Bioclues Newsletter April-June 2023

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Jun 30, 2023, 2:41:52 AM6/30/23
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Quarterly newsletter of Bioclues.org
April - June 2023 | Vol 14 | Issue 2
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BIOCLUES SPEAKS

“For good ideas and true innovation, you need human interaction, conflict, argument, debate”. 
                                                                                                                        Margaret Heffernan
 

 

Dear Biocluers,

Bioclues is a non-profit virtual organization for, by, and of the Indian Bioinformaticians. A largest bioinformatics societies in India. Bioclues was built on the foundation of connecting people. Bioclues aims to bring together the Indian bioinformaticians, foster a strong working mentor-mentee relationship, provide access to bioinformatics resources, organize conferences and workshops besides imparting information about research, training, education, employment, and current events and news from bioinformatics, genomics, and related fields.

Read on to know more about our latest events and members

Stay Safe and be healthy!
Editors: Indrani Biswas, Rajul Jain, Sandeep Kumar and Rashmi Sukumaran

With inputs from Prashanth N Suravajhala 

Accolades of Rajeev Varshney, PhD!

Bioclues wishes Rajeev Varshney, our ardent adviser and a doyen, heartiest congratulations for being awarded as Fellow of the Royal Society. He is the fourth Indian Agricultural Research Scientist to receive this prestigious fellowship. 
On this special occasion, he shared his thoughts, “I feel humbled and honored to have been elected as a Fellow of the Royal Society. This is like a dream come true for any scientist. I am thrilled to be included alongside the stalwarts and giants such as Norman Borlaug, MS Swaminathan, Jim Peacock, Gurudev Khush, who have been inspirations and role models not only for me but for all agricultural scientists across the world". He added, "I am grateful to my colleagues and collaborators from Australia, India, Germany and many countries in Asia, Africa and America with whom I had the privilege of working with over the last 25 years. 

Student Representatives of Bioclues 

Hi! I'm Goldy Singh Student chapter Chair of BIOCLUES. “I'm pursuing MSc in Biotechnology from Amrita School of Biotechnology, Amritapuri and have also completed my bachelor's degree from Amrita. I have done a project under the guidance of Dr. Prashant Suravajhala -  Principal Scientist, Bioclues- on the topic "Metagenomics and neurodegenerative diseases".

“I'm Malavika J, one of the Student Chapter Chairs of BIOCLUES.
I have done my Bachelor's in Biotechnology from Amrita Vishwa Vidyapeetham, Kerala and completed my dissertation under the guidance of Dr. Prashant Suravajhala-Principal Scientist, Systems Genomics Lab, Amrita Vishwa Vidyapeetham, on the topic "Inferring recombination events in SARS- CoV 2 in silico".
Currently, I am pursuing my Masters in Biotechnology at Vellore Institute of Technology, Tamil Nadu.
Writing, blogging, reading as well as networking are my hobbies as it helps in honing my communication and interpersonal skills. Hope to meet all the bioinformatics enthusiasts in Bioclues and have fruitful discussions”.

  Bioinformatics and Computational Biology: 
Background and Rationale in Life Sciences

In the ever-evolving field of life sciences, advancements in technology have transformed the way we explore and understand the complexities of living organisms. One area that has played a pivotal role in this revolution is bioinformatics and computational biology. Combining biology, computer science, and statistics, these interdisciplinary fields have revolutionized our ability to analyze vast amounts of biological data and extract meaningful insights.


Bioinformatics involves the development and application of computational methods to study biological data. It encompasses a wide range of areas, including genomics, proteomics, transcriptomics, and metabolomics, encompassing system biology altogether. By leveraging computational tools and algorithms, researchers efficiently analyze and interpret complex biological data, leading to discoveries and communication in various life science domains.
The rapid advancement of DNA sequencing technologies has been a major catalyst for the growth of bioinformatics. The ability to generate massive amounts of genomic data quickly and cost-effectively has presented researchers with a new set of challenges: how to store, analyze, and interpret this vast amount of information. This is where bioinformatics and computational biology come into play, providing the tools and techniques necessary to extract meaningful knowledge from genomic data. This sets the primary goal of bioinformatics is to decode the information encoded within genomes. By analyzing DNA sequences, researchers identify genes, regulatory elements, and functional regions within the genome enhancing the understanding of genetic basis of diseases, identifying potential drug targets, and exploring the evolutionary relationships between different organisms. 


