We often hear the following question: "Is there any way to know if the whole pathway or the whole GO is upregulated or downregulated? The results table shows p-values and DE numbers, but I want to know if that [...]
You are a life scientist undertaking cutting edge research that involves experiments in which you collect omics data: transcriptomics, genomics, proteomics, methylation, RNASeq, ATACSeq, single cell, etc. You are working on an exciting and very important problem. You have great [...]
In the world of bioinformatics, we all need to be careful when analyzing our data. I receive countless questions about what reference set should be used when analyzing gene expression or protein expression data. If you are thinking “what’s a [...]
Methylprednisolone effective in treating critically ill patients Almost exactly one year ago, the US was experiencing the first wave of COVID-19. In March 2020, SARS-CoV2 is defying all modern medical knowledge and technology killing people at a rate of 1,500 [...]
AdvaitaBio, a leading provider of bioinformatics to core facilities, researchers and pharmaceutical companies, recently conducted a global poll of bioinformatics service providers in order to determine what factors improve the overall quality, productivity and customer satisfaction. Bioinformatics core facilities [...]
Genome Biology recently published a peer-reviewed paper containing a comprehensive benchmarking and comparison of 13 widely-used pathway analysis methods across more than 1,000 analyses. We highlight the most important findings below. The problem: Many high-throughput experiments compare two phenotypes [...]
Inqaba Biotechnical Industries partners with Advaita Bioinformatics to provide advanced pathway analysis software in Sub-Saharan Africa ANN ARBOR, MI – October 14, 2019— Advaita Bioinformatics, the leader in the interpretation of high-throughput biomedical data, today announced a new distribution partnership [...]
You might think that spending thousands of dollars to meet your bioinformatics needs guarantees the most accurate analysis on the market. Well, it’s actually a lot more complicated than that! Expensive pathway analysis tools such as Qiagen’s Ingenuity Pathway Analysis [...]
Is this you? You provide expert bioinformatics services to your organization You have great analysts in your group, but not enough of them Your organization does extremely important work in biomedical research, but you have to live on a budget [...]
How are you currently analyzing your RNASeq and proteomics data? Are you currently using one of the many free tools available for pathway analysis, such as DAVID? Or, are you perhaps using Qiagen's Ingenuity Pathway Analysis (IPA)? If yes, [...]
You may be interested this recent story in GenomeWeb about how Advaita is taking the lead in the pathway analysis of RNASeq and proteomics data. We are excited that more and more people are gaining access to iPathwayGuide and [...]
A while ago, I was doing the pathway analysis of a data set coming from a fat remodeling experiment in mice. This experiment involved a drug candidate known to transform the "regular fat" or white adipose tissue into "brown fat" [...]
Orthologs in Systems Biology A recent paper by Renaud, et al., (Environmental Pollution, Vol 244, January 2019, pp 926-937) points out the significant hazard posed by endocrine disrupting chemical (EDC) exposure for aquatic organisms. Renaud, et al., employed iPathwayGuide as [...]
My previous post, Pathway Analysis vs Gene Set Analysis, ended with an interesting question: has anybody really compared side-by-side gene set analysis methods and pathway analysis methods on the same data sets? Well, the answer is: not yet! The [...]
To some, pathway analysis and gene set analysis are synonyms. However, there are important distinctions between these two groups of methods, and they provide different results. This is part of a series of articles on pathway analysis methods. Pathway [...]