ALBERT — All Library Books, journals and Electronic Records Telegrafenberg

1

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Protein synthesis rate is the predominant regulator of protein expression during differentiation (2013)

Anders R Kristensen; Joerg Gsponer; Leonard J Foster

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-09-18

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.47 Authors: Anders R Kristensen, Joerg Gsponer & Leonard J Foster

Electronic ISSN: 1744-4292

Topics: Biology

Published by Springer Nature on behalf of The European Molecular Biology Organization (EMBO).

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Human disease locus discovery and mapping to molecular pathways through phylogenetic profiling (2013)

Yuval Tabach; Tamar Golan; Abrahan Hernández-Hernández; Arielle R Messer; Tomoyuki Fukuda; Anna Kouznetsova; Jian-Guo Liu; Ingrid Lilienthal; Carmit Levy; Gary Ruvkun

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-10-02

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.50 Authors: Yuval Tabach, Tamar Golan, Abrahan Hernández-Hernández, Arielle R Messer, Tomoyuki Fukuda, Anna Kouznetsova, Jian-Guo Liu, Ingrid Lilienthal, Carmit Levy & Gary Ruvkun

Electronic ISSN: 1744-4292

Topics: Biology

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3

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Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction (2013)

Edward J O’Brien; Joshua A Lerman; Roger L Chang; Daniel R Hyduke; Bernhard Ø Palsson

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-10-02

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.52 Authors: Edward J O’Brien, Joshua A Lerman, Roger L Chang, Daniel R Hyduke & Bernhard Ø Palsson

Electronic ISSN: 1744-4292

Topics: Biology

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RNAi screening reveals a large signaling network controlling the Golgi apparatus in human cells (2013)

Joanne Chia; Germaine Goh; Victor Racine; Susanne Ng; Pankaj Kumar; Frederic Bard

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-06-12

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.34 Authors: Joanne Chia, Germaine Goh, Victor Racine, Susanne Ng, Pankaj Kumar & Frederic Bard

Electronic ISSN: 1744-4292

Topics: Biology

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The HDAC interaction network (2013)

Ilana Livyatan; Eran Meshorer

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-06-12

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.33 Authors: Ilana Livyatan & Eran Meshorer

Electronic ISSN: 1744-4292

Topics: Biology

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6

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Construction of human activity-based phosphorylation networks (2013)

Robert H Newman; Jianfei Hu; Hee-Sool Rho; Zhi Xie; Crystal Woodard; John Neiswinger; Christopher Cooper; Matthew Shirley; Hillary M Clark; Shaohui Hu; Woochang Hwang; Jun Seop Jeong; George Wu; Jimmy Lin; Xinxin Gao; Qiang Ni; Renu Goel; Shuli Xia; Hongkai Ji; Kevin N Dalby; Morris J Birnbaum; Philip A Cole; Stefan Knapp; Alexey G Ryazanov; Donald J Zack; Seth Blackshaw; Tony Pawson; Anne-Claude Gingras; Stephen Desiderio; Akhilesh Pandey; Benjamin E Turk; Jin Zhang; Heng Zhu; Jiang Qian

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-04-03

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.12 Authors: Robert H Newman, Jianfei Hu, Hee-Sool Rho, Zhi Xie, Crystal Woodard, John Neiswinger, Christopher Cooper, Matthew Shirley, Hillary M Clark, Shaohui Hu, Woochang Hwang, Jun Seop Jeong, George Wu, Jimmy Lin, Xinxin Gao, Qiang Ni, Renu Goel, Shuli Xia, Hongkai Ji, Kevin N Dalby, Morris J Birnbaum, Philip A Cole, Stefan Knapp, Alexey G Ryazanov, Donald J Zack, Seth Blackshaw, Tony Pawson, Anne-Claude Gingras, Stephen Desiderio, Akhilesh Pandey, Benjamin E Turk, Jin Zhang, Heng Zhu & Jiang Qian

Electronic ISSN: 1744-4292

Topics: Biology

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7

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Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling (2013)

Judith A H Wodke; Jacek Puchałka; Maria Lluch-Senar; Josep Marcos; Eva Yus; Miguel Godinho; Ricardo Gutiérrez-Gallego; Vitor A P Martins dos Santos; Luis Serrano; Edda Klipp; Tobias Maier

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-04-03

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.6 Authors: Judith A H Wodke, Jacek Puchałka, Maria Lluch-Senar, Josep Marcos, Eva Yus, Miguel Godinho, Ricardo Gutiérrez-Gallego, Vitor A P Martins dos Santos, Luis Serrano, Edda Klipp & Tobias Maier

Electronic ISSN: 1744-4292

Topics: Biology

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SH3 interactome conserves general function over specific form (2013)

Xiaofeng Xin; David Gfeller; Jackie Cheng; Raffi Tonikian; Lin Sun; Ailan Guo; Lianet Lopez; Alevtina Pavlenco; Adenrele Akintobi; Yingnan Zhang; Jean-François Rual; Bridget Currell; Somasekar Seshagiri; Tong Hao; Xinping Yang; Yun A Shen; Kourosh Salehi-Ashtiani; Jingjing Li; Aaron T Cheng; Dryden Bouamalay; Adrien Lugari; David E Hill; Mark L Grimes; David G Drubin; Barth D Grant; Marc Vidal; Charles Boone; Sachdev S Sidhu; Gary D Bader

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-04-03

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.9 Authors: Xiaofeng Xin, David Gfeller, Jackie Cheng, Raffi Tonikian, Lin Sun, Ailan Guo, Lianet Lopez, Alevtina Pavlenco, Adenrele Akintobi, Yingnan Zhang, Jean-François Rual, Bridget Currell, Somasekar Seshagiri, Tong Hao, Xinping Yang, Yun A Shen, Kourosh Salehi-Ashtiani, Jingjing Li, Aaron T Cheng, Dryden Bouamalay, Adrien Lugari, David E Hill, Mark L Grimes, David G Drubin, Barth D Grant, Marc Vidal, Charles Boone, Sachdev S Sidhu & Gary D Bader

Electronic ISSN: 1744-4292

Topics: Biology

Published by Springer Nature on behalf of The European Molecular Biology Organization (EMBO).

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9

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Plant stem cell maintenance involves direct transcriptional repression of differentiation program (2013)

Ram Kishor Yadav; Mariano Perales; Jérémy Gruel; Carolyn Ohno; Marcus Heisler; Thomas Girke; Henrik Jönsson; G Venugopala Reddy

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-04-03

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.8 Authors: Ram Kishor Yadav, Mariano Perales, Jérémy Gruel, Carolyn Ohno, Marcus Heisler, Thomas Girke, Henrik Jönsson & G Venugopala Reddy

Electronic ISSN: 1744-4292

Topics: Biology

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10

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A map of cell type-specific auxin responses (2013)

Bastiaan O R Bargmann; Steffen Vanneste; Gabriel Krouk; Tal Nawy; Idan Efroni; Eilon Shani; Goh Choe; Jiří Friml; Dominique C Bergmann; Mark Estelle; Kenneth D Birnbaum

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-09-11

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.40 Authors: Bastiaan O R Bargmann, Steffen Vanneste, Gabriel Krouk, Tal Nawy, Idan Efroni, Eilon Shani, Goh Choe, Jiří Friml, Dominique C Bergmann, Mark Estelle & Kenneth D Birnbaum

Electronic ISSN: 1744-4292

Topics: Biology

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11

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Barriers to transmission of transcriptional noise in a c-fos c-jun pathway (2013)

Khyati Shah; Sanjay Tyagi

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-09-11

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.45 Authors: Khyati Shah & Sanjay Tyagi

