naveenbioinformatics,bioinformtics,bioinformatics jobs


The SingularityU The Netherlands Summit is aimed at bringing awareness about exponential technologies and their impact on business and policy.


We'll introduce you to Singularity University and the themes of accelerating change and help you understand how emerging technologies will impact your industry and regulatory environment. This will enable you to prepare your organization for future developments.


  • Connect with 900+ European C-level executives, innovators, entrepreneurs, investors, NGOs and policy makers.
  • See brand new content by the world’s leading domain experts and SU faculty members.
  • Meet and learn from our local SingularityU The Netherlands faculty members.
  • Gain key insights into the future of Energy, Mobility, Finance, Security, Health, Work and Humanity.
  • Experience and interact with the latest cutting-edge technologies from our Innovation Hub.


  • Artificial Intelligence & Robotics
  • Biotechnology & Bioinformatics
  • Networks & Computing Systems
  • Medicine & Neuroscience
  • Nanotechnology & Digital Fabrication
  • Blockchain & Security
  • Entrepreneurship & Future Organizations
  • Energy & Abundance
  • Society & Ethics
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Spencer Hall is a fourth year Statistics major and Philosophy minor. Hall plans on attending graduate school to pursue a master’s in Statistics with a concentration in Bioinformatics. Hall has had first-hand experience with a chronic illness that could be benefited by the application of bioinformatics. His talk is about how the massive amount of genetic data available today is too large to be analyzed without statistical methods, and has consequences so important that we cannot afford not to study it.
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“Big data” is a catchall term for any data set of exceedingly large volume. It could be transaction information at a credit card company, invoice data at an online retailer, meteorological measurements from a weather station. All these data sets have unique characteristics that make it extremely difficult to use conventional computing technologies and techniques to store and process them for analysis. Their variety is daunting, and high velocity is required to handle them in a timely manner.

  •  People working in fields such as physics, bioinformatics, statistics, political science and psychology are already heavy users and analyzers of a large amount of data. Transition from these types of disciplines to big data analytics could be relatively smooth.
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[right-post]Position-Specific Iterated BLAST (PSI-BLAST) is a user-friendly version of a profile-based search.BLAST does not always find all homologs because no search program is 100% sensitive. To find putative homologs that BLAST does not find, search with mathematical representation of the protein family. It is important to note that PSI-BLAST finds putative homologs. It is best to confirm the homology in the wet lab or in the dry lab.

in Personalized Medical Treatment[right-post]

naveenbioinformatics,bioinformatics jobs,bioinformatics phd

We’re excited about our work with the hospitals and research institutions using bioinformatics to achieve major healthcare breakthroughs and unlock the mysteries of the human body.This eBook highlights the important work bioinformatics organizations are undertaking and explains how we are helping them achieve their mission. The stories of these four organizations illustrate what is possible with the AWS Cloud:
  1. The National Institute of Health’s Human Microbiome Project (HMP) – Researchers from all over the globe can now access HMP data through Nephele, an AWS-supported platform, and use that information to identify possible microbial causes of preterm births, diabetes, inflammatory bowel syndrome, and other disorders.
  2. The INOVA Translational Medicine Institute (ITMI) – AWS architecture facilitates the storage and management of this secure data, and enables Inova researchers to develop personalized treatments and predictive care for newborns suffering from congenital disorders and patients of all ages with cancer-causing genetic mutations.
  3. University of California, San Diego’s  Center for Computational Biology & Bioinformatics (CCBB) – CCBB has seven core AWS-supported analysis pipelines, all optimized to handle next-generation sequencing data. Each pipeline is targeted at identifying small but important molecular differences, whether in a tumor’s DNA or in the microbiome, enabling doctors to tailor treatment on an individual level.
  4. GenomeNext – GenomeNext’s AWS based platform represents the newest technological benchmark in the history of genomic analysis, and allows even small research groups to complete genomic sequencing in a matter of hours at a fraction of the traditional cost.
Read More Download the eBook

the future of healthcare[right-post]

[fquote]"Genetic engineering techniques are now cheap and widespread enough that any knowledgeable individual can order every material they need off the Internet and download the software to do experiments on themselves," said Raymond McCauley, Biotechnology and Bioinformatics Chair, Singularity University.[/fquote]
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[fquote]The PhD opportunity will be carried out at OncoImmunity resulting in a PhD awarded through the University of Oslo. The candidate will have academic mentors and supervisors at the University of Oslo, in addition to main supervisors in the OncoImmunity development and scientific team. This PhD position involves the research and development of novel machine learning algorithms to identify immunogenic mutations from patient genomes. The candidates background should be in machine-learning, big data and statistics. The ideal candidate will have a background in the analysis of cancer next generation sequencing (NGS) and research interests in developing novel methods that will allow for discoveries at the interplay between cancer and immunology, in order to identify improved personalized cancer immunotherapy.[/fquote]

Required experience 

  • We are looking for applicants who have an MSc degree in bioinformatics, statistics, computational biology, computer science, or applied mathematics.

Roles and responsibilities 

  • Apply machine-learning and statistical methods to NGS and associated proteomics information Excellent communication skills, and capable of providing clear visualization of data and results Experience in computer programming with strong familiarity with languages and technologies needed for statistical data analysis and machine-learning (Python, R, etc) Develop and implement pipelines for NGS data analysis Work closely in a scientific team developing a software solution, which relies on statistical analysis and machine-learning from next generation sequencing (NGS) of DNA. Work with other developers, the software development manager, CEO and the CSO, to develop key machine-learning and statistical methodology in the software solution. Passion to build an innovative software solution which will benefit cancer patients by empowering the development of ground-breaking immunotherapies. 


