Gene Regulation and Systems Biology

2015:9

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 Available

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

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
Original research | Published on 10 Sep 2015

2014:8

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

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

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

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

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

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
Original research | Published on 10 Mar 2014

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

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

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
Original research | Published on 08 May 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

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

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

2013:7

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

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
Original research | Published on 06 Feb 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
Original research | Published on 20 Feb 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

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

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

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

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

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

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

2012:6

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

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)

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

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
Original research | Published on 11 Apr 2012

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

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 Available

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
Original research | Published on 25 Jun 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

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

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

2011:5

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
Original research | Published on 27 Feb 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

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

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

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

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

2010:4

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

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

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

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

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

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

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

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
Original research | Published on 20 Oct 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

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

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

2009:3

Patterns of Stochastic Behavior in Dynamically Unstable High-Dimensional Biochemical Networks
Simon Rosenfeld
Gene Regulation and Systems Biology 2009:3 1-10
Original research | Published on 29 Jan 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
Original research | Published on 19 Feb 2009

A Novel Function of Ethylene
Aiko Amagai
Gene Regulation and Systems Biology 2009:3 21-30
Original research | 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
Original research | Published on 12 Mar 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

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

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
Original research | Published on 19 Jun 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

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

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

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
Original research | Published on 08 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

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
Original research | Published on 21 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

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

2008:2

Pharmacodynamic Modeling of Acute and Chronic Effects of Methylprednisolone on Hepatic Urea Cycle Genes in Rats
Anasuya Hazra, Debra C. DuBois, Richard R. Almon, Grayson H. Snyder and William J. Jusko
Gene Regulation and Systems Biology 2008:2 1-19
Original research | Published on 14 Feb 2008

Gene Expression Analysis of Biological Systems Driving an Organotypic Model of Endometrial Carcinogenesis and Chemoprevention
Doris M. Benbrook, Stan Lightfoot, James Ranger-Moore, Tongzu Liu, Shylet Chengedza, William L. Berry and Igor Dozmorov
Gene Regulation and Systems Biology 2008:2 21-42
Original research | Published on 10 Feb 2008

Oxygen and Cell Fate Decisions
Qun Lin, Yuri Kim, Rodolfo M. Alarcon and Zhong Yun
Gene Regulation and Systems Biology 2008:2 43-51
Original research | Published on 10 Feb 2008

Reconstructing a Network of Stress-Response Regulators via Dynamic System Modeling of Gene Regulation
Wei-Sheng Wu, Wen-Hsiung Li and Bor-Sen Chen
Gene Regulation and Systems Biology 2008:2 53-62
Original research | Published on 10 Feb 2008

TAK1 mRNA Expression in the Tumor Tissue of Locally Advanced Head and Neck Cancer Patients
Beatriz Honorato, Juan Alcalde, Rafael Martinez-Monge, Natalia Zabalegui and Jesús Garcia-Foncillas
Gene Regulation and Systems Biology 2008:2 63-70
Original research | Published on 14 Feb 2008

Gene Regulation System of Vasopressin and Corticotoropin-Releasing Hormone
Masanori Yoshida
Gene Regulation and Systems Biology 2008:2 71-88
Original research | Published on 03 Mar 2008

Association of Vascular Endothelial Growth Factor Polymorphisms with Asthma in Tunisian Children
Jihene Lachheb, Hanene Chelbi, Imen Ben Dhifallah, Jamel Ammar, Kamel Hamzaoui and Agnès Hamzaoui
Gene Regulation and Systems Biology 2008:2 89-96
Original research | Published on 10 Apr 2008

Calcitriol and TO-901317 Interact in Human Prostate Cancer LNCaP Cells
Jing-Huan Wang and Pentti Tuohimaa
Gene Regulation and Systems Biology 2008:2 97-105
Original research | Published on 17 Mar 2008

Image Analysis and Data Normalization Procedures are Crucial for Microarray Analyses
Ali Kpatcha Kadanga, Christine Leroux, Muriel Bonnet, Stéphanie Chauvet, Bruno Meunier, Isabelle Cassar-Malek and Jean-François Hocquette
Gene Regulation and Systems Biology 2008:2 107-112
Original research | Published on 17 Mar 2008

