Best Practices for Sci Computing
http://journals.PLOS.org/plosbiology/article?id=10.1371/journal.pbio.1001745 Usual stuff (GitHub, profilers, assertions) + some gems (turn bugs into test cases)
The impact of #SVs on…gene expression
http://biorxiv.org/content/early/2016/06/09/055962 24k in 147 people in GTEx pilot act as causal variants in 3-7% of ~25k eQTLs
The impact of structural variation on human gene expression
Colby Chiang, Alexandra J Scott, Joe R Davis, Emily
K Tsang, Xin Li, Yungil Kim, Farhan N Damani, Liron Ganel, GTEx Consortium, Stephen B Montgomery, Alexis Battle, Donald F Conrad, Ira M Hall
doi: https://doi.org/10.1101/055962
A gradient of childhood #selfcontrol predicts health, wealth & public safety http://www.PNAS.org/content/108/7/2693.full From following 1K kids from 0 to 32 yrs
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
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
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!
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
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
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