Blog News from ecSeq


Bringing the power of Big Data to biomedical researchers


Posted on July 28, 2017


Great article about ecSeq Bioinformatics's work and vision in the current issue of 'Healthcare Journal of Baton Rouge'. Thanks to Dr. Claudia S. Copeland (LinkedIn Profile) for this understandable article about a very complex topic


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NGS Data Analysis Workshop, June 2017


Posted on June 30, 2017


btS Logo

Our workshop “Next-Generation Sequencing Data Analysis: A Practical Introduction” in Frankfurt this week was a full success. Our two trainers gave the 18 participants from 7 different countries (Germany, Croatia, South Korea, Netherlands, Israel, Czech Republik and Finland) an introduction on how to work with linux and how to handle RNA-Seq and DNA-Seq data correctly. The gained knowledge will allow the researchers to start their own analyses and it will help them to discuss their bioinformatics problems or questions with bioinformaticians on an almost equal level.


UPCOMING NGS DATA ANALYSIS WORKSHOPS:

1st Berlin Summer School in NGS Data Analysis

  • Date: September 11 - 15, 2017
  • Location: Berlin, Germany

RNA-Seq Data Analysis Workshop

  • Date: October 9 - 12, 2017
  • Location: Leipzig, Germany

Metagenomics Analysis with MEGAN6

  • Date: October 17 - 19, 2017
  • Location: Frankfurt, Germany

DNA Methylation Data Analysis

  • Date: November 29 - December 1, 2017
  • Location: Berlin, Germany

Next-Generation Sequencing Data Analysis: A Practical Introduction

  • Date: December 6 - 8, 2017
  • Location: Munich, Germany


Additional RNA-Seq Course 2017


Posted on June 29, 2017


Additional RNA-Seq Course in October 2017

Due to an extraordinary run on our "1st Berlin Summer School" in September in Berlin and an astounding long waiting list, we decided to offer an additional RNA-Seq course with almost the same topics in October in Leipzig.


RNA-Seq Data Analysis Workshop

  • Date: October 9 - 12, 2017
  • Location: Leipzig, Germany


RNA-Seq Data Analysis in Leipzig, Germany


NGS Data Analysis Workshop, May 2017


Posted on May 11, 2017


btS Logo

Our workshop “Next-Generation Sequencing Data Analysis: A Practical Introduction” in Munich last week was a full success. Our two trainers gave the 20 participants from 8 different countries (Germany, USA, Saudi Arabia, UK, Romania, Belgium, Slovenia and Turkey) an introduction on how to work with linux and how to analyze RNA-Seq and DNA-Seq data correctly. The gained knowledge will allow the researchers to start their own analyses and it will help them to discuss their bioinformatics problems or questions with bioinformaticians on an almost equal level.


UPCOMING NGS DATA ANALYSIS WORKSHOPS:

Next-Generation Sequencing Data Analysis: A Practical Introduction

  • Date: June 26 - 28, 2017
  • Location: Frankfurt, Germany

1st Berlin Summer School in NGS Data Analysis

  • Date: September 11 - 15, 2017
  • Location: Berlin, Germany

Metagenomics Analysis with MEGAN6

  • Date: October 17 - 19, 2017
  • Location: Frankfurt, Germany

DNA Methylation Data Analysis

  • Date: November 29 - December 1, 2017
  • Location: Berlin, Germany

Next-Generation Sequencing Data Analysis: A Practical Introduction

  • Date: December 6 - 8, 2017
  • Location: Munich, Germany


Five Year Anniversary


Posted on April 15, 2017


CELEBRATING OUR 5TH YEAR ANNIVERSARY TODAY!

Today marks 5 years exactly that ecSeq Bioinformatics entered the highly competitive and innovative world of life sciences. In the last 5 years we have learned a lot, shared a lot, taught a lot and built a lot. We have seen substantial growth take place with the sequencing technology. We truly believe this technology and industry will develop rapidly in the coming years.

We have had the pleasure of working with some amazing clients, building great solutions and relationships that extend well beyond typical client/contractor engagements. We also want to send a special shout out to our sequencing partners who give us a much needed helping hand to deliver high quality solutions for our clients.

We have some exciting things in the works for the remainder of the year, so stay tuned. As we continue our journey, we are excited to see what the next 5 years and beyond will bring.


Five Year Anniversary


RNA-Seq Data Analysis Workshop, March 2017


Posted on March 25, 2017


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Our workshop “RNA-Seq Data Analysis Workshop: Quality Control, Read Mapping, Visualization and Downstream Analyses” in Berlin last week was a full success. Our three trainers gave the 25 participants from 11 different countries (Germany, USA, Qatar, Netherlands, Hungary, Belgium, China, United Kingdom, Poland, Croatia and Italy) an introduction on how to work with linux and how to analyze RNA-Seq data correctly. The gained knowledge will allow the researchers to start their own analyses and it will help them to discuss their bioinformatics problems or questions with bioinformaticians on an almost equal level.