  • Cover letter CV Documentation of a relevant completed M.Sc. or equivalent degree. Course and grade list of bachelor and/or master degrees

[fquote]A three-year Ph.D. studentship in evolutionary biology is available in the laboratory of Andreas Wagner at the University of Zurich. We are looking for a researcher to study the origins of evolutionary innovations and phenotypic diversity in genetic systems, such as metabolic networks, regulatory circuits, and enzymes. Lab members are a group with very diverse backgrounds and research projects, unified by their interests in evolution and life’s fundamental organizational principles. Ongoing work in the lab ranges from the directed evolution of enzymes to laboratory evolution in E.coli and computational analyses of genetic networks (e.g., Hayden et al., Nature 2011; Payne and Wagner, Science 2014). A sample of the laboratory’s research can be found at [/fquote]

University of Zurich - Universität Zürich - UZH

  • The successful candidate will have a strong background in bioinformatics and computational biology. Fluency in a major scripting language such as perl, and experience in software development is a must. Also desirable is a strong background in biology. Applications without a demonstrated interest and research history in evolutionary biology will not be considered further. We are looking for an individual with a Masters Degree or equivalent, who is highly self-motivated and can work independently. 
  • The working language in the laboratory is English. German skills, although helpful, are not essential. Zurich is a highly attractive city in beautiful surroundings, with a multinational population, and many educational and recreational opportunities. 
  • To be considered, please send a single (!) PDF file merged from the following parts to [email protected]: CV including publication list, academic transcripts, a statement of research interests not exceeding three pages, and three academic references. Please include the word “PEVOLPHD16” in the subject line. Applications will be considered until April 22, 2016, or until the position is filled, whichever comes first. The position is available from the fall of 2016.

I can imagine a future where functional medicine is built into a bioinformatic system which analyzes your history, medical history, analyzes lab tests that can be done by yourself at a local pharmacy or anywhere or maybe a kit that’s sent to your home. That data gets put into a system. It’s driven through an artificial intelligence decision support system. It spits out guidelines and recommendations for you to do. You find other people to do it with in your community. 
[fquote]You learn how to actually connect the resources that are around you that link everything together. I mean, Uber didn’t invent anything new; it just linked together all sorts of resources to make things easy, and that can happen in medicine to help people change their lifestyle and behavior. It can link people in the community who want to get healthy together, who want to learn how to shop and cook and do all kinds of things.[/fquote]
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South by Southwest (SXSW) is right around the corner, so we created a Custom List in Mattermark to help you track them. We found 282 companies that will be represented at SXSW this year and below are the 23 fastest growing ones that are not public or acquired and have raised less than $100 million in funding. We used the Mattermark Growth Score to rank all 282 companies. The Custom List in Mattermark provides each company’s Growth Score, Mindshare Score, URL, location, total funding, all investors, employee count, employee count month-over-month change, current funding stage, location, estimated monthly uniques, and last funding date. Below are the top 23 on the list.
[fquote]Desktop Genetics (Mattermark Growth Score: 138) – A bioinformatics company, which develops technologies at the intersection of biotechnology, information management and laboratory automation.[/fquote]

It was a rallying call for investment in maths and physics research in Africa. The "Next Einstein" slogan became a mission for the organisation Neil Turok had founded to bring Africa into the global scientific community: the African Institute of Mathematical Sciences (AIMS). That search for an African Einstein now has some results, with 15 "Next Einstein Fellows" and 54 "Next Einstein Ambassadors" announced at an event last month. These are young African scientists, often leaders in their fields, working and studying in Africa.
[fquote]There are advantages in other fields, too. For scientists using bioinformatics to explore the origins of genetic disease, Africa holds a unique place as the cradle of humanity - and therefore the repository of our oldest genetic information.[/fquote] Read More

