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Applied bioinformatics – interdisciplinary curriculum built on open source technology

Ilie Dorin Acu, Valerie Lawson, Maria-Sofia Domide, Kei-Leung Lun & Kennedy Cheuryiot
Classic bioinformatics curricula are limited by a relatively rigid course compartmentalization, employment of expensive IT/Bioinformatics proprietary tools, and limited grading system as an outcome for completing the course. Here we present a curriculum infused with real-life research-based projects such as whole genome analysis, gene expression array and molecular dynamics, applied for aging, cancer and pharmacogenomics. These projects serve as pivotal points for integrating biomedical, computer science and statistics into one coherent interdisciplinary subject known as...

PhyPipe: an automated pipeline for phylogenetic reconstruction from multilocus sequences

Nicolás D. Franco-Sierra, Mateo Gómez-Zuluaga, Juan F. Díaz-Nieto & Javier C. Alvarez
Phypipe is a pipeline for performing phylogenetic analysis with probabilistic methods using DNA sequences from multiple loci.

It takes FASTA nucleotide files (one per locus) containing sequences for the taxa to be analyzed and outputs the phylogenetic tree reconstructed by the method of choice (Bayesian Inference or Maximum Likelihood).

Phypipe's workflow covers sequence alignment, DNA evolution model selection for partitions, phylogenetic reconstruction and topological tests, using specific software tools for each step handling all intermediate configuration files.

Phypipe...

Burden of pneumocystis pneumonia in HIV-infected adults in sub-Saharan Africa: a systematic review and meta-analysis

Sean Wasserman, Mark Engel, Rulan Griesel & Marc Mendelson
Background
Seroprevalence data and clinical studies in children suggest that the burden of pneumocystis pneumonia (PCP) in Africa may be underestimated. A more accurate knowledge of the epidemiology of PCP will inform interpretation of diagnostic tests, development of empiric treatment guidelines and allocation of scarce resources. We performed a systematic review to determine the prevalence and attributable mortality of PCP amongst HIV-infected adults in sub-Saharan Africa.

Conclusion
PCP is an important opportunistic infection amongst HIV-infected adults in sub-Saharan...

HLA-MA: Efficient and Reliable HTS Data/Sample Consistency Check based on HLA Types

Clemens Messerschmidt, Manuel Holtgrewe & Dieter Beule
The HLA (human leukocyte antigen) type consists of 6 alleles of the highly variable MHC class I genes, overall more than 11.000 different alleles are known today (Robinson et al., 2014). A combination of alleles will almost certainly be unique for any individual and therefore can serve as a fingerprint for any human sample. Recent algorithmic progress (Szolek et al., 2014) allows for proper analysis of the highly variable HLA genes with high-throughput sequencing (HTS)....

PRED-TMBB2: Improved topology prediction and detection of beta-barrel outer membrane proteins

Konstantinos Tsirigos, Arne Elofsson & Pantelis Bagos
PRED-TMBB was presented for the first time in 2004 and is one of the most cited methods regarding the topology prediction and detection of beta-barrel outer membrane proteins. Here, we present an update to this method, PRED-TMBB2, which contains several new features that improve its performance significantly. The major difference is the incorporation of evolutionary information in the form of Multiple Sequence Alignments (MSAs), which drastically improves the topology prediction capability and makes it able...

Confident variant calling in NGS data – a mission impossible?

Sarah Sandmann, Aniek De Graaf, Bert Van Der Reijden, Joop Jansen & Martin Dugas
For decades of years Sanger sequencing has been the gold standard in the field of sequencing. The launching of next-generation sequencing (NGS) techniques has reduced time and costs of sequencing. However, data often contains false positive calls and even today Sanger sequencing is still used to validate the called variants in NGS data.

Considering three common next-generation sequencers – Roche 454, Ion Torrent PGM and Illumina NextSeq – we developed optimized variant calling pipelines to automatically...

One health prevention and control of antibiotic resistance

Carrie Walker & Kaja Abbas
In this study, we analyze scientific evidence to understand antibiotic use and misuse in animal, human and environmental health, and recommend one health solutions and multi-sectoral collaborations to mitigate the risks of antibiotic resistance.

De-identified meerkat data and code

Saul J. Newman, Simon Eyre, Catherine H. Kimble, Mauricio Arcos-Burgos, Carolyn Hogg & Simon Easteal
README.text contains a description of the contents. Instructions are included in the R code as comments.

Stratification of phaco-trabectome surgery results using a glaucoma severity index

Pritha Roy, Ralitsa Loewen, Hardik Parikh, Yalong Dang, Joel Schuman & Nils Loewen
The outcomes of phacoemulsification combined with trabectome surgery was analyzed using a glaucoma severity index based on preoperative intraocular pressure (IOP), number of preoperative medications, and visual field damage. Despite a less absolute indication to lower IOP, a substantial pressure reduction was seen in patients with more advanced glaucoma.

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