Cancer Genomes and Personalized Medicine – are we there yet?

April 29th, 2013

Bioinformatics WideShot(Cropped)

Cancer is and was always a disease that frightened humankind. The diagnosis of the disease meant a death sentence some decades ago. However, things are changing for the better. Armed with the initial human genome sequence available in 2001 and hundreds of cancer genomes, we can now use targeted drugs for specific defects in cancer cells. Treatment for the disease will not be based in the tissue the cancer came from (examples include prostate, colon, breast, brain and others) like years ago, but in the genomic features of the cancer. A tumor from brain can have similar genetic defects and resemble more a tumor from prostate or even breast compared to other brain tumors. Most of these genetic flaws that have been identified with human cancer genome projects are relative newcomers to medical terminology, as are most of the anticancer drugs, still in early testing, that are aimed at them. Development of the new drugs has been affected by the falling cost and increased speed of decoding the DNA from cancer cells and the prospects of premium prices for drugs that specifically attack the molecular drivers of cancer (for more information see the article by Anne Eisenberg in the NY Times “Variations on a Gene, and Tools to Find Them”). The web is also helping in the fight against cancer. Data repositories have been created to guide doctors and patients that suffer from cancer helping them find the right drug for their disease type. One of such tools is the portal “My Cancer Genome” created by researchers at the Vanderbilt University in Tennessee, United States. The website started two years ago and now has more than fifty contributors from twenty institutions all over the world. The website lists mutations in different cancer types, as well as drug therapies that may or may not be of benefit for patients. Most of the drugs described in the website are in clinical trials and only a few have been approved by the Food and Drug Administration (FDA). However, the portal is free and doctors, researchers, patients, relatives and institutions can access, easing the translation of the findings in research laboratories to the bedside of patients. The users can also select a type of cancer, such as “melanoma” and add a gene or gene defect, let’s say “BRAF,” for instance, or “lung cancer” and “BRAF,” and see all types of mutations in the BRAF gene that occur in those cancer types. The users can then check for national and international drug trials aimed at these alterations. Another internet tool that is focused in cancer patients is the website “CancerDriver”. This solution is a Search Engine connected to a database that facilitates the identification of the right biomarker for different disease outcomes. These solutions can use data crowdsourcing to identify specific disease types, leveraging information to the final consumer – the cancer patient. The sequencing of cancer genomes with accumulating information in databases and the use of internet solutions by health care professionals and patients will definitely facilitate cancer treatment. Personalized Medicine for cancer is already here. Now we have to make good use of it to help treating this deadly disease in the years to come.

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Can Microbes Help Us Loose Weight?