Butyrate Induced Cell Cycle Arrest in Bovine Cells through Targeting Gene Expression Relevant to DNA Replication Apparatus
Cong-jun Li and Robert W. Li
Gene Regulation and Systems Biology 2008:2 113-123
Original research | Published on 17 Mar 2008

Comparison of Statistical Data Models for Identifying Differentially Expressed Genes Using a Generalized Likelihood Ratio Test
Kok-Yong Seng, Robb W. Glenny, David K. Madtes, Mary E. Spilker, Paolo Vicini and Sina A. Gharib
Gene Regulation and Systems Biology 2008:2 125-139
Original research | Published on 17 Mar 2008

Pharmacodynamic/Pharmacogenomic Modeling of Insulin Resistance Genes in Rat Muscle After Methylprednisolone Treatment: Exploring Regulatory Signaling Cascades
Zhenling Yao, Eric P. Hoffman, Svetlana Ghimbovschi, Debra C. DuBois, Richard R. Almon and William J. Jusko
Gene Regulation and Systems Biology 2008:2 141-161
Original research | Published on 23 Apr 2008

Multi-Target Approaches in Colon Cancer Chemoprevention Based on Systems Biology of Tumor Cell-Signaling
Suresh Guruswamy and Chinthalapally V. Rao
Gene Regulation and Systems Biology 2008:2 163-176
Original research | Published on 02 May 2008

MicroRNAs Regulate Osteogenesis and Chondrogenesis of Mouse Bone Marrow Stromal Cells
Salla Suomi, Hanna Taipaleenmäki, Anne Seppänen, Tommi Ripatti, Kalervo Väänänen, Teuvo Hentunen, Anna-Marja Säämänen and Tiina Laitala-Leinonen
Gene Regulation and Systems Biology 2008:2 177-191
Original research | Published on 22 Apr 2008

Centrality Analysis Methods for Biological Networks and Their Application to Gene Regulatory Networks
Dirk Koschützki and Falk Schreiber
Gene Regulation and Systems Biology 2008:2 193-201
Original research | Published on 15 May 2008

RNA Processing and mRNA Surveillance in Monogenic Diabetes
Jonathan M. Locke and Lorna W. Harries
Gene Regulation and Systems Biology 2008:2 203-212
Original research | Published on 21 May 2008

Gene Expression in Pre-MBT Embryos and Activation of Maternally-Inherited Program of Apoptosis to be Executed at around MBT as a Fail-Safe Mechanism in Xenopus Early Embryogenesis
Koichiro Shiokawa, Mai Aso, Takeshi Kondo, Hiroaki Uchiyama, Shinsaku Kuroyanagi, Jun-Ichi Takai, Senji Takahashi, Masayuki Kajitani, Chikara Kaito, Kazuhisa Sekimizu, Eiji Takayama, Kazuei Igarashi and Hiroshi Hara
Gene Regulation and Systems Biology 2008:2 213-231
Original research | Published on 29 May 2008

Level of Expression of the Nonmutant Ferrochelatase Allele is a Determinant of Biochemical Phenotype in a Mouse Model of Erythropoietic Protoporphyria
Joseph Bloomer, Yongming Wang and Dongquan Chen
Gene Regulation and Systems Biology 2008:2 233-241
Original research | Published on 29 May 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
Original research | Published on 20 Jun 2008

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
Original research | Published on 24 Nov 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
Original research | Published on 27 Aug 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
Original research | Published on 22 Sep 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
Original research | Published on 22 Jul 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
Original research | Published on 10 Oct 2008

2007:1

Systems Biology-Based Identification of Crosstalk between E2F Transcription Factors and the Fanconi Anemia Pathway
Moe Tategu, Takako Arauchi, Rena Tanaka, Hiroki Nakagawa and Kenichi Yoshida
Gene Regulation and Systems Biology 2007:1 1-8
Original research | Published on 01 May 2007

Evaluation of Two Outlier-Detection-Based Methods for Detecting Tissue-Selective Genes from Microarray Data
Koji Kadota, Tomokazu Konishi and Kentaro Shimizu
Gene Regulation and Systems Biology 2007:1 9-15
Original research | Published on 01 May 2007

Developing a Systems Biology Approach to Study Disease Progression Caused by Heterodera glycines in Glycine max
Vincent P. Klink, Christopher C. Overall and Benjamin F. Matthews
Gene Regulation and Systems Biology 2007:1 17-33
Original research | Published on 05 Jun 2007