UPCOMING NGS DATA ANALYSIS WORKSHOPS:

Next-Generation Sequencing Data Analysis: A Practical Introduction

  • Date: June 26 - 28, 2017
  • Location: Frankfurt, Germany

1st Berlin Summer School in NGS Data Analysis

  • Date: September 11 - 15, 2017
  • Location: Berlin, Germany

Next-Generation Sequencing Data Analysis: A Practical Introduction

  • Date: December 6 - 8, 2017
  • Location: Munich, Germany


Joint project with Fraunhofer IME


Posted on February 08, 2017


dandelion

Rubber from dandelions

In recent years the Russian dandelion Taraxacum koksaghyz, a previously neglected wild plant, has been investigated to be re-introduced as a valuable rubber crop that grows in moderate climates, like in Germany. The milky sap of the dandelion shows similarities to that of the rubber tree, and most importantly contains caoutchouc, the raw material for rubber production.

Together with the Fraunhofer Institute for Molecular Biology and Applied Ecology IME, ESKUSA GmbH and hortilab, ecSeq GmbH will generate a high-resolution genetic map of Russian dandelion.


Christian Schulze Gronover

Dr. Christian Schulze Gronover (Fraunhofer IME) received the 2015 Joseph von Fraunhofer Prize for his work on the Russian dandelion and its application as a source of natural rubber. He is the coordinator of the project, which is funded by the German Federal Ministry of Education and Research (BMBF).


Fred Eickmeyer

Dr. Fred Eickmeyer (ESKUSA GmbH) specialized on breeding of dandelion. He wants to optimize and establish Russian dandelion to an alternative raw material for natural rubber.

sponsored by BMBF

Cooperation Agreement with Emmanuelle Charpentier's Laboratory


Posted on February 01, 2017


Today we signed a cooperation agreement with Prof. Dr. Emmanuelle Charpentier.

We are looking forward to this great partnership.


Prof. Dr. Emmanuelle Charpentiers

Prof. Dr. Emmanuelle Charpentier is best known for her role in deciphering the molecular mechanisms of the bacterial CRISPR-Cas9 immune system and repurposing it into a tool for genome editing. In particular she uncovered the mechanism beyond the maturation of non-coding RNA key for the CRISPR-Cas9 function. In collaboration with Jennifer Doudna's laboratory, Charpentier's laboratory showed that Cas9 could be used to make cuts in any DNA sequence desired. The method they developed involved the combination of Cas9 with easily created synthetic "guide RNA" molecules. Researchers worldwide have employed this method successfully to edit the DNA sequences of plants, animals, and laboratory cell lines.




Sources: Picture and text from wikipedia.org; Video from youtube.com (DFG channel)


Outstanding research - New macromolecule with influence on Burkitt lymphoma detected


Posted on January 27, 2017


Dr. Gero Doose

Dr. Gero Doose is head of research and development at ecSeq GmbH. He developed RNA folding and protein solubility prediction algorithms before he started working with high-throughput sequencing data. Gero implemented detection pipelines for circularized and trans-spliced transcripts. As an expert for split-read alignment analysis, he also developed a sophisticated method to detect differential alternative splicing.


PNAS
Outstanding Research


The transcription factor MYC plays a key role in carcinogenesis. Together with scientists around Dr. Ingram Iaccarino (Christian Albrechts University) and Dr. Dr. Steve Hoffmann (University of Leipzig), Dr. Doose discovered a long non-coding RNA that is able to modulate MYC’s transcriptional network. This finding therefore has the potential to open new therapeutic opportunities for MYC associated cancers. The results were published in the renowned journal “Proceeding of the National Academy of Science of the United States of America” (PNAS).



Reference:

Doose G, Haake A, Bernhart SH, López C, Duggimpudi S, Wojciech F, Bergmann AK, Borkhardt A, Burkhardt B, Claviez A, Dimitrova L, Haas S, Hoell JI, Hummel M, Karsch D, Klapper W, Kleo K, Kretzmer H, Kreuz M, Küppers R, Lawerenz C, Lenze D, Loeffler M, Mantovani-Löffler L, Möller P, Ott G, Richter J, Rohde M, Rosenstiel P, Rosenwald A, Schilhabel M, Schneider M, Scholz I, Stilgenbauer S, Stunnenberg HG, Szczepanowski M, Trümper L, Weniger MA; ICGC MMML-Seq Consortium, Hoffmann S, Siebert R, Iaccarino I: 'MINCR is a MYC-induced lncRNA able to modulate MYCs transcriptional network in Burkitt lymphoma cells'. PNAS, 112(38):E5261-70. (2015)




Next-Generation Sequencing Data Analysis: A Practical Introduction, December 2016


Posted on December 13, 2016


btS Logo

Our workshop “Next-Generation Sequencing Data Analysis: A Practical Introduction” in Munich last week was a full success. Our two trainers gave the twenty participants from eight different countries an introduction on how to work with linux and how to analyze NGS data correctly. The gained knowledge will allow the researchers to start their own analyses and it will help them to discuss their bioinformatics problems or questions with bioinformaticians on an almost equal level.


UPCOMING NGS DATA ANALYSIS WORKSHOP:

RNA-Seq Data Analysis Workshop

  • Date: March 21 - 24, 2017
  • Location: Berlin, Germany

Please find detailed information and a course program on the workshop's page.



Keynote at bionection 2016 in Halle (Saale)


Posted on September 23, 2016


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bionection is an international event for technology transfer in life sciences. Thus, participants from industry and academia will present and discuss their latest inventions in this hot research field. The venerable Leopoldina provides an amazing scene for inspiring discussions, extraordinary thoughts and exchange of innovative ideas.

