• Searching elegansNet
• About elegansNet

• Animated & fun science - for grades 4 - 10, or older! (BrainPOP, LLC.)
• Amphibians
• Bioinformatics
• Cell
• Cells-Molecules-Organisms
• D. Discoideum
• Mouse
• Nematodes - ACeKit
• Nucleic Acid
• Sea Urchin
• Yeast

Weizmann Institute

• What is Bioinformatics?

Indiana University

• Introduction to Databases, Finding Genes, Protein Models

Rensselaer Polytechnic Institute

• Bioinformatics & Molecular Biology (Silvaggi, NR)
• Algorithms for nucleic acid and protein sequence analysis (Michael Zuker)

India.com

• List of News Topics

Clinton-Gore Admin.

• Bioinformatics in the 21^st Century - A Report to the Research Resources and Infrastructure Working Group Subcommittee on Biotechnology National Science and Technology Council White House Office of Science and Technology Policy.

• Why study them? U. Wisconsin

• Bioluminescence & GFP
• Bugs in the News
• Cell - Much information about cells and subcellular structures; includes graphics.
• Cells Live - How Big is a cell ? The size of viruses, bacteria, human cells? & More.
• Why Files
• Why is mouse an ideal model organism?
  • Wellcome Trust
  • Mouse Genetics (Silver)

• Model System in motion

• ACeKit: A C. elegans Survival Kit - Introductions & Informatics

• Why study them?

Yeast

• Using as Model

• Introduction - Fred Sherman

• Databases
• Projects Cheminfo
• Resources

• PubChem
• ChemBank: Small Molecule Bioactives DB
• Cheminformatics Links Collection @ CI.org

Projects Cheminformatics

• Center for Chemical Methodology and Library Development

Resources

• Cheminformatics.org
  • Cheminformatics Links
  • Data Sets

• System-Biology Org
• Publication

• Whole-istic Biology

GENOME BROWSERS

• Ensembl
• euGenes
• NCBI
• UCSC

GENE TRAP

• Genome Survey Sequences Database (dbGSS & NCBI)

• International Gene Trap Consortium

• BayGenomics

• German Gene Trap Consortium
• Gene Trap Mutagenesis
  • gene trap database
• Lexicon Genetics Inc.
• Mammalian Function Genomics Center

• Sanger Gen Trap Resources

• Gene Trap Paradigm

• Gene-trap mutagenesis: past, present and beyond
• Homologous Recombination
• Functional Genomics

• Contemporary gene targeting strategies for the novice.

• Cre-LoxP System - Animation

• Hit & Run Gene Targeting

• Tag & Exchange Gene Targeting

• Stable tag-exchange gene targeting

• Tools for targeted manipulation of mouse genome

• Confirming gene trap insertion site

• DATABASES
• SERVICES
• PROJECTS
• PORTALS  to more links
• PUBLICATIONS

• DCPD - Drosophila core promoter database
• DBTSS - Database of Transcriptional Start Sites (human)
• Eukaryotic Promoter
• EPD - Eukaryotic Promoter Database
• MotifDic database
• PLACE -Plant cis-acting regulatory DNA elements database
• SCPD - Saccharomyces cerevisiae promoter database
• TRANSFAC database

SERVICES -ciselemments

• Cis-teria !
• Cis-element clusters:
  • Cis-analyst
  • Fly enhancer
  • ModelGenerator and ModelInspector
  • Transcription Factor Binding Site Clusters in the Human Genome

• Phylogenetic footprinting:

  • ACUTS - Ancient Conserved UnTranslated Sequences
  • PipMaker
  • Vista
• TRES - Transcription Regulatory Element Search -
  a tool for Comparative Promoter Analysis

PROJECTS-ciselemments

||||Cis elements@Wheaton College

• A DNA motif lexicon (for example, for C.elegans)
• "Favorite gene" projects
• A catalogue of inverted repeats (IR)

