Welcome to the InSyBio blog

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In InSyBio (Intelligent Systems Biology), we have developed an on-line suite of software tools which assists biology researchers in extracting valuable biological knowledge from experimental data. Our team comprises of four enthusiastic software engineering researchers (Christos, Kostas, Christos and Aigli)  with long year experience in the area of informatiion technology and specially bioinformatics. Our work is strongly supported by Dr. Mavroudi,  a highly experienced academician in the fields of Computational Intelligence and Bioinformatics.

Our research experience on methodologies and algorithms for mining and processing biological data concluded to the development of an integrated bioinformatics tool platform called InSyBio Suite. This platform consists of tools for providing integrated biological information from various sources, while at the same time it is empowered with robust, user-friendly and installation-free bioinformatics tools based on intelligent algorithms and methods. You can find more about InSyBio Suite by visiting our site http://www.insybio.com

In this blog, we indent to share with you our thoughts, knowledge as well as interesting announces referring to the world of bioinformatics. Feel free to contribute to this blog with comments or even articles with your fresh ideas or thoughts.

We welcome you to our blog!

The InSyBio team

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InSyBio taking steps to help tackle the opioid crisis through precision medicine

In an effort to find a better alternative to the traditionally prescribed opioid analgesics, InSyBio worked in collaboration with Clarity Science and the OPERA study (Optimizing Patient Experience and Response to Topical Analgesics) to utilize advanced machine learning methods to not only predict patient response to treatment but also to stratify chronic pain patients into individuals who will benefit from topical analgesics treatment and those who will not in order to personalize treatment for optimal therapeutic results.  InSyBio showed that its analysis application can predict, with high accuracy (AUC 73.8-87.2%), patient response, allowing for a first-of-its-kind precision medicine approach to treating chronic pain.

Peter Hurwitz, President of Clarity Science states: “The OPERA Study showed that there are alternative pain management treatment options available for healthcare professionals to help address a patient’s pain. These options may lead to a reduced focus on Opioid prescribing and other oral analgesics that have side effects and have a significant impact on patient care and outcomes. Collaborating with InSyBio allowed us to identify, using predictive analytics, patients who are most likely to benefit from these alternative forms of treatment without having them trial the medication first, leading to faster patient response, reduced risk of treatment failure, improved patient outcomes, and a better Quality of Life. Incorporating this methodology across other health conditions will have an immense impact on global patient health and will change current strategies and approaches to healthcare treatment.”

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As the opioid use epidemic reaches an all-time high, an option for a less addictive substitute to existing pain treatments has never been more needed. Often Opioids are over-utilized due to their established ability in treating chronic pain and a lack of a proper therapeutic alternative with comparable efficacy. However, Topical agents have the potential to provide analgesic effects without the risk of abuse, misuse, and addiction or many of the systemic adverse events associated with oral analgesics. Through the use of these topical agents, in combination with InSyBio’s superior machine learning tools, a very real option to addictive oral pain medication is enabled.

Labros Digonis, CEO of InSyBio states: “Understanding which patients could benefit from an alternative prescription not only lowers their risk of addiction but also has much larger implications on a national level through the lowering of opioid abuse and related negative consequences. The answer to this epidemic lies in an improved understanding of best treatment options and InSyBio is tackling this incredible feat by acknowledging individual variability, predicting response and stratifying patients into ideal therapeutic groups. This precision pain therapy ability is a breakthrough for the industry!”

This research has been recently presented by InSyBio CSO, Dr. Mavroudi, at the 10th International conference on Information, Intelligence, Systems and Applications  (IISA 2019 – http://iisa2019.upatras.gr/ ).

About InSyBio: InSyBio is an international pioneer bioinformatics revolutionizing the medical field, clinical trials and food/nutrition industries through targeted biomarker discovery and highly-accurate predictive analytics.

