Volume 6

Molecular Systems Biology

Volume 6

1

Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data

Choi, Hyungwon, Kim, Sinae, Gingras, Anne-Claude, Nesvizhskii, Alexey I

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.62 MB

english, 2010

2

Epistatic relationships reveal the functional organization of yeast transcription factors

Zheng, Jiashun, Benschop, Joris J, Shales, Michael, Kemmeren, Patrick, Greenblatt, Jack, Cagney, Gerard, Holstege, Frank, Li, Hao, Krogan, Nevan J

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 3.58 MB

english, 2010

3

Different sets of QTLs influence fitness variation in yeast

Romano, Gal Hagit, Gurvich, Yonat, Lavi, Ofer, Ulitsky, Igor, Shamir, Ron, Kupiec, Martin

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.10 MB

english, 2010

4

A systematic screen for protein–lipid interactions in Saccharomyces cerevisiae

Gallego, Oriol, Betts, Matthew J, Gvozdenovic-Jeremic, Jelena, Maeda, Kenji, Matetzki, Christian, Aguilar-Gurrieri, Carmen, Beltran-Alvarez, Pedro, Bonn, Stefan, Fernández-Tornero, Carlos, Jensen, Lar

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.65 MB

english, 2010

5

Target mRNA abundance dilutes microRNA and siRNA activity

Arvey, Aaron, Larsson, Erik, Sander, Chris, Leslie, Christina S, Marks, Debora S

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 435 KB

english, 2010

6

Networking the nucleus

Rajapakse, Indika, Scalzo, David, Tapscott, Stephen J, Kosak, Steven T, Groudine, Mark

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.65 MB

english, 2010

7

The endocannabinoid system links gut microbiota to adipogenesis

Muccioli, Giulio G, Naslain, Damien, Bäckhed, Fredrik, Reigstad, Christopher S, Lambert, Didier M, Delzenne, Nathalie M, Cani, Patrice D

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 3.78 MB

english, 2010

8

Patterns of basal signaling heterogeneity can distinguish cellular populations with different drug sensitivities

Singh, Dinesh Kumar, Ku, Chin-Jen, Wichaidit, Chonlarat, Steininger, Robert J, Wu, Lani F, Altschuler, Steven J

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.11 MB

english, 2010

9

DamID in C. elegans reveals longevity-associated targets of DAF-16/FoxO

Schuster, Eugene, McElwee, Joshua J, Tullet, Jennifer M A, Doonan, Ryan, Matthijssens, Filip, Reece-Hoyes, John S, Hope, Ian A, Vanfleteren, Jacques R, Thornton, Janet M, Gems, David

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 719 KB

english, 2010

10

Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana

Van Leene, Jelle, Hollunder, Jens, Eeckhout, Dominique, Persiau, Geert, Van De Slijke, Eveline, Stals, Hilde, Van Isterdael, Gert, Verkest, Aurine, Neirynck, Sandy, Buffel, Yelle, De Bodt, Stefanie, M

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.74 MB

english, 2010

11

Reconstruction annotation jamborees: a community approach to systems biology

Thiele, Ines, Palsson, Bernhard Ø

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 623 KB

english, 2010

12

Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control

Jiao, Yuling, Meyerowitz, Elliot M

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.45 MB

english, 2010

13

Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model

Pokhilko, Alexandra, Hodge, Sarah K, Stratford, Kevin, Knox, Kirsten, Edwards, Kieron D, Thomson, Adrian W, Mizuno, Takeshi, Millar, Andrew J

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 495 KB

english, 2010

14

A comprehensive map of the mTOR signaling network

Caron, Etienne, Ghosh, Samik, Matsuoka, Yukiko, Ashton-Beaucage, Dariel, Therrien, Marc, Lemieux, Sébastien, Perreault, Claude, Roux, Philippe P, Kitano, Hiroaki

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 38.40 MB

english, 2010

15

A comprehensive molecular interaction map of the budding yeast cell cycle

Kaizu, Kazunari, Ghosh, Samik, Matsuoka, Yukiko, Moriya, Hisao, Shimizu-Yoshida, Yuki, Kitano, Hiroaki

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 17.00 MB

english, 2010

16

A diffusion-based neurite length-sensing mechanism involved in neuronal symmetry breaking