Think your DNA is all human? Think again. And a new discovery suggests it's even less human than scientists previously thought.Nineteen new pieces of non-human DNA -- left by viruses that first infected our ancestors hundreds of thousands of years ago -- have just been found, lurking between our own genes.
[fquote]The simple reason that software has bugs (that result in errors) is that writing software is hard.Let's take a simple example and say you want to write some software to determine if a genetic variant meets an autosomal recessive inheritance pattern. This is easy, right!? Just find sites where the affected parent is het, the unaffected is homozygous reference and the proband is heterozygous. Done. Too easy.[/fquote]
[accordion] [item title="£75M investment in bioinformatics"]UK Minister for Universities and Science David Willetts joined key stakeholders in the Cambridge biotechnology cluster today to celebrate the opening of a new Technical Hub for bioinformatics. The European Bioinformatics Institute's new South Building will be home to the ELIXIR Directorate, which will coordinate bioinformatics activities throughout Europe in order to increase the availability and uptake of biological data in commercial and non-commercial.Read More[/item] [item title="Scientists develop high-sensitivity software for searching massive DNA databases"]A new computer program was designed by Russian and American scientists and specialized for searching massive DNA databases for distant similarities, reports Institute for information transmission problems of the Russian Academy of Sciences (IITP RAS) press-service. Anna Kaznadzey, a junior researcher at IITP RAS took part in this work.Read More[/item] [item title="Teaching children how to be a sequence "]As part of a PhD it is anticipated1 that you will share your science with various audiences; fellow PhD students, peers in the field and the various publics. Every year, the university celebrates British Science Week with a Science Fair, inviting possibly the most difficult public to engage with: children. Over three days the fair serves to educate and entertain 1700 pupils from over 30 schools based across Mid Wales, and this year I volunteered2 to run a stand.Read More[/item] [item title="ISCB’s initial reaction to New England Journal of Medicine"]The recent editorial by Dr Longo and Dr Drazen in the New England Journal of Medicine (Longo and Drazen, 2016) has stirred up quite a bit of controversy. As Executive Officers of the International Society of Computational Biology, Inc. (ISCB), we express our deep concern about the restrictive and potentially damaging opinions voiced in this editorial, and while ISCB works to write a detailed response, we felt it necessary to promptly address the editorial with this reaction. Although some of the concerns voiced by the authors of the editorial are worth considering, large parts of the statement purport an obsolete view of hegemony over Read More[/item] [item title="Assistant Professor of Bioinformatics "]The Department of Molecular and Biomedical Sciences at the University of Maine is seeking to fill a tenure-track position at the Assistant Professor level in the area of Bioinformatics/Computational Biology. The successful applicant will establish and lead a productive research program in the areas of bioinformatics/computational biology that provides research opportunities for both undergraduate and graduate students. Specific research areas of interest for this position include but are not limited to genomics and systems biology including gene expression, evolution, population genetics, and microbiomics. Analysis of other datasets such as lipidomics, metabolomics, transcriptomics, epigenomics, etc. are also of interest. The Department of Molecular and Biomedical Sciences has an active research core in the areas of host-pathogen interactions, toxicology, and cell signaling, and an outstanding zebrafish facility that supports broad research areas. Other units on campus also offer areas for collaboration such as wildlife genomics, mouse models, and others. As a founding and active member of The University of Maine's Graduate School of Biomedical Sciences and Engineering, the reach and collaborations available to members of the Department extend to the physical and computational sciences and to institutions across the state of Maine, including the Mt. Desert Island Biological Laboratory, The Jackson Laboratory, and Maine Medical Center Research Institute. The department is actively developing a new Masters degree program in Bioinformatics and includes a phage genomics course in its undergraduate core curriculum. The applicant will teach within the Department of Molecular and Biomedical Sciences with emphasis on the development of new courses in computational biology at the advanced undergraduate and graduate level. The position is a 75% research/25% teaching position with a start date of January 1, 2017 or later.Read More[/item] [item title="Will Spark Power the Data behind Precision Medicine?"]The promise of precision medicine that President Obama envisions with this statement is a far-reaching goal that will require sweeping changes to the ways physicians treat patients, health data is collected, and global collaborative research is performed. Precision medicine typically describes an approach for treating and preventing disease that takes into account a patient’s individual variation in genes, lifestyle, and environment. Achieving this mission relies on the intersection of several technology innovations and a major restructuring of health data to focus on the genetic makeup of an individual. Read More[/item] [item title="Paper: “Undergraduate Bioinformatics Workshops Provide Perceived Skills”"]Bioinformatics is becoming an important part of undergraduate curriculum, but expertise and well-evaluated teaching materials may not be available on every campus. Here, a guest speaker was utilized to introduce bioinformatics and web-available exercises were adapted for student investigation. Students used web-based nucleotide comparison tools to examine the medical and evolutionary relevance of a unidentified genetic sequence. Based on pre- and post-workshop surveys, there were significant gains in the students understanding of bioinformatics, as well as their perceived skills in using bioinformatics tools. The relevance of bioinformatics to a student’s career seemed dependent on career aspirations.Read More[/item] [item title="More ancient viruses lurk in our DNA than we thought"]Think your DNA is all human? Think again. And a new discovery suggests it's even less human than scientists previously thought.Nineteen new pieces of non-human DNA -- left by viruses that first infected our ancestors hundreds of thousands of years ago -- have just been found, lurking between our own genes.Read More[/item] [item title=" What is the reason for most software errors in Bioinformatics "]The simple reason that software has bugs (that result in errors) is that writing software is hard.Let's take a simple example and say you want to write some software to determine if a genetic variant meets an autosomal recessive inheritance pattern. This is easy, right!? Just find sites where the affected parent is het, the unaffected is homozygous reference and the proband is heterozygous. Done. Too easy.Read More[/item] [item title="International Conference on Bioinformatics and Computational Biology (BICoB)"]In recent years, computational biology and medical informatics have seen significant advances driven by computational techniques in bioinformatics making bioinformatics and computational biology among the most vibrant research areas. The 7th international conference on Bioinformatics and Computational Biology (BICoB-2016) provides an excellent venue for researchers and practitioners in the fields of bioinformatics and computational biology to present and publish their research results and techniques. The BICoB conference seeks original and high quality papers in the fields of bioinformatics, computational biology, systems biology, medical informatics and the related disciplines.Read More[/item] [item title="The 100 Best Bioinformatics(Computer Science) Programs in the World"]At Princeton, one can research problems in Bitcoin and Crypto currencies, bioinformatics, computational neuroscience, geo-replicated cloud storage and any number of other leading subfields of information theory. Not surprisingly given Princeton’s focus, all its students, even undergraduates, are required to do at least one design or research-related project before graduation.Read More[/item] [item title="Software Architecture Training Conference in La Jolla"]creating applications for bioinformatics, finance, and retail. To make byte code more accessible, he created the open-source Java Assembler Kit (JAK) which provides a fluent API for producing Java byte code and includes a REPL to allow for interactive experimentation.Read More[/item] [item title="Wellcome Trust and COAF Open Access Spend, 2014-15"]Once a year we ask all those institutions in receipt of an open access (OA) grant from the Trust to provide details on how the grant has been spent. In 2014 six research funders established the Charity Open Access Fund (COAF) in order to provide a single funding mechanism to cover Article Processing Charges (APCs). The data supplied by institutions for the 2014-15 report therefore covers APC spend on articles arising from research funded by Arthritis Research UK, Breast Cancer Now, Bloodwise, British Heart Foundation, Cancer Research UK and the Wellcome Trust.Read More[/item] [item title="A new approach to sequence and assemble primate genomes"]A new sequencing technology based on longer sequence reads allows missing genes and missing forms of genetic variation to be discovered for the first time. This assembly offers new biological insights into a living species that is second only to chimps in its evolutionary closeness to humans.Read More[/item] [item title="Science relies on computer modelling"]From the transforming discovery of penicillin to the theories of relativity and quantum mechanics, science progressed with mind-boggling speed even before there were computers. Much of this is down to the robustness of the scientific method: scientific results are validated by being replicated and extended by other scientists.Read More[/item] [item title="MOOC Course Report: April 2016"]A big welcome to “Bioinformatics: Introduction and Methods” from Peking University! In this MOOC you will become familiar with the concepts and computational methods in the exciting interdisciplinary field of bioinformatics and their applications in biology, the knowledge and skills in bioinformatics you acquired will help you in your future study and research.Read More[/item] [item title="Roche and Discuva in superdrug partnership"]The two companies announced on 28 February that they have entered a collaboration and licence agreement for the discovery and the development of antibiotics. The drugs are to treat infections caused by multi-drug resistant Gram-negative bacteria using Discuva’s Selective Antibiotic Target IdentificatioN (SATIN) technology. This next-generation sequencing and bioinformatics platform will be used to identify bacteria and select promising drug candidates.Read More[/item] [item title="Sample size calculation while controlling false discovery "]RNA-Sequencing (RNA-seq) experiments have been popularly applied to transcriptome studies in recent years. Such experiments are still relatively costly. As a result, RNA-seq experiments often employ a small number of replicates. Power analysis and sample size calculation are challenging in the context of differential expression analysis with RNA-seq data. One challenge is that there are no closed-form formulae to calculate power for the popularly applied tests for differential expression analysis. In addition, false discovery rate (FDR), instead of family-wise type I error rate, is controlled for the multiple testing error in RNA-seq data analysis. So far, there are very few proposals on sample size calculation for RNA-seq experiments.Read More[/item] [item title="24 phenomenal founders crashing the tech party"]A mathematician with a PhD in molecular evolution and bioinformatics, Nora Khaldi founded Nuritas in 2014 to ‘make the future of food’. Combining AI and DNA sequencing, Khaldi’s pioneering approach to bioinformatics has seen the company revolutionise how we study food. Khaldi will be speaking at Inspirefest this summer.Read More[/item] [/accordion]