Its solutions provide the R&D departments of Pharma, Research Institutes and Food/Nutrition companies, with the means both analytically and computationally to meet their challenging research and innovation goals (such as robust biomarker discovery and accurate predictive models). This is done through a sophisticated, software-as-a-service, machine learning platform which comprehensively integrates multi-omics data reducing the number of samples and additional validation experiments needed. Since 2013, InSyBio has worked with hundreds of academics, large and small companies, hospitals and research centers allowing them to succeed in their biomarker discovery tasks with an increase of at least 10% in predictive accuracy and decrease of at least 80% in overall time and cost.

Visit www.insybio.com to see how InSyBio can help you reach your R&D goals in the era of Precision Medicine and Nutrition.

About Clarity Science LLC: Clarity Science is an international scientific outcomes research Company assisting biopharmaceutical, specialty pharmacies, and other healthcare Companies with the coordination and execution of scientific, IRB-approved, outcomes studies. Managed by a seasoned staff of healthcare professionals, scientific researchers, outcomes statisticians, and guided by physician experts across multiple therapeutic areas, Clarity Science currently coordinates and administers outcomes studies in pain, allergy, podiatry, scar/wound healing, cardio-metabolic, psychiatry, urology, and genomic testing fields. Whether through improving treatment methodologies or identifying new ones, we aspire to make a global positive impact on patient health and to improve the quality of life for patients and their families. Our goal is to conduct scientifically rigorous and valid research that advances innovation in science and ultimately helps healthcare professionals provide improved patient care, leading to improved patient health worldwide. www.claritysciences.com

For any further detail contact our Business Development Manager, Mackenzie Hastings, at m.hastings@insybio.com

InSyBio awarded on Ignite Ideas program organised by Nestle Hellas

InSyBio has been recently awarded for its superior performance in the context of the Ignite Ideas program (https://igniteideas.gr/en/ ) which was organised by Nestle Hellas.

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InSyBio has participated in this program, with its revolutionary idea of personalizing the coffee blend and type selection combining input from a saliva test and responses to questionnaires in order to maximize taste satisfaction as well as other metrics such as quality of sleep and athletic performance. This personalization is empowered with InSyBio’s proprietary biomarker discovery and predictive analytics technologies.

The whole program lasted approximately 6 months and it consisted of three intense phases including extended mentoring from experts from Nestle Hellas and the Athens Center for Entepreneurship and Innovation. During this project we had the chance to optimize the business plan for the personalized coffee selection services we provide and design a first pilot project with Nestle Hellas.

On the 23rd of May, our CEO Labros Digonis, presented our project in front of Nestle Hellas top executives together with the other 5 awarded teams (Coffeco, foodakai, bio2chp, Bespot, shopmind). Within the next 6 months our R&D team will be closely working with Nestle Hellas for implementing the pilot project that has been designed in the context of this program. The outcome of this project will be a personalized coffee selection system which will allow for the first time coffee consumers to select the coffee blend and preparation type that fit their genome and their demographic and lifestyle characteristics in order to maximize taste satisfaction.

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About Ignite Ideas:  “Ignite Ideas” is a Nestlé Hellas initiative aiming to support new ventures (startups) with similar business interests. The initiative is co-organised by the Athens Center for Entrepreneurship and Innovation (ACEin) , the incubation center of the Athens University of Economics and Business. The program aims at developing a (virtual) accelerator of innovative ideas by equipping the participating startups with knowledge, skills, tools and the confidence required to further develop their ideas.
Innovation has been at the heart of Nestlé Group since its beginning. The inventions of Farine Lactée, the first food for infants, by Henri Nestlé in 1867, the “champagne of waters” or the Perrier water that we all know by Sir John Harmsworth in 1903, Nescafé instant coffee by a team of experts in 1929 and Nespresso by Eric Favre, a Nestlé employee back in 1975, are just some of the milestones that prove that behind every bright idea there is an equally bright mind. Today, Nestlé Group steadily invests in Research and Development, nutrition science and passion for quality. Consequently, Nestlé has the world’s largest private food and nutrition research organization, involving about 5000 people located in more than 30 R&D facilities worldwide.
Recognizing the significant presence of innovative ideas in the new Greek entrepreneurship, Nestlé Hellas through its “Ignite Ideas” program is aiming to locate the ideas that have potential for expansion and support them in order to contribute in the productive reconstruction of the country.

