The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Complexity and Approximation

This paper defines techniques for the slicing of UML models, that is, for the restriction of models to those parts which specify the properties of a subset of the elements within them. The purpose of this restriction is to produce a smaller model which permits more effective analysis and comprehension than the complete model, and also to form a step in factoring of a model. We consider class diagrams, individual state machines, and communicating sets of state machines.

Slicing of UML models using model transformations

A genetic algorithm for the Flexible Job-shop Scheduling Problem

Concrete mathematics, a foundation for computer science, by Ronald L. Graham, Donald E. Knuth and Oren Patashnik. Pp 625. £24·95. 1989. ISBN 0-201-14236-8 (Addison-Wesley)

Increasing the weight of minimum spanning trees

We study the problem of finding a spanning tree with maximum number of leaves. We present a simple 2-approximation algorithm for the problem, improving on the approximation ratio of 3 achieved by the best previous algorithms. We also study the variant in which a given set of vertices must be leaves of the spanning tree, and we present a 5/2-approximation algorithm for this version of the problem.

/pdf/2-approximation-algorithm-for-finding-a-spanning-tree-with-4rnz9rqf4p.pdf

2-Approximation Algorithm for Finding a Spanning Tree with Maximum Number of Leaves

https://people.idsia.ch/~monaldo/papers/EJOR-varJsp-05.pdf

Roberto Solis-Oba

Papers

Increasing the weight of minimum spanning trees

2-Approximation Algorithm for Finding a Spanning Tree with Maximum Number of Leaves

Approximation schemes for job shop scheduling problems with controllable processing times

2-Approximation Algorithm for Finding a Spanning Tree with Maximum Number of Leaves

Rectangle packing with one-dimensional resource augmentation