Recommended links

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Links by subject area:

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General reference

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Conferences

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Technology and techniques

  • Journal of Visualized Experiments (JoVE)

    JoVE is an online journal that publishes visualized (video-based) biological research studies. The web site aims to solve some of the most difficult problems in contemporary life-science research, such as the time-consuming learning of experimental techniques, and how to reliably reproduce biological experiments.

  • Nature Protocols

    Nature Protocols, which launched in June 2006, provides an online, comprehensive, recipe-like collection of biological and biomedical protocols. Nature Protocols articles are commissioned and peer reviewed, and cover diverse subjects, guaranteeing that there is something for everyone. Alongside the commissioned protocols, the web site presents the freely available interactive 'Protocols Network', into which anyone can upload their laboratory procedures.

  • Cold Spring Harbor (CSH) Protocols

    If you are looking for information on methods, head for CSH Protocols. For decades, participants in the hands-on courses and users of its laboratory manuals have gained access to the most reliable methods in molecular and cellular biology, and now this access is moving online.

  • Biological Research Protocol Books

    An up-to-date, comprehensive and organized compendium of research manuals and protocol books in the life sciences.

  • Biocompare

    Biocompare's mission is "to facilitate scientific discovery by providing objective product information to the life science community". Their web site provides information to allow you to compare reagent purchasing, and it has evolved to also include several other useful sections, such as New Technologies, News and Professional Reviews.

  • Protocols online

    This web site contains a collection of molecular and cell biology techniques from named labs. Includes a forum where scientists can share techniques, tools and tips.

  • Virtual Library — Microscopy

    Microscopy centres in various institutes, information on equipment, protocols, and images galore.

  • The green fluorescent protein applications page

    All about the myriad uses of green fluorescent protein (GFP): movies, product information and links to other GFP sites.

  • The Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

    The homepage of a US National Research Resource Center dedicated to the development of new technologies for specimen preparation and image analysis to study the three-dimensional structure of cells and tissues.

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Cell adhesion

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Cell death

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Cell growth and division

  • MitoCheck

    The integrative 'MitoCheck' consortium aims to carry out an audit of all the genes that are required during cell division to understand better this precisely choreographed process. It will also study the subcellular localization and the involvement of a subset of the gene products in protein complexes.

  • Modeling the Budding Yeast Cell Cycle

    This web site presents a mathematical model of cell-cycle control in budding yeast and is an enhancement of a research paper by the groups of John Tyson, Bela Novak and Frederick Cross. Browsing the site should give experimentalists a feel for the potential of mathematical modelling and how its predictive power can be useful to design new experiments.

  • Kohn interaction maps

    Kurt Kohn's information-packed graphical representations of protein interactions in the cell cycle and DNA repair. Makes the New York subway seem intuitive.

  • The Salmon lab

    Ted Salmon's lab maintains mitosis world and the cytokinetic mafia — an original web site for people who are "passionate about cytokinesis".

  • The Tumor Gene Database

    Searchable resource of proto-oncogenes and tumour-suppressor genes, with extensive references.

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Cell signalling

  • Pathway Interaction Database

    The Pathway Interaction Database (PID) is a highly structured, curated collection of information about known biomolecular interactions and cellular processes assembled into signalling pathways. This database is a collaborative project between academia and scientific publishing and is designed to support simple browsing across predefined pathways, the construction of larger networks, and analysis and visualization of lists of targeted molecules in the context of predefined and novel networks.

  • Cell Signalling Biology

    On the Cell Signalling Biology web site, which launched in 2006, Michael J. Berridge provides a large, comprehensive resource that discusses all aspects of cell signalling and integrates emerging cell-signalling findings.

  • The Pawson Lab

    Members of The Pawson Lab focus on studying the mechanisms that underlie intracellular signal transduction, and their web site contains useful information including data on Protein Interaction Domains.

  • The EF-Hand Calcium-Binding Proteins Data Library

    This web site is a useful resource that contains "...a growing collection of published sequence, structural, functional, and other information about EF-hand calcium-binding proteins and their roles in cellular signal transduction".