About InSyBio: InSyBio is an international bioinformatics pioneer company in precision medicine and nutrition, which focuses on developing computational frameworks and tools for the analysis of complex life-science and biological data.

Its solutions provide the R&D departments of Pharma, Research Institutes and Food/Nutrition companies, with the means both analytically and computationally to meet their challenging research and innovation goals (such as robust biomarker discovery and accurate predictive models). This is done through a sophisticated, software-as-a-service, machine learning platform which comprehensively integrates multi-omics data reducing the number of samples and additional validation experiments needed. Since 2013, InSyBio has worked with hundreds of academics, large and small companies, hospitals and research centers allowing them to succeed in their biomarker discovery tasks with an increase of at least 10% in predictive accuracy and decrease of at least 80% in overall time and cost.

Visit www.insybio.com to see how InSyBio can help you reach your R&D goals in the era of Precision Medicine and Nutrition.

For any further detail contact our Business Development Manager, Mackenzie Hastings at m.hastings@insybio.com

InSyBio Suite V2.5 has been launched and Includes for the first time a complete pipeline for the analysis of RNA-sequencing data

The new version of InSyBio Suite enables the fast and accurate discovery of transcriptomics predictive biomarkers.

  • The newly introduced pipeline in InSyBio ncRNAseq tool offers efficient, user friendly and secure pre-processing of RNA-sequencing data without having to manually define parameters or select the best algorithm to be used in each step.
  • The interpretation of the revealed biosignatures is now reaching a supreme level with our patent pending functional annotation and enrichment tools as well as our network analytics techniques.
  • This new version will enable users generating transcriptomics data to join InSyBio Suite userss community and speed up the accomplishment of their research tasks towards high quality scientific publications and top research outcomes.

InSyBio Suite version 2.5 has been officially launched as of Monday May 9th, 2019. The Chief Scientific Officer of InSyBio, Dr. Seferina Mavroudi, stated that “Our transcriptome contains information combining our genetic predisposition and more advanced epigenetic mechanisms. With the new version of InSyBio Suite we enable the discovery of predictive biomarkers and models from transcriptomics data in an unbiased, error-free optimal manner”.

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InSyBio Suite now offers the following unique features:

  • In InSyBio ncRNAseq tool: An optimized semi-automatically adjusted pipeline for the RNA-sequencing data (fastq or bam files) linked with the rest of the biomarker discovery pipeline offered by InSyBio Suite.
  • In InSyBio Interact tool: Access to a human interactome knowledge base using our patent-pending technology 1 which includes functional annotation of more than 95% of the human proteome. New functional enrichment functionalities were also incorporated.
  • In InSyBio BioNets tool: Incorporation of prior knowledge networks into the process of reconstructing biological networks with correlation or mutual information-based mechanisms.

The CEO of InSyBio, Labros Digonis, stated that “According to recent reports the global transcriptomics market is expected to exceed $3B in 2019 with the RNA-sequencing services part of it being one of the fastest growing. At InSyBio, we had been servicing this market previously with tools for the analysis of non-coding RNAs but were continuously getting requests from the users of our platform and our collaborators for a pipeline for the preprocessing and analysis of RNA-sequencing data reducing the number of parameters that the user need define. Our group of programmers and researchers did their best [work] during the last months and we are now able to offer a user-friendly interface for our RNA-sequencing pre-processing pipeline which can provide results fast, is linked to the rest of our platform’s functionality and requires minimum bioinformatics expertise by the users. Our company’s vision is to act as a catalyst to accelerate discovery of novel biomarkers from multi-omics data and speed up the disruption of the pharma industry in the new era of precision medicine.”

