Tuesday, April 17, 2018

biogrid PPI


read my old codes:

applejack:qin.biogrid.code hqin$ pwd
/Users/hqin/data/biogrid/qin.biogrid.code


My code took 'physical' interactions from biogrid, and found only unique interactions.

Saturday, April 7, 2018

multiplicity of eigen value


The number of linearly independent eigenvectors associated with a given eigen value $lambda$ is called the geometric multiplicity of eigenvalue $lambda$.



matrix Jordan cannonical form and eigen values



http://mathworld.wolfram.com/JordanCanonicalForm.html

Eigen values in Jordan cannobucak form of matrix

estimate protein interactions based on network evolution

estimate protein interactions based on network evolution

https://www.sciencedirect.com/science/article/pii/S037843711730924X

qin 2003 pnas

Friday, April 6, 2018

*** naked mole rat, non-aging model?


elife:
Naked mole-rat mortality rates defy
Gompertzian laws by not increasing with
age
J Graham Ruby, Megan Smith, Rochelle Buffenstein*

Calico Life Sciences LLC, South San Francisco, United States


TODO: exponential signal + white noises :: exponential fitting
Gompertiz signal + white noises :: exponential fitting vs Gompertz fitting. Perhaps, there is just not enough statistical power?

Wednesday, March 28, 2018

NIH uncolicited applications



Did you know that the majority of funded NIH proposals are unsolicited?  That is, they are not in response to a specific funding opportunity announcement!

https://www.niaid.nih.gov/grants-contracts/unsolicited-investigator-initiated-research  although this guidance is specific to NIAID (allergy and infectious disease), the same applies to almost all of NIH – especially NCI – the wealthiest of all at NIH.


Please see the attached presentation from Program Officer, Dr. David Berrigan at NCI.  Last week at meetings at UTK, he took us through the top 10 list of research gems from the Division of Cancer Control and Population Sciences.  These are applicable to anywhere at NIH, not just NCI.


Tuesday, March 27, 2018

Zoom course instruction with iPad


1) Zoom on MacBook, sharescreen with iPad through airplay or cable. (Sometimes, airplay or cable does not work).

2) Zoom on Mackbook, iPad screen shared with Zoom App.  Make sure microphone is muted. Record on both Mackbook.  Make sure personal app, emails are closed.

Monday, March 26, 2018

journal of computational biology



Journal Cover
 
Special Issue: The 13th International Symposium on Bioinformatics Research and Applications (ISBRA2017)
This Special Issue includes a selection of papers presented at the 13th International Symposium on Bioinformatics Research and Applications (ISBRA 2017) which was held in Honolulu, Hawaii on May 30–June 2, 2017. ISBRA provides a forum for the exchange of ideas and results among researchers, developers, and practitioners working on all aspects of bioinformatics and computational biology and their applications.
Enjoy FREE ACCESS through April 9, 2018.
Read Now:
Reconstructing One-Articulated Networks with Distance Matrices
Kuang-Yu Chang, Yun Ciu, Siu-Ming Yiu, Wing-Kai Hon  Read Now
ICON-MIC: Implementing a CPU/MIC Collaboration Parallel Framework for ICON on Tianhe-2 Supercomputer
Zihao Wang, Yu Chen, Jingrong Zhang, Lun Li, Xiaohua Wan, Zhiyong Liu, Fei Sun, Fa Zhang  Read Now
Estimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry
Michał Aleksander Ciach, Mateusz Krzysztof Łącki, Błażej Miasojedow, Frederik Lermyte, Dirk Valkenborg, Frank Sobott, Anna Gambin  Read Now
Convolutional Neural Network for Histopathological Analysis of Osteosarcoma
Rashika Mishra, Ovidiu Daescu, Patrick Leavey, Dinesh Rakheja, Anita Sengupta  Read Now
An Optimized Method for Bayesian Connectivity Change Point Model
Xiuchun Xiao, Bing Liu, Jing Zhang, Xueli Xiao, Yi Pan  Read Now
Unbiased Taxonomic Annotation of Metagenomic Samples
Bruno Fosso, Graziano Pesole, Francesc Rosselló, Gabriel Valiente  Read Now

Sunday, March 18, 2018