miRNA silencing for…therapy targeted to the [acidic] tumor microenviron., w/ #pHLIP
http://www.nature.com/nature/journal/v518/n7537/abs/nature13905.html miR-155 moves beyond biomarker
Posts Tagged ‘from’
MicroRNA silencing for cancer therapy targeted to the tumour microenvironment : Nature : Nature Publishing Group
April 8, 2016DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data | BMC Systems Biology | Full Text
April 8, 2016DREM…reconstruction of…regulatory #networks from time-series expression http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-6-104 Classic approach using 3-level IO #HMMs
SF424 (R&R) Application and Electronic Submission Information for NIH
March 26, 2016Yet more thoughts on squeezing in stuff:
Margins: 0.5 inches all around
Normal: Arial 11 pt
Spacing:
– 12 pt spacing exactly & 0 before & after + 4 pt before major heads (except for in-line figures, then automatic ‘single spacing’) such as INNOVATION
– no widow/orphan control
– no spaces before paragraphs, just indents
– bullet (*) lists (eg for people)
Hyphenate! (Menu: Page Layout, Page Setup, Hyphenation, Automatic) ****
Legends: Arial 8.5 pt, Spacing exactly 8.4 pt. Hyphenated. ****
Titles: Cambria 12 pt looks nice, but flexible.
References: NIH Style EndNote. [1]
QT:{{”
NIH instructions write: “Use an Arial, Helvetica, Palatino Linotype, or Georgia typeface, a black font color, and a font size of 11 points or larger. (A Symbol font may be used to insert Greek letters or special characters; the font size requirement still applies.). Type density, including characters and spaces, must be no more than 15 characters per inch. Type may be no more than six lines per inch (1 inch = 72 points, six lines/inch = 12 pt exact spacing). Use standard paper size (8 ½” x 11) . Use at least one-half inch margins (top, bottom, left, and right) for all pages. No information should appear in the margins.”
“}}
QT:{{”
11. Descriptive Title of Applicant’s Project
Enter a brief descriptive title of the project. This field is required.
A “new” application must have a different title from any other PHS project with the same PD/PI. A “resubmission” or “renewal” application should normally have the same title as the previous grant or application. If the specific aims of the project have significantly changed, choose a new title.
A “revision” application must have the same title as the currently funded grant.
NIH and other PHS agencies limit title character length to 81 characters, including the spaces between words and punctuation. Titles in excess of 81 characters will be truncated. Be sure to only use standard characters in the descriptive title: A through Z, a through z, 0 through 9, space ( ), and underscore (_).
“}}
The above is OLD. Now you can go above 81 characters.
QT:{{”
Font
Prepare the application using Arial, Helvetica, Palatino Linotype, or Georgia typeface in black font color. After text attachments are converted to PDF, font size in each final PDF document must be at least 11 points (or larger). (A Symbol font may be used to insert Greek letters or special characters; the font size requirement still applies.) Since some PDF converters may reduce font sizes, it is important to confirm that type density in each final PDF document, including both characters and spaces, is no more than 15
characters+spaces per linear inch and no more than six lines per vertical inch.
“}}
Note: 72 points/inch so 6 lines/inch at 11pt type translates into a line spacing of 11 pts + 1pt per line.
QT:{{”
Paper Size and Page Margins
Final PDF documents should be formatted to be no larger than standard paper size (8 ½” x 11). The final PDF document should have at least one-half inch margins (top, bottom, left, and right) for all pages. No information should appear in the margins, including the PI’s name and page numbers.
….
Figures, Graphs, Diagrams, Charts, Tables, Figure Legends, and Footnotes You may use a smaller type size but it must be in a black font color, readily legible, and follow the font typeface requirement. Color can be used in figures; however, all text must be in a black font color, clear and legible.
“}}
An expanded sequence context model broadly explains variability in polymorphism levels across the human genome : Nature Genetics : Nature Publishing Group
March 26, 2016Expanded seq. context model…explains variability in polymorphism[s] http://www.nature.com/NG/journal/vaop/ncurrent/full/ng.3511.html Reminiscent of GOR sec. structure prediction
AlgoRun, a Docker-based packaging system for platform-agnostic implemented algorithms
March 19, 2016http://dx.doi.org/10.1093/bioinformatics/btw120
http://AlgoRun.org, #Docker-based packaging [w/ web GUI & workflow mgt] for platform-agnostic implement[ations]
http://Bioinformatics.Oxfordjournals.org/content/early/2016/03/02/bioinformatics.btw120
Hosny, A. et al. AlgoRun, a Docker-based packaging system for platform-agnostic implemented algorithms. Bioinformatics Advance Access, Mar 2, 2016.
