ZENCODE-ITN

The scientific focus of the ZENCODE-ITN consortium is to understand genome regulation through combined experimental and computational approaches in a model vertebrate. The consortium recognises the urgent need for highly skilled young scientists trained in both computational biology and experimental wet lab biology. This network provides multi-disciplinary skills for a solid foundation in computational biology and developmental genomics.

We aim to comprehensively annotate functional epigenetic and transcribed elements, decipher genomic codes of transcription, as well as coding and non-coding gene function during vertebrate development and enhance zebrafish as an attractive developmental, comparative genomic and disease model. The participants include major zebrafish genomics laboratories, eminent computational biologists and world-class genomics technology experts.

The training program is designed for 15 ESRs, with more than 40 intersectoral and interdisciplinary secondments available, 7 training courses and 2 workshops/conferences. Through a trans-national network of public and private partners we aim to enhance the employability of the recruited ESRs through exposure to both academia and enterprise, thus extending the traditional academic research training setting and eliminating cultural and other barriers to mobility.

We aim to develop a cohort of Europe’s best young researchers to be, first and foremost, purposeful thinkers who aspire to solve a major scientific problem who will then translate this new understanding into solutions to medical needs.

There are two central aims.

• First, is to ensure that finished ESRs are highly skilled scientists: proficient in a variety of technologies and able to cross scientific disciplines.
• Second, is to ensure that ESRs acquire entrepreneurial aspirations coupled to the skills required to work across academia and industry and forge valuable links.

The ZENCODE-ITN Network Partners

• University of Birmingham, UK (Coordinator)
  Professor Ferenc Mueller
  Dr Aditi Kanhere
  
  
• Imperial College London, UK
  Dr Boris Lenhard
  
  
• Max Planck Institute, Münster, Germany
  Dr Juan M Vaquerizas
  vaquerizaslab.org
  
  
• Karolinska Instiutet, Stockholm, Sweden
  Dr Carsten O Daub
  Daub Lab
  
  
• King's College London, UK
  Dr Fiona Wardle
  Wardle Lab
  
  
• University of Liege, Belgium
  Dr Bernard Peers
  
  
• IDIBAPS, Barcelona, Spain
  Professor Jorge Ferrer
  Dr Josep Oriola
  idibaps.org
  
  
• Karlsruhe Institute of Technologie, Germany
  Professor Uwe Straehle
  Dr Robert Geisler
  
  
• Riken, Yokohama, Japan
  Dr Piero Carninci
  
  
• BGI Europe / University of Copenhagen, Denmark
  Dr Guojie Zhang
  Professor Albin Sandelin
  bgitechsolutions.com
  
  
• ZFIN, Oregon, USA
  www.zfin.org

Claudia Dominguez Valls

I was born in Barcelona, Spain where I studied Biology at the University of Barcelona and got my specialization in Biomedical sciences. Before finishing my Degree, I obtained an international exchange scholarship to perform an internship at University of Chile where I joined the research group of Prof. Julio Alcayaga in the laboratory of Cellular Physiology and Neurobiology. After graduating, I continued working in the Lab for 2 years evaluating the effect of hypoxia in petrosal ganglion neurons in rabbit. In September 2013, I started my master in Genetics and Genomics at the University of Barcelona. During my M.Sc. thesis I studied the effect of Juvenile Hormone on Insulin-Like peptides (ILPs) expression levels in Blatella germanica in the laboratory of Dr. Jose Luis Maestro situated in the Institut de Biología Evolutiva (IBE),CSIC-UPF, in Barcelona, Spain.

In September 2015, I joined the ZENCODE Marie Curie Initial Training Network as a Early Stage Researcher. I am pursuing my PhD at Zebrafish Development and Disease Model (ZDDM) Lab in GIGA at Université de Liège (Belgium). Under the supervision of Dr. Bernard Peers, the main goal of my PhD is to study the transcriptomic and epigenomic modifications of pancreatic beta and alpha cells in response to the metabolic status in Zebrafish.

Ana Lopez

I grew up in Alfaro, a town in the north of Spain. I always was interested in Sciences, so when I was 18 I decided to move to Pamplona to study Biology and Biochemistry at University of Navarra. During the first year they offered us the opportunity to obtain a Diploma in Bioinformatics and I decided to do it. I spent 6 years purchasing these three degrees at Pamplona. Besides, I decided to be involved in the Erasmus network and I did the 5th year in Rome, at La Sapienza University. When I finished all my degrees, I decided to do a master, so I moved to London. I spent one year there obtaining my MSc in Applied Biosciences and Biotechnology at Imperial College London. During that year I decided to continue my career in research in something related to the developmental biology. Last September, I started my PhD at GIGA Research Center that belong to the University of Liège (Belgium).

