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Questions tagged [literature-search]

Use this tag when looking for a reference of a method, data, result or discussion.

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Kinetics “Master Equation”

In stochastic (probabilistic) models, the evolution of a system over time is calculated using a "Master Equation" which also factors the external and internal noise / perturbations in order to more ...
4
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1answer
67 views

Attractor Landscape Analysis

I have come across a modeling toolbox, ATLANTIS, which is able to determine cell fates in silico based on the input models provided. This MATLAB-based toolbox is built on a method called "Attractor ...
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P21 mutant Colon Cancer cell lines (RNA SEQ)

I need to obtain RNA sequence datasets for my project. The datasets should include P21 mutation, knockout and wild type in any Colon Cancer cell lines, Preferably in the same study. I'm not sure if ...
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3answers
109 views

Fast and reliable alternatives to blast

After some unexpected results (and previously reported) I heard that there are other tools for finding similar sequences besides blast that are faster and more accurate. I only found hmmer, but I don'...
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1answer
130 views

Error correction within the long read

I am going to get some data from plasmid sequencing to identify SNPs on the plasmids. What is done in the lab is the following: The plasmids are purified by size. We amplify the plasmids using the ...
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1answer
28 views

Build a Pubmed query given long gene list

I would like to search the literature using the Pubmed search engine for a set of genes that are associated with a brain region of interest. Unfortunately, there are a lot of them. It's possible there ...
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1answer
58 views

How to calculate Moreau-Broto autocorrelation, Moran autocorrelation, Geary autocorrelation from protein (amino acid) sequences?

I want to code Moreau-Broto autocorrelation, Moran autocorrelation, Geary autocorrelation in Python 3.6 from the scratch for amino acid sequences without using any package. Unfortunately, I have not ...
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What is the most efficient method to identify a protein that has undergone post-translational modifications by an enzyme?

I am in the process of conducting research on a wide array of proteins that are all post-translationally modified by the human enzyme GSK-3beta. What is the best to show (using peer-reviewed research ...
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2answers
179 views

Books on bioinformatics algorithms

I'm looking for a book about bioinformatics algorithms, such as alignment, BLAST search, and variant calling. I'm hoping reading about this subject will give me a deeper understanding of the ...
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2answers
230 views

What is the distribution of indel sizes in a healthy human genome? of insertion:deletion ratios?

My understanding is that indels are from 1bp to 10Kb, and a healthy genome has ~400K-500K Indels. Surely most of these are small. What is the distribution of insertion sizes in a healthy human ...
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1answer
103 views

Influential papers in bioinformatics [closed]

As a newcomer, what are some influential research papers published in the past few years that I should read to catch up in the field? Edit: @Devon Ryan answered it perfectly. I tried a google search ...