SF424 (R&R) Application and Electronic Submission Information for NIH
March 19, 2016More thoughts on this. One person’s condensed summary of this for Word:
QT:{{
Margins: 0.5 inches all around
Normal: Arial 11 pt
Spacing: 12 pt exactly (except for in-line figures, then automatic ‘single spacing’)
Hyphenate! (Menu: Page Layout, Page Setup, Hyphenation, Automatic) **** Legends: Arial 8.5 pt, Spacing exactly 8.4 pt. Hyphenated. **** Titles: Cambria 12 pt looks nice, but flexible.
References: NIH Style EndNote. [1]
NIH instructions write: “Use an Arial, Helvetica, Palatino Linotype, or Georgia typeface, a black font color, and a font size of 11 points or larger. (A Symbol font may be used to insert Greek letters or special characters; the font size requirement still applies.). Type density, including characters and spaces, must be no more than 15 characters per inch. Type may be no more than six lines per inch (1 inch = 72 points, six lines/inch = 12 pt exact spacing). Use standard paper size (8 ½” x 11) . Use at least one-half inch margins (top, bottom, left, and right) for all pages. No information should appear in the margins.”
“}}
QT:{{”
11. Descriptive Title of Applicant’s Project
Enter a brief descriptive title of the project. This field is required.
A “new” application must have a different title from any other PHS project with the same PD/PI. A “resubmission” or “renewal” application should normally have the same title as the previous grant or application. If the specific aims of the project have significantly changed, choose a new title.
A “revision” application must have the same title as the currently funded grant.
NIH and other PHS agencies limit title character length to 81 characters, including the spaces between words and punctuation. Titles in excess of 81 characters will be truncated. Be sure to only use standard characters in the descriptive title: A through Z, a through z, 0 through 9, space ( ), and underscore (_).
“}}
The above is OLD. Now you can go above 81 characters.
QT:{{”
Font
Prepare the application using Arial, Helvetica, Palatino Linotype, or Georgia typeface in black font color. After text attachments are converted to PDF, font size in each final PDF document must be at least 11 points (or larger). (A Symbol font may be used to insert Greek letters or special characters; the font size requirement still applies.) Since some PDF converters may reduce font sizes, it is important to confirm that type density in each final PDF document, including both characters and spaces, is no more than 15
characters+spaces per linear inch and no more than six lines per vertical inch.
“}}
Note: 72 points/inch so 6 lines/inch at 11pt type translates into a line spacing of 11 pts + 1pt per line.
QT:{{”
Paper Size and Page Margins
Final PDF documents should be formatted to be no larger than standard paper size (8 ½” x 11). The final PDF document should have at least one-half inch margins (top, bottom, left, and right) for all pages. No information should appear in the margins, including the PI’s name and page numbers.
….
Figures, Graphs, Diagrams, Charts, Tables, Figure Legends, and Footnotes You may use a smaller type size but it must be in a black font color, readily legible, and follow the font typeface requirement. Color can be used in figures; however, all text must be in a black font color, clear and legible.
“}}
EM algorithm
March 11, 2016What’s the EM #algorithm?
http://www.nature.com/nbt/journal/v26/n8/full/nbt1406.html Description of its essence in simple contexts (ie coin toss) & as soft version of kmeans
What is the expectation maximization algorithm? : Article : Nature Biotechnology
Primer
Nature Biotechnology 26, 897 – 899 (2008)
doi:10.1038/nbt1406
Chuong B Do & Serafim Batzoglou
Abstract
The expectation maximization algorithm arises in many computational biology applications that involve probabilistic models. What is it good for, and how does it work?
without too much math
SVM movie
March 5, 2016quick video for visualizing the power of kernels in SVM
https://www.youtube.com/watch?v=3liCbRZPrZA
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription: Cell
March 4, 2016CTCF-Mediated…3D Genome Architecture
http://www.cell.com/cell/abstract/S0092-8674(15)01504-4 SNPs give different #chromatin topologies, including strong #allelic effects
Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins : Nature Genetics : Nature Publishing Group
March 3, 2016Gene-gene & gene-env interactions…by #transcriptome…in twins by @dermitzakis lab
http://www.nature.com/ng/journal/v47/n1/full/ng.3162.html Nice model for ASE HT @cjieming
Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins
Alfonso Buil, Andrew Anand Brown, Tuuli Lappalainen, Ana Viñuela, Matthew N Davies, Hou-Feng Zheng, J Brent Richards, Daniel Glass, Kerrin S Small, Richard Durbin, Timothy D Spector & Emmanouil T Dermitzakis