Archive for the 'SciLit' Category

Sequence of events in prostate cancer

October 5, 2018

Sequence of events in prostate #cancer, by @MarkARubin1
http://www.Nature.com/articles/d41586-018-06029-5 Discusses the high prevalence of AR-enhancer amplifications in recent studies
QT:{{”
“Quigley and colleagues performed whole-genome sequencing of 101 samples of metastatic, castration-resistant prostate-cancer tissue obtained from previous studies11,12. The most frequently altered genomic site identified was the AR-enhancer region, which was amplified in 81% of samples. The high prevalence of this type of amplification is notable because enhancer amplifications identified so far for other cancer types generally arise at much lower
frequency13–16. Moreover, the high prevalence of this AR-enhancer amplification in the data presented by Viswanathan and Quigley contrasts with its occurrence in only 1 of 54 previously published whole-genome sequences of prostate-cancer samples obtained before clinical treatment had commenced17.”
“}}

GTEx sex differential expression paper

September 5, 2018

https://www.nature.com/articles/nature24265
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0352-z

+
TCGA sex differences
https://www.cell.com/cancer-cell/abstract/S1535-6108(16)30111-8

The Scientific Prize Network Predicts Who Pushes the Boundaries of Science

September 3, 2018

https://arxiv.org/pdf/1808.09412.pdf

Mind control as a guide for the mind | Nature Human Behaviour

August 18, 2018

Mind control as a guide for the mind | Nature Human Behaviour

https://www.nature.com/articles/s41562-017-0119

Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data: Biophysical Journal

August 18, 2018

Modeling RNA Secondary Structure with Sequence Comparison &
Experimental Mapping Data
https://www.Cell.com/biophysj/fulltext/S0006-3495(17)30689-6 combines TurboFold sec. structure prediction w/ results of SHAPE assays

Zhen Tan
Gaurav Sharma
David H. Mathews

Open Archive Published:July 20, 2017
DOI:https://doi.org/10.1016/j.bpj.2017.06.039

Addressing the minimum fleet problem in on-demand urban mobility | Nature

August 17, 2018

Addressing the minimum fleet problem in on-demand urban mobility by @mmvazifeh, @stevenstrogatz et al.
https://www.Nature.com/articles/s41586-018-0095-1 Solved by putting taxis & their riders into a large #network

Muons: the little-known particles helping to probe the impenetrable

August 17, 2018

Muons: the little-known particles helping to probe the impenetrable, via @NaturePodcast https://www.Nature.com/articles/d41586-018-05254-2 Using “muography” to see into the ground, beneath volcanos & into pyramids

New study finds cell line difference across labs

August 16, 2018

https://www.nature.com/articles/s41586-018-0409-3
QT:{{”
“… comprehensive genomic characterization of 27 strains of the common breast cancer cell line MCF7 uncovered rapid genetic
diversification. Similar results were obtained with multiple strains of 13 additional cell lines.
“}}

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