Results 21 to 30 of about 57,228 (156)

Optimized Sequence Library Design for Efficient In Vitro Interaction Mapping [PDF]

, 2017
Sequence libraries that cover all k-mers enable universal, unbiased measurements of binding to both oligonucleotides and peptides. While the number of k-mers grows exponentially in k, space on all experimental platforms is limited.
Berger Leighton, Bonnie, Fordyce, Polly, Kim, Ryan, Orenstein, Yaron, Puccinelli, Robert   +4 more
core   +1 more source

Percolation of linear $k$-mers on square lattice: from isotropic through partially ordered to completely aligned state

, 2012
Numerical simulations by means of Monte Carlo method and finite-size scaling analysis have been performed to study the percolation behavior of linear $k$-mers (also denoted in the literature as rigid rods, needles, sticks) on two-dimensional square ...
Laptev, Valeri V., Lebovka, Nikolai I., Tarasevich, Yuri Yu.   +2 more
core   +1 more source

Diminishing Return for Increased Mappability with Longer Sequencing Reads: Implications of the k-mer Distributions in the Human Genome [PDF]

, 2013
The amount of non-unique sequence (non-singletons) in a genome directly affects the difficulty of read alignment to a reference assembly for high throughput-sequencing data.
Freudenberg, Jan, Li, Wentian, Miramontes, Pedro   +2 more
core   +2 more sources

Determination of the Critical Exponents for the Isotropic-Nematic Phase Transition in a System of Long Rods on Two-dimensional Lattices: Universality of the Transition

, 2008
Monte Carlo simulations and finite-size scaling analysis have been carried out to study the critical behavior and universality for the isotropic-nematic phase transition in a system of long straight rigid rods of length $k$ ($k$-mers) on two-dimensional ...
A. J. Ramirez-Pastor, Binder K., D. A. Matoz-Fernandez, D. H. Linares, Fisher M. E., Flory P. J., Ghosh A., Kamieniarz G., Privman V., Selke W., Selke W., Tomé T., Vroege G. J.   +12 more
core   +1 more source

Transcriptome‐wide analysis of circRNA and RBP profiles and their molecular relevance for GBM

Molecular Oncology, EarlyView.
CircRNAs are differentially expressed in glioblastoma primary tumors and might serve as therapeutic targets and diagnostic markers. The investigation of circRNA and RNA‐binding proteins (RBPs) interactions shows that distinct RBPs play a role in circRNA biogenesis and function.
Julia Latowska‐Łysiak, Żaneta Zarębska, Marcin P. Sajek, Adriana Grabowska, Alessia Buratin, Paweł Głodowicz, Julia O. Misiorek, Konrad Kuczyński, Stefania Bortoluzzi, Marek Żywicki, Jan G. Kosiński, Agnieszka Rybak‐Wolf, Rafał Piestrzeniewicz, Anna M. Barciszewska, Katarzyna Rolle   +14 more
wiley   +1 more source

Fast Spaced Seed Hashing [PDF]

, 2017
Hashing k-mers is a common function across many bioinformatics applications and it is widely used for indexing, querying and rapid similarity search. Recently, spaced seeds, a special type of pattern that accounts for errors or mutations, are routinely ...
Comin, Matteo, Girotto, Samuele, Pizzi, Cinzia   +2 more
core   +1 more source

Co‐expression of HSV‐1 ICP34.5 enhances the expression of gene delivered by self‐amplifying RNA and mitigates its immunogenicity

FEBS Open Bio, EarlyView.
ICP34.5 is one of the most important antihost response proteins. The saRNA‐encoding HSV‐1 neurovirulence protein ICP34.5 clearly mediated the eukaryotic initiation factor 2 alpha subunit (eIF2α) dephosphorylation and significant suppression of innate immune responses in vitro, leading to enhanced expression of the saRNA‐encoded gene.
Xuemin Lu, Yabin Wu, Chunye Zhao, Jie Zheng, Shangwu Chen, Yigang Wang, Yulong Xia   +6 more
wiley   +1 more source

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. [PDF]

, 2015
BackgroundThe problem of supervised DNA sequence classification arises in several fields of computational molecular biology. Although this problem has been extensively studied, it is still computationally challenging due to size of the datasets that ...
Close, Timothy J, Lonardi, Stefano, Ounit, Rachid, Wanamaker, Steve   +3 more
core   +2 more sources

Toward Personalized Stationary Chromatography Phases: Equipping Commercial Silica Phases with Selected Peptide‐Based Binding Domains to Tailor Affinity

Advanced Materials Interfaces, EarlyView.
The 7‐mer peptide motifs QFFLFFQ, QFFEFFQ, and QFQQSFF, known as good, medium, and poor binders for the photosensitizers m‐THPC and Chlorin E6 are covalently immobilized on commercial amino‐functionalized silica particles by inverse electron‐demand Diels‐Alder ligation.
Steffen A. Busche, Lukas D. Bangert, Raoul D. Brand, Tommy Kröger, Enrico Heyl, Hans G. Börner   +5 more
wiley   +1 more source

Pattern formation in a two-dimensional two-species diffusion model with anisotropic nonlinear diffusivities: a lattice approach

, 2017
Diffusion in a two-species 2D system has been simulated using a lattice approach. Rodlike particles were considered as linear $k$-mers of two mutually perpendicular orientations ($k_x$- and $k_y$-mers) on a square lattice.
Burmistrov, Andrei S., Laptev, Valeri V., Lebovka, Nikolai I, Tarasevich, Yuri Yu.   +3 more
core   +1 more source