Besides Thermo Fischer and Thyssenkrupp Industrial Solutions, ecSeq’s CEO Dr. David Langenberger will be one of the three keynote speakers at the event. On the second day of the conference, David will talk about today's challenges in NGS bioinformatics. Our business area, NGS bioinformatics, fits very well into the overall aim of bionection, where the latest progress in medical and bio-technologies, as well as current questions in life sciences will be presented.

The German National Academy of Sciences was founded in 1652. Since then it is “dedicated to the advancement of science for the benefit of humankind and to the goal of shaping a better future”. ecSeq GmbH is honored to speak in such history-charged halls in Halle (Saale).


bionection Logo


Nature Genetics - DNA Methylome Analysis


Posted on September 15, 2016


Nature Genetics Cover

Great News:

The two trainers of our upcoming epigenomics workshop 'DNA Methylation Data Analysis' got their research work published in Nature Genetics.

Dr. Helene Kretzmer and Dr. Christian Otto identified differentially methylated regions in Burkitt and follicular lymphoma using exactly the bisulfite sequencing data analysis method that they will teach in the workshop.


Workshop:

22-25 November 2016 in Leipzig, Germany: DNA Methylation Data Analysis

Publication:

Kretzmer et al.: 'DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control', Nature Genetics (2015)


Helene Kretzmer     Dr. Helene Kretzmer (University Leipzig) is working on DNA methylation analyses using NGS since 2011. She is responsible for the bioinformatics analysis of the MMML-Seq study of the International Cancer Genome Consortium (ICGC).
 
Christian Otto     Dr. Christian Otto (CCR Bio-IT) is one of the developers of bisulfite read mapping tool segemehl and is an expert on implementing efficient algorithms for NGS data analysis.

ecSeq's NGS Experts


Posted on July 28, 2016


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Up-to-date expert knowledge is the key to generating impactful biological insights.

To address this unavoidable need, we established an extensive network of outstanding scientists, covering all research fields relevant to NGS. Together with a project-specific expert panel ('think tank'), we will analyze your data in a scientifically proven manner to provide you with meaningful, knowledge-driven results.

 

 

 

Go through the complete list of scientists and check the extraordinary experts in our expert-network:

btS Logo

   

Start a knowledge-driven project with ecSeq Bioinformatics


Please also check our upcoming workshops in fall 2016:


Next-Generation Sequencing Data Analysis: A Practical Introduction, June/July 2016


Posted on July 06, 2016


Group Picture

Our workshop “Next-Generation Sequencing Data Analysis: A Practical Introduction” in Munich two weeks ago was a full success. Our two trainers gave the twenty participants from nine different countries an introduction on how to work with linux and how to analyze NGS data correctly. The gained knowledge will allow the researchers to start their own analyses and it will help them to discuss their bioinformatics problems or questions with bioinformaticians on an almost equal level.

For everyone who was not able to attend we will organize a second workshop in December 2016. It will be at the same location in Munich and it will cover the exact same topics. Perfect for beginners.


UPCOMING NGS DATA ANALYSIS WORKSHOP:

Next-Generation Sequencing Data Analysis: A Practical Introduction

  • Date: December 7 - 9, 2016
  • Location: Munich, Germany

Please find detailed information and a course program on the workshop's page.


Besides this introduction course we have planned three more workshops in fall 2016:


Lab journal with a portrait of ecSeq GmbH


Posted on May 04, 2016


Loborjounral cover

We recently received a visit by Tobias Hoffmann, a journalist from the German "Laborjournal" (German for lab journal). In its latest issue (from May 2nd, 2016) ecSeq GmbH and its founders, Dr. David Langenberger and Dr. Mario Fasold, are portrayed in a double-page article.

The article talks about our two founders, how they gained their doctorates from professor Stadler in Leipzig and their way to ecSeq GmbH. One of our business areas are workshops which train the participants how to analyze NGS data. We want to impart a discretionary competence as well as evaluation skills with the courses. Public workshops take place in Munich, Berlin, Prague or Oxford with about one third of the participants having an industrial (non-academic) background. This knowledge is important because nowadays every research application contains NGS analyzes.

Secondly, Hoffmann introduces our network of 45 highly skilled NGS experts to the readers. During project consulting ecSeq GmbH accompanies NGS projects which require complex bioinformatics solutions. Customers can book nearly everything: the analyses, the software or the complete planning of an experiment. All NGS experts are working in the background together with ecSeq GmbH.

Of course, the author asks the follow up question: 'Why should customers approach ecSeq and not the experts directly?' The answer is pretty simple: 'Because academic researchers with their reservations are often not very open-minded about inquiries from companies.' With ecSeq GmbH as intermediary, a trustful and well-managed collaboration is possible. This separation of industry and academia is very important for both, the companies and the researchers in our network.

We thank the "Laborjournal" for this great introduction of our company! You can get your free copy of the "Laborjournal" at universities and research facilities or on their website.


Let's Talk About Starting Your Own Company - ecSeq at Life Sciences Career Day Dresden


Posted on April 26, 2016


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At the Life Sciences Career Day Dresden students from biology, biotechnology, biochemistry, medicine & pharmacy can get an impression about how their future could look like. We at ecSeq GmbH are very honored to represent the career path of a start-up company in the field of life sciences and to embold young scientists to realize their own ideas!

Deciding where to go after university is by far not trivial and has to be well thought out. Researchers have to realize that an academic career with the aim to get a professorship or the industrial path as an employee are not the only possibilities. We will explain and picture an interesting, but challenging middle course, the entrepreneurship. During our presentation we will tell the exciting story about starting our own company. We will describe how to turn the dream of a business into reality, talk about the initial period and finally, demonstrate how our daily work routine looks like. Afterwards, all upcoming questions will be answered.