Toriyama, Michinori, Sakumura, Yuichi, Shimada, Tadayuki, Ishii, Shin, Inagaki, Naoyuki

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 6.09 MB

english, 2010

17

A modular gradient-sensing network for chemotaxis in Escherichia coli revealed by responses to time-varying stimuli

Shimizu, Thomas S, Tu, Yuhai, Berg, Howard C

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 712 KB

english, 2010

18

microRNA-122 as a regulator of mitochondrial metabolic gene network in hepatocellular carcinoma

Burchard, Julja, Zhang, Chunsheng, Liu, Angela M, Poon, Ronnie T P, Lee, Nikki P Y, Wong, Kwong-Fai, Sham, Pak C, Lam, Brian Y, Ferguson, Mark D, Tokiwa, George, Smith, Ryan, Leeson, Brendan, Beard, R

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.00 MB

english, 2010

19

Metabonomic, transcriptomic, and genomic variation of a population cohort

Inouye, Michael, Kettunen, Johannes, Soininen, Pasi, Silander, Kaisa, Ripatti, Samuli, Kumpula, Linda S, Hämäläinen, Eija, Jousilahti, Pekka, Kangas, Antti J, Männistö, Satu, Savolainen, Markku J, Jul

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.02 MB

english, 2010

20

HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology

Gille, Christoph, Bölling, Christian, Hoppe, Andreas, Bulik, Sascha, Hoffmann, Sabrina, Hübner, Katrin, Karlstädt, Anja, Ganeshan, Ramanan, König, Matthias, Rother, Kristian, Weidlich, Michael, Behre,

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 13.53 MB

english, 2010

21

Emergent cooperation in microbial metabolism

Wintermute, Edwin H, Silver, Pamela A

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 772 KB

english, 2010

22

Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli

Goodarzi, Hani, Bennett, Bryson D, Amini, Sasan, Reaves, Marshall L, Hottes, Alison K, Rabinowitz, Joshua D, Tavazoie, Saeed

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.93 MB

english, 2010

23

A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion

Sommer, Morten OA, Church, George M, Dantas, Gautam

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 798 KB

english, 2010

24

Metabolomic and transcriptomic stress response of Escherichia coli

Jozefczuk, Szymon, Klie, Sebastian, Catchpole, Gareth, Szymanski, Jedrzej, Cuadros-Inostroza, Alvaro, Steinhauser, Dirk, Selbig, Joachim, Willmitzer, Lothar

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.30 MB

english, 2010

25

Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli

Atsumi, Shota, Wu, Tung-Yun, Machado, Iara M P, Huang, Wei-Chih, Chen, Pao-Yang, Pellegrini, Matteo, Liao, James C

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.76 MB

english, 2010

26

Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism

Jerby, Livnat, Shlomi, Tomer, Ruppin, Eytan

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.36 MB

english, 2010

27

A side effect resource to capture phenotypic effects of drugs

Kuhn, Michael, Campillos, Monica, Letunic, Ivica, Jensen, Lars Juhl, Bork, Peer

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 503 KB

english, 2010

28

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

Lewis, Nathan E, Hixson, Kim K, Conrad, Tom M, Lerman, Joshua A, Charusanti, Pep, Polpitiya, Ashoka D, Adkins, Joshua N, Schramm, Gunnar, Purvine, Samuel O, Lopez-Ferrer, Daniel, Weitz, Karl K, Eils,

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.02 MB

english, 2010

29

Dynamic interaction networks in a hierarchically organized tissue

Kirouac, Daniel C, Ito, Caryn, Csaszar, Elizabeth, Roch, Aline, Yu, Mei, Sykes, Edward A, Bader, Gary D, Zandstra, Peter W

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.41 MB

english, 2010

30

Modelling and experimental analysis of hormonal crosstalk in Arabidopsis

Liu, Junli, Mehdi, Saher, Topping, Jennifer, Tarkowski, Petr, Lindsey, Keith

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 999 KB

english, 2010

31

Dynamics within the CD95 death-inducing signaling complex decide life and death of cells

Neumann, Leo, Pforr, Carina, Beaudouin, Joel, Pappa, Alexander, Fricker, Nicolai, Krammer, Peter H, Lavrik, Inna N, Eils, Roland