Electronic ISSN: 1744-4292

Topics: Biology

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12

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Chromosome segregation by the Escherichia coli Min system (2013)

Barbara Di Ventura; Benoît Knecht; Helena Andreas; William J Godinez; Miriam Fritsche; Karl Rohr; Walter Nickel; Dieter W Heermann; Victor Sourjik

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-09-11

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.44 Authors: Barbara Di Ventura, Benoît Knecht, Helena Andreas, William J Godinez, Miriam Fritsche, Karl Rohr, Walter Nickel, Dieter W Heermann & Victor Sourjik

Electronic ISSN: 1744-4292

Topics: Biology

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13

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Dissection of a Krox20 positive feedback loop driving cell fate choices in hindbrain patterning (2013)

Yassine X Bouchoucha; Jürgen Reingruber; Charlotte Labalette; Michel A Wassef; Elodie Thierion; Carole Desmarquet-Trin Dinh; David Holcman; Pascale Gilardi-Hebenstreit; Patrick Charnay

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-09-25

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.46 Authors: Yassine X Bouchoucha, Jürgen Reingruber, Charlotte Labalette, Michel A Wassef, Elodie Thierion, Carole Desmarquet-Trin Dinh, David Holcman, Pascale Gilardi-Hebenstreit & Patrick Charnay

Electronic ISSN: 1744-4292

Topics: Biology

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14

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Biomedically relevant circuit-design strategies in mammalian synthetic biology (2013)

William Bacchus; Dominique Aubel; Martin Fussenegger

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-09-25

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.48 Authors: William Bacchus, Dominique Aubel & Martin Fussenegger

Electronic ISSN: 1744-4292

Topics: Biology

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15

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Competition between species can stabilize public-goods cooperation within a species (2012)

Hasan Celiker; Jeff Gore

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-11-14

Description: Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.54 Authors: Hasan Celiker & Jeff Gore

Electronic ISSN: 1744-4292

Topics: Biology

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16

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Modelling reveals novel roles of two parallel signalling pathways and homeostatic feedbacks in yeast (2012)

Jörg Schaber; Rodrigo Baltanas; Alan Bush; Edda Klipp; Alejandro Colman-Lerner

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-11-14

Description: Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.53 Authors: Jörg Schaber, Rodrigo Baltanas, Alan Bush, Edda Klipp & Alejandro Colman-Lerner

Electronic ISSN: 1744-4292

Topics: Biology

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17

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Regulation of yeast central metabolism by enzyme phosphorylation (2012)

Ana Paula Oliveira; Christina Ludwig; Paola Picotti; Maria Kogadeeva; Ruedi Aebersold; Uwe Sauer

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-11-14

Description: Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.55 Authors: Ana Paula Oliveira, Christina Ludwig, Paola Picotti, Maria Kogadeeva, Ruedi Aebersold & Uwe Sauer

Electronic ISSN: 1744-4292

Topics: Biology

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18

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Novel biomarkers for pre-diabetes identified by metabolomics (2012)

Rui Wang-Sattler; Zhonghao Yu; Christian Herder; Ana C Messias; Anna Floegel; Ying He; Katharina Heim; Monica Campillos; Christina Holzapfel; Barbara Thorand; Harald Grallert; Tao Xu; Erik Bader; Cornelia Huth; Kirstin Mittelstrass; Angela Döring; Christa Meisinger; Christian Gieger; Cornelia Prehn; Werner Roemisch-Margl; Maren Carstensen; Lu Xie; Hisami Yamanaka-Okumura; Guihong Xing; Uta Ceglarek; Joachim Thiery; Guido Giani; Heiko Lickert; Xu Lin; Yixue Li; Heiner Boeing; Hans-Georg Joost; Martin Hrabé de Angelis; Wolfgang Rathmann; Karsten Suhre; Holger Prokisch; Annette Peters; Thomas Meitinger; Michael Roden; H-Erich Wichmann; Tobias Pischon; Jerzy Adamski; Thomas Illig

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-09-26

Description: Novel biomarkers for pre-diabetes identified by metabolomics Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.43 Authors: Rui Wang-Sattler, Zhonghao Yu, Christian Herder, Ana C Messias, Anna Floegel, Ying He, Katharina Heim, Monica Campillos, Christina Holzapfel, Barbara Thorand, Harald Grallert, Tao Xu, Erik Bader, Cornelia Huth, Kirstin Mittelstrass, Angela Döring, Christa Meisinger, Christian Gieger, Cornelia Prehn, Werner Roemisch-Margl, Maren Carstensen, Lu Xie, Hisami Yamanaka-Okumura, Guihong Xing, Uta Ceglarek, Joachim Thiery, Guido Giani, Heiko Lickert, Xu Lin, Yixue Li, Heiner Boeing, Hans-Georg Joost, Martin Hrabé de Angelis, Wolfgang Rathmann, Karsten Suhre, Holger Prokisch, Annette Peters, Thomas Meitinger, Michael Roden, H-Erich Wichmann, Tobias Pischon, Jerzy Adamski & Thomas Illig

Electronic ISSN: 1744-4292

Topics: Biology

Published by Springer Nature on behalf of The European Molecular Biology Organization (EMBO).

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19

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Need-based activation of ammonium uptake in Escherichia coli (2012)

Minsu Kim; Zhongge Zhang; Hiroyuki Okano; Dalai Yan; Alexander Groisman; Terence Hwa

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-09-26

Description: Need-based activation of ammonium uptake in Escherichia coli Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.46 Authors: Minsu Kim, Zhongge Zhang, Hiroyuki Okano, Dalai Yan, Alexander Groisman & Terence Hwa

Electronic ISSN: 1744-4292

Topics: Biology

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20

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Cell-cycle regulation of NOTCH signaling during C. elegans vulval development (2012)

Stefanie Nusser-Stein; Antje Beyer; Ivo Rimann; Magdalene Adamczyk; Nir Piterman; Alex Hajnal; Jasmin Fisher

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-10-10

Description: Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.51 Authors: Stefanie Nusser-Stein, Antje Beyer, Ivo Rimann, Magdalene Adamczyk, Nir Piterman, Alex Hajnal & Jasmin Fisher

Electronic ISSN: 1744-4292

Topics: Biology

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21

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A model of spatially restricted transcription in opposing gradients of activators and repressors (2012)

Michael A White; Davis S Parker; Scott Barolo; Barak A Cohen

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-09-26

Description: A model of spatially restricted transcription in opposing gradients of activators and repressors Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.48 Authors: Michael A White, Davis S Parker, Scott Barolo & Barak A Cohen

Electronic ISSN: 1744-4292

Topics: Biology

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22

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Properties of cell death models calibrated and compared using Bayesian approaches (2013)

Hoda Eydgahi; William W Chen; Jeremy L Muhlich; Dennis Vitkup; John N Tsitsiklis; Peter K Sorger

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-02-06

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2012.69 Authors: Hoda Eydgahi, William W Chen, Jeremy L Muhlich, Dennis Vitkup, John N Tsitsiklis & Peter K Sorger

Keywords: apoptosisBayesian estimationbiochemical networksmodeling

Electronic ISSN: 1744-4292

Topics: Biology

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23

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Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli (2013)

Martin Dragosits; Vadim Mozhayskiy; Semarhy Quinones-Soto; Jiyeon Park; Ilias Tagkopoulos

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-02-06

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2012.76 Authors: Martin Dragosits, Vadim Mozhayskiy, Semarhy Quinones-Soto, Jiyeon Park & Ilias Tagkopoulos

Keywords: cross-stress protectionevolutionary trade-offsmicrobial evolutionstress adaptation

