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.

APPLY TO THE INTERNATIONAL PHD PROGRAMME

[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. 
[/info]

PHD PROJECTS OFFERED - IPP SUMMER CALL 2016

  • 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.

ELIGIBILITY

  • 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. 

[slide] [item url="https://www.imb-mainz.de/students-postdocs/international-phd-programme/" src="http://i.imgur.com/THKjAKN.png" [/item] [item url="https://www.imb-mainz.de/students-postdocs/international-phd-programme/" src="http://i.imgur.com/HXCrukO.png" [/item] [item url="https://www.imb-mainz.de/students-postdocs/international-phd-programme/" src="http://i.imgur.com/RdB0UFE.png" [/item] [/slide]

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: www.wiley.com/go/pevsnerbioinformatics.
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.
     
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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.

Syllabus

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

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Overview 

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.

Audience

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.

Outcomes

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
Read More

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 (https://bioconductor.org/packages/GenVisR) under GPLv3. Support is available via GitHub (https://github.com/griffithlab/GenVisR/issues) 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.
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

[vtab]
  [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]
[/vtab]

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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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
















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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MARI themes

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