Results 41 to 50 of about 566,210 (290)

Discovery of large genomic inversions using long range information. [PDF]

, 2017
BackgroundAlthough many algorithms are now available that aim to characterize different classes of structural variation, discovery of balanced rearrangements such as inversions remains an open problem.
Alkan, Can, Amemiya, Chris T, Antonacci, Francesca, Chiatante, Giorgia, Eichler, Evan E, Eslami Rasekh, Marzieh, Miroballo, Mattia, Tang, Joyce, Ventura, Mario   +8 more
core   +3 more sources

App-SpaM: phylogenetic placement of short reads without sequence alignment

Bioinformatics Advances, 2021
AbstractMotivationPhylogenetic placement is the task of placing a query sequence of unknown taxonomic origin into a given phylogenetic tree of a set of reference sequences. A major field of application of such methods is, for example, the taxonomic identification of reads in metabarcoding or metagenomic studies.
Matthias Blanke, Burkhard Morgenstern
openaire   +2 more sources

A multi-platform reference for somatic structural variation detection

Cell Genomics, 2022
Summary: Accurate detection of somatic structural variation (SV) in cancer genomes remains a challenging problem. This is in part due to the lack of high-quality, gold-standard datasets that enable the benchmarking of experimental approaches and ...
Jose Espejo Valle-Inclan, Nicolle J.M. Besselink, Ewart de Bruijn, Daniel L. Cameron, Jana Ebler, Joachim Kutzera, Stef van Lieshout, Tobias Marschall, Marcel Nelen, Peter Priestley, Ivo Renkens, Margaretha G.M. Roemer, Markus J. van Roosmalen, Aaron M. Wenger, Bauke Ylstra, Remond J.A. Fijneman, Wigard P. Kloosterman, Edwin Cuppen   +17 more
doaj   +1 more source

An efficient and scalable graph modeling approach for capturing information at different levels in next generation sequencing reads [PDF]

, 2013
BACKGROUND: Next generation sequencing technologies have greatly advanced many research areas of the biomedical sciences through their capability to generate massive amounts of genetic information at unprecedented rates.
Hesham H Ali, Julia D Warnke
core   +1 more source

Linked-read sequencing for detecting short tandem repeat expansions

Scientific Reports, 2022
Detection of short tandem repeat (STR) expansions with standard short-read sequencing is challenging due to the difficulty in mapping multicopy repeat sequences.
Readman Chiu, Indhu-Shree Rajan-Babu, Inanc Birol, Jan M. Friedman   +3 more
doaj   +1 more source

Identification of stress-related genes by co-expression network analysis based on the improved turbot genome

Scientific Data, 2022
Measurement(s) whole genome sequencing Technology Type(s) PacBio long-read and Illumina short-read sequencing ...
Xi-wen Xu, Weiwei Zheng, Zhen Meng, Wenteng Xu, Yingjie Liu, Songlin Chen   +5 more
doaj   +1 more source

Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads

BMC Genomics, 2021
Background Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks.
Seth Commichaux, Kiran Javkar, Padmini Ramachandran, Niranjan Nagarajan, Denis Bertrand, Yi Chen, Elizabeth Reed, Narjol Gonzalez-Escalona, Errol Strain, Hugh Rand, Mihai Pop, Andrea Ottesen   +11 more
doaj   +1 more source

DiBELLA: Distributed long read to long read alignment [PDF]

, 2019
We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers [29]. While long sequences of DNA offer enormous advantages
Buluç, A, Ellis, M, Guidi, G, Oliker, L, Yelick, K   +4 more
core   +2 more sources

Can long-read sequencing tackle the barriers, which the next-generation could not? A review

Pathology and Oncology Research
The large-scale heterogeneity of genetic diseases necessitated the deeper examination of nucleotide sequence alterations enhancing the discovery of new targeted drug attack points.
Nikolett Szakállas, Barbara K. Barták, Gábor Valcz, Gábor Valcz, Zsófia B. Nagy, István Takács, Béla Molnár   +6 more
doaj   +1 more source

AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization [PDF]

Journal of Computational Biology, 2011
High-throughput sequencing coupled to chromatin immunoprecipitation (ChIP-Seq) is widely used in characterizing genome-wide binding patterns of transcription factors, cofactors, chromatin modifiers, and other DNA binding proteins. A key step in ChIP-Seq data analysis is to map short reads from high-throughput sequencing to a reference genome and ...
Daniel, Newkirk, Jacob, Biesinger, Alvin, Chon, Kyoko, Yokomori, Xiaohui, Xie   +4 more
openaire   +2 more sources