Electronic ISSN: 1744-4292

Topics: Biology

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24

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Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit (2012)

Katja Baerenfaller; Catherine Massonnet; Sean Walsh; Sacha Baginsky; Peter Bühlmann; Lars Hennig; Matthias Hirsch-Hoffmann; Katharine A Howell; Sabine Kahlau; Amandine Radziejwoski; Doris Russenberger; Dorothea Rutishauser; Ian Small; Daniel Stekhoven; Ronan Sulpice; Julia Svozil; Nathalie Wuyts; Mark Stitt; Pierre Hilson; Christine Granier; Wilhelm Gruissem

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-08-29

Description: Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.39 Authors: Katja Baerenfaller, Catherine Massonnet, Sean Walsh, Sacha Baginsky, Peter Bühlmann, Lars Hennig, Matthias Hirsch-Hoffmann, Katharine A Howell, Sabine Kahlau, Amandine Radziejwoski, Doris Russenberger, Dorothea Rutishauser, Ian Small, Daniel Stekhoven, Ronan Sulpice, Julia Svozil, Nathalie Wuyts, Mark Stitt, Pierre Hilson, Christine Granier & Wilhelm Gruissem

Electronic ISSN: 1744-4292

Topics: Biology

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25

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Inferring transcriptional and microRNA-mediated regulatory programs in glioblastoma (2012)

Manu Setty; Karim Helmy; Aly A Khan; Joachim Silber; Aaron Arvey; Frank Neezen; Phaedra Agius; Jason T Huse; Eric C Holland; Christina S Leslie

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-08-29

Description: Inferring transcriptional and microRNA-mediated regulatory programs in glioblastoma Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.37 Authors: Manu Setty, Karim Helmy, Aly A Khan, Joachim Silber, Aaron Arvey, Frank Neezen, Phaedra Agius, Jason T Huse, Eric C Holland & Christina S Leslie

Electronic ISSN: 1744-4292

Topics: Biology

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Dynamics of protein noise can distinguish between alternate sources of gene-expression variability (2012)

Abhyudai Singh; Brandon S Razooky; Roy D Dar; Leor S Weinberger

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-08-29

Description: Dynamics of protein noise can distinguish between alternate sources of gene-expression variability Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.38 Authors: Abhyudai Singh, Brandon S Razooky, Roy D Dar & Leor S Weinberger

Electronic ISSN: 1744-4292

Topics: Biology

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27

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Deciphering a global network of functionally associated post-translational modifications (2012)

Pablo Minguez; Luca Parca; Francesca Diella; Daniel R Mende; Runjun Kumar; Manuela Helmer-Citterich; Anne-Claude Gavin; Vera van Noort; Peer Bork

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-18

Description: Deciphering a global network of functionally associated post-translational modifications Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.31 Authors: Pablo Minguez, Luca Parca, Francesca Diella, Daniel R Mende, Runjun Kumar, Manuela Helmer-Citterich, Anne-Claude Gavin, Vera van Noort & Peer Bork

Electronic ISSN: 1744-4292

Topics: Biology

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28

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Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels (2012)

Sylvia C Tippmann; Robert Ivanek; Dimos Gaidatzis; Anne Schöler; Leslie Hoerner; Erik van Nimwegen; Peter F Stadler; Michael B Stadler; Dirk Schübeler

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-18

Description: Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.23 Authors: Sylvia C Tippmann, Robert Ivanek, Dimos Gaidatzis, Anne Schöler, Leslie Hoerner, Erik van Nimwegen, Peter F Stadler, Michael B Stadler & Dirk Schübeler

Electronic ISSN: 1744-4292

Topics: Biology

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29

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INDI: a computational framework for inferring drug interactions and their associated recommendations (2012)

Assaf Gottlieb; Gideon Y Stein; Yoram Oron; Eytan Ruppin; Roded Sharan

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-18

Description: INDI: a computational framework for inferring drug interactions and their associated recommendations Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.26 Authors: Assaf Gottlieb, Gideon Y Stein, Yoram Oron, Eytan Ruppin & Roded Sharan

Electronic ISSN: 1744-4292

Topics: Biology

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The glucose-deprivation network counteracts lapatinib-induced toxicity in resistant ErbB2-positive breast cancer cells (2012)

Kakajan Komurov; Jen-Te Tseng; Melissa Muller; Elena G Seviour; Tyler J Moss; Lifeng Yang; Deepak Nagrath; Prahlad T Ram

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-18

Description: The glucose-deprivation network counteracts lapatinib-induced toxicity in resistant ErbB2-positive breast cancer cells Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.25 Authors: Kakajan Komurov, Jen-Te Tseng, Melissa Muller, Elena G Seviour, Tyler J Moss, Lifeng Yang, Deepak Nagrath & Prahlad T Ram

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Global biogeography of SAR11 marine bacteria (2012)

Mark V Brown; Federico M Lauro; Matthew Z De; Maere; Les Muir; David Wilkins; Torsten Thomas; Martin J Riddle; Jed A Fuhrman; Cynthia Andrews-Pfannkoch; Jeffrey M Hoffman; Jeffrey B McQuaid; Andrew Allen; Stephen R Rintoul; Ricardo Cavicchioli

Springer Nature

In: Molecular Systems Biology

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Description: Global biogeography of SAR11 marine bacteria Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.28 Authors: Mark V Brown, Federico M Lauro, Matthew Z DeMaere, Les Muir, David Wilkins, Torsten Thomas, Martin J Riddle, Jed A Fuhrman, Cynthia Andrews-Pfannkoch, Jeffrey M Hoffman, Jeffrey B McQuaid, Andrew Allen, Stephen R Rintoul & Ricardo Cavicchioli

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Cells, shared memory and breaking the PTM code (2012)

Pau Creixell; Rune Linding

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-18

Description: Cells, shared memory and breaking the PTM code Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.33 Authors: Pau Creixell & Rune Linding

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Metabolic rewiring drives resistance to targeted cancer therapy (2012)

Jason W Locasale

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-18

Description: Metabolic rewiring drives resistance to targeted cancer therapy Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.30 Author: Jason W Locasale

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Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers (2012)

I-Ming Wang; Bin Zhang; Xia Yang; Jun Zhu; Serguei Stepaniants; Chunsheng Zhang; Qingying Meng; Mette Peters; Yudong He; Chester Ni; Deborah Slipetz; Michael A Crackower; Hani Houshyar; Christopher M Tan; Ernest Asante-Appiah; Gary O'Neill; Mingjuan Jane Luo; Rolf Thieringer; Jeffrey Yuan; Chi-Sung Chiu; Pek Yee Lum; John Lamb; Yves Boie; Hilary A Wilkinson; Eric E Schadt; Hongyue Dai; Christopher Roberts

Springer Nature

In: Molecular Systems Biology

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Description: Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.24 Authors: I-Ming Wang, Bin Zhang, Xia Yang, Jun Zhu, Serguei Stepaniants, Chunsheng Zhang, Qingying Meng, Mette Peters, Yudong He, Chester Ni, Deborah Slipetz, Michael A Crackower, Hani Houshyar, Christopher M Tan, Ernest Asante-Appiah, Gary O'Neill, Mingjuan Jane Luo, Rolf Thieringer, Jeffrey Yuan, Chi-Sung Chiu, Pek Yee Lum, John Lamb, Yves Boie, Hilary A Wilkinson, Eric E Schadt, Hongyue Dai & Christopher Roberts

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Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells (2012)

Silvia Stingele; Gabriele Stoehr; Karolina Peplowska; Jürgen Cox; Matthias Mann; Zuzana Storchova

