Bioinformatics Articles this Week

It is time to find the best bioinformatics contributions of 2013 .The original idea came to us after noticing that the yearly reviews in Science and Nature celebrated the large experimental projects, whereas bioinformatics tools like BLAST, BWA or SOAPdenovo rarely got mentioned despite their immense contribution to biology. More importantly, papers discussing elegant computational algorithms got recognized years after their publication (Pevzner’s dBG, Myers’ string graph) or never got recognized (Ross Lippert’s 2005 papers on using Burrows Wheeler Transform in genomics). So, we wanted to give recognition to the major computation discoveries in biology and try to bring attention to under-appreciated contributions with potential long-term benefit.
Anton Korobeynikov is a member of Algorithmic Biology Lab of St. Petersburg Academic University of the Russian Academy of Sciences and part of Faculty of Mathematics and Mechanics at Saint Petersburg State University, Russia. He contributed to the development of very useful NGS algorithms, such BayesHammer for error correction and SPAdes for genome assembly.
Eran Elhaik, a researcher in evolutionary genomics, finished his post doctoral research at Johns Hopkins and is leaving next month to become a professor in University of Sheffield, UK.
Heng Li is currently a research scientist at Broad Institute. He is the author of several outstanding bioinformatics tools, including BWA and samtools.
Istvan Albert is a professor at Penn State University. Biostar is his most popular contribution, but he wrote many other interesting papers in bioinformatics and theoretical physics.
Jared Simpson joined Ontario Institute for Cancer Research as a Fellow this year. If we cannot keep him distracted, he will develop another efficient genome assembler.
Joanna Sulkowska is a researcher working on protein folding and topological properties of biomolecules at the Center for Theoretical Biological Physics at UCSD and Instytut Fizyki Polskiej Akademii Nauk of Polish Academy of Sciences.
Nikolay Vyahhi is a Visiting Scholar in the Department of Computer Science and Engineering at University of California San Diego (UCSD). Together with Phillip Compeau, he co-founded Rosalind, a free online resource for learning algorithmic biology. Nikolay directs the M.S. Program in Bioinformatics in the Academic University of St. Petersburg, Russian Academy of Sciences and recently founded the Bioinformatics Institute in St. Petersburg as well as Stepic, a project focusing on content delivery for online education.
Rayan Chikhi is a post-doctoral researcher working with Paul Medvedev at Penn State University. He worked on bioinformatics algorithms and data structures during his PhD at IRISA/Ecole Normale Supérieure of Brittany (France). He is co-author of the Minia assembler, which won our last year’s assembler award.
Please note that we like to make the process fun and enjoyable for all of us and not another huge time sink with deadlines, etc. So, we will try to minimize formalities and make sure we reach the stated goal in the best way. As an example, one judge mentioned that he will be away during Christmas and may not be able to access the internet. Others may have similar constraint. If that delays our dates for decision by a week or two, we will be flexible.
We like to find elegant papers and methods, which are currently under-appreciated, but will have major impact in the future (in the opinion of judges). You can consider the process similar to investors trying to find promising early-stage start-ups except that we do not have anything to invest apart from our reputation. There is some risk involved, because, five years down the road, the paper/algorithm selected by the judges may not turn out to be as promising as expected.
We may keep similar set of categories as last year, but all other suggestions are welcome. (i) bioinfomatics in general, (ii) NGS assembly and alignment algorithms, (iii) teaching tools, (iv) blogs and twitter feeds, (v) journals.
i) Nomination from readers (and judges):
At first, we will build a large list of contributions. All readers are free to nominate as many papers as they want, provided they include a short paragraph mentioning why they find the paper as the best. The list can include papers from the judges as well. We do not like to be biased by high-profile journals and would like to include arxiv and blog posts in our consideration.
ii) Preliminary screening:
iii) Final voting:
Bioinformatics is one of the fastest emerging interdisciplinary research areas, which may be defined as an ‘interface between biological and computational sciences’. Most of the Bioinformatics work can be described as analyzing biological data, although a growing number of projects deal with the organization of biological information. Though the US remains the largest market in the world, Asia-Pacific countries (particularly India and China) are witnessing the fastest growth and are anticipated to emerge as the dominating forces in the future.
RNAseqViewer let you visualize the various data from the RNA-Seq analyzing process, for single or multiple samples. By focusing on gene expression and transcript isoforms, the program offers innovative ways to present the transcriptome data.
RNAseqViewer currently supports 7 types of data often used in RNA-Seq analysis (see table 1). Different types of view for each data set allow the visualization of different levels of information, including heatmap-like views for informative and yet very compact tracks, making possible to visualize dozens of samples simultaneously.
The user interface has been design to enable smooth browsing of the data. RNAseqViewer supports dynamic zooming and panning using the mouse, the keyboard or the buttons of the interface. Direct access to a specific position is possible by specifying coordinates or a gene's name.
Special attention has been given to the memory management, so that very large data sets can be visualized without exceeding memory limits nor affecting the fluidity of the user interface.
Other features include the possibility to hide intronic regions, the choice of the interface language (currently English, Chinese or French) and the possibility to print out the graphs or to export to PDF or image format.
RNAseqViewer is written in Python 3 and makes use of some additional libraries. Hence you have two options to run it. The first one is to download the source code, install Python and the necessary libraries, and run the program as a Python script. The other and easier option is to download the program as an executable which includes the Python interpreter and the necessary libraries.
The source code and binaries are freely available for academic use.
Please read the installation guide and the illustrated quick start tutorial.
Windows 32bit installer (12 Mb)
Download and run the installer to install the program.
Tested on Windows XP pro SP3 and Windows 7 SP1.
Windows 64bit installer (13 Mb)
Download and run the installer to install the program.
Tested on Windows XP pro SP3 and Windows 7 SP1.
Ubuntu and openSUSE binaries (15 Mb)
Download and uncompress the package, then run the executable "RNAseqViewer".
Tested on Ubuntu 12.04 and openSUSE 12.2.
Debian binaries (16 Mb)
Download and uncompress the package, then run the executable "RNAseqViewer".
Tested on Debian 7.
The expert provider of bioinformatics software and services across a wide range of life science and other sectors, has announced the final closing of a £1 million fundraising, as it continues to expand and develop new bioinformatics products. Eagle uses advanced computing to answer complex biological problems, from fighting cancer to breeding better crops.
David Flanders, CEO of Eagle said: "With the fundraising now secured, we can really begin to make progress in achieving our commercial goals. We have already begun our expansion, and the development of ElasticAP relationship is underway – all while we continue to grow the consulting side of the business."
Anthony Clarke, London Business Angels CEO, comments: "Following completion of its £1m funding round, Eagle Genomics is now well placed to exploit its high growth potential in the exciting bio-informatics market. I am delighted that a syndicate of LBA investors led by one of our Angel Investors, including our EIS Roundtable Syndicate Fund 2013, has been able to contribute circa £200k to this funding round alongside the Angel CoFund with many of these investors being sector experts who will able to add real value to the company going forwards."
PATRIC is the Bacterial Bioinformatics Resource Center, an information system designed to support the biomedical research community’s work on bacterial infectious diseases via integration of vital pathogen information with rich data and analysis tools. PATRIC sharpens and hones the scope of available bacterial phylogenomic data from numerous sources specifically for the bacterial research community, in order to save biologists time and effort when conducting comparative analyses. The freely available PATRIC platform provides an interface for biologists to discover data and information and conduct comprehensive comparative genomics and other analyses in a one-stop shop. PATRIC is a NIH-NIAID -funded project of Virginia Tech’s Cyberinfrastructure Division.
PATRIC has three primary types of experiment data, Taxonomy or Genome level, Gene or CoDing Sequence level, and Your Own Uploaded Experiment data. Learn about these types of experiment data, where you can find them, and some of the potential analyses you can do.
A new study at Mayo Clinic is using genomic sequencing to develop customized treatments for men with castration-resistant prostate cancer, a progressive and incurable stage of prostate cancer, which no longer responds to hormone therapies that stop or slow testosterone production.
Fellow researchers have described him as "one of the greatest scientists of any generation" and as "a real hero" of British science.
He is considered the "father of genomics" after pioneering methods to work out the exact sequence of the building blocks of DNA.
Dr Sanger also developed techniques to determine the structure of proteins.
He was born in 1918 in Gloucestershire and initially planned to follow his father into medicine.
However, he followed a career in biochemistry at the University of Cambridge.
It is impossible to exaggerate the impact of Fred Sanger's work on modern biomedical science.
Prof Colin Blakemore
At the time he attributed his success to fellow researchers and his wife: "I was married to Margaret Joan Howe in 1940. Although not a scientist herself she has contributed more to my work than anyone else by providing a peaceful and happy home."
He worked until the age of 65 when he retired to spend more time gardening and "messing about in boats".
"His invention of the two critical technical advances - for sequencing proteins and nucleic acids - opened up the fields of molecular biology, genetics and genomics.
I’ve lived through the era of the Human Genome Project, then the Personal Genome Project, after that, the race to lower the price of genome sequencing, but what if sequencing your genome would cost nothing and you shouldn’t have to send your samples to laboratories full of sequencing machines, but you could sequence your genome at home using a USB stick.
To sequence anything longer than a few hundred base pairs, scientists mince up thousands of copies of the target DNA, sequence all the fragments, and use software to painstakingly reconstruct the order of the DNA bases by matching overlap within fragments. A new approach, called nanopore sequencing, can handle long strands of DNA at once, eliminating the need for overlap analysis. As a result, nanopore sequencers could be cheaper, faster, and more compact than other DNA sequencers. They can also accurately sequence stretches with many repeating base pairs. The MinION from Oxford Nanopore Technologies connects to a USB port. Soon, anyone with $1,000 and a computer will be able to sequence DNA.
Memory specialist Micron has announced a new accelerator processor that it claims outperforms Intel's chips when it comes to dealing with streaming data.
The design is based on an adaption of memory architecture and exploits "the inherent bit-parallelism of traditional SDRAM," according to a Micron paper describing the technology. This sets it apart from Intel's "Xeon Phi" accelerator, which gets its number-crunching skills from an array of many, many low-power wimpy x86 chips.
Frontiers in Neuroscience for Young Minds is a scientific journal that includes young people (from 8 to 18) in the review of articles. This has the double benefit of bringing kids into the world of scientific research – many of them for the first time – and offering active scientists a platform for reaching out to the broadest of all publics.
New research or review articles are reported on a subject area that fits into one of the categories mentioned above. This can be work published by Frontiers or any other publisher;
The scientists write up their research for submission to the Journal, following our editorial guidelines as outlined below;
The report is handled by one of our prestigious associate editors, who will manage the process of peer review ;
Your article is reviewed by a young mind, mentored by a scientist with experience in peer review.
The young mind and mentor will require that the authors write clearly, concisely and with enthusiasm!
The articles are then validated by the Associate Editor, revised and forwarded to the Frontiers office for production;
The text is typeset and published on kids.frontiersin.org.
The identities of the reviewers (first name only for the young mind) and author are published with the article.
If you are interested in becoming a Frontiers Young Minds Reviewer, please contact our editorial office with a short biography and a letter. Is there someone among your family or friends who is a scientist and who can act as mentor for the project?
If you would like information about becoming a Young Minds mentor, please send your contact information and to our editorial office and we can explore these opportunities together.
If you are an author, send us an abstract with the reference to the original research article, or a short summary if you are planning to submit a review. In both cases, please indicate into which subject area above your contribution should be placed. You will then be contacted by an Associate Editor, who will be handling the review of your Young Minds paper. In the second half of 2014, we will open our manuscript submission and review platform to handle Young Minds papers; in the interim, please submit your materials with a cover letter to [email protected]. Once approved, we will ask you submit a two to three page article appropriate for our community of Young Minds, including two or three figures, and a very short list of references (no more than 5). Please make a special effort for the figures — these will help get you message across to the readers of this site.
If you are a teacher, keep an eye on this website: PDF versions of all the articles will soon be available, along with an e-book of the first round of articles for use in the classroom.
USA
I love books and articles with wry humor, and think my father is the funniest guy in the world. My other love is mechanisms, and I am frustrated that I have not yet learned all the math needed to build a spaceship. But I am working on it, meanwhile honing my logical skills by reviewing.
Canada
I'm a Canadian girl who just began grade 8. I like reading, dancing, acting, swimming and multiple other activities. My favorite colours are green, blue, purple and black. When I grow up I want to be a teacher, geologist, palaeontologist or another kind of science researcher. My favourite subjects in school are French, music, geography, English and science
California, USA
I am in 7th grade, and my parents are neuroscientists. I like to play sports, especially basketball. My favorite TV show is the Simpsons. When I grow up, I want to be an engineer and invent cool and important things.
Cambridge, MA, USA
3rd grader who plays the piano and loves to sing and dance. She participates in Science Club for Girls and she and her Mom will be performing in their second opera this year.
London, United Kingdom
I study how emotion influences decision making. I use a technology called fMRI which enables me to measure brain activity while people perform mental tasks. Outside of work I listen to jazz, rhythm and blues, and opera. I am an avid hiker, reader of literature and enjoy fly fishing.
Berlin, Germany
Doing neuroscience research is fun! I conduct experiments to understand how we make decisions when we interact with other people. I want to understand how we value other people's opinions and how their opinions can motivate our behavior. When I'm not doing science, I like to draw odd geometrical shapes, and I love watching movies as well.
Jerusalem, Israel
Studies how we use our different senses (e.g., vision and audition), to understand our surroundings (e.g., that there is a yellow car approaching the crosswalk fast, and we should wait before crossing). We see the car, we hear its engine, and we plan our actions accordingly.
Berkeley, USA
Associate Professor of Electrical Engineering and Neuroscience at the University of California, Berkeley, and Co-Director of the Center for Neural Engineering and Prostheses at UC Berkeley and UC San Francisco. He is interested in how the brain controls movement, and in the design of neuroprosthetic systems for people suffering with paralysis and other neurological conditions.
Davis, USA
I study how thinking develops, particularly thinking about number, space, time and emotions or feelings. To do this, I study both typically developing people and people who have developmental disorders like autism and fragile X syndrome.
Boston, USA
He studies how sleep and dreaming make our memories stronger and last longer, while also trying to figure out what they really mean, and whether they are even worth keeping. His work suggests that sleeping is a big part of learning, and sometimes as important as studying!
Lausanne, Switzerland
Professor at the Center for Neuroprosthetics of the École Polytechnique Fédérale de Lausanne (EPFL). He received a PhD in computer science from the Technical University of Catalonia, Barcelona (Spain) and has worked in Italy, US and Switzerland. He has received several awards for his work on brain-machine interfaces and brain-controlled robots.
Chicago, USA
Director of the High Performance Electrical Neuroimaging (HPEN) Laboratory, Stephanie studies how one's social relationships modify one's brain, and vice versa. She has received several awards for her work on the science of social connection and pair bond.