Mugsy: fast multiple alignment of closely related whole genomes.

Motivation: The relative ease and low cost of current generation sequencing technologies has led to a dramatic increase in the number of sequenced genomes for species across the tree of life. This increasing volume of data requires tools that can quickly compare multiple whole-genome sequences, millions of base pairs in length, to aid in the study of populations, pan-genomes, and genome evolution.

Results: We present a new multiple alignment tool for whole genomes named Mugsy.

Quake: quality-aware detection and correction of sequencing errors.

We introduce Quake, a program to detect and correct errors in DNA sequencing reads. Using a maximum likelihood approach incorporating quality values and nucleotide specific miscall rates, Quake achieves the highest accuracy on realistically simulated reads. We further demonstrate substantial improvements in de novo assembly and SNP detection after using Quake.

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes.

COMBREX (http://combrex.bu.edu) is a project to increase the speed of the functional annotation of new bacterial and archaeal genomes.

Clustering metagenomic sequences with interpolated Markov models.

Background: Sequencing of environmental DNA (often called metagenomics) has shown tremendous potential to uncover the vast number of unknown microbes that cannot be cultured and sequenced by traditional methods. Because the output from metagenomic sequencing is a large set of reads of unknown origin, clustering reads together that were sequenced from the same species is a crucial analysis step. Many effective approaches to this task rely on sequenced genomes in public databases, but these genomes are a highly biased sample that is not necessarily representative of environments interesting to many metagenomics projects.

Do-it-yourself genetic testing.

We developed a computational screen that tests an individual's genome for mutations in the BRCA genes, despite the fact that both are currently protected by patents.

Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification.

Background: Bacterial pathogens often show significant intraspecific variations in ecological fitness, host preference and pathogenic potential to cause infectious disease. The species of Listeria monocytogenes, a facultative intracellular pathogen and the causative agent of human listeriosis, consists of at least three distinct genetic lineages. Two of these lineages predominantly cause human sporadic and epidemic infections, whereas the third lineage has never been implicated in human disease outbreaks despite its overall conservation of many known virulence factors.

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (∼1.

Genome sequence of the dioxin-mineralizing bacterium Sphingomonas wittichii RW1.

Pollutants such as polychlorinated biphenyls and dioxins pose a serious threat to human and environmental health. Natural attenuation of these compounds by microorganisms provides one promising avenue for their removal from contaminated areas. Over the past 2 decades, studies of the bacterium Sphingomonas wittichii RW1 have provided a wealth of knowledge about how bacteria metabolize chlorinated aromatic hydrocarbons.

How good patient blood management leads to excellent outcomes in Jehovah's witness patients undergoing cardiac surgery.

Objectives: The refusal of blood products makes open-heart surgery in Jehovah's witnesses (JW) an ethical challenge. We demonstrate how patient blood management strategies lead to excellent surgical outcomes.

Methods: From 2003 to 2008, 16 JW underwent cardiac surgery at our institution.

Real life cardio-thoracic surgery training in Europe: facing the facts.

The objective of this study was to determine the current status of training in cardio-thoracic surgery in Europe and the residents' perception of the effects of the full implementation of the European Working Time Directive (EWTD) on training. We conducted a web-based survey of trainees registered with the European Association of Cardio-Thoracic Surgery and 79 respondents form the basis for this analysis. A majority of trainees (69.

Assembly of large genomes using second-generation sequencing.

Second-generation sequencing technology can now be used to sequence an entire human genome in a matter of days and at low cost. Sequence read lengths, initially very short, have rapidly increased since the technology first appeared, and we now are seeing a growing number of efforts to sequence large genomes de novo from these short reads. In this Perspective, we describe the issues associated with short-read assembly, the different types of data produced by second-gen sequencers, and the latest assembly algorithms designed for these data.

Between a chicken and a grape: estimating the number of human genes.

Many people expected the question 'How many genes in the human genome?' to be resolved with the publication of the genome sequence in 2001, but estimates continue to fluctuate.

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.