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-09-12

Description: Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.40 Authors: Silvia Stingele, Gabriele Stoehr, Karolina Peplowska, Jürgen Cox, Matthias Mann & Zuzana Storchova

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The changing privacy landscape in the era of big data (2012)

Eric E Schadt

Springer Nature

In: Molecular Systems Biology

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Description: The changing privacy landscape in the era of big data Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.47 Author: Eric E Schadt

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Gene location and DNA density determine transcription factor distributions in Escherichia coli (2012)

Thomas E Kuhlman; Edward C Cox

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-09-12

Description: Gene location and DNA density determine transcription factor distributions in Escherichia coli Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.42 Authors: Thomas E Kuhlman & Edward C Cox

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A feel for systems (2012)

Eberhard O Voit; Wendy C Newstetter; Melissa L Kemp

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-09-12

Description: A feel for systems Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.41 Authors: Eberhard O Voit, Wendy C Newstetter & Melissa L Kemp

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Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma (2012)

Jacek R Wiśniewski; Paweł Ostasiewicz; Kamila DuśDorota F Zielińska; Florian Gnad; Matthias Mann

Springer Nature

In: Molecular Systems Biology

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Description: Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.44 Authors: Jacek R Wiśniewski, Paweł Ostasiewicz, Kamila Duś, Dorota F Zielińska, Florian Gnad & Matthias Mann

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Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation (2012)

Aarash Bordbar; Monica L Mo; Ernesto S Nakayasu; Alexandra C Schrimpe-Rutledge; Young-Mo Kim; Thomas O Metz; Marcus B Jones; Bryan C Frank; Richard D Smith; Scott N Peterson; Daniel R Hyduke; Joshua N Adkins; Bernhard O Palsson

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In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.21 Authors: Aarash Bordbar, Monica L Mo, Ernesto S Nakayasu, Alexandra C Schrimpe-Rutledge, Young-Mo Kim, Thomas O Metz, Marcus B Jones, Bryan C Frank, Richard D Smith, Scott N Peterson, Daniel R Hyduke, Joshua N Adkins & Bernhard O Palsson

Keywords: constraint-based modelingimmunometabolismmetabolic network reconstructionRAW 264.7

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Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours (2012)

Takuji Yamada; Alison S Waller; Jeroen Raes; Aleksej Zelezniak; Nadia Perchat; Alain Perret; Marcel Salanoubat; Kiran R Patil; Jean Weissenbach; Peer Bork

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In: Molecular Systems Biology

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Description: Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.13 Authors: Takuji Yamada, Alison S Waller, Jeroen Raes, Aleksej Zelezniak, Nadia Perchat, Alain Perret, Marcel Salanoubat, Kiran R Patil, Jean Weissenbach & Peer Bork

Keywords: genomicsmetabolic pathwaysmetagenomicsneighbourhood informationorphan enzymes

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Transcription start site associated RNAs in bacteria (2012)

Eva Yus; Marc Güell; Ana P Vivancos; Wei-Hua Chen; María Lluch-Senar; Javier Delgado; Anne-Claude Gavin; Peer Bork; Luis Serrano

Springer Nature

In: Molecular Systems Biology

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Description: Transcription start site associated RNAs in bacteria Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.16 Authors: Eva Yus, Marc Güell, Ana P Vivancos, Wei-Hua Chen, María Lluch-Senar, Javier Delgado, Anne-Claude Gavin, Peer Bork & Luis Serrano

Keywords: non-coding RNAssmall RNAstranscriptiontranscriptomics

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Competing G protein-coupled receptor kinases balance G protein and β-arrestin signaling (2012)

Domitille Heitzler; Guillaume Durand; Nathalie Gallay; Aurélien Rizk; Seungkirl Ahn; Jihee Kim; Jonathan D Violin; Laurence Dupuy; Christophe Gauthier; Vincent Piketty; Pascale Crépieux; Anne Poupon; Frédérique Clément; François Fages; Robert J Lefkowitz; Eric Reiter

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: Competing G protein-coupled receptor kinases balance G protein and β-arrestin signaling Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.22 Authors: Domitille Heitzler, Guillaume Durand, Nathalie Gallay, Aurélien Rizk, Seungkirl Ahn, Jihee Kim, Jonathan D Violin, Laurence Dupuy, Christophe Gauthier, Vincent Piketty, Pascale Crépieux, Anne Poupon, Frédérique Clément, François Fages, Robert J Lefkowitz & Eric Reiter

Keywords: β-arrestin7 transmembrane receptorsdynamical modelingG proteinsignal transduction

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Multi-layered stochasticity and paracrine signal propagation shape the type-I interferon response (2012)

Ulfert Rand; Melanie Rinas; Johannes Schwerk; Gesa Nöhren; Melanie Linnes; Andrea Kröger; Michael Flossdorf; Kristóf Kály-Kullai; Hansjörg Hauser; Thomas Höfer; Mario Köster

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In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: Multi-layered stochasticity and paracrine signal propagation shape the type-I interferon response Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.17 Authors: Ulfert Rand, Melanie Rinas, Johannes Schwerk, Gesa Nöhren, Melanie Linnes, Andrea Kröger, Michael Flossdorf, Kristóf Kály-Kullai, Hansjörg Hauser, Thomas Höfer & Mario Köster

Keywords: bacterial artificial chromosomesgene expressioninterferon regulatory factor-7live-cell microscopymulti-scale modelling

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Comparative transcriptomics of pathogenic and non-pathogenic Listeria species (2012)

Omri Wurtzel; Nina Sesto; J R Mellin; Iris Karunker; Sarit Edelheit; Christophe Bécavin; Cristel Archambaud; Pascale Cossart; Rotem Sorek

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In: Molecular Systems Biology

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Description: Comparative transcriptomics of pathogenic and non-pathogenic Listeria species Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.11 Authors: Omri Wurtzel, Nina Sesto, J R Mellin, Iris Karunker, Sarit Edelheit, Christophe Bécavin, Cristel Archambaud, Pascale Cossart & Rotem Sorek

Keywords: comparative genomicsListeria monocytogenesRNA-seqtranscriptomeTSS map

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A framework for mapping, visualisation and automatic model creation of signal-transduction networks (2012)

Carl-Fredrik Tiger; Falko Krause; Gunnar Cedersund; Robert Palmér; Edda Klipp; Stefan Hohmann; Hiroaki Kitano; Marcus Krantz

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In: Molecular Systems Biology

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Description: A framework for mapping, visualisation and automatic model creation of signal-transduction networks Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.12 Authors: Carl-Fredrik Tiger, Falko Krause, Gunnar Cedersund, Robert Palmér, Edda Klipp, Stefan Hohmann, Hiroaki Kitano & Marcus Krantz

Keywords: combinatorial complexitymathematical modellingnetwork mappingsignal transductionvisualisation

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A genomic bias for genotype–environment interactions in C. elegans (2012)

Vladislav Grishkevich; Shay Ben-Elazar; Tamar Hashimshony; Daniel H Schott; Craig P Hunter; Itai Yanai

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: A genomic bias for genotype–environment interactions in C. elegans Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.19 Authors: Vladislav Grishkevich, Shay Ben-Elazar, Tamar Hashimshony, Daniel H Schott, Craig P Hunter & Itai Yanai

Keywords: C. elegansgenome regulationgenomic sequencinggenotype-environment interactiontranscriptomics

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Towards an ‘Oceans Systems Biology’ (2012)

Eric Karsenti

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: Towards an ‘Oceans Systems Biology’ Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.8 Author: Eric Karsenti

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Differential network biology (2012)

Trey Ideker; Nevan J Krogan

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: Differential network biology Molecular Systems Biology 8, (2012). doi:10.1038/msb.2011.99 Authors: Trey Ideker & Nevan J Krogan

