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humansandviruses.blogspot.com

Humans and Viruses: November 2014

http://humansandviruses.blogspot.com/2014_11_01_archive.html

Sunday, November 30, 2014. Preventing Infection by Shutting Down Host Cell Receptors? While most anti-virals tend to target the virus itself, as in the case of influenza virus where there is rapid mutation, viruses are capable of finding ways to render the drug ineffective. If attacking the virus directly doesn't work, what could be another way of halting viral infection? Hopefully this is good news for the improvement of anti-viral drugs and anti-viral treatments! Since the advent of genome mapping, the...

karchinlab.org

Karchin Lab Johns Hopkins University

http://karchinlab.org/people.html

The William R. Brody Faculty Scholar, Johns Hopkins University. Institute for Computational Medicine, Department of Biomedical Engineering, Department of Oncology. About the Karchin Lab. Dave Masica, Ph.D. Department of Biomedical Engineering. Institute for Computational Medicine. Department of Biomedical Engineering. Institute for Computational Medicine. Department of Biomedical Engineering. Institute for Computational Medicine. Department of Biomedical Engineering. Institute for Computational Medicine.

karchinlab.org

Karchin Lab Johns Hopkins University POSE

http://karchinlab.org/apps/appPose.html

POSE @ Karchin lab. POSE (Phenotype-optimized Sequence Ensembles). Is a supervised learning method that predicts the functional significance of missense mutations in a specific protein. Current release is POSE 0.60, last updated on 01/12/2015. POSE software is intended for those with substantial bioinformatics and Python expertise. POSE is free for non-commercial use. Commercial users should contact the Johns Hopkins Technology Transfer office. Documentation for the developer.

karchinlab.org

Karchin Lab Johns Hopkins University SNVBox

http://karchinlab.org/apps/appSnvBox.html

SNVBox @ Karchin lab. SNVBox is intended for those with substantial bioinformatics and Linux system expertise and access to a large-memory Linux server. It is free for non-commercial use. For more details please refer to our Software License. Commercial users should contact the Johns Hopkins Technology Transfer office. SNVBox can be used independently of CHASM and VEST software, however these tools use SNVBox as a source of predictive features, and SNVBox currently shares a Wiki site with them.

karchinlab.org

Karchin Lab Johns Hopkins University

http://karchinlab.org/publications.html

Tokheim C, Papdopoulis N, Kinzler KW, Vogelstein B, Karchin R (2016) Evaluating the evaluation of cancer driver genes. J Am Med Inform Assoc Jun 21 pii: ocw069. doi: 10.1093/jamia/ocw069. [Epub ahead of print]. Mascia DL, Karchin R (2016) Towards increasing the clinical relevance of in silico methods to predict pathogenic missense variants. PLoS Computational Biology. May 12;12(5):e1004725. Cancer Research. Apr. 28.pii: canres.3190.2015. [Epub ahead of print]. Douville C, Masica DL, Stenson PD, Cooper DN...

karchinlab.org

Karchin Lab Johns Hopkins University SCHISM

http://karchinlab.org/apps/appSchism.html

SCHISM @ Karchin lab. SCHISM (SubClonal Hierarchy Inference from Somatic Mutations). Is a computational framework that reconstructs tumor subcolonal phylogenies using somatic mutation cellularities in patient's tumor sample(s). SCHISM combines information about somatic mutation cellularity (aka mutation cancer cell fraction) across all tumor sample(s) available from a patient in a hypothesis testing framework to identify the statistical support for the lineage relationship between each pair of mutations ...

karchinlab.org

Karchin Lab Johns Hopkins University VEST

http://karchinlab.org/apps/appVest.html

VEST @ Karchin lab. VEST (Variant Effect Scoring Tool). Is a machine learning method that predicts the functional significance of missense mutations observed through genome sequencing, allowing mutations to be prioritized in subsequent functional studies, based on the probability that they impair protein activity. It is free for non-commercial use. For more details please refer to our Software License. Commercial users should contact the Johns Hopkins Technology Transfer office. Documentation for the user.

karchinlab.org

Karchin Lab Johns Hopkins University POSE

http://karchinlab.org/apps/appMoca.html

MOCA @ Karchin lab. MOCA (Multivariate Organization of Combinatorial Alterations). Is a non-parametric algorithm to discover constellations of dichotomous features that predict a phenotype of interest with high sensitivity and specficity. Current release is MOCA 0.75, last updated on 02/04/2014. MOCA software is intended for those with substantial bioinformatics and Python expertise. MOCA is free for non-commercial use. Commercial users should contact the Johns Hopkins Technology Transfer office.