News

- 9 September 2016-
SCIS - a toolbox for in silico stem cell biology
Stem cells' capacity for self-renewal and differentiation into mature cells holds enormous potential for regenerative medicine. Extensive research has generated large amounts of data, which pose considerable challanges to researchers. To facilitate the usage of complex molecular datasets in stem cell biology, we have started to implement a suite of connected and free to use web tools called the Stem Cell In Silico (SCIS) Toolbox. (For people, who missed out on Latin in school: scis means in Latin "you know" ;-). At the INFORUM 2016 José will present today the first two SCIS components, StemCellNet and StemChecker and will give an outlook on future developments.


- 8 September 2016-
SysBioLab participates in two European Cost Actions
The SysBioLab takes part in two new Cost Actions: Harmonising standardisation strategies to increase efficiency and competitiveness of European life-science research (CHARME) and Gene Regulation Ensemble Effort for the Knowledge Commons (GRECO). Both Cost Actions aim to facilitate the usage and interchange of biological data and hence are of major interest for the SysBioLab. Matthias is national delegate in the Management Committees of both Cost Actions and is additionally work group leader in GRECO.


- 8 August 2016-
Agapios Sachinidis visits the SysBioLab
Prof. Agapios Sachinidis from the Institute of Neurophysiology of the University of Cologne (Germany) is visiting the SysBioLab. It is the first visit within the FCT-DAAD project and will serve to interpret the results gained from the bioinformatic analyses of in vivo data for cardiomyogenesis as well as to coordinate the further collaboration.


- 15 June 2016 -
CyanoEXpress (almost) under the midnight sun
Matthias presented the CyanoEXpress database at the Norplantbio 2016 - the Norwegian Plant Biology conference, which was held in Trondheim. Strikingly, the sun only sets a little before midnight there and rises already at 3am in the morning again! Matthias used the extended daylight not only to present the new CyanoExpress version and the work published recently in Scientific Reports, but also to initiate collaborations in the area of green systems and synthetic biology with the PhotoSynLab led by Martin Hohmann-Marriott.


- 29 February 2016 -
Photosynthesis: How to cope successfully with an ever-changing environment
For many organisms, environmental conditions are in constant flow and require the adaptation of numerous internal processes to keep homeostasis. Thus, the ability to adapt is a fundamental feature to successful life forms. Photosynthetic organisms, in particular, need to adjust various processes to daily changes in light intensity and nutrient availability. In a new study published today in Scientific Reports, we present a holistic picture of how Synechocystis, a model organism for photosynthesis, adapts its gene expression to various environmental perturbations. Strikingly, the photosynthetic apparatus responded most strongly, but in a highly coordinated fashion to changes in conditions. Detailed inspection of the integrated data led to the discovery a variety of regulatory patterns and novel putative photosynthetic genes. Together with the extended CyanoEXpress database, the presented analysis will contribute to a better understanding of regulation of photosynthesis and its coordination with other processes on a systems level, as well as help to establish Synechocystis as a photosynthetic model organism for systems and synthetic biology studies.


- 17 February 2016 -
UPR-HD: an online tool for the study of the unfolded protein response in Huntington's disease
Huntington's disease (HD) is a fatal neurodegenerative disease, for which no cure has yet been found. Besides other mechanisms, the unfolded protein response (UPR) has been put forward to play a role in the pathogenesis in HD. As an adaptive response, UPR can counter-balance accumulation of mis-folded proteins, but can also trigger cell death if it persists. Our recently published analysis indicates that the UPR is activated in various disease models of HD, and that the UPR presents an attractive target for therapeutic interventions. To help independent researchers to study the role of UPR in HD, we implemented a new online tool called UPR-HD. It enables researchers to search, interactively analyze and visualize the expression patterns of UPR-associated genes across various HD expression data sets, and may contribute to find novel ways to treat HD.


- 7 October 2015 -
HeartEXpress 1.0 online: Diving into the sea of expression patterns for cardiomyogenesis and heart development
Heart development is a highly complex process with a series of precisely spatially and temporally ordered events on molecular level. To understand how these events are controlled and coordinated, it is necessary to study the underlying gene expression and its regulation. To help researchers in this formidable task, we have established HeartEXpress, a web-based platform for the analysis of integrated expression datasets associated with cardiomyogenesis. The current version comprises human and murine gene expression data from independent microarray experiments for stem cell differentiation, in vitro or in vivo reprogramming, in the context of cardiomyogenesis, and heart development. We hope that this resource will support the development of new therapies in cardiac regenerative medicine.


