Posts Tagged ‘kky’

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:

search variants in 10000+ genomes

December 5, 2016

Hum. Longevity

Universality of human microbial dynamics : Nature : Nature Research

September 5, 2016

Universality of human #microbial dynamics Addressed via simulations & graphs comparing counts of species v organisms

Punctuated equilibrium in the large-scale evolution of programming languages | Journal of The Royal Society Interface

September 22, 2015

Punctuated equilibrium in the large-scale #evolution of #programming languages Clustering groups these into trees

Punctuated equilibrium in the large-scale evolution of programming languages
Sergi Valverde, Ricard V. Solé

related to the scaling you like

March 13, 2015

Statistical Basis for Predicting Technological Progress

Béla Nagy,
J. Doyne Farmer,
Quan M. Bui,
Jessika E. Trancik

Published: February 28, 2013
DOI: 10.1371/journal.pone.0052669

BoxPlotR: a web tool for generation of box plots

September 21, 2014

They published a paper on a web tool to generate box plots !! QT:{{”
Despite the obvious advantages of the box plot for simultaneous representation of data set and statistical parameters, this method is not in common use, in part because few available software tools allow the facile generation of box plots. For example, the standard spreadsheet tool Excel is unable to generate box plots.

M.S. and J.W. conceived of the box plot tool


By The Numbers: Search NIH Grant Data By Institution

September 19, 2014

Genome-scale functional characterization of Drosophila developmental enhancers in vivo : Nature : Nature Publishing Group

August 13, 2014

Functional characterization of… developmental #enhancers in vivo: 3.5k of 7.7k tested active in fly embryo stages

cancer genomics

January 19, 2014

An article on how Eric Schadt tries to treat a cancer patient by sequencing…