Practical Lessons from Theoretical Models about the Somitogenesis
Aitor González and Ryoichiro Kageyama
Gene Regulation and Systems Biology 2007:1 35-42
Original research | Published on 28 May 2007

A Discussion Concerning the Inclusion of Variety Effect when Analysis of Variance is Used to Detect Differentially Expressed Genes
Guri Feten, Are Halvor Aastveit, Lars Snipen and Trygve Almøy
Gene Regulation and Systems Biology 2007:1 43-47
Original research | Published on 15 Jun 2007

The Effect of Aromatic Hydrocarbon Receptor on the Phenotype of the Hepa 1c1c7 Murine Hepatoma Cells in the Absence of Dioxin
Feng Wang, Ruixue Zhang, Shengli Shi and Oliver Hankinson
Gene Regulation and Systems Biology 2007:1 49-56
Original research | Published on 18 Sep 2007

Intensity Dependent Confidence Intervals on Microarray Measurements of Differentially Expressed Genes: A Case Study of the Effect of MK5, FKRP and TAF4 on the Transcriptome
Werner Van Belle, Nancy Gerits, Kirsti Jakobsen, Vigdis Brox, Marijke Van Ghelue and Ugo Moens
Gene Regulation and Systems Biology 2007:1 57-72
Original research | Published on 17 Jul 2007

Insulin Sensitizing Pharmacology of Thiazolidinediones Correlates with Mitochondrial Gene Expression rather than Activation of PPARγ
Charles W. Bolten, Patrick M. Blanner, William G. McDonald, Nicholas R. Staten, Richard A. Mazzarella, Graciela B. Arhancet, Martin F. Meier, David J. Weiss, Patrick M. Sullivan, Alexander E. Hromockyj, Rolf F. Kletzien and Jerry R. Colca
Gene Regulation and Systems Biology 2007:1 73-82
Original research | Published on 17 Sep 2007

The Remarkable Mechanism of Prostaglandin E2 on Synaptic Plasticity
Yukio Akaneya
Gene Regulation and Systems Biology 2007:1 83-89
Original research | Published on 09 May 2008

Computational Systems Biology in Cancer: Modeling Methods and Applications
Wayne Materi and David S. Wishart
Gene Regulation and Systems Biology 2007:1 91-110
Original research | Published on 17 Sep 2007

Role of Fetal Stem Cells in Maternal Tissue Regeneration
Jiang F. Zhong and Leslie P. Weiner
Gene Regulation and Systems Biology 2007:1 111-115
Original research | Published on 06 Sep 2007

CGI: Java Software for Mapping and Visualizing Data from Array-based Comparative Genomic Hybridization and Expression Profiling
Joyce Xiuweu-Xu Gu, Michael Yang Wei, Pulivarthi H. Rao, Ching C. Lau, Sanjiv Behl and Tsz-Kwong Man
Gene Regulation and Systems Biology 2007:1 131-136
Original research | Published on 06 Oct 2007

New Insights into the Genetic Regulation of Plasmodium Falciparum Obtained by Bayesian Modeling
Svetlana Bulashevska, Ezekiel Adebiyi, Benedikt Brors and Roland Eils
Gene Regulation and Systems Biology 2007:1 137-149
Original research | Published on 29 Nov 2007

Nonlinear Dynamic Trans/Cis Regulatory Circuit for Gene Transcription via Microarray Data
Yu-Hsiang Chang, Yu-Chao Wang and Bor-Sen Chen
Gene Regulation and Systems Biology 2007:1 151-166
Original research | Published on 12 Oct 2007

The Role and Regulation of Receptor-Like Kinases in Plant Defense
Kerry E. Goff and Katrina M. Ramonell
Gene Regulation and Systems Biology 2007:1 167-175
Original research | Published on 26 Sep 2007

β1-Integrin Signaling is Essential for Lens Fiber Survival
Andrew R. Samuelsson, Richard Belvindrah, Chuanyue Wu, Uli Müller and Willi Halfter
Gene Regulation and Systems Biology 2007:1 177-189
Original research | Published on 12 Oct 2007

Enterobacterial Small Mobile Sequences Carry Open Reading Frames and are Found Intragenically—Evolutionary Implications for Formation of New Peptides
Nicholas Delihas
Gene Regulation and Systems Biology 2007:1 191-205
Original research | Published on 16 Oct 2007

