Bioclues Newsletter July-September 2021

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Sep 29, 2021, 3:27:06 AMSep 29
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Quarterly newsletter of Bioclues.org
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July - September 2021 | Vol 12 | Issue 3
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BIOCLUES SPEAKS
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Dear Members,

Bioclues is a non-profit virtual organization for, by, and of the Indian Bioinformaticians. One of the fastest growing 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 | Be healthy
Editors: Sakshi Singh, Mohankumar Megha and Rashmi Sukumaran

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As Bioclues.org enters 17th year of service, take a look at the result of people connecting to do science! Here's list of 40+ publications of Bioclues over the years. 

#India #bioinformatics #OpenAccess #OpenScience

Publications of 2021

  • Book chapter: Manjari, K.S., Chakraborty, D., Kumar, A. and Singh, S. (2021). Biodiversity and Importance of Plant Bioprospecting in Cosmetics. In Bioprospecting of Plant Biodiversity for Industrial Molecules (eds S.K. Upadhyay and S.P. Singh). https://doi.org/10.1002/9781119718017.ch10
  • Editorial Perspective: Shukla N, Prasad A, Kanga U, Suravajhala R, Nigam VK, Kishor PK, Polavarapu R, Chaubey G, Singh KK, Suravajhala P. SARS-CoV-2 Transgressing LncRNAs Uncovers the Known Unknowns. Physiol Genomics. 2021 Sep 7. https://doi.org/10.1152/physiolgenomics.00075.2021. Epub ahead of print. PMID: 34492207.
  • Review: Choudhary C, Sharma S, Meghwanshi KK, Patel S, Mehta P, Shukla N, Do DN, Rajpurohit S, Suravajhala P, Shukla JN. Long Non-Coding RNAs in Insects. Animals (Basel). 2021 Apr 14;11(4):1118. https://doi.org/10.3390/ani11041118. PMID: 33919662; PMCID: PMC8069800.
  • Research: Suravajhala R, Parashar A, Choudhir G, Kumar A, Malik B, Nagaraj VA, Padmanaban G, Polavarapu R, Suravajhala P, Kishor PBK. Molecular docking and dynamics studies of curcumin with COVID-19 proteins. Netw Model Anal Health Inform Bioinform. 2021;10(1):44. https://doi.org/10.1007/s13721-021-00312-8. Epub 2021 Jun 10. PMID: 34131556; PMCID: PMC8192041.
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Remembering a great scientist!
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Prof. N. Srinivasan (1 April 1962 - 3 September 2021)

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Head of Proteins: Structure, Function and Evolutionary Group (N. S. Group) at the Molecular Biophysics Unit of the Indian Institute of Science

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Deeply saddened to hear that Prof N Srinivasan of IISc Bangalore is no more. He has been a doyen of StructuralBiology and a scientist  par excellence. He is one of the advisers of @Bioclues.
Our heartfelt condolences to the family. 

A great loss to India and Science!

May his soul rest in eternal peace.

Sympathetically
Team Bioclues

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Tributes to Prof. N. Srinivasan from Bioclues Community

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By Prof. M. Michael Gromiha, IIT Madras
I had a long association with Prof. Srinivasan and I admire his passion for structural bioinformatics research. I had several occasions to interact with him both personally and scientifically. It is memorable about his interactions with our family and his way of explaining major concepts in a simple approach is extremely impressive. He is very enthusiastic about his research on protein structures and I remember our lengthy conversation about his Structure paper for more than 30 minutes over the phone. Last year he attended our 5th IIT Madras – Tokyo Tech joint symposium on Bioinformatics and his lecture on Ramachandran map was fascinating. He told us that he would come again for the next meeting and we really miss him a lot. I am lucky to examine his last student’s thesis and it is the longest thesis I have ever read. He cordially relates with others and respects the works of fellow researchers. His smiling face is not forgettable. It is a great loss to science and everyone who knows him. Our deep condolences to Sowhdamini and Jayashree, and I am sure his presence will always be with us in some ways.

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By Dr. Tikam Chand Dakal, Asst Professor, MLS University, Rajasthan
Great scientists always wear a smile on their faces and have a simple lifestyle. They always inspire others with their smile and simplicity. Late Prof N.Srinivasan was one such scientist.
Saying "no" to anyone, known or unknown, was not in the nature of Prof Srinivasan. Once, I approached him with an invitation for a talk, he accepted the invitation humbly with eternal simplicity and a smile on his face. I was neither his student anytime but he profess me many things in few seconds. I had a few opportunities to talk with him and he was always ready to help me in possible ways.
His sudden demise is really painful.
A heartfelt condolence

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By Dr. Harpreet Singh, Head PG Department of Bioinformatics, 
Hans Raj Mahila Maha Vidyalaya Jalandhar

Like for everyone in the field of Bioinformatics, particularly those working on Structural Bioinformatics, Prof. N. Srinivasan has always been a role model. It was just like a dream come true when Prof. Srinivasan along with Prof. R Sowdhamini, visited our college during the Indian Conference on Bioinformatics 2019 (InBix'19). The keynote talk delivered by Prof. Prof. Srinivasan mesmerized everyone while showcasing the power of Structural Bioinformatics and set the stage for this prestigious conference. Everyone among the participants was highly motivated with his level of knowledge and his simplicity. His two day stay in our college was memorable and was full of excitement, knowledge and encouragement for all of us. His sudden loss is irreparable and has created a void which may never be filled, but he will remain as our role model inspiring us for years to come.