March 31st, 2013

Gut Microbes may be key players in the weight battle, according to new studies. In people, microbial cells outnumber the human ones in several orders of magnitude, and recent studies reflect a growing awareness of the crucial role played by trillions of bacteria and other microorganisms that live in a specific ecosystem in the gut. Perturbations in this environment can have profound and sometimes devastating effects for the host. Microbiome, which is the totality of microbes, their genetic elements (genomes), and environmental interactions in a defined environment, have been a subject of research since they may be able to explain some complex diseases opening new opportunities for drug development and therapies. Studies mainly funded by the National Institutes of Health (NIH) in the United States for the Human Microbiome Project (HMP) demonstrate important correlations between the microbiome and human health and disease. These projects will leverage advances made by the HMP’s large scale sequencing efforts, with the advancement of new tools and technology to examine the relationship between changes in the human microbiome and diseases of interest. Fifteen Projects studying the relationship of microbiomes with cancer, autoimmune diseases and other factors are ongoing (for more information see NIH Human Microbiome Project’s Webpage). In one of such studies, the results obtained suggest that the specific effects of gastric bypass surgery (generally used to decrease the size of the stomach in obese people, so they can loose weight) on the microbiota contribute to its ability to cause weight loss and that finding ways to manipulate microbial populations to mimic those effects could become a valuable new tool to address obesity (see more in the article “Gut Microbes could help us loose weight” by Emily Singer at the MIT Technology Review). Previous studies with people and mice have found that the nature of microbes in the intestines changes after gastric bypass, with some groups growing more prominent and others decreasing in number. However, nobody was able to demonstrate whether the altered microbial composition was merely a side effect of the bypass surgery, or whether shifting bacterial populations could help people lose weight. In order to address this question, Kaplan and colleagues used a diet rich in fat to feed mice and then performed either bypass or a “placebo” surgery on the animals. Mice in the bypass group lost around 30 percent of their body weight within three weeks of the procedure. But even before the mice dropped weight, those in the bypass group already had an altered mix of intestinal bacteria. In addition, the bypass mice had more of certain types of microbes called Gamma proteobacteria, particularly Escherichia species compared to the other group. Some species of Escherichia are pathogenic, but others help prevent inflammation and maintain intestinal health. Mice that did a bypass surgery also had more Akkermansia bacteria, which can feed cells in the intestines with mucus, particularly when the host is cutting calories (for more information check the scientific article “Conserved Shifts in the Gut Microbiota Due to Gastric Bypass Reduce Host Weight and Adiposity” by Liou et al). The group speculates that the microbes somehow trigger fat-burning changes in the host’s metabolism. The researchers are now testing the effects of altering levels of individual microbes, as well as some of the chemicals they produce to see the effects. For example, gastric bypass changed the ratio of molecules called short-chain fatty acids, which often serve as chemical signals. Depending on the results, scientists might be able to create a cocktail of weight-loss microbes. So the answer is yes, our little friends (the microbes), could be of some help for people that need to loose weight. Maybe specific microbiota “pills” will be produced in the future, so you could just “rebuild” your gut microbial population to avoid getting fat and sick. Who knows? Let’s wait and see… (Image Source: Science Clarified)

 

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Silver Linings, epigenetics and our environment

February 26th, 2013

After watching ‘Silver Linings Playbook‘ based on a book with the same title (the movie received eight Academy Award nominations and Jennifer Lawrence got one Oscar for her amazing performance as Tiffany) I just figured: Whom can we call as a normal person? I think that to a level we are all screwed up in the mind. We all tweak our mind to live in society; we all have our little “OCDness” and bipolarity. ‘Silver Linings Playbook’ touches something that society prefers to keep in a safe; it is ugly to say that you or a family member has any kind of mental illness. However, the world today is somehow bipolar. We all need to handle a “wired” world and be successful in all tasks at work, at home, etc. We all are scrutinized by society in a daily basis.  Who can handle that? I really liked the way the director of the movie approached mental illness, showing how family support is very important and anybody can be happy (yes, it is a love story with a happy ending) even with lots of “ups” and “downs”. Well, the environment can play a significant role in metal illness such as schizophrenia, bipolar disorders and other mood disorders. In the movie, the character played by Bradley Cooper (also nominated for an Oscar) “Pat” would always have a nervous breakdown in stressful situations or when hearing a song that reminded him of bad experiences in his life. These are all “environmental triggers”, and medication can indeed help to keep these symptoms dormant. A recent essay by Elyn R. Saks in the NYTimes (see the article “Successful and Schizophrenic”) shows that anybody with mental disorders could be happy, married and successful. Elyn writes that when she was diagnosed with schizophrenia her prognosis was “grave” and she would never live independently, hold a job, find a loving partner, or get married. Well, guess what?! She is married now, holds a Ph.D. and is a successful tenured Law Professor at the University of Southern California. She has also written books about her illness. Of course in her essay she mentions that it was never easy, with lots of treatment and medication during the course of her life. Scientifically, two fields of study – epigenetics and how the environment affects genetic profiles – have been trying to understand and study people with mental illness; cases such as Elyn that somehow control her illness and also people that have very grave symptoms without a “normal” life. Epigenetics is a field that deals with how changes in our environment could modify our molecular profiles based on our lifestyle, what we eat, where we live, if we smoke or not, etc. Studies have been showing that genetic or epigenetic differences cause discordance between monozygotic twins as a clue to a molecular basis for mental disorders (for more details check the article by Kato et al “Genetic or epigenetic difference causing discordance between monozygotic twins as a clue to molecular basis of mental disorders”). This study points that genetics is not enough to cause and/or maintain a “mental illness state”. Interestingly, the environment can modify our genetic profile in different ways, which is mainly through epigenetics – gene expression control and phenotypic changes in our brain cells. For bipolar disorders, for example, epigenetic mechanisms might be relevant to the pathophysiology based on several lines of evidence such as the relatively high degree of discordance in monozygotic twins, characteristic age at onset, parent-of-origin effects, and fluctuation of the disease course (see the article “Epigenetics and bipolar disorder: New opportunities and challenges”). Even though there are lots of complexity involved in understanding mental illness, since all of them are classified as complex diseases and have multiple factors involved, research from the last decade pointed towards epigenetic mechanisms and the environment as factors to explain the differences in the symptoms that people have during their lifetime. Coming back to the movie ‘Silver Linings Playbook’, it is clear that mental illness is a serious condition and can have extreme impacts in a person’s life, but it is not a death sentence or a way for society to exclude these individuals completely. The take home message of the movie is that everybody during their lives will have to deal with bad and good situations and the big difference is the attitude that these individuals will have towards these events. Thus, as “Pat” says in the movie, “this is what I believe to be true; you have to do everything you can, you have to work your hardest and if you stay positive, you have a shot at a silver lining…”I see silver linings and happiness as environmental triggers that could change anybody’s life in a good way. The truth is that we all want to have the big shot at a silver lining! (Image Source: Wired Magazine)