- 5 August 2015 -
Shining light on the dual role of the unfolded protein response in Huntington's disease
The so-called unfolded protein response (UPR) is an important control mechanism to ensure correct folding of proteins. While its main function is to counter-balance the accumulation of un- or mis-folded proteins in the endoplasmic reticulum, its persistent activation can have severe consequences: the triggering of inflammation and apoptosis leading to cell death. To elucidate this dual role in Huntington's disease (HD), a lethal hereditary neurodegenerative disorder, we carried out the first comprehensive analysis of UPR activation in HD and elucidate potential links to pathogenetic mechanisms within a systems biology framework. We evaluated expression profiles of UPR genes and discovered the dysregulation of the UPR in many HD models. Most importantly, the study published in F1000Research pinpoints pivotal genes that connect HD, UPR and apoptosis, and that can serve as promising molecular targets to establish effective therapies for HD.


- 7 July 2015 -
Epigenetic stemness signature discovered
It is well known that epigenetic modifications of DNA and chromatin play an important role in the control of pluripotency and differentiation. In contrast, the possibility that such epigenetic modifications might also give us novel biomarkers for stem cells has not been assessed so far. Such novel biomarkers could help us to define more accurate the state of stem cells - an important prerequisite for safe application of stem cell technology.
In a pilot study led by Paul de Sousa from the MRC Centre for Regenerative Medicine at the University of Edinburgh, we could demonstrate that such epigenetic biomarkers do exist for human embryonic stem cells (hESC). By comparing methylation patterns in hESCs and in somatic tissue, we identify conserved patterns for pluripotent cells. Remarkably, follow up experimental validation showed several genes associated with the detected conserved methylation pattern can not only serve as biomarkers, but are also novel potent regulators of pluripotency.


- 24 May 2015 -
StemChecker: Screening for stemness genes
Stem cells have a remarkable capacity: They can self-renew as well as differentiate into other types of cells. Which genes are responsible for this intriguing feature called stemness is one of the key question in stem cell biology and further beyond. Many groups have put forward sets of genes associated with stemness based on various approaches. These so-called stemness signatures have been proven to be helpful not only for stem cell biologists, but also for researchers working on human diseases. However, their broad usage was hindered, as many of these signatures remained hidden in supplementary materials of publications or were dispersed on the web. To facilitate researcher the use of stemness signatures, we have developed StemChecker, a web-server for the discovery and exploration stemness signatures in gene sets given by the user. Its features are described in an article published online today in Nucleic Acids Resarch, which includes two case studies illustrating its use in stem cell biology and cancer research. Naturally, the team behind StemChecker was happy about that!


- 12 May 2015 -
Enhanced Internal Training
Throughout this week, Isabel is giving hands-on tutorials for the advanced usage of Unix, R, and software for microarray and NGS analysis. Be sure to be there in time, as this tutorial is popular and space is limited!


- 23 April 2015 -
Hunting Huntington's disease modifiers more efficiently
Protein-protein interaction (PPI) networks provide a powerful basis for the analysis of molecular processes. However, most approaches using PPI networks have a big draw-back: They neglect that these network are not static but vary considerably between different tissues and biological states. To make PPI networks more specific, we have developed together with the Lab for Proteomics and Molecular Mechanisms of Neurodegenerative Diseases led by Erich Wanker (MDC, Berlin, Germany), a simple but efficient filtering procedure. Application to Huntington's disease (HD), a fatal neurodegenerative disorder, enabled us to identify a novel potent disease modifier (CRMP1), that showed specific differentially expression in the brain area affected by the disease. Subsequent experiments could demonstrate that CRMP1 is indeed a potent suppressor of neurotoxicity and protein aggregation in vitro and in vivo, and may serve as a valuable target for novel therapies of HD. The study published today in Genome Research also illustrates how the combination of computational and experimental approaches helps to make headways in the study of human diseases.


