Results 71 to 80 of about 574,806 (288)

Towards Better Understanding of Artifacts in Variant Calling from High-Coverage Samples [PDF]

, 2015
Motivation: Whole-genome high-coverage sequencing has been widely used for personal and cancer genomics as well as in various research areas. However, in the lack of an unbiased whole-genome truth set, the global error rate of variant calls and the ...
Li, Heng
core   +1 more source

A Sequence-Based Novel Approach for Quality Evaluation of Third-Generation Sequencing Reads [PDF]

Genes, 2019
The advent of third-generation sequencing (TGS) technologies, such as the Pacific Biosciences (PacBio) and Oxford Nanopore machines, provides new possibilities for contig assembly, scaffolding, and high-performance computing in bioinformatics due to its long reads.
Zhang, Wenjing, Huang, Neng, Zheng, Jiantao, Liao, Xingyu, Wang, Jianxin, Li, Hong-Dong   +5 more
openaire   +2 more sources

Protein pyrophosphorylation by inositol pyrophosphates — detection, function, and regulation

FEBS Letters, EarlyView.
Protein pyrophosphorylation is an unusual signaling mechanism that was discovered two decades ago. It can be driven by inositol pyrophosphate messengers and influences various cellular processes. Herein, we summarize the research progress and challenges of this field, covering pathways found to be regulated by this posttranslational modification as ...
Sarah Lampe, Tanmay Kumar Mohanty, Rashna Bhandari, Dorothea Fiedler   +3 more
wiley   +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

The newfound relationship between extrachromosomal DNAs and excised signal circles

FEBS Letters, EarlyView.
Extrachromosomal DNAs (ecDNAs) contribute to the progression of many human cancers. In addition, circular DNA by‐products of V(D)J recombination, excised signal circles (ESCs), have roles in cancer progression but have largely been overlooked. In this Review, we explore the roles of ecDNAs and ESCs in cancer development, and highlight why these ...
Dylan Casey, Zeqian Gao, Joan Boyes
wiley   +1 more source

Clinical application of high throughput molecular screening techniques for pharmacogenomics. [PDF]

, 2011
Genetic analysis is one of the fastest-growing areas of clinical diagnostics. Fortunately, as our knowledge of clinically relevant genetic variants rapidly expands, so does our ability to detect these variants in patient samples.
Schrijver, Iris, Wiita, Arun P
core   +1 more source

Third-Generation Cytogenetic Analysis: Diagnostic Application of Long-Read Sequencing.

The Journal of molecular diagnostics : JMD, 2022
Copy number variants (CNVs) play important roles in the pathogenesis of several genetic syndromes. Traditional and molecular karyotyping are considered the first-tier diagnostic tests to detect macroscopic and cryptic deletions/duplications. However, their time-consuming and laborious experimental protocols protract diagnostic times from 3 to 15 days ...
Magini, Pamela, Mingrino, Alessandra, Gega, Barbara, Mattei, Gianluca, Semeraro, Roberto, Bolognini, Davide, Mongelli, Patrizia, Desiderio, Laura, Pittalis, Maria Carla, Pippucci, Tommaso, Magi, Alberto   +10 more
openaire   +2 more sources

In situ molecular organization and heterogeneity of the Legionella Dot/Icm T4SS

FEBS Letters, EarlyView.
We present a nearly complete in situ model of the Legionella Dot/Icm type IV secretion system, revealing its central secretion channel and identifying new components. Using cryo‐electron tomography with AI‐based modeling, our work highlights the structure, variability, and mechanism of this complex nanomachine, advancing understanding of bacterial ...
Przemysław Dutka, Yuxi Liu, Stefano Maggi, Debnath Ghosal, Jue Wang, Prashant P. Damke, Stephen D. Carter, Wei Zhao, Sukhithasri Vijayrajratnam, Joseph P. Vogel, Carrie L. Shaffer, Grant J. Jensen   +11 more
wiley   +1 more source

An improved protocol for small RNA library construction using High Definition adapters [PDF]

, 2015
Next generation sequencing of small RNA (sRNA) libraries is widely used for studying sRNAs in various biological systems. However, cDNA libraries of sRNAs are biased for molecules that are ligated to adapters more or less efficiently than other molecules.
Aravin, Baran, Bushati, Edgar, Git, Hafner, He, Jagadeeswaran, Jayaprakash, Kawano, Mallory, Mortazavi, Munafó, Pease, Prüfer, Raabe, Reddy, Song, Sorefan, Stocks, Sun, Szittya, Szittya, Tian, Vigneault, Viollet, Willenbrock, Zhang, Zhuang   +28 more
core   +1 more source

Sequence determinants of RNA G‐quadruplex unfolding by Arg‐rich regions

FEBS Letters, EarlyView.
We show that Arg‐rich peptides selectively unfold RNA G‐quadruplexes, but not RNA stem‐loops or DNA/RNA duplexes. This length‐dependent activity is inhibited by acidic residues and is conserved among SR and SR‐related proteins (SRSF1, SRSF3, SRSF9, U1‐70K, and U2AF1).
Naiduwadura Ivon Upekala De Silva, Puspa Kunwar, Md Ibnul Rifat Rahman, Joanna Koryo Kwao, Nathan Lehman, Zihan Zhang, Trenton Paul, Claire Cheng, Nicholas Truex, Hui‐Ting Lee, Jun Zhang   +10 more
wiley   +1 more source