Top down or Bottom up approach?

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How to add an outgroup while using supermatrix approach for species tree reconstruction?

I have 12 species from same genus. For supermatrix approach we generally use the multiple sequence alignment single copy orthologs sequences then concatenate them and remove the badly aligned...

11 December 2017 3,868 4 View

What is the difference between analysis of recombination and selection pressure when using multiple Genus vs multiple species?

I read several papers where researchers use several strains of same species for analysis of recombination or selection pressure however there are few papers in which researchers use the multiple...

09 October 2017 8,848 4 View

Do I need to stick with single copy orthologs, while estimating selection pressure with PAML?

The ortholog groups of 5 species proteins look like: Group1: sp1 sp2 sp3 sp4 sp5 Group2: sp1 sp2_seq1 sp2_seq2 sp3 sp4_seq1 sp4_seq2 sp5 (sp is for species here) As here one can see the Group1...

05 June 2017 6,710 1 View

How can I evaluate the accuracy of predicted protein protein interactions with ROCR package?

I need to evaluate the accuracy of predicted interactome of an insect species which I constructed by interolog method. I read that I can use ROCR package for it. I got a gold standard positive PPI...

02 March 2017 9,554 1 View

Which type of Tree is needed for codeml PAML analysis?

I need to run codeml for ortholog clusters from different related genus. Do I need to generate a species tree for it that I can use for all the clusters or I need to generate gene tree for all the...

01 February 2017 2,304 3 View

How to identify irreversible reactions and inconsistency of KEGG reactions?

Lets see an example. The reaction R00344 is mentioned as irrversible in KEGG

06 July 2016 4,805 3 View

Which journals you regularly follow to increase your knowledge-base?

In principle, this questions is like quora flavor. Here, I am asking this question for a bioinformatician perspective but surely would like to know you opinion about the other journals that are...

04 May 2016 7,593 2 View

How the large scale signaling network can be converted into Boolean model?

PS: I have single time point gene expression data for around half of the gene in the signaling network.

04 May 2016 3,055 2 View

How can I apply z-test for significance changes in the protein-protein interaction network properties while comparing with random networks?

I have created a PPI network, now I want to compare it with random networks. I can generate the random network. In general, I am interested in the comparision plots of (i) degree vs betweenness...

03 April 2016 10,079 4 View

What is the biological significance of under-representation of differentially expressed genes?

I understand the over-representation of GO term in FDR test against reference gene sets but the under-representation seems confusing. My test set is infection induced differentially expressed...

03 April 2016 3,359 5 View

Could you recommend some articles on Urban Transportation System optimization and Innovation?

13 August 2024 2,595 3 View

Which Scopus Journal provides the most affordable fees?

"PUBLISHING IN A SCOPUS JOURNAL" Researchers are now at a cross road. The critical need to publish in a Scopus or ISI, etc journal is ever vital. Journal Publication fees must be submitted....

10 August 2024 8,621 1 View

Seeking Advice on Viability and Execution of Undergraduate Thesis Topic?

Hello everyone, I am currently developing a thesis proposal and would appreciate your input on its viability and how to effectively carry it out. My proposed topic is: "Does the perceived threat...

10 August 2024 8,992 0 View

Who will be moral responsible for the death of thousands of people in the event of an earthquake?

Who will bear moral responsibility for the deaths of thousands of people in the event of an earthquake? Weeks and months remain before the onset of strong earthquakes that bring death to...

08 August 2024 6,134 12 View

Hello all, Looking for international reviewer to review Ph.D thesis in wireless sensor network.Can anybody help?

My name is Apurva Saoji. I am a Ph.D scholar in Computer engineering in India. I am looking for international expert in reviewing my PhD thesis, "Competitive Optimization Techniques to Minimize...

07 August 2024 4,600 2 View

Are there any instruments for studying time similar to the way it is in space?

There are a huge number of methods for studying objects in space, according to the senses (and not only). Mechanical, thermal, optical, acoustic, electrical, magnetic, based on particle beams,...

06 August 2024 7,102 0 View

Weak DAPI staining after immunohistochemistry - how to improve?

After immunohistochemistry of previously fixed in PFA and EtOH and then frozen 20 μm sections of zebrafish brain, DAPI staining is very weak (right) compared to the same sections stained without...

05 August 2024 9,637 2 View

Why did the authors extrapolate a phenotype that they experimentally proved in one bacterial strain across the whole genus of the organism?

I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...

05 August 2024 6,787 4 View

The Curse of Evolution and Complexity?

Brain and body mass together are positively correlated with lifespan (Hofman 1993). The duration of neural development is one of the best predictors of brain size, and conception is the best...

05 August 2024 6,247 3 View

In the case of a wound l recurrence after radical breast cancer and sentinel lymph node biopsy. Are the sentinel lymph node procedure recommended?

In the case of a wound l recurrence after radical breast cancer and sentinel lymph node biopsy. Are the sentinel lymph node procedure recommended? If no axillary lymph node dissection was not...

05 August 2024 8,056 1 View