Recent Articles In Bioinformatics

  • Bioinformatics - Master's Programme
  • Penn and UGA Awarded $23.4 Million Contract for Pathogen Genomics Database
  • Spain to become a full member of ELIXIR
  • Bioinformaticians shed light into the data jungle
  • Measuring the success of an online bioinformatics resource
  • Why doesn't Santa age?
  • Ebola outbreak:
  • NHS DNA scheme to fight cancer and genetic diseases
  • P&G signs bioinformatics deal to speed new product research
  • Google's secretive Calico looking to hire bioinformatics pro
  • 2014 in Review: A Year of Great Science
  • Roche Buys Bioinformatics Firm
  • Global Synthetic Biology Market - Forecast to 2018
  • UTSA receives NIH grant to develop bioinformatics tools
  • Make Your Program Slower With Threads
  • Bioinformatics firm Eagle adds to senior team
  • Funding boost for clinical genomics company Congenica
  • PhosFox: a bioinformatics tool
  • UCLA will Integrate Big Data to Solve Biomedical Problems
  • repDNA: a Python package
  • ECOD: An Evolutionary Classification of Protein Domains
  • How to code in schools: a teacher and student's guide
  • Machine Intelligence Cracks Genetic Controls
  • Computer Neural Network as Good as Primate Brain in Identifying Objects
  • The host metabolite D-serine contributes to bacterial niche specificity

Bioinformatics - Master's Programme

  • The bioinformatics masters programme will provide you with a broad specialist competence in bioinformatics. You will also develop your own individual ability to solve problems related to biology, to plan and carry out analyses on molecular biology and biomedical data, and to collect, process and critically judge results from such data.
What will you study?The curriculum contains courses focusing on analysis of large-scale molecular biological and biomedical data, bioinformatics algorithms as well as research and development in bioinformatics. There is a computer science part of the programme, where you will concentrate on courses in Perl programming as well as the statistical language R, which are both highly used in bioinformatics. You will also carry out a master's degree project in the field of bioinformatics.
  • During your studies, lectures will be mixed with computer laboratory work. You will learn how to use various computerized tools for compiling and analyzing data from research projects and biological experiments, and to use various methods for analysis, for example sequence analysis and gene expression analysis.


  • Global consumer products giant Procter & Gamble (P&G) has turned to Cambridge bioinformatics technology to accelerate certain areas of research.
  • P&G’s Global Biotechnology and Life Sciences Department will use Eagle’s bioinformatics software platform, eaglecore, to help accelerate research of new products, organise existing data and integrate legacy data with more recent data for analysis across the company.
“By using our platform, P&G will able to better reference, manage and use all of their data to develop new insights and products, saving both time and development costs.”
  • He said eaglecore improves bioinformatics research to help accelerate the development of new products, including pharmaceuticals, consumer goods, food and beverages, livestock and crop development, and biofuels. eaglecore allows its users to integrate, tag and reference all of their research data in a single place allowing researchers to better use their data with new insights, and new developments.

Penn and UGA Awarded $23.4 Million Contract 

  • At the turn of the millennium, the cost to sequence a single human genome exceeded $50 million, and the process took a decade to complete. Microbes have genomes, too, and the first reference genome for a malaria parasite was completed in 2002 at a cost of roughly $15 million. But today researchers can sequence a genome in a single afternoon for just a few thousand dollars. Related technologies make it possible to capture information about all genes in the genome, in all tissues, from multiple individuals.
“This database has expedited research in many ways,” UGA’s Kissinger said. “Vaccine scientists frequently want to examine how proteins have changed over time, to identify those with signatures indicating that they provoke the human immune system. Those studying a specific antigen may wish to examine its structure and diversity, in order to prioritize those regions that might be most promising and relatively unlikely to develop resistance.”
  • Using EuPathDB and other resources, researchers around the world can now conduct cutting-edge research “in silico,”on the computer, maximizing the chance of success when translated to the lab or clinic.