High-throughput mRNA sequencing (RNA-Seq) promises simultaneous transcript discovery and abundance estimation. However, this would require algorithms that are not restricted by prior gene annotations and that account for alternative transcription and splicing. Here we introduce such algorithms in an open-source software program called Cufflinks.

Routine off-pump coronary artery bypass grafting is safe and feasible in high-risk patients with left main disease.

Background: Coronary artery bypass graft surgery (CABG) remains the method of choice for patients with left main disease (LMD). The precise role of off-pump coronary artery bypass graft surgery (OPCABG) remains unclear in this setting. We report the safety and feasibility of a routine OPCABG approach to patients with LMD.

Detection and correction of false segmental duplications caused by genome mis-assembly.

Diploid genomes with divergent chromosomes present special problems for assembly software as two copies of especially polymorphic regions may be mistakenly constructed, creating the appearance of a recent segmental duplication. We developed a method for identifying such false duplications and applied it to four vertebrate genomes. For each genome, we corrected mis-assemblies, improved estimates of the amount of duplicated sequence, and recovered polymorphisms between the sequenced chromosomes.

Mind the gaps.

By grouping short reads derived from the same long genomic fragment, the reads can easily be assembled into fragments that approach the length of capillary sequencing reads.

Despite modern off-pump coronary artery bypass grafting women fare worse than men.

Female gender is an established risk factor for worse outcomes after cardiac surgery. Avoiding cardiopulmonary bypass (CPB) for coronary bypass grafting has an unknown effect on gender differences. Herein, we evaluate if gender has an impact on outcomes after modern off-pump coronary artery bypass grafting (OPCAB).

Searching for SNPs with cloud computing.

As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the SNP caller SOAPsnp. Executing in parallel using Hadoop, Crossbow analyzes data comprising 38-fold coverage of the human genome in three hours using a 320-CPU cluster rented from a cloud computing service for about $85.

Left atrial appendage clip occlusion: early clinical results.

Objective: Atrial fibrillation puts patients at significant risk for embolic stroke originating from the left atrial appendage. Few means are available for safe, effective, and durable left atrial appendage occlusion. A new clip device was evaluated with regard to safety and effectiveness for epicardial left atrial appendage occlusion.

Severe cardiomyopathy following treatment with the tumour necrosis factor-alpha inhibitor adalimumab for Crohn's disease.

Adalimumab belongs to the group of tumour necrosis factor-alpha inhibitors and has been approved for the treatment Crohn's Disease since 2007. Herein we report a severe adverse reaction to adalimumab in a 25-year-old female patient. One week after the initial-dose of adalimumab (160 mg), which was initiated due to an acute exacerbation of Crohn's disease, the patient developed a fulminant cardiomyopathy.

Efficient oligonucleotide probe selection for pan-genomic tiling arrays.

Background: Array comparative genomic hybridization is a fast and cost-effective method for detecting, genotyping, and comparing the genomic sequence of unknown bacterial isolates. This method, as with all microarray applications, requires adequate coverage of probes targeting the regions of interest. An unbiased tiling of probes across the entire length of the genome is the most flexible design approach.

"When Aneurysm Ain't Aneurysm": sinus of Valsalva aneurysm mimicked by healed abscess cavity under the aortic valve.

In a 70-year-old patient with severe aortic valve stenosis, preoperative standard imaging (transthoracic echocardiography and angiography) detected an unclear subannular cavity structure. Initially interpreted as an aneurysm of Valsalva, the structure was identified intraoperatively as a huge chronic abscess cavity and exclusion was carried out by pericardial patch plasty. This case draws attention to the importance of a differential diagnosis of an abscess due to infective endocarditis in cases of unclear subannular structures rashly diagnosed as aneurysm of Valsalva.

Impact of preoperative nesiritide on renal function after mitral valve surgery.

Nesiritide, a recombinant B-type natriuretic peptide used for the intravenous treatment of acute decompensated congestive heart failure. Concerns have been raised about the long-term use of nesiritide, but data is scarce regarding its use in acute congestive heart failure and during cardiac surgery. We conducted a retrospective data review to address the safety of nesiritide for pretreatment of patients undergoing mitral valve surgery.