Monday, May 4, 2015

Insilico Medicine SuperPharman Challenge: Looking for Superheroes to Fight Cancer and Aging

Super Heroes Needed at Insilico Medicine to Fight Cancer and Age-related Diseases

Aging fighters at Insilico Medicine are looking for relentless doers who dream big, but are not afraid to get their hands dirty with basic tasks. Doers, who have trouble sleeping at night, because they know that millions of people are suffering and dying of cancer and age-related diseases and their own clock is ticking as well. Doers with both programming and database management skills and knowledge of biology. You will need to know or quickly learn how to use huge multi-omics data to find alternative uses of currently available drugs and distribute many micro tasks to the crowd, freelancers or colleagues, while keeping the big picture in mind. 

We know that we are looking for a needle in the haystack, but this is how our team has come to be and you will be in great company. We have relentless super heroes in the US, UK, Switzerland, Poland, Israel, Russia and China. If you know someone amazing, who fits that profile amazing, ask him. Maybe he or she is already working for us. He goes through the day doing a boring academic job, but at night he is hacking away.

Our first frontier is transforming the pharmaceutical industry, repurposing known drugs and finding the new ones. When we launch, the world will become a better place. And if you are that super hero with bold ideas and hands on experience, ready to unleash maniacal energy to hack aging, send us a signal and we will respond right away or start watching you to see if you fit.

Here is a link to what Insilico Medicine is doing: 

In partnerships they can also do in vitro and in vivo validation, humouse clinical trials and even organ-on-a-chip and body-on-a-chip validation. 
They are looking for someone with similar skill set and energy as Alex Zhavoronkov ( to work together with him, gradually replace him and then find someone to replace yourself as the company grows or you decide to start a subsidiary. 

Minimum requirements:
  • Python, MySQL, Hadoop, AWS Services, IBM Watson
  • Experience working with multi-omics data and/or clinical trials/biomedical text data
  • SVM and deep learning algorithms
  • Basic knowledge of signaling and metabolic pathways
  • Experience working with GEO, ArrayExpress, KEGG, TCGA, LINCS, Connectivity Map, Drugbank, Clinical Trials, WHO databases, etc.
  • Personal network of contacts in academia and large pharmaceutical companies
  • Excellent writing skills
  • Ability to give public talks and generate publicity is a plus
  • Knowledge of Russian, Chinese or Hebrew is a plus

Sunday, January 4, 2015

From cancer to longevity and policy

Here is a great conference to attend in February

Friday, October 3, 2014

Everyday drugs could give extra years of life - New Scientist

Great article on New Scientist by the talented science journalist Clare Wilson covering the Aging Forum.

Everyday drugs could give extra years of life - health - 01 October 2014 - New Scientist

Thursday, August 14, 2014

Pathway Pharmaceuticals developed a method for analyzing transcriptomic data in a platform-agnostic manner

Scientists from Pathway Pharmaceuticals and the Biogerontology Research Foundation (BGRF), a UK-based charity founded to support ageing research and address the challenges of a rapidly ageing population, propose a new concept for signalome-wide analysis of changes in intracellular pathways, called OncoFinder, which allows for accurate and robust cross-platform analysis of gene expression data. This new technique will allow scientists to derive useful information from and compare the hundreds of thousands of data sets obtained using legacy equipment as well as data sets obtained from biological samples preserved in paraffin blocks and partially-degraded samples.

The original research, published in the journal Frontiers in Molecular Biosciences, shows that the OncoFinder method significantly reduces errors introduced by transcriptome-wide experimental techniques. Scientists compared gene expression data for the same biological samples obtained by both next generation sequencing (NGS) and microarray methods, finding that these different techniques have almost no correlation between the gene expression values for all datasets analysed. In contrast, when the OncoFinder algorithm is applied to the data, a clear correlation between next generation sequencing and microarray gene expression datasets was seen.