My project is focused on the analysis of the transcriptome and epigenome of the zebrafish embryonic endodermal cells during their specification towards a pancreatic fate. Incubation of zebrafish gastrulae with retinoic acid drives endodermal cells mostly into a pancreatic or hepatic fate. Inversely, incubation of zebrafish gastrulae with the RA antagonist BMS493 triggers anterior endoderm and blocks pancreatic and hepatic fate. I will use this tricks to analyze the modifications of the transcriptome and epigenome during the specification of endodermal cells towards mid-truck identity fate.

Andrea Mariossi

Originally from Italy, Andrea completed his marine biology Masters degree at the University of Padova in 2014. He focused on aquatic toxicology and ecotoxicology and during his final year he studied the effects of different pollutants on detoxifying systems and antioxidant defense systems in three-spined stickleback in Joachim Sturve’s lab at university of Gothenburg. After graduating he won a Leonardo da Vinci scholarship under the Project Unipharma Graduates 10 and spent six months at the Institute of Ecopreneurship (FHNW) where he focused on identification of proteins involved in the degradation of sulfonamides antibiotics by Microbacterium strain BR1. Following the completion of the placement, he started his PhD at King's College London under the ZENCODE-ITN programme, studying transcriptional regulation during endoderm formation in zebrafish applying next-generation sequencing techniques. The focus is on the network of genes downstream of the Sox family members, Sox32 and Sox17, ChIP-seq will identify sites of transcriptions factors binding and histone modifications and RNA-seq will profile gene expression levels. Integration of the different data will help understand the relationship of DNA elements and their protein regulators and how they work in conjunction during different stages of zebrafish development.

The main objective of the project is to identify direct targets of key Sox family members, Sox32 and Sox17, during endoderm formation in zebrafish. ChIP-seq will identify sites of transcriptions factors binding and histone modifications and RNA-seq will profile gene expression levels. Integration of the different data will help understand the relationship of DNA elements and their protein regulators and how they work in conjunction during different stages of zebrafish development.

Swarnima Joshi

Presently I am employed as a PhD student (ZENCODE-ITN) in Karlsruhe Institute of Technology, Germany. My research focuses on characterizing different zebrafish mobility mutants. Mutated zebrafish strains will also be examined by genome sequencing to identify the mutation leading to the observed phenotype, further the examination will be done to elucidate the role of the mutated gene during zebrafish development. I obtained my master degree in Molecular biology and biotechnology from Vytautas Magnus University, Lithuania. Erasmus+ EU programme gave me an opportunity to go to Julius Maximillian’s university of Wuerzburg, Germany where I did my master thesis entitled Microscopic analysis of serotonergic input onto the Mauthner neuron in Zebrafish brain. I did my bachelors in Pharmaceutical Sciences from Banasthali University, India.

Sanamjeet Virdi

Joined Prof. Straehle group as a PhD student in Institute of toxicology and genetics at KIT in October 2015. Currently pursuing research on the topic of development of a pipeline for identification of mutations in ENU mutants in Zebrafish. Graduated as Master of Science in Bioinformatics from University of Tampere, Finland, in October 2014. Master’s thesis was on Mutational analysis of non-coding genome in Prostate Cancer using whole genome sequencing under the supervision of Prof. Matti Nykter. Previous education includes a Bachelor of Engineering from Panjab University, Chandigarh, India in Biotechnology. Research technique expertise consists of analyzing next generation sequencing data (WGS) using various open source tools and ability to work on other types DNA or protein sequences data using Python and R.

The aim of my project is to focus on development of a software pipeline for data analysis, and validating it by sequencing of 3 previously uncharacterized myogenesis mutants which mimic myopathies and neuropathies of humans. The identified mutations will be further characterized by transcriptional profiling using RNA sequencing. Confirmation of the results by biological means will be performed in collaboration with researchers working on myogenesis mutations in the laboratory of Prof. Uwe Strähle.

Sanjana Pillay

I have a Master’s in Biotechnology. Before joining the University of Birmingham, as an Early Stage Researcher, I worked as a research fellow in CSIR- Institute of Genomics & Integrative Biology, Delhi (India) for two years. There, my study focussed on the role of DNA methylation on gene expression and it’s impact on disease development. My stay at CSIR-IGIB has given me a first hand introduction to cutting-edge research like Next Generation Sequencing. I worked on some excellent projects and been part of scientific discussions which have lead to my overall development as an effective researcher. My project here at Birmingham focusses on the role of non-coding RNA’s in zebrafish development. Non-coding RNAs (ncRNAs) have been shown to be involved in chromatin modification, cell fate determination and X chromosome inactivation. A few of them have been shown to play a role in regulating the expression of the protein coding genes. However the function of vast majority of these ncRNAs still remains unknown. Our aim will be to identify ncRNA’s association and modification of chromatin and study their function in regulating the expression of protein coding genes during different developmental stages in zebrafish.