Additionally, bioinformatics plays a crucial role in the field of comparative genomics. By comparing the genomes of different species, researchers gain insights into evolutionary processes, identify conserved regions, and understand the genetic basis of traits. Comparative genomics has been instrumental in studying the evolution of species, uncovering the genetic underpinnings of human diseases, and even shedding light on our shared ancestry with other organisms. Proteomics, the study of proteins and their functions, is another area greatly influenced by bioinformatics. Proteins play essential roles in various biological processes, and understanding their functions is critical for deciphering the complexities of life. Bioinformatics tools enable the identification and characterization of proteins, prediction of protein structures, and analysis of protein-protein interactions. These insights aid in understanding protein functions, pathways, and the underlying mechanisms of diseases. Transcriptomics, on the other hand, focuses on studying the transcriptome, which represents the complete set of RNA molecules in a cell or tissue. 


Bioinformatics tools allow researchers to analyze gene expression patterns, identify differentially expressed genes, and uncover potential biomarkers associated with diseases. This knowledge has significant implications in personalized medicine, where tailored treatments can be developed based on an individual's unique molecular profile. Moreover, bioinformatics and computational biology have made substantial contributions to drug discovery and development. By utilizing computational methods such as virtual screening, molecular docking, and quantitative structure-activity relationship (QSAR) modeling, researchers expedite the identification of potential drug candidates, optimize their properties, and predict their efficacy. These computational approaches reduce the time and cost associated with traditional drug discovery methods, accelerating the development of novel therapeutics.


In addition to their impact on genomics, proteomics, and transcriptomics, the recent development in bioinformatics and computational biology have also paved the way for the emergence of systems biology—a holistic approach to understanding biological systems as interconnected networks of molecules and processes. Systems biology integrates data from various biological levels, such as genes, proteins, and metabolites, to gain a comprehensive understanding of complex biological phenomena. This interdisciplinary field has enormous potential for advancements in personalized medicine, drug discovery, and the development of innovative therapies.
As the field of bioinformatics continues to evolve, professionals in this field have a promising and fulfilling career ahead. From analyzing large-scale genomic data to developing computational models of biological systems, the application of bioinformatics tools opens up a plethora of opportunities for those pursuing a career at the intersection of life sciences and computational sciences. By harnessing the power of bioinformatics and computational biology, researchers and professionals can unlock new frontiers in understanding life's intricacies and make transformative contributions to the field of biology.

                                                                                                                                                   Rajul Jain, PhD
                                                                                 Joint Secretary and Women in Biology Chair 

Lankan Conference in Bioinformatics (Lanbix, 2023)

Session 1
Imbalance datasets in Machine learning - Challenges and Techniques

Pramod P Nair, PhD. Assistant Professor, Department of Mathematics, Amrita Vishwa Vidyapeetham, Kollam, India

The talk commences with the distribution of datasets and introduction to terms like biased productive models, overfitting etc. How deep learning algorithms are used in evaluation matrices, the techniques of under sampling, over sampling, cost sensitive sampling and ensemble methods are discussed extensively. According to the output the researcher aims to get, the option of the precision method can be used. On the other hand, methods like F1 scores, area under the curve etc can be misleading many of the times.  Undersampling for binary links using Tomek links, is assumed to be for noisy or ambiguous instances. Data points are shown to be highly overlapping in such cases. An explanation about Smote - Synthetic Minority Oversampling technique, an undersampling technique, where synthetic instances are created to replicate or duplicate data in the datasets, is provided.  It is done to generate instances of minority class. Moving on, the importance of cost sensitive learning is also discussed by Pramod P Nair. The concepts of class weights, cost sensitive algorithms and threshold moving are extensively elaborated.
Ensemble methods like bagging, booting and decision trees are also covered. Data imbalance affects the machine learning algorithm and model in a detrimental way. Choosing the right technique depends on the class distribution. Likewise, choosing the appropriate evaluation matrix depends on the problem in hand, as well as the various hybrid balancing techniques. It was indeed an insightful talk, by  Pramod Nair. 

