp. 67-72. by Martin Weigt, Robert A. White, Hendrik Szurmant, James A. Hoch, Terence Hwa posted to protein_binding protein_structure by akraemer on 2009-01-07 17:45:34 as along with 6 people and 2 groups orr cactus haisent sobolevnrm sjcockell hmk KeatingJClub baker-group
	A gene regulatory network in mouse embryonic stem cells. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 42. (16 October 2007), pp. 16438-16443. by Q. Zhou, H. Chipperfield, D. A. Melton, W. H. Wong posted to reprogramming by akraemer on 2009-01-06 19:45:35 as along with 1 person FJ
	Reprogramming stem cells is a microenvironmental task [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 41. (14 October 2008), pp. 15637-15638. by Mina J. Bissell, Jamie Inman posted to reprogramming by akraemer on 2009-01-06 19:34:24 as along with 1 person inesdesantiago
	Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks [My Copy] Proceedings of the National Academy of Sciences (25 November 2008) by Avi Ma'ayan, Guillermo A. Cecchi, John Wagner, Ravi A. Rao, Ravi Iyengar, Gustavo Stolovitzky posted to networks by akraemer on 2009-01-06 19:14:23 as along with 5 people jmenche schwartzjmc sg45653 grahamc jjray
	On the origin and highly likely completeness of single-domain protein structures. [My Copy] Proc Natl Acad Sci U S A, Vol. 103, No. 8. (21 February 2006), pp. 2605-2610. by Y. Zhang, I. A. Hubner, A. K. Arakaki, E. Shakhnovich, J. Skolnick posted to protein_structure by akraemer on 2009-01-05 22:52:05 as along with 2 people nigham dgront
	Scientific Computing in the Cloud [My Copy] (31 Dec 2008) by J. J. Rehr, J. P. Gardner, M. Prange, L. Svec, F. Vila posted to cloud by akraemer on 2009-01-05 19:46:47 as along with 5 people and 1 group claudiushauptmann tnhh Vanakoji verma7 agbiotec Cloud Computing
	Identification of functional information subgraphs in complex networks. [My Copy] Physical review letters, Vol. 100, No. 23. (13 June 2008) by L. M. Bettencourt, V. Gintautas, M. I. Ham posted to information network by akraemer on 2009-01-05 05:06:59 as
	Mesoscale modeling of molecular machines: cyclic dynamics and hydrodynamical fluctuations. [My Copy] Physical review. E, Statistical, nonlinear, and soft matter physics, Vol. 77, No. 5 Pt 1. (May 2008) by A. Cressman, Y. Togashi, A. S. Mikhailov, R. Kapral posted to gaussian_network_model by akraemer on 2009-01-05 05:04:14 as
	Prediction of binding sites in receptor-ligand complexes with the Gaussian Network Model. [My Copy] Physical review letters, Vol. 100, No. 22. (6 June 2008) by T. Haliloglu, E. Seyrek, B. Erman posted to gaussian_network_model by akraemer on 2009-01-05 05:01:24 as
	Cooperativity, sensitivity, and noise in biochemical signaling. [My Copy] Physical review letters, Vol. 100, No. 25. (27 June 2008) by W. Bialek, S. Setayeshgar posted to noise by akraemer on 2009-01-05 04:58:02 as
	Functional modularity in a large-scale mammalian molecular interaction network [My Copy] Computational Systems Bioinformatics Conference, 2005. Workshops and Poster Abstracts. IEEE In Computational Systems Bioinformatics Conference, 2005. Workshops and Poster Abstracts. IEEE (2005), pp. 161-163. by A. Kramer, D. R. Richards, J. O. Bowlby, R. M. Felciano posted to network_modularity by akraemer on 2009-01-04 01:04:35 as
	Fast 3D molecular superposition and similarity search in databases of flexible molecules [My Copy] Journal of Computer-Aided Molecular Design, Vol. 17, No. 1. (1 January 2003), pp. 13-38. by Andreas Krämer, Hans W. Horn, Julia E. Rice posted to molecular_similarity by akraemer on 2009-01-04 01:04:15 as
	FLASHFLOOD: A 3D Field-based similarity search and alignment method for flexible molecules [My Copy] Journal of Computer-Aided Molecular Design, Vol. 15, No. 7. (1 July 2001), pp. 587-612. by Michael C. Pitman, Wolfgang K. Huber, Hans Horn, Andreas Krämer, Julia E. Rice, William C. Swope posted to molecular_similarity by akraemer on 2009-01-04 01:03:43 as
	Superinsulator Phase of Two-Dimensional Superconductors [My Copy] Physical Review Letters, Vol. 81, No. 16. (19 October 1998), 3523. by A. Krämer, S. Doniach posted to superinsulator by akraemer on 2009-01-04 01:03:12 as
	Entanglement of flux lines in superconductors with finite thickness [My Copy] Physica C: Superconductivity, Vol. 309, No. 1-2. (1 December 1998), pp. 33-38. by A. Krämer posted to vortices superconductor by akraemer on 2009-01-04 01:02:50 as

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transcriptional_regulation	10
information	8
superconductor	8
reprogramming	7
vortices	7
aps2009	5
cell_fate	4
network	4
protein_binding	4
combinatorial_regulation	3
development	3
gaussian_network_model	3
immune_system	3
network_modularity	3
networks	3
biological_network	2
boolean_networks	2
cellular_transport	2
chemical_physics	2
density_functional	2
molecular_similarity	2
protein_structure	2
self_assembly	2
t_cells	2
b_cells	1
causality	1
cloud	1
digital_library	1
flux_balance_analysis	1
metabolic_network	1
noise	1
spin_glasses	1
stochastic_simulation	1
superinsulator	1
virus	1

akraemer's library 72 articles Export

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