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Where is Science going?

January 29th, 2013

Science is changing fast and it is not hypothesis-driven anymore like it used to be. Any kind of research now faces increasing amounts of information and data to deal with. Fields such as astronomy, genomics, physics, drug discovery in biomedicine, and several others have been using Information Technology (IT) to analyze lots of data and make sense of it. We’ve got to a point that hypotheses are generated after you get the data from experiments. Then, high-throughput computer technology together with mathematical algorithms are used to answer questions. In other words, instead of generating data based on a specific hypothesis, you generate huge amounts of data and then ask the questions, thus formulating a hypothesis – it is backwards! This could be explained by the overlap we have been noticing of Information Technology with any kind of research. Well, we have always used computers for specific tasks, especially in research. But now computers are fast, the internet is even faster and we are creating an enormous gap. Science and young scientists (and I mean generally) are not prepared for this information overload named “Big Data”. One example is genomics, mainly because DNA sequencing machines are evolving in a pace that is leaving Moore’s Law in the dust (for more information see the article “Big Data in Genomics: challenges and solutions”). We are generating more data in the last years than we have produced in our entire existence. And the Big Data revolution is definitely impacting scientific and biomedical research. A specific example is the ENCODE project that is trying to map all functional regions in a person’s DNA (check the article “ENCODE: Big Data to deal with human complexity” for more information). As I mentioned before, science is facing an increasing deficit in people to not only handle big data, but more importantly to have the knowledge and skills to generate value from this data. How to aggregate and filter data, how to present the data, how to analyze it and gain insights, how to use the insights to aid in decision-making, and then how to integrate all the information is important for the future of science and scientific progress. The problem is that researchers need a toolbox of techniques, skills, processes and abilities to construct new solutions based on this accumulation of information. And they need the ability to create a user interface that turns their abstract findings into something others can understand. Scientists also need the skills to create elegant ways to transform raw data into information, and then investigate it. A Wired article put it all in a very nice essay: we are forgetting scientific theory and philosophy because of the Big Data. We are now giving lots of credit to computational power and are forgetting the main scientific ingredient that are human curiosity and instinct; and computers do not have these two ingredients. We’ve reached a point where supercomputers are fast enough to crunch data just as easily as anything else. This could be good or bad, depends on how we use this power. Time will tell, but for now, let me go back to my “hypothesis-generator”, or should I say my computer…Scientists have to work! (Image Credits: Nature Magazine)

