By Jeffrey M. Perkel Structure Made Simple A step-by-step guide to reaching into structural biology databases and extracting the most for your research. There’s certainly no shortage of structural biology data today, but that doesn’t make it easy to use. Between technical advances and high-throughput structural genomics, structure databases are stuffed to overflowing with multicolored renderings of proteins, nucleic acids, and macromolecul

By Jeffrey M. Perkel Can Mass Spec Really Do That? Unexpected applications of a technique best known as a proteomics powerhouse. Mass spectrometry (MS) is not just about proteomics, though its star in that field certainly shines bright. As anyone in the drug discovery, food science, petroleum, or chemistry industries can tell you, mass spec is considerably broader than that. “Traditionally it was a technique for looking at relatively small compou

By Jeffrey M. Perkel Tailor-Made Mass Spec Mass spec tinkerers describe their custom fixes for commercial hardware limitations. Once upon a time, mass spectrometers were open-platform devices that could be tweaked as new applications arose. Today’s mass specs, though, are tightly engineered black boxes: sample in, data out. “As the level of sophistication of software and components has improved, it’s almost impossible to

By Jeffrey M. Perkel Surpassing the Law of Averages How to expose the behaviors of genes, RNA, proteins, and metabolites in single cells. By necessity or convenience, almost everything we know about biochemistry and molecular biology derives from bulk behavior: From gene regulation to Michaelis-Menten kinetics, we understand biology in terms of what the “average” cell in a population does. But, as Jonathan Weissman of the University of Califo

By Jeffrey M. Perkel Sequencing On Target Techniques for pulling out and sequencing selected areas of the genome It's time for a genomics reality check. Despite the constant, glowing coverage of speedy, low-cost next-generation DNA sequencing, whole-genome analysis, and consumer genomics, researchers still have no idea what the vast majority of human genomic DNA does, nor the functional consequence of variations in those sequences. Thus, few researchers

Making the most of mass spectrometry imaging.

How to troubleshoot sample preparation for cryo-electron microscopy, an up-and-coming structural biology technique.

Protein-protein interaction assays for all occasions.

How to conduct your next large-scale epigenetic analysis

Researcher: Richard Young, member, Whitehead Institute for Biomedical Research, Cambridge, Mass. Project: Mapping transcription factor binding across the yeast genome. Problem: Chromatin immunoprecipita

Credit: © 2008 Illumina Inc. All Rights Reserved." /> Credit: © 2008 Illumina Inc. All Rights Reserved. Researcher: Steven Jones, head, Bioinformatics, Genome Sciences Center, British Columbia Cancer Research Center, Vancouver, BC, Canada Project: Mapping transcription-factor binding in interferon-gamma-stimulated and unstimu

Credit: Courtesy of John Greally, Albert Einstein College of Medicine, and PLoS ONE" /> Credit: Courtesy of John Greally, Albert Einstein College of Medicine, and PLoS ONE Researcher: John Greally, associate professor of Molecular Genetics, Albert Einstein College of Medicine, NY Project: Comparing ep