“For several years the potential for the use of gene expression data in research and clinical applications has been underappreciated due to the inconsistency of the data coming from the various types of equipment. There is just too much variation and complexity when comparing the massive number of individual genes. But when this complexity is reduced and the gene expression is mapped onto signalling pathways, we can evaluate the pathway activation drift and analyse the changes and transitions much more effectively. The OncoFinder algorithm enables scientists to characterise the functional states of transcriptomes more accurately than before and we hope that this will become a method of choice in genetics, physiology, biomedicine and molecular diagnostics,” said Alex Zhavoronkov, PhD, director of the BGRF and co-author of the study.

The original research paper is available to view and download here.

Wednesday, March 5, 2014

From Cancer to Aging Drug Discovery

Aging is one of the major challenges of the modern society. The advances in biomedicine and healthcare systems have led to the unprecedented long lives of the population after the retirement leading to the increased burden on the economies. There is an urgent need to develop and validate interventions with geroprotective properties to increase the productive health spans of the working population and maintaining performance and avoiding loss of function.
Experiments with animal models already resulted in significant breakthroughs resulting in up to 1,000 percent increases in lifespans. But extrapolating these advances to humans or other mammals proved to be extremely challenging. Human live orders of magnitude longer than the short-lived model organisms and there is no comprehensive set of aging biomarkers, allowing to track the effects of the many drugs that may extend lifespan. We are also  different from other animals and the many drugs that work on mice do not work on humans.
To address these challenges the international team comprised of biogerontologists, geneticists, computer scientists and biomathematicians proposed using a computer simulation and laboratory validation approach using human cells and model organisms to predict what drugs may help fight aging in humans.
The Human Genome Project and the following revolution in sequencing and laboratory diagnostics resulted in the vast data on genetic and epigenetic profiles of cells and tissues from people of various ages. The proposed method uses this data to construct the cloud of molecular signalling pathways involved in aging and longevity and evaluates the effects of the very large number of drugs and drug combinations to simulate the young state of the cells and tissues. Scientists hope that this method may be used to find new drugs with aging-suppressive properties and predict the activity of the drugs that are already on the market. Also, people respond to the drugs differently and this method may be able to personalize the geroprotective therapy to the individual patients and help the drug companies conduct better clinical trials.
"There are thousands of compounds with known molecular targets and some  are already used in the clinic. Due to high cost and the time it takes to complete the experimental work, it may not be possible to test all of the effects of these drugs even in mice. And the fact that the drug works in mice does not guarantee the same effect in humans. There needs to be a better way to predict the efficacy of the drug in humans.  We proposed a method for doing that in silico using the multiple sources of data and we hope to validate this method in the very near future.", said Alex Zhavoronkov, PhD, the director of the Biogerontology Research Foundation in the UK. "Also, people are different, age at different rates and respond to drugs differently. The proposed method may be used to predict the personalized geroprotector regiments.", he added.
Many pharmaceutical companies already expressed their interest in bringing aging research into clinical practice, but the absence of the business models, accurate validation methods, and the inability to classify aging as the curable disease are major impediments to mainstream development of geroprotective drugs. In silico drug discovery may help accelerate this process. The group plans to present the results of their experimental work using this method at the Practical Applications of Aging Research Symposium at MipTek 2014 in Basel, Switzerland attended by over 3,000 delegates from the pharmaceutical industry.  
“The decreases in cost and increased availability of genetic and epigenetic research as well as the breakthroughs in computer technologies are already helping make better decisions in biomedicine. The proposed method may take the in silico approach to drug discovery to the next level. If the can validate it in the laboratory, and we are working on that as we speak, this may revolutionize aging research”, said Anton Buzdin, the director of the First Oncology Research and Advisory Center.

The paper describing the new approach to screening and ranking of geroprotective drugs was published in the reputable scientific journal Frontiers in Genetics.

Citation: Zhavoronkov A, Buzdin AA, Garazha AV, Borissoff N and Moskalev AA (2014). Signaling pathway cloud regulation for in silico screening and ranking of the potential geroprotective drugs. Front. Genet. 5:49. doi: 10.3389/fgene.2014.00049 - See more at:

Signaling pathway cloud regulation for in silico screening and ranking of the potential geroprote...

