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JOURNAL

Gene Regulation and Systems Biology


An international, peer reviewed, open access journal focusing on the regulation of genes and the proteins they encode and the relationship between gene regulation and the wider field of systems biology.  The journal recognizes that regulation of genes and the proteins they encode is at the core of systems biology, and therefore understanding the role of gene regulation in the context of the entire system as it relates to disease processes will aid therapeutic development.  Combining knowledge of gene expression and promoter control, improving gene and protein networks, and determining the role of signal transduction will enhance our ability to treat complex diseases.

Editor in Chief: Professor James Willey

ISSN: 1177-6250

Processing Speed: High quality, constructive peer review and rapid editorial decision within an average of four weeks.



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FOXO1 Up-Regulates Human L-selectin Expression Through Binding to a Consensus FOXO1 Motif
Yuefen Lou, Xiaojiong Lu and Xitong Dang
Gene Regulation and Systems Biology 2012:6 139-149
Original Research | Published on 29 Oct 2012



A Next-Generation Sequencing Approach to Study the Transcriptomic Changes During the Differentiation of Physarum at the Single-Cell Level
Israel Barrantes, Jeremy Leipzig and Wolfgang Marwan
Gene Regulation and Systems Biology 2012:6 127-137
Original Research | Published on 01 Oct 2012



Ruminant Metabolic Systems Biology: Reconstruction and Integration of Transcriptome Dynamics Underlying Functional Responses of Tissues to Nutrition and Physiological Statea
Massimo Bionaz and Juan J. Loor
Gene Regulation and Systems Biology 2012:6 109-125
Review | Published on 25 Jun 2012



Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA
Michael R. Leuze, Tatiana V. Karpinets, Mustafa H. Syed, Alexander S. Beliaev and Edward C. Uberbacher
Gene Regulation and Systems Biology 2012:6 93-107
Original Research | Published on 30 May 2012 | Video abstract



Quantification of Transcriptome Responses of the Rumen Epithelium to Butyrate Infusion using RNA-seq Technology
Ransom L. Baldwin VI, Sitao Wu, Weizhong Li, Congjun Li, Brian J. Bequette and Robert W. Li
Gene Regulation and Systems Biology 2012:6 67-80
Original Research | Published on 16 May 2012



Unique Sex-Based Approach Identifies Transcriptomic Biomarkers Associated with Non-Syndromic Craniosynostosis
Brendan D. Stamper, Sarah S. Park, Richard P. Beyer, Theo K. Bammler and Michael L. Cunningham
Gene Regulation and Systems Biology 2012:6 81-92
Original Research | Published on 16 May 2012



A Flexible and Qualitatively Stable Model for Cell Cycle Dynamics Including DNA Damage Effects
Clark D. Jeffries, Charles R. Johnson, Tong Zhou, Dennis A. Simpson and William K. Kaufmann
Gene Regulation and Systems Biology 2012:6 55-66
Short Report | Published on 11 Apr 2012



Regulatory Mechanisms in Bone Following Mechanical Loading
Sara M. Mantila Roosa, Charles H. Turner and Yunlong Liu
Gene Regulation and Systems Biology 2012:6 43-53
Original Research | Published on 17 Jan 2012



Identification of cis-Regulatory Elements in the dmyc Gene of Drosophila Melanogaster
Jasmine Kharazmi, Cameron Moshfegh and Thomas Brody
Gene Regulation and Systems Biology 2012:6 15-42
Original Research | Published on 21 Dec 2011 | Highly accessed (previous month)



Alpha-Tocopherol Alters Transcription Activities that Modulates Tumor Necrosis Factor Alpha (TNF-a) Induced Inflammatory Response in Bovine Cells
Cong-Jun Li, Robert W. Li, Stanislaw Kahl and Theodore H. Elsasser
Gene Regulation and Systems Biology 2012:6 1-14
Original Research | Published on 05 Dec 2011



Biomolecular Self-Defense and Futility of High-Specificity Therapeutic Targeting
Simon Rosenfeld
Gene Regulation and Systems Biology 2011:5 89-104
Perspective | Published on 21 Nov 2011



Application of Structure Equation Modeling for Inferring a Serial Transcriptional Regulation in Yeast
Sachiyo Aburatani
Gene Regulation and Systems Biology 2011:5 75-88
Original Research | Published on 10 Nov 2011