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 3.21 MB

english, 2010

32

A model of yeast cell-cycle regulation based on multisite phosphorylation

Barik, Debashis, Baumann, William T, Paul, Mark R, Novak, Bela, Tyson, John J

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.26 MB

english, 2010

33

A tunable dual-promoter integrator for targeting of cancer cells

Nissim, Lior, Bar-Ziv, Roy H

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1006 KB

english, 2010

34

Cooperation and Hamilton's rule in a simple synthetic microbial system

Chuang, John S, Rivoire, Olivier, Leibler, Stanislas

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 360 KB

english, 2010

35

Chromatin regulators as capacitors of interspecies variations in gene expression

Tirosh, Itay, Reikhav, Sharon, Sigal, Nadejda, Assia, Yael, Barkai, Naama

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 576 KB

english, 2010

36

Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch

Lou, Chunbo, Liu, Xili, Ni, Ming, Huang, Yiqi, Huang, Qiushi, Huang, Longwen, Jiang, Lingli, Lu, Dan, Wang, Mingcong, Liu, Chang, Chen, Daizhuo, Chen, Chongyi, Chen, Xiaoyue, Yang, Le, Ma, Haisu, Chen

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.75 MB

english, 2010

37

Evolving a robust signal transduction pathway from weak cross-talk

Siryaporn, Albert, Perchuk, Barrett S, Laub, Michael T, Goulian, Mark

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.49 MB

english, 2010

38

GroEL dependency affects codon usage—support for a critical role of misfolding in gene evolution

Warnecke, Tobias, Hurst, Laurence D

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.83 MB

english, 2010

39

Design principles of nuclear receptor signaling: how complex networking improves signal transduction

Kolodkin, Alexey N, Bruggeman, Frank J, Plant, Nick, Moné, Martijn J, Bakker, Barbara M, Campbell, Moray J, van Leeuwen, Johannes P T M, Carlberg, Carsten, Snoep, Jacky L, Westerhoff, Hans V

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1013 KB

english, 2010

40

Emergence of tissue polarization from synergy of intracellular and extracellular auxin signaling

Wabnik, Krzysztof, Kleine-Vehn, Jürgen, Balla, Jozef, Sauer, Michael, Naramoto, Satoshi, Reinöhl, Vilém, Merks, Roeland M H, Govaerts, Willy, Friml, Jiří

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 4.40 MB

english, 2010

41

Defining the budding yeast chromatin-associated interactome

Lambert, Jean-Philippe, Fillingham, Jeffrey, Siahbazi, Mojgan, Greenblatt, Jack, Baetz, Kristin, Figeys, Daniel

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.77 MB

english, 2010

42

Defining the transcriptome and proteome in three functionally different human cell lines

Lundberg, Emma, Fagerberg, Linn, Klevebring, Daniel, Matic, Ivan, Geiger, Tamar, Cox, Juergen, Älgenäs, Cajsa, Lundeberg, Joakim, Mann, Matthias, Uhlen, Mathias

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 574 KB

english, 2010

43

Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action

Kapitzky, Laura, Beltrao, Pedro, Berens, Theresa J, Gassner, Nadine, Zhou, Chunshui, Wüster, Arthur, Wu, Julie, Babu, M Madan, Elledge, Stephen J, Toczyski, David, Lokey, R Scott, Krogan, Nevan J

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.83 MB

english, 2010

44

Integrative model of genomic factors for determining binding site selection by estrogen receptor-α

Joseph, Roy, Orlov, Yuriy L, Huss, Mikael, Sun, Wenjie, Li Kong, Say, Ukil, Leena, Fu Pan, You, Li, Guoliang, Lim, Michael, Thomsen, Jane S, Ruan, Yijun, Clarke, Neil D, Prabhakar, Shyam, Cheung, Edwi

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.67 MB

english, 2010

45

mRNA turnover rate limits siRNA and microRNA efficacy

Larsson, Erik, Sander, Chris, Marks, Debora

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 151 KB

english, 2010

46

Single-gene tuning of Caulobacter cell cycle period and noise, swarming motility, and surface adhesion