The Life Science Career Day takes place on June 3rd, 2016 at the "Hörsaalzentrum" in Dresden, Germany.

It is organized by the biotechnology students initiative btS. We are looking forward to meet enthusiastic students who would like to discuss bioinformatics and its future with us.

These questions will be answered:

  • What is Next-Generation Sequencing?
  • What role does it already play in research and the daily clinical business?
  • Can a start-up in the field of NGS bioinformatics be successful?

Membership in life science cluster 'biosaxony'


Posted on April 01, 2016


Biosaxony Logo

It is always important to have a good network of partner corporations and institutes to learn from each other. To this end, ecSeq GmbH is now a member of biosaxony, the cluster of the biotechnology and life sciences sector in Saxony. The organization hosts projects with participating scientists and companies, provides its members useful services and know-how, has the aim to develop the branch and strengthens the business location Saxony. It combines members from areas of economy, science and politics like young start ups, universities, research institutes, municipalities as well as large-scale enterprises.

We are looking forward to an interesting exchange with the Saxon biotechnology network!


RNA Expert - Dr. Martin Smith


Posted on March 21, 2016


Dr. Martin Smith

We are very pleased to introduce Dr. Martin Smith as a member of our NGS Expert Network.

Dr. Martin Smith is a computational biologist with a strong background in biology. As a child he grew up in Canada and he always dreamt of becoming a biologist. He majored as an undergraduate in microbiology and immunology at the University of Montreal, but he quickly realised this wasn’t his field. Switching to the emerging field of bioinformatics was an enthusiastic yet challenging decision for him, as it required rewiring his brain around abstract informatics concepts and discrete mathematics.

To this day, he is very passionate about bioinformatics and would recommend a cross-disciplinary career path to anyone. He has worked in 5 different cities across 3 different continents, namely Montreal (University of Montreal); Quebec City (Infectious Disease Research Centre—CHUL); Brisbane (Institute for Molecular Bioscience); Leipzig (Interdisciplinary Center for Bioinformatics); and Sydney (Garvan). He received his doctorate in Genomics and Computational Biology from the University of Queensland in 2012. His doctor's thesis was supervised by Prof. Dr. John Mattick and Prof. Dr. Peter F. Stadler.

His research revolves around characterising the “regulome”, i.e. the biological mechanisms that control how genes are activated and repressed. He is particularly interested in how non-protein coding regions of the genome can regulate gene expression at the level of RNA.




Evaluation: Annual Survey - Public NGS Workshops


Posted on February 29, 2016


Feedback

Around the turn of the year (2015/2016), we asked the question:
What courses would you like us to prepare for 2016?

We analyzed all votes (~200 single votes) and below you can find the result of the survey. Based on your voting, we put together the following workshop agenda for 2016:

In February we already covered the following courses:



We thank all attendees! We hope that our agenda fits your expectations!



Assembly Expert - Dr. Alexander Donath


Posted on February 25, 2016


Dr. Alexander Donath

We are very pleased to introduce Dr. Alexander Donath as a member of our NGS Expert Network.

Dr. Alexander Donath is head of section for Computational Genomics at the Zoological Research Museum Alexander Koenig. Since 2011 he is working on NGS data analysis and de novo assembly of non-model organisms. He is involved in a number of large-scale transcriptome and genome research projects, for example 1KITE and i5k.


Assembly Workshop 2016

Besides being part of the NGS Expert Network, he also designed our hands-on workshop for de novo transcriptome analysis, which will cover assembly and differential gene expression analysis in non-model organisms.

September 28 - 30, 2016 in Leipzig, Germany
De Novo Transcriptome Analysis - Assembly and Differential Gene Expression


Outstanding Research

In 2014 Dr. Alexander Donath co-authored the Science paper Phylogenomics resolves the timing and pattern of insect evolution, which was honoured as a research highlight by Nature Reviews Genetics.

'... In this research, novel approaches were used to produce a robust phylogenomic tree of insects, which will now serve as a reference point for future research.' (Nature)

Science Magazine      '... The study authors, who are part of an international consortium working on the 1K Insect Transcriptome Evolution (1KITE) project, began their work in 2011 in hopes of using newly available sequencing technology to clarify insect relationships previously only investigated using morphological evidence or smaller molecular datasets. They sequenced transcriptomes from 103 insect species distributed across all living insect orders. They also drew data from previously published whole-genome sequences of 14 arthropod species, as well as from transcriptomes of 27 additional species. They then narrowed down their genetic data to 1,478 protein-coding genes that are present in all of the species analyzed. ...'
from TheScientist