Developmental Regulation of Genes Encoding Universal Stress Proteins in Schistosoma mansoni
Raphael D. Isokpehi, Ousman Mahmud, Andreas N. Mbah, Shaneka S. Simmons, LĂ­via Avelar, Rajendram V. Rajnarayanan, Udensi K. Udensi, Wellington K. Ayensu, Hari H. Cohly, Shyretha D. Brown, Centdrika R. Dates, Sonya D. Hentz, Shawntae J. Hughes, Dominique R. Smith-McInnis, Carvey O. Patterson, Jennifer N. Sims, Kelisha T. Turner, Baraka S. Williams, Matilda O. Johnson, Taiwo Adubi, Judith V. Mbuh, Chiaka I. Anumudu, Grace O. Adeoye, Bolaji N. Thomas, Oyekanmi Nashiru and Guilherme Oliveira
Gene Regulation and Systems Biology 2011:5 61-74
Original Research | Published on 19 Sep 2011



Identification of New SRF Binding Sites in Genes Modulated by SRF Over-Expression in Mouse Hearts
Xiaomin Zhang, Gohar Azhar, Scott Helms, Brian Burton, Chris Huang, Ying Zhong, Xuesong Gu, Hong Fang, Weida Tong and Jeanne Y. Wei
Gene Regulation and Systems Biology 2011:5 41-59
Original Research | Published on 12 Jul 2011



Critical Self-Organized Self-Sustained Oscillations in Large Regulatory Networks: Towards Understanding the Gene Expression Initiation
Simon Rosenfeld
Gene Regulation and Systems Biology 2011:5 27-40
Original Research | Published on 22 Mar 2011



Biology of the Mi-2/NuRD Complex in SLAC (Stemness, Longevity/Ageing, and Cancer)
Yue Zhang
Gene Regulation and Systems Biology 2011:5 1-26
Review | Published on 27 Feb 2011



Molecular Cloning of the Genes Encoding the PR55/Bβ/δ Regulatory Subunits for PP-2A and Analysis of Their Functions in Regulating Development of Goldfish, Carassius auratus
Jun-Qiong Zhao, Si-Si Xie, Wen-Bin Liu, Ya-Mei Xiao, Xiao-Ming Zeng, Mi Deng, Lili Gong, Jin-Ping Liu, Pei-Chao Chen, Jie Zhou, Xiao-Hui Hu, Jia-Han Lv, Xiang-Qian Yu, Dao Wang, Chi Li, Yun-Lei Peng, Gao-Peng Liao, Yun Liu and David Wan-Cheng Li
Gene Regulation and Systems Biology 2010:4 135-148
Original Research | Published on 20 Dec 2010



Identifying a Transcription Factor's Regulatory Targets from its Binding Targets
Fred Lai, Julie S. Chang and Wei-Sheng Wu
Gene Regulation and Systems Biology 2010:4 125-133
Original Research | Published on 08 Dec 2010



Alpha-Tocopherol Modulates Transcriptional Activities that Affect Essential Biological Processes in Bovine Cells
Cong-jun Li, Robert W. Li and Theodore H. Elsasser
Gene Regulation and Systems Biology 2010:4 109-124
Original Research | Published on 22 Nov 2010



Overexpression of Colligin 2 in Glioma Vasculature is Associated with Overexpression of Heat Shock Factor 2
Dana A.M. Mustafa, Anieta M. Sieuwerts, Ping Pin Zheng and Johan M. Kros
Gene Regulation and Systems Biology 2010:4 103-107
Short Report | Published on 20 Oct 2010



Omega-6 Fat Supplementation Alters Lipogenic Gene Expression in Bovine Subcutaneous Adipose Tissue
Sandeep J. Joseph, Scott L. Pratt, Enrique Pavan, Romdhane Rekaya and Susan K. Duckett
Gene Regulation and Systems Biology 2010:4 91-101
Original Research | Published on 19 Oct 2010



HO1 mRNA and Protein do not Change in Parallel in Bronchial Biopsies of Patients After Long Term Exposure to Sulfur Mustard
Mohammad Reza Nourani, Samaneh Yazdani, Mehryar Habibi Roudkenar, Majid Ebrahimi, Raheleh Halabian, Leila Mirbagheri, Mostafa Ghanei and Abbas Ali Imani Fooladi
Gene Regulation and Systems Biology 2010:4 83-90
Original Research | Published on 01 Oct 2010