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Science and Technology as Human Endeavors

December 30th, 2012

Science is a system of knowledge based on repeatable observation and experimentation to test different hypothesis. Technology is the application of the knowledge acquired by science to practical aims of human endeavors. Both science and technology are often interconnected. Scientific accomplishments help facilitate our daily lives, since we have evolved as rational humans. For example, the military, all businesses in general, and even the common citizen have always been interested in the advantages that scientific and technological accomplishments can bring to our homes and even to protect our countries (in the case of military research). It is common knowledge that most scientific work is funded by different federal agencies such as The National Institutes of Health (NIH), The National Science Foundation (NSF), The Department of Energy (DOE) and several others in the United States (taking the United States as an example). Liberation of human potential is something we should seek and it implies certain confidence about our nature and the value of just what the human potential is. Plato, the Greek philosopher, mathematician and student of Socrates, believed that we are human to the extent that we are rational, can think, analyze and take conclusions based on the observations of the world around us. Liberal education (geared toward leadership) and vocational training (geared towards career development) have guided curricula away from the chancy investment in someone’s possible leadership potential and toward the less speculative trainability of a person to fill a slot in the scientific culture to become a scientist. I believe that in a “healthy” society, leadership involves confrontation with the perpetual mystery of the future in concert with single-minded exploration of alternatives for adaptive change. But tragically, we are usually asked to choose and specialize prematurely in our careers; if relevance of education is equated with the ability to satisfy basic human needs; in other words, if we wish a goal-directed focus and direct engagement of practical problems, a world–vocational training is the obvious choice. If we wish to engage broad social, intellectual, or ethical problems and if we want to help provide our culture in society with the enlarged spectrum of alternatives provided by open discovery in science and technology, then liberal education is indeed the obvious choice. Alienation from either science or technology is very unhealthy for a society. The United States, for example, have been though “the atomic age” with the development of the atomic bomb, the “telecom” age with fundamental advancements in telecommunications and technology, the “space age” with the man landing in the moon in the 1960’s and nowadays we are in the “medicine and health care age” with the advances in technologies such as genomics and personalized medicine. The world is changing with globalization and faster information flow, but science and technology are still behind in transforming discoveries in products or solutions to daily problems for common citizens (specially in medicine with the development of new drugs for diseases), mainly because of the increasing lack of funding by the federal agencies lately and less career driven education for students that have great potential to become extraordinary scientists. We desperately need changes in the educational system in the United States for kids with intellectual potential and interest in becoming scientists to develop new technologies and discover cures for diseases, because in the end, science and technology are the moving gear of our society.

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Kids doing Grownup Science: Blackawton Bees