Apart from being a hardworking person, I interest myself in reading all kinds of books, mostly intellectual, which helps in my overall growth as a person. Traveling is my other passion and I welcome the opportunity to work with people from all kinds of cultures. 

Goutham Atla

I have a bachelor’s degree in Pharmacy and masters degree in "Pharmacoinformatics" from National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, India. During my master's degree, I have studied bioinformatics along with the computational approaches for drug discovery. I learned the computational techniques for analyzing the High Throughput Sequencing data during my stay as a Bioinformatics Associate at Centre for Cellular and Molecular Platforms (C-CAMP) @ NCBS, Bangalore India. I joined Prof. Jorge Ferrer's lab at IDIBAPS, Barcelona, Spain with an aim of understanding the human genome regulation in diabetes.

Genome regulation in insulin producing pancreatic islet cells is central for our understanding of human diabetes. My focus in Zencode-ITN project is to use the high throughput sequencing data in a panel of human islet samples exposed to different glucose concentrations and employ integrative analysis to show how environmental and genetic factors modulate promoter usage. Other sub projects includes understanding the role of regulatory sequence variants in diabetes and understanding how regulatory defects can impact 3D chromosomal structure and gene transcription in human islets. I will use the Zebrafish as a model organism to validate the findings.

Abdul Kadir Mukarram

I am a PhD student in the research group of Carsten O. Daub at Karolinska Institutet, Sweden. My research focus is mainly in the area of genome annotation and comparative genomics to strengthen zebrafish as an attractive model organism to answer medically relevant problems in human. To achieve this goal, I will analyse and integrate various next-generation sequencing data (including RNA-seq, ChIP-seq, CAGE, ATAC-seq and methylation data) of zebrafish and relate them to corresponding genomic features in human. My educational background is Bachelor of Pharmacy from Airlangga University, Indonesia, followed by Master of Bioinformatics from University of Malaya, Malaysia.

Matthias Hörtenhuber

Before coming to Sweden, I studied mathematics as well as biomedical engineering in Vienna, Austria. As I liked the analytical approach in mathematics and the cell biological aspect in biomedical engineering, bioinformatics became the next logical step. Besides investigating the genome function using statistical methods, I am also interested in visualizations as a discovery tool for bioinformaticians as well as non-bioinformaticians.

My project is split into two parts. The first one consists of developing a zebrafish genome database (available at danio-code.zfin.org), including its database schema, data input design, data views/visualizations and genome annotation. In the second part I use this platform to study gene regulation in early developmental stages and compare it to human data.

Benjamin Hernandez

I have a strong interest in the function and structure of the genome. Specifically, in the regulation of the genomic activity that takes place during embryonic development, which in an extraordinarily organized and robust fashion ensures the coordinated arousal of entirely different cell types from a yet common genetic background.

I am under the supervision of Dr. Juan M. Vaquerizas at the Max Planck Institute for Molecular Biomedicine. As part of the ZENCODE network, I currently analyze the extent and functionality of monoallelic gene expression during the early stages of embryonic development.

Dunja Vucenovic

I am a PhD candidate in the Computational Regulatory Genomics group at Imperial College London, UK. Before starting my studies here, I carried out both my undergraduate and M.Sc. degrees in Molecular Biology at The Faculty of Science, Croatia. For a long time I have been interested in computational biology, and it was this interest which initially led me to take part in a project aimed at characterising the mechanisms of formation and evolution of chimeric transcripts. Following on from this, I became interested in the interplay of different OMICs technologies; due to their ability to assemble a range of information formats into a single picture, overall affording us a better understanding of disease. This underlying concept formed the foundation of my my Master’s thesis - where I used genomic, epigenomic and glycomic data from 4000 patients in an attempt to identify potential biomarkers of lower-back pain.

Being able to meet likeminded people, pursue my interests, learn a lot and apply gained knowledge, I am looking forward to the three-year research training within the ZENCODE-ITN.

Fabio D'Orazio

I am a PhD student in the Ferenc Muller's group based at the University of Birmingham. Previously, I have got a Bachelor's degree in Biotechnology and a Master's degree in Molecular Biology (2010-2015) at the University of Rome Tor Vergata. During my Diploma thesis I worked in Francois Spitz's lab at EMBL in Heidelberg, where I focused on enhancer-promoter interactions by studying a mouse genetic disease. This experience allowed me to develop a strong interest in how histone modifications and chromatin architecture can influence gene expression. For these reasons, I decided to pursue my postgraduate studies in the field of epigenetics, by joining my current group.