Fractal Topology of Gene Promoter Networks at Phase Transitions
Preston R. Aldrich, Robert K. Horsley, Yousuf A. Ahmed, Joseph J. Williamson and Stefan M. Turcic
Gene Regulation and Systems Biology 2010:4 75-82
Original Research | Published on 28 Jul 2010



Do DNA Microarrays Tell the Story of Gene Expression?
Simon Rosenfeld
Gene Regulation and Systems Biology 2010:4 61-73
Debate | Published on 29 Jun 2010



Model-Based Analysis of FGF23 Regulation in Chronic Kidney Disease
Hiroki Yokota, Ana Pires, João F. Raposo and Hugo G. Ferreira
Gene Regulation and Systems Biology 2010:4 53-60
Original Research | Published on 09 Jun 2010



GA-based Design Algorithms for the Robust Synthetic Genetic Oscillators with Prescribed Amplitude, Period and Phase
Bor-Sen Chen and Po-Wei Chen
Gene Regulation and Systems Biology 2010:4 35-52
Original Research | Published on 24 May 2010



Inference of Cancer-specific Gene Regulatory Networks Using Soft Computing Rules
Xiaosheng Wang and Osamu Gotoh
Gene Regulation and Systems Biology 2010:4 19-34
Original Research | Published on 31 Mar 2010



Transcriptional Response Of E. coli Upon FimH-mediated Fimbrial Adhesion
Prasanna Bhomkar, Wayne Materi, Valentyna Semenchenko and David S. Wishart
Gene Regulation and Systems Biology 2010:4 1-17
Original Research | Published on 24 Mar 2010



Microarray Data Analysis of Gene Expression Evolution
Honghuang Lin
Gene Regulation and Systems Biology 2009:3 211-214
Short Commentary | Published on 27 Nov 2009



Hereditary Inclusion Body Myopathy (HIBM2)
Chris M. Jay, Nick Levonyak, Gregory Nemunaitis, Phillip B. Maples and John Nemunaitis
Gene Regulation and Systems Biology 2009:3 181-190
Review | Published on 21 Oct 2009



Characteristics of Transcriptional Activity in Nonlinear Dynamics of Genetic Regulatory Networks
Simon Rosenfeld
Gene Regulation and Systems Biology 2009:3 159-179
Original Research | Published on 19 Oct 2009



Stochastic Spatio-Temporal Dynamic Model for Gene/Protein Interaction Network in Early Drosophila Development
Cheng-Wei Li and Bor-Sen Chen
Gene Regulation and Systems Biology 2009:3 191-210
Original Research | Published on 19 Oct 2009



Evolution and Origin of HRS, a Protein Interacting with Merlin, the Neurofibromatosis 2 Gene Product
Leonid V. Omelyanchuk, Julia A. Pertseva, Sarah S. Burns and Long-Sheng Chang
Gene Regulation and Systems Biology 2009:3 143-157
Short Report | Published on 08 Oct 2009



Evaluation of the Role of FGF23 in Mineral Metabolism
Hiroki Yokota, João F. Raposo, Andy Chen, Chang Jiang and Hugo G. Ferreira
Gene Regulation and Systems Biology 2009:3 131-142
Original Research | Published on 03 Aug 2009



The Goldfish SG2NA Gene Encodes Two α-Type Regulatory Subunits for PP-2A and Displays Distinct Developmental Expression Pattern
Hai-Li Ma, Yun-Lei Peng, Lili Gong, Wen-Bin Liu, Shuming Sun, Jiao Liu, Chun-Bing Zheng, Hu Fu, Dan Yuan, Junqiong Zhao, Pei-Chao Chen, Si-si Xie, Xiao-Ming Zeng, Ya-Mei Xiao, Yun Liu and David Wan-Cheng Li
Gene Regulation and Systems Biology 2009:3 115-129
Original Research | Published on 21 Jul 2009



Application of Petri Nets in Bone Remodeling
Lingxi Li and Hiroki Yokota
Gene Regulation and Systems Biology 2009:3 105-114
Original Research | Published on 06 Jul 2009



