La Folie, Quo Vadis, Evo-Devo?

1989
Li, K. C. and Duan, N. (1989). Regression analysis under link violation. Ann. Statist. 17, 1009-1052.

http://www.nature.com/nrg/journal/v10/n1/full/nrg2510.html

Rosetta Inpharmatics, LLC / Merck & Company, Inc.

Theodosius Dobzhansky:
"Nothing in biology makes sense except in the light of evolution"

這是我在碩士班時學的~~這要感謝老許的指導
一樣依照我個人風格, 本篇文章一率採用cluster寫作法, 並且dynamic update....

達爾文在天國一定會保佑我的, 雖然我知道他一定是被打入地獄, 但這兩篇可以讓他上天堂(完全不知道這三句怎麼來的...XD)

http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-2958.2008.06221.x
Molecular Microbiology, doi:10.1111/j.1365-2958.2008.06221.x

The evolution of molecular biology into systems biology
ature Biotechnology 22, 1249 - 1252 (2004)

http://www.sciencemag.org/content/vol319/issue5871/index.dtl

HCL - Hierarchical clustering
Eisen, M.B., P.T. Spellman, P.O. Brown, and D. Botstein. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95:14863-14868.

Systems Biology Markup Language

Proc Natl Acad Sci U S A. 2001 November 20; 98(24): 13763–13768.
Published online 2001 November 6. doi: 10.1073/pnas.231499798.

Systems biology is a new field in the molecular life sciences. It is new as molecular biology was in the fifties and as cell biology was in the seventies. In my definition, systems biology is a science that aims to elucidate the general principles that govern the emergence of biological function from the interactions of components of living systems. Biological function is defined as all it takes for an organism to survive momentarily and under various stresses that reflect what its ancestors have been subject to in evolution. The components are the biological macromolecules, largely (although not completely) encoded by the genome, or higher order aggregates of such components. Indeed, biology appears to be organized in a modular fashion. This is clear in the sense of structure, with examples such as the structure of catalytic units (enzymes), confinement units (membranous vesicles), and inheritable information (chromatin). It is less clear perhaps in the sense of units of function such as metabolic pathways, endocytosis and division. Yet, if only to make understanding by the human mind possible, systems biology also aims to understand cell function in terms of those well- and ill-defined higher order modules.

Transcriptional regulation networks in cells orchestrate gene expression. In this network the 'nodes' are operons, and each 'edge' is directed from an operon that encodes a transcription factor to an operon that it directly regulates (an operon is one or more genes transcribed on the same mRNA). We asked whether one can decompose such networks into basic building blocks. To accomplish this, we generalize the concept of motifs, widely used in analyzing sequences, to the level of networks. We define 'network motifs', patterns of interconnections that recur in many different parts of a network, at frequencies much higher than in randomized networks that preserve the number of incoming an outgoing edges for each node. We developed algorithms for detecting network motifs and applied them to one of the best-characterized regulation network, that of transcriptional interactions in Escherichia coli. We find that much of the network is composed of repeated appearances of three highly significant motifs. Each network motif has a specific function in determining gene expression, such as generating temporal expression programs and governing the responses to fluctuating external signals. The motifs also allow an easily interpretable view of the entire known transcriptional network of the organism. This work is available in pdf form. The transcriptional database contains 577 interactions between 116 TFs and 419 operons. It was based on an existing database (RegulonDB). We enhanced RegulonDB by an extensive literature search, adding 35 new TFs, including alternative sigma factors, and over a hundred new interactions from the literature. The dataset consists of established interactions in which a TF directly binds a regulatory site.

http://www.wretch.cc/album/show.php?i=tear2001&b=1&f=1135926837&p=1

http://www.wretch.cc/album/show.php?i=tear2001&b=1&f=1135926836&p=0
Network biology offers a quantifiable description of the networks that characterize various biological systems.Here we define the most basic network measures that allow us to compare and characterize different complex networks.

D. Rind

With the discovery of DNA, the completion of genome sequencing of a number of organisms, and the advent of powerful high-throughput measurement technologies such as microarrays, it is now commonly said that biology has gone through a revolution. But I also have heard it said that biology is only about to go through a scientific revolution, much as physics did in the 17th century. In messianic hopes, people foretell the coming of the Newton of biology, but it is up to us, the scientific community, to set the stage for that to happen.