PORTALS (more links)-ciselemments

• BioBencHelper
• Cis-teria!
• TRES

PUBLICATIONS

• Estrogen receptor α target genes and response elements in breast tumor cells

Reviews

• Highlights of 2003 Reviewed
• Breakthrough of the year - 2002 - Citation links
• History and Overview Introduction
• Other RNA World
• Genome Defense

• Reviews

   NATURE, 415, 197-243, 2002

• Cardiac excitation contraction coupling
• Seven transmembrane -spanning receptors and heart function
• Cardiac channelopathies
• New ideas about atrial fibrillation 50 years on
• The failing heart
• Myocardial gene therapy
• Myocyte renewal and ventricular remodelling

• New
• Main GFP Pages
• Criteria for selecting a pair of xFPs
• Gene Expression Probing 
• Quantitation, HTS, & ScreeningGFP
• Material & Methods
• News GroupGFP
• References & Links
• SensitivityGFP
• Vendors

• PA GFP

Main GFP Pages

• Clontech Living Colors Main Page
• Yahoo Green Fluorescent Protein Links
• GFP Applications Page by Wallace Marshall
• Molecular Motion Tools - fluorescent proteins (Thomas Hughes, Yale U.)
  • GFP information for making fluorescent constructs
  • Key papers on the properties of fluorescent proteins
  • Links to GFP resources & reagents
  • Cool applications of GFP

GFP-Probing Gene Expression (UMBC, Jincai Li)

• Application of Green Fluorescent Protein(GFP) on Gene Expression
  General Applications of GFP
  • Attributes of GFP
  • Green mouse?
  • Links to application

• MRC Imaging facility Links

News Group GFP

• Bionet Fluorescent Proteins

Quantitation & ScreeningGFP

• ABC of Quantitation -   1, 2, 3
• Quantitative monitoring of gene expression (Jincai Li)
  • Why quantitative
  • GFP sensor
  • Bioprocess control and monitoring
  • High-throughout screening
• Multiple color
• GFP colony picker (Genetix)

References GFP

• Reference & Links @UMBC,  Jincai Li

Sensitivity GFP

• b-gal vs. GFP

Vendors GFP

• BD Biosciences Clontech - Living Colors (TM) FluorescentGFP
• Omega Optical's DsRed sets are designed to work with the new red fluorescent protein

• Underhill &  Ozinsky, Current Opinion in Immunology 2002, 14:103*110
• O'Neill, Science's STKE, 8 August 2000.

TLRs & Imd

• Imd & Toll Pathways
  • IRAK-4
• Tlr-1
• Tlr-2 - Microbial ligands; NO-dependence & NO-Independence; peptidoglycans (gram-positive bacteria); Lipoprotein; LPS; Lipoarabinomannan
• Tlr-3 - ds RNA
• Tlr-4 - LPS Gram-negative; Taxol; F protein (RS virus); hsp60; fibronectin
• Tlr-5 - Flagellin
• Tlr-6
• Tlr-7 - Small anti-viral compounds
• Tlr-8
• Tlr-9 - CpG
• Tlr-10

Subunit Interactions

• ABC
• Which polymerase & when?
• Selected PCR Polymerases
• SOE PCR
• Quantitative PCR Primer Database (QPPD) - NCI

Which polymerase & when?

• KOD, Pfu Turbo, Taq
• PFU vs. Pwo
• Which Polymerase & When? Scientist 12[1]:17, Jan. 05, 1998. Also see Novagen
• DNA Polymerases Compared P1 & P2

Selected PCR Polymerases

• KOD HiFi DNA Polymerase - elongation rate and processivity are 5 times and 10–15 times higher, respectively, than Pfu. Fidelity?
• KOD Hot Start DNA Polymerase
• KOD XL DNA Polymerase
• High Fidelity + Long range PCR
• High fidelity - Pwo DNA Polymerase
• Stutter" or "Shadow" bands
• Taq + Pwo - Polishing Ends

• ABC Shuffle
• Examples - Summaries
• Labs shufflings
• Publications
• Shuffling Method Variants

• How DNA Shuffling  works  Cohen J, Science, 2001 Jul 13; 293 (5528):237.
• Animation of Molecular Breeding @Maxygen
• Directed Enzyme Evolution - Arnold FH, Caltech

Publications shuffle

• All Authors
• Maxygen Papers
  • Genome shuffling (Nature 2002).