Reference:
Bernhard Misof, Shanlin Liu, Karen Meusemann, Ralph S. Peters, Alexander Donath, Christoph Mayer, Paul B. Frandsen, Jessica Ware, Tomáš Flouri, Rolf G. Beutel, Oliver Niehuis, Malte Petersen, Fernando Izquierdo-Carrasco, Torsten Wappler, Jes Rust, Andre J. Aberer, Ulrike Aspöck, Horst Aspöck, Daniela Bartel, Alexander Blanke, Simon Berger, Alexander Böhm, Thomas R. Buckley, Brett Calcott, Junqing Chen, Frank Friedrich, Makiko Fukui, Mari Fujita, Carola Greve, Peter Grobe, Shengchang Gu, Ying Huang, Lars S. Jermiin, Akito Y. Kawahara, Lars Krogmann, Martin Kubiak, Robert Lanfear, Harald Letsch, Yiyuan Li, Zhenyu Li, Jiguang Li, Haorong Lu, Ryuichiro Machida, Yuta Mashimo, Pashalia Kapli, Duane D. McKenna, Guanliang Meng, Yasutaka Nakagaki, José Luis Navarrete-Heredia, Michael Ott, Yanxiang Ou, Günther Pass, Lars Podsiadlowski, Hans Pohl, Björn M. von Reumont, Kai Schütte, Kaoru Sekiya, Shota Shimizu, Adam Slipinski, Alexandros Stamatakis, Wenhui Song, Xu Su, Nikolaus U. Szucsich, Meihua Tan, Xuemei Tan, Min Tang, Jingbo Tang, Gerald Timelthaler, Shigekazu Tomizuka, Michelle Trautwein, Xiaoli Tong, Toshiki Uchifune, Manfred G. Walzl, Brian M. Wiegmann, Jeanne Wilbrandt, Benjamin Wipfler, Thomas K. F. Wong, Qiong Wu, Gengxiong Wu, Yinlong Xie, Shenzhou Yang, Qing Yang, David K. Yeates, Kazunori Yoshizawa, Qing Zhang, Rui Zhang, Wenwei Zhang, Yunhui Zhang, Jing Zhao, Chengran Zhou, Lili Zhou, Tanja Ziesmann, Shijie Zou, Yingrui Li, Xun Xu, Yong Zhang, Huanming Yang, Jian Wang, Jun Wang, Karl M. Kjer, Xin Zhou: 'Phylogenomics resolves the timing and pattern of insect evolution', Science 346 (6210): 763-767 (2014).

small RNA-Seq Expert - Prof. Dr. Manja Marz


Posted on January 19, 2016


Prof. Dr. Manja Marz

We are very pleased to introduce Prof. Dr. Manja Marz as a member of our NGS Expert Network.

Prof. Dr. Manja Marz studied biology and computer science at the University of Leipzig, and received her Ph.D. in bioinformatics from the University of Leipzig in 2009. After leading a Group at the Philipss-University of Marburg and Junior-Professorship at the Friedrich-Schiller-University Jena, she got two calls for professorships at University of Lübeck and Friedrich Schiller University Jena in 2014. Since 2015 she holds a full professorship at Friedrich Schiller University Jena. She is also Founding member of MSCJ (Michael Stifel Zentrum Jena for Data-Driven and Simulation Science), Board member of ZAJ (Aging Research Center Jena), Founding and board member of FIFI (Fördervereinverein des Instituts für Informatik) and Group leader at Leibniz Institute for Age Research – Fritz Lipmann Institute.

Her research interest include High Throughput Sequencing Analysis, Comparative Genomics, Identification and Annotation of Non-coding RNAs, Bioinformatic Analysis and System Biology of Viruses, Coevolution of Proteins and RNAs, Algorithmic Bioinformatics and Phylogenetic Analysis.



Happy New Year 2016


Posted on December 30, 2015


With 2015 coming to an end we can't help but feel a little nostalgic and look back at what the past twelve months have brought us. We couldn't be happier with what we do and we have all of you, our loyal customers to thank for our success.

During the past 360 or so days, we have been hard at work to train you in NGS data analysis and analyze your NGS data. We are extremely thankful for all the support and word-of-mouth advertising for our services.

We are all set for 2016 and can't wait to see what the New Year is going to bring to the NGS world.

Wishing you a Happy Holiday and a joyful New Year.
Best wishes from the complete team at ecSeq GmbH.


Feedback

Annual Survey - Public NGS Workshops


Posted on December 10, 2015


Feedback

This year, again, we offered several hands-on bioinformatics NGS workshops. We widened our range and went to different venues across Europe in order to make our service available to more and more interested researchers. Besides basic NGS introduction courses, we always try to extend our portfolio to cover further NGS applications.

Our question: What courses would you like us to prepare for 2016?


Fill out our survey today and win a 50% off voucher for one of our NGS workshops!


RNA-Seq Expert - Prof. Dr. Ivo Hofacker


Posted on November 04, 2015


Prof. Dr. Ivo Hofacker

We are very pleased to introduce Prof. Dr. Ivo Hofacker as a member of our NGS Expert Network.

Since 2010 Prof. Dr. Ivo Hofacker holds a double professorship at the faculties of Chemistry and Computer Science. He is currently head of the Research Group Bioinformatics and Computational Biology.

His scientific interests fit mostly under the computational biology umbrella. Much of his work focuses on RNA Bioinformatics, the most visible part perhaps being the Vienna RNA Package for prediction and comparison of RNA secondary structures, which he and his coworkers have developed for over 15 years.


Prof. Dr. Rolf Backofen

Conntect with us on Facebook


Posted on November 02, 2015


Meet us in Facebook

Check out our Facebook page and learn more about our products, our hands-on workshops, our research topics and our expertise in NGS data analysis. Share your ideas and stay conntected.

In our Facebook group 'Next-Generation Sequencing Data Analysis' you will learn about upcoming events, open jobs, and interesting information about the rapidly growing field of Next-Generation Sequencing. So connect with us and discover the world of ecSeq Bioinformatics.


