Brown and his colleagues developed experimental methods for using DNA microarrays to investigate basic principles of genome organization, gene expression, cell regulation and specialization, physiology, development and disease, and the microbiome, along with statistical and computational tools for visualizing and interpreting the resulting large volumes of data. This work was especially revealing for the molecular portraits of many human cancers including lymphomas such as DLBCL, breast cancers, and other tumors, as part of diverse global collaborations including David Botstein, Michael Eisen, Lou Staudt, Ash Alizadeh, and others. Microarray technologies are widely used for comparing gene expression patterns and other genome features among individuals and their tissues and cells, providing information on disease subcategories, disease prognosis, and treatment outcome. Starting in the late 1990s, Brown began publicly voicing concern over what he called "a fundamentally flawed process of scientific publishing," in which academics typically published results of publicly funded research in private, commercial publishing houses that charged subscription fees for access to journals. “We viewed this entire process as being patently unfair. Not only were scientists in poor countries being denied access to the latest and best information out there, but the public who supports this research was being denied access as well. We felt there simply had to be a better way to do it," Brown told a University of Chicago medical journal. Brown began a collaboration with other scientists, including Harold Varmus (then director of the National Institutes of Health), David J. Lipman (then director of the National Center for Biotechnology Information), and Michael Eisen of Lawrence Berkeley National Laboratory, to overhaul the scientific and medical publishing systems to make papers available on the rapidly developing Internet platforms such as Usenet and the World Wide Web. "Why should publishers be able to control what I can do with information that was published by my scientific colleagues whose motivation was exactly to have their discoveries contribute to future discoveries? ... We had already existing tools that we could use to so to speak hyperlink things so that you could reorganize information in systematic ways, but they weren't really being exploited by the conventional scientific literature," Brown said in an interview with BioMedCentral Biology. The magazine Nature reported that the scientists' open-access movement could "spell the end for many print titles"; Brown called subscription-based scientific journals "anachronisms." In 2001, Brown, Eisen and Varmus co-founded the Public Library of Science (PLOS) to