Systems biology
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- Hereditary Inclusion Body Myopathy (HIBM2)
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- Stochastic Spatio-Temporal Dynamic Model for Gene/Protein Interaction Network in Early Drosophila Development
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Journal: Biomedical Engineering and Computational Biology
No abstract provided.
Evolution and Origin of HRS, a Protein Interacting with Merlin, the Neurofibromatosis 2 Gene Product (08/Oct/2009)
Hepatocyte growth factor receptor tyrosine kinase substrate (HRS) is an endosomal protein required for trafficking receptor tyrosine kinases from the early endosome to the lysosome. HRS interacts with Merlin, the Neurofibromatosis 2 (NF2) gene product, and this interaction may be important for Merlin’s tumor suppressor activity. Understanding the evolution, origin,...
Evaluation of the Role of FGF23 in Mineral Metabolism (03/Aug/2009)
Fibroblast growth factor 23 (FGF23) has recently been identified as a critical regulatory factor in phosphate (P) metabolism. Although the exact molecular mechanism of FGF23 synthesis through sensing the concentration of P is yet to be determined, experimental and clinical data indicate the influential role of FGF23 in P and...
Application of Petri Nets in Bone Remodeling (06/Jul/2009)
Understanding a mechanism of bone remodeling is a challenging task for both life scientists and model builders, since this highly interactive and nonlinear process can seldom be grasped by simple intuition. A set of ordinary differential equations (ODEs) have been built for simulating bone formation as well as bone resorption....
Simon Rosenfeld and Izet Kapetanovic DHHS/NIH/National Cancer Institute/Division of Cancer Prevention, EPN, 6130 Executive Blvd, Bethesda, MD 20892, U.S.A. Abstract In this paper, we outline the status quo and approaches to further development of the systems biology concepts with focus on applications in cancer prevention science. We...
Advances in Antisense Oligonucleotide Development for Target Identification, Validation, and as Novel Therapeutics (22/Sep/2008)
Moizza Mansoor and Alirio J. Melendez Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore. Abstract Antisense oligonucleotides (As-ODNs) are single stranded, synthetically prepared strands of deoxynucleotide sequences, usually 18–21 nucleotides in length, complementary to the mRNA sequence of the target gene....
Yoshiya L. Murashima, Jiro Suzuki and Mitsunobu Yoshii Division of Psychobiology, Tokyo Institute of Psychiatry, Tokyo, Japan. Abstract Purpose: Epileptic mutant EL mice show secondary generalized seizures. Seizure discharges initiate in the parietal cortex and generalize through the hippocampus. We have previously demonstrated an increase in the...
Molecular Mechanisms of Uterine Leiomyosarcomas: Involvement of Defect in LMP2 Expression (22/Jul/2008)
Takuma Hayashi1,6, Yuto Shimamura1, Taro Saegusa1, Akiko Horiuchi2, Yukihiro Kobayashi3, Nobuyoshi Hiraoka4, Yae Kanai4, Hiroyuki Aburatani5, Kenji Sano3 and Ikuo Konishi2 1Dept. of Immunology and Infectious Disease, Shinshu University Graduate School of Medicine. 2Dept. of Obstetrics and Gynecology, Shinshu University Medical School. 3Dept. of Laboratory Medicine, Shinshu...
Evidence of Highly Regulated Genes (in-Hubs) in Gene Networks of Saccharomyces Cerevisiae (14/Jul/2008)
Jesper Lundström1,2,3, Johan Björkegren1,3 and Jesper Tegnér2,3 1The Computational Medicine group, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Solna, SE-171 76 Stockholm, Sweden. 2Division of Computa- tional Biology, Department of Physics, Linköpings Institute of Technology, Linköping University, SE-581 83 Linköping, Sweden. 3Clinical Gene Networks,...
Testing the Accuracy of Eukaryotic Phylogenetic Profiles for Prediction of Biological Function (18/Jun/2008)
Saurav Singh and Dennis P. Wall Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115. Abstract A phylogenetic profile captures the pattern of gene gain and loss throughout evolutionary time. Proteins that interact directly or indirectly within the cell to perform a biological function will...
