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Article
Open AccessFunctional antibodies exhibit light chain coherence
The vertebrate adaptive immune system modifies the genome of individual B cells to encode antibodies that bind particular antigens1. In most mammals, antibodies are composed of heavy and light chains that are gen...
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Article
Open AccessEvaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly
De novo reference assemblies that are affordable, practical to produce, and of sufficient quality for most downstream applications, remain an unattained goal for many taxa. Insects, wh...
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Article
Comprehensive variation discovery in single human genomes
David Jaffe and colleagues report a new algorithm, DISCOVAR, for variant calling and de novo genome assembly. They test the algorithm on a new reference variant call set and demonstrate improved variant calling, ...
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Article
Open AccessThe genomic substrate for adaptive radiation in African cichlid fish
Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced t...
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Article
Open AccessAssemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many ...
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Article
Open AccessCharacterizing and measuring bias in sequence data
DNA sequencing technologies deviate from the ideal uniform distribution of reads. These biases impair scientific and medical applications. Accordingly, we have developed computational methods for discovering, ...
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Article
Open AccessThe African coelacanth genome provides insights into tetrapod evolution
The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar...
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Article
Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing
Anthony Bleyer, Eric Lander, Mark Daly and colleagues show that frameshift mutations in a large VNTR of MUC1 cause medullary cystic kidney disease type 1. Their discovery sheds light on the biology of this diseas...
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Article
Open AccessA high-resolution map of human evolutionary constraint using 29 mammals
The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the ...
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Article
Open AccessAnalyzing and minimizing PCR amplification bias in Illumina sequencing libraries
Despite the ever-increasing output of Illumina sequencing data, loci with extreme base compositions are often under-represented or absent. To evaluate sources of base-composition bias, we traced genomic sequen...
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Article
Open AccessA scalable, fully automated process for construction of sequence-ready barcoded libraries for 454
We present an automated, high throughput library construction process for 454 technology. Sample handling errors and cross-contamination are minimized via end-to-end barcoding of plasticware, along with molecu...
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Chapter
CA3 Cells: Detailed and Simplified Pyramidal Cell Models
From rodents to humans, the hippocampus has been implicated in a variety of cognitive functions, including spatial navigation, memory storage, and recall (Hölscher, 2003). The classic anatomical representation...
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Article
Open AccessALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jum**) reads from five microbial genomes of varied GC composi...
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Article
Open AccessAssisted assembly: how to improve a de novo genome assembly by using related species
We describe a new assembly algorithm, where a genome assembly with low sequence coverage, either throughout the genome or locally, due to cloning bias, is considerably improved through an assisting process via...
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Article
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
Gnirke et al. present a bead-based method for capturing sequences of interest in the human genome for massively parallel sequencing. Using long, biotinylated RNA probes to pull down PCR-amplified DNA fragments, t...
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Article
High-resolution map** of copy-number alterations with massively parallel sequencing
Massively parallel sequencing is a precise way to analyze copy-number variations given the right computational tools. An algorithm now facilitates the detection and fine map** of copy-number gains and losses...
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Article
Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing
This variant ascertainment algorithm, or VAAL, uses short sequence reads of haploid bacterial genomes to first locally assemble the reads and then compare these assemblies to the reference genome. This allows ...
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Article
Genome-scale DNA methylation maps of pluripotent and differentiated cells
DNA methylation, an important mechanism of epigenetic modification that produces different patterns of gene expression from a single DNA sequence, is vital to normal development and its malfunction can cause c...
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Article
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromat...
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Article
A genome-wide map of diversity in Plasmodium falciparum
Genetic variation allows the malaria parasite Plasmodium falciparum to overcome chemotherapeutic agents, vaccines and vector control strategies and remain a leading cause of global morbidity and mortality1. Here ...
