e-NIOS

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Seven Bridges & e-NIOS Partnership to Break the Biomarker Bottleneck

Press:

GenomeWeb

PR Newswire

Cambridge, Mass. and Athens, Greece., Sept 11, 2018. Seven Bridges, the leading biomedical data platform and analytics company, and e-NIOS, a biological knowledge discovery start-up, announced a strategic partnership towards data-driven discovery of biomarker signatures. Derivation of robust biomarkers from next generation sequencing and multi-omic data is currently a major bottleneck in precision medicine initiatives. This bottleneck continues to limit the transformation of genomic information into biomedical insights that will improve clinical outcomes through more efficient drug target discovery and more effective patient stratification.

Together, we are leveraging machine learning and physiology to improve and partially automate interpretation of potential biomarkers. Currently, interpretation is largely performed manually, relying on expert decisions. Human experts are both costly and inconsistent. Our partnership will develop efficient and standardized interpretation frameworks which harness the inherent complexity of molecular networks. This partnership has the potential to shift from listing all statistical correlations towards focusing on a smaller set of causal associations.

e-NIOS’ innovative technology enables unsupervised, intelligent translation of -omics data through BioInfoMiner, a cloud platform that resolves biological complexity and derives molecular signatures suitable for data-driven interpretation in different conditions, physiological states and datasets. Additionally, it allows the integration of different -omic layers (genomic, epigenomic, transcriptomic, proteomic, variants). BioInfoMiner can also drive discovery in studies related to plant and microbial systems.

According to e-NIOS’ co-founder Aristotelis Chatziioannou (CEO), “e-NIOS and Seven Bridges share the same vision for data-driven, streamlined computational genomics, integrating all steps from raw data to actionable biological interpretation. The Seven Bridges Platform is a valuable, high-performance cloud environment for the deployment of complex workflows and streamlined processing of massive, genomic datasets. Seven Bridges has been an excellent technological partner for our company as we work together to enable innovative, automated, data-driven biomarker industrial services and applications in the area of precision medicine.”
As Brandi Davis-Dusenbery, CEO of Seven Bridges, explained, “e-NIOS’ technology has the unique ability to combine biological network information with data-driven models. Here we bring together the technical and scientific strengths of both companies to provide a complete solution for the prediction of biomarker associations from raw data. Our strategic partnership supports Seven Bridges’ mission to connect the world’s biomedical information and rapidly transform it into actionable information.”

About Seven Bridges

Seven Bridges is the biomedical data analysis company accelerating breakthroughs in genomics research for cancer, drug development, and precision medicine. Thousands of researchers in government, biotech, and academia use Seven Bridges, including leading global pharmaceutical companies and national genomics projects such as the U.S. National Cancer Institute-funded Cancer Genomics Cloud, the Gabriella Miller Kids’ First Data Center, the Million Veteran Program, and the U.S. National Institutes of Health Data Commons Pilot. To find out more, contact us.

About e-NIOS

e-NIOS Applications P.C. is a spin-off company of the National Hellenic Research Foundation, founded by a multidisciplinary team with expertise in the fields of Bioinformatics, Genomics, Artificial Intelligence, Data Mining, Operational Research and Decision Support Systems. The company participates in many funded EU Horizon 2020 Research & Innovation networks and has developed sustainable international collaborations with partners such as the National University of Ireland, Galway, the French National Institute of Health and Medical Research (INSERM) the German Anticancer Institute Deutsches Krebsforschungszentrum  (DKFZ, Heidelberg) and many Universities and research groups across Europe. Research results obtained through e-NIOS technology have been published in high impact journals (EMBO Molecular Medicine, Cell Metabolism, FASEB, Scientific Reports and Nature Communications). e-NIOS recently filed a joint international patent with INSERM, France, entitled “Method of therapy selection for patients suffering from Glioblastoma”, exploiting results generated through BioInfoMiner. To find out more, contact us.

 

 

New paper involving BioInfoMiner analysis validates proteostasis imbalance as a driver of tumor aggressiveness in Glioblastoma (EMBO Mol. Med.)

Proteostasis imbalance is emerging as a major hallmark of cancer, driving tumor aggressiveness. Evidence suggests that the endoplasmic reticulum (ER), a major site for protein folding and quality control, plays a critical role in cancer development. This concept is valid in glioblastoma multiform (GBM), the most lethal primary brain cancer with no effective treatment.

It was previously demonstrated that the ER stress sensor IRE1α (referred to as IRE1) contributes to GBM progression. The new study entitled “Dual IRE1 RNase functions dictate glioblastoma development” published in EMBO Molecular Medicine provides the first demonstration of a dual role of IRE1 downstream signaling in cancer and opens a new therapeutic window to abrogate tumor progression.

BioInfoMiner analysis was employed in order to define specific IRE1‐dependent gene expression signatures that were confronted to human GBM transcriptomes and shed light to the antagonistic roles of XBP1 mRNA splicing and RIDD on tumor outcomes, mainly through selective remodeling of the tumor stroma.

The research was carried out by an international consortium with the participation of e-NIOS, including among others Université de Bordeaux, Université de Rennes 1, University of Ireland Galway, University of Chile, INSERM, CNRS, National Hellenic Research Foundation and Harvard School of Public Health.