Tuesday, October 1, 2013

Mineralization of the connective tissue with age may be involved in cancer

When you open a 70-year old patient on the operating table and touch the aorta, the feeling may resemble touching an eggshell or sand paper. It is stiffer than the heart of a young person and the key reasons for this are the abundant calcium deposits in the connective tissue that accumulate with age.

The many factors leading to mineralization of the connective tissue include genetic and acquired diseases, inflammation, reactive oxygen species, but the major problem is that it occurs spontaneously during aging as calcium-containing molecules are trapped in the extracellular matrix and develop into apatite over time.

Despite its relative significance, compared to the many other areas of aging research, mineralization of the connective tissue is rarely mentioned in scientific publications and few teams are working on preventing or clearing out the extracellular aggregates.  To address the problem, a multidisciplinary team of physicians, bioinformatitians, biochemists and physicists performed a comprehensive bioinformatics analysis of the many factors involved in mineralization, identified key molecular targets and proposed a list of possible drugs to address the issue.

The results of the study were accepted for publication by a high-impact journal in biogerontology “Rejuvenation Research” and will be published shortly and can be cited as “Mineralization of the connective tissue: a complex molecular process leading to age-related loss of function”, Anastasia Shindyapina, Garik V Mkrtchyan, Tatiana Gneteeva, Sveatoslav Buiucli, M Kulka, B Tancowny, Alexander Aliper, Alexander Zhavoronkov, Rejuvenation Research, ahead of print. doi:10.1089/rej.2013.1475, , PMID 23902273

Anastasia Shindyapina together with her collaborators presented the results of the study on the 5th of September at the SENS6 conference in Cambridge, UK.

“Aging inevitably leads to the loss of function on many levels. Mineralization of the connective tissue is one of the causes and consequences of aging and is a complex multifactorial process. Metabolic activity, diseases and external stress factors may cause calcification, but most importantly, it occurs spontaneously. Our goal is to identify least toxic ways to both prevent calcification and to repair the accumulated  aggregates.”, said Anastasia Shindyapina, ASUS Fellow for Bioinformatics and Medical Information Technology, PhD-candidate at the Moscow State University and researcher at FOIRMYS.

"Mineralization of connective tissue with age is one of the many aspects of aging that are examples of "accumulation of eventually pathogenic extracellular material", an issue that attracts too little attention within the academic community. The accumulation of advanced glycation endproducts (AGEs) and of mineral deposits both result in increased stiffness of connective tissue, impair homeostasis and contribute to a broad range of age-related diseases. Through comprehensive bioinformatic analysis of the many molecular processes involved in mineralization, Zhavoronkov's team has identified possible molecular interventions. Additionally they proposed that mineralization and AGEs work in concert and should be addressed concurrently. Anastasia Shyndyapina, the lead author on the paper, recently presented this work at the SENS6 conference in Cambridge.", commented Dr. Aubrey de Grey, Chief Science Officer of SENS Research Foundation and International Adjunct Professor at the Moscow Institute of Physics and Technology (MIPT).

The First Open Institute for Regenerative Medicine for Young Scientists (FOIRMYS) is a non-profit volunteer initiative bringing together over a thousand enthusiast young scientists and physicians interested in regenerative medicine. It was first organized by Alex Zhavoronkov, PhD in collaboration with Sergey Yakovenko, PhD, Sergey Roumiantsev, PhD and Oleg Korzinov in Moscow with support from Anna Chapman.
FOIRMYS provides regular weekly lectures by the top academic and industry thought leaders, investors and regulators. The list of presenters includes Paolo Macchiarini (Karolinska Institute), Alexey Aravin (Caltech), Charles Cantor (Boston U, ex-director of the Human Genome Project), Augustinus Bader (Leipzig University), top managers from Beijing Genomics Institute, Malaysian Genome Resource Center, Indigo Capital Partners and many others. As part of the curriculum students participate in practicums at “Altravita IVF, FRCCPH, FORCC, Quantum Pharmaceuticals, Biopharmcluster “Northern” and Moscow Institute of Physics and Technology.
Members work in small teams comprised of scientists and physicians on ambitious outlier projects in aging and regenerative medicine with topics ranging from mineralization of connective tissue, HGPS and regulation of endometriosis to industry overviews and healthcare economics. The projects are coordinated in a crowdsourced environment and rely heavily on popular tools like Facebook, Dropbox and Google Apps. FOIRMYS developed a concept called “Personalized Medicine”, where projects are centered around the problems of a single patient, who provides samples and helps coordinate the project. Members also learn how to promote their work, create personal science blogs (including Women in Science initiative) and engage in industry outreach.
Participation in practical group projects resulted in success stories including young scientists’ publications in peer-reviewed journals, fellowships, participation in international conferences, gainful employment of young scientists and international collaborations.