International PhD Programme (IPP) gives talented and enthusiastic students the opportunity to undertake PhD research at the cutting edge of modern biology. Projects within the Programme address key questions related to the overarching theme of Gene Regulation, Epigenetics & Genome Stability.

  • Our groups cover a broad range of expertise in biochemistry, genetics, cell and developmental biology, bioinformatics, systems biology, and applied physics.The fields we study range from embryonic development, ageing and disease to analysis of high-throughput datasets, modeling of regulatory gene networks and the development of ground breaking super-resolution microscopes. This range of expertise and the open and vibrant atmosphere within the Programme encourages multidisciplinary collaborations and innovative research. Moreover, a range of scientific and social events are organised to ensure high levels of exchange and collaboration between the participating groups.

Institute of Molecular Biology

The Programme is coordinated by the Institute of Molecular Biology - a recently founded centre of excellence in the life sciences. Participating groups are located at the:

There are 38 groups participating in the IPP. For a full list, please see IPP Groups.

  • Core funding for the International PhD Programme comes from the Boehringer Ingelheim Foundation. As a PhD student your research will be overseen by an expert Thesis Advisory Committee who will be there to support you in your research and provide you with advice. This programme thus provides an excellent opportunity to interact closely with a number of top scientists during the course of your study.
  • To download our flyer for the International PhD Programme, please click here: PDF. If you have any questions that are not answered here, you can contact us using the details on the contact page.


[info title="Info message" icon="info-circle"] Registration deadline: 1 May 2016 Application deadline: 8 May 2016 All applicants will be informed about the result of the selection process latest in the first week of June 2016. Shortlisted applicants will be invited to Interview Days at IMB, which will be held 25 - 27 July 2016. Successful applicants will start their PhD studies between September 2016 and March 2017. 


  • The International PhD Programme includes groups at the Institute of Molecular Biology (IMB), Johannes Gutenberg University (JGU), Mainz's University Medical Centre (UMC) and the Max Planck Institute for Polymer Research (MPI-P). Please visit the IPP groups page for an overview of all groups involved in the IPP. Note that not all groups involved in the IPP offer a new position every call. 
  • You can select up to 5 recruiting groups in your field of interest and you can still modify or extend this selection if you are invited to our interview days and come to know the Group Leaders in person.


  • The IPP wants to attract the brightest minds from all over the world. We are looking for creative and ambitious students in the field of life sciences who are looking for challenging work at the cutting edge of science. Our student community currently consists of more than 90 PhD students from 20 different countries. Each call we receive about 500 applications from students all over the world, for approximately 10 – 15 positions. 

Working language

  • As IMB is an international institution the first criterion for eligibility is that you are able to communicate in English, which is our working language.
  • Education and experience
You should have prior experience in a research environment and have, or be about to complete, a Master's or equivalent degree (at least 4 years of university education).

Application Process

1) Online registration

  • Register online to provide us with your contact details and the details of at least two referees. Referees should be senior scientists who know you well.  
  • Once you have completed the registration form, your nominated referees will receive a personalised link to the standard reference form and upload page. You will be notified by email when a reference letter is submitted.  
  • We will not consider applications until 2 reference letters are received. Therefore, please ensure that you contact your referees in advance of registering to inform them of your intention to apply to the IPP, and to confirm that they are able to provide a reference by the specified deadline (8 May 2016).