Shuffle Variants

• DOGS - Gibbs et al. Gene 271 (2001) 13-20
• RPR - Random Priming Recombination - Shao et al. NAR 26, 681-683 (1998)
• RACHITT - Enchira
• RM-PCR - No homology needed.
• SCRATCHY - Homology independent; PNAS 98, 11248-11253 (2001)
• StEP - staggered extension process - Nat. Biotechnol. (1998)16:258-261.

Labs shufflings

• Arnold FH, Caltech

Examples - Summaries enzshuf

• Bacterial Activities
  • Enzyme DNA Shuffling - A summary table from Arnold lab.
• Mammalian & Viral Activities
  • Summary examples @elegansNet + Original paper citations.

• All  spectroscopy  SpectroscopyNow.com - All spectroscopy, from infrared to Raman (John Wiley).
• Mass spectroscopy i-mass.com - A comprehensive web site dedicated to the scientific discipline of mass spectrometry and the concept of mass.
  

• Atlas
• Calculators, Converters & Tables
• Chemical/physical Topics
• DATA - Chemical & Physical
• Dictionary
• Directories/Portal
• Manuals
• Measurements
• Nature Physicsportal
• Organic Chem.
• Periodic Tables

• Physical Reference Data

• Tables (Martindale's)

Chemistry & Physics Topics (Dave Young's + elegansNet)

• Introduction

  Selected Topics in Computational Chemistry

  Visual Quantum Mechanics - Essential concepts of quantum physics. Physics Education Research Group, Kansas State U.

• Models, Approximations and Reality
• Introduction to Computational Chemistry
• Computational Techniques in the Drug Design Process
• Computational Modeling of Molecular Vibrations
• QM/MM
• Finding Transition Structures
• Calculating Electronic Excited States
• SCF Convergence and Chaos Theory
• Spin Contamination

  Other Topics in Chemistry

• States of Matter
• Equations of State
• Introduction to Magnetochemistry
• Formulation Chemistry
• Winners of the Nobel Prize in Chemistry
• Holy Grails of Chemistry

  Physics topics

• Quantum Experiments and the Foundations of Physics (Anton Zeilinger at the University of Vienna).

  Quick Reference Guides

• Absolute Beginners Guide to Gaussian
• Using Gaussian Checkpoint Files
• Absolute Beginners Guide to MOPAC
• Most used UNIX commands
• Using the vi editor
• Using Motif Windows
• Computer Security Basics

  Links

• Chemistry related links
• General interest links

Directories ChemPhysics

• HyperPhysics -a broad-ranging interactive physics exploration environment (Rod Nave, Georgia State University).
• Organic chemistry resources world wide
• Wired Chemist

Manuals Chemistry

• Chemistry Web Book Easily searchable (NIST).

• Entropy on the World Wide Web - promotes appreciation of entropy in its many forms

• Merck

  • Home Edition

• Worthington Enzymes

   

Periodic Tables

• WebElements Periodic Table - Mark Winter [The University of Sheffield and WebElements Ltd, UK]

• The Pictorial Periodic Table - Chris Heilman

• Basics
• Databases
• Dictionary
• General Immunology
• Glossary
• Immune System
• HIV
  • More Immunodeficiency Resources
• Immunologic Diseases
  • CliniWeb
  • Karolinska Institute
• Immunological Synapse
  • Dendritic Cells
  • Toll-like Receptors
• Labs - Immunology
• MHC
• Monoclonal antibodies & therapies
• Search - MedMark
• Toll-like Receptors
• More Links