Wednesday, May 15, 2013

One book to pre-order for the Summer – Ageless Generation: How Advances in Biomedicine Will Transform the Future of the Global Economy

The end of retirment by extending healthy life or by an unprecedented economic collapse
 If you were to pre-order one book for this Summer consider this one. The Ageless Generation: How Advances in Biomedicine Will Transform the Future of the Global Economy.

Accelerating aging research to extend healthy productive lifespan seems to be in everyone's best interest. There are few people on this planet, who would chose to age and gradually succumb to diseases of aging if they were given a choice to live longer and healthier lives.

However, up until recently, the many failed promises of science made many of us resistant to accepting the possibility of the interventions that may take us way beyond the lifespans of our parents and grandparents.
Well, now it is time to open up to these possibilities and get actively involved, because the urgency to accelerate aging research now stems from the economic fundamentals of the aging population in the developed countries.

Aging populations in the developed countries are now the single biggest threat to the global economy. People that are retiring today and that are due to retire in the next decade are going to live extraordinarily long lives due to the advances in biomedicine and propagation of these advanced into the clinical setting.
 "The Ageless Generation: How Advances in Biomedicine Will Transform the Global Economy",  a book by Alex Zhavoronkov, PhD in very simple layman language drills down into the history of retirement and social security and the present state of the social security, healthcare and the unfunded liabilities of the developed countries. It also takes the reader on a tour of the laboratories in the US, Europe and China, where scientists toil on solving the complex puzzles of regenerative medicine, longevity genes and technologies that will extend our lifespans. Then it looks at the future of retirement and presents the real possibility of the near-term Economic Collapse. There are some solutions and policy proposals, but chances are very small that we will be able to avoid the crisis before we can significantly extend healthy lifespans.

The book will be published by Palgrave Macmillan in June 2013 and is available for pre-order at Amazon and most bookstores worldwide.

Barnes and Noble:

The main idea of this book is that in record time the US must start a coordinated program to increase healthy productive lives of the two generations that are nearing retirement or the whole world will face several decades of economic decline and possible collapse. The need to fight aging is no longer an altruistic initiative, but a real economic necessity.

Recent advances in biomedicine will extend the lifespans of the two generations due to retire within the next twenty years; however, unless there are programs in place to keep them healthy and working, the burden of the aging population will drive the global economy into the state of depression or even worse. Developed countries should re-focus the research programs from just extending lifespans to extending health spans and the retirement age to remain solvent and this initiative must be led by the beating heart and the brain of the world's economy - the United States of America.

Every reader of this post must consider the possibility of radical extension of healthy life through biomedicine. One thing you should do right now is to stretch the expected horizons to 150 years.  Yes, it is possible! Even if we let some of the major advances that already happened to converge and reach the clinic, 150 years of life is the very minimum of what a 40-year old today should expect.

One way to prepare for it is to pack up and prepare yourself and your family to live through the economic collapse. Another way is to actively engage in supporting aging research by engaging in government lobbying, supporting research directly or even engaging in research personally.

Here is a link to Macmillan's page for this book: 

And here is a Facebook page: 

Signal Transduction Pathways

Signal Transduction Pathways
RTK, GPCR, GF, Cytokine, Wnt, Death Factors & Shh pathways