BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

The central goal of human genetics is to understand the inherited basis of human variation in phenotypes, elucidating human physiology, evolution and disease. Rare mutations have been found underlying two thousand mendelian diseases; more recently, it has become possible to assess systematically the contribution of common SNPs to complex disease. The known role of copy-number alterations in sporadic genomic disorders, combined with emerging information about inherited copy-number variation, indicate the importance of systematically assessing copy-number variants (CNVs), including common copy-number polymorphisms (CNPs), in disease. Here we discuss evidence that CNVs affect phenotypes, directions for basic knowledge to support clinical study of CNVs, the challenge of genotyping CNPs in clinical cohorts, the use of SNPs as markers for CNPs and statistical challenges in testing CNVs for association with disease. Critical needs are high-resolution maps of common CNPs and techniques that accurately determine the allelic state of affected individuals.

Copy number variation in association studies of human disease

This paper addresses the following relay sensor placement problem: given the set of duty sensors in the plane and the upper bound of the transmission range, compute the minimum number of relay sensors such that the induced topology by all sensors is globally connected. This problem is motivated by practically considering the tradeoff among performance, lifetime, and cost when designing sensor networks. In our study, this problem is modelled by a NP-hard network optimization problem named Steiner Minimum Tree with Minimum number of Steiner Points and bounded edge length (SMT-MSP). In this paper, we propose two approximate algorithms, and conduct detailed performance analysis. The first algorithm has a performance ratio of 3 and the second has a performance ratio of 2.5.

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Relay sensor placement in wireless sensor networks

Ingredients of Locational Analysis (J. Krarup & P. Pruzan). The p-Median Problem and Generalizations (P. Mirchandani). The Uncapacitated Facility Location Problem (G. Cornuejols, et al.). Multiperiod Capacitated Location Models (S. Jacobsen). Decomposition Methods for Facility Location Problems (T. Magnanti & R. Wong). Covering Problems (A. Kolen & A. Tamir). p-Center Problems (G. Handler). Duality: Covering and Constraining p-Center Problems on Trees (B. Tansel, et al.). Locations with Spatial Interactions: The Quadratic Assignment Problem (R. Burkard). Locations with Spatial Interactions: Competitive Locations and Games (S. Hakimi). Equilibrium Analysis for Voting and Competitive Location Problems (P. Hansen, et al.). Location of Mobile Units in a Stochastic Environment (O. Berman, et al.). Index.

https://link.springer.com/content/pdf/10.1057%2Fjors.1991.208.pdf

Discrete location theory

The rapidly growing field of computational social choice, at the intersection of computer science and economics, deals with the computational aspects of collective decision making. This handbook, written by thirty-six prominent members of the computational social choice community, covers the field comprehensively. Chapters devoted to each of the field's major themes offer detailed introductions. Topics include voting theory (such as the computational complexity of winner determination and manipulation in elections), fair allocation (such as algorithms for dividing divisible and indivisible goods), coalition formation (such as matching and hedonic games), and many more. Graduate students, researchers, and professionals in computer science, economics, mathematics, political science, and philosophy will benefit from this accessible and self-contained book.

/pdf/handbook-of-computational-social-choice-12i1xbv1b8.pdf

Handbook of Computational Social Choice

Parameterized computational complexity of control problems in voting systems

Parameterized complexity of control problems in Maximin election

Minimum Common String Partition (MCSP) has drawn much attention due to its application in genome rearrangement. In this paper, we investigate three variants of MCSP: MCSP c , which requires that there are at most c elements in the alphabet; d-MCSP, which requires the occurrence of each element to be bounded by d; and x-balanced MCSP, which requires the length of blocks being in range (n/k?x,n/k+x), where n is the length of the input strings, k is the number of blocks in the optimal common partition and x is a constant integer. We show that MCSP c is NP-hard when c?2. As for d-MCSP, we present an FPT algorithm which runs in O ?((d!)2k ) time. As it is still unknown whether an FPT algorithm only parameterized on k exists for the general case of MCSP, we also devise an FPT algorithm for the special case x-balanced MCSP parameterized on both k and x.

/pdf/minimum-common-string-partition-revisited-1fu5iamscg.pdf

Minimum common string partition revisited

The ability to predict protein-protein binding sites has a wide range of applications, including signal transduction studies, de novo drug design, structure identification and comparison of functional sites. The interface in a complex involves two structurally matched protein subunits, and the binding sites can be predicted by identifying structural matches at protein surfaces. We propose a method which enumerates “all” the configurations (or poses) between two proteins (3D coordinates of the two subunits in a complex) and evaluates each configuration by the interaction between its components using the Atomic Contact Energy function. The enumeration is achieved efficiently by exploring a set of rigid transformations. Our approach incorporates a surface identification technique and a method for avoiding clashes of two subunits when computing rigid transformations. When the optimal transformations according to the Atomic Contact Energy function are identified, the corresponding binding sites are given as predictions. Our results show that this approach consistently performs better than other methods in binding site identification. Our method achieved a success rate higher than other methods, with the prediction quality improved in terms of both accuracy and coverage. Moreover, our method is being able to predict the configurations of two binding proteins, where most of other methods predict only the binding sites. The software package is available at http://sites.google.com/site/guofeics/dobi
 for non-commercial use.

/pdf/protein-protein-binding-site-identification-by-enumerating-4j32pj0zei.pdf

Protein-protein binding site identification by enumerating the configurations

In this article, we present a new data structure, called the permutation tree, to improve the running time of sorting permutation by transpositions and sorting permutation by block interchanges. The existing 1.5-approximation algorithm for sorting permutation by transpositions has time complexity O(n3/2 √logn). By means of the permutation tree, we can improve this algorithm to achieve time complexity O(nlogn). We can also improve the algorithm for sorting permutation by block interchanges to take its time complexity from O(n2) down to O(nlogn).

Daming Zhu

Papers

Parameterized computational complexity of control problems in voting systems

Parameterized complexity of control problems in Maximin election

Minimum common string partition revisited

Protein-protein binding site identification by enumerating the configurations

Faster algorithms for sorting by transpositions and sorting by block interchanges