Genotype to phenotype relationships in ASD http://www.nature.com/neuro/journal/v18/n2/abs/nn.3907.html Expression differences in #brain development for LOF-containing, M v F, &c
Also, netbag finds subnets assoc w autism
Archive for the 'SciLit' Category
Genotype to phenotype relationships in autism spectrum disorders : Nature Neuroscience : Nature Publishing Group
February 26, 2015Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq
February 21, 2015Human & mouse [mRNA] #methylomes revealed by m6A-seq http://www.nature.com/nature/journal/v485/n7397/full/nature11112.html Conservation across species & conditions (for most sites)
Dan Dominissini,
Sharon Moshitch-Moshkovitz,
Schraga Schwartz,
…
Rotem Sorek
& Gideon Rechavi
Nature 485, 201–206 (10 May 2012) doi:10.1038/nature11112
Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators : Nature : Nature Publishing Group
February 21, 2015Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators http://www.nature.com/nature/journal/v508/n7497/full/nature13206.html Reconstructed #evolution across 8 species
Daniel W. Bellott,
Jennifer F. Hughes,
…
Richard A. Gibbs,
Richard K. Wilson
& David C. Page
Nature 508, 494–499 (24 April 2014) doi:10.1038/nature13206
Space-time wiring specificity supports direction selectivity in the retina : Nature : Nature Publishing Group
February 21, 2015Spacetime wiring specificity supports…selectivity in the retina http://www.nature.com/nature/journal/v509/n7500/full/nature13240.html @eye_wire citizenscience traces neural connectivity
finds a time lag circuit
Jinseop S. Kim,
Matthew J. Greene,
…
H. Sebastian Seung
& the EyeWirers
Nature 509, 331–336 (15 May 2014) doi:10.1038/nature13240
High-resolution mapping reveals a conserved, widespread, dynamic meiotically regulated mRNA methylation program
February 21, 2015High-res mapping reveals a conserved…mRNA methylation program http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3956118/ Predicting methyl sites w/ seq., structure & position
Cell. 2013 Dec 5; 155(6): 1409–1421.
Published online 2013 Nov 21. doi: 10.1016/j.cell.2013.10.047 PMCID: PMC3956118
NIHMSID: NIHMS550466
High-resolution mapping reveals a conserved, widespread, dynamic meiotically regulated mRNA methylation program
Schraga Schwartz,1,* Sudeep D. Agarwala,2,* Maxwell R. Mumbach,1 Marko Jovanovic,1 Philipp Mertins,1 Alexander Shishkin,1 Yuval Tabach,3,4 Tarjei S Mikkelsen,1 Rahul Satija,1 Gary Ruvkun,3,4 Steven A. Carr,1 Eric S. Lander,1,5,6 Gerald R. Fink,1,2,8 and Aviv Regev 1,7,8
Privacy in Pharmacogenetics: An End-to-End Case Study of Personalized Warfarin Dosing | USENIX
February 20, 2015Privacy in Pharmacogenetics…Personalized Warfarin Dosing
https://www.usenix.org/conference/usenixsecurity14/technical-sessions/presentation/fredrikson_matthew Model-inversion attack; differential privacy doesn’t help
Authors:
Matthew Fredrikson, Eric Lantz, and Somesh Jha, University of Wisconsin—Madison; Simon Lin, Marshfield Clinic Research Foundation; David Page and Thomas Ristenpart, University of Wisconsin—Madison
Awarded Best Paper!
Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles
February 17, 2015Analysis of high-throughput B-cell sequencing
http://www.pnas.org/content/early/2015/02/05/1417683112.abstract Successful locus-level application of #personalgenome construction
Genome Biology | Full text | Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation
February 13, 2015WGBS…reveals complementary roles of promoter & gene-body
#methylation in…regulation http://genomebiology.com/content/15/7/408 Has model for gene expression
Hysteresis in a quantized superfluid atomtronic circuit : Nature : Nature Publishing Group
February 10, 2015Hysteresis in a quantized #superfluid atomtronic circuit
http://www.nature.com/nature/journal/v506/n7487/full/nature12958.html Moving atoms instead of electrons for future storage devices
Stephen Eckel,
Jeffrey G. Lee,
Fred Jendrzejewski,
Noel Murray,
Charles W. Clark,
Christopher J. Lobb,
William D. Phillips,
Mark Edwards
& Gretchen K. Campbell
Nature 506, 200–203 (13 February 2014) doi:10.1038/nature12958
QT:{{”
Atomtronics1, 2 is an emerging interdisciplinary field that seeks to develop new functional methods by creating devices and circuits where ultracold atoms, often superfluids, have a role analogous to that of electrons in electronics. Hysteresis is widely used in electronic circuits—it is routinely observed in superconducting circuits3 and is essential in radio-frequency superconducting quantum interference devices4. Furthermore, it is as fundamental to superfluidity5 …. “}}
Why Most Published Research Findings are false
February 7, 2015Why Most Published Research Findings are False http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.0020124 Evaluating 2×2 confusion matrix, effects of bias & multiple studies
PLoS Medicine | www.plosmedicine.org 0696
August 2005 | Volume 2 | Issue 8 | e124
QT:{{"
Published research fi ndings are sometimes refuted by subsequent evidence, with ensuing confusion and disappointment. Refutation and controversy is seen across the range of research designs, from clinical trials and traditional epidemiological studies [1–3] to the most modern molecular research [4,5]. There is increasing concern that in modern research, false fi ndings may be the majority or even the vast majority of published research claims [6–8]. However, this should not be surprising. It can be proven that most claimed research fi ndings are false. Here I will examine the key
…
Research fi ndings are defi ned here as any relationship reaching formal statistical signifi cance, e.g., effective interventions, informative predictors, risk factors, or associations. “Negative” research is also very useful. “Negative” is actually a misnomer, and the misinterpretation is widespread. However, here we will target relationships that investigators claim exist, rather than null fi ndings. As has been shown previously, the probability that a research fi nding is indeed true depends on the prior probability of it being true (before doing the study), the statistical power of the study, and the level of statistical signifi cance [10,11]. Consider a 2 × 2 table in which research fi ndings are compared against the gold standard of true relationships in a scientifi c fi eld. In a research fi eld both true and false hypotheses can be made about the presence of relationships. Let R be the ratio of the number of “true relationships” to “no relationships” among those tested in the fi eld. R
is characteristic of the fi eld and can vary a lot depending on whether the fi eld targets highly likely relationships or searches for only one or a few true relationships among thousands and millions of hypotheses that may be postulated. Let us also consider, for computational simplicity, circumscribed fi elds where either there is only one true relationship (among many that can be hypothesized) or the power is similar to fi nd any of the several existing true relationships. The pre-study probability of a relationship being true is R⁄(R + 1). The probability of a study fi nding a true relationship refl ects the power 1 − β (one minus the Type II error rate). The probability of claiming a relationship when none truly exists refl ects the Type I error rate, α. Assuming that c relationships are being probed in the fi eld, the expected values of the 2 × 2 table are given in Table 1. After a research fi nding has been claimed based on achieving formal statistical signifi cance, the post-study probability that it is true is the positive predictive value, PPV. The PPV is also the complementary probability of what Wacholder et al. have called the false positive report probability [10]. According to the 2 × 2 table, one gets PPV = (1 − β)R⁄(R − βR + α). A research fi nding is thus
"}}
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