Session 2
AI in Biology - a different perspective

V R Manoj, PhD, Professor and HoD, Veltech University - Department of Bioengineering 

It is an enlightening session in which he elaborates about AI BIO applications like, drug discovery, disease diagnosis, genomics, ecology etc. Emergent areas, like synthetic biology, precision agriculture, digital image analysis etc. Some new terms like genetic circuits, omics etc are also introduced. Recent applications of AI include XENOBOT, Microfluidic chips, microbiome evaluation, bioprinting etc.It is an imperative talk on which he stated that AI can be used in medical biotechnology, industrial biotechnology, animal biotechnology as well as agriculture.
He also mentioned the top 10 biotechnology innovations and trends of 2023 with respect to AI. Gene sequencing, bio manufacturing and precision medicine etc will rule the field of bioinformatics and biotechnology in the years to come. 
V R Manoj discussed the numerous applications of XENOBOT which can reveal entire development information about organisms. It is one of the recent advancements of AI in the field of regenerative medicine.
The concept of smart materials, neural networks, deep learning etc were also discussed extensively in this talk. Smart materials are those materials that are capable of complex behavior, due to incorporation of nanocomputers and nanomachines. Hybrid neural systems and their applications in healthcare are also introduced. Their stimulation of neurons and treatment of diseases, are shed light onto. The complex evolution of structures and patterns in biology are instrumental in developing similar patterns in computers, to better aid in understanding networks.

 

Artificial Intelligence and Machine Learning in healthcare

K. Sri Manjari, PhD,  Secretary, Bioclues.org

K. Sri Manjari starts with the most important idea of whether machines can think or not. From that point, the discussion takes on interesting directions. AI, Machine learning and deep learning are employed widely in health sectors in the modern world today. AI assisted robotic surgery, medical diagnosis, treatment, medical data security are the key areas in which different types of technological advancements like programming and artificial intelligence are employed.
Medical image analysis can be used to look for lesions, scratches or internal injuries for better diagnostic purposes. She also elaborates on the complex neural networks and informed AI networks. K. Sri Manjari also discusses how AI is used to decipher the cognitive abilities of the brain and understand the complex interaction between the neurons, to help foster connections. She also elaborates about the various steps required to create imaging of healthy and unhealthy tissues with informative illustrations and figures. Radiopharmaceuticals and radiochemistry analysis are being worked on to generate such high quality images in such good resolution in the modern world today. Differences between Translational medicine and precision medicine are also discussed. 
The common factors being modern based data integration, biomarker guided trial designs and Artificial intelligence playing major roles in both of the types of medicinal approaches. An interesting diagram about the multi omic approaches, clinical trials, disease endotypes, and comparison diagnostics, biomarker guided clinical trial designs under precision medicine is also extensively conveyed by K. Sri Manjari. Additionally, the various influences of Big data analytics in healthcare are analyzed. They imply that the results are dependent on the human mind and health, with respect to Artificial intelligence and applications. Data fusion and integration with concepts like linear regression is discussed with enthralling, catchy diagrams and flowcharts. Data labeling, modeling, reporting, data collection, medical analysis are the few of the many steps elaborated by K Sri Manjari. This interesting field has many outcomes including the increase of health coverage as well as better prevention and treatment of infections, diseases as well as outbreaks.

 