Keywords: genetic interactionsnetworksprotein interactions

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Glucose deprivation activates a metabolic and signaling amplification loop leading to cell death (2012)

Nicholas A Graham; Martik Tahmasian; Bitika Kohli; Evangelia Komisopoulou; Maggie Zhu; Igor Vivanco; Michael A Teitell; Hong Wu; Antoni Ribas; Roger S Lo; Ingo K Mellinghoff; Paul S Mischel; Thomas G Graeber

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: Glucose deprivation activates a metabolic and signaling amplification loop leading to cell death Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.20 Authors: Nicholas A Graham, Martik Tahmasian, Bitika Kohli, Evangelia Komisopoulou, Maggie Zhu, Igor Vivanco, Michael A Teitell, Hong Wu, Antoni Ribas, Roger S Lo, Ingo K Mellinghoff, Paul S Mischel & Thomas G Graeber

Keywords: cancermetabolismphosphataseproteomicsreactive oxygen species

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A regulatory role for repeated decoy transcription factor binding sites in target gene expression (2012)

Tek-Hyung Lee; Narendra Maheshri

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: A regulatory role for repeated decoy transcription factor binding sites in target gene expression Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.7 Authors: Tek-Hyung Lee & Narendra Maheshri

Keywords: bimodalitytandem repeatstranscription factor decoystranscriptional regulation

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A direct look at RNAi screens (2012)

Alexis R Barr; Chris Bakal

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: A direct look at RNAi screens Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.14 Authors: Alexis R Barr & Chris Bakal

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Proteomic and protein interaction network analysis of human T lymphocytes during cell-cycle entry (2012)

Stephen J Orr; Daniel R Boutz; Rong Wang; Constantinos Chronis; Nicholas C Lea; Thivyan Thayaparan; Emma Hamilton; Hanna Milewicz; Eric Blanc; Ghulam J Mufti; Edward M Marcotte; N Shaun B Thomas

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: Proteomic and protein interaction network analysis of human T lymphocytes during cell-cycle entry Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.5 Authors: Stephen J Orr, Daniel R Boutz, Rong Wang, Constantinos Chronis, Nicholas C Lea, Thivyan Thayaparan, Emma Hamilton, Hanna Milewicz, Eric Blanc, Ghulam J Mufti, Edward M Marcotte & N Shaun B Thomas

Keywords: cell cyclecell sizemass spectrometryproteomicsT cells

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The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops (2012)

Alexandra Pokhilko; Aurora Piñas Fernández; Kieron D Edwards; Megan M Southern; Karen J Halliday; Andrew J Millar

Springer Nature

In: Molecular Systems Biology

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Description: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.6 Authors: Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar

Keywords: biological clockscircadian rhythmsgene regulatory networksmathematical modelsystems biology

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miRNAs versus oncogenes: the power of social networking (2012)

Marcos Malumbres

Springer Nature

In: Molecular Systems Biology

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Description: miRNAs versus oncogenes: the power of social networking Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.2 Author: Marcos Malumbres

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Single-cell analysis of population context advances RNAi screening at multiple levels (2012)

Berend Snijder; Raphael Sacher; Pauli RämöPrisca Liberali; Karin Mench; Nina Wolfrum; Laura Burleigh; Cameron C Scott; Monique H Verheije; Jason Mercer; Stefan Moese; Thomas Heger; Kristina Theusner; Andreas Jurgeit; David Lamparter; Giuseppe Balistreri; Mario Schelhaas; Cornelis A M De Haan; Varpu Marjomäki; Timo HyypiäPeter J M Rottier; Beate Sodeik; Mark Marsh; Jean Gruenberg; Ali Amara; Urs Greber; Ari Helenius; Lucas Pelkmans

Springer Nature

In: Molecular Systems Biology

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Description: Single-cell analysis of population context advances RNAi screening at multiple levels Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.9 Authors: Berend Snijder, Raphael Sacher, Pauli Rämö, Prisca Liberali, Karin Mench, Nina Wolfrum, Laura Burleigh, Cameron C Scott, Monique H Verheije, Jason Mercer, Stefan Moese, Thomas Heger, Kristina Theusner, Andreas Jurgeit, David Lamparter, Giuseppe Balistreri, Mario Schelhaas, Cornelis A M De Haan, Varpu Marjomäki, Timo Hyypiä, Peter J M Rottier, Beate Sodeik, Mark Marsh, Jean Gruenberg, Ali Amara, Urs Greber, Ari Helenius & Lucas Pelkmans

Keywords: cell-to-cell variabilityimage analysispopulation contextRNAivirus infection

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Combined experimental and computational analysis of DNA damage signaling reveals context-dependent roles for Erk in apoptosis and G1/S arrest after genotoxic stress (2012)

Andrea R Tentner; Michael J Lee; Gerry J Ostheimer; Leona D Samson; Douglas A Lauffenburger; Michael B Yaffe

Springer Nature

In: Molecular Systems Biology

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Description: Combined experimental and computational analysis of DNA damage signaling reveals context-dependent roles for Erk in apoptosis and G1/S arrest after genotoxic stress Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.1 Authors: Andrea R Tentner, Michael J Lee, Gerry J Ostheimer, Leona D Samson, Douglas A Lauffenburger & Michael B Yaffe

Keywords: apoptosiscell-cycle checkpointDNA damageErksignal transduction

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Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels (2012)

Milana Frenkel-Morgenstern; Tamar Danon; Thomas Christian; Takao Igarashi; Lydia Cohen; Ya-Ming Hou; Lars Juhl Jensen

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.3 Authors: Milana Frenkel-Morgenstern, Tamar Danon, Thomas Christian, Takao Igarashi, Lydia Cohen, Ya-Ming Hou & Lars Juhl Jensen

Keywords: cell cyclenon-optimal codonstranslation regulationtRNA expression during cell cyclewobbling

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Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium (2012)

Vera van Noort; Jan Seebacher; Samuel Bader; Shabaz Mohammed; Ivana Vonkova; Matthew J Betts; Sebastian Kühner; Runjun Kumar; Tobias Maier; Martina O'Flaherty; Vladimir Rybin; Arne Schmeisky; Eva Yus; Jörg Stülke; Luis Serrano; Robert B Russell; Albert JR Heck; Peer Bork; Anne-Claude Gavin

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In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.4 Authors: Vera van Noort, Jan Seebacher, Samuel Bader, Shabaz Mohammed, Ivana Vonkova, Matthew J Betts, Sebastian Kühner, Runjun Kumar, Tobias Maier, Martina O'Flaherty, Vladimir Rybin, Arne Schmeisky, Eva Yus, Jörg Stülke, Luis Serrano, Robert B Russell, Albert JR Heck, Peer Bork & Anne-Claude Gavin

Keywords: kinaseN-acetyltransferasenetworkphosphatasepost-translational modification

Electronic ISSN: 1744-4292

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Global microRNA level regulation of EGFR-driven cell-cycle protein network in breast cancer (2012)

Stefan Uhlmann; Heiko Mannsperger; Jitao David Zhang; Emöke-Ágnes Horvat; Christian Schmidt; Moritz Küblbeck; Frauke Henjes; Aoife Ward; Ulrich Tschulena; Katharina Zweig; Ulrike Korf; Stefan WiemannÖzgür Sahin

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: Global microRNA level regulation of EGFR-driven cell-cycle protein network in breast cancer Molecular Systems Biology 8, (2012). doi:10.1038/msb.2011.100 Authors: Stefan Uhlmann, Heiko Mannsperger, Jitao David Zhang, Emöke-Ágnes Horvat, Christian Schmidt, Moritz Küblbeck, Frauke Henjes, Aoife Ward, Ulrich Tschulena, Katharina Zweig, Ulrike Korf, Stefan Wiemann & Özgür Sahin