  1. K Theofilatos, C Dimitrakopoulos, S Mavroudi, A Korfiati, C Alexakos, Protein functional and sub-cellular annotation in a proteome, US Patent App. 15/361,461

InSyBio is offering a one-month free license to use InSyBio Suite including the new version of ncRNAseq tool. Request your free trial now by completing a simple form at: https://www.insybio.com/request.html

About InSyBio: InSyBio is an international bioinformatics pioneer company in precision medicine and nutrition, which focuses on developing computational frameworks and tools for the analysis of complex life-science and biological data.

Its solutions provide the R&D departments of Pharma, Research Institutes and Food/Nutrition companies, with the means both analytically and computationally to meet their challenging research and innovation goals (such as robust biomarker discovery and accurate predictive models). This is done through a sophisticated, software-as-a-service, machine learning platform which comprehensively integrates multi-omics data reducing the number of samples and additional validation experiments needed. Since 2013, InSyBio has worked with hundreds of academics, large and small companies, hospitals and research centers allowing them to succeed in their biomarker discovery tasks with an increase of at least 10% in predictive accuracy and decrease of at least 80% in overall time and cost.

Visit www.insybio.com to see how InSyBio can help you reach your R&D goals in the era of Precision Medicine and Nutrition.

For any further detail contact our Business Development Manager, Mackenzie Hastings at m.hastings@insybio.com

InSyBio reveals novel diagnostic and prognostic biosignature for Glioblastoma and announces its presentation at the 11th annual RECOMB/ISCB Conference on Regulatory & Systems Genomics

InSyBio’s R&D team applying the company’s proprietary predictive biomarker technology to a collection of data from open omics repositories came up with a novel biosignature of 13 transcripts and a predictive model for glioblastoma diagnosis and treatment. The biosignature not only increases significantly the diagnostic accuracy for glioblastoma but it is able to differentiate it from other types of brain tumors. Additional validation experiments are planned by InSyBio team, as this biosignature, combined with the trained machine learning models can become a strong tool in the hands of physicians not only for diagnostic-screening purposes but also for personalizing glioblastoma treatment by classifying patients into meaningful genomic phenotypes.

This work entitled as “Combining Network Theory and Machine Learning to Identify a Diagnostic and Prognostic Biosignature for Glioblastoma” was accepted for a poster presentation (poster #54) at the 11th Annual RECOMB/ISCB Conference on Regulatory & Systems Genomics, 10-12 December 2018, New York. It will be presented on the Poster Session 5:30 pm – 7:00 pm on Monday 10th of December 2018.

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Mackenzie Hastings, the neuroscientist of InSyBio, business development associate and the company’s representative in the conference stated: “Glioblastoma is the most aggressive and lethal form of brain cancer but with InSyBio’s novel approach of biological network comparison, we were able to take an unparalleled leap in the pursuit of better diagnosis and treatment through our discovery of a novel, 13-transcript biomarker signature capable of diagnosing both tumor subtype and genetic profile with higher predictive accuracy than any other state-of-the-art method.”. Mackenzie will be present in all three days of the conference and everyone interested in arranging an one-to-one meeting with her in the context of the conference should contact her before the conference via email at m.hastings@insybio.com .

InSyBio’s CEO, Labros Digonis, stated that: “InSyBio has been enrolled for the fight against cancer and specifically against aggressive, currently untreated forms of Cancer such as Glioblastoma. RECOMB/ISCB is considered among the top international conferences for computational and systems biology research and we consider it as a perfect match for us to present our research. Though our participation in this conference we are seeking for collaborators which can contribute to validating and interpreting the glioblastoma biosignature we have uncovered as well as molecular biologists who can benefit from the utilization of our biomarker discovery technology”.

About the conference: The RECOMB/ISCB Conference on Regulatory and Systems Genomics with DREAM Challenges (https://www.iscb.org/recomb-regsysgen2018) is one of the premier annual meetings in the fields of regulatory genomics, systems biology, and network visualization. This multidisciplinary conference brings together both computational and experimental researchers from across the world to discuss recent discoveries about genomic and molecular regulatory networks as well as innovative, integrative methods for developing a systems-level understanding of biological activity.