November 28th, 2012

Every scientist is a kid in the purest way. Science has the potential to amaze, transform and inspire the way every single person on earth thinks of the world and themselves. The parallel between children and science is simple: every kid always wants to know the “whys” of things. When I was a kid, I remember being very curious about everything. I wanted to know every detail on the world surrounding my family and me. This characteristic even drove my mother crazy since she used to call me the boy of the “whys”; but it was the indication that I wanted to be a real scientist. This feeling got even deeper when in high school I had a biology teacher that gave classes on genetics and Mendel’s law. That was the moment I knew I wanted to work with genetics! And why am I writing about this curiosity that was always haunting me? Well, science is cool because we can try (at least…) to understand the “whys”. The instinct of curiosity is inside every kid, shy or outgoing, because children is always asking about the stuff around them. Kids in secondary school routinely carry out scientific experiments for classes and science fairs. However, the “discoveries” and/or “inventions” presented by them are never published; except for the kids from a group of British schoolchildren that might be the youngest “scientists” ever to have their work published in a peer-reviewed journal. The article was published in Biology Letters, and is authored by twenty-five 8- to 10-year-old children from Blackawton Primary School. These kids reported that buff-tailed bumblebees can learn to recognize nourishing flowers based on colors and patterns (see their article “Blackawton bees” here). The kids from this school asked the questions, hypothesized the answers, designed “games” to test it (which corresponded to the experiments), analyzed the data and wrote the article in “kids language”. Of course all of this had adult supervision by the British scientist Beau Lotto and teachers from the Blackawton Primary School (see more information in the article “Schoolchildren announce bumble-bee breakthrough in top science journal” from The Guardian). Using simple puzzles to direct bees to colors having sugar or salt, the kids discovered that bumblebees can use a combination of color and spatial relationships to decide which flowers they are directed to; this indicates that bees can indeed “memorize” information. In real life this might mean that bees are able to collect information and remember it when going to different fields in nature. The article was featured in a TED Talk by Lotto and one of the students named Amy O’Toole (all twenty-five kids were authors of the article) and also in a Featured Editor’s Choice from the prestigious Science Magazine. In addition, there was a special comment about their article in the journal that it was published and discussions about it in the scientific community all over the world. After this breakthrough (I mean the first kids publishing their discoveries in a peer-reviewed journal), it is a fact that the students of Blackawton Primary School are very lucky because they have had an educational experience which, sadly, most school science students never get to have (and I myself didn’t). They carried out a genuinely original piece of work and published it, or in other words, they went through all the scientific process from discovery to publication (it is worth to note that it took almost 2 years from the time of writing to the acceptance and publication of the article!). The kids also wrote in their article a conclusion that every scientist has come to at one point in their career: “Science is cool and fun because you get to do stuff that no one has ever done before”. Well, I wanted to describe this exceptional example about the kids from Blackawton Primary School to show that every scientist is like children – we want to know the answers to the “whys” in the world surrounding us. It does not mean it is an easy job, but that is why we love what we do!

 

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Genetic Diseases: new horizons, new hopes

October 23rd, 2012

Monogenic genetic diseases are frequent causes of neonatal morbidity and mortality, and disease presentations are often undiagnosed. Scientists have already identified genetic problems for more than 7,000 genetic diseases and around 500 of these already have applicable treatments. Thousands of disorders caused by a single gene defect have been characterized at molecular levels, but clinical testing is available for only some of them and many have clinical and genetic heterogeneity. Hence, unmet need exists for improved care and molecular diagnosis in infants. Because for some of these disorders the progression of the disease is extremely rapid, albeit heterogeneous, molecular diagnoses must occur quickly to be relevant for clinical decision-making. Fortunately, in the last three years, faster DNA sequencing machines or the so-called Next Generation Sequencing (NGS) together with improved data analysis tools have been able to facilitate the diagnosis of genetic disorders in days rather than weeks, and we can expect to do it in hours since technologies in this field are evolving fast. Whole genome sequencing, for example, can already identify new genetic defects, never seen or described before. Health care professionals can group children that have the same symptoms and genetic mutations, providing new clues on how to proceed to treat these patients. Armed with computer program searches for genes based on the baby’s symptoms, they can diagnose genetic diseases with more certainty (for more information see “Rapid Whole-Genome Sequencing for Genetic Disease Diagnosis in Neonatal Intensive Care Units” by Saunders et al.). This way, new genetic disorders can be identified combining DNA sequencing with bioinformatics and the symptoms or morphological defects of the children. Diagnosing unidentified diseases will add more information to the biomedical field and help pharmaceutical companies identify and test new drugs (see also “Rapid test pinpoints newborns’ genetic diseases in days” by Monya Baker). These tests could represent one of the first practical fruits of the revolution in sequencing an individual’s entire DNA (see the article “Infant DNA Tests Speed Diagnosis of Rare Diseases” by Gina Kolata in the NYTimes). This brings new market opportunities for genetic testing, biotechnology and pharmaceutical companies. Tests such as whole genome sequencing that reveals fatal genetic diseases could also improve genetic counseling by informing parents on their probabilities of having new children with the same defects. Most genetic diseases have no treatments yet; however, for the ones that are identified and there are treatments, this type of test will increase the chances for the babies to survive and avoid the problems caused by an undiagnosed condition. Whole genome sequencing still cannot diagnose all genetic diseases; however these new breakthroughs in medical genetics will enable a better diagnosis for many cases that would otherwise have remained harrowing mysteries. More research needs to be done before these tests make it to market and are covered by the healthcare system (it is still expensive, costing between 8,000-15,000 dollars), but these studies bring new hope for families of kids with genetic disorders. (Image Source: GEN News)