Information required for registration:

  • Personal data, including your address and contact details
  • Contact details of your referees
Please register here: LINK TO ONLINE REGISTRATION FORM (Deadline for registration 1 May 2016)

2) Online application form

  • Once you have registered, you will receive a link to the online application form. It will ask you to provide the information and documents listed below.
  • As the form cannot be saved, we strongly advise you to prepare the necessary information before you begin. Texts can then be pasted into the form as required. The application must be completed in English.  

Information required for application (click here to download an example):

  • Details of your degrees (BSc, MSc)
  • Details of any other post-graduate degrees, awards, honours or distinctions (description with a maximum of 250 words)
  • Details of past research experiences
  • A list of your publications (PubMed format, maximum of 300 words) and your conference contributions (title of presentation, date and location of the conference)
  • Which groups you are interested in working with; up to 5 may be selected. Please note: not all groups offer projects in every call!
  • A motivational statement describing your interest in the IPP and your chosen groups as well as your scientific goals (maximum of 300 words)

You will be asked to upload the following documents in PDF format:

  • Curriculum vitae (max size 3 MB)
  • A single file (max size 4 MB) containing:
  1. High school certificate
  2. University studies (including certificates of qualification and transcripts of records)
  3. English language test certificate (not mandatory, only if available)

[info title="Info message" icon="info-circle"]If degree forms and records from your university are not available in English, we do not require authorised translations for this application. If you encounter any technical problems, please contact the IPP coordinator (email).[/info]

3) Interview days

Shortlisted students will be invited to Mainz for interviews from 25 - 27 July 2016. The interviews will be held over 3 days and include presentations by the Group Leaders and the applicants as well as in-depth interviews in the group(s) you could imagine to work with. You must register by 1 May 2016 to be eligible to apply for the summer call. 

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Widely received in its previous editions, Bioinformatics and Functional Genomics offers the most broad-based introduction to this explosive new discipline. Now in a thoroughly updated and expanded third edition, it continues to be the go-to source for students and professionals involved in biomedical research.
This book provides up-to-the-minute coverage of the fields of bioinformatics and genomics. Features new to this edition include:
  • Extensive revisions and a slight reorder of chapters for a more effective organization
  • A brand new chapter on next-generation sequencing
  • An expanded companion website, also updated as and when new information becomes available
  • Greater emphasis on a computational approach, with clear guidance of how software tools work and introductions to the use of command-line tools such as software for next-generation sequence analysis, the R programming language, and NCBI search utilities

The book is complemented by lavish illustrations and more than 500 figures and tables - many newly-created for the third edition to enhance clarity and understanding. Each chapter includes learning objectives, a problem set, pitfalls section, boxes explaining key techniques and mathematics/statistics principles, a summary, recommended reading, and a list of freely available software. Readers may visit a related Web page for supplemental information such as PowerPoints and audiovisual files of lectures, and videocasts of how to perform many basic operations:
Bioinformatics and Functional Genomics, Third Edition serves as an excellent single-source textbook for advanced undergraduate and beginning graduate-level courses in the biological sciences and computer sciences. It is also an indispensable resource for biologists in a broad variety of disciplines who use the tools of bioinformatics and genomics to study particular research problems; bioinformaticists and computer scientists who develop computer algorithms and databases; and medical researchers and clinicians who want to understand the genomic basis of viral, bacterial, parasitic, or other diseases.

Table of Contents

Part I Analyzing DNA RNA and Protein Sequences

  • Introduction 3
  • Access to Sequence Data and Related Information 19
  • Pairwise Sequence Alignment 69
  • Basic Local Alignment Search Tool (BLAST) 121
  • Advanced Database Searching 167
  • Multiple Sequence Alignment 205
  • Molecular Phylogeny and Evolution 245

Part II Genomewide Analysis of DNA RNA and Protein

  • DNA: The Eukaryotic Chromosome 307
  • Analysis of Next-Generation Sequence Data 377
  • Bioinformatic Approaches to Ribonucleic Acid (RNA) 433
  • Gene Expression: Microarray and RNA-seq Data Analysis 479
  • Protein Analysis and Proteomics 539
  • Protein Structure 589
  • Functional Genomics 635

Part III Genome Analysis

  • Genomes Across the Tree of Life 699
  • Completed Genomes: Viruses 755
  • Completed Genomes: Bacteria and Archaea 797
  • Eukaryotic Genomes: Fungi 847
  • Eukaryotic Genomes: From Parasites to Primates 887
  • Human Genome 957
  • Human Disease 1011
Read More

Teens awarded more than $1 million for scientific innovations at the 2016 Intel Science Talent Search, and for the first time in the event’s 75-year history more than half of the finalists were female. These projects scored three teens — Amol Punjabi, Paige Brown and Maya Varma — top honors, including $150,000 each at the 2016 Intel Science Talent Search (Intel STS), held at the National Building Museum in Washington, D.C., on March 15.

First Place: Amol Punjabi (computational biology and bioinformatics)

  • First Place: Amol Punjabi, 17, of Marlborough, Massachusetts For his computational biology and bioinformatics project, Punjabi developed software to help drug makers develop new therapies for cancer and heart disease. He is the lead author of a paper on nanoparticles published in ACS Nano and co-author of a paper on a related topic in Nanoscale.
Read More

In this course, you will learn how entire genomes are assembled from millions of short overlapping pieces of DNA. The scale of this problem (the human genome is 3 billion nucleotides long!) implies that computers must be involved. Yet the problem is even more complex than it may appear ... to solve it, we will need to travel back in time to meet three famous mathematicians, and learn about algorithms based on graph theory.


