Improving RNA-Seq expression estimates by correcting for fragment bias

BY IN Journal Club, RNA-Seq NO COMMENTS YET , , , ,

Preparation steps for RNA-Seq lead to both positional bias, whereby fragments are preferential located towards either the beginning or end of transcripts, and sequence-specific bias, whereby the sequence surrounding the beginning or end of potential fragments affects their likelihood of being selected for sequencing, in sequenced fragments. If such biases are not corrected for, expression

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New resampling method for evaluating stability of clusters

BY IN Journal Club, Machine learning, Methods NO COMMENTS YET , ,

A measure of cluster stability is needed to discriminate between real clusters from random ones, which arise due to random variation of gene expression measurements from both technical and biological variation. In this study, Gana Dresen et al. propose a new “continuous weights” method to measure cluster stability that uses resampling in a manner similar

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Enabling a Genomics Aware EHR

BY IN Medical informatics, Opinion NO COMMENTS YET , ,

The genome is particularly useful for assessing inherited disease risk and the modulation of drug response. To improve the precision of diagnosis and treatment for personalized medicine, multiple sources of information, including genomic information, will likely need to be combined (Altman, 2013). However, to be successful in personalized medicine, the integration of genomic information into

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Computer-Stored Medical Records – Their Future Role in Medical Practice

BY IN History, Journal Club, Medical informatics, Viewpoint NO COMMENTS YET , ,

The idea of an electronic health record, by which a patient’s information would be stored electronically instead of on paper, has been around since the late 1960s. One of the first medical record systems was developed by the Regenstrief Institute in 1972. In this article, McDonald and Tierney of the Regenstrief Institute discuss benefits of

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Personal Genomic Measurements: The Opportunity for Information Integration

BY IN Journal Club, Medical informatics, Viewpoint NO COMMENTS YET , , , ,

The genome is particularly useful for assessing inherited disease risk and the modulation of drug response. To improve the precision of diagnosis and treatment for personalized medicine, multiple sources of information, including genomic information from high-throughput genomics technologies, will likely need to be combined. In this commentary, Altman argues that this integration of personal genomic

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Region-based segmentation and object detection

BY IN Journal Club, Machine learning NO COMMENTS YET , , , ,

Current computer vision models for image segmentation and object detection use awkward feature mappings and uncoupled subtask representations making joint inference clumsy and leaving the classification of many parts of the scene ambiguous. Gould et al. propose combining image segmentation and object detection in a hierarchical model to reason simultaneously about pixels, regions, and objects

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Genomic Medicine, Health Information Technology, and Patient Care

BY IN Journal Club, Medical informatics, Viewpoint NO COMMENTS YET , , , ,

In this viewpoint article, Chute and Kohane propose three key criteria that must be met to enable the health care system to address the genomic medicine challenge and ultimately enhance the genomic understanding of medicine to usher in improvements in health care effectiveness by the end of this decade: the emergence of a coherent, consistent,

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Cancer genome landscapes

BY IN Cancer genomics, Journal Club, Review NO COMMENTS YET , , , , ,

Over the past decade, comprehensive sequencing efforts have revealed the genomic landscapes of common forms of human cancer. In this review, Vogelstein at el. summarize what has been learned about cancer genomes from these sequencing studies and what this information has taught us about cancer biology and future cancer management strategies. Some key points of

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The Use of Orthologous Sequences to Predict the Impact of Amino Acid Substitutions on Protein Function

BY IN Comparative genomics, Functional impact prediction, Journal Club NO COMMENTS YET , ,

For nonsynonymous coding variants, functional impact prediction algorithms frequently make use of conservation of amino acid substitutions observed among homologous proteins at a given site under the assumption substitutions occurring at well-conserved sites will deleteriously impact protein function and substitutions occurring at less conserved sites will be tolerated. In this study, Marini et al. examine

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In silico analysis of missense substitutions using sequence-alignment based methods

BY IN Functional impact prediction, Journal Club, Review NO COMMENTS YET , , , , , , , ,

Computational classifiers classify missense substitutions as pathogenetic or neutral based on inferences from evolutionary conservation using protein multiple sequence alignments (PMSAs) of the gene of interest (and other features). In this review, Tavtigian et al. make suggestions with respect to the important aspects of creating PMSAs that are informative for classification (and more). In using

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