  • Calmodulin Target Database

    This database was pioneered by the Ikura laboratory at the Ontario Cancer Institute, Canada, and it offers an introduction to the EF-hand-containing Ca2+-receptor calmodulin that, on binding Ca2+, changes shape and can bind to various targets.

  • GPCRDB

    A web site all about G-protein-coupled receptors, containing information about various aspects — from phylogenetic trees to ligand-dissociation constants.

  • The Signaling Gateway

    "The Alliance for Cellular Signaling (AfCS)-Nature Signaling Gateway is a comprehensive and up-to-the-minute resource for anyone interested in signal transduction. This Gateway represents a unique collaboration between academia and scientific publishing and is designed to facilitate navigation of the complex world of research into cellular signaling. Information and data presented here are freely available to all." The site provides access to the 'Molecule Pages', a weekly updated section called 'Signaling Update', and the AfCS Data Center.

  • Biomolecular Interaction Network Database (BIND)

    BIND is an expanding database that contains information on biomolecular interactions, pathways and complexes. It includes high-throughput data submissions and hand-curated information that has been collected from the scientific literature.

  • Cytokines & Cells Online Pathfinder Encyclopaedia (COPE)

    Horst Ibelgauft's classic resource for cytokine enthusiasts. Contains an extensive glossary of terms, with references.

  • The Wnt Homepage

    Roel Nusse's guide to Wnt signalling, including comparative tables, lists of target genes, and links to PubMed and the sequence databases.

  • BioCarta

    Colourful signalling-pathway maps with extensive database links.

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Cellular microbiology

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Chromosome biology

  • Chromatin Structure and Function Page

    James Bone’s clearing house of chromatin-related information, containing continually updated news and links plus a section on employment opportunities for chromatin researchers.

  • Nucleosome and chromatin pages

    Information on DNA, histones, nucleosomes, higher-order chromatin structure and histone acetylation.

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Cytoskeleton

  • Virtual Cell

    A unique software modelling environment for quantitative cell biological research for scientists from diverse fields, from cell biologists to theoretical biophysicists.

  • Cell Migration Gateway

    Updated monthly, the Cell Migration Gateway is a free resource that highlights the latest developments in the field of cell migration. The site is divided into three main sections. Cell Migration Update presents the latest news and selected highlights of key articles, an up-to-date library of essential papers and a conference calendar listing forthcoming cell migration-related events around the world. Cell Migration Knowledgebase contains key factfiles for molecules relevant to cell migration. CMC Activity Center describes the various projects being carried out by members of the Cell Migration Consortium. Included in this section is a large and growing public repository of primary data and lists of resources available to migration researchers.

  • The myosin homepage

    Everything you ever wanted to know about myosin, but were afraid to ask. Hosted by the Myosin Group at the MRC Laboratory of Molecular Biology and the Cambridge Institute for Medical Research.

  • The kinesin homepage

    Liz Green and Steve Henikoff's colourful resource including research methods, extensive information on kinesin and its family members, and lots of movies showing these well-studied molecular motors in action.

  • Cell intelligence

    How do cells know where to go? Well-structured site with attractive images and movies.

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Developmental biology

  • WormAtlas

    WormAtlas aims to make the anatomy of Caenorhabditis elegans simple and accessible. The site has many useful features, including an illustrated handbook of worm anatomy and a description of staining and electron-microscopy methods. It is funded by a grant from the National Institutes of Health and is in close collaboration with WormBase.

  • Virtual Library - Developmental Biology

    Maintained by the Society for Developmental Biology, this jump-station has, among other things, an invaluable subject index linking to the homepages of many prominent developmental cell biologists.

  • Homeobox genes database

    All about hox genes: maps, networks, expression patterns, evolutionary relationships...

  • The Interactive Fly

    Comprehensive and regularly updated database of genes, developmental pathways, images, movies and more.

  • Zygote

    Scott Gilbert's online textbook of developmental cell biology; contains a plethora of beautiful images.