Basic Immunology

• The Immune system: Innate & Acquired

Databases Immunology

• Cytokine Family Database
• dbMHC database
• Kabat Database of Sequences of Proteins of Immunological Interest (Johnson, G and Wu, TT (2001) Nucleic Acids Research, 29: 205- 206).
• ImMunoGeneTics - integrated db specializing in Immunoglobulins (Ig), T cell receptors
  (TcR) and Major Histocompatibility Complex (MHC) molecules of all vertebrate species (created in 1989 by Marie-Paule Lefranc (Université
  Montpellier II, CNRS).
• IMGT/HLA Database provides a specialist databases for sequences of the human major histocompatibility complex (HLA) and includes the official sequences for the WHO HLA Nomenclature Committee For Factors of the HLA System. 
• IPD-MHC RAT Sequence Database
• Major Histocompatibility Complex (MHC) Binding Peptides Database - MHCPEP @ WEHI  

Labs - Immunology

• Reith, Walter , Geneva U., Faculty of Medicine

MHC

• ABC
  • MHC I 
  • MHC II
  • MHC I+II
• dbMHC Home@ NCBI
• IMGT/HLA Database - sequences of the human major histocompatibility complex (HLA)
• IPD-MHC RAT Sequence Database
• The MHC Haplotype Project (Wellcome Trust, Sanger Inst., UK.)
• MHC Haplotypes, Genetics, & Role in Transplantation. (pdf) - Richard Hunt
  med.sc.edu
• Major Histocompatibility Complex and Human Leukocyte Antigen Resources ashi-hla.org
• Major Histocompatibility Complex (MHC) Binding Peptides Database - MHCPEP @ WEHI
• WHO Nomenclature and HLA sequences at ANRI

Immunological Synapse

• Immunological Synapse--a Multitasking System
• How and Why Does the Immunological Synapse Form? Physical Chemistry Meets Cell Biology Science's STKE, 5 March 2002

• Databases & Tools
• Data Standard
• Chips, arrays, microarrays
• Glossary
• Interactomes
• Periodic Table of protein structures
• Phylogenetic Information
  • Surface-Mapping
• Portals
• Reviews
• Search
• Societies

• Pathway Specific Microarrays
  • SuperArray Biosience Corp
• Multiplexed protein profiling by rolling-circle amplification
• Protein Chips
• Reverse Transfection & Transfected cell microarrays - [Microarrays of cells expressing defined cDNAs. Nature 411, 3 May 2001]. Two uses include: (i) drug targets identification; (ii) expression cloning system for discovery of gene products that alter cellular physiology. (Sabatini Lab, Whitehead Institute for Biomedical Research).
  • Itegral Molecular (Akceli Inc.) - distribute reverse transfection or transfected cell microarray technology.
  • Cell Microarrays (Sabatini lecture).
• Small molecule microarrays
• Frozen Cell Microarray

Databases & Tools p&roteomics

• Data analysis and molecular databases for Genomic & Proteomic Research.
  • Biozon.org - Unified view of data from SwissProt, PDB, BIND, Genbank, KEGG and other databases.
  • MatchMiner: Batch-translates among many types of gene and protein identifiers.
  • GoMiner: Leverages the Gene Ontology for biological interpretation of microarrays data, etc.
  • MedMiner: Searches and organizes the PubMed literature on genes and drugs.
  • CIMminer: Produces Clustered Image Maps (CIMs) (i.e., clustered .heat maps.).
  • MIMminer: Electronically navigates Kohn Molecular Interaction Maps.
  • Also: An (opinionated) guide to microarray data analysis.
  • Coming soon: AbMiner: A database resource on available monoclonal antibodies
• Dart: To locate protein neighbors by domain architecture, learn about NCBI's new Domain Architecture Retrieval Tool.

