Gene Regulation and Systems Biology

tRNA-Derived Short Non-coding RNA as Interacting Partners of Argonaute Proteins
Megumi Shigematsu and Yohei Kirino
Gene Regulation and Systems Biology 2015:9 27-33
Review | Published on 10 Sep 2015

Effects of High Fat Feeding on Adipose Tissue Gene Expression in Diabetic Goto-Kakizaki Rats
Bai Xue, Jing Nie, Xi Wang, Debra C. DuBois, William J. Jusko, and Richard R. Almon
Gene Regulation and Systems Biology 2015:9 15-26
Original Research | Published on 10 Aug 2015

p53 Contributes to Differentiating Gene Expression Following Exposure to Acetaminophen and Its Less Hepatotoxic Regioisomer Both In Vitro and In Vivo
Brendan D. Stamper, Michael L. Garcia, Duy Q. Nguyen, Richard P. Beyer, Theo K. Bammler, Frederico M. Farin, Terrance J. Kavanagh and Sidney D. Nelson
Gene Regulation and Systems Biology 2015:9 1-14
Original Research | Published on 01 Jun 2015 | Video abstract

A Hypothetical Protein of Alteromonas macleodii AltDE1 (amad1_06475) Predicted to be a Cold-Shock Protein with RNA Chaperone Activity
Arafat Rahman Oany, Shah Adil Ishtiyaq Ahmad, KM Kaderi Kibria, Mohammad Uzzal Hossain and Tahmina Pervin Jyoti
Gene Regulation and Systems Biology 2014:8 141-147
Original Research | Published on 18 Dec 2014

A Comprehensive Profile of ChIP-Seq-Based PU.1/Spi1 Target Genes in Microglia
Jun-ichi Satoh, Naohiro Asahina, Shouta Kitano and Yoshihiro Kino
Gene Regulation and Systems Biology 2014:8 127-139
Original Research | Published on 08 Dec 2014

Endothelin-1 but not Endothelial Nitric Oxide Synthase Gene Polymorphism is Associated with Sickle Cell Disease in Africa
Tanya J. Thakur, Aldiouma Guindo, Londyn R. Cullifer, Yi Li, Ikhide G. Imumorin, Dapa A. Diallo and Bolaji N. Thomas
Gene Regulation and Systems Biology 2014:8 119-126
Original Research | Published on 25 May 2014

Species-Specific Regulation of t-PA and PAI-1 Gene Expression in Human and Rat Astrocytes
Anna Tjärnlund-Wolf, Karin Hultman, Fredrik Blomstrand, Michael Nilsson, Robert L. Medcalf and Christina Jern
Gene Regulation and Systems Biology 2014:8 113-118
Short Report | Published on 08 May 2014

Overfeeding Dairy Cattle During Late-Pregnancy Alters Hepatic PPARα-Regulated Pathways Including Hepatokines: Impact on Metabolism and Peripheral Insulin Sensitivity
M. Jawad Khan, Carolina B. Jacometo, Daniel E. Graugnard, Marcio N. Corrêa, Eduardo Schmitt, Felipe Cardoso and Juan J. Loor
Gene Regulation and Systems Biology 2014:8 97-111
Original Research | Published on 03 Apr 2014

DNA Conformational Transitions Induced by Supercoiling Control Transcription in Chromatin
Andrey N. Luchnik
Gene Regulation and Systems Biology 2014:8 89-96
Consise Review | Published on 12 Mar 2014 | Video abstract

Tissue-Specific Gene Expression and Regulation in Liver and Muscle Following Chronic Corticosteroid Administration
Tung T. Nguyen, Richard R. Almon, Debra C. DuBois, Siddharth Sukumaran, William J. Jusko, and Ioannis P. Androulakis
Gene Regulation and Systems Biology 2014:8 75-87
Methodology | Published on 10 Mar 2014

Tetracycline Derivative Minocycline Inhibits Autophagy and Inflammation in Concanavalin-A-Activated Human Hepatoma Cells
Michel Desjarlais, Jonathan Pratt, Amine Lounis, Catherine Mounier, Khadidja Haidara and Borhane Annabi
Gene Regulation and Systems Biology 2014:8 63-73
Original Research | Published on 04 Mar 2014

Discovery of Emphysema Relevant Molecular Networks from an A/J Mouse Inhalation Study Using Reverse Engineering and Forward Simulation (REFS™)
Yang Xiang, Ulrike Kogel, Stephan Gebel, Michael J. Peck, Manuel C. Peitsch, Viatcheslav R. Akmaev and Julia Hoeng
Gene Regulation and Systems Biology 2014:8 45-61
Original Research | Published on 19 Feb 2014

