Posts Tagged ‘lab’

West campus storage closet

August 18, 2018

MS surface 2

May 18, 2018
note taking to a whole different level

IvyPlus Exchange Program + Imperial, UCL and U of London

May 10, 2018

a link to details on IvyPlus exchange program:

turns out Imperial College London is the institution that left U of London. UCL is still part of U of London

Highlights of 2016

March 26, 2017

I recently had to complete my 2016 Faculty Activity Report (FAR), summarizing key lab “activities” of the past year.

* Here are dump directories with some excerpts:–cv57/–cv57/

These include:

* A full updated CV describing my lab’s activities (in too much detail):–cv57/M-Gerstein-Public-CV–bld1dec16.cv57.pdf

The CV is based on :

– Compiling the people in the lab, viz:–cv57/cv57-22-bld1dec16-AdaptedFrom–Gerstein_Lab_Personnel_112016.pdf–cv57/cv57-23-bld1dec16–EditOn–Corrected-Past-Postdoctoral-Associates-and-Fellows.notrkchg.pdf

– A dump up to the end of ’16 of all of our scientific papers and our “other writings” too.–cv57/cv57-26-bld1dec16–addendum-Rest–Just-Other-Writings.pdf–cv57/cv57-30-bld1dec16–papers-simple–reformatted.pdf

– There’s also an update on lectures in ’16:

* Finally, I’ve done little write up of some highlights, viz:

During 2016 the lab had a number of research highlights. We have published three interlinked tools: Stress, Frustration, and
Intensification, for assessing the impact of rare genomic variants using knowledge of molecular structure. The tools are of particular interest to the medical genetics community because as they can help explain various cancer mutations as well as variants associated with genetic diseases. Another highlight is our publishing a framework for quantifying privacy risks as a result of linking clinical and phenotype variables. This paper is a timely work given the ongoing debate on data sharing. Apart from these works, we have a few research papers on topics in genomics, such as analyzing allele-specific binding and gene expression analysis, and several review articles on the role of non-coding variants, network comparison, and the cost of sequencing.

Regarding service, I worked on further developing the computational biology program at Yale. In particular, I co-chaired a committee about moving toward a Center for Biomedical Data Science at the Medical School. My lab served the research community in participating in many consortiums, such as PCAWG (the Pan-Cancer Analysis Working Group), the ENCODE consortium, PsychENCODE, 1000 Genomes’ structural variation group (and its follow-ons), and the Extracellular RNA Communication Consortium. In 2016, I gave talks and participated in many meetings, including an important data-science education forum at the Cold Spring Harbor Laboratory.

Regarding teaching, I further developed my course in Bioinformatics by including more practical hands-on materials. For example, we introduced a collaborative programming assignment utilizing the GitHub site.

(Private link, with authentication only for my reference:

For reference, this involved updating a variety of places on the wiki, viz:

The RedMonk Programming Language Rankings: June 2016 – tecosystems

August 7, 2016

.@RedMonk Programming Language Rankings Now in a period of little change after an initial “Cambrian” diversification

Gerstein Lab Highlights in 2015

January 31, 2016

I recently had to complete my 2015 Faculty Activity Report (FAR), summarizing key lab “activities” of last year. (Sounds a bit like summer camp.)

Here are some excerpts:

* A full updated CV describing my lab’s activities (in too much detail):

* This is mostly based on compiling the people in the lab in ’15 & the papers they’ve worked on :

There’s also an update on lectures in ’15:

* Finally, I’ve done little write up of some highlights, viz:

Highlights for 2015 include a number of technical computational biology papers, discussing such things as structural variant breakpoint analysis, regulatory network characterization in terms of logical circuits, and the identification of recurrent cancer variants. We also participated in some major consortium papers (1000G, PsychENCODE, and TCGA Prostate & Kidney) and had some popular-interest pieces (eg a SF Chronicle op-ed on website regulation). There were a few important lectures (eg keynote at Genome Informatics ’15). Finally, we received new grants such as the renewal of the Yale CMG sequencing center.

(Private link, with authentication only for my reference:

DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data

August 28, 2015

DeconRNASeq…framework for #deconvolution of heterogeneous tissue samples “App note” w/ very concise code snippet

30 lines of R?

Brief history of

June 15, 2013

From MF, in chronological order

1. — physical machine in Bass

2. — physical machine in ITS
(mirrored to — physical machine in Bass)

3. — qemu virtualized machine in ITS

4. mirrored to — VMware virtualized machine in Gibbs

5. forked — VMware virtual machine in Gibbs

6. — consolidated in EC2