Molecular Systems Biology

Functional genomics

2009

Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance

Stephanie Plantegenet, Johann Weber, Darlene R Goldstein, Georg Zeller, Cindy Nussbaumer, Jérôme Thomas, Detlef Weigel, Keith Harshman & Christian S Hardtke

doi:10.1038/msb.2008.79
Published online: 17 February 2009

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Environment-specific combinatorial cis-regulation in synthetic promoters

Jason Gertz & Barak A Cohen

doi:10.1038/msb.2009.1
Published online: 17 February 2009

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Adaptable gene-specific dye bias correction for two-channel DNA microarrays

Thanasis Margaritis, Philip Lijnzaad, Dik van Leenen, Diane Bouwmeester, Patrick Kemmeren, Sander R van Hooff & Frank CP Holstege

doi:10.1038/msb.2009.21
Published online: 28 April 2009

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How selection affects phenotypic fluctuation

Yoichiro Ito, Hitoshi Toyota, Kunihiko Kaneko & Tetsuya Yomo

doi:10.1038/msb.2009.23
Published online: 28 April 2009

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Genome-wide allele- and strand-specific expression profiling

Julien Gagneur, Himanshu Sinha, Fabiana Perocchi, Richard Bourgon, Wolfgang Huber & Lars M Steinmetz

doi:10.1038/msb.2009.31
Published online: 16 June 2009

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Comparative systems biology of human and mouse as a tool to guide the modeling of human placental pathology

Brian Cox, Max Kotlyar, Andreas I Evangelou, Vladimir Ignatchenko, Alex Ignatchenko, Kathie Whiteley, Igor Jurisica, S Lee Adamson, Janet Rossant & Thomas Kislinger

doi:10.1038/msb.2009.37
Published online: 16 June 2009

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Prevalence of transcription promoters within archaeal operons and coding sequences

Tie Koide, David J Reiss, J Christopher Bare, Wyming Lee Pang, Marc T Facciotti, Amy K Schmid, Min Pan, Bruz Marzolf, Phu T Van, Fang-Yin Lo, Abhishek Pratap, Eric W Deutsch, Amelia Peterson, Dan Martin & Nitin S Baliga

doi:10.1038/msb.2009.42
Published online: 16 June 2009

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Coordinated posttranscriptional mRNA population dynamics during T-cell activation

Neelanjan Mukherjee, Patrick J Lager, Matthew B Friedersdorf, Marshall A Thompson & Jack D Keene

doi:10.1038/msb.2009.44
Published online: 28 July 2009

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The organization of the transcriptional network in specific neuronal classes

Kellen D Winden, Michael C Oldham, Karoly Mirnics, Philip J Ebert, Christo H Swan, Pat Levitt, John L Rubenstein, Steve Horvath & Daniel H Geschwind

doi:10.1038/msb.2009.46
Published online: 28 July 2009

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Positive selection for elevated gene expression noise in yeast

Zhihua Zhang, Wenfeng Qian & Jianzhi Zhang

doi:10.1038/msb.2009.58
Published online: 18 August 2009

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Evidence for a major role of antisense RNAs in cyanobacterial gene regulation

Jens Georg, Björn Vo s zlig , Ingeborg Scholz, Jan Mitschke, Annegret Wilde & Wolfgang R Hess

doi:10.1038/msb.2009.63
Published online: 15 September 2009

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Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis

Maria Piques, Waltraud X Schulze, Melanie Höhne, Björn Usadel, Yves Gibon, Johann Rohwer & Mark Stitt

doi:10.1038/msb.2009.68
Published online: 13 October 2009

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Harnessing gene expression to identify the genetic basis of drug resistance

Bo-Juen Chen, Helen C Causton, Denesy Mancenido, Noel L Goddard, Ethan O Perlstein & Dana Pe'er

doi:10.1038/msb.2009.69
Published online: 13 October 2009

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Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression

Larsson Omberg, Joel R Meyerson, Kayta Kobayashi, Lucy S Drury, John F X Diffley & Orly Alter

doi:10.1038/msb.2009.70
Published online: 13 October 2009

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Application of an integrated physical and functional screening approach to identify inhibitors of the Wnt pathway

Bryan W Miller, Garnet Lau, Chris Grouios, Emanuela Mollica, Miriam Barrios-Rodiles, Yongmei Liu, Alessandro Datti, Quaid Morris, Jeffrey L Wrana & Liliana Attisano

doi:10.1038/msb.2009.72
Published online: 13 October 2009

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2008

A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1

Véronique de Berardinis, David Vallenet, Vanina Castelli, Marielle Besnard, Agnès Pinet, Corinne Cruaud, Sumitta Samair, Christophe Lechaplais, Gabor Gyapay, Céline Richez, Maxime Durot, Annett Kreimeyer, François Le Fèvre, Vincent Schächter, Valérie Pezo, Volker Döring, Claude Scarpelli, Claudine Médigue, Georges N Cohen, Philippe Marlière, Marcel Salanoubat & Jean Weissenbach

doi:10.1038/msb.2008.10
Published online: 04 March 2008

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Selection to minimise noise in living systems and its implications for the evolution of gene expression

Ben Lehner

doi:10.1038/msb.2008.11
Published online: 04 March 2008

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Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression

Sujun Hua, Caleb B Kallen, Ruby Dhar, Maria T Baquero, Christopher E Mason, Beth A Russell, Parantu K Shah, Jiang Liu, Andrey Khramtsov, Maria S Tretiakova, Thomas N Krausz, Olufunmilayo I Olopade, David L Rimm & Kevin P White

doi:10.1038/msb.2008.25
Published online: 15 April 2008

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From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions

