Posts Tagged ‘fromtalk’

Quantifying the local resolution of cryo-EM density maps | Nature Methods

November 14, 2017

Quantifying the local resolution of #cryoEM density maps
https://www.Nature.com/articles/nmeth.2727 “Theory…based on the following idea: a L Angstrom feature exists at a pt…if a 3D local sinusoid of wavelength L is statistically detectable above noise at that point.”

QT:{{”
We propose a mathematical theory and an efficient algorithm for measuring local resolution that address all of the above limitations. The theory (Online Methods) is based on the following idea: a λ-Å feature exists at a point in the volume if a three-dimensional (3D) local sinusoid of wavelength λ is statistically detectable above noise at that point. A likelihood-ratio hypothesis test of the local sinusoid versus noise can detect this feature at a given P value (typically P = 0.05). We define the local resolution at a point as the smallest λ at which the local sinusoid is detectable, and we account for multiple testing with an FDR procedure.
“}}

Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element. – PubMed – NCBI

October 30, 2017

Comparative…3D chromosomal architecture identifies a novel fetal Hb reg. element http://GenesDev.cshlp.org/content/31/16/1704.abstract #Pseudogene shifts v. promotor

Welcome | ScienceHill-CryoEM

October 28, 2017

http://sciencehill-cryoem.yale.edu/
cryoem.yale.edu
https://medicine.yale.edu/ccmi/

Visualizing the molecular sociology at the HeLa cell nuclear periphery | Science

October 26, 2017

http://science.sciencemag.org/content/351/6276/969.long

#Visualizing the molecular sociology [of complexes] at the HeLa cell nuclear periphery, w/ #CryoET at 10 Ang. res. http://science.ScienceMag.org/content/351/6276/969.long

Science. 2016 Feb 26;351(6276):969-72. doi: 10.1126/science.aad8857.
Visualizing the molecular sociology at the HeLa cell nuclear periphery.
Mahamid J1, Pfeffer S2, Schaffer M2, Villa E3, Danev R2, Cuellar LK2, Förster F2, Hyman AA4, Plitzko JM2, Baumeister W1.

ALK Mutations Confer Differential Oncogenic Activation and Sensitivity to ALK Inhibition Therapy in Neuroblastoma: Cancer Cell

May 22, 2015

ALK Mutations Confer Differential Oncogenic Activation
http://www.cell.com/cancer-cell/abstract/S1535-6108%2814%2900393-6 MD modeling better assessing #SNV impact than stats, ie sift

ALK Mutations Confer Differential Oncogenic Activation and Sensitivity to ALK Inhibition Therapy in Neuroblastoma

Scott C. Bresler
Daniel A. Weiser
Peter J. Huwe

Ravi Radhakrishnan
Mark A. Lemmon
Yaël P. Mossé

DOI: http://dx.doi.org/10.1016/j.ccell.2014.09.019

Convergent transcriptional specializations in the brains of humans and song-learning birds

March 15, 2015

Convergent…specializations in brains of humans & songbirds http://www.sciencemag.org/content/346/6215/1256846.long Both have matching expression patterns across regions

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

February 21, 2015

Human & 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

High-resolution mapping reveals a conserved, widespread, dynamic meiotically regulated mRNA methylation program

February 21, 2015

High-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