Archive for the 'SciLit' Category

genome-wide starr-seq + sources of experimental bias

August 12, 2018

quite relevant
https://www.nature.com/articles/nmeth.4534

Resolving systematic errors in widely used enhancer activity assays in human cells

Felix Muerdter
, Łukasz M Boryń
, Ashley R Woodfin
, Christoph Neumayr
, Martina Rath
, Muhammad A Zabidi
, Michaela Pagani
, Vanja Haberle
, Tomáš Kazmar
, Rui R Catarino
, Katharina Schernhuber
, Cosmas D Arnold
& Alexander Stark

Nature Methods volume 15, pages141–149 (2018)

text mining and privacy

August 4, 2018

Don’t quote me: reverse identification of research participants in social media studies

John W. Ayers,
Theodore L. Caputi,
Camille Nebeker &
Mark Dredze

npj Digital Medicine
volume 1, Article number: 30 (2018)

https://www.nature.com/articles/s41746-018-0036-2

Induced Structural Disorder as a Molecular Mechanism for Enzyme Dysfunction in Phosphoglucomutase 1 Deficiency – ScienceDirect

July 28, 2018

Induced Structural Disorder as a Molecular Mechanism for Enzyme Dysfunction in Phosphoglucomutase 1 Deficiency – ScienceDirect https://www.sciencedirect.com/science/article/pii/S0022283616001625

GA4GH’s paper on data sharing

July 27, 2018

Perspective | OPEN | Published: 23 July 2018

Responsible sharing of biomedical data and biospecimens via the “Automatable Discovery and Access Matrix” (ADA-M)

J. Patrick Woolley,
Emily Kirby,
Josh Leslie,
Francis Jeanson,
Moran N. Cabili,
Gregory Rushton,
James G. Hazard,
Vagelis Ladas,
Colin D. Veal,
Spencer J. Gibson,
Anne-Marie Tassé,
Stephanie O. M. Dyke,
Clara Gaff,
Adrian Thorogood,
Bartha Maria Knoppers,
John Wilbanks &
Anthony J. Brookes

npj Genomic Medicinevolume 3, Article number: 17 (2018) | Download Citation

new paper in Nature Genomic Medicine:
https://www.nature.com/articles/s41525-018-0057-4

Journal Club by JG

July 27, 2018

TWAS of 229k women identifies new candidate susceptibility genes for breast cancer https://www.Nature.com/articles/s41588-018-0132-x Metascan approach. Derive model for imputing transcriptome from #GTEx & validate against TCGA. Application to BCAC.

Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder | Nature Neuroscience

July 27, 2018

Genome-wide prediction & functional characterization of the genetic basis of autism spectrum disorder, by @OlgaTroyanskaya lab
https://www.Nature.com/articles/nn.4353 Intersected candidate #ASD genes w/ #BrainSpan gene expression to find a pre-natal signal for the disease

Leveraging molecular QTL to understand the genetic architecture of diseases and complex traits | bioRxiv

July 11, 2018

https://www.biorxiv.org/content/early/2017/10/15/203380

Leveraging molecular QTL to understand the genetic architecture of diseases and complex traits

Farhad Hormozdiari, Steven Gazal, Bryce van de Geijn, Hilary Finucane, Chelsea J.-T. Ju, Po-Ru Loh, Armin Schoech, Yakir Reshef, Xuanyao Liu, Luke O’Connor, Alexander Gusev, Eleazar Eskin, Alkes Price
doi: https://doi.org/10.1101/203380

Survey of variation in human transcription factors reveals prevalent DNA binding changes | Science

July 11, 2018

http://science.sciencemag.org/content/351/6280/1450.long

Bioconda: sustainable and comprehensive software distribution for the life sciences | Nature Methods

July 11, 2018

https://www.nature.com/articles/s41592-018-0046-7

kbase out

July 10, 2018

https://www.nature.com/articles/nbt.4163