How Do We Assemble Genomes? (Graph Algorithms)

  • Exploding Newspapers
  • The String Reconstruction Problem
  • String reconstruction as a walk in the overlap graph
  • Another graph for string reconstruction
  • Walking in the de Bruijn graph
  • The seven bridges of Konigsberg
  • Euler's Theorem
  • From Euler's Theorem to an Algorithm for Finding Eulerian Cycles
  • Assembling genomes from read-pairs
  • Epilogue: Genome assembly faces real sequencing data

How Do We Sequence Antibiotics? (Brute Force Algorithms)

  • The Discovery of Antibiotics
  • How Do Bacteria Make Antibiotics?
  • Dodging the Central Dogma
  • Sequencing Antibiotics by Shattering them into Pieces
  • A Brute Force Algorithm for Cyclopeptide Sequencing
  • A Branch-and-Bound Algorithm for Cyclopeptide Sequencing
  • Just How Fast Is This Algorithm?
  • Adapting Cyclopeptide Sequencing for Spectra with Errors
  • From 20 to More than 100 Amino Acids
  • The Spectral Convolution Saves the Day
  • Epilogue: From Simulated to Real Spectra

Bioinformatics Application Challenge: Sequencing a Staphylococcus aureus genome

Read More


The aim of this course is to provide principal investigators with an introduction to the challenges of working with biological data as a research leader; to provide guidance on strategies for managing data and the importance of data sharing; how to encourage bioinformatics development in your team and / or work with collaborators and what resources are available across the life sciences.


This course is aimed at principal investigators and other senior scientists in the molecular life sciences, especially those currently supervising others who are using bioinformatics in their research, or plan to include bioinformatics to their research in the future.
Participants do not require any previous experience of using bioinformatics resources or methods.


After this course you should be able to:

  • Define the potential and pitfalls of bioinformatics use in your research
  • Identify your team needs in terms of bioinformatics use and support
  • Develop appropriate plans for the management and sharing of data
  • Support the development of bioinformatics skills within your team
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Visualizing and summarizing data from genomic studies continues to be a challenge. Here we introduce the GenVisR package to addresses this challenge by providing highly customizable, publication-quality graphics focused on cohort level genome analyses. GenVisR provides a rapid and easy-to-use suite of genomic visualization tools, while maintaining a high degree of flexibility by leveraging the abilities of ggplot2 and bioconductor. Availability and Implementation: GenVisR is an R package available via bioconductor ( under GPLv3. Support is available via GitHub ( and the Bioconductor support website.
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ISCB is pleased to invite you to attend ISMB 2016, July 8-12, 2016, in Orlando, Florida. The conference provides a multidisciplinary forum for disseminating the latest developments in bioinformatics and computational biology. ISMB 2016 offers a diverse, engaging scientific program and the broadest scope of any international bioinformatics/computational biology conference. ISMB 2016 is accepting submissions for proceedings, highlight talks, and posters.
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Microbial eukaryotes cover the widest phylogenetic diversity in the eukaryotic tree of life and are essential components of all Earth’s ecosystems. Paradoxically, they remain largely unknown, hiding a wealth of genes and genomes that are key to understand the ecology and evolution of microbial ecosystems. SINGEK is a H2020 Marie-Skłodowska-Curie Innovative Training Network (MSCA-ITN) project aimed at providing a unique and structured training programme to 15 Early Stage Researchers (ESRs) to study microeukaryotes at the single-cell level.
[fquote] ESRs will be trained in the use of an array of laboratory methods (cell sorting and molecular tools for nucleic acid amplification and high throughput sequencing), bioinformatic techniques (genome and transcriptome assembly and functional gene annotations), and will work on scientific questions in the fields of microbial ecology and evolution in order to investigate microeukaryotes in unparalleled detail. The training structure is a central part of SINGEK project and will include: local and network-wide activities, secondments to other network.[/fquote]
  • All positions are for 3-years contracts starting in October 1st, 2016, most of them leading to a PhD degree. Specific conditions may apply to individual positions depending on local regulations.
  • Top-level graduates in biology, bioinformatics, microbial ecology, molecular biology, evolutionary biology, biodiversity, biotechnology, physics, nanoscience, engineering or computer science are encouraged to apply. No discrimination will be made on the basis of nationality, gender, race, religion or disability.
  • H2020 EU funding imposes strict eligibility criteria: At the time of recruitment the researcher must not have resided or carried out his/her main activity (work, studies, etc…) in the country of the host institute for more than 12 months in the 3 years immediately prior to his/her recruitment under the project.The researcher should also be in the first four years of their research careers at the time of recruitment by the host organisation and have not been awarded a doctoral degree.
  • Candidates may apply through the SINGEK applications system, which will request the following information:
  1. An application form, including a CV overview, ESRs’ positions of interest (up to 3), and a statement of their motivation for applying.
  2. A full CV.
  3. An academic record, with a scan of the degree qualifications.
  4. Two recommendation letters.
[info title="Info message" icon="info-circle"]Each project supervisor will revise the candidates’ documentation and, on the basis of the completeness and adequacy of the requested material and quick eligibility check, will score candidates based on: (1) academic profile; (2) personal motivation; (3) scientific skills and relevant experience; and (4) English proficiency. Shortlisted candidates will be invited to teleconference interviews with the relevant project supervisor(s).Application deadline: 17:00 GMT on the 15th April 2016[/info] Read More


[fquote]This international graduate program is a close cooperation with our partner program "MADD-Gen" at Simon Fraser University (SFU), Vancouver, Canada.Research will focus on the development of methods of high importance for the practical comparative analysis of genomes, in particular in view of both the variation between individuals (diversity) and the change in populations over time (dynamics). Our program aims at training specialists in handling big data related to genomics and molecular biology.[/fquote]

  • PhD students will hold 3-year positions, payed according to German TV-L 13 table, i.e., a monthly gross salary of approximately 3200 Euros. The graduate program involves a six-months research stay at Simon Fraser University or one of the other partner institutions in Vancouver, Canada. (Additional funds to support parents and handicapped persons are available.)

