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Whole genome and exome sequencing usually include reads containing mitochondrial DNA (mtDNA). Yet, state-of-the-art pipelines and services for human nuclear genome variant calling and annotation do not handle ...
BMC Bioinformatics 2017 18:373
Published on: 18 August 2017
Research Article
Recently, many standalone applications have been proposed to correct sequencing errors in Illumina data. The key idea is that downstream analysis tools such as de novo genome assemblers benefit from a reduced err...
BMC Bioinformatics 2017 18:374
Published on: 18 August 2017
Research Article
Coreference resolution is the task of finding strings in text that have the same referent as other strings. Failures of coreference resolution are a common cause of false negatives in information extraction fr...
BMC Bioinformatics 2017 18:372
Published on: 17 August 2017
Software
Multi-label classification has recently gained great attention in diverse fields of research, e.g., in biomedical application such as protein function prediction or drug resistance testing in HIV. In this cont...
BMC Bioinformatics 2017 18:371
Published on: 17 August 2017
Research Article
Discriminating driver mutations from the ones that play no role in cancer is a severe bottleneck in elucidating molecular mechanisms underlying cancer development. Since protein domains are representatives of ...
BMC Bioinformatics 2017 18:370
Published on: 16 August 2017
Research Article
Named Entity Recognition (NER) is a key task in biomedical text mining. Accurate NER systems require task-specific, manually-annotated datasets, which are expensive to develop and thus limited in size. Since s...
BMC Bioinformatics 2017 18:368
Published on: 15 August 2017
Research Article
Drug resistance in HIV treatment is still a worldwide problem. Predicting resistance to antiretrovirals (ARVs) before starting any treatment is important. Prediction accuracy is essential, as low-accuracy pred...
BMC Bioinformatics 2017 18:369
Published on: 15 August 2017
Research Article
Traction Force Microscopy (TFM) is a widespread technique to estimate the tractions that cells exert on the surrounding substrate. To recover the tractions, it is necessary to solve an inverse problem, which i...
BMC Bioinformatics 2017 18:365
Published on: 10 August 2017
Research Article
As more and more biological reaction data become available, the full exploration of the enzymatic potential for the synthesis of valuable products opens up exciting new opportunities but is becoming increasing...
BMC Bioinformatics 2017 18:366
Published on: 10 August 2017
Software
Rapid generation of omics data in recent years have resulted in vast amounts of disconnected datasets without systemic integration and knowledge building, while individual groups have made customized, annotate...
BMC Bioinformatics 2017 18:367
Published on: 10 August 2017
Research Article
Many biases and spurious effects are inherent in RNA-seq technology, resulting in a non-uniform distribution of sequencing read counts for each base position in a gene. Therefore, a base-level strategy is requ...
BMC Bioinformatics 2017 18:364
Published on: 9 August 2017
Software
Next-generation sequencing (NGS) approaches are commonly used to identify key regulatory networks that drive transcriptional programs. Although these technologies are frequently used in biological studies, NGS...
BMC Bioinformatics 2017 18:363
Published on: 8 August 2017
Software
Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density...
BMC Bioinformatics 2017 18:362
Published on: 7 August 2017
Methodology Article
Probabilistic assessments of clinical care are essential for quality care. Yet, machine learning, which supports this care process has been limited to categorical results. To maximize its usefulness, it is imp...
BMC Bioinformatics 2017 18:361
Published on: 7 August 2017
Research Article
MicroRNAs carry out post-transcriptional gene regulation in animals by binding to the 3' untranslated regions of mRNAs, causing their degradation or translational repression. MicroRNAs influence many biologica...
BMC Bioinformatics 2017 18:359
Published on: 3 August 2017
Research Article
Histopathology images are critical for medical diagnosis, e.g., cancer and its treatment. A standard histopathology slice can be easily scanned at a high resolution of, say, 200,000×200,000 pixels. These high ...
BMC Bioinformatics 2017 18:360
Published on: 3 August 2017
Methodology Article
High-throughput sequence (HTS) data exhibit position-specific nucleotide biases that obscure the intended signal and reduce the effectiveness of these data for downstream analyses. These biases are particularl...
BMC Bioinformatics 2017 18:357
Published on: 1 August 2017
Research Article
Disease progression models are important for understanding the critical steps during the development of diseases. The models are imbedded in a statistical framework to deal with random variations due to biolog...
BMC Bioinformatics 2017 18:358
Published on: 1 August 2017
Research Article
Computational prediction of transcription factor (TF) binding sites in different cell types is challenging. Recent technology development allows us to determine the genome-wide chromatin accessibility in vario...
BMC Bioinformatics 2017 18:355
Published on: 27 July 2017
Software
LINCS L1000 is a high-throughput technology that allows gene expression measurement in a large number of assays. However, to fit the measurements of ~1000 genes in the ~500 color channels of LINCS L1000, every...
BMC Bioinformatics 2017 18:356
Published on: 27 July 2017
Methodology Article
Epigenetic heterogeneity within a tumour can play an important role in tumour evolution and the emergence of resistance to treatment. It is increasingly recognised that the study of DNA methylation (DNAm) patt...
BMC Bioinformatics 2017 18:354
Published on: 25 July 2017
Research article
Large sample sets of whole genome sequencing with deep coverage are being generated, however assembling datasets from different sources inevitably introduces batch effects. These batch effects are not well und...
BMC Bioinformatics 2017 18:351
Published on: 24 July 2017
Software
Given the current influx of 16S rRNA profiles of microbiota samples, it is conceivable that large amounts of them eventually are available for search, comparison and contextualization with respect to novel sam...
BMC Bioinformatics 2017 18:353
Published on: 24 July 2017
Research Article
Characterizing membrane dynamics is a key issue to understand cell exchanges with the extra-cellular medium. Total internal reflection fluorescence microscopy (TIRFM) is well suited to focus on the late steps ...
BMC Bioinformatics 2017 18:352
Published on: 24 July 2017
Methodology Article
Gene Ontology (GO) is a community effort to represent functional features of gene products. GO annotations (GOA) provide functional associations between GO terms and gene products. Due to resources limitation,...
BMC Bioinformatics 2017 18:350
Published on: 21 July 2017
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