@article {19160,
	title = {Dirichlet Mixtures, the Dirichlet Process, and the Structure of Protein Space},
	journal = {Journal of Computational Biology},
	volume = {20},
	number = {1},
	year = {2013},
	abstract = {The Dirichlet process is used to model probability distributions that are mixtures of an unknown number of components. Amino acid frequencies at homologous positions within related proteins have been fruitfully modeled by Dirichlet mixtures, and we use the Dirichlet process to derive such mixtures with an unbounded number of components. This application of the method requires several technical innovations to sample an unbounded number of Dirichlet-mixture components. The resulting Dirichlet mixtures model multiple-alignment data substantially better than do previously derived ones. They consist of over 500 components, in contrast to fewer than 40 previously, and provide a novel perspective on the structure of proteins. Individual protein positions should be seen not as falling into one of several categories, but rather as arrayed near probability ridges winding through amino acid multinomial space.},
	keywords = {ALIGNMENT, computational molecular biology, dynamic programming, multiple alignment, sequence analysis},
	doi = {10.1089/cmb.2012.0244},
	author = {Nguyen,Viet-An and Jordan Boyd-Graber and Altschul, Stephen F.}
}
@conference {14723,
	title = {PLANet: an active internetwork},
	booktitle = {IEEE INFOCOM {\textquoteright}99. Eighteenth Annual Joint Conference of the IEEE Computer and Communications Societies. Proceedings},
	volume = {3},
	year = {1999},
	month = {1999/03/21/25},
	pages = {1124-1133 vol.3 - 1124-1133 vol.3},
	publisher = {IEEE},
	organization = {IEEE},
	abstract = {We present PLANet: an active network architecture and implementation. In addition to a standard suite of Internet-like services, PLANet has two key programmability features: (1) all packets contain programs; and (2) router functionality may be extended dynamically. Packet programs are written in our special purpose programming language PLAN, the Packet Language for Active Networks, while dynamic router extensions are written in OCaml, a dialect of ML. Currently, PLANet routers run as byte-code-interpreted Linux user-space applications, and support Ethernet and IP as link layers. PLANet achieves respectable performance on standard networking operations: on 300 MHz Pentium-II{\textquoteright}s attached to 100 Mbps Ethernet, PLANet can route 48 Mbps and switch over 5000 packets per second. We demonstrate the utility of PLANet{\textquoteright}s activeness by showing experimentally how it can nontrivially improve application and aggregate network performance in congested conditions},
	keywords = {100 Mbit/s, 300 MHz, 48 Mbit/s, active internetwork, active network architecture, active network implementation, byte-code-interpreted applications, Computer architecture, Computer languages, Computer networks, congested conditions, dynamic programming, dynamic router extensions, Ethernet, Ethernet networks, INFORMATION SCIENCE, Internet, Internet-like services, internetworking, IP, IP networks, link layers, Linux user-space applications, Local area networks, ML dialect, Network performance, networking operations, OCaml, Packet Language for Active Networks, packet programs, packet switching, Pentium-II, performance, performance evaluation, PLAN, PLANet, Planets, programmability features, programming languages, router functionality, special purpose programming language, Switches, telecommunication network routing, Transport protocols, Web and internet services},
	isbn = {0-7803-5417-6},
	doi = {10.1109/INFCOM.1999.751668},
	author = {Hicks, Michael W. and Moore,J. T and Alexander,D. S and Gunter,C. A and Nettles,S. M}
}
@conference {14579,
	title = {A SIMD solution to the sequence comparison problem on the MGAP},
	booktitle = {International Conference on Application Specific Array Processors, 1994. Proceedings},
	year = {1994},
	month = {1994/08/22/24},
	pages = {336 - 345},
	publisher = {IEEE},
	organization = {IEEE},
	abstract = {Molecular biologists frequently compare an unknown biosequence with a set of other known biosequences to find the sequence which is maximally similar, with the hope that what is true of one sequence, either physically or functionally, could be true of its analogue. Even though efficient dynamic programming algorithms exist for the problem, when the size of the database is large, the time required is quite long, even for moderate length sequences. In this paper, we present an efficient pipelined SIMD solution to the sequence alignment problem on the Micro-Grain Array Processor (MGAP), a fine-grained massively parallel array of processors with nearest-neighbor connections. The algorithm compares K sequences of length O(M) with the actual sequence of length N, in O(M+N+K) time with O(MN) processors, which is AT-optimal. The implementation on the MGAP computes at the rate of about 0.1 million comparisons per second for sequences of length 128},
	keywords = {AT-optimal algorithm, Biological information theory, biology computing, biosequence comparison problem, computational complexity, Computer science, Costs, database size, Databases, DNA computing, dynamic programming, dynamic programming algorithms, fine-grained massively parallel processor array, Genetics, Heuristic algorithms, maximally similar sequence, MGAP parallel computer, Micro-Grain Array Processor, Military computing, molecular biology, molecular biophysics, Nearest neighbor searches, nearest-neighbor connections, Parallel algorithms, pipeline processing, pipelined SIMD solution, sequence alignment problem, sequences},
	isbn = {0-8186-6517-3},
	doi = {10.1109/ASAP.1994.331791},
	author = {Borah,M. and Bajwa,R. S and Hannenhalli, Sridhar and Irwin,M. J}
}