Role of SP-1 in SDS-Induced Adipose Differentiation Related Protein Synthesis in Human Keratinocytes
Emanuela Corsini, Omar Zancanella, Laura Lucchi, Barbara Viviani, Marina Marinovich and Corrado L. Galli
Gene Regulation and Systems Biology 2007:1 207-215
Original research | Published on 04 Oct 2007

Signaling Mechanisms of Endogenous Angiogenesis Inhibitors Derived from Type IV Collagen
Akulapalli Sudhakar and Chandra S. Boosani
Gene Regulation and Systems Biology 2007:1 217-226
Original research | Published on 14 Oct 2007

Trichoderma Biocontrol: Signal Transduction Pathways Involved in Host Sensing and Mycoparasitism
Susanne Zeilinger and Markus Omann
Gene Regulation and Systems Biology 2007:1 227-234
Original research | Published on 08 Nov 2007

Variability of DNA Microarray Gene Expression Profiles in Cultured Rat Primary Hepatocytes
Jun Xu, Xutao Deng, Victor Chan, Nancy Kelley-Loughnane, Brent W Harker, Leming Shi, Saber M. Hussain, John M. Frazier and Charles Wang
Gene Regulation and Systems Biology 2007:1 235-249
Original research | Published on 18 Nov 2007

Proposed Regulation of Gene Expression by Glucose in Rodent Heart
Martin E. Young, Jie Yan, Peter Razeghi, Robert C. Cooksey, Patrick H. Guthrie, Stanislaw M. Stepkowski, Donald A. McClain, Rong Tian and Heinrich Taegtmeyer
Gene Regulation and Systems Biology 2007:1 251-262
Original research | Published on 05 Nov 2007

MicroRNA Expression in Alzheimer Blood Mononuclear Cells
Hyman M. Schipper, Olivier C. Maes, Howard M. Chertkow and Eugenia Wang
Gene Regulation and Systems Biology 2007:1 263-274
Original research | Published on 20 Dec 2007

Transcription Initiation by Mix and Match Elements: Flexibility for Polymerase Binding to Bacterial Promoters
India G. Hook-Barnard and Deborah M. Hinton
Gene Regulation and Systems Biology 2007:1 275-293
Original research | Published on 17 Dec 2007

Current Status of Monocyte Differentiation-Inducing (MDI) Factors Derived from Human Fetal Membrane Chorion Cells Undergoing Apoptosis after Influenza Virus Infection
Noboru Uchide and Hiroo Toyoda
Gene Regulation and Systems Biology 2007:1 295-302
Original research | Published on 12 Nov 2007

Vectors Encoding Seven Oikosin Signal Peptides Transfected into CHO Cells Differ Greatly in Mediating Gaussia luciferase and Human Endostatin Production although mRNA Levels are Largely Unaffected
Christiane Tröße, Hanne Ravneberg, Beate Stern and Ian F. Pryme
Gene Regulation and Systems Biology 2007:1 303-312
Original research | Published on 11 Dec 2007

Prostate Cancer Epigenetics: A Review on Gene Regulation
Lena Diaw, Karen Woodson and John W. Gillespie
Gene Regulation and Systems Biology 2007:1 313-325
Original research | Published on 11 Dec 2007

Genomic Loci Modulating the Retinal Transcriptome in Wound Healing
Félix R. Vázquez-Chona, Lu Lu, Robert W. Williams, Eldon E. Geisert
Gene Regulation and System Biology 2007:1 327-348
Original research | Published on 14 Feb 2008

Gene Module Identification from Microarray Data Using Nonnegative Independent Component Analysis
Ting Gong, Jianhua Xuan, Chen Wang, Huai Li, Eric Hoffman, Robert Clarke and Yue Wang
Gene Regulation and Systems Biology 2007:1 349-363
Original research | Published on 15 Jan 2008

Early Onset of Heat-Shock Response in Mouse Embryos Revealed by Quantification of Stress-Inducible hsp70i RNA
Cristina Hartshorn, Aleksandra Anshelevich, Yanwei Jia and Lawrence J. Wangh
Gene Regulation and Systems Biology 2007:1 365-373
Original research | Published on 06 Dec 2007