Therapy Resistance in Malignant Glioma

This paper may contain information useful for interpretation of high-throughput data sets on glioma: link

Using Pre-existing Microarray Datasets to Increase Experimental Power

A recent PLoS paper outlines a method for combining of multiple legacy microarray datasets as means to improve data accuracy. Link

Differential profiling of plasma proteome leads to a new breast cancer biomarker candidate

As was recently reported by BMC Cancer, biotinidase content in human blood plasma is lowered in all grades of breast cancer. This study was done in the lab; it would be interesting to see whether this result could be confirmed by computational means (using only data older than this study). Link: here

Gene Expression Biomarkers are NOT Yet Ready for Clinical Use

At least this is what NCI has to say about the lung cancer progrnostic biomarkers based on gene expression data. The markers themselves do exist, they are just not useful for the clinic, write Jyothi Subramanian, Ph.D., and Richard Simon of the biometric research branch at the NCI. The common problems include poor statistical validation of markers and lack of medical utility.

Recently Started or Completed Projects

11/02/2009 IFXworks LLC has engaged on a project with Baxter Biosciences. Dr. Makarov, IFXworks LLC Principal, is leading this effort, focused on laboratory informatics and long-term information preservation.

09/01/2009 Dr. X-F. Chen, IFXworks LLC Principal, has engaged on a project with Battelle Memorial Institute, working on bioinformatics and systems biology.

11/15/2008 IFXworks LLC announces plans to enter into a partnership with the University of South Dakota to work on informatics support of bioenergy research projects. This effort is a representation of our committment as a company to the environmentally-friendly energy industry in the United States and towards eventual energy independence of our home country.

10/21/2008 Research outsourcing marketplace for a Fortune-50 pharmaceutical company.

This fall marks an anniversary of the inaugural project that got our company started. On October 21, 2008, IFXworks LLC Principal, Dr. Vladimir Makarov, closed a long-term software development project that he had managed for the previous 12 months on behalf of a major pharmaceutical company based in La Jolla, CA. The main focus of this effort was creation of the industry-leading electronic marketplace for contract research services specific to pharmaceutical research and development. “Today the pharmaceutical industry is shifting to the business model based on outsourcing of various business processes. Outsourced work may include such steps as target discovery, parallel organic synthesis, and screening, in addition to traditionally outsourced clinical research. As this trend is spreading through the industry, we expect that demand for contract reaserch services would explode. This growth, in turn, necessitates the need for specialized exchange platforms”, commented Dr. Makarov. IFXworks played a management consulting role in this project and collaborated with off-shore development partners to deliver the system on time and under budget.

ISB, MD Anderson Will Use $7.9M NCI Grant to Analyze TCGA Data

The Institute for Systems Biology has received a $7.9 million grant to create and run, together with MD Anderson Cancer Center, a data analysis center for the Cancer Genome Atlas project. See full text on GenomeWeb.

Pharmaceutical companies are getting comfortable with cloud computing

According to this article in Bio-IT World, large pharmas are getting comfortable with cloud computing, and in particular, cloud computing provided as a service. This may be bad news for makers of Linux clusters, but great for Amazon.com and the R&D divisions that need to save money.