- 21 Abril 2015 -
SysBioLab goes to the Parliament!
José and Matthias attended the 8th International Meeting of the Stem Cell Network NRW, which was held in the former German Parliament. Not only the presented progress in stem cell biology and regenerative medicine was impressive, but apparently also the comfort of the chairs there!


- 30 March 2015 -
Ravi moves to Mozart city
Ravi is heading to Salzburg - the birth place of Mozart - to start his new postdoc position at the Experimental and Clinical Cell Therapy Institute, where he will be the key bioinformatics person. After four years close to the sea, this will also be quite a change in the surrounding landscape. So we could not resist having a last gathering at the beach. Good luck, Ravi, with your new position and learning German (with a strong Austrian accent, of course)!


- 19 January 2015 -
Bem-vindo, Miquel!
The SysBioLab has a new member: Miquel Bovea Marco. Miquel has a BSc. degree in Biotechnology form the University of Valencia and will enforce our Spanish work-force for the study of cyanobacteria. ¡Bienvenido, Miquel!


- 13 January 2015 -
Cancer research: Fruitful link with the Link lab
Two new publications show how local collaborations between computational and experimental scientists can tackle big challenges in cancer research. In the first study led by the local Link Lab and published today in Carcinogenesis, Ravi compared publicly available expression profiles of existing molecular markers for melanoma and tribbles2 (TRIB2) - a pseudokinase studied by the Link Lab. Ravi could show that TRIB2 correlates strongly with the presence of melanoma - a finding that was subsequently validated experimentally and that suggests TRIB2 as novel diagnostic biomarker for melanoma . In the second study published recently in Breast Cancer Research, Ravi (again) analysed transcriptome data produced by the Link Laboratory. These data describe the response of cancer cell lines to inhibitors of PI3 - kineases that are commonly activated in cancer. The results have helped to understand the molecular details how these inhibitors target cancer cells.


- 11 December 2014 -
Highlight of the year: SysBioLab Retreat!
Today, we got together for our lab retreat - a day filled with presentations ranging from cyanobacteria to stem cells, lively discussions and a little bit of poolin between.


- 10 November 2014 -
Bem-vindo, Tânia!
Tânia Barata has arrived today at the SysBioLab. She will be a visiting scholar for the next six month, and will focus on the systems biology of stem cells. Previously, she has worked on the identification of small molecules that affect human embryonic vascular development. Thus, her background will certainly be of great value for the targeting molecular networks for drug research .


- 30 October 2014 -
Miguel heads off to Down Under
The SysBioLab loses his first post-doc: Miguel. After more than 4 years in the SysBioLab, Miguel has accepted an offer for a position in the lab of Min Chen at the University of Sydney, where the chlorophyll f has been discovered. Good on you, mate! But before leaving, we had an esquisite farewell party at Matthias' beach house.


- 1 October 2014 -
Cyanobacteria speak Spanish in the SysBioLab
Joaquín Giner Lamia is joining the SysBioLab. Directly from nearby Sevilla, he will help us to study the regulation of photosynthesis in cyanobacteria. Joaquin has acquired a profound knowledge of microbiology during his PhD and has extensive experience with Synechocystis. Welcome, Joaquín!


- 23 July 2014 -
New version of CyanoEXpress
We have made some changes concerning labeling and ordering of samples in the the CyanoEXpress database to facilitate the interpretation of transcriptional response patterns.


- 2 July 2014 -
Toward a systems-level understanding of cyanobacteria
Cyanobacteria are very versatile group of microorganisms, and have a unique position in the living world, as they are the only prokaryotes capable of performing oxygenic photosynthesis. Their living habitats range from desert crusts to open ocean. Recently, cyanobacteria moved into the focus of biotechnological research, as potential vehicles for a clean generation of bio-fuel and other high value products. In a review published today in a special issue of Frontiers in Genetics, we comprehensively review how different omics technologies and systems biology approaches can be applied to elucidate the fascinating world of cyanobacteria.