Testing the Accuracy of Eukaryotic Phylogenetic Profiles for Prediction of Biological Function (18/Jun/2008)
Saurav Singh and Dennis P. Wall Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115. Abstract A phylogenetic profile captures the pattern of gene gain and loss throughout evolutionary time. Proteins that interact directly or indirectly within the cell to perform a biological function will...
Centrality Analysis Methods for Biological Networks and Their Application to Gene Regulatory Networks (15/May/2008)
Dirk Koschützki1,2 and Falk Schreiber1,3 1Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Gatersleben, Germany. 2Department of Computer and Electrical Engineering, Furtwangen University of Applied Sciences, Robert-Gerwig-Platz 1, 78120 Furtwangen, Germany. 3Institute for Computer Science, Martin-Luther-University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120...
Multi-Target Approaches in Colon Cancer Chemoprevention Based on Systems Biology of Tumor Cell-Signaling (02/May/2008)
Suresh Guruswamy and Chinthalapally V. Rao Department of Medicine, Hematology-Oncology Section, University of Oklahoma Health Sciences Center, Oklahoma City, OK, U.S.A. Abstract Colorectal cancer is the leading cause of cancer related deaths in the United States. Although it is preventable, thousands of lives are lost each year...
Zhenling Yao1, Eric P. Hoffman3, Svetlana Ghimbovschi3, Debra C. DuBois1,2, Richard R. Almon1,2 and William J. Jusko1 1Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, 2Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York. 3Children’s National Research Center, Washington D.C. Abstract...
Borges Dilemma, Fundamental Laws, and Systems Biology (10/Apr/2008)
Ping Ao Department of Mechanical Engineering and Department of Physics, University of Washington, Seattle, WA 98195, U.S.A.
Association of Vascular Endothelial Growth Factor Polymorphisms with Asthma in Tunisian Children (10/Apr/2008)
Jihene Lachheb1, Hanene Chelbi1, Imen Ben Dhifallah1, Jamel Ammar1,2, Kamel Hamzaoui1 and Agnès Hamzaoui2 1Medicine University of Tunis, Homeostasis and cell Dysfunction Unit Research 99/UR/08-40, Tunis, Tunisia. 2Pneumology Hospital A Mami, Pavillon B; Department of Pediatric and Respiratory Diseases, Ariana, Tunisia. Abstract Background: Previous studies demonstrated that...
TAK1 mRNA Expression in the Tumor Tissue of Locally Advanced Head and Neck Cancer Patients (14/Feb/2008)
Beatriz Honorato1, Juan Alcalde2, Rafael Martinez-Monge3, Natalia Zabalegui4 and Jesús Garcia-Foncillas1 1Clinical Genetics Unit and Oncology Department, University Clinic of Navarra, Pamplona, Spain. 2Otolaringology Department, University Clinic of Navarra, Pamplona, Spain. 3Radiotherapy-Oncology Department, University Clinic of Navarra, Pamplona, Spain. 4Immunotherapy Laboratory, CIMA University of Navarra, Pamplona, Spain....
Reconstructing a Network of Stress-Response Regulators via Dynamic System Modeling of Gene Regulation (10/Feb/2008)
Wei-Sheng Wu1,2, Wen-Hsiung Li2,3 and Bor-Sen Chen1 1Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan. 2Department of Evolution and Ecology, University of Chicago, 1101 East 57th Street, Chicago, IL, 60637, U.S.A. 3Genomics Research Center, Academia Sinica, Taipei, Taiwan. Abstract...
Transcription Initiation by Mix and Match Elements: Flexibility for Polymerase Binding to Bacterial Promoters (17/Dec/2007)
India G. Hook-Barnard and Deborah M. Hinton Gene Expression and Regulation Section, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes Digestive and Kidney Diseases, National Institutes of Health, Bldg. 8 Room 2A-13, Bethesda, MD 20892-0830. Abstract Bacterial RNA polymerase is composed of...
Christiane Tröße1*, Hanne Ravneberg1, Beate Stern1,2 and Ian F. Pryme1,2 1UniTargetingResearch AS, Thormøhlensgt. 51, N-5006 Bergen, Norway. 2Department of Biomedicine, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway. *Present address: National Institute of Nutrition and Seafood Research, N-5817 Bergen, Norway. Abstract: The...