Keywords: breast cancerEGFR signalingmicroRNAmiRNA–protein interaction networknetwork analysis

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Widespread translational control contributes to the regulation of Arabidopsis photomorphogenesis (2012)

Ming-Jung Liu; Szu-Hsien Wu; Ho-Ming Chen; Shu-Hsing Wu

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: Widespread translational control contributes to the regulation of Arabidopsis photomorphogenesis Molecular Systems Biology 8, (2012). doi:10.1038/msb.2011.97 Authors: Ming-Jung Liu, Szu-Hsien Wu, Ho-Ming Chen & Shu-Hsing Wu

Keywords: photomorphogenesispolysometranslation

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Competing pathways control host resistance to virus via tRNA modification and programmed ribosomal frameshifting (2012)

Nathaniel D Maynard; Derek N Macklin; Karla Kirkegaard; Markus W Covert

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: Competing pathways control host resistance to virus via tRNA modification and programmed ribosomal frameshifting Molecular Systems Biology 8, (2012). doi:10.1038/msb.2011.101 Authors: Nathaniel D Maynard, Derek N Macklin, Karla Kirkegaard & Markus W Covert

Keywords: bacteriophage lambdahost-virusiron-sulfur clustersprogrammed ribosomal frameshiftingtRNA modification

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Bistability in feedback circuits as a byproduct of evolution of evolvability (2012)

Hiroyuki Kuwahara; Orkun S Soyer

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: Bistability in feedback circuits as a byproduct of evolution of evolvability Molecular Systems Biology 8, (2012). doi:10.1038/msb.2011.98 Authors: Hiroyuki Kuwahara & Orkun S Soyer

Keywords: environmental fluctuationsgene regulatory networknoisephenotypic variabilitystochastic switching

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Signaling for death: tyrosine phosphorylation in the response to glucose deprivation (2012)

Bryan D Bryson; Forest M White

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: Signaling for death: tyrosine phosphorylation in the response to glucose deprivation Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.27 Authors: Bryan D Bryson & Forest M White

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Asymmetric positive feedback loops reliably control biological responses (2012)

Alexander V Ratushny; Ramsey A Saleem; Katherine Sitko; Stephen A Ramsey; John D Aitchison

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: Asymmetric positive feedback loops reliably control biological responses Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.10 Authors: Alexander V Ratushny, Ramsey A Saleem, Katherine Sitko, Stephen A Ramsey & John D Aitchison

Keywords: heterodimerkinetic modelpositive feedbackregulatory network motifrobustness

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Positive roles for negative regulators in the mating response of yeast (2012)

John R Houser; Eintou Ford; Michal J Nagiec; Beverly Errede; Timothy C Elston

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: Positive roles for negative regulators in the mating response of yeast Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.18 Authors: John R Houser, Eintou Ford, Michal J Nagiec, Beverly Errede & Timothy C Elston

Keywords: Dig2perfect adaptationprotective protein complexesSte12transcriptional regulation

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A dynamical model of the spindle position checkpoint (2012)

Ayse Koca Caydasi; Maiko Lohel; Gerd Grünert; Peter Dittrich; Gislene Pereira; Bashar Ibrahim

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-07-09

Description: A dynamical model of the spindle position checkpoint Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.15 Authors: Ayse Koca Caydasi, Maiko Lohel, Gerd Grünert, Peter Dittrich, Gislene Pereira & Bashar Ibrahim

Keywords: Bfa1mitotic exit networkmodeling and simulationspindle position checkpointTem1

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Natural sequence variants of yeast environmental sensors confer cell-to-cell expression variability (2013)

Steffen Fehrmann; Hélène Bottin-Duplus; Andri Leonidou; Esther Mollereau; Audrey Barthelaix; Wu Wei; Lars M Steinmetz; Gaël Yvert

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-10-09

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.53 Authors: Steffen Fehrmann, Hélène Bottin-Duplus, Andri Leonidou, Esther Mollereau, Audrey Barthelaix, Wu Wei, Lars M Steinmetz & Gaël Yvert

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Temporal control of self-organized pattern formation without morphogen gradients in bacteria (2013)

Stephen Payne; Bochong Li; Yangxiaolu Cao; David Schaeffer; Marc D Ryser; Lingchong You

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-10-09

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.55 Authors: Stephen Payne, Bochong Li, Yangxiaolu Cao, David Schaeffer, Marc D Ryser & Lingchong You

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A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities (2013)

Franco J Vizeacoumar; Roland Arnold; Frederick S Vizeacoumar; Megha Chandrashekhar; Alla Buzina; Jordan T F Young; Julian H M Kwan; Azin Sayad; Patricia Mero; Steffen Lawo; Hiromasa Tanaka; Kevin R Brown; Anastasia Baryshnikova; Anthony B Mak; Yaroslav Fedyshyn; Yadong Wang; Glauber C Brito; Dahlia Kasimer; Taras Makhnevych; Troy Ketela; Alessandro Datti; Mohan Babu; Andrew Emili; Laurence Pelletier; Jeff Wrana; Zev Wainberg; Philip M Kim; Robert Rottapel; Catherine A O’Brien; Brenda Andrews; Charles Boone; Jason Moffat

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In: Molecular Systems Biology

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Publication Date: 2013-10-09

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.54 Authors: Franco J Vizeacoumar, Roland Arnold, Frederick S Vizeacoumar, Megha Chandrashekhar, Alla Buzina, Jordan T F Young, Julian H M Kwan, Azin Sayad, Patricia Mero, Steffen Lawo, Hiromasa Tanaka, Kevin R Brown, Anastasia Baryshnikova, Anthony B Mak, Yaroslav Fedyshyn, Yadong Wang, Glauber C Brito, Dahlia Kasimer, Taras Makhnevych, Troy Ketela, Alessandro Datti, Mohan Babu, Andrew Emili, Laurence Pelletier, Jeff Wrana, Zev Wainberg, Philip M Kim, Robert Rottapel, Catherine A O’Brien, Brenda Andrews, Charles Boone & Jason Moffat

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A competitive protein interaction network buffers Oct4-mediated differentiation to promote pluripotency in embryonic stem cells (2013)

Silvia Muñoz Descalzo; Pau RuéFernando Faunes; Penelope Hayward; Lars Martin Jakt; Tina Balayo; Jordi Garcia-Ojalvo; Alfonso Martinez Arias

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In: Molecular Systems Biology

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Publication Date: 2013-10-09

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.49 Authors: Silvia Muñoz Descalzo, Pau Rué, Fernando Faunes, Penelope Hayward, Lars Martin Jakt, Tina Balayo, Jordi Garcia-Ojalvo & Alfonso Martinez Arias

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Root systems analysis branches out (2013)

Klaus Palme; William Teale

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In: Molecular Systems Biology

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Publication Date: 2013-10-23

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.51 Authors: Klaus Palme & William Teale

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Sequential induction of auxin efflux and influx carriers regulates lateral root emergence (2013)

Benjamin Péret; Alistair M Middleton; Andrew P French; Antoine Larrieu; Anthony Bishopp; Maria Njo; Darren M Wells; Silvana Porco; Nathan Mellor; Leah R Band; Ilda Casimiro; Jürgen Kleine-Vehn; Steffen Vanneste; Ilkka Sairanen; Romain Mallet; Göran Sandberg; Karin Ljung; Tom Beeckman; Eva Benkova; Jiří Friml; Eric Kramer; John R King; Ive De Smet; Tony Pridmore; Markus Owen; Malcolm J Bennett