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ENCODE: Our Guide to the Human Genome

September 26th, 2012

Early in 2001, the Human Genome Project gave us a complete read out of our DNA. The elucidation of the human DNA sequence was important to give us all the instructions to make a human being; however we are just starting to realize how the instructions are indeed incomplete. Researchers were able able to uncover 3 billion letters of the DNA molecule, but just roughly 2% (around 25,000 protein-coding genes) corresponded to the building blocks (or proteins) of the cells. Based on that, many biologists suspected that the information responsible for the complexity in human cells could be somewhere in the “deserts” between the protein-coding genes. ENCODE, which stands for Encyclopedia of DNA Elements (for more information see the article “The Human Encyclopaedia” on Nature) is a project that started in 2003 with a massive data-collection effort uniting several laboratories all over the world. The main objective was to understand the deserts between protein-coding genes, catalogue the “functional” parts of the DNA sequence and understand their regulation. In summary, the objective of the ENCODE Project was to show if the rest of the genome, more specifically the non-coding areas, were doing something important inside the cells. An interesting fact from ENCODE is that it was a consortia created between groups that are generally competitors. These groups generated an incredible amount of information that was collected, stored and analyzed. Indeed, science today is increasingly “social”, especially in fields such as genomics in which huge amounts of data are generated. In such projects, collaboration between groups is key. This project was only possible because of collaboration. It was also a good training for researchers in big scientific projects that will be more common from now on. In these projects, tons of data are generated, stored, transferred and analyzed. After almost 10 years of intensive data analysis, researchers involved in this Project published their results in 30 papers across three different journals. According to ENCODE’ s main conclusions, more than 80 percent of our genome has a “biochemical function”. These regions were classified as “junk” for a long time, but ENCODE is showing that they are the opposite. Tom Gingeras, one of the study main scientists, declared that “Almost every single nucleotide is associated with a function of some sort or another in the genome” (see more in the DISCOVER Magazine), reinforcing the idea of functionality for most genome. And what about the remaining 20 percent of human’s DNA? Researchers believe that these remaining regions are not “junk” either. ENCODE looked at hundreds of cell types, but the human body has thousands. A given part of the genome might control a functional element in one cell type, but not in others, and the complexity of information could be even higher. Again, the researchers claim that ENCODE has one important implication, which is to redefine what is a “gene”. This new study has changed the view of the genome as we knew it since the functional elements have lots of overlap. And since we are the most complex organism out there, it is not surprising that the results are the same way. The new definition for a “gene” suggests that it is a collection of transcripts, united by a common factor, with a function that could be either in the genome itself or in biochemical reactions within a cell. Human genome research is far from finished, and this could go on for decades (if not forever…). For those who though that the elucidation of the sequence of the human DNA was enough to understand a human being, a big lesson has been learned. The complexity of the information from ENCODE will probably need another decade to be fully understood. In fact, ENCODE is just the start for a big journey inside human cell’s DNA. We are just beginning to build a guide for our genome (Image Source: Nature Journal).

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A new way to storage digital information?