• Motif & Domain Search

  FingerPRINTScan

  PatternFind

  pfam

  PRINTS

  Prosite

  SMART

  VAST - Searches for

  similarity between

  proteins

• Protein Database Search Engine - Protein DBS system provides Protein Global-to-Global Tertiary Structure Matching.
• PDBsum: A database of the known 3D structures of proteins and nucleic acids
• Proteome Analysis@EBI - 45 proteomes included with comprehensive statistical and comparative analyses of the predicted proteomes of fully sequenced organisms. The analysis is compiled using InterPro, CluSTr and GO, and is performed on the non-redundant complete proteome sets of SWISS-PROT and TrEMBL entries (ebi.ac.uk)
• C. elegans Proteome (EBI, UK).
• EC Enzyme
• ExPASy
• HIP - Harvard Institute of Proteomics.
• HUGE
• Human Serum Proteome
• MODBASE, a database of three-dimensional protein models calculated by comparative modeling (Rockefeller U). 
• NCBI
• Owl
• PDB - single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR.
• PIR
• Protein Chips of yeat - Science, Sept 14, 01
• Proteome Sanger Centre
• PROMISE - The Prosthetic groups and Metal Ions in Protein Active Sites Database Version 2.0 (U. of Leeds).
• Protein MSPcrunch: A BLAST post-processing filter - searches SWIR (non-redundant data bases of SwisProt, SP-TREMBL, & WormPep)(Sonnhammer &, Durbin).

• Protein Kinases: C. elegans; S. cerevisiae;

  Mammalian; Other

• Proteome Analysis comparing the Complete S. cerevisiae and C. elegans Proteomes: Orthology and Divergence (Steve Chervitz; 6/18/99).

• PSORT - Protein Cellular localization sites in Cells
• Pedant - a protein extraction, description, and analysis tool. Supplies computational analysis of sequences, genome analysis and annotation, and information on unfinished sequences (HMS Beagle; 5/12/00).
• POD - Comparing the Complete S. cerevisiae and C. elegans Proteomes: Orthology and Divergence (Steve Chervitz; Stanford U.)
• Parse Protein Pedigrees: offers automatic hierarchical classification of proteins. Proteins are processed using a novel clustering algorithm which relies on their sequence distances (Hebrew U).
• Serum Proteome
• Worm PD

Data Standard

Standards at last!

• MIAME Guidelines ((Nature Genetics 29, 365–371; 2001)

• Checklist of variables that should be included in every microarray publication

• Submission of microarray data to either of two databases: GEO; ArrayExpress

Interactomes

Interactomes

• Yeast proteins that interact and the peptide recognition domains involved. Science Jan 02
• Functional organization of the yeast proteome by systematic analysis of protein complexes.  Nature 415, 141 - 147, 2002.

Portals proteomics

• ProteomicsSURF - A proteomics directory of  methods & protocols for novice and advanced users. Also included are links to Bioinformatics, Genomics, Microarrays, PCR, Crystallography, NMR, & Chromatography.

Protein Reviews

• Proteomic Reviews (Nature)
• PROW: Search Protein Reviews On the Web is an online resource that features PROW Guides, authoritative short, structured reviews on proteins and protein families.

Search proteomics

• pfam text search
• PROW: Search

Societies proteomics

• Proteome

SEARCH ENGINES

Chubba

• Google Scholar

• CrossRef

• Google's University Search

• Access a large List

• Directory of Open Access Journals
• Search
• Specific Journals
• Essays & Reviews
• Protein Reviews

• elegansNet-Selected
• C. elegans related
• Journal Abbreviations
• Email alert setup

• Google Scholar

• Google's University Search

• Citation db
• Current Content
• Directory of Open Access Journals
• High Wire Press (over 230 journals listed).
• Electronic Journal Miner
• Medline (Evaluated)
• Medline Workbench
  • Abbreviated
  • Full content.
• Ovid
• Ovid Java
• PubMed
• BioMed Central (BMC)
• Science Functional Genomics
• Vandy Library Catalog
• Vandy Electronic Journals
• Worm Lit. Search