Facebook

RNA-Seq Expert - Prof. Dr. Rolf Backofen


Posted on October 30, 2015


Prof. Dr. Rolf Backofen

We are very pleased to introduce Prof. Dr. Rolf Backofen as a member of our NGS Expert Network.

Prof. Dr. Rolf Backofen studied computer science at the University of Erlangen, and received his Ph.D. in computer science from the University of Saarland in December 1994, where he worked at the German Research Center for Artificial Intelligence (DFKI). He received his habilitation from the University Munich (LMU) in February 2000. He was holding the chair for bioinformatics at the University of Jena from November 2001 till June 2005. In 2004 he became the holder of the chair for Bioinformatics at the University of Freiburg, Institute of Computer Science.

His research interest include constraint programming, structure prediction in simplified protein models, investigation of protein energy landscapes, detection of RNA sequence/structure motifs, prediction and evaluation of alternative splice forms, description and detection of regulatory sequences.


Prof. Dr. Rolf Backofen

Nature Genetics - DNA Methylome Analysis


Posted on October 09, 2015


Nature Genetics Cover

Great News:

The two trainers of our upcoming epigenomics workshop 'DNA Methylation Data Analysis' got their research work published in Nature Genetics.

Helene Kretzmer and Dr. Christian Otto identified differentially methylated regions in Burkitt and follicular lymphoma using exactly the bisulfite sequencing data analysis method that they will teach in the workshop.


Workshop:

15-17 December 2015 in Leipzig, Germany: DNA Methylation Data Analysis

Publication:

Kretzmer et al.: 'DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control', Nature Genetics (2015)


Helene Kretzmer     Helene Kretzmer (University Leipzig) is working on DNA methylation analyses using NGS since 2011. She is responsible for the bioinformatics analysis of the MMML-Seq study of the International Cancer Genome Consortium (ICGC).
 
Christian Otto     Dr. Christian Otto (CCR Bio-IT) is one of the developers of bisulfite read mapping tool segemehl and is an expert on implementing efficient algorithms for NGS data analysis.

Introducing Knowledge-Driven NGS Solutions


Posted on September 16, 2015


Knowledge-Driven NGS Solutions

Nobody can be an expert in everything. However, biomedical projects increasingly demand expert knowledge in more than a single field. In fact, up-to-date expert knowledge is key to generating impactful biological insights.

To this end, we established an extensive network of outstanding scientists, covering various research fields relevant to NGS. The idea is that, together with the customer, we assemble a panel of experts that is able to develop an optimal strategy for the specific challenges of the project (see our white paper).

Our bioinformatics team can then rapidly implement a software solutions since we already have a library of analysis modules for many NGS applications.

Get more information here.


Enabling end-to-end NGS solutions through our partnership with AllGenetics


Posted on April 07, 2015


AllGenetics

We are now able to offer end-to-end analysis solutions for the NGS applications RNA-Seq, small-RNA-Seq, and DNA-seq. This includes essential steps from sample preparation and sequencing to extensive bioinformatics data analysis. This is enabled by our partnership with AllGenetics, a biotech company specialized in NGS research projects. Our partnership with AllGenetics ensures that projects can be completed smoothely and effectively from project design to data analysis.


Upcoming NGS Workshop in Prague, CZ


Posted on March 19, 2015


Workshop

We happily announce that the next NGS workshop will take place September 7-11 in Prague. The course entitled 'PRAGUE SUMMER SCHOOL - NEXT-GEN SEQ DATA ANALYSIS' spans a whole week and is organized by SEQme in cooperation with ecSeq Bioinformatics. The workshop specifically addresses the needs of beginners in the field of NGS bioinformatics.

Please click here to visit the workshop website.


Meet us at the Illumina User Group Meeting, EMBL


Posted on February 26, 2015


Illumina

The Illumina User Group Meeting (UGM) Central Europa is taking place on March 10-11 at the EMBL in Heidelberg, Germany. Dr. Mario Fasold will present new possibilities for bioinformatic analysis of RNA-seq data and also be available for discussions on the afternoon of March 11. Please contact us if you would like to schedule a meeting there.


Upcoming: NGS Workshop in Leipzig, Germany


Posted on November 27, 2014


Workshop

In March 2015 our NGS data analysis are again taking place in Leipzig. The workshop has been redesigned and adapted to the needs of beginners in the field of NGS bioinformatics. There are now two optional courses on RNA-seq data analysis (model and non-model organisms). Building on the knowledge covered in the main course allows us to cover the many relvant aspects of downstream RNA-seq analyses.

Link to the workshop page.


NGS Workshop at 'Programming for Evolutionary Biology' in Bogota, Colombia


Posted on October 29, 2014


evop

In this intensive course, students will learn how to survive in a Linux environment, get hands-on experience in two widely used programming languages (Perl and R), and statistical data analysis. The classes will be given by experts in the field and consist of lectures and exercises with the computer. The aim of the course is to provide the students with the necessary background and skills to perform computational analyses with a focus on solving research questions related to genomics and evolution. The philosophy of the course will be “learning by doing”, which means that the computational skills will be taught using examples and real data from evolutionary biology for the exercises. During the course, students will also propose projects of their own interest and perform them as final projects in small groups under the supervision of a teaching assistant. This November school the school goes to Colombia. It is open for students from all countries, but specially, from the Americas. It is mainly targeted toward PhD students, MSc students and Postdocs of evolutionary biology or related research fields with no or little programming experience who want to become proficient in computational evolutionary biology in a couple of weeks.