Within the ZENCODE network, my project aims to better understand the mechanisms behind the flow of information through zebrafish generations

Michael Dong

As a Bioinformatics Technician, I will be involved in the collection and annotation of ZENCODE-ITN genomics and transcriptomics datasets as well as their storage in databases. These datasets will be quality controlled, structured, annotated and shared in the consortium and ultimately opened to the public. I will also be involved in the development and maintenance of the database and the web interface related to this project.The final objective of this project is to produce a web resource of immediate utility in the domain of comparative genomics, presenting zebrafish as a “bench mark” research model to study vertebrates, giving a new point of view to human disease-based researches.

Quirze Rovira

As a biologist interested in all kinds of ‘omics' data I am interested in approaches that shorten the bridge that connects Life Science and Bioinformatics. To contribute in filling in that gap, I studied a Master Degree in Bioinformatics in the Autonomous University of Barcelona.

My research interest is focused on the study of mobile elements in the genome. I was first introduced to transposable elements (TEs) as a research topic in the Institute of Evolutionary Biology (IBE-CSIC-UPF) under the supervision of Josefa Gonzalez, where I studied the TEs related to stress response in fruit fly genome. Afterwards, I moved to the lab of Manuel Irimia in the Center for Genomic Regulation (CRG) to study the role of TEs in the regulation of alternative splicing during early development stages of mammalian genomes.

Within ZENCODE-ITN I aim to characterise regulatory mechanisms involved in the control of TEs expression in the zebrafish genome. To explore this interesting biological challenge, I’ve joined the lab of Dr. Juanma Vaquerizas at the Max Plank Institute for Molecular Biomedicine in Münster, where I’ll be using different next generation sequencing data.

Amanda Evans

I have a bachelor’s degree in biomedical sciences with an honours specialization in Microbiology and Immunology from the University of Western Ontario, Canada. There I completed my undergraduate thesis project developing a bead-based model in vitro assay to study the signalling pathway of phagocytic receptor CD16A using fluorescent microscopy. Continuing at the University of Western Ontario, I completed my Master’s degree in Microbiology and Immunology with a specialization in Molecular Imaging. In my project, I identified two rapidly adapting domains through bioinformatic analysis in phagocytic receptor MERTK, and used in vitro assays to demonstrate this rapid adaption to be a form of antagonistic coevolution to evade viral hijacking by enveloped viruses such as Ebola. Apart from my education, I worked as a research assistant throughout my undergraduate degree in a physiology and pharmacology laboratory focusing on G protein signalling, and an immunology laboratory studying phagocytes. I also completed a co-op placement at the London Regional Cancer Program in a laboratory studying prostate cancer metastasis using in vivo imaging of avian embryo models.

The main objectives of my project at King’s College London are to develop a low cell ChIP-seq method to enable identification of regulatory elements involved in zebrafish endoderm development, and develop a single cell CAGE method using developing zebrafish to enable TSS-based promoter reconstruction.

I have a Bachelors in Biological Sciences from Hunter College in New York. I studied organic chemistry at Yale University for two semesters. I also have a background in preclinical medicine.

My research interests span several areas, from computational to experimental biology. I am interested in algorithmic approaches for integrative analysis of NGS data, but also in epigenomics and the role of enhancers during development and aging.

Final Meeting 28th-31st October 2018

The ZENCODE-ITN final meeting was held in the beautiful surroundings of Cape Sounio, Greece. The three day conference proved very successful with esteemed invited speakers, Pi's and ESRs attending and presenting as well as fun social activities and dinners, all thoroughly enjoyed by everyone. 

AT7 Barcelona May 7th - 8th 2018

Hosted by Hospital Clinic de Barcelona, the goal of ATC7 was to 'Understand how genome sequencing is being used in practical clinical setting'

A two-day workshop in Barcelona with external speakers, the workshop also featured a visit to the Centro Nacional de Análisis Genómico-Centro de Regulación Genómica (CNAG-CRG), an SB meeting where all PI's attended, network/poster session and an evening social where all PIs and ESRs joined in.

ATC6 27th Nov - 1st Dec 2017

Hosted by the King’s and the Imperial Colleges, ATCs 6 was held in London.

The event spread over five days, with the main goal of training the ESRs on both transferable skills and Next-Generation-Sequencing data analysis.