- 1 July 2014 -
StemCellNet: A new and unique resource for Stem Cell Biology
Stem cells have evoked considerable interest, not only due to their potential in regenerative medicine, but also because of their role in major diseases such as cancer. Recent experiments have begun to probe the molecular networks underlying stem cell maintenance and differentiation, and to define molecular signatures for stemness, but their analysis is challenging due to the complexity and the lack of powerful software tools. To equip the research community with a resource that exploits the data generated in various studies and to shed light in the molecular mechanisms of stem cells, we have developed an interactive web server called StemCellNet. It can help you to generates focused networks, to select and prioritize genes for further research, and to integration of heterogenous data in stem cell biology. A publication in this year´s Web Server issue of Nuclear Acids Research describes its various features.


- 3 June 2014 -
Targeting molecular networks for drug research
Molecular networks have moved into the focus of biomedical research. While their study have certainly provided new insights into physiological and pathophysiological processes, the challenge now is how to modify or even restructure these networks for means of treatment of diseases or enhance regenerative mechanisms. Of different possiblities for altering networks, the use of drugs is presently the most feasible. In a short review published today in Frontiers in Genetics, we have present an concise overview how analysis of molecular interaction networks can contribute to pharmacology (e.g., by identifying new drug targets or prediction of drug side effects) for improved treatment of diseases and for application in regenerative medicine.


- 15 May 2014 -
Bem-vindo, Isabel and Daniel!
The SysBioLab welcomes two new members: Isabel Duarte and Daniel Oliveira. Isabel has previously been involved in various bioinformatics project and has great expertice in computational biology, whereas Daniel has worked experimentally on the stem cell differentation, so both contribute complementary skills to the project.


- 1 April 2014 -
SysBioLab is looking for Master´s students
Looking for a topic for Master´s thesis at the UAlg and interested in Computational Biology? Then you should definitely check out our current listing of thesis topics, which include proposals for purely computational as well combined experimental and computational research work.


- 18 March 2014 -
Unified Interactome is ready to download
The UniHI web site includes now an option for downloading the full integrated human interactome.


- 14 February 2014 -
Cheers to Rui
Rui defended successfully his thesis "Analysis of the Transcriptional Regulatory Network underlying Heart Development" and has received his Master´s degree in Biomedical Sciences. A day of celebration in the SysBiolab: Cheers, Rui!


- 14 January 2014 -
Congrats to José
José was selected for a FCT postdoc scholarship in last year´s highly competitive call. His research proposal comprises the development of software and computational algorithms dedicated to stem cell differentiation and cellular reprogramming.


- 1 January 2014 -
UniHI 7: Making sense of complex networks
Trying to make sense of the confusing tangles representing molecular interaction networks? Then our new version of UniHI , which is described in this year´s database issue of Nucleic Acids Research, is the place for you to start your investigations! Interaction networks - even for a small number of genes or proteins - are frequently highly complex and difficult to interpret. To tackle the formidable challenge to make sense of them, we have equipped UniHI 7 with a unique set of powerful tools ranging from simple filtering options to advanced network analysis methods. Besides accumulating now almost 350 000 molecular interactions between genes, proteins and drugs, UniHI includes numerous types of data and information that help users to bridge the gap between geno- and phenotype and to build highly specific networks underlying molecular mechanisms in human health and disease. Its user-friendly interface also enables researchers less acquainted with network analysis to perform state-of-the-art network-based investigations. So your next stop in network biology: UniHI 7 !


- 25 November 2013 -
CyanoEXpress version 1.4 online: New datasets included
A new version of CyanoEXpress has gone online, with three new datasets measuring circadian expression as well as the transcriptional response to copper depletion and and during low carbon acclimation.


- 20 November 2013 -
CyanoEXpress meets CyanoFactory
The CyanoEXpress team traveled to Porto to present their work and the latest features of CyanoExpress at the first meeting of the CyanoFactory consortia.


- 8 July 2013 -
CyanoEXpress version 1.3 online
An additional data preprocessing step facilitates now the detection and interpretation of expression changes in Synechocystis during the day-night cycle.


- 30 May 2013 -
Fairwell to Dulce
After joining the SysBioLab last year and working on the effects of phosporylation of alpha-synuclein phosphorylation on gene expression in a collaborative project with Sandra Tenreiro (IMM, Lisbon), Dulce will soon move to Braga, where she is offered a scholarship at the Life and Health Sciences Research Institute of Universidade do Minho. (Parabens, Dulce!) Before she was taking the road towards Braga, however, we had a very enjoyable farewell party and what could be a better place than the beach for this. Good luck & much success, Dulce!