August 26th, 2012

Information, of all kinds, has been increasing since humans learned how to write in stones in ancient times. Now that there is an explosion of information, mainly digital information, we are in need of better ways to storage it in a safe and stable manner. One solution that is becoming reality is the “cloud”, a service that companies provide for information storage. Companies such as Apple, Dropbox, Google and other offer server space to store all types of digital information (books, movies, photos, etc) for a fair price. However, it looks like nature already had one simple and stable way to store data. A recent article in Science by Harvard Professor George Church (for more information see “Next-Generation Digital Information Storage in DNA”) demonstrates that indeed nature has a better way to do information storage using the DNA molecule. DNA has many potential advantages over other systems since it is very stable and most times immutable (except if exposed to mutagens that cause mutations in the bases, changing its sequence). Dr Church’s group developed a strategy that encoded the digital information of a whole printed book using a novel scheme of next-generation DNA synthesis and sequencing technologies. The group converted 53,426 words, 11 images and 1 Java Script Program into 5.27 megabit bitstream, that were encoded onto 54,898X 159 oligonucleoties (which are small pieces of DNA). After the codification the oligonucleotides were synthesized, printed and linked together to form a stable DNA molecule. The newly synthesized DNA was further sequenced to recover the information, which was done with success. This article is a milestone not just in storing information inside a biological molecule, but in showing that nature itself have smart ways to “save” and codify information. Well, DNA encode for entire cellular programs inside the cells of organisms. Importantly, we are still trying to decipher DNA’s cellular code since it is composed by different layers of information, not just the sequential bases of the “linear” DNA. Examples include chemical modifications in the DNA such as methylation or acetylation, which could change the meaning of specific regions. The fact is that DNA is very suitable for immutable, high-latency, sequential access applications such as archival storage – cells already utilize it. So, why we did not think about using DNA to store information before? Mainly because now we have all the technology to do it, before we did not. We can synthesize long stretches of DNA, print it on glass slides and also sequence it fast, since DNA sequencing technologies are evolving faster than the speed of computers. In fact, Moore’s law does not apply to DNA sequencing. The costs of DNA synthesis and sequencing have been dropping at exponential rates of 5- and 12- fold per year, respectively. This is much faster that electronic media, that is just 1.6- fold a year. Additionally, DNA has other advantages such as density, stability and energy efficiency to store information. I believe this might be just the start for digital information to be stored in the DNA molecule. Information will continue to accumulate; long-term and stable solutions like the one presented by this group will be able to store it. The take home message is that nature is teaching us – the tools are already here, we just have to learn how to use them.

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Bioinformatics now! It is time to learn computer coding

July 30th, 2012

The science of bioinformatics or computational biology is increasingly being used to improve the quality of life as we know it. Bioinformatics has developed out of the need to understand the molecule of DNA, also known as the code of life. Massive DNA sequencing projects became a reality with the advent of next generation technologies and has added in the growth of the science of bioinformatics. DNA, the basic molecule of life, together with other layers of information in the cells, directly controls the fundamental biology of life. It codes for genes (both protein-coding and non-coding) that act in concert with some environmental factors to determine the biological makeup of humans or any living organism. It is variations and errors in the genomic DNA (such as mutations and polymorphisms), which ultimately define the likelihood of developing diseases or resistance to these same disorders. This way, the ultimate goal of bioinformatics is to uncover the wealth of biological information hidden in the mass of sequence, structure, literature and other biological data obtaining a clearer insight into the fundamental biology of organisms and to use this information to enhance the standard of life. The science of bioinformatics grows together with computer science since the more breakthroughs the better for both fields. Recently, with the explosion of genetic data and genomics information, bioinformatics became an essential tool to life sciences. In other words, the need to deal with complex types and sources of data from living organisms is increasing the importance of computer science for biology. Never in history, computers and biology were so close to each other. I believe that, in the future, every laboratory from academic and private sectors will need to have a group dedicated to bioinformatics. This is already happening in several institutions and companies. Genomics and the projects related to it are adding amounts of data that our brain cannot process. Big challenges will be faced in order to facilitate the interconnection between computer science and biology. Computer scientists have no biology or medical training and biologists know little on the language used by “computer coders”. Thus, to be a multitasking scientist today, an individual needs lots of computer skills. And by computer skills I do not mean just knowing how to use a computer. A deeper knowledge is needed to deal with big amounts of data being generated by genetics and genomics right now.

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