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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Removing Gap Columns from MSA

BY IN Code, Python, Tutorials NO COMMENTS YET ,

Consider the following multiple sequence alignment: >HUMAN —————–METTNGT-ETWYESLHAVLKALNATLHSNLLCRPGPGL–G– >MOUSE —————–METSNGT-ETWYMSLHAVLKALNTTLHSHLLCRPGPGP–G– >CHICKEN —————–MEEDNRT-EPWHHSLQAMLDALNQTLHRAILHP-ST——- … Let’s say you want to remove the columns from the alignment where the query (human) protein sequence has a gap. You may want to do this for a number of reasons though I had to do this trick to get my local

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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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5 Useful Python One Liners for Lists

BY IN Code, Python, Tutorials NO COMMENTS YET

Five useful Python one liners for making and manipulating lists: 1. From text file to list: code: [line.strip() for line in open(file)] example file proteins_list.txt: Q8N465 O95452 Q14524 Q86YC2 P11413 Q8IWV7 example: >>> [line.strip() for line in open(‘proteins_list.txt’)] [‘Q8N465’, ‘O95452’, ‘Q14524’, ‘Q86YC2’, ‘P11413’, ‘Q8IWV7’] 2. Get a list of strings from list that contains a

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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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