- 8 May 2013 -
Cat invasion of the SysBioLab!
The SysBioLab has new (and very cute) members: 3 kittens! Someone has thought that Matthias needs some company in his beach cottage and left them in front of his door. As they still quite young (less than a month), they need to be fed every other hour. Thus, Matthias brings them along when he goes to work, where they have now a reserved space on the terrace. And of course, they have become an instant attraction for the whole group and the rest of the Centre. Moreover, Miguel found a homeless kitten, too, so the SysBioLab keeps growing rapidly!


- 20 April 2013 -
Presentation in Blue
Matthias gave an overview of CyanoExpress and our meta-analysis of the Synechocytis gene expression data at the ESF-EMBO Symposium. Best of all: Even in a fresh and stylish blue shirt - thanks to his generous room-mate Vicente Rubio! Unfortunately, Matthias´s own luggage preferred to stay at the Airport in Faro.


- 28 March 2013 -
The Swinging Interactome
Our study of the dynamic organization of the protein interactome during the day/night cycle was published in PLOS Genetics. In this work, we introduced the concept of dynamic interactions and predicted dynamic complexes whose abundance periodically change following a circadian rhythm. Examining their role in the network context, we detected an intriguing temporal organization of the interactome and discovered that many cellular functions and processes tend to be coupled by dynamic interactions. The study is the result of a close collaboration with the Laboratory of Chronobiology at the Charité in Berlin.

- 4 February 2013 -
José joins the SysBioLab
José Pinto has started his FCT fellowship in our lab. He has obtained a PhD in Bioinformatics from the University of Minho, where he developed software tools for the analysis of metabolic networks. He will join the FCT project PTDC/BIA-GEN/116519/2010, in which we study alternative splicing and its impact on molecular interaction networks during stem cell differentiation. José will also help to further develop our UniHI webserver. Bem vindo, José!


- 23 January 2013 -
CyanoEXpress goes to Poland
CyanoExpress will be presented at the ESF-EMBO Symposium "Molecular Bioenergetics Of Cyanobacteria: Shaping The Environment" which will take place in Pultusk, Poland from 15th to 20th April 2013. Miguel and Matthias were selected to present our recent work on the transcriptional response of Synechocystis to iron depletion and on the integration of expression data for Synechocystis. See you there!


- 19 December 2012 -
Early Christmas present by the FCT
Our project proposal was successful in this year´s FCT call! In the project, we will elucidate the molecular regulation of photosynthesis and its coordination with other processes through an innovative genomic approach complemented by integrative computational analyses at the systems level. The objective is to provide a rational basis for targeted bioengineering and synthetic biology approaches for enhanced biofuel production in phototrophic organisms. The starting date will be the 1st of April 2013. Here is a pic of our celebration!


- 1 December 2012 -
Handling the Double-edged Sword
Iron presents a double-edged sword for cyanobacteria. On one side, it is a necessary component of photosynthesis; on the other side, it can lead to the production of highly toxic molecules. Thus, cyanobacteria are likely to have evolved dedicated mechanisms to regulate iron homeostasis. In the work published today in G3: Genes, Genomes, Genetics, we have simultaneously monitored the expression of protein-coding and non-coding transcripts in the model cyanobacterium Synechocystis under iron deprivation and discovered a wide range of transcriptional changes. The results of our analyses indicate an extensive transcriptional response, affecting various processes and a complex regulatory network involving both proteins and regulatory RNAs.

- 22 November 2012 -
Matthias gives a talk at the MDC in Berlin
Matthias presents the findings of our recently published analyses of therapeutic targets for Huntington´s disease at the Max-Delbrück-Centre in Berlin. He has been invited by Erich Wanker, head of the research group for Proteomics and Molecular Mechanisms of Neurodegenerative Diseases at the Max-Delbrück-Centre.


- 3 September 2012 -
Rui joins the SysBioLab
Rui Machado has started his Master thesis in our lab. The topic is "Analysis of the transcriptional regulatory network underlying heart development". He will combine expression and interaction data to gain a detailed picture of the dynamic regulatory mechanisms underlying heart development. José Bragança will serve as co-supervisor. As several other groups at the CBME working experimentally on cardiomyogenesis, Rui´s work will certainly be of great interest for many people here! Bem vindo, Rui!