Link to the workshop page.


Upcoming: NGS Workshop in Oxford, UK


Posted on October 27, 2014


Workshop

The purpose of this workshop is to get a deeper understanding in Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discovered. The participants will be trained on understanding their own HTS data, finding potential problems/errors therein and finally performing their own analyses using open source tools. In the course we will use a RNA-seq dataset from the current market leader, Illumina.

Link to the workshop page.


New Publication in Nature Communications


Posted on October 08, 2014


Nature

Sarah A. Munro, Steven P. Lund, P. Scott Pine, Hans Binder, Djork-Arné Clevert, Ana Conesa, Joaquin Dopazo, Mario Fasold, Sepp Hochreiter, Huixiao Hong, Nadereh Jafari, David P. Kreil, Paweł P. Łabaj, Sheng Li, Yang Liao, Simon M. Lin, Joseph Meehan, Christopher E. Mason, Javier Santoyo-Lopez, Robert A. Setterquist, Leming Shi, Wei Shi, Gordon K. Smyth, Nancy Stralis-Pavese, Zhenqiang Su, Weida Tong, Charles Wang, Jian Wang, Joshua Xu, Zhan Ye, Yong Yang, Ying Yu & Marc Salit: 'Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures, Nature Communications, 5:5125.


New Publication in Nature Biotechnology


Posted on September 10, 2014


Nature

Su Z, Labaj PP, Li S, Thierry-Mieg J, Thierry-Mieg D, Shi W, Wang C, Schroth GP, Setterquist RA, Thompson JF, Jones WD, Xiao W, Xu W, Jensen RV, Kelly R, Xu J, Conesa A, Furlanello C, Gao H, Hong H, Jafari N, Letovsky S, Liao Y, Lu F, Oakeley EJ, Peng Z, Praul CA, Santoyo-Lopez J, Scherer A, Shi T, Smyth GK, Staedtler F, Sykacek P, Tan XX, Thompson EA, Vandesompele J, Wang MD, Wang J, Wolfinger RD, Zavadil J, Auerbach SS, Bao W, Binder H, Blomquist T, Brilliant MH, Bushel PR, Cai W, Catalano JG, Chang CW, Chen T, Chen G, Chen R, Chierici M, Chu TM, Clevert DA, Deng Y, Derti A, Devanarayan V, Dong Z, Dopazo J, Du T, Fang H, Fang Y, Fasold M, Fernandez A, Fischer M, Furió-Tari P, Fuscoe JC, Caimet F, Gaj S, Gandara J, Gao H, Ge W, Gondo Y, Gong B, Gong M, Gong Z, Green B, Guo C, Guo L, Guo LW, Hadfield J, Hellemans J, Hochreiter S, Jia M, Jian M, Johnson CD, Kay S, Kleinjans J, Lababidi S, Levy S, Li QZ, Li L, Li L, Li P, Li Y, Li H, Li J, Li S, Lin SM, López FJ, Lu X, Luo H, Ma X, Meehan J, Megherbi DB, Mei N, Mu B, Ning B, Pandey A, Pérez-Florido J, Perkins RG, Peters R, Phan JH, Pirooznia M, Qian F, Qing T, Rainbow L, Rocca-Serra P, Sambourg L, Sansone SA, Schwartz S, Shah R, Shen J, Smith TM, Stegle O, Stralis-Pavese N, Stupka E, Suzuki Y, Szkotnicki LT, Tinning M, Tu B, van Delft J, Vela-Boza A, Venturini E, Walker SJ, Wan L, Wang W, Wang J, Wang J, Wieben ED, Willey JC, Wu PY, Xuan J, Yang Y, Ye Z, Yin Y, Yu Y, Yuan YC, Zhang J, Zhang KK, Zhang W, Zhang W, Zhang Y, Zhao C, Zheng Y, Zhou Y, Zumbo P, Tong W, Kreil DP, Mason CE, Shi L.: 'A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium', Nature Biotechnology, 32(9):903-914.



Posted on July 30, 2014


We are looking for a student with background in web development. The project can be undertaken as part of an internship, as student employee or as part of a bachelor/master/diploma thesis. This project is a collaboration with the bioinformatics group of Prof. Peter F. Stadler at the University of Leipzig.

Find more information in our job flyer (only in German).


New member of the Scientific Advisory Board:
Prof. Dr. Peter F. Stadler


Posted on May 09, 2014


Genome Biology

We are very pleased to announce that Prof. Dr. Peter F. Stadler has joined our Scientific Advisory Board.

Prof. Dr. Peter F. Stadler received his Ph.D. in Chemistry from the University of Vienna in 1990 following studies in chemistry, mathematics, physics and astronomy. After a PostDoc at the Max Planck Institute for Biophysical Chemistry in Goettingen he returned to Vienna to work in the area to theoretical biochemistry. Since 1994 he is External Professor at the Santa Fe Institute, a research center focussed on Complex Systems. In 2002 he moved to the University of Leipzig as Full Professor of Bioinformatics. Furthermore, he is Senior Scientific Advisor at the RNomics Group at the Fraunhofer Institute for Cell Therapy and Immunology (IZI) in Leipzig, Principal Investigator at the Center for non-coding RNA in Technology and Health (RTH) in Copenhagen, External Scientific Member of the Max Planck Society affiliated with the MPI for Mathematics in the Sciences in Leipzig, Guest Lecturer at the Institute for Theoretical Chemistry of the University of Vienna and Corresponding Member Abroad of the Austrian Academy of Sciences. He published more than 400 scientific papers and articles and is Member of the Editorial Boards of seven scientific journals.