Studying at the University of Bielefeld

  • Candidates should hold an excellent Master degree (or equivalent) in Bioinformatics, Computer Science, Mathematics, or a related area. They have to demonstrate broad background in the interdisciplinary field of bioinformatics in general, with a focus on computer science and deep knowledge in the area they apply for (see project descriptions for detailed requirements). As students must be able to communicate their work in the research training group, and have to quickly integrate into both the Bielefeld and Vancouver environment, good communication skills are demanded. Knowledge of the English language is required, whereas German is not necessary. Applications from suitably qualified handicapped and severely handicapped persons are explicitly encouraged.
  • Bielefeld University has received a number of awards for its achievements in the provision of equal opportunity and has been recognized as a family friendly university. The university welcomes applications from women. This is particularly true with regard both to academic and technical posts as well as positions in Information Technology and trades and crafts. Applications are handled according to the provisions of the state equal opportunity statutes.

[info title="Info message" icon="info-circle"]The application deadline is on Sunday, May 8, 2016 at midnight (any time zone).
Two to three weeks later, the most promising candidates will be invited to an application workshop, taking place at Bielefeld University in mid-June.[/info]

Application Instructions

  [content title=" Choose projects"]Within the general scope of the program, we offer several specific PhD projects you can apply for. Please choose up to three projects of your interest. You will have to enter their number in the application form (step 3 below).For the description of the projects including prospective supervisors, follow this link.[/content]
  [content title="Verify your interest in this program"]Now that you've read the project descriptions, you know better what our research program is about. Please also inform yourself about the qualification program and reconsider the requirements mentioned above: "Candidates [...] have to demonstrate broad background in the interdisciplinary field of bioinformatics in general, with a focus on computer science and deep knowledge in the area they apply for."Only if you think that you qualify for this program, proceed.[/content]
[content title="Complete the application form"]The following pdf form can be filled electronically, e.g., with Adobe Acrobat Reader:Application form[/content]

Provide further documents

[info title="Info message" icon="info-circle"]Your application has to contain the following documents. Do not send any documents other than the required ones.Include English or German translations of all official documents, in case the documents are neither in English nor German. (For the selection procedure, the translations do not need to be certified. In case you are selected for a position, you will have to provide certified translations.)[/info]
Letter of application:
  • Stating your motivation, qualification, main scientific experiences, and a brief outline of your current and future scientific interests (1 page).
Short tabular CV:
  • Data should be in tabular form, maximum 2 pages, including start and end dates (mm/yyyy) where applicable. List your personal information, contact details, languages, and all relevant secondary education, profession and trainings after leaving high school (college, Gymnasium etc.). Also include a list of all conferences you attended, your honors/prizes (e.g. scholarships), and your publications, including thesis (title), journal publications (citations only), conference talks (title and conference) and posters.
Transcript of records, including:
  • 1st university degree or intermediate examination (e.g. B.Sc., Vordiplom)
  • 2nd university degree (e.g. Master, Diploma), or intermediate results if in progress
  • if applicable: transcript of additional university degree(s)
Letters of recommendation:
  • Include two letters of recommendation from qualified referees (e.g. group leaders). For reasons of privacy, the letters can also be sent to us by the referees directly (to [email protected]).
Handicapped or severely handicapped persons should indicate this status on the application form and in the CV to be accounted for.

Submit your application

[info title="Info message" icon="info-circle"]All documents (including the form) have to be provided in a single PDF file not larger than 5MB.Send the PDF to [email protected] by May 08, 2016 (any time zone).(Applying via email is preferred. However, applications might also be sent by mail to: Bielefeld University, Faculty of Technology, Int. Research Training Group 1906 (DiDy), P.O. Box 10 01 31, 33501 Bielefeld, Germany.)Incomplete or incorrect applications will not be considered.If you have questions, contact: [email protected][/info]
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development in Africa

[fquote]The National Institutes of Health (USA) has committed 5 years of funding to the Bioinformatics Network of the Human Heredity and Health in Africa initiative. This pan-African network aims to develop capacity for bioinformatics research, in order to provide support to human health genomics research programs ongoing on the continent. Over the 5 years of funding, it is imperative to track changes in bioinformatics capacity at the funded centres and to document how the funding has translated into capacity development during this time frame.[/fquote]