Lin, Yihan, Crosson, Sean, Scherer, Norbert F

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.67 MB

english, 2010

47

Nonsense-mediated decay targets have multiple sequence-related features that can inhibit translation

Zhang, Zhenguo, Zhou, Li, Hu, Landian, Zhu, Yufei, Xu, Heng, Liu, Yang, Chen, Xianfen, Yi, Xianfu, Kong, Xiangyin, Hurst, Laurence D

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 638 KB

english, 2010

48

Bacterial adaptation through distributed sensing of metabolic fluxes

Kotte, Oliver, Zaugg, Judith B, Heinemann, Matthias

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 738 KB

english, 2010

49

Feedback between p21 and reactive oxygen production is necessary for cell senescence

Passos, João F, Nelson, Glyn, Wang, Chunfang, Richter, Torsten, Simillion, Cedric, Proctor, Carole J, Miwa, Satomi, Olijslagers, Sharon, Hallinan, Jennifer, Wipat, Anil, Saretzki, Gabriele, Rudolph, K

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 5.33 MB

english, 2010

50

Inferring condition-specific transcription factor function from DNA binding and gene expression data

McCord, Rachel Patton, Berger, Michael F, Philippakis, Anthony A, Bulyk, Martha L

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 730 KB

english, 2010

51

mRNA turnover rate limits siRNA and microRNA efficacy

Larsson, Erik, Sander, Chris, Marks, Debora

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 525 KB

english, 2010

52

Metabolism gets lucky

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 183 KB

english, 2010

53

Global coordination of transcriptional control and mRNA decay during cellular differentiation

Amorim, Maria J, Cotobal, Cristina, Duncan, Caia, Mata, Juan

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.83 MB

english, 2010

54

Control of ATP homeostasis during the respiro-fermentative transition in yeast

Walther, Thomas, Novo, Maite, Rössger, Katrin, Létisse, Fabien, Loret, Marie-Odile, Portais, Jean-Charles, François, Jean-Marie

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 5.62 MB

english, 2010

55

Short-term memory in gene induction reveals the regulatory principle behind stochastic IL-4 expression

Mariani, Luca, Schulz, Edda G, Lexberg, Maria H, Helmstetter, Caroline, Radbruch, Andreas, Löhning, Max, Höfer, Thomas

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.19 MB

english, 2010

56

Ecological distribution and population physiology defined by proteomics in a natural microbial community

Mueller, Ryan S, Denef, Vincent J, Kalnejais, Linda H, Suttle, K Blake, Thomas, Brian C, Wilmes, Paul, Smith, Richard L, Nordstrom, D Kirk, McCleskey, R Blaine, Shah, Manesh B, VerBerkmoes, Nathan C,

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.01 MB

english, 2010

57

Develop reusable and combinable designs for transcriptional logic gates

Zhan, Jian, Ding, Bo, Ma, Rui, Ma, Xiaoyu, Su, Xiaofeng, Zhao, Yun, Liu, Ziqing, Wu, Jiarui, Liu, Haiyan

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 426 KB

english, 2010

58

Connecting cell fate decision networks in hematopoeisis from the outside in

Gaudet, Suzanne

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 302 KB

english, 2010

59

Molecular characterization of the evolution of phagosomes

Boulais, Jonathan, Trost, Matthias, Landry, Christian R, Dieckmann, Régis, Levy, Emmanuel D, Soldati, Thierry, Michnick, Stephen W, Thibault, Pierre, Desjardins, Michel

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 3.74 MB

english, 2010

60

Genetic interactions reveal the evolutionary trajectories of duplicate genes

VanderSluis, Benjamin, Bellay, Jeremy, Musso, Gabriel, Costanzo, Michael, Papp, Balázs, Vizeacoumar, Franco J, Baryshnikova, Anastasia, Andrews, Brenda, Boone, Charles, Myers, Chad L

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 442 KB

english, 2010

61

GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome

Sekedat, Matthew D, Fenyö, David, Rogers, Richard S, Tackett, Alan J, Aitchison, John D, Chait, Brian T

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 3.04 MB

english, 2010

62

Structured digital tables on the Semantic Web: toward a structured digital literature

