Posts Tagged ‘cbb752’

Explore Erudite – BD2K Training Coordinating Center

December 6, 2016

http://bigdatau.org/explore_erudite

Needleman–Wunsch algorithm – Wikipedia

November 11, 2016

https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm

relates to

https://en.wikipedia.org/wiki/Wagner%E2%80%93Fischer_algorithm

https://en.wikipedia.org/wiki/Michael_J._Fischer

QT:{{"

Historical notes and algorithm development[edit]

The original purpose of the algorithm described by Needleman and Wunsch was to find similarities in the amino acid sequences of two proteins.[1]

Needleman and Wunsch describe their algorithm explicitly for the case when the alignment is penalized solely by the matches and mismatches, and gaps have no penalty (d=0). The original publication from 1970 suggests the recursion

A better dynamic programming algorithm with quadratic running time for the same problem (no gap penalty) was first introduced[3] by David Sankoff in 1972. Similar quadratic-time algorithms were discovered independently by T. K. Vintsyuk[4] in 1968 for speech processing ("time warping"), and by Robert A. Wagner and Michael J. Fischer[5] in 1974 for string matching.

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Visualization of Statistical Power Analysis

July 28, 2016

Visualization of Power Analysis http://amarder.GITHUB.io/power-analysis/ Useful sliders giving one a feel of the #statistics

How does multiple testing correction work?

June 13, 2016

How does multiple-testing correction work
http://www.nature.com/nbt/journal/v27/n12/abs/nbt1209-1135.html Intuition for teaching: genome-wide error rate on a single gene v family

The role of regulatory variation in complex traits and disease : Nature Reviews Genetics : Nature Publishing Group

June 12, 2016

Reg. variation in cplx traits by @LeonidKruglyak
http://www.nature.com/nrg/journal/v16/n4/full/nrg3891.html nice teaching figure for #eQTLs, showing how mostly cis + hotspots http://www.nature.com/nrg/journal/v16/n4/full/nrg3891.html

Plant endophytes as a platform for discovery-based undergraduate science education : Abstract : Nature Chemical Biology

March 26, 2016

Ex. of extreme project oriented course

http://www.nature.com/nchembio/journal/v3/n7/abs/nchembio0707-356.html

EM algorithm

March 11, 2016

What’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, 2016

quick video for visualizing the power of kernels in SVM
https://www.youtube.com/watch?v=3liCbRZPrZA

Visualizing matrix multiplication as a linear combination – Eli Bendersky’s website

February 20, 2016

http://eli.thegreenplace.net/2015/visualizing-matrix-multiplication-as-a-linear-combination/

MIT Linear Algebra, Lecture 3: Matrix Multiplication and Inverse Matrices – good coders code, great coders reuse

February 20, 2016

http://www.catonmat.net/blog/mit-linear-algebra-part-three/