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Planning Algorithms
, 2004
"... This book presents a unified treatment of many different kinds of planning algorithms. The subject lies at the crossroads between robotics, control theory, artificial intelligence, algorithms, and computer graphics. The particular subjects covered include motion planning, discrete planning, planning ..."
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Cited by 1108 (51 self)
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This book presents a unified treatment of many different kinds of planning algorithms. The subject lies at the crossroads between robotics, control theory, artificial intelligence, algorithms, and computer graphics. The particular subjects covered include motion planning, discrete planning
The SWISSMODEL Workspace: A webbased environment for protein structure homology modelling
 BIOINFORMATICS
, 2005
"... Motivation: Homology models of proteins are of great interest for planning and analyzing biological experiments when no experimental threedimensional structures are available. Building homology models requires specialized programs and uptodate sequence and structural databases. Integrating all re ..."
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Cited by 555 (5 self)
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Motivation: Homology models of proteins are of great interest for planning and analyzing biological experiments when no experimental threedimensional structures are available. Building homology models requires specialized programs and uptodate sequence and structural databases. Integrating all
Homological Algebra of Mirror Symmetry
 in Proceedings of the International Congress of Mathematicians
, 1994
"... Mirror Symmetry was discovered several years ago in string theory as a duality between families of 3dimensional CalabiYau manifolds (more precisely, complex algebraic manifolds possessing holomorphic volume elements without zeroes). The name comes from the symmetry among Hodge numbers. For dual Ca ..."
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Cited by 529 (3 self)
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Mirror Symmetry was discovered several years ago in string theory as a duality between families of 3dimensional CalabiYau manifolds (more precisely, complex algebraic manifolds possessing holomorphic volume elements without zeroes). The name comes from the symmetry among Hodge numbers. For dual CalabiYau manifolds V, W of dimension n (not necessarily equal to 3) one has dim H p (V, Ω q) = dim H n−p (W, Ω q). Physicists conjectured that conformal field theories associated with mirror varieties are equivalent. Mathematically, MS is considered now as a relation between numbers of rational curves on such a manifold and Taylor coefficients of periods of Hodge structures considered as functions on the moduli space of complex structures on a mirror manifold. Recently it has been realized that one can make predictions for numbers of curves of positive genera and also on CalabiYau manifolds of arbitrary dimensions. We will not describe here the complicated history of the subject and will not mention many beautiful contsructions, examples and conjectures motivated
Rho GTPases and the actin cytoskeleton
 Science
, 1998
"... The actin cytoskeleton mediates a variety of essential biological functions in all eukaryotic cells. In addition to providing a structural framework around which cell shape and polarity are defined, its dynamic properties provide the driving force for cells to move and to divide. Understanding the b ..."
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Cited by 589 (4 self)
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), leading to the assembly of a meshwork of actin filaments at the cell periphery to produce lamellipodia and membrane ruffles (Fig. 1E) (2). More recently, activation of Cdc42, a third member of the Rho subfamily, was shown to induce actinrich surface protrusions called filopodia (Fig. 1G) (3, 4
Large margin methods for structured and interdependent output variables
 JOURNAL OF MACHINE LEARNING RESEARCH
, 2005
"... Learning general functional dependencies between arbitrary input and output spaces is one of the key challenges in computational intelligence. While recent progress in machine learning has mainly focused on designing flexible and powerful input representations, this paper addresses the complementary ..."
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Cited by 612 (12 self)
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Learning general functional dependencies between arbitrary input and output spaces is one of the key challenges in computational intelligence. While recent progress in machine learning has mainly focused on designing flexible and powerful input representations, this paper addresses the complementary issue of designing classification algorithms that can deal with more complex outputs, such as trees, sequences, or sets. More generally, we consider problems involving multiple dependent output variables, structured output spaces, and classification problems with class attributes. In order to accomplish this, we propose to appropriately generalize the wellknown notion of a separation margin and derive a corresponding maximummargin formulation. While this leads to a quadratic program with a potentially prohibitive, i.e. exponential, number of constraints, we present a cutting plane algorithm that solves the optimization problem in polynomial time for a large class of problems. The proposed method has important applications in areas such as computational biology, natural language processing, information retrieval/extraction, and optical character recognition. Experiments from various domains involving different types of output spaces emphasize the breadth and generality of our approach.
A greedy algorithm for aligning DNA sequences
 J. COMPUT. BIOL
, 2000
"... For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic programming approaches and yet produce an alignment that is guaranteed to be theoretically optimal. We introduce a new greedy a ..."
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Cited by 576 (16 self)
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For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic programming approaches and yet produce an alignment that is guaranteed to be theoretically optimal. We introduce a new greedy alignment algorithm with particularly good performance and show that it computes the same alignment as does a certain dynamic programming algorithm, while executing over 10 times faster on appropriate data. An implementation of this algorithm is currently used in a program that assembles the UniGene database at the National Center for Biotechnology Information.
Construction of Escherichia coli K12 inframe, singlegene knockout mutants: the Keio collection. Mol. Syst. Biol 2:2006.0008
, 2006
"... We have systematically made a set of precisely defined, singlegene deletions of all nonessential genes in Escherichia coli K12. Openreading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a onestep method for inactivation of chromosom ..."
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Cited by 701 (7 self)
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We have systematically made a set of precisely defined, singlegene deletions of all nonessential genes in Escherichia coli K12. Openreading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a onestep method for inactivation of chromosomal genes and primers designed to create inframe deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in highthroughput studies, two independent mutants were saved for every deleted gene. These mutants—the ‘Keio collection’—provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genomewide testing of mutational effects in a common strain background, E. coli K12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase
String theory and noncommutative geometry
 JHEP
, 1999
"... We extend earlier ideas about the appearance of noncommutative geometry in string theory with a nonzero Bfield. We identify a limit in which the entire string dynamics is described by a minimally coupled (supersymmetric) gauge theory on a noncommutative space, and discuss the corrections away from ..."
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Cited by 801 (8 self)
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counterpart. We obtain a new perspective on noncommutative gauge theory on a torus, its Tduality, and Morita equivalence. We also discuss the D0/D4 system, the relation to Mtheory in DLCQ, and a possible noncommutative version of the sixdimensional (2, 0) theory. 8/99
Studies of transformation of Escherichia coli with plasmids
 J. Mol. Biol
, 1983
"... Factors that affect he probability of genetic transformation f Escherichia coli by plasmids have been evaluated. A set of conditions is described under which about one in every 400 plasmid molecules produces a transformed cell. These conditions include cell growth in medium containing elevated level ..."
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Cited by 1609 (1 self)
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levels of Mg 2+. and incubation of the cells at 0 ~ in a solution of Mn 2+, ("a 2+, Rb + or K +, dimethyl sulfoxide, dithiothreitol, and hexamine cobalt (III). Transibrmation efficiency declines linearly with increasing plasmid size. Relaxed and supercoiled plasmids transfol'm with similar
Results 1  10
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118,257