Archive for the 'SciLit' Category

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illumina platinum genomes paper

January 10, 2017

Set of 5.4M phased…variants…from seq. a 3-gen. 17-member [CEPH] pedigree, centered on #NA12878
http://genome.cshlp.org/content/early/2016/11/25/gr.210500.116 $ILMN Pt genomes

A reference data set of 5.4 million phased human
variants validated by genetic inheritance from
sequencing a three-generation 17-member pedigree

Michael A. Eberle,1 Epameinondas Fritzilas,2 Peter Krusche,2 Morten Källberg,2 Benjamin L. Moore,2 Mitchell A. Bekritsky,2 Zamin Iqbal,3 Han-Yu Chuang,1 Sean J. Humphray,2 Aaron L. Halpern,1 Semyon Kruglyak,1 Elliott H. Margulies,1 Gil McVean,3,4 and David R. Bentley2

http://genome.cshlp.org/content/early/2016/11/25/gr.210500.116

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new CommonMind paper

December 22, 2016

Gene expr. elucidates functional impact of…risk for SCZ
http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4399.html CMC resource contains >2.1M #eQTLs involving ~1.6M SNPs

NATURE NEUROSCIENCE | ARTICLE

Gene expression elucidates functional impact of polygenic risk for schizophrenia

Menachem Fromer,
Panos Roussos,
Solveig K Sieberts,
Jessica S Johnson,
David H Kavanagh,
Thanneer M Perumal,
Douglas M Ruderfer,
….
Eric E Schadt,
Keisuke Hirai,
Kathryn Roeder,
Kristen J Brennand,
Nicholas Katsanis,
Enrico Domenici,
Bernie Devlin
& Pamela Sklar

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Gamma frequency entrainment attenuates amyloid load and modifies microglia : Nature : Nature Research

December 19, 2016

Gamma frequency entrainment attenuates amyloid load & modifies microglia http://www.nature.com/nature/journal/v540/n7632/full/nature20587.html Buying a 40 Hz light to fight Alzheimer’s!

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Protein-structure-guided discovery of functional mutations across 19 cancer types : Nature Genetics : Nature Research

December 11, 2016

Protein-structure-guided discovery of functional mutations across 19 #cancer types http://www.nature.com/ng/journal/v48/n8/abs/ng.3586.html Cancer3D relates SNVs to drugs

http://www.nature.com/ng/journal/v48/n8/abs/ng.3586.html

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A scored human protein-protein interaction network to catalyze genomic interpretation : Nature Methods : Nature Research

December 9, 2016

Scored…PPI #network to catalyze genomic interpretation http://www.Nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4083.html >500k links from lit. mining; up weights small-scale expt

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Access : Mining electronic health records: towards better research applications and clinical care : Nature Reviews Genetics

December 6, 2016

http://www.nature.com/nrg/journal/v13/n6/full/nrg3208.html

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Classification and characterization of microsatellite instability across 18 cancer types : Nature Medicine : Nature Research

December 4, 2016

http://www.nature.com/nm/journal/v22/n11/abs/nm.4191.html

"Classification and characterization of
microsatellite instability across 18 cancer types" by Hause,
Pritchard, Shendure and Salipante from Nature Medicine, 2016

Characterization of microsatellite instability across 18 cancer types http://www.nature.com/nm/journal/v22/n11/abs/nm.4191.html Classifier finds cancer-associated #MSI loci

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PLOS Computational Biology: PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

November 28, 2016

PredictSNP…Consensus Classifier for Prediction of Disease-Related
Mutations http://journals.PLOS.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003440 Demo of various #ensemble approaches

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De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets | BMC Genomics | Full Text

November 25, 2016

De novo prediction of cis-regulatory…modules through integrative analysis of a large number of ChIP datasets
http://BMCGenomics.BiomedCentral.com/articles/10.1186/1471-2164-15-1047 [1/2]
Only calls modules w/ overrepresented pairs of TFBSes – based on observation that well-known promotors have extensive co-regulation [2/2]

De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets

Meng Niu,
Ehsan S Tabari and
Zhengchang Su

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Health Care Infrastructure for Financially Sustainable Clinical Genomics

November 15, 2016

http://jmd.amjpathol.org/article/S1525-1578(16)30086-1/pdf
billing figure

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