Gene Expression and Gene Ontology Enrichment Analysis for H3K4me3 and H3K4me1 in Mouse Liver and Mouse Embryonic Stem Cell Using ChIP-Seq and RNA-Seq
Ngoc Tam L. Tran and Chun-Hsi Huang
Gene Regulation and Systems Biology 2014:8 33-43
Original Research | Published on 20 Jan 2014

Central Role of the PPARγ Gene Network in Coordinating Beef Cattle Intramuscular Adipogenesis in Response to Weaning Age and Nutrition
Sonia J. Moisá, Daniel W. Shike, Dan B. Faulkner, William T. Meteer, Duane Keisler and Juan J. Loor
Gene Regulation and Systems Biology 2014:8 17-32
Original Research | Published on 08 Jan 2014

Innate Immunity Interactome Dynamics
Asmaa Elzawahry, Ashwini Patil, Yutaro Kumagai, Yutaka Suzuki and Kenta Nakai
Gene Regulation and Systems Biology 2014:8 1-15
Original Research | Published on 06 Jan 2014

Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases
Jun-ichi Satoh, Natsuki Kawana and Yoji Yamamoto
Gene Regulation and Systems Biology 2013:7 139-152
Original Research | Published on 04 Nov 2013

CEBPG Exhibits Allele-Specific Expression in Human Bronchial Epithelial Cells
Thomas M. Blomquist, Ronald D. Brown, Erin L. Crawford, Ivana de la Serna, Kandace Williams, Youngsook Yoon, Dawn-Alita Hernandez and James C. Willey
Gene Regulation and Systems Biology 2013:7 125-138
Original Research | Published on 04 Jul 2013

Dietary Lipid During Late-Pregnancy and Early-Lactation to Manipulate Metabolic and Inflammatory Gene Network Expression in Dairy Cattle Liver with a Focus on PPARs
Haji Akbar, Eduardo Schmitt, Michael A. Ballou, Marcio N. Corrêa, Edward J. DePeters and Juan J. Loor
Gene Regulation and Systems Biology 2013:7 103-123
Original Research | Published on 11 Jun 2013

Investigation of dmyc Promoter and Regulatory Regions
Jasmine Kharazmi and Cameron Moshfegh
Gene Regulation and Systems Biology 2013:7 85-102
Original Research | Published on 15 May 2013

Yin Yang 1 and Adipogenic Gene Network Expression in Longissimus Muscle of Beef Cattle in Response to Nutritional Management
Sonia J. Moisá, Daniel W. Shike, William T. Meteer, Duane Keisler, Dan B. Faulkner and Juan J. Loor
Gene Regulation and Systems Biology 2013:7 71-83
Original Research | Published on 16 Apr 2013

Butyrate Induced IGF2 Activation Correlated with Distinct Chromatin Signatures Due to Histone Modification
Joo Heon Shin, Robert W. Li, Yuan Gao, Derek M. Bickhart, George E. Liu, Weizhong Li, Sitao Wu and Cong-jun Li
Gene Regulation and Systems Biology 2013:7 57-70
Original Research | Published on 26 Mar 2013

A Comprehensive Profile of ChIP-Seq-Based STAT1 Target Genes Suggests the Complexity of STAT1-Mediated Gene Regulatory Mechanisms
Jun-ichi Satoh and Hiroko Tabunoki
Gene Regulation and Systems Biology 2013:7 41-56
Original Research | Published on 26 Mar 2013

Global Consensus Theorem and Self-Organized Criticality: Unifying Principles for Understanding Self-Organization, Swarm Intelligence and Mechanisms of Carcinogenesis
Simon Rosenfeld
Gene Regulation and Systems Biology 2013:7 23-39
Perspective | Published on 20 Feb 2013

Implications of Systemic Dysfunction for the Etiology of Malignancy
Sarah S. Knox and Michael F. Ochs
Gene Regulation and Systems Biology 2013:7 11-22
Perspective | Published on 06 Feb 2013

Extensive Ethnogenomic Diversity of Endothelial Nitric Oxide Synthase (eNOS) Polymorphisms
Bolaji N. Thomas, Tanya J. Thakur, Li Yi, Aldiouma Guindo, Dapa A. Diallo and Jurg Ott,
Gene Regulation and Systems Biology 2013:7 1-10
Original Research | Published on 15 Jan 2013

Effects of High Fat Feeding on Liver Gene Expression in Diabetic Goto-Kakizaki Rats
Richard R. Almon, Debra C. DuBois, Siddharth Sukumaran, Xi Wang, Bai Xue, Jing Nie and William J. Jusko
Gene Regulation and Systems Biology 2012:6 151-168
Original Research | Published on 28 Nov 2012

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 | Highly accessed (previous month)

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

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, Lívia 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