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371
Assembly of Designer TAL Effectors by Golden Gate Cloning
, 2011
"... Generation of customized DNA binding domains targeting unique sequences in complex genomes is crucial for many biotechnological applications. The recently described DNA binding domain of the transcription activator-like effectors (TALEs) from Xanthomonas consists of a series of repeats arranged in t ..."
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Cited by 15 (0 self)
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in tandem, each repeat binding a nucleotide of the target sequence. We present here a strategy for engineering of TALE proteins with novel DNA binding specificities based on the 17.5 repeat-containing AvrBs3 TALE as a scaffold. For each of the 17 full repeats, four module types were generated, each with a
A novel fluorescence-based genetic strategy identifies mutants of Saccharomyces cerevisiae defective for nuclear pore complex assembly. Mol. Biol. Cell 9:2439–2461
, 1998
"... Nuclear pore complexes (NPCs) are large proteinaceous portals for exchanging macromolecules between the nucleus and the cytoplasm. Revealing how this transport apparatus is assembled will be critical for understanding the nuclear transport mechanism. To address this issue and to identify factors tha ..."
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Cited by 14 (2 self)
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that regulate NPC formation and dynamics, a novel fluorescence-based strategy was used. This approach is based on the functional tagging of NPC proteins with the green fluorescent protein (GFP), and the hypothesis that NPC assembly mutants will have distinct GFP-NPC signals as compared with wild-type (wt) cells
CLP-based protein fragment assembly
"... The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor— also developed for this work — from a database of known protein structures that clusters and classi ..."
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The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor— also developed for this work — from a database of known protein structures that clusters
CLP-based protein fragment assembly
"... Abstract. The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor—also developed for this work — from a database of known protein structures that clusters a ..."
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Abstract. The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor—also developed for this work — from a database of known protein structures that clusters
Improved Assembly Accuracy by Integrating Base-Calling, Error Correction and Assembly
"... Motivation. With the recent advent of a multitude of next-generation sequencing (NGS) technologies (characterized by high throughput but relatively shorter read length), de novo DNA sequence assembly has become again one of the most prominent problems in Genomics and Computational Biology. Although ..."
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algorithmic improvements play an important role in sequence assembly, the complexity of the problem is strongly reduced if higher quality (low error rate) sequences can be generated. For this reason, base-calling and error correction tools, together with novel assembly strategies, have begun to play a
Biography
"... Article number = k056 Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem ..."
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Article number = k056 Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem
A sparse marker extension tree algorithm for selecting the best set of haplotype tagging single nucleotide polymorphisms
- Genet. Epidemiol
, 2005
"... Single nucleotide polymorphisms (SNPs) play a central role in the identification of susceptibility genes for common diseases. Recent empirical studies on human genome have revealed block-like structures, and each block contains a set of haplotype tagging SNPs (htSNPs) that capture a large fraction o ..."
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Cited by 5 (5 self)
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of the haplotype diversity. Herein, we present an innovative sparse marker extension tree (SMET) algorithm to select optimal htSNP set(s). SMET reduces the search space considerably (compared to full enumeration strategy), and therefore improves computing efficiency. We tested this algorithm on several datasets
Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel
"... Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth ..."
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Cited by 1 (0 self)
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10K project with 2,184 haplotypes from the 1000 Genomes Project. Finally, we introduce a novel approximation that maintains speed without sacrificing impu-
Towards the Design of Heuristics by Means of Self-Assembly
"... The current investigations on hyper-heuristics design have sprung up in two different flavours: heuristics that choose heuristics and heuristics that generate heuristics. In the latter, the goal is to develop a problem-domain independent strategy to automatically generate a good performing heuristic ..."
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Cited by 3 (1 self)
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components. This idea arises from previous works in which computational models of self-assembly were subject to evolutionary design in order to perform the automatic construction of user-defined structures. Then, the aim of this paper is to present a novel methodology for the automated design of heuristics
An Efficient Strategy for Developing a Simulator for a Novel Concurrent Multithreaded Processor Architecture
- in International Symposium on Modeling, Analysis and Simulation of Computer and Telecommunication Systems
, 1998
"... In developing a simulator for a new processor architecture, it often is not clear whether it is more efficient to write a new simulator from scratch or whether it is better to try and modify an existing simulator. Writing a new simulator has the advantages of needing to understand only the new proce ..."
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Cited by 12 (6 self)
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processor architecture itself and being the "owner" of the final code. However, it also forces the processor architect to develop or adapt all of the related software tools, such as compilers, assemblers, and so forth. On the other hand, modifying an existing simulator and related tools can
Results 21 - 30
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371