About InSyBio: InSyBio is an international bioinformatics pioneer company in precision medicine and nutrition, which focuses on developing computational frameworks and tools for the analysis of complex life-science and biological data.

Its solutions provide the R&D departments of Pharma, Research Institutes and Food/Nutrition companies, with the means both analytically and computationally to meet their challenging research goals (such as robust biomarker discovery and accurate predictive models). Since 2013, InSyBio has worked with hundreds of academics, companies, hospitals and research centers allowing them to succeed in their biomarker discovery tasks with an average increase of 10% in predictive accuracy and decrease of at least 80% in overall time and cost.

Visit www.insybio.com to see how InSyBio can help you reach your R&D goals in the era of Precision Medicine and Nutrition.

InSyBio participates in the NBG Business Seeds and the International Accelerator Programs.

For any further detail contact our Business Development Associate Joseph Woodworth (j.woodworth@insybio.com)

InSyBio Suite V2.4 has been launched and includes for the first time the InSyBio Biomarkers Tool

The new version of InSyBio Suite has a significant increase in speed and refinement of the predictive biomarkers process.

  • The pioneer InSyBio Biomarkers tool is a unique tool offering single and multi-omics biomarker discovery with a combination of statistical, machine learning and biological network methods.
  • It allows its users to use InSyBio’s patent pending pipeline for biomarker discovery with increased predictive accuracy and decreased requirements for sample size and validation experiments.
  • with this new version the company keeps innovating whilst focused on its mission to transform and improve the world of precision medicine, ultimately guaranteeing safer and more effective treatments.
  • this new version will improve the experience of more than 400 active users of InSyBio Suite and help them succeed in their research tasks.

InSyBio Suite version 2.4 has been officially launched on Monday 26th of November 2018. The Chief Scientific Officer of InSyBio, Dr. Seferina Mavroudi, stated that “At InSyBio we are crazy enough to think that we can revolutionize the biomarker discovery process – and maybe we have”.

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InSyBio Biomarkers tool offers the following key features:

  • Data preprocessing using a combination of normalization, filtering, scaling and missing values imputation techniques
  • Semi-automatic statistical analysis: automatically select the best statistical test for your dataset
  • Bioinformatics visualization of your omics data with heatmaps, volcano plots, boxplots and excel-like tabular files
  • Identification of multiple biomarker solutions and training machine learning predictors with them
  • Using trained machine learning models and identified multiple biomarkers to predict the phenotype on new data

Other important updates include:

  • Functional characterization of >95% of the human proteome using our patent-pending in silico pipeline.
  • New advanced technique for miRNA target prediction using as input a series of a set of genes and a set of miRNAs and exploring all the potential miRNA:mRNA target sites among them with a computational technique which provides >98% accuracy.
  • Extended changes in the interface of the tool to improve user experience.

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The CEO of InSyBio, Labros Digonis, stated that “Big data—and, more importantly, its effective analysis—enable an unprecedented understanding of the world around us, and make it possible to improve Pharmaceutical and Food/Nutrition Industries to work more effectively and efficiently. Knowing the great added value the Suite brings on, we believe the Insybio Suite will be established as the analysis platform of choice, ‘the SAP’ for Pharma and Nutrition Industries’ R&D”

About InSyBio: InSyBio is an international bioinformatics pioneer company in precision medicine and nutrition, which focuses on developing computational frameworks and tools for the analysis of complex life-science and biological data.

Its solutions provide the R&D departments of Pharma, Research Institutes and Food/Nutrition companies, with the means both analytically and computationally to meet their challenging research goals (such as robust biomarker discovery and accurate predictive models). Since 2013, InSyBio has worked with hundreds of academics, companies, hospitals and research centers allowing them to succeed in their biomarker discovery tasks with an average increase of 10% in predictive accuracy and decrease of at least 80% in overall time and cost.

Visit www.insybio.com to see how InSyBio can help you reach your R&D goals in the era of Precision Medicine and Nutrition.