Cheung, Kei-Hoi, Samwald, Matthias, Auerbach, Raymond K, Gerstein, Mark B

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.96 MB

english, 2010

63

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

Bordbar, Aarash, Lewis, Nathan E, Schellenberger, Jan, Palsson, Bernhard Ø, Jamshidi, Neema

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.07 MB

english, 2010

64

Intracellular transactivation of HIV can account for the decelerating decay of virus load during drug therapy

Althaus, Christian L, De Boer, Rob J

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 4.62 MB

english, 2010

65

Understanding the physiology of Lactobacillus plantarum at zero growth

Goffin, Philippe, van de Bunt, Bert, Giovane, Marco, Leveau, Johan H J, Höppener-Ogawa, Sachie, Teusink, Bas, Hugenholtz, Jeroen

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 465 KB

english, 2010

66

Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G-protein action

Pandey, Sona, Wang, Rui-Sheng, Wilson, Liza, Li, Song, Zhao, Zhixin, Gookin, Timothy E, Assmann, Sarah M, Albert, Réka

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.70 MB

english, 2010

67

Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape

Frise, Erwin, Hammonds, Ann S, Celniker, Susan E

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 3.31 MB

english, 2010

68

Revealing a signaling role of phytosphingosine-1-phosphate in yeast

Cowart, L Ashley, Shotwell, Matthew, Worley, Mitchell L, Richards, Adam J, Montefusco, David J, Hannun, Yusuf A, Lu, Xinghua

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.17 MB

english, 2010

69

Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity

Fendt, Sarah-Maria, Buescher, Joerg Martin, Rudroff, Florian, Picotti, Paola, Zamboni, Nicola, Sauer, Uwe

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.02 MB

english, 2010

70

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers

Lefebvre, Celine, Rajbhandari, Presha, Alvarez, Mariano J, Bandaru, Pradeep, Lim, Wei Keat, Sato, Mai, Wang, Kai, Sumazin, Pavel, Kustagi, Manjunath, Bisikirska, Brygida C, Basso, Katia, Beltrao, Pedr

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.06 MB

english, 2010

71

A general lack of compensation for gene dosage in yeast

Springer, Michael, Weissman, Jonathan S, Kirschner, Marc W

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 351 KB

english, 2010

72

Chromosomal periodicity and positional networks of genes in Escherichia coli

Mathelier, Anthony, Carbone, Alessandra

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 948 KB

english, 2010

73

Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network

Arda, H Efsun, Taubert, Stefan, MacNeil, Lesley T, Conine, Colin C, Tsuda, Ben, Van Gilst, Marc, Sequerra, Reynaldo, Doucette-Stamm, Lynn, Yamamoto, Keith R, Walhout, Albertha J M

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.60 MB

english, 2010

74

Clustering phenotype populations by genome-wide RNAi and multiparametric imaging

Fuchs, Florian, Pau, Gregoire, Kranz, Dominique, Sklyar, Oleg, Budjan, Christoph, Steinbrink, Sandra, Horn, Thomas, Pedal, Angelika, Huber, Wolfgang, Boutros, Michael

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.58 MB

english, 2010

75

Automated identification of pathways from quantitative genetic interaction data

Battle, Alexis, Jonikas, Martin C, Walter, Peter, Weissman, Jonathan S, Koller, Daphne

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.81 MB

english, 2010

76

The phosphoproteome of toll-like receptor-activated macrophages

Weintz, Gabriele, Olsen, Jesper V, Frühauf, Katja, Niedzielska, Magdalena, Amit, Ido, Jantsch, Jonathan, Mages, Jörg, Frech, Cornelie, Dölken, Lars, Mann, Matthias, Lang, Roland

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 778 KB

english, 2010

77

Coordination of frontline defense mechanisms under severe oxidative stress

Kaur, Amardeep, Van, Phu T, Busch, Courtney R, Robinson, Courtney K, Pan, Min, Pang, Wyming Lee, Reiss, David J, DiRuggiero, Jocelyne, Baliga, Nitin S

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.70 MB

english, 2010

78

Pre-dispositions and epigenetic inheritance in the Escherichia coli lactose operon bistable switch

Robert, Lydia, Paul, Gregory, Chen, Yong, Taddei, François, Baigl, Damien, Lindner, Ariel B

