Results 71 to 80 of about 334,258 (285)

Somatic mutational landscape in von Hippel–Lindau familial hemangioblastoma

Molecular Oncology, EarlyView.
The causes of central nervous system (CNS) hemangioblastoma in Von Hippel–Lindau (vHL) disease are unclear. We used Whole Exome Sequencing (WES) on familial hemangioblastoma to investigate events that underlie tumor development. Our findings suggest that VHL loss creates a permissive environment for tumor formation, while additional alterations ...
Maja Dembic, Anne Nørremølle, Lilian Bomme Ousager, Lars van Brakel Andersen, Marie Louise Mølgaard Binderup, Mads Thomassen   +5 more
wiley   +1 more source

A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data [PDF]

, 2012
Deep shotgun sequencing and analysis of genomes, transcriptomes, amplified single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystems. However, sampling variation in short-read data sets and high sequencing
Brom, Timothy H., Brown, C. Titus, Howe, Adina, Pyrkosz, Alexis B., Zhang, Qingpeng   +4 more
core   +1 more source

OMSim : a simulator for optical map data [PDF]

, 2017
Motivation: The Bionano Genomics platform allows for the optical detection of short sequence patterns in very long DNA molecules (up to 2.5 Mbp). Molecules with overlapping patterns can be assembled to generate a consensus optical map of the entire ...
Audenaert, Pieter, Fostier, Jan, Miclotte, Giles, Plaisance, Stéphane, Rombauts, Stephane, Van de Peer, Yves   +5 more
core   +2 more sources

dUTPase is essential in zebrafish development and possesses several single‐nucleotide variants with pronounced structural and functional consequences

FEBS Open Bio, EarlyView.
dUTPases are involved in balancing the appropriate nucleotide pools. We showed that dUTPase is essential for normal development in zebrafish. The different zebrafish genomes contain several single‐nucleotide variations (SNPs) of the dut gene. One of the dUTPase variants displayed drastically lower protein stability and catalytic efficiency as compared ...
Viktória Perey‐Simon, Angéla Békesi, Latifa Kazzazy, Jázmin Mihály, Máté Varga, Beáta G. Vértessy, Kinga Nyíri   +6 more
wiley   +1 more source

SATRAP: SOLiD Assembler TRAnslation Program. [PDF]

PLoS ONE, 2015
SOLiD DNA sequences are typically analyzed using a reference genome, while they are not recommended for de novo assembly of genomes or transcriptomes. This is mainly due to the difficulty in translating the SOLiD color-space data into normal base-space ...
Davide Campagna, Fabio Gasparini, Nicola Franchi, Lucia Manni, Andrea Telatin, Nicola Vitulo, Loriano Ballarin, Giorgio Valle   +7 more
doaj   +1 more source

Current challenges in de novo plant genome sequencing and assembly [PDF]

, 2012
: Genome sequencing is now affordable, but assembling plant genomes de novo remains challenging.
McCombie, W. R., Schatz, M. C., Witkowski, J.   +2 more
core   +1 more source

Methods for De-novo Genome Assembly

, 2020
Despite advances in algorithms and computational platforms, de-novo genome assembly remains a challenging process. Due to the constant innovation in sequencing technologies (Sanger, SOLiD, Illumina, 454, PacBio and Oxford Nanopore), genome assembly has evolved to respond to the changes in input data type.
Bayat, Arash, Gamaarachchi, Hasindu, Deshpande, Nandan P., Wilkins, Marc R., Parameswaran, Sri   +4 more
openaire   +2 more sources

Extreme-Scale De Novo Genome Assembly [PDF]

, 2017
De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality end-to-end de novo assembler designed for extreme scale analysis, via efficient parallelization of the Meraculous code ...
Georganas, Evangelos, Hofmeyr, Steven, Egan, Rob, Buluc, Aydin, Oliker, Leonid, Rokhsar, Daniel, Yelick, Katherine   +6 more
openaire   +2 more sources

Multi‐omics and low‐input proteomics profiling reveals dynamic regulation driving pluripotency initiation in early mouse embryos

FEBS Open Bio, EarlyView.
Mouse pre‐implantation development involves a transition from totipotency to pluripotency. Integrating transcriptomics, epigenetic profiling, low‐input proteomics and functional assays, we show that eight‐cell embryos retain residual totipotency features, whereas cytoskeletal remodeling regulated by the ubiquitin‐proteasome system drives progression ...
Wanqiong Li, Xi Xiao, Lingbin Qi, Chanyi Li, Sirui Song, Jiaying Qin, Zhigang Xue, Jinfeng Xue, Huaifang Li   +8 more
wiley   +1 more source

A novel mutation in NDUFB11 unveils a new clinical phenotype associated with lactic acidosis and sideroblastic anemia [PDF]

, 2017
NDUFB11, a component of mitochondrial complex I, is a relatively small integral membrane protein, belonging to the 'supernumerary' group of subunits, but proved to be absolutely essential for the assembly of an active complex I.
Bertini, Enrico, Bianchi, Marzia, Carrozzo, Rosalba, Christodoulou, John, Di Nottia, Michela, Diodato, Daria, Dionisi Vico, Carlo, Francisci, Silvia, Gelmetti, Vania, Guo, Yiran, Lucarelli, Barbarella, Martinelli, Diego, Montanari, Arianna, Niceta, Marcello, Piemonte, Fiorella, Riley, Lisa, Rizza, Teresa, Sorrentino, Francesco, Tartaglia, Marco, Torraco, Alessandra, Valente, Enza Maria, Verrigni, Daniela   +21 more
core   +2 more sources