 

Announcement of BioS Online Seminars: Digital Skills on Computational Biology for Health Professionals, 15-16 October 2020

Within the framework of the Erasmus days, the BioS project offers further online seminars on modules 1 to 3 to deepen and apply the knowledge acquired in the course. We would like to invite you to join us.

https://www.erasmusdays.eu/event/bios-project/

To participate in the BioS Online Seminar, please register under:

https://docs.google.com/forms/d/e/1FAIpQLSfBTZyQs3pFRskynuEkocOzqzW_vc5TeTodxWDlG375VvrqDg/viewform

After registration, you receive the direct link to the online seminar.

The BioS project offers three online seminars on the topics:

  • INTRODUCTION TO BIOINFORMATICS
  • COMMERCIAL PERSONALIZED GENOMICS SERVICES IN PATIENT CARE
  • COMPUTATIONAL STATISTICS FOR CLINICAL DOCTORS

The online seminars give you the opportunity to acquire valuable knowledge for your professional career, to discuss live with experts highly topical issues and to connect with peer learners all around Europe.

Online Seminar 1:
Systemic interpretation of data from different –omic layers and derivation of diagnostic, personalized signatures of molecular biomarkers, assisting medical decision.

e-nios, module 1, Thursday 15th of October, 13.00 – 15.00 CEST

In this online seminar the audience is introduced to the secrets of multi-omic analysis and robust systemic interpretation. This process manages to reveal those active, functional, molecular modules, providing consistent, mechanistic understanding of the myriad of interactions occurring, and enables in-silico extraction of signatures of molecular biomarkers, for a more accurate and robust clinical diagnosis/prognosis. The interpretation of the various types of omics data streams is effected through the web platform BioInfoMiner of e-NIOS, integrating the results of diverse analytic workflows showcasing how to extract predictive signatures for several diseases, without requiring advanced programming skills. Two examples of the data-driven interpretation and extraction of diagnostic signatures both at the gene and variant level will be performed on case studies including data from patients suffering from different cancer types.

Online Seminar 2:
BIOS PROJECT- COMPUTATIONAL STATISTICS FOR CLINICAL DOCTORS – HOW TO EVALUATE DIAGNOSTIC INFORMATION?

BGU, module 2, Friday, 16th of October,
10.00 – 12.00 CEST

In this online seminar, the theoretical material taught during the BioS course is transformed into practical and applicable skills by working with contemporary examples. You will learn how to use predictive methods, such as COVID19 PCR tests, how to interpret results, and how evidence affects the test credibility.

Online Seminar 3:
BIOS PROJECT – COMMERCIAL PERSONALIZED GENOMICS SERVICES IN PATIENT CARE – THE ROLE OF TUMOR GENETIC PROFILING, MOLECULAR IMAGING AND TARGETED THERAPIES IN THE TREATMENT OF NON-SMALL CELL LUNG CANCER

GOC, module 3, Friday, 16th of October,
13.00 – 15.00 CEST

In this online seminar, the role of tumor genetic profiling, molecular imaging and targeted therapies in the treatment of non-small cell lung cancer will be presented.

Registration

To participate in the BioS Online Seminar, please register under:

https://docs.google.com/forms/d/e/1FAIpQLSfBTZyQs3pFRskynuEkocOzqzW_vc5TeTodxWDlG375VvrqDg/viewform

After registration, you receive the direct link to the online seminar.

BioInfoMiner elucidates the role of the early secretory pathway in SARS-CoV-2 infection

https://doi.org/10.1083/jcb.202006005

Here, we analyze and discuss the contribution of the molecular machines operating in the early secretory pathway in the biogenesis of SARS-CoV-2 and their relevance for potential antiviral targeting. The fact that these molecular machines are conserved throughout evolution, together with the redundancy and tissue specificity of their components, provides opportunities in the search for unique proteins essential for SARS-CoV-2 biology that could also be targeted with therapeutic objectives. Finally, we provide an overview of recent evidence implicating proteins of the early secretory pathway as potential antiviral targets with effective therapeutic applications.

The journeys of CoV-2 in the host cell. Coronavirus infection starts with the binding of the spike protein to cognate receptors. This drives conformational changes that promote fusion of the viral particle with the host cell’s plasma membrane. Once in the cytoplasm, viral particles are uncoated, and the viral RNA genome is translated, producing two polyproteins (pp1a and pp1ab). These polypeptides are proteolytically processed by host and viral proteases, generating nonstructural proteins (nsps). nsps assemble to form the replicase (R), which together with pp1a/pp1ab produces the replicase–polymerase complex. Replicase polymerase complex is responsible for the replication of the viral genome and for the production of subgenomic RNAs. The latter are translated to form structural proteins nucleocapsid (N), spike (S), membrane (M), and envelope (E). In addition to these genomic elements shared by other CoVs, the SARS-CoV-2 genome also contains eight ORFs coding for accessory proteins. Structural proteins are subjected to diverse posttranslational modifications in the ER and Golgi compartments, including disulfide bond and formation N- and O-glycosylation. Structural proteins concentrate in the ERGIC, where they assemble around the genome–nucleocapsid complexes. Mature virions are packed and budded in smooth-walled vesicles and then transported along downstream organelles of the exocytic pathway.