Sponsors' Talks

Amit Bhattacharya, PhD: TissueGnostics

Amit Bhattacharya, working at TissueGnostics, discussed their technology called TissueFAXS. TissueFAXS is a bio-image informatics approach to cellular analysis of tissues, which is based on the use of computational techniques to analyze bio-images, particularly microscopy images, especially cellular and morphological images at large scale, to obtain useful knowledge out of complicated and heterogeneous biological images. The technology focuses on the use of computational techniques to analyze bio-images in this case microscopy images, especially cellular and morphological images at large scale. Dr. Bhattacharya explained that bio-image informatics is a branch of data science and bioinformatics that is strictly based on images of microscopy. The technology is a combination of bioinformatics and computational biology that focuses on analyzing bio-images in large scale and high throughput.
Bhattacharya discussed how the subject of bioinformatics as a discipline has focused mainly on microscopy images, particularly cellular and morphological images. Because microscopy images are heterogeneously complicated, they generate a huge amount of data that requires data image management, building an image repository, ontologies, annotation of images, and cloud computing to analyze using machine learning techniques, particularly deep learning. He explains that tissues are spatially heterogeneous, and the ROI for data analysis should be as small as possible to address this problem. Therefore, they collect data from single cells in a tissue, in a biologically relevant way, using the subject of cytometry. Cytometry is the process of collecting data from single cells and from each cell, multiple parameters and taking data from all cells in a system or in a tissue section. He also explains that they use TissueFAXS to identify single cells in a section and collect data from them without breaking up the tissue and losing special information.
Overall, he highlighted the importance of using bio-image informatics and computational techniques to analyze complicated and heterogeneous biological images and extract useful knowledge from them. He also demonstrated how tissue FAX is used to collect data from single cells in a tissue section, which is crucial for understanding the spatial heterogeneity of tissues.

 

Sponsors' Talks

Revolutionizing Biology with AI: What Young Scientists Need to Know 
Rajul Jain, PhD 

Rajul Jain believes that there is a dire need for a new revolution in biological studies, particularly in the current global health threats and environmental crisis, and that AI holds immense potential to revolutionize biology. She explains the difference and relationship between AI, machine learning, and deep learning, and emphasizes the importance of collaboration between biologists, AI experts, clinicians, and technicians, as well as attention to data quality, computing power, ethical considerations, validation, and interpretation of results.  Rajul Jain also discusses the advantages of using AI in biology, such as increased efficiency, accuracy, and the ability to analyze large amounts of data much faster than humans. She uses Alzheimer's disease as an example of how AI can be applied to deal with various types of data available for prediction, identification, and treatment of the disease.

 

Video Abstract

  1. Priyanka Sonar- New Visions in Infection Control
  2. Natte Sai Bharath - Oral Cancer Detection Using machine learning.
  3. Adhithya Sudeesh- Data Imbalance in Multilabel Classification
  4. Sneha K H- Biologically inspired ChaosNet architecture for Hypothetical Protein classification.
  5. Ranjana Raju- Benchmarking Exome pipeline for inferring consensus variants.
  6. Anjali Krishna. A- Inferring variants of Unknown
  7. Bhargavi – Prostate Cancer Genomics
  8. BRITE Fellows- Rare Diseases
  9. Sana Fatima- Artificial Intelligence in Agriculture

 

Session 3

An epilogue over Galaxy with ML 
Kiran K Telukunta, PhD

Kiran K Telukunta has a PhD in pharmaceutical bioinformatics and is an expert in the use of the Galaxy data analysis platform. His talk was on "An Epilogue over Galaxy with ML" and he provides an overview of how Galaxy can be used with machine learning techniques.
Kiran Telukunta then delves into the use of machine learning techniques with Galaxy. He provides examples of how machine learning can be used in different applications such as image recognition, protein structure prediction, and drug discovery. He emphasizes that Galaxy provides a user-friendly interface for users who may not have a background in programming or machine learning.  Kiran  Telukunta also discusses the benefits of using Galaxy for machine learning, such as the ability to automate repetitive tasks and the availability of pre-built tools and workflows. He also touches on the challenges of using machine learning with Galaxy, such as the need for large datasets and the importance of proper data preprocessing. Towards the end of his talk,  Kiran encourages the audience to become part of the Galaxy community and contribute to the development of the platform. He explains that the Galaxy Training Network provides resources for users to learn how to use the platform and contribute to its development.
Overall, KiranTelukunta's talk provided an informative overview of how the Galaxy platform can be used for machine learning, and encourages users to become part of the Galaxy community.

