Zeev Smilansky

Automatic registration for images of two-dimensional protein gels

Two‐dimensional polyacrylamide gel electrophoresis 1 (2‐D PAGE 1) is currently the method of choice for separating complex mixtures of cellular proteins. Despite its usefulness, 2‐D PAGE is not being applied to its full potential because of difficulties with both the method and analysis of the results. One of the key problems is the difficulty and slowness of image analysis, especially registration (image alignment), which is laborious and the results unsatisfactory. We have developed a novel system for analysis of 2‐D PAGE images, called Z3, that performs the analysis faster and more precisely. The Z3 system employs novel approaches to image registration, image display, computation of differential expression, and the design and analysis of 2‐D gel experiments. This paper describes in detail the registration algorithm, and briefly discusses the merits of complementary pseudocolor display. The registration algorithm is novel in that for the first time raw‐image‐based registration technology is applied to 2‐D gel analysis.

Precalibration of matrix‐assisted laser desorption/ionization‐time of flight spectra for peptide mass fingerprinting

Identification of proteins using matrix‐assisted laser desorption/ionization‐time of flight (MALDI‐TOF) peptide mass fingerprinting (PMF) is a key technique in proteomics. The method is known to be sensitive as well as amenable to high‐throughput operation, but the resulting identifications suffer from a relatively low level of confidence. One way of increasing the confidence is by improving measurement accuracy using one of several calibration methods. This paper presents a new strategy for calibration of MALDI‐TOF PMF spectra that makes use of the phenomenon of peptide mass clustering, and enables spectrum calibration prior to the step of database interrogation, before or after peak extraction. Typically, mass errors are reduced by 40–60%. Accuracy improvement at this early stage can help avoid losing protein candidates, reduce the number of external calibration spots, eliminate internal calibrants, and reduce the number of candidates being scored, thereby reducing analysis time. Different variants of the method are discussed and compared to known calibration methods, such as relying on known calibrants or comparison to putative database candidates. In order to allow precise description of the method and to place the results in perspective, theoretical considerations of peptide databases and scoring functions are also discussed.

Decomposability of polytopes and polyhedra

In this paper decomposability of polytopes (and polyhedral sets) is studied by investigating the space of affine dependences of the vertices of the dual polytope. This turns out to be a fruitful approach and leads to several new results, as well as to simpler proofs and generalizations of known results. One of the new results is that a 3-polytope with more vertices than facets is decomposable; this leads to a characterization of the decomposability of 3-polytopes.

Convex hulls of generalized moment curves

We consider the family of curves inR4: {fx115-1}, wherep andq are positive integers, and determine the facial structure of the convex hull of these curves.

Automatic defect classification system for semiconductor wafers

The problem of automated defect classification has been recognized as one of the biggest challenges to successful integration of automated inspection into wafer manufacturing process. The high degree of customization required for each application adds another dimension to the inherent difficulties. For example, the input to an automatic classifier of printed circuit boards defects will be completely different from the input to a semiconductor defect classifier. Also, the heuristics used for classification will differ greatly. Furthermore, even in similar applications, different manufacturers will have different notions of how defects ought to be classified. In this paper we describe a system which attempts to automate the defect classification process, offering a high degree of adaptivity, customization and automation, with special emphasis on minimizing the need for input from a skilled user. Using Orbots wafer inspection system, we concentrated on classification of defects on patterned wafers.

Bi-cyclic 4-polytopes

AbstractIn a previous paper [2] we studied the facial structure of convex hulls of certain curves that lie on the torus

A non-geometric shelling of a 3-polytope

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Intensity-based statistical scorer for tandem mass spectrometry.

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Apparatus and method for color calibration

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