Letter to the Editor: Does Dicer Expression Affect shRNA Processing?
Neil Senzer, Donald Rao and John Nemunaitis
Gene Regulation and Systems Biology 2009:3 103-104
Letter to Editor | Published on 19 Jun 2009



Safety and in vivo Expression of a GNE-Transgene: A Novel Treatment Approach for Hereditary Inclusion Body Myopathy-2
Anagha P. Phadke, Chris Jay, Salina J. Chen, Courtney Haddock, Zhaohui Wang, Yang Yu, Derek Nemunaitis, Gregory Nemunaitis, Nancy S. Templeton, Neil Senzer, Phillip B. Maples, Alex W. Tong and John Nemunaitis
Gene Regulation and Systems Biology 2009:3 89-101
Original Research | Published on 08 May 2009



Sigma Factors for Cyanobacterial Transcription
Sousuke Imamura and Munehiko Asayama
Gene Regulation and Systems Biology 2009:3 65-87
Review | Published on 22 Apr 2009



An Effective Tri-Clustering Algorithm Combining Expression Data with Gene Regulation Information
Ao Li and David Tuck
Gene Regulation and Systems Biology 2009:3 49-64
Original Research | Published on 15 Apr 2009



A Novel Function of Ethylene
Aiko Amagai
Gene Regulation and Systems Biology 2009:3 21-30
Review | Published on 07 Apr 2009



Post-Transcriptional Control of Chloroplast Gene Expression
Eva M. del Campo
Gene Regulation and Systems Biology 2009:3 31-47
Published on 12 Mar 2009



RNAi-Mediated Knockdown Showing Impaired Cell Survival in Drosophila Wing Imaginal Disc
Makoto Umemori, Okiko Habara, Tatsunori Iwata, Kousuke Maeda, Kana Nishinoue, Atsushi Okabe, Masahiko Takemura, Kuniaki Takahashi, Kaoru Saigo, Ryu Ueda and Takashi Adachi-Yamada
Gene Regulation and Systems Biology 2009:3 11-20
Published on 19 Feb 2009



Patterns of Stochastic Behavior in Dynamically Unstable High-Dimensional Biochemical Networks
Simon Rosenfeld
Gene Regulation and Systems Biology 2009:3 1-10
Published on 29 Jan 2009



The MAPK Signaling Cascade is a Central Hub in the Regulation of Cell Cycle, Apoptosis and Cytoskeleton Remodeling by Tripeptidyl-Peptidase II
Ramakrishna Sompallae, Vaia Stavropoulou, Mathieu Houde and Maria G. Masucci
Gene Regulation and Systems Biology 2008:2 253-265
Published on 24 Nov 2008



Systems Biology and Cancer Prevention: All Options on the Table
Simon Rosenfeld and Izet Kapetanovic
Gene Regulation and Systems Biology 2008:2 307-319
Published on 10 Oct 2008



Advances in Antisense Oligonucleotide Development for Target Identification, Validation, and as Novel Therapeutics
Moizza Mansoor and Alirio J. Melendez
Gene Regulation and Systems Biology 2008:2 275-295
Published on 22 Sep 2008



Role of Cytokines During Epileptogenesis and in the Transition from the Interictal to the Ictal State in the Epileptic Mutant EL Mouse
Yoshiya L. Murashima, Jiro Suzuki and Mitsunobu Yoshii
Gene Regulation and Systems Biology 2008:2 267-274
Published on 27 Aug 2008



Molecular Mechanisms of Uterine Leiomyosarcomas: Involvement of Defect in LMP2 Expression
Takuma Hayashi, Yuto Shimamura, Taro Saegusa, Akiko Horiuchi, Yukihiro Kobayashi, Nobuyoshi Hiraoka, Yae Kanai, Hiroyuki Aburatani, Kenji Sano and Ikuo Konishi
Gene Regulation and Systems Biology 2008:2 297-305
Published on 22 Jul 2008



Preclinical Assessment of wt GNE Gene Plasmid for Management of Hereditary Inclusion Body Myopathy 2 (HIBM2)
Chris Jay, Greg Nemunaitis, John Nemunaitis, Neil Senzer, Stephan Hinderlich, Daniel Darvish, Julie Ogden, John Eager, Alex Tong and Phil Maples
Gene Regulation and Systems Biology 2008:2 243-252
Published on 20 Jun 2008



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