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.16 MB

english, 2010

79

Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide

Botta, Marco, Haider, Syed, Leung, Ian X Y, Lio, Pietro, Mozziconacci, Julien

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.09 MB

english, 2010

80

Quantitative analysis of regulatory flexibility under changing environmental conditions

Edwards, Kieron D, Akman, Ozgur E, Knox, Kirsten, Lumsden, Peter J, Thomson, Adrian W, Brown, Paul E, Pokhilko, Alexandra, Kozma-Bognar, Laszlo, Nagy, Ferenc, Rand, David A, Millar, Andrew J

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 448 KB

english, 2010

81

An interdomain sector mediating allostery in Hsp70 molecular chaperones

Smock, Robert G, Rivoire, Olivier, Russ, William P, Swain, Joanna F, Leibler, Stanislas, Ranganathan, Rama, Gierasch, Lila M

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.71 MB

english, 2010

82

Impact of translational error-induced and error-free misfolding on the rate of protein evolution

Yang, Jian-Rong, Zhuang, Shi-Mei, Zhang, Jianzhi

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.59 MB

english, 2010

83

Identifying the genetic determinants of transcription factor activity

Lee, Eunjee, Bussemaker, Harmen J

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.96 MB

english, 2010

84

Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5′-phosphate synthesis

Kim, Juhan, Kershner, Jamie P, Novikov, Yehor, Shoemaker, Richard K, Copley, Shelley D

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 973 KB

english, 2010

85

A global protein–lipid interactome map

Brehme, Marc, Vidal, Marc

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 296 KB

english, 2010

86

Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences

Tirosh, Itay, Sigal, Nadejda, Barkai, Naama

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.30 MB

english, 2010

87

Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast

Fendt, Sarah-Maria, Oliveira, Ana Paula, Christen, Stefan, Picotti, Paola, Dechant, Reinhard Christoph, Sauer, Uwe

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 628 KB

english, 2010

88

Single-cell quantification of IL-2 response by effector and regulatory T cells reveals critical plasticity in immune response

Feinerman, Ofer, Jentsch, Garrit, Tkach, Karen E, Coward, Jesse W, Hathorn, Matthew M, Sneddon, Michael W, Emonet, Thierry, Smith, Kendall A, Altan-Bonnet, Grégoire

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 3.53 MB

english, 2010

89

Lysogen stability is determined by the frequency of activity bursts from the fate-determining gene

Zong, Chenghang, So, Lok-hang, Sepúlveda, Leonardo A, Skinner, Samuel O, Golding, Ido

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 725 KB

english, 2010

90

Chaperonin activity modulates codon adaptation

Han, Sangjo, Kim, Philip M

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 143 KB

english, 2010

91

Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network

Plata, Germán, Hsiao, Tzu-Lin, Olszewski, Kellen L, Llinás, Manuel, Vitkup, Dennis

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 522 KB

english, 2010

92

Systems parasitology: effects of Fasciola hepatica on the neurochemical profile in the rat brain

Saric, Jasmina, Li, Jia V, Utzinger, Jürg, Wang, Yulan, Keiser, Jennifer, Dirnhofer, Stephan, Beckonert, Olaf, Sharabiani, Mansour T A, Fonville, Judith M, Nicholson, Jeremy K, Holmes, Elaine

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.01 MB

english, 2010

93

Proteome-wide identification of mycobacterial pupylation targets

Poulsen, Christian, Akhter, Yusuf, Jeon, Amy Hye-Won, Schmitt-Ulms, Gerold, Meyer, Helmut E, Stefanski, Anja, Stühler, Kai, Wilmanns, Matthias, Song, Young-Hwa

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 802 KB

english, 2010

94

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

Vogel, Christine, de Sousa Abreu, Raquel, Ko, Daijin, Le, Shu-Yun, Shapiro, Bruce A, Burns, Suzanne C, Sandhu, Devraj, Boutz, Daniel R, Marcotte, Edward M, Penalva, Luiz O

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 961 KB

english, 2010

95

Zebrafish Pou5f1-dependent transcriptional networks in temporal control of early development