InSyBio participates in the NBG Business Seeds and the International Accelerator Programs.

For any further detail contact our Business Development Associate Joseph Woodworth (j.woodworth@insybio.com)

Only three days remain until InSyBio Suite V2.4 is launched!

InSyBio Suite version 2.4 will be launched on Monday 26th of November 2018 and it will include among others for the first time InSyBio Biomarkers tool: a unique tool to offer single and multi-omics biomarker discovery with a combination of statistical, machine learning and biological network methods. The addition of InSyBio Biomarkers tool in InSyBio Suite allows its users for the first time to use InSyBio’s patent pending pipeline for biomarker discovery with increased predictive accuracy and decreased requirements for sample size and validation experiments.

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To request a free one-month license or to request a quote for the full version of InSyBio Suite v2.4 please email us at info@insybio.com

InSyBio Biomarkers tool offers the following key features:

  • Data preprocessing using a combination of normalization, filtering, scaling and missing values imputation techniques
  • Semi-automatic statistical analysis: automatically select the best statistical test for your dataset
  • Bioinformatics visualization of your omics data with heatmaps, volcano plots, boxplots and excel-like tabular files
  • Identification of multiple biomarker solutions and training machine learning predictors with them
  • Using trained machine learning models and identified multiple biomarkers to predict the phenotype on new data

insybio_image1

Other important updates include:

  • Functional characterization of >95% of the human proteome using our patent-pending in silico pipeline
  • New advanced technique for miRNA target prediction using as input a series of a set of genes and a set of miRNAs and exploring all the potential miRNA:mRNA target sites among them with a computational technique which provides >98% accuracy.
  • Extended changes in the interface of the tool to improve user experience.

insybio_figure2

About InSyBio: InSyBio is a bioinformatics pioneer company in personalized healthcare which focuses on developing computational frameworks and tools for the analysis of complex life-science and biological data.

For Pharma, Research Institutes and Food/Nutrition companies, who need efficient means both analytically and computationally in order to meet research goals (such as robust biomarker discovery and accurate predictive models), our solution is the best option because we offer a sophisticated, software-as-a-service, adaptable machine learning platform ensured by patent-pending powerful computational pipelines that provide an increase of at least 10% in predictive accuracy and decrease of at least 80% in overall time and cost.

Our brand is better than other well known open source and commercial solutions due to our ability to integrate multiple omics data within a single platform, and to reduce the number of samples and additional validation experiments needed.

Find more details at www.insybio.com

InSyBio is taking another step towards expanding in the US biotechnology market

It’s been only a few months since we have established our presence in USA by setting up InSyBio Inc with premises in Austin Texas with the help of International Accelerator (https://internationalaccelerator.com/ ). Our first steps have been extremely successful being able to attract funding from Angel Investors, acquire new clients and collaborate with some of the significant Texas-based research institutions. We are now in the happy position to announce hiring our second Business Development Associate in Austin, Mr.
Joseph Woodworth. Joseph will work as a full-time employee in our premises in Austin and he will be responsible for disseminating our technology and products in pharma and nutrition industries.

Joseph holds a B.Sc in Biological Sciences (2012) with an emphasis on Molecular, Cellular, and Developmental Biology from the University of California, Santa Barbara. He has worked in the Molecular Diagnostic industry with Cepheid Inc., focusing on viral, bacterial, and genetic disease detection and specification using RT-PCR. Prior to this, he contributed in clinical care as an Emergency Room Scribe at Northridge Medical Center, and in Behavioral Health treatment administration. Joseph has 4 years experience working with technical/product support and product implementation, in customer facing roles.

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About InSyBio: InSyBio is a bioinformatics pioneer company in personalized healthcare which focuses on developing computational frameworks and tools for the analysis of complex life-science and biological data. The key objective of our analysis lies in the discovery of predictive integrated biomarkers (biomarkers of various categories) with applications in pharma, nutrition and cosmetics industries. Find more details at www.insybio.com