Mapping neuron connections in the brain

June 23, 2005

Debut of the new open access journalPLoS Computational Biology

The human brain contains from 10 to 100 billion neurons, and each has hundreds of connections with neighboring neurons. Making sense of these intricate connections is essential to understanding brain function, and the task is a monumental one.

Thanks to a new theoretical approach to mapping neuron connectivity published in PLoS Computational Biology by Bagrat Amirikian, a researcher at the Department of Neuroscience at the University of Minnesota, the task is now feasible. In the past, mapping connections between neurons was limited to either highly simplified formulations or tedious experimental methods requiring precise three-dimensional reconstructions of neuron arbors, tremendously branched structures formed by neurons.

Part of the difficulty in mapping lies in the complex structure of arbors. Amirikian has improved on past methods by developing a theoretical framework requiring only two-dimensional drawings of arbors. Such drawings are already available in the neuroscience literature for many types of neurons. With this method, neuron connection maps could be used to create computer simulations of neural circuits involving tens of thousands of neurons with biologically realistic connections--and provide a practical way to begin untangling the mysteries of the brain.
Citation: Amirikian B (2005) A phenomenological theory of spatially structured local synaptic connectivity. PLoS Comp Biol 1(1): e11.

Bagrat Amirikian
University of Minnesota
Announcing the debut of a new open access journal from the Public Library of Science -PLoS Computational Biology.

The Public Library of Science (PLoS) and the International Society for Computational Biology (ISCB) are pleased to announce the June 24 launch of PLoS Computational Biology (, a new open-access, peer-reviewed journal reporting major biological advances achieved through computation. Unique in its scope, the journal publishes research from one of the most rapidly growing and exciting areas of scientific inquiry. As a collaboration between a scholarly society and an open access publisher, the journal also provides further momentum to the shift towards unrestricted access and use of all scientific and medical literature.

"Today we have taken a very important first step to a new era of data and knowledge integration which has the potential to fundamentally change the way we do science," says Dr. Philip E. Bourne, editor-in-chief of PLoS Computational Biology. Bourne is a professor in the Department of Pharmacology at the University of California San Diego, co-director of the Protein Data Bank and senior advisor to the Life Sciences at the San Diego Supercomputer Center.

In the inaugural issue, founding editors Philip E. Bourne, Steven E. Brenner, and Michael B. Eisen explain the vision behind PLoS Computational Biology: "What motivates us to start a new journal at this time? Computation, driven in part by the influx of large amounts of data at all biological scales, has become a central feature of research and discovery in the life sciences."

"Until the appearance of PLoS Computational Biology, there has been no single publication with a focus on the important contributions of computational studies to the understanding of living systems," writes Michael Gribskov, president of ISCB, in an accompanying editorial.

Open access - free availability and unrestricted use - to all articles published in the journal is central to the mission of PLoS Computational Biology, and distinguishes this new journal from most scientific journals which still needlessly restrict access to their contents. Open access revolutionizes the way we use research literature, and takes much inspiration from the field of computational biology itself. Gribskov reminds us that "free availability of protein and nucleic acid sequences, protein structures, and other biological data is critical to practitioners of computational biology."

We invite you to explore the full complement of research in PLoS Computational Biology at


All works published in PLoS Computational Biology are open access. Everything is immediately available without cost to anyone, anywhere - to read, download, redistribute, include in databases, and otherwise use - subject only to the condition that the original authorship is properly attributed. Copyright is retained by the authors, and all works are licensed under the Creative Commons Attribution License.

The Public Library of Science (PLoS) is a non-profit organization of scientists and physicians committed to making the world's scientific and medical research a public resource. PLoS publishes open-access journals of original peer-reviewed research, including PLoS Biology and PLoS Medicine, which are available at no cost to anyone in the world with a connection to the Internet. More information can be found at and .

The International Society for Computational Biology (ISCB) is a scholarly society dedicated to advancing the scientific understanding of living systems through computation, with an emphasis on the role of computing and informatics in advancing molecular biology. Founded in 1997, the ISCB serves a global membership with the goal of increased understanding of the significance of bioinformatics in the scientific community, government, and the public at large. More about the ISCB can be found at

Rocky Choi
Publications Assistant
Public Library of Science
185 Berry Street, Suite 3100
San Francisco, CA USA 94107
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U.K.: +44-1223-494493


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