Questions tagged [bioinformatics]

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Mathematical modeling of multi-site reaction-diffusion

(I asked a similar question on Mathematics SE, but based on the Help section it might be better suited for this site, as it is focused on research-level mathematical modeling.) I am wondering if ...
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1answer
114 views

Matching two sequences between each other

Given the sequence of symbols $A$ (contains ~10,000 symbols) and sequence of blocks $B$ (contains ~3,000 blocks, ~30 symbols inside each block) I need to exclude some blocks from sequence $B$ so that ...
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2answers
389 views

Human brains considered as directed graphs

I assume that human brains can be considered as directed graphs with neurons as nodes and synapses as edges. I explicitly don't want to consider the weights, the dynamics of neural activity (based on ...
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2answers
293 views

Neighbourhood of a word and Levenshtein distance

The Levenshtein distance or Edit distance $$ lev(U,V) $$ between two strings $U$ and $V$ over a finite alphabet $\Sigma$ of size $ \left| \Sigma \right| = \sigma ,$ is the minimal number of insertions,...
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2answers
1k views

Industry jobs involving mathematics, machine learning and biology [closed]

I have a MSc in Mathematics and a PhD in Bioinformatics (in two different European countries); during the PhD I was developing computational methods to analyse DNA sequence data, mainly using a ...
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1answer
149 views

Generating spatially-aware degree-preserving random graphs?

In the study of biological neural networks, researchers sometimes compare hypotheses vs. a degree-preserving random null model. One major criticism against this approach is that connections in neural ...
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1answer
319 views

Maximal difference between k randomly drawn numbers from 1 to n – Looking for formula to sequence

Hello! I have an interesting problem that seemed simple to me, but I'm unable to solve it on my own. Suppose I am drawing k numbers out of n numbers labeled from 1 to n. Considering all $\binom{n}{k}$...
3
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1answer
448 views

Cover a line segment randomly with smaller line segments

Covering a circle randomly with arcs has been well studied in the past (Geometric Probability - Solomon). But the problem when the circle is changed to a line segment doesn't seem to have been ...
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3answers
422 views

MicroArray, tesing if a sample is the same with high variance data.

I'll explain the problem but what I am looking for is a few suggested methods to approach this problem. You don't need to know what a microarray but if you are interested look here link text The info ...
4
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3answers
2k views

Correspondence between Viterbi algorithm and Smith-Waterman

Viterbi is an algorithm for finding the maximum likelihood assignment to the hidden variables of an HMM, given the observed variables (we know the transition and emission probabilities of the HMM). ...