Jakub Truszkowski

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Illumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16S rRNA gene. Publicly available tools are needed to assemble overlapping paired-end reads while correcting mismatches and uncalled bases; many errors could be corrected to obtain higher sequence yields using quality information. PANDAseq assembles paired-end(More)
Existing hidden Markov model decoding algorithms do not focus on approximately identifying the sequence feature boundaries. We give a set of algorithms to compute the conditional probability of all labellings "near" a reference labelling λ for a sequence y for a variety of definitions of "near". In addition, we give optimization algorithms to find the best(More)
Identifying recombinations in HIV is important for studying the epidemiology of the virus and aids in the design of potential vaccines and treatments. The previous widely-used tool for this task uses the Viterbi algorithm in a hidden Markov model to model recombinant sequences. We apply a new decoding algorithm for this HMM that improves prediction(More)
Rollating walkers are popular mobility aids used by older adults to improve balance control. There is a need to automatically recognize the activities performed by walker users to better understand activity patterns, mobility issues and the context in which falls are more likely to happen. We design and compare several techniques to recognize walker related(More)
We consider the problem of phylogenetic placement, in which large numbers of sequences (often next-generation sequencing reads) are placed onto an existing phylogenetic tree. We adapt our recent work on phylogenetic tree inference, which uses ancestral sequence reconstruction and locality-sensitive hashing, to this domain. With these ideas, new sequences(More)
Recently, we have identified a randomized quartet phylogeny algorithm that has O(n logn) runtime with high probability, which is asymptotically optimal. Our algorithm has high probability of returning the correct phylogeny when quartet errors are independent and occur with known probability, and when the algorithm uses a guide tree on O(loglogn) taxa that(More)
Marek Cygan, Guy Kortsarz and Zeev Nutov. Steiner Forest Orientation Problems Daniel Delling and Renato Werneck. Better Bounds for Graph Bisection Matthias Bernt, Kun-Mao Chao, Jyun-Wei Kao, Martin Middendorf and Eric Tannier. Preserving Inversion Phylogeny Reconstruction Manisha Bansal, Naveen Garg and Neelima Gupta. A 5-approximation for capacitated(More)
Open anterior fontanel cerebral ultrasonography was performed in 113 children aged between 1 month and 2 years, infants with purulent meningitis and encephalitis. It revealed early CNS complications in 50 patients (44.2%). The treatment protocol was adjusted for different types of complications. All children were discharged home and referred for further(More)