Onichtchouk, Daria, Geier, Florian, Polok, Bozena, Messerschmidt, Daniel M, Mössner, Rebecca, Wendik, Björn, Song, Sungmin, Taylor, Verdon, Timmer, Jens, Driever, Wolfgang

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 5.89 MB

english, 2010

96

Dissecting spatio-temporal protein networks driving human heart development and related disorders

Lage, Kasper, Møllgård, Kjeld, Greenway, Steven, Wakimoto, Hiroko, Gorham, Joshua M, Workman, Christopher T, Bendsen, Eske, Hansen, Niclas T, Rigina, Olga, Roque, Francisco S, Wiese, Cornelia, Christo

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.87 MB

english, 2010

97

Transcript counting in single cells reveals dynamics of rDNA transcription

Tan, Rui Zhen, van Oudenaarden, Alexander

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.09 MB

english, 2010

98

Chemical combinations elucidate pathway interactions and regulation relevant to Hepatitis C replication

Owens, Christopher M, Mawhinney, Christina, Grenier, Jill M, Altmeyer, Ralf, Lee, Margaret S, Borisy, Alexis A, Lehár, Joseph, Johansen, Lisa M

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.79 MB

english, 2010

99

Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing

Yang, Scott Cheng-Hsin, Rhind, Nicholas, Bechhoefer, John

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 790 KB

english, 2010

100

Precision and scaling in morphogen gradient read-out

Morton de Lachapelle, Aitana, Bergmann, Sven

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 442 KB

english, 2010

101

From bench to website

Lemberger, Thomas

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 93 KB

english, 2010

102

An atlas of gene regulatory networks reveals multiple three-gene mechanisms for interpreting morphogen gradients

Cotterell, James, Sharpe, James

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 3.90 MB

english, 2010

103

Quantitative analysis of the transcription control mechanism

Mao, Changhui, Brown, Christopher R, Falkovskaia, Elena, Dong, Shawfeng, Hrabeta-Robinson, Eva, Wenger, Lauren, Boeger, Hinrich

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.10 MB

english, 2010

104

Pre-steady and stable morphogen gradients: can they coexist?

Morton de Lachapelle, Aitana, Bergmann, Sven

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 99 KB

english, 2010

105

Chromatin regulators shape the genotype–phenotype map

Landry, Christian R, Rifkin, Scott A

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 201 KB

english, 2010

106

Violations of robustness trade-offs

Kitano, Hiroaki

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.54 MB

english, 2010

107

Evolutionary fates within a microbial population highlight an essential role for protein folding during natural selection

Peña, Matthew I, Davlieva, Milya, Bennett, Matthew R, Olson, John S, Shamoo, Yousif

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.03 MB

english, 2010

108

Transcriptional regulation is only half the story

Plotkin, Joshua B

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 215 KB

english, 2010

109

Towards whole-body systems physiology

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 486 KB

english, 2010

110

Dynamic CRM occupancy reflects a temporal map of developmental progression

Wilczyński, Bartek, Furlong, Eileen E M

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.40 MB

english, 2010

111

Kinase/phosphatase overexpression reveals pathways regulating hippocampal neuron morphology

Buchser, William J, Slepak, Tatiana I, Gutierrez-Arenas, Omar, Bixby, John L, Lemmon, Vance P

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 3.51 MB

english, 2010

112

Coupling governs entrainment range of circadian clocks

Abraham, Ute, Granada, Adrián E, Westermark, Pål O, Heine, Markus, Kramer, Achim, Herzel, Hanspeter

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.14 MB

english, 2010

113

Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo

Fakhouri, Walid D, Ay, Ahmet, Sayal, Rupinder, Dresch, Jacqueline, Dayringer, Evan, Arnosti, David N

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.60 MB

english, 2010

114

Nucleosome patterning evolution: steady aim despite moving targets

Hittinger, Chris Todd, Hesselberth, Jay R

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 190 KB

english, 2010

115

A sequestration feedback determines dynamics and temperature entrainment of the KaiABC circadian clock

Brettschneider, Christian, Rose, Rebecca J, Hertel, Stefanie, Axmann, Ilka M, Heck, Albert J R, Kollmann, Markus

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 535 KB

english, 2010

116

A matter of timing and precision

Jaeger, Johannes

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 102 KB

english, 2010