 

Summary and Conclusions By Sandeep Kumar, PhD 

Lastly the session was concluded by Sandeep Kumar by thanking the eminent speakers and Bioclues team for their efforts in organizing the conference. There were a total of 170 registrations and video abstracts. The conference discussed different areas of AI, and the audience learned a lot from the sessions. The success of this conference depends on how the participants will use the information in their research. The Bioclues team requests everyone to get involved in ML and AI and use the tools in their future research. Bioclues organizations also look forward to future partnerships with the participants and request more active participation in future collaborations. This concludes by thanking all the participants and speakers for their time and valuable knowledge sharing.

OUR PAST EVENTS

In ‘Sci’versation with Prash:

K. Sri Manjari, Ph.D.

GenepoweRx, India

on May 3, 2023.

View recording >>
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In ‘Sci’versation with Prash:

Sahitha Lulu, Ph.D & Vino S. Ph.D

VIT, Vellore

on May 24, 2023.

View recording >>
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On eve of International Mothers' Day

Charu Lata, Ph.D, NIScPR, New Delhi

Saranjeet Dhawan, Ph.D, University of Ladakh

Kavitha Thirumurugan, Ph.D, VIT, Vellore

on May 13, 2023.

View recording >>
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GCCI: Genetic Counseling in Prenatal Genomic Diagnosis

Usha P. Dave, Ph.D, D.H.A, Lab Director, Navigene on May 13, 2023.

View recording >>
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           R Programming Workshop                              Python Programming Workshop

   K. Sri Manjari, Ph.D, GenepoweRx, Hyderabad                    Prashanth N. Suravajhala, Ph.D, Amrita 

   on April 27-28, June 17-20, 2023                                                School of Biotechnology, Amritapuri

                                                                                                                                on May 1-4, 2023.

View recording >>
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Systematic review and Meta-Analysis workshop

One of the successful and longest duration events conducted in the month of May, 2023 was a workshop on systematic review and meta-analysis, by Mrs. Shinduja Vikas, who has extensive experience in scientific writing and has been working as a Copy Editor in Taylor and Francis. This workshop focussed on theoretical and practical sessions. A detailed overview was provided regarding the importance and rationale of systematic and meta-analysis review. The difference and applications of these reviews were explained as a hands -on workshop session. For this kind of review analysis, implementation of PRISMA guidelines is necessary, which was illustrated during the session. Further, all of the participants were taught hands-on sessions to work with R studio, which facilitated participants to interact and learn. It reached participation beyond 25 participants. 

 

Introducing IN-KIND Life Memberships

Dear Members,

Bioclues as a non-profit organization would like to introduce 100 "in-kind" Life Members (LM) of our society and accorded from all States and Union Territories of India. In the next one month, we want to have 100 "in-kind" LMs who are needy, facing financial problems, but love doing bioinformatics, and are eager to join this society. If you have any student who is deprived of taking services at the expense of not being able to pay the membership fee, please let us know! The members would be given a full fee waiver for Life Membership. We anticipate that these less-privileged members will bring one paid LM each in due course.

Contact our secretary, Dr. K. Sri Manjari, to express your interest at  s...@bioclues.org

LIFE MEMBERSHIP

 

Welcome to our new Life Members!

  1. Swarkar Sharma
  2. Kshipra Chauhan
  3. Krupa S
  4. Vipul Kumar
  5. Aadya Kapoor
  6. Shinduja R

     
Become a Life Member!
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Benefits enjoyed by a Life Member

Our heartfelt Condolences

Team Bioclues offers sincere condolences and deepest sympathies to the family of and friends of Christian Schonback, Professor of Bioinformatics in Nazarbayev University, Kazakhstan on the latter’s sad demise.

Christian served as an APBionet past president and had contributed to some of the best works on transcriptional landscape and functional genomic databases.

OUR INDUSTRY PARTNERS

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TissueGnostics

A solution provider for Precision Medicine / Next-Generation Digital Pathology and provides fully integrated cutting-edge tissue cytometers

WOULD YOU LIKE TO CONTRIBUTE?

We would love to publish your research highlights, achievements, popular science articles, poems, drawing, cartoon or photographs. 

Write to us at indrani...@gmail.com, kc.sa...@jainuniversity.ac.in.

Newsletter Editors: Team Bioclues

BIOinformatics CLUb for Experimenting Scientists (BIOCLUES)
Mail: ad...@bioclues.org
 

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