Nice graph of seq. machine output v time
http://www.cell.com/molecular-cell/abstract/S1097-2765(15)00340-8
Archive for the 'SciLit' Category
Found this review
May 31, 2015Machine learning applications in genetics and genomics : Nature Reviews Genetics : Nature Publishing Group
May 30, 2015#Machinelearning applications in…genomics
http://www.nature.com/nrg/journal/v16/n6/full/nrg3920.html Nice overview of key distinctions betw generative & discriminative models
In their review, “Machine learning in genetics and genomics”, Libbrecht and Noble overview important aspects of application of machine learning to genomic data. The review presents illustrative classical genomics problems where machine learning techniques have proven useful and describes the differences between supervised, semi-supervised and unsupervised learning as well as generative and discriminative models. The authors discuss considerations that should be made when selecting the right machine learning approach depending on the biological problem and data at hand, provide general practical guidelines and suggest possible solutions to common challenges.
Identification of Asthma Phenotypes Using Cluster Analysis in the Severe Asthma Research Program (ATS Journals)
May 30, 2015Identification of #Asthma Phenotypes Using Cluster Analysis
http://www.atsjournals.org/doi/abs/10.1164/rccm.200906-0896OC#.VWk-gFxViko 5 canonical groups based on lung function, meds usage, &c
Canonical clustering of asthmatic patients into different groups
Noninvasive Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of Asthma (ATS Journals)
May 30, 2015Analysis of the Sputum Transcriptome Discriminates Clinical Phenotypes of Asthma http://www.atsjournals.org/doi/abs/10.1164/rccm.201408-1440OC Consistent blood expression patterns
Noninvasive Analysis of the Sputum Transcriptome Discriminates
Clinical Phenotypes of Asthma (ATS Journals)
Yan, X., Chu, J.-H., Gomez, J., Koenigs, M., Holm, C., He, X., Perez,
M. F., Zhao, H., Mane, S., Martinez, F. D., Ober, C., Nicolae, D. L.,
Barnes, K. C., London, S. J., Gilliland, F., Weiss, S. T., Raby, B.
A., Cohn, L., and Chupp, G. L. “Non-Invasive Analysis of the Sputum
Transcriptome Discriminates Clinical Phenotypes of Asthma” American
Journal of Respiratory and Critical Care Medicine (2015):
doi:10.1164/rccm.201408-1440OC,
QT:{{"
Conclusions: There are common patterns of gene expression in the
sputum and blood of children and adults that are associated with near
fatal, severe and milder asthma.
"}}
Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding
May 25, 2015Mtn gorilla genomes reveal…impact of long-term…inbreeding http://www.sciencemag.org/content/348/6231/242 Pop. variation so low that very deleterious SNPs purged
Science 10 April 2015:
Vol. 348 no. 6231 pp. 242-245
DOI: 10.1126/science.aaa3952
Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding
Yali Xue1,*,
Javier Prado-Martinez2,*,
Peter H. Sudmant3,*,
…
Tomas Marques-Bonet2,12,
Chris Tyler-Smith1,†,
Aylwyn Scally13,†
ALK Mutations Confer Differential Oncogenic Activation and Sensitivity to ALK Inhibition Therapy in Neuroblastoma: Cancer Cell
May 22, 2015ALK Mutations Confer Differential Oncogenic Activation
http://www.cell.com/cancer-cell/abstract/S1535-6108%2814%2900393-6 MD modeling better assessing #SNV impact than stats, ie sift
ALK Mutations Confer Differential Oncogenic Activation and Sensitivity to ALK Inhibition Therapy in Neuroblastoma
Scott C. Bresler
Daniel A. Weiser
Peter J. Huwe
…
Ravi Radhakrishnan
Mark A. Lemmon
Yaël P. Mossé
Comparative genomics reveals insights into avian genome evolution and adaptation
May 16, 2015Comparative #genomics reveals insights into avian…#evolution http://www.sciencemag.org/content/346/6215/1311 Less repeats & dups in birds; woodpecker, an exception
Science 12 December 2014:
Vol. 346 no. 6215 pp. 1311-1320
DOI: 10.1126/science.1251385
Comparative genomics reveals insights into avian genome evolution and adaptation
Guojie Zhang1,2,*,†,
Cai Li1,3,*,
….
Avian Genome Consortium§,
Erich D. Jarvis20,†,
M. Thomas P. Gilbert3,56,†,
Jun Wang1,55,57,58,59,†
Characterization of structural variants with single molecule and hybrid sequencing approaches
May 16, 2015Characterization of #SVs w. single molecule & hybrid sequencing http://bioinformatics.oxfordjournals.org/content/30/24/3458.abstract Probabilistic read mapping, re-evaluating adjacencies
QT:{{"
We present MultiBreak-SV, an algorithm to detect structural variants
(SVs) from single molecule sequencing data, paired read sequencing
data, or a combination of sequencing data from different platforms.
"}}
Rebooting MOOC Research
May 15, 2015Rebooting #MOOC Research https://www.sciencemag.org/content/347/6217/34.summary
Perspective from an #education institution: How to measure engagement of the student?