Igor Ulitsky, Tomer Shlomi, Martin Kupiec & Ron Shamir

doi:10.1038/msb.2008.42
Published online: 15 July 2008

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Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression

Itai Yanai, L Ryan Baugh, Jessica J Smith, Casey Roehrig, Shai S Shen-Orr, Julia M Claggett, Andrew A Hill, Donna K Slonim & Craig P Hunter

doi:10.1038/msb.2008.6
Published online: 12 February 2008

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The liver pharmacological and xenobiotic gene response repertoire

Georges Natsoulis, Cecelia I Pearson, Jeremy Gollub, Barrett P Eynon, Joe Ferng, Ramesh Nair, Radha Idury, May D Lee, Mark R Fielden, Richard J Brennan, Alan H Roter & Kurt Jarnagin

doi:10.1038/msb.2008.9
Published online: 25 March 2008

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On the relation between promoter divergence and gene expression evolution

Itay Tirosh, Adina Weinberger, Dana Bezalel, Mark Kaganovich & Naama Barkai

doi:10.1038/msb4100198
Published online: 15 January 2008

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2007

The gene and the genon concept: a functional and information-theoretic analysis

Klaus Scherrer & Jürgen Jost

doi:10.1038/msb4100123
Published online: 13 March 2007

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Backup without redundancy: genetic interactions reveal the cost of duplicate gene loss

Jan Ihmels, Sean R Collins, Maya Schuldiner, Nevan J Krogan & Jonathan S Weissman

doi:10.1038/msb4100127
Published online: 27 March 2007

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Prediction of phenotype and gene expression for combinations of mutations

Gregory W Carter, Susanne Prinz, Christine Neou, J Patrick Shelby, Bruz Marzolf, Vesteinn Thorsson & Timothy Galitski

doi:10.1038/msb4100137
Published online: 27 March 2007

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

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

doi:10.1038/msb4100140
Published online: 17 April 2007

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The protein network of bacterial motility

Seesandra V Rajagopala, Björn Titz, Johannes Goll, Jodi R Parrish, Katrin Wohlbold, Matthew T McKevitt, Timothy Palzkill, Hirotada Mori, Russell L Finley, Jr & Peter Uetz

doi:10.1038/msb4100166
Published online: 31 July 2007

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Construction of consecutive deletions of the Escherichia coli chromosome

Jun-ichi Kato & Masayuki Hashimoto

doi:10.1038/msb4100174
Published online: 14 August 2007

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2006

Global analysis of gene function in yeast by quantitative phenotypic profiling

James A Brown, Gavin Sherlock, Chad L Myers, Nicola M Burrows, Changchun Deng, H Irene Wu, Kelly E McCann, Olga G Troyanskaya & J Martin Brown

doi:10.1038/msb4100043
Published online: 17 January 2006

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Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110

Koji Hayashi, Naoki Morooka, Yoshihiro Yamamoto, Katsutoshi Fujita, Katsumi Isono, Sunju Choi, Eiichi Ohtsubo, Tomoya Baba, Barry L Wanner, Hirotada Mori & Takashi Horiuchi

doi:10.1038/msb4100049
Published online: 21 February 2006

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Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection

Tomoya Baba, Takeshi Ara, Miki Hasegawa, Yuki Takai, Yoshiko Okumura, Miki Baba, Kirill A Datsenko, Masaru Tomita, Barry L Wanner & Hirotada Mori

doi:10.1038/msb4100050
Published online: 21 February 2006

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Core transcriptional regulatory circuitry in human hepatocytes

Duncan T Odom, Robin D Dowell, Elizabeth S Jacobsen, Lena Nekludova, P Alexander Rolfe, Timothy W Danford, David K Gifford, Ernest Fraenkel, Graeme I Bell & Richard A Young

doi:10.1038/msb4100059
Published online: 02 May 2006

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Adaptively inferring human transcriptional subnetworks

Debopriya Das, Zaher Nahlé & Michael Q Zhang

doi:10.1038/msb4100067
Published online: 06 June 2006

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When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation

M T A P Kresnowati, W A van Winden, M J H Almering, A ten Pierick, C Ras, T A Knijnenburg, P Daran-Lapujade, J T Pronk, J J Heijnen & J M Daran

doi:10.1038/msb4100083
Published online: 12 September 2006

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Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability

Andrew C Tolonen, John Aach, Debbie Lindell, Zackary I Johnson, Trent Rector, Robert Steen, George M Church & Sallie W Chisholm

doi:10.1038/msb4100087
Published online: 03 October 2006

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2005

A global view of pleiotropy and phenotypically derived gene function in yeast

Aimée Marie Dudley, Daniel Maarten Janse, Amos Tanay, Ron Shamir & George McDonald Church

doi:10.1038/msb4100004
Published online: 29 March 2005

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Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium

Amos Tanay, Israel Steinfeld, Martin Kupiec & Ron Shamir

doi:10.1038/msb4100005
Published online: 29 March 2005

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Monitoring dynamics of single-cell gene expression over multiple cell cycles

Scott Cookson, Natalie Ostroff, Wyming Lee Pang, Dmitri Volfson & Jeff Hasty

doi:10.1038/msb4100032
Published online: 22 November 2005

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Gene function prediction from congruent synthetic lethal interactions in yeast

Ping Ye, Brian D Peyser, Xuewen Pan, Jef D Boeke, Forrest A Spencer & Joel S Bader

doi:10.1038/msb4100034
Published online: 22 November 2005

Synopsis | Full Text | PDF (257K) | Supplementary information

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