As part of the training, the ESRs have faced with the challenge of introducing a motivated group of high school students to some aspects of medical research and the importance of model organisms. Applied science has revealed of great interest for the teenagers who got engaged with enthusiasm and fun!

The week finished on a more technical note with in depth training of RNA-seq data analysis.

Gene-Regulatory Systems in Development 27th-29th March 2017, Carmona, Spain

Our jointly organised conference with fellow ITN project DevCom proved a great success. Set in the beautiful town of Carmona, just outside Seville in Spain. It created a beautiful backdrop for an interesting and fruitful conference that all our students were able to attend and take part in the poster session. Invaluable time was spent networking with prominent invited speakers and a session with the editor of Nat Genet was another highlight for our group.

ATC4&5 and Mid-Term Review Meeting 11th-13th Jan 2017

Our 3rd training event (ChIP-seq and MedIP-seq analysis; organised by MPI, Imperial) was held in Munster, Germany, hosted by the Max Planck Institute. Arranged over 3 days it also incorporated our Mid-Term Review Meeting where all the ESRs presented updates on their projects, along with some background information for our EU project Officer and reviewer. Social events included a tour of Munster and two evening dinners, all very much enjoyed by our ESRs and Pi's.

ATC2&3 25th April-5th May 2016, Liege, Belgium

Our second training event ATC2/3 took place at the University of GIGA in Liege, Belgum. 14 ZENCODE PhD students, from Japan, Sweden, Germany, England, Spain and Belgium, attended the 2 weeks training course on the CAGE-seq and ChIP-seq technologies. A Network and Supervisory Board meeting was also held on the last day where all students presented updates on their projects so far and plans for the future. 

ATC1 19th-21st Oct 2015, Kidderminster, UK

ATC1 Network Meeting 19th-21st October 2015The first ZENCODE Network and training event took place in the wonderful, picturesque place of Bewdley, near Kidderminster at the Hotel Mercure.

Monday 19th Oct and Tuesday 20th Oct focused on student training events (basic computational biology) and then Wed 21st Oct, the PIs introduced their labs to the students followed by a social in the afternoon/evening. There was also an advisory board meeting to discuss matters of the network.

The last day of the meeting took place at the stunning Spring Grove House, Safari Park, Kidderminster.

DANIO-CODE is an international collaborative effort that aims to annotate the functional elements of the zebrafish genome.

Zebrafish are increasingly used to successfully model human disease, to screen drugs and to study environmental toxicity in addition to being a model for embryonic development. Zebrafish genome is the third most complete but further annotation is essential to better realize the power of this model organism in diverse areas of biomedical research and to further strengthen its role in biomedical research.

DANIO-CODE partners work together to provide a central resource of publicly available data and genome annotation of the zebrafish genome. DANIO-CODE combines a large variety of genome wide datasets including protein-coding and non-coding transcribed genome elements, non-coding functional elements such as cis-regulatory modules and associated epigenetic features.

DANIO-CODE was established at a workshop held in Imperial College London in December 2014 (see meeting report published in Zebrafish) where members of the zebrafish genomics research community and previous contributors to ENCODE and FANTOM genome annotation projects identified key aims.

Key Links:

Data Co-ordination Centre

This WIKI provides up-to-date information about the status of DANIO-CODE activities, guide documents and forum for discussion. The WIKI is managed by Anne Eagle at ZFIN

Newsgroup email address

By registering at the WIKI, members will access the DANIO-CODE email server and newsgroup with the danio-code@zfin.org address

Data Annotation Jamboree, University of Liege, Belgium, 6th May 2016

Video recordings of Data Annotation Jamboree 6th May 2016

DANIO-CODE DCC Upload Tutorial by Matthias Hörtenhuber

Sequence Conservation Analysis by ANCORA by Boris Lenhard

Considerations for the Integration of Zebrafish Gene Expression Database with Genomics Datasets by Dunja Vucenovic

Danio-Code in the light of modENCODE by Ben Brown

Considerations for the publication of the first DANIO-CDE by Carsten Daub

Towards a first publication of a DANIO-CODE by Ferenc Mueller

Introduction of the DANIO-CODE Data Coordination Centre by Carsten Daub

DanioPeaks: Computational analysis Resource for DANIO-CODE by Boris Lenhard

Introduction to the International Consortium Effort, DANIO-CODE by Ferenc Mueller

Professor Ferenc Mueller - ZENCODE-ITN Coordinator

Professor of Developmental Genetics
Department of Cancer and Genomic Sciences
College of Medicine and Health
Edgbaston
Birmingham, B15 2TT
UK

Tel: +44 (0)121 414 2895
Email: f.mueller@bham.ac.uk