Cells

Components of Cell Biochemistry

• BIOCHEMISTRY
• Garrett and Grisham Web Site
• 
  
• STRUCTURAL/TRANSPORT
• Globin Gene Server home page
• 
  
• ACID NUCLEIC BINDING
• The Sanger Centre: RNA recognition motif
• RNA binding strategies of ribosomal proteins (review on Nucleic Acids Research, Draper and Reynaldo, 1999)
• 
  
• SIGNALS AND RECEPTORS
• Cytokine and Cytokine Receptor Pleiotropy and Redundancy
• TGF-beta family
• NRSAS - Nuclear Receptor Structure Analysis Servers (Bettler et al., 2003)
• 
  
• PROTEIN KINASES AND SIGNAL TRANSDUCTION
• ***Signal Transduction Knowledge Environment
• Alliance for Cellular Signaling - Relationships between sets of inputs and outputs in signaling cells<>Protein Kinase Resource   |   Protein Kinases & Medicine
• NPG web focus: Kinases in cancer - Focus
• Pathway Interaction Database - An authoritative database for exploring signaling pathways
• 
  
• METABOLISM
• Enzyme Nomenclature - Enzyme Database
• BRENDA - (BRaunschweig ENzyme DAtabase): protein function database (Schomburg et al., 2004 update)
• PRECISE - a Database of Predicted and Consensus Interaction Sites in Enzymes (Sheu et al., 2004)
• EzCatDB - the Enzyme Catalytic-mechanism Database (Nagano 2005)
• Titles in NetBiochem
• 
  
• PROTEIN INTERACTIONS
• Interaction Databases List
• The GRID - The General Repository for Interaction Datasets (paper in GenomeBiology 2003)
• Protein Interaction Prediction (links)
• STRING - known and predicted protein-protein associations, integrated and transferred across organisms (von Mering et al., 2005)
• Database of Interacting Proteins (Salwinski et al., 2004)
• BIND - The Biomolecular Interaction Network Database (Alfarano et al., 2005)
• IntAct (HermJacob et al., 2004)
• Biocarta - graphical view of pathways
• ERGO (Integrated Genomics) curated database DNA, with connected similarities, functions, pathways
• Yeast protein complex database
• The Human Protein Reference Database (PRD) - integrated information about human proteins (Peri et al., 2003)

Cell simulation

• Whole Cell Simulation (Tomita, 2001)
• E-Cell Project   | Science -- Normile 284 (5411): 80
• Cellular Programming - Evolution of Parallel Cellular Machines
• MEG - Model Extender for Gepasi - building models of differentiated and heterogeneous biochemical systems
• Genetic Circuits Research Group - building genome-based models of bacteria (University of California, San Diego)
• The CyberCell Database (CCDB): a self-updating, relational database for in silico modeling of E. coli (Sundararaj et al., 2004)
• Genetic Programming.org   |   Pacific Symposium on Biocomputing 2001 - John Koza's method
• The virtual cell - National Resource for Cell Analysis and Modeling (NRCAM)
• MCell - A General Monte Carlo Simulator of Cellular Microphysiology (The Salk Institute / Pittsburgh Supercomputing Center)
• In Silico Cell at Physiome, written in CellML (www.CellML.org)
• Department of Energy Microbial Cell Project  - Understanding How a Cell Works
• Artificial cells: prospects for biotechnology (Pohorille andDeamer2002)
• STOCKS: STOChastic Kinetic Simulation of biochemical processes with Gillespie algorithm
• Other Links about Simulation of biological systems
• Arkin Laboratory for Dynamical Genomics
• Reactome - a knowledgebase of biological pathways (Joshi-Tope et al., 2005)
• GeneNet in 2005 (Ananko et al., 2005)
• LINCS - network-based understanding of biology by cataloging changes
  
• Brain Simulation: Human Brain Project - Blue Brain Project - Brain Scales - Allen Institute
  

Cell organization

• Cell biology: Join the crowd - Nature, Sep 8, 2003
• Cellular organelles
• The cytoskeleton - Nature Insights
• Exocytosis
• Phagocytosis
• Protein transport

Cell collections

• Cell Line Data Base (CLDB): information on 3500 human and animal cell lines available in Italy and Europe.
• The CABRI Project - Simple Search of the CABRI Catalogues

Stem Cells

• Focus on stem cells - Nature - Web focus
• A Stem Cell Molecular Signature - Science, October 18, 2002
• "Stemness": Transcriptional Profiling of Embryonic and Adult Stem Cells - Science, October 18, 2002
• From Adult Bone Marrow to to Multinucleate Muscle in Fiber Response to Injury  - (LaBarge and Blau, 2002)
• Cellule staminali umane da embrioni e da organismi adulti - R. Colombo (Ita)
• Candidate Genes Associated With Pluripotency and Lineage Specificity - Tanaka et al., Genome Res 2002
• Cell plasticity: Flexible arrangement - Nature, Sep 4, 2003
• Developmental reprogramming: Take a cell, any cell... - Nature, 2003
• Intestinal stem cells protect their genome by selective segregation of template DNA strands (Potten et al. , 2002)

Apoptosis

• Apoptosis in Development
• Cell Death - Opening page

Images

• Cells alive: a gallery of images and movies with cells
• Home(page) Movies
• DNALC: Biology Animation Library

Microbiology

• Microbiology Resources: selected by smu

Books

• Djaczenko - Biologia - CISU, 1980

DNA