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In: Molecular Systems Biology

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Publication Date: 2013-10-23

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.43 Authors: Benjamin Péret, Alistair M Middleton, Andrew P French, Antoine Larrieu, Anthony Bishopp, Maria Njo, Darren M Wells, Silvana Porco, Nathan Mellor, Leah R Band, Ilda Casimiro, Jürgen Kleine-Vehn, Steffen Vanneste, Ilkka Sairanen, Romain Mallet, Göran Sandberg, Karin Ljung, Tom Beeckman, Eva Benkova, Jiří Friml, Eric Kramer, John R King, Ive De Smet, Tony Pridmore, Markus Owen & Malcolm J Bennett

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The inoculum effect and band-pass bacterial response to periodic antibiotic treatment (2012)

Cheemeng Tan; Robert Phillip Smith; Jaydeep K Srimani; Katherine A Riccione; Sameer Prasada; Meta Kuehn; Lingchong You

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-10-10

Description: Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.49 Authors: Cheemeng Tan, Robert Phillip Smith, Jaydeep K Srimani, Katherine A Riccione, Sameer Prasada, Meta Kuehn & Lingchong You

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Insulin/IGF-1-mediated longevity is marked by reduced protein metabolism (2013)

Gerdine J Stout; Edwin C A Stigter; Paul B Essers; Klaas W Mulder; Annemieke Kolkman; Dorien S Snijders; Niels J F van den Broek; Marco C Betist; Hendrik C Korswagen; Alyson W Mac; Innes; Arjan B Brenkman

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In: Molecular Systems Biology

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Publication Date: 2013-07-03

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.35 Authors: Gerdine J Stout, Edwin C A Stigter, Paul B Essers, Klaas W Mulder, Annemieke Kolkman, Dorien S Snijders, Niels J F van den Broek, Marco C Betist, Hendrik C Korswagen, Alyson W MacInnes & Arjan B Brenkman

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Apoptosis and other immune biomarkers predict influenza vaccine responsiveness (2013)

David Furman; Vladimir Jojic; Brian Kidd; Shai Shen-Orr; Jordan Price; Justin Jarrell; Tiffany Tse; Huang Huang; Peder Lund; Holden T Maecker; Paul J Utz; Cornelia L Dekker; Daphne Koller; Mark M Davis

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In: Molecular Systems Biology

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Publication Date: 2013-07-03

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.37 Authors: David Furman, Vladimir Jojic, Brian Kidd, Shai Shen-Orr, Jordan Price, Justin Jarrell, Tiffany Tse, Huang Huang, Peder Lund, Holden T Maecker, Paul J Utz, Cornelia L Dekker, Daphne Koller & Mark M Davis

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Targeted proteomics reveals strain-specific changes in the mouse insulin and central metabolic pathways after a sustained high-fat diet (2013)

Eduard SabidóYibo Wu; Lucia Bautista; Thomas Porstmann; Ching-Yun Chang; Olga Vitek; Markus Stoffel; Ruedi Aebersold

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In: Molecular Systems Biology

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Publication Date: 2013-07-17

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.36 Authors: Eduard Sabidó, Yibo Wu, Lucia Bautista, Thomas Porstmann, Ching-Yun Chang, Olga Vitek, Markus Stoffel & Ruedi Aebersold

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Network quantification of EGFR signaling unveils potential for targeted combination therapy (2013)

Bertram Klinger; Anja Sieber; Raphaela Fritsche-Guenther; Franziska Witzel; Leanne Berry; Dirk Schumacher; Yibing Yan; Pawel Durek; Mark Merchant; Reinhold Schäfer; Christine Sers; Nils Blüthgen

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In: Molecular Systems Biology

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Publication Date: 2013-06-12

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.29 Authors: Bertram Klinger, Anja Sieber, Raphaela Fritsche-Guenther, Franziska Witzel, Leanne Berry, Dirk Schumacher, Yibing Yan, Pawel Durek, Mark Merchant, Reinhold Schäfer, Christine Sers & Nils Blüthgen

Keywords: cancerEGFR signalingmathematical modelingmodular response analysissignal transduction

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The functional interactome landscape of the human histone deacetylase family (2013)

Preeti Joshi; Todd M Greco; Amanda J Guise; Yang Luo; Fang Yu; Alexey I Nesvizhskii; Ileana M Cristea

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In: Molecular Systems Biology

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Publication Date: 2013-06-12

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.26 Authors: Preeti Joshi, Todd M Greco, Amanda J Guise, Yang Luo, Fang Yu, Alexey I Nesvizhskii & Ileana M Cristea

Keywords: HDACI-DIRTinteractionsproteomicsSAINT

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Effects of diet and development on the Drosophila lipidome (2012)

Maria Carvalho; Julio L Sampaio; Wilhelm Palm; Marko Brankatschk; Suzanne Eaton; Andrej Shevchenko

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-08-15

Description: Effects of diet and development on the Drosophila lipidome Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.29 Authors: Maria Carvalho, Julio L Sampaio, Wilhelm Palm, Marko Brankatschk, Suzanne Eaton & Andrej Shevchenko

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Integration of clinical data with a genome-scale metabolic model of the human adipocyte (2013)

Adil Mardinoglu; Rasmus Agren; Caroline Kampf; Anna Asplund; Intawat Nookaew; Peter Jacobson; Andrew J Walley; Philippe Froguel; Lena M Carlsson; Mathias Uhlen; Jens Nielsen

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In: Molecular Systems Biology

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Publication Date: 2013-03-20

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.5 Authors: Adil Mardinoglu, Rasmus Agren, Caroline Kampf, Anna Asplund, Intawat Nookaew, Peter Jacobson, Andrew J Walley, Philippe Froguel, Lena M Carlsson, Mathias Uhlen & Jens Nielsen

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Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines (2013)

Alessandro Ori; Niccolò Banterle; Murat Iskar; Amparo Andrés-Pons; Claudia Escher; Huy Khanh Bui; Lenore Sparks; Victor Solis-Mezarino; Oliver Rinner; Peer Bork; Edward A Lemke; Martin Beck

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In: Molecular Systems Biology

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Publication Date: 2013-03-20

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.4 Authors: Alessandro Ori, Niccolò Banterle, Murat Iskar, Amparo Andrés-Pons, Claudia Escher, Huy Khanh Bui, Lenore Sparks, Victor Solis-Mezarino, Oliver Rinner, Peer Bork, Edward A Lemke & Martin Beck

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Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures (2013)

Peter D Gould; Nicolas Ugarte; Mirela Domijan; Maria Costa; Julia Foreman; Dana Mac; Gregor; Ken Rose; Jayne Griffiths; Andrew J Millar; Bärbel Finkenstädt; Steven Penfield; David A Rand; Karen J Halliday; Anthony J W Hall

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In: Molecular Systems Biology

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Publication Date: 2013-03-20

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.7 Authors: Peter D Gould, Nicolas Ugarte, Mirela Domijan, Maria Costa, Julia Foreman, Dana MacGregor, Ken Rose, Jayne Griffiths, Andrew J Millar, Bärbel Finkenstädt, Steven Penfield, David A Rand, Karen J Halliday & Anthony J W Hall

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A fluorescent reporter for mapping cellular protein-protein interactions in time and space (2013)

Daniel Moreno; Joachim Neller; Hans A Kestler; Johann Kraus; Alexander Dünkler; Nils Johnsson

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In: Molecular Systems Biology

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Publication Date: 2013-03-20

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.3 Authors: Daniel Moreno, Joachim Neller, Hans A Kestler, Johann Kraus, Alexander Dünkler & Nils Johnsson

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Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast (2013)