RA-map: a state-of-the-art interactive knowledge base for rheumatoid arthritis

RA-map is a fully annotated, expert validated, state-of-the-art knowledge base for RA in the form of a molecular map. BioInfoMiner was used for topological, functional and pharmacogenomic analysis.

The publication is accessible at:

Vidisha Singh, George D Kalliolias, Marek Ostaszewski, Maëva Veyssiere, Eleftherios Pilalis, Piotr Gawron, Alexander Mazein, Eric Bonnet, Elisabeth Petit-Teixeira, Anna Niarakis, RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis, Database, Volume 2020, 2020, baaa017, https://doi.org/10.1093/database/baaa017

New publication on bioinformatic analysis of phage display experiments

In this publication, we introduce PepSimili, an integrated workflow tool, which performs mapping of massive peptide repertoires on whole proteomes and delivers a streamlined, systems-level biological interpretation.

https://www.frontiersin.org/articles/10.3389/fphys.2019.01160/full

Find our new paper here.

The molecular mechanisms underlying inflammatory bowel diseases remain currently not completely understood, and therapeutic options are scarce.

Herein, we have identified that a normally endoplasmic reticulum resident protein, AGR2, exhibits tightly regulated secretion mechanisms that are perturbed in Crohn’s disease. We demonstrate that the extracellular release of AGR2 leads to the chemoattraction of monocytes, thereby suggesting extracellular AGR2’s pro‐inflammatory functions, that can be blocked using specific antibodies.

As a consequence, this discovery could represent an appealing therapeutic approach to attenuate the inflammatory burden in Crohn’s disease.

Join us at Bio-IT World 2019 Boston

e-NIOS is excited to participate in Bio-IT World, 16-18 April 2019, Boston. Join us at Seven Bridges’ booth #332 in the Exhibit Hall, for a demonstration of signature-based interpretation on the Seven Bridges Platform with BioInfoMiner!

 

Collaborative publication with DKFZ, ACCC and NHRF on Radiogenomics and Colorectal Cancer towards Precision Medicine

This is a new e-NIOS’ collaborative work on composite biomarker signatures, combining genomics with positron emission tomography (PET) measurements.

Online paper (open access)

The Athens Comprehensive Cancer Center (ACCC) was founded in 2017, in partnership with  the German Cancer Research Center (DKFZ) (Heidelberg, Germany) and aims to position itself as the first comprehensive cancer center in Greece based on innovative strategies for precision oncology.

 

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Meet us at the ECCB 2018 Conference

e-NIOS is excited to sponsor and participate in the 7th European Conference on Computational Biology, 8-12 September, 2018, Athens.

ECCB is the main computational biology event in Europe and will welcome scientists working in a variety of disciplines, including bioinformatics, computational biology, biology, medicine, and systems biology.

On Tuesday September 11, 2018 Eleftherios Pilalis, CTO, will present the BioInfominer platform for streamlined genomic interpretation at the Applications track.

e-NIOS signature-based stratification presented at the PERMIDES Final Conference

The joint project, entitled “Prioritization and pathway Analysis by MachinE LeArning”, between e-NIOS and Genosalut clinical genomics company, was presented at the PERMIDES Final Conference held on June 12, 2018, in Utrecht, The Netherlands, where fourteen of the best projects presented their results.

The project aimed at the development of an innovative precision medicine application, which integrates clinical and computational expertise, as a decision support tool for diagnosis and treatment of complex diseases. More particularly, an integrated workflow was successfully deployed for patient stratification based on BioInfoMiner biomarker signatures derived from Exome-seq data.

PERMIDES is one out of five European INNOSUP-1-2015 – Cluster facilitated projects for new value chains (funded under EC Call for proposal: H2020-INNOSUP-2015-1), promoting innovation in Personalized Medicine as an Emerging Industry in Europe. PERMIDES targets key solutions for the reconfiguration of the biopharmaceutical value chain towards a Health Economy 4.0 with a special focus on oncology.

New publication involving BioInfoMiner analysis suggests induction of IRE1α-dependent Anticancer Immunosurveillance by low-protein diet (Cell Metabolism)

A new paper involving the participation of e-NIOS and a BioInfoMiner-derived biomarker signature was published in the high impact journal Cell Metabolism.

Dietary restriction was shown to impact on tumor growth with very variable effects depending on the cancer type. However, how dietary restriction limits cancer progression remains largely unknown. In this publication,  we demonstrate that feeding mice a low-protein isocaloric diet but not a low-carbohydrate diet reduced tumor growth in three independent mouse cancer models. Surprisingly, this effect relies on anticancer immunosurveillance. Mechanistically, we established that a low protein diet induces the unfolded protein response (UPR) in tumor cells through the activation of IRE1α and RIG1 signaling, thereby resulting in cytokine production and mounting an efficient anticancer immune response.

http://www.cell.com/cell-metabolism/fulltext/S1550-4131(18)30120-7

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