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Gene expression

  • Transcription Regulatory Regions Database

    The Transcription Regulatory Regions Database is a unique information resource that contains information (only experimental) on the structural and functional organization of transcription regulatory regions of eukaryotic genes.

  • Center for Biological Timing

    Links to meetings, institutes and courses, with the common thread of biological rhythms.

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Lipids, membranes and membrane traffic

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Metabolic pathways

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Nuclear structure and transport

  • Nuclear Protein Database (NPD)

    This searchable, curated database — which is regularly updated — contains information (for example, protein size and sequence, isoelectric point, and subnuclear compartment) on more than 1,000 vertebrate proteins, mainly from mice and humans, that are thought, or known, to be localized to the nucleus.

  • The Sedat Lab

    Research group focusing on nuclear architecture and chromosome organization.

  • Cellnucleus.com

    A community-driven web site for those interested in the structure and function of the nucleus.

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Nucleic-acid metabolism

  • The RNA World Website

    If you're looking for information about RNA, head for The RNA World Website. Set up and maintained by the Institute for Molecular Biology in Jena (now the Leibniz Institute for Age Research – Fritz Lipmann Institute), Germany, this site does a sterling job of bringing together RNA-related web resources to make the search for relevant information much easier.

  • The European Ribosomal RNA database

    Ribosomal RNA (rRNA) sequence data listed by organism; secondary-structure prediction programmes and other software; and links to related sites.

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Protein structure and metabolism

  • Peptide Atlas

    The PeptideAtlas is a multi–organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. PeptideAtlas was developed by the Seattle Proteome Center (SPC), a highly interactive, multidisciplinary group that brings together scientific expertise from diverse areas such as biology, chemistry, proteomics, physics, bioinformatics and statistics. The aim of SPC is to enhance and develop innovative proteomics technologies and software tools and apply them to biological questions.

  • PRoteomics IDEntifications Database

    PRIDE is an open-source database of protein identifications that is designed to allow researchers to store, share and compare their results. This free-to-use database aims to provide access to published, peer-reviewed, standardized data on protein identification from many different sources. PRIDE is closely linked to the Human Proteomics Organization's Proteomics Standards Initiative (HUPO-PSI) and will allow users to transfer data using the standards that are currently being developed as part of PSI.

  • NetPro™

    One of the largest and most comprehensive collections of completely curated protein–protein, gene–protein, gene–small-molecule interactions from the scientific literature.

  • UniProt database

    Three world-class protein databases — Swiss-Prot, the translated EMBL nucleotide sequence database (TrEMBL) and the Protein Information Resource-Protein Sequence Database (PIR-PSD) — have now been united to create the UniProt database. UniProt is available at three mirror sites (http://www.ebi.uniprot.org, http://www.expasy.uniprot.org and http://www.pir.uniprot.org), and provides free access to comprehensive and up-to-date information on protein sequence and function.

  • Human Protein Reference Database

    However you find your protein of choice, in the user-friendly Human Protein Reference Database (HPRD), information on every possible feature — alternative names, function, sequence, domains, motifs, interactions, expression, localization, post-translational modifications, substrates and any disease association — is just a click away.

  • InterPro

    This "integrated resource of protein domains and functional sites" combines all the commonly used protein domain databases in one resource.

  • Glycoforum

    Well-organized glycobiology site, including educational information and recent press releases.

  • Prolysis

    Proteases, proteasome and protease inhibitors. Includes CUTTER, a programme to generate and analyse proteolytic fragments.

  • SMART

    Simple Modular Architecture Research Tool, written by Peer Bork's group at the European Molecular Biology Laboratory in Heidelberg, is a powerful tool for putting modular protein domains in context.

  • Structural Classification of Proteins

    When the Structural Classification of Proteins (SCOP) database was launched, its aims were to provide a detailed and comprehensive description of structural and evolutionary relationships, as well as to provide links to co-ordinates, images of the structure, interactive viewers, sequence data and literature references. It now does this, and much more.

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