Celebrating two years ecSeq Bioinformatics


Posted on April 07, 2014


We're celebrating the 2nd Anniversary of ecSeq Bioinformatics and want to thank all clients and workshop participants for the awesome two years. You placed confidence and trust in us to provide a needed service - we did not take this responsibility lightly. We would like to express gratitude to our partners and our great team.


Announcing the 2014 NGS workshops


Posted on March 28, 2014


Do you think your skills in sequencing data analysis could need some improvement? Then our NGS workshop series taking place in October 2014 might be interesting for you. As usual, these hands-on workshops have a strong focus on practical experience meaning that you analyze typical NGS datasets. Our trainers will directly interact with you and give valuable feedback.

Our workshop series 2014 will consist of four separate courses:

For beginners, we have the RNA-seq Bioinformatics: A Practical Introduction course which will cover all the basics required for NGS analysis like file formats, quality control, read processing and read alignment, all based on an example RNA-seq dataset.

We are very happy that we could convince Dr. Michael Hackenberg, the developer of one of the most-used microRNA gene prediction tools for small RNA-seq data (miRanalyzer) to join us for our microRNA workshop. This course titled microRNA Analysis Using High-Throughput Sequencing will cover the essential steps of small RNA-seq analysis from microRNA prediction to extensive downstream analyses.

We also have a workshop on DNA Methylation Analysi where Helene Kretzschmer will show you how she took care of her data in the MMML-Seq study of the International Cancer Genome Consortium (ICGC).

Lastly, there is the workshop Discovering standard and non-standard RNA transcripts where Gero Doose will train you on advanced methods of transcriptome analysis. Gero has a strong background in transcriptome analysis, finding different isoforms, fusion-transcripts or circularized RNAs.

There is an early-bird discount which applies until end of april.


small RNA-Seq Presentation at Forschungsmuseum KOENIG


Posted on March 10, 2014


At March 27, the presentation 'Inferring non-coding RNAs from RNA-Seq Data' will be held in Bonn, Germany.


NGS Workshop at 3rd Programming for Evolutionary Biology Course


Posted on March 05, 2014


At March 22, the presentation 'Analysis of high-throughput sequencing data' will be given at the 3rd Programming for Evolutionary Biology Course in Leipzig, Germany.


New Publication in Genome Biology


Posted on February 10, 2014


Genome Biology

Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt L, Teupser D, Hackermüeller J, Stadler PF: 'A multi-split mapping algorithm for circular RNA, splicing, trans-splicing, and fusion detection', Genome Biology, 15:R34, doi:10.1186/gb-2014-15-2-r34


New Book Chapter in Methods in Molecular Biology


Posted on January 28, 2014


Springer

Hertel J, Langenberger D, Stadler PF: 'Computational prediction of microRNA genes' in J. Gorodkin, W.L. Ruzzo, (eds).: RNA Sequence, Structure and Function: Computational and Bioinformatic Methods. Volume 1097 of Methods in Molecular Biology, Humana Press, New York.


Poster Presentation at 55th ASH Annual Meeting and Exposition


Posted on December 05, 2013


Blood

Hezaveh K, Bernhart S, Hoffmann S, Langenberger D, Schlesner M, Stadler PF, Binder V, Lenze D, Siebert R, Hummel M, Borkhardt A: 'In-Depth miRNA Profiling Of Germinal Center Derived B-Cell Lymphomas By Next Generation Sequencing: A Report From The German Icgc-Mmml-Seq Project', Blood 122 (21), 2500-2500.


New Publication in Nature Magazine


Posted on August 16, 2013


Nature

Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SAJR, Behiati S, Biankin AV, Bignell GR, Bolli N, Borg A, Boerresen-Dale A, Boyault S, Burkhardt B, Butler AP, Caldas C, Davies HR, Desmedt C, Eils R, Eyfjord JE, Foekens JA, Greaves M, Hosoda F, Hutter B, Ilicic T, Imbeaud S, Imielinsk M, Jäger N, Jones DTS, Jones D, Knappskog S, Kool M, Lakhani SR, López-Otín C, Martin S, Munshi NC, Nakamura H, Northcott PA, Pajic M, Papaemmanuil E, Paradiso A, Pearson JV, Puente XS, Raine K, Ramakrishna M, Richardson AL, Richter J, Rosenstiel P, Schlesner M, Schumacher TN, Span PN, Teague JW, Totoki Y, Tutt ANJ, Valdés-Mas R, van Buuren MM, van 't Veer L, Vincent-Salomon A, Waddell N, Yates LR, Australian Pancreatic Cancer Gen Initiative, ICGC Breast Cancer Consortium, ICGC MMML-Seq Consortium, ICGC PedBrain, Zucman-Rossi J, Futreal PA, McDermott U, Lichter P, Meyerson M, Grimmond SM, Siebert R, Campo E, Shibata T, Pfister SM, Campbell PJ, Stratton MR: 'Signatures of mutational processes in human cancer', Nature, 500(7463):415-21.

News from ecSeq

On our blog you will find major news, background stories and press releases.

More frequent updates are provided on the following pages: