Questions tagged [literature-search]

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

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22 views

Appropriate value to replace outliers in clinical studies

I am working on clinical study where I am focusing on binary classification problem. There are few variables which has outliers. I am trying to know which would be the right value to replace ...
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1answer
50 views

Replicate papers (beginner) [closed]

I have a strong mathematical and computer background (also with machine learning) and would like to switch to bioinformatics. I know a fair amount of biology. But I find it hard to find real world ...
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0answers
29 views

Literature mining tools and methods

"As a first step, we sought to systematically establish the complete set of genes implicated in the physiological response to SCI. We conducted a systematic analysis of the SCI literature, reviewing ...
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2answers
29 views

how to search NCBI to find all available reviewed accession numbers for a protein family

what is the most optimal keyword search query to input into NCBI In order to find all the available proteins accession numbers for a specific family? For example, how would I find all the reviewed ...
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1answer
74 views

Merging transcriptomes coming from different experiments

I'm planning to build a transcriptome by pooling all existing transcriptomes in SRA for a non-model species (which has no reference genome) to study differentially expressed genes and the like. It ...
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0answers
27 views

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 ...
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1answer
77 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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0answers
36 views

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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5answers
407 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'...
4
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1answer
212 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
38 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
128 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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0answers
24 views

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
200 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
303 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
106 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 ...