- 7 August 2012 -
CyanoEXpress presented at the ISPP 2012, Porto
We presented CyanoEXpress at the 14th International Symposium on Phototrophic Prokaryotes in Porto, Portugal. The poster presentation can be found (here). We would like thank again for the great interest!!


- 6 July 2012 -
CyanoEXpress Publication in Bioinformation
The CyanoEXpress database, its features and implementation are described in the new issue of Bioinformation (Abstract+Pdf).


- 2 July 2013 -
Dulce joins the SysBioLab
Dulce Almeida, who has a Master degree in Biological Engineering, is starting her FCT fellowship in our lab. She will join the PTDC/BIA-BCM/117975/2010 project, which is led by Sandra Tenreiro from the Instituto de Medicina Molecular, Lisbon. In this project, we will examine the role and regulation of alpha-synuclein phosphorylation in Parkinson´s disease. Alpha-synuclein is a small protein which plays a central role in neurodegeneration. Previous investigations indicated that phosphorylation of alpha-synuclein has a crucial influence on its effects in Parkinson´s disease. Dulce will carry out various bioinformatic analyses to identify factors which can be linked to the observed changes of alpha-synuclein phosphorylation. Bem vindo, Dulce!


- 28 June 2012 -
Elucidating the complexity of Huntington´s disease
Two of the most puzzling features of Huntington´s disease have been the variability in its clinical manifestation, as well as the complexity of underlying molecular changes; both are in apparent contradiction to the known monogenic nature of the disease. Our analyses published today in BMC Neurology helps to elucidate these puzzling features. Analysing a comprehensive set of therapeutic target genes for Huntington´s disease, we identified a strikingly large number of biological processes which can be associated with the disease and which may provide new targets for its treatment. Also, we derived a candidate set of 24 novel genetic modifiers. To facilitate other researchers following-up studies, we have provided a compendium of molecular mechanisms linked to Huntington´s diseases at http://hdtt.sysbiolab.eu .


- 31 May 2012 -
Release of CyanoEXpress Version 1.0
The first version of web-based CyanoEXpress database has become publicly accessible. It currently comprises expression data for 3073 genes and 178 environmental and genetic perturbations obtained in over 30 independent studies. The developed web interface supports interactive inspection of co-expression patterns. At present, CyanoEXpress constitutes the most comprehensive collection of expression data available for Synechocystis.


- 25 January 2012 -
Make the most out of your blood stem cells
Haematopoiesis, the formation of new blood cells, is a vital, life-long process. The basis for this process is a pool of hematopoietic stem cells, which need to proliferate, to provide sufficient new blood cells. For the maintenance of hematopoietic stem cells , endothelial cells (ECs) play therefore an important role, as they contribute in the regulation of hematopoietic cell proliferation and trafficking. In a microarray study carried out by Gürkan Bal and co-workers at the Institute for Transfusion Medicine, Charité, Berlin and published in Cell Transplantation, Matthias helped in the identification of new expansion factors for hematopoietic stem cell. Such factors could be useful to increase the efficiency of bone marrow transplantations.


- 16 January 2012 -
Book chapter featuring UniHI published
A book chapter, descripting UniHI, its implementation and its use, has been published in Two Hybrid Technologies, Methods in Molecular Biology. A pre-print version can be found here: pdf

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- 2 January 2012 -
Kick-starting the new year - UniHI 6 goes online
UniHI 6 can be now publicly accessed at www.unihi.org. With almost 300,000 human molecular interactions included, UniHI 6 constitutes one of the most comprehensive platforms for the query, visualization and analysis of molecular networks in human. UniHI 6 has been especially designed for intuitive usage, so it is applicable by a wide community of scientists both in biology and medicine. In particular, it aims to help researchers, who are less acquainted with computational analyses, to perform state-of-the-art investigations into human molecular networks. UniHI 6 is based on a complete re-implementation of previous versions of UniHI (described in Nucleic Acids Research 2007 & 2009) but has a widely extended scope and functionality. While it continues to be an comprehensive resource for interaction data, UniHI 6 puts now more emphasis on the interactive analysis and interrogation of molecular networks by the user.