Spain to become a full member of ELIXIR

  • Spain will become a full member of ELIXIR, the European bioinformatics infrastructure created to optimise biological data obtained from life sciences research. Spain participates in ELIXIR through the National Bioinformatics Institute(INB), a platform of the National Institute of Health Carlos III (ISCIII), whose central node is hosted at the Spanish National Cancer Research Centre (CNIO). Six INB institutions are participating in ELIXIR: the Spanish National Cancer Research Centre (CNIO), the Centre for Genomic Regulation (CRG), the Institute for Research in Biomedicine (IRB Barcelona), the Pompeu Fabra University (UPF), the Barcelona Supercomputing Center (BSC) and the Centro Nacional de Análisis Genómico (CNAG).
Spain provides ELIXIR with key services in the areas of biocomputing and bioinformatics, including the assessment of bioinformatics methods, genomic and biomedical data analysis, and data mining. Furthermore, the Spanish team ELIXIR co-leads the development of the European Genome-phenome Archive (EGA) database, the main repository for genomic data of biomedical interest, which is an essential component of the bioinformatics infrastructure for data analysis on rare diseases
  • ELIXIR was officially launched in December 2013. So far, its full members are the European Molecular Biology Laboratory (EMBL) and 11 countries: the Czech Republic, Denmark, Estonia, Finland, Israel, the Netherlands, Norway, Portugal, Sweden, Switzerland and the United Kingdom.

Bioinformaticians shed light into the data jungle

  • The University of Tübingen could be said to have played a pioneering role in the field of bioinformatics. The first ever bioinformatics course in Germany was established at the University of Tübingen way back in 1998. According to Prof. Dr. Oliver Kohlbacher, Tübingen now offers a service structure that is still quite unique in Germany. “In Germany, I would say the centre is the only one of its kind and I only know of a few similar centres in the EU,” Kohlbacher says. Tübingen University realised very early on that the university’s skills needed to be pooled in a central bioinformatics unit in order to achieve the objective of getting everyone pulling together in the same direction and as effectively as possible. As the units are closely integrated, Kohlbacher is one of three ZBIT directors as well as being QBiC director and coordinator of the CiBi.
But first things first: the Tübingen Centre for Bioinformatics (ZBIT) is effectively an old lady, at least in terms of bioinformatics. It was established back in 2000 and is the central bioinformatics research and teaching unit at the University of Tübingen. Its service portfolio has grown enormously over the years. “High-throughput technologies meant that we had to expand our services considerably, as our life sciences colleagues were finding it increasingly difficult without outside assistance to cope with the large amount of accumulated data,” says Kohlbacher. Three years ago, Tübingen won a tender to provide core facilities. The goal was to make bioinformatics services available.
  • The most recent addition to the Tübingen bioinformatics infrastructure is the Center for Integrative Bioinformatics (CiBi), which is jointly run by the QBiC and the ZBIT. The CiBi is one of six bioinformatics centres in Germany that together make up the “de.NBI”, the German Network for Bioinformatics Infrastructure, a BMBF infrastructure initiative aimed at expanding and improving the availability of hardware, data resources and bioinformatics tools in the life sciences, and securing them in the long term.

Measuring the success of an online bioinformatics resource

  • Like many other journals, PLOS Computational Biology aims to publish research that helps to further the field and develop the community that the journal serves. From time to time, however, we publish a paper that makes a significant impact not as research but as a resource. One such article is a Perspective entitled An Online Bioinformatics Curriculum by David Searls, one of our Associate Editors, who presents a bioinformatics curriculum in the form of a virtual ‘course list’, together with editorial commentary, and an assessment of strengths, weaknesses, and likely future directions for open online learning in bioinformatics.

Why doesn't Santa age?

  • Every living thing has a genome - information in the form of DNA that orchestrates all of the processes that take place inside each cell. This information is contained in a sequence of chemicals - the DNA letters A, C, G, T - around three billion of them in the case of humans. If we can find out the sequence of letters in a genome, it gives us clues about every aspect of how the organism works and came to be the way it is.

Ebola outbreak:

  • Throughout this week researchers have gathered in Melbourne to share what they know about the field of bioinformatics."Bioinformatics brings together mathematicians, statisticians, computer scientists and biologists to address some of the big problems in the life sciences," Dr Jonathan Keith from Monash University said.Dr Keith, a statistician, said if you considered the eradication of Ebola to be a battle, bioinformatics provided the back up for the foot soldiers on the ground.
"What bioinformatics provides is a better understanding of what the parts are, and how they work together and that's a really crucial thing for laboratory researchers to know what should be targeted."
  • "Principally it's the biologists who are at the front line who have to understand the biology and generate the physical quantities [of the vaccination]," he said.
  • "But the bioinformaticians will be searching through very large databases, trying to find significant patterns, trying to understand what works with what within the genome.

NHS DNA scheme to fight cancer and genetic diseases

  • A new genetics project could help "unlock a series of secrets about devastating diseases", the NHS says.

P&G signs bioinformatics deal to speed new product research

  • Procter & Gamble (P&G) has signed a four-year agreement to use bioinformatics software to help boost the development of new products including pharmaceuticals, consumer goods and biofuels.
  • The firm will use Eagle Genomics' secure, cloud-based, Eaglecore platform to organise existing data and integrate existing data with new analysis from across the company.

Google's secretive Calico looking to hire bioinformatics pro

  • Calico is Google's secretive anti-aging R&D biotech company that is trying to leverage IT to take on the ultimate challenge—​changing the way we age.
  • Calico is now looking for a head of bioinformatics to lead development of the infrastructure and tools necessary for the copmany to effectively acquire and process sequence data, FireceBiotech IT reports.
Computational bioinformatics is a specialized field that involves genomic sequencing, flow cytometry, metabolomics, and other highly complex areas of expertise.
If you have a PhD in bioinformatics and a world-class publication record, you may be eligible to apply for the high-level computational bioinformatics job at Google.
  • Calico is small, but growing. The company is engaged in the task of understanding the aging process and developing IT-related healthcare interventions based on that genomic knowledge.

2014 in Review: A Year of Great Science


Roche Buys Bioinformatics Firm

Roche has acquired Bina Technologies, a privately-owned biotech company based in California. The biotech’s first product was the Bina Box, a platform for secondary genomic analysis, sequence alignment, and variant calling, but since 2012, it has developed other products and platforms. Bina’s co-founder and CEO Narges Bani Asadi said in a statement that the relationship will be mutually beneficial to both firms. “We found great alignment between our company’s vision and values, and we are very excited about the possibilities of working with Roche's global team and serving the academic and translational and clinical research markets together in the future,” she said.
  • “We’re going to have the support of Roche to develop and scale our company much faster than before, and also have access to really deep experience and knowledge in Roche,” she said.

Global Synthetic Biology Market - Forecast to 2018

  • The synthetic biology market is highly competitive with a large number of players, including both big and small players, operating in this market. Synthetic biology is an emerging area of research and is broadly described as the design and construction of novel organisms or devices, artificial biological pathways, and the redesign of existing natural biological systems.

UTSA receives NIH grant to develop bioinformatics tools

  • According to the American Cancer Society, breast cancer is the most common cancer among American women, except for skin cancers, and about one in eight women in the United States will develop invasive breast cancer during their lifetime. The National Institutes of Health recently awarded a $1.08 million grant to The University of Texas at San Antonio (UTSA) to combine computational modeling with biological information to advance our understanding of what may cause breast cells to become cancerous.

Make Your Program Slower With Threads

  • Years ago, while taking a numerical methods course, I wrote some code to calculate the expected number of shared birthdays in a group. The code is very simple: each attempt constructs a vector of N birthdays, then counts the duplicates. The outer loop runs millions of attempts, and calculates the mean number of shared birthdays across all the samples. It's little more than a tight loop around a pseudo-random number generator.

Bioinformatics firm Eagle adds to senior team

  • Eagle has appointed Michael Reynolds as vice president of global sales as it prepares to launch a new bioinformatics software platform that will allow 'intelligent sharing' of genomic data later this year.
  • Reynolds joins the Cambridge, UK-based company from Pilgrim Software, where he was director of EMEA sales, and during a 20-year pharma and life sciences career his prior roles include stints at Smart Analyst, APC Pharma and Etrials.

Funding boost for clinical genomics company Congenica

  • Wellcome Trust spin-out bioinformatics company Congenica has secured ‘up to £1 million’ new investment from Cambridge Innovation Capital (CIC).
  • The clinical genomics company based on the Wellcome Trust Genome Campus outside Cambridge uses a platform called Sapientia for analysis and interpretation of genome sequences, based on knowledge developed  at (and licensed from) the Wellcome Trust Sanger Institute as part of the ongoing Deciphering Developmental Disorders (DDD) project. This is using whole exome and genome sequencing to try and identify genetic causes of learning disability and developmental delay in children.

PhosFox: a bioinformatics tool

  • PhosFox: a bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data
  • It is possible to identify thousands of phosphopeptides and -proteins in a single experiment with mass spectrometry-based phosphoproteomics. However, a current bottleneck is the downstream data analysis which is often laborious and requires a number of manual steps.

UCLA will Integrate Big Data to Solve Biomedical Problems

  • UCLA has announced a new institute to help medical and biology researchers make sense of 'big data.'
  • Millions upon millions of medical records and test results; countless DNA sequences; hard drives stuffed with images of all kinds — pictures of cells, scans of body parts; it's all part of the deluge of information often known as "big data," an ever-growing stockpile of digital material that scientists hope will reveal insights about biology and lead to improvements in medical care.

repDNA: a Python package

  • repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects
  • In order to develop powerful computational predictors for identifying the biological features or attributes of DNAs, one of the most challenging problems is to find a suitable approach to effectively represent the DNA sequences.

ECOD: An Evolutionary Classification of Protein Domains

  • Understanding the evolution of a protein, including both close and distant relationships, often reveals insight into its structure and function. Fast and easy access to such up-to-date information facilitates research.
  • ECOD (Evolutionary Classification of protein Domains) is distinct from other structural classifications in that it groups domains primarily by evolutionary relationships (homology), rather than topology (or “fold”).

How to code in schools: a teacher and student's guide

  • The UK is, according to Codeacademy's founder Zach Sims, well ahead of the pack when it comes to teaching the next generation to code.
"Before the term started, a lot of people were feeling under-confident, especially in primary schools," says Swidenbank. "All evidence now shows confidence is on the up." The biggest challenge remains the knowledge gaps, she asserts. But Codeacademy's own figures show the extent of the dent being made in that area. It has had 100,000 new student signups in the past three months and has partnered with more than 2,000 schools since September, bringing its total to more than 3,000.
  • The biggest change, has been a growth in confidence -- in both teachers and students. Keeping on top of the learning is the key to ensuring that confidence thrives, and Swidenbank has seen the results of that firsthand.

Machine Intelligence Cracks Genetic Controls

  • Every cell in your body reads the same genome, the DNA-encoded instruction set that builds proteins. But your cells couldn’t be more different. Neurons send electrical messages, liver cells break down chemicals, muscle cells move the body. How do cells employ the same basic set of genetic instructions to carry out their own specialized tasks? The answer lies in a complex, multilayered system that controls how proteins are made.

Computer Neural Network as Good as Primate Brain in Identifying Objects

  • For years, neuroscientists have been hard at work designing computer networks imbued with the capability to mimic visual skills that the human brain efficiently does. In a study, researchers from the Massachusetts Institute of Technology finally found a computer model called "deep neural networks" that can match a primate's brain in recognizing objects.

The host metabolite D-serine contributes to bacterial niche specificity

  • Escherichia coli comprise a diverse array of both commensals and niche-specific pathotypes. The ability to cause disease results from both carriage of specific virulence factors and regulatory control of these viaenvironmental stimuli. Moreover, host metabolites further refine the response of bacteria to their environment and can dramatically affect the outcome of the host–pathogen interaction.