The scientific output by faculty in the Columbia University Department of Systems Biology has resulted in over 300 publications over the last five years. About one-third were published in journals with an impact factor higher than 13, reserved for the top 10% of scientific journals.

Among publications by Columbia faculty are several seminal contributions within the field of systems biology. For example, Columbia investigators assembled the first regulatory networks within cancer cells to be validated experimentally 1-4 , identified a previously unknown layer of post-transcriptional regulation involving microRNAs 5 , found a functional gene network associated with autism 6 , and demonstrated that nucleotide sequence determines the width of the DNA minor groove, which then determines the ways in which Hox transcription factors bind to DNA 7,8 . This last result suggests new ways to integrate insights from structural biology into the practice of systems biology. See our complete list of publications for more information.

The Department of Systems Biology has also been competitive in attracting funding to support our research. We have been awarded seven distinct center of excellence grants in systems biology, six of which are funded by the National Institutes of Health. This accomplishment reflects not only the relevance of the science being conducted at Columbia but also the highly collaborative and interdisciplinary nature of our program.

In addition to basic scientific discoveries, Columbia investigators have also developed many algorithms and software tools for predicting protein structure and the function of regulatory networks. Through a platform called geWorkbench , these tools are freely available and have been widely adopted within the research community. These efforts are supported by a major center grant from the Integrative Cancer Biology Program at the National Cancer Institute to maintain the Center for Multiscale Analysis of Genomic and Cellular Networks (MAGNet).


References

1 Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A. Reverse engineering of regulatory networks in human B cells. Nat Genet. 2005;37:282-90.

2 Wang K, Saito M, Bisikirska BC, Alvarez MJ, Lim WK, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin AA, Klein U, Dalla-Favera R, Califano A. Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat Biotechnol. 2009;27:829-39.

3 Carro MS, Lim WK, Alvarez MJ, Bollo RJ, Zhao X, Snyder EY, Sulman EP, Anne SL, Doetsch F, Colman H, Lasorella A, Aldape K, Califano A, Iavarone A. The transcriptional network for mesenchymal transformation of brain tumors. Nature. 2010;463:318-25.

4 Zhao X, D’Arca D, Lim WK, Brahmachary M, Carro MS, Ludwig T, Cardo CC, Guillemot F, Aldape K, Califano A, Iavarone A, Lasorella A. The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain. Dev Cell. 2009;17:210-21.

5 Sumazin P, Yang X, Chiu HS, Chung WJ, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M, Guarnieri P, Silva J, Califano A. An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell. 2011 Oct 14;147(2):370-81.

6 Gilman SR, Iossifov I, Levy D, Ronemus M, Wigler M, Vitkup D. Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses. Neuron. 2011 Jun 9;70(5):898-907.

7 Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B. The role of DNA shape in protein-DNA recognition. Nature. 2009 Oct 29;461(7268):1248-53.

8 Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A, Crickmore MA, Jacob V, Aggarwal AK, Honig B, Mann RS. Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell. 2007 Nov 2;131(3):530-43.