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[slide] [item url="" src="" title="PhD @ The University of Luxembourg "]The University of Luxembourg has the following vacancy in its Systems Biology Group at the Life Sciences Research Unit, Faculty of Science, Technology and Communication:[/item] [item url="" src="" title="Two PhD positions in genetics/epigenetics/bioinformatics/statistics"]Two PhD positions are available, funded by the Norwegian Research Council. The studentships will be based in the Department of Medical Genetics, Oslo University Hospital and University of Oslo. We offer an excellent research infrastructure with very well equipped facilities.[/item] [item url="Image_Link_URL" src="" title="Doctoral student in computational biochemistry"]Research in the field of Biochemistry at Linnaeus University is carried out at the Department of Chemistry and Biomedical Sciences within the Faculty of Health and Life Sciences. We are interested in a wide range of research disciplines, including molecular interactions, enzymology, immunology, virology, plant molecular biology, chemistry and biomaterials.[/item] [item url="" src="" title="13 Fully Funded Ph.D. Student Positions"]13 fully funded Ph.D. student positions of the Research Training Group "3D Tissue Models for Studying Microbial Infections by Human Pathogens" (RTG 2157)[/item] [item url="v" src="" title="Bioinformatics Scientist"]Ph.D. candidate position in the area of single cell epigenomics. The project is based on the development of computational methods for analysis and integration of single cell ATAC-Seq, ChIP-Seq and RNA-Seq. This project will be performde in collaboration with stem cell specialists from the Medical Faculty and includes the analysis of in-house generated data.[/item] [/slide] [accordion] [item title=" PhD programs at Hannover Biomedical Research School"]To apply for the PhD programs at Hannover Biomedical Research School you first have to register. After registration you will receive an email including your activation hyperlink. By clicking on this hyperlink, you will confirm your registration and you will be able to logon to (link is external). Please note: if you had already applied to our HBRS in previous years, you need to create a new login/register new (new email, login, password)! The confirmation email should come at once. Recently we had difficulties with addresses like and, probably due to spam filters. Please let us know if you face problems. Follow the instructions during the application process and submit your application after you filled in all required fields. Please be aware, that you won't be able to edit your application after submission. As a part of the application you will have to choose two referees who will write a letter of recommendation on your behalf. Please ensure that the email of your referee is correct. The system will send a link and login to your referee, so that he/she will be able to directly fill in and upload the evaluation form to your application. You can submit your application even though references are not there yet. We accept the evaluations till April 11th.Read More[/item] [item title="2016 John Goldman Fellowships: Applications Invited"]We are pleased to invite applications for the 2016 John Goldman Fellowships. These prestigious awards have been created in honour of Professor John Goldman (1938 – 2013), a renowned haematologist, a pioneer in the treatment of leukaemia and founding Chairman of Leuka. The fellowship awards are aimed at those with a passion for science, a desire to develop new ideas and translate scientific advances into clinical practice.Read More[/item] [item title="Post Doctoral Research Fellow Patient Genomics Data Visualization"]A Postdoctoral Research Fellow position is available immediately to work on a collaborative project between the laboratory of Eric Holland and Hamid Bolouri in the Human Biology Division of the Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA. The postdoctoral fellow will join ongoing efforts under the auspices of the Solid Tumor Translational Research Initiative ( to develop data analysis and visualization methods for large-scale, molecularly-detailed, patient timeline data (see,, and Now[/item] [item title="IRB Barcelona International PhD Fellowships 2016"]3 PhD grants are offered for the academic year 2016-2017 within the “la Caixa”-Severo Ochoa International PhD Programme (herein referred to as “la Caixa”- Severo Ochoa Grants). Furthermore, 6 fellowships will be offered, these funded by the MINECO (“Ministerio de Economía y Competitividad”), through the “Contratos predoctorales Severo-Ochoa para la Formación de doctores” 2016 call.Read More[/item] [/accordion]

The Harvard Chan Bioinformatics Core

[fquote]The Harvard Chan Bioinformatics Core (HBC) acts as a center for bioinformatics research, services and training at the Harvard Chan School of Public Health. Integral to the Harvard Chan School, the Harvard Stem Cell Institute, the Harvard NeuroDiscovery Center and Harvard Medical School, our multi-disciplinary team works with researchers across the Harvard, MIT and Broad biomedical community, providing a comprehensive portfolio of infrastructure, data analysis, training and development. We seek an experienced computational biologist to become a key member of our team.[/fquote]

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held in Vashi

[fquote]Around 100 students from colleges in Mumbai, Thane and Navi Mumbai attended a two-day free workshop on Bioinformatics conducted by Indian Women Scientists Association in Vashi. The students gained theoretical and practical knowledge on Bioinformatics, which would help them with application of information technology and computer science into the field of biology. They were taught about sequence and molecular file formats, sequence alignment programs and 3D visualization tools. Students also participated in a practical session demonstrating designing of PCR primers for applications on Sunday.[/fquote]

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as a Bioinformatician 

[fquote]Patrick Gagné is innu. He is studying bioinformatics at Université Laval, and he is working at the Department of Natural Resources Canada. He shares his positive experience with the federal public service, in a position he obtained through the Federal Student Work Experience Program (FSWEP).[/fquote]
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[fquote] Since the birth of DNA sequencing in 1977, the technology has seen a drastic decrease in sequencing costs. Nowadays a human genome can be sequenced for as little as $1,000. Unfortunately, computers are not evolving as quickly. Lower cost, and hence greater scale of genomic sequencing, is producing enormous amounts of data, resulting in major central processing unit (CPU) and storage problems. Since manipulating such enormous data sets requires computational resources beyond the power of a standard computer, there are two ways to solve the problem.[/fquote]



[fquote]NGS 2016 Glasgow, the 3rd annual Next Generation Sequencing conference to take place in Scotland will be held on 27th & 28th April 2016 at the IET Teacher building in the heart of Glasgow city centre.  This event is held in partnership with NHS West of Scotland Genetics Service and the University of Glasgow’s Polyomics research facility.  In conjunction with the conference there will be a one day workshop on 26th April that will provide Next Generation Sequencing data analysis training to those working in the wetlab who want to be able to analyse the data and understand the data analysis workflows.[/fquote]

[tab] [content title="When"]CONFERENCE ON 27TH & 28TH APRIL WORKSHOP ON 26TH APRIL[/content] [content title="Where"]IET TEACHER BUILDING, GLASGOW [/content] [content title="SPEAKERS"]Prof Dame Janet Thornton, EMBL-EBI Prof Sir John Burn, International Centre for Life[/content] [content title="REGISTRATION"][/content] [/tab]
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MARI themes

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