New Insights into the Genetic Regulation of Plasmodium Falciparum Obtained by Bayesian Modeling (29/Nov/2007)
Svetlana Bulashevska1, Ezekiel Adebiyi2, Benedikt Brors2 and Roland Eils2,3 1Division ‘Theoretical Bioinformatics’, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. 2Department of Computer and Information Sciences, Covenant University, PMB 1023, Ota, Nigeria. 3Department ‘Bioinformatics and Functional Genomics’, Institute of Pharmacy and...
Variability of DNA Microarray Gene Expression Profiles in Cultured Rat Primary Hepatocytes (18/Nov/2007)
Jun Xu1, Xutao Deng1,2, Victor Chan3, Nancy Kelley-Loughnane4, Brent W Harker5, Leming Shi6, Saber M. Hussain7, John M. Frazier7 and Charles Wang1,2 1Department of Medicine and Burns and Allen Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048; 2David Geffen School of Medicine at UCLA, Los Angeles, CA 90048; 3Alion...
Noboru Uchide1,2 and Hiroo Toyoda1 1Department of Clinical Molecular Genetics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan. 2Department of Medicine, Division of Infectious Disease, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, U.S.A.Abstract: Influenza virus infection induces...
Trichoderma Biocontrol: Signal Transduction Pathways Involved in Host Sensing and Mycoparasitism (08/Nov/2007)
Susanne Zeilinger and Markus Omann Vienna University of Technology, Institute for Chemical Engineering, Research Area of Gene Technology and Applied Biochemistry, Working Group Molecular Biochemistry of Fungi, Getreidemarkt 9, A-1060 Vienna, Austria.Abstract: Fungi of the genus Trichoderma are used as biocontrol agents against several plant pathogenic fungi like Rhizoctonia spp.,...
1Martin E. Young, 2Jie Yan, 3Peter Razeghi, 4Robert C. Cooksey, 3Patrick H. Guthrie, 5Stanislaw M. Stepkowski, 4Donald A. McClain, 2Rong Tian and 3Heinrich Taegtmeyer 1USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, Houston, Texas. 2Division of Cardiovascular Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts. 3Division...
Nicholas Delihas Department of Molecular Genetics and Microbiology, School of Medicine, SUNY, Stony Brook, NY 11794-5222, U.S.A.Abstract: Intergenic repeat units of 127-bp (RU-1) and 168-bp (RU-2), as well as a newly-found class of 103-bp (RU-3), represent small mobile sequences in enterobacterial genomes present in multiple intergenic regions. These repeat sequences...
Signaling Mechanisms of Endogenous Angiogenesis Inhibitors Derived from Type IV Collagen (14/Oct/2007)
Akulapalli Sudhakar1,2,3 and Chandra S. Boosani1 1Cell Signaling and Tumor Angiogenesis Laboratory, Department of Genetics, Boys Town National Research Hospital, Omaha, NE 68132. 2Department of Biomedical Sciences, Creighton University, School of Medicine, Omaha, NE, 68178. 3Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198.Abstract: Vascular...
Andrew R. Samuelsson1, Richard Belvindrah2, Chuanyue Wu3, Uli Müller2 and Willi Halfter1 1Department of Neurobiology, University of Pittsburgh, 1402 E Biological Science Tower, Pittsburgh PA 15261; 2Department of Cell Biology and Institute for Childhood and Neglected Disease, Scripps Research Institute, La Jolla, CA 92037; 3Department of Pathology, 707 Scaife Hall, University...
Nonlinear Dynamic Trans/Cis Regulatory Circuit for Gene Transcription via Microarray Data (12/Oct/2007)
Yu-Hsiang Chang, Yu-Chao Wang and Bor-Sen Chen Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan.Abstract: The trans-regulatory circuit is considered as the regulatory interactions between upstream regulatory genes and transcription factor binding site motifs or cis elements. And the cis-regulatory circuit...
Joyce Xiuweu-Xu Gu1, Michael Yang Wei1, Pulivarthi H. Rao1, Ching C. Lau1, Sanjiv Behl2 and Tsz-Kwong Man1 1Department of Pediatrics, Baylor College of Medicine and Texas Children’s Cancer Center, Houston, Texas. 2Department of Computer Science, University of Houston, Victoria, Texas.Abstract: With the increasing application of various genomic technologies in biomedical...