Guillermo G Zampar; Anne Kümmel; Jennifer Ewald; Stefan Jol; Bastian Niebel; Paola Picotti; Ruedi Aebersold; Uwe Sauer; Nicola Zamboni; Matthias Heinemann

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In: Molecular Systems Biology

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Publication Date: 2013-04-03

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.11 Authors: Guillermo G Zampar, Anne Kümmel, Jennifer Ewald, Stefan Jol, Bastian Niebel, Paola Picotti, Ruedi Aebersold, Uwe Sauer, Nicola Zamboni & Matthias Heinemann

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Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli (2013)

Douglas McCloskey; Bernhard Ø Palsson; Adam M Feist

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In: Molecular Systems Biology

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Publication Date: 2013-05-01

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.18 Authors: Douglas McCloskey, Bernhard Ø Palsson & Adam M Feist

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Systematic identification of proteins that elicit drug side effects (2013)

Michael Kuhn; Mumna Al Banchaabouchi; Monica Campillos; Lars Juhl Jensen; Cornelius Gross; Anne-Claude Gavin; Peer Bork

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-05-01

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.10 Authors: Michael Kuhn, Mumna Al Banchaabouchi, Monica Campillos, Lars Juhl Jensen, Cornelius Gross, Anne-Claude Gavin & Peer Bork

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Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding (2013)

Murat Iskar; Georg Zeller; Peter Blattmann; Monica Campillos; Michael Kuhn; Katarzyna H Kaminska; Heiko Runz; Anne-Claude Gavin; Rainer Pepperkok; Vera van Noort; Peer Bork

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In: Molecular Systems Biology

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Publication Date: 2013-05-01

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.20 Authors: Murat Iskar, Georg Zeller, Peter Blattmann, Monica Campillos, Michael Kuhn, Katarzyna H Kaminska, Heiko Runz, Anne-Claude Gavin, Rainer Pepperkok, Vera van Noort & Peer Bork

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A global S. cerevisiae small ubiquitin-related modifier (SUMO) system interactome (2013)

Tharan Srikumar; Megan C Lewicki; Brian Raught

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-05-29

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.23 Authors: Tharan Srikumar, Megan C Lewicki & Brian Raught

Electronic ISSN: 1744-4292

Topics: Biology

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The Neurospora photoreceptor VIVID exerts negative and positive control on light sensing to achieve adaptation (2013)

Elan Gin; Axel C R Diernfellner; Michael Brunner; Thomas Höfer

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-05-29

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.24 Authors: Elan Gin, Axel C R Diernfellner, Michael Brunner & Thomas Höfer

Electronic ISSN: 1744-4292

Topics: Biology

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Phosphoproteome dynamics reveal novel ERK1/2 MAP kinase substrates with broad spectrum of functions (2013)

Mathieu Courcelles; Christophe Frémin; Laure Voisin; Sébastien Lemieux; Sylvain Meloche; Pierre Thibault

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-05-29

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.25 Authors: Mathieu Courcelles, Christophe Frémin, Laure Voisin, Sébastien Lemieux, Sylvain Meloche & Pierre Thibault

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Topics: Biology

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Synthetic mammalian transgene negative autoregulation (2013)

Vinay Shimoga; Jacob T White; Yi Li; Eduardo Sontag; Leonidas Bleris

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-06-05

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.27 Authors: Vinay Shimoga, Jacob T White, Yi Li, Eduardo Sontag & Leonidas Bleris

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The selective control of glycolysis, gluconeogenesis and glycogenesis by temporal insulin patterns (2013)

Rei Noguchi; Hiroyuki Kubota; Katsuyuki Yugi; Yu Toyoshima; Yasunori Komori; Tomoyoshi Soga; Shinya Kuroda

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-05-15

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.19 Authors: Rei Noguchi, Hiroyuki Kubota, Katsuyuki Yugi, Yu Toyoshima, Yasunori Komori, Tomoyoshi Soga & Shinya Kuroda

Keywords: computational modelglucose metabolisminsulinnetwork motiftemporal coding

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Metabolic reconstruction identifies strain-specific regulation of virulence in Toxoplasma gondii (2013)

Carl Song; Melissa A Chiasson; Nirvana Nursimulu; Stacy S Hung; James Wasmuth; Michael E Grigg; John Parkinson

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-11-20

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.62 Authors: Carl Song, Melissa A Chiasson, Nirvana Nursimulu, Stacy S Hung, James Wasmuth, Michael E Grigg & John Parkinson

Keywords: flux balance analysismetabolic reconstructionstrain differencesToxoplasma gondii

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Topics: Biology

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Imaging the transcriptome (2013)

Timothée Lionnet

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-11-27

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.67 Author: Timothée Lionnet

Electronic ISSN: 1744-4292

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Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis (2013)

Victor Chubukov; Markus Uhr; Ludovic Le Chat; Roelco J Kleijn; Matthieu Jules; Hannes Link; Stephane Aymerich; Jörg Stelling; Uwe Sauer

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2013-11-27

Description: Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.66 Authors: Victor Chubukov, Markus Uhr, Ludovic Le Chat, Roelco J Kleijn, Matthieu Jules, Hannes Link, Stephane Aymerich, Jörg Stelling & Uwe Sauer

Electronic ISSN: 1744-4292

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Mapping the human phosphatome on growth pathways (2012)

Francesca Sacco; Pier Federico Gherardini; Serena Paoluzi; Julio Saez-Rodriguez; Manuela Helmer-Citterich; Antonella Ragnini-Wilson; Luisa Castagnoli; Gianni Cesareni

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-08-15

Description: Mapping the human phosphatome on growth pathways Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.36 Authors: Francesca Sacco, Pier Federico Gherardini, Serena Paoluzi, Julio Saez-Rodriguez, Manuela Helmer-Citterich, Antonella Ragnini-Wilson, Luisa Castagnoli & Gianni Cesareni

Electronic ISSN: 1744-4292

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Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS (2012)

Zia Khan; Joshua S Bloom; Sasan Amini; Mona Singh; David H Perlman; Amy A Caudy; Leonid Kruglyak

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-08-15

Description: Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.34 Authors: Zia Khan, Joshua S Bloom, Sasan Amini, Mona Singh, David H Perlman, Amy A Caudy & Leonid Kruglyak

Electronic ISSN: 1744-4292

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Dissecting sources of quantitative gene expression pattern divergence between Drosophila species (2012)

Zeba Wunderlich; Meghan D Bragdon; Kelly B Eckenrode; Tara Lydiard-Martin; Sivanne Pearl-Waserman; Angela H De; Pace

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In: Molecular Systems Biology

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Publication Date: 2012-08-15

Description: Dissecting sources of quantitative gene expression pattern divergence between Drosophila species Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.35 Authors: Zeba Wunderlich, Meghan D Bragdon, Kelly B Eckenrode, Tara Lydiard-Martin, Sivanne Pearl-Waserman & Angela H DePace

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Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS (2012)

Iwona Stelniec-Klotz; Stefan Legewie; Oleg Tchernitsa; Franziska Witzel; Bertram Klinger; Christine Sers; Hanspeter Herzel; Nils Blüthgen; Reinhold Schäfer

Springer Nature

In: Molecular Systems Biology

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Publication Date: 2012-08-15

Description: Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS Molecular Systems Biology 8, (2012). doi:10.1038/msb.2012.32 Authors: Iwona Stelniec-Klotz, Stefan Legewie, Oleg Tchernitsa, Franziska Witzel, Bertram Klinger, Christine Sers, Hanspeter Herzel, Nils Blüthgen & Reinhold Schäfer

Electronic ISSN: 1744-4292

Topics: Biology

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