Subject archive

Chromatin & Transcription

2009

Backup in gene regulatory networks explains differences between binding and knockout results

Anthony Gitter, Zehava Siegfried, Michael Klutstein, Oriol Fornes, Baldo Oliva, Itamar Simon & Ziv Bar-Joseph

doi:10.1038/msb.2009.33
Published online: 16 June 2009

A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability

Amy K Schmid, David J Reiss, Min Pan, Tie Koide & Nitin S Baliga

doi:10.1038/msb.2009.40
Published online: 16 June 2009

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

Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture

Raja Jothi, S Balaji, Arthur Wuster, Joshua A Grochow, Jörg Gsponer, Teresa M Przytycka, L Aravind & M Madan Babu

doi:10.1038/msb.2009.52
Published online: 18 August 2009

Control and signal processing by transcriptional interference

Antoine Buetti-Dinh, Rosemarie Ungricht, János Z Kelemen, Chetak Shetty, Prasuna Ratna & Attila Becskei

doi:10.1038/msb.2009.61
Published online: 18 August 2009

Dissection of a complex transcriptional response using genome-wide transcriptional modelling

Martino Barenco, Daniel Brewer, Efterpi Papouli, Daniela Tomescu, Robin Callard, Jaroslav Stark & Michael Hubank

doi:10.1038/msb.2009.84
Published online: 17 November 2009

2008

Ultrasensitive gene regulation by positive feedback loops in nucleosome modification

Kim Sneppen, Mille A Micheelsen & Ian B Dodd

doi:10.1038/msb.2008.21
Published online: 15 April 2008

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

Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation

Ophir Shalem, Orna Dahan, Michal Levo, Maria Rodriguez Martinez, Itay Furman, Eran Segal & Yitzhak Pilpel

doi:10.1038/msb.2008.59
Published online: 14 October 2008

p53-repressed miRNAs are involved with E2F in a feed-forward loop promoting proliferation

Ran Brosh, Reut Shalgi, Atar Liran, Gilad Landan, Katya Korotayev, Giang Huong Nguyen, Espen Enerly, Hilde Johnsen, Yosef Buganim, Hilla Solomon, Ido Goldstein, Shalom Madar, Naomi Goldfinger, Anne-Lise Børresen-Dale, Doron Ginsberg, Curtis C Harris, Yitzhak Pilpel, Moshe Oren & Varda Rotter

doi:10.1038/msb.2008.65
Published online: 25 November 2008

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

2007

Tissue-specific regulatory elements in mammalian promoters

Andrew D Smith, Pavel Sumazin & Michael Q Zhang

doi:10.1038/msb4100114
Published online: 16 January 2007

Reconstructing dynamic regulatory maps

Jason Ernst, Oded Vainas, Christopher T Harbison, Itamar Simon & Ziv Bar-Joseph

doi:10.1038/msb4100115
Published online: 16 January 2007

Genome-wide transcriptional plasticity underlies cellular adaptation to novel challenge

Shay Stern, Tali Dror, Elad Stolovicki, Naama Brenner & Erez Braun

doi:10.1038/msb4100147
Published online: 24 April 2007

Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae

Hung Pham, Roberto Ferrari, Shawn J Cokus, Siavash K Kurdistani & Matteo Pellegrini

doi:10.1038/msb4100194
Published online: 18 December 2007

2006

Systems-level analyses identify extensive coupling among gene expression machines

Karolina Maciag, Steven J Altschuler, Michael D Slack, Nevan J Krogan, Andrew Emili, Jack F Greenblatt, Tom Maniatis & Lani F Wu

doi:10.1038/msb4100045
Published online: 17 January 2006

Deciphering principles of transcription regulation in eukaryotic genomes

Dat H Nguyen & Patrik D'haeseleer

doi:10.1038/msb4100054
Published online: 18 April 2006

A quantitative study of the benefits of co-regulation using the spoIIA operon as an example

Dagmar Iber

doi:10.1038/msb4100084
Published online: 22 August 2006

Communication between levels of transcriptional control improves robustness and adaptivity

Alexander M Tsankov, Christopher R Brown, Michael C Yu, Moe Z Win, Pamela A Silver & Jason M Casolari

doi:10.1038/msb4100106
Published online: 28 November 2006

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