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By Dr. Prashanth, Principal Scientist, Systems Biology, Amrita School of Biotechnology, Amrita University Kerala

                                      SRINI’S  PRASH

It was a night full of thoughts and I was thinking of a person who is an inspiration to many, also to me and many others who are directly or indirectly related to bioinformatics, computational  systems biology and more precisely - “Biophysics”. I was reminiscing about the greatest gift someone has given me in my life, indicating that P-R-A-S-H has all positively charged amino acids. This was the very first slide in his opening talk. It was a surprise for me and more than that I felt it as a great honour and blessing from someone whom we looked up to. Such analogy could only be possible by a Biophysicist and for a school of thought: Late Prof. N SRINIVASAN.

 
The prefixed words make me feel very emotional and I never expected that this was the word I could probably use to our “SRINI” the very next morning. I got the news of his demise and had to confirm this at least twice and wish this was not true. I have had two wonderful meetings that I could think of which gave me a push to move forward in life:

 

The very first occasion was in 2016 when I moved to India after my several years of postdoctoral stint and hiatus. Even before that, I had numerous exchange of emails with Sir and Sowdhamini, who are always down-to-earth. Whence 2016, I knocked on his door at his IISc office without taking an a prior appointment. He was talking to his PhD fellow and warmly welcomed me, gave me almost an hour’s time to discuss science with green tea, all through hypothetical protein research that I carried out, domains of unknown function and, he was working on de-DUFfing works which was a great read. By then, I did not accept any position and was going through places as a “banjara” and taking knowledge and inspiration. That was a perfect moment and at the back of my mind, I felt I finished the 8th year of my Postdoc within just one hour of interaction with him. 
 
The second, of course, was when we organised InBix’17 in Jaipur and later in InBix’19 with Harpreet as a host, their hospitality mesmerized him so much that he wanted another visit to lovely Punjab.  All through his two day stay, he would interact with as many students and would feel apologetic with his trademark simplistic smile, if he had to cut short the discussions on account of time. There were occasions he would also speak about his daughter and her career. 

 

As an adviser of Bioclues, he would give us wonderful suggestions, but in the last few years he couldn’t. We felt it a great honour to nominate him for ISCB accomplishment awards for which he has kindly provided his CV. Glancing at it, I felt the covet could be Srini and a feather would be added to ISCB for honoring him. However, it was otherwise and after the result, he modestly put it, “Prash, maybe it’s time I have grown up.” I bowed to his simplicity, positive approach and school of thought. Wish, I could give him back the “biophysical nomenclature of SRINI” and what all I could think from his name is:  He is Srinivasan - An abode - ‘Lord Venkateshwara/Balaji - Vishnu Avatar’ that he has left for, in void for researchers like us. God loves those who interpret structures and Srini’s excellence was required for this.

 

Srini would always celebrate the success of his students and others as his, and the discussions he would have with P. Balram and Sir Tom Blundell are noteworthy, impeccable to be written in annals of Biophysics.

 

Sir, never ever did we think of this sorry news. We hope and promise that the generations to come will remain unto your expectations. The void within would be covered by Sodhwamini madam as obituaries are to be replaced with excellent papers decorated on your name. Our deepest condolences to the family. Thank you again for the wonderful gift. You have brought a positive facet to my name and I will remain unto your expectations. 

 

Gratefully yours
Prash 

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OUR PAST EVENTS
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ATOPlex: a solution for customized targeted sequencing

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by Ravi Kumar Chilukoti, PhD
on July 07, 2021.

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View recording >>

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Research and Career Opportunities in Europe

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by Hirakjyoti Das (PhD), University of Frieburg, Germany on July 17, 2021.

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View recording >>

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In ‘Sci’versation with Prash: 
Dr. Nirmal K. Lohiya

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Emeritus Medical Scientist, University of Rajasthan, Jaipur on July 22, 2021.

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View recording >>

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GCCI Webinar: Pathophysiology of Colorectal Cancer

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by Dr. Anshu, MGIMS, Sevagram
on September 8, 2021.

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View recording >>

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In ‘Sci’versation with Prash: 
Dr. Mohit Mazumder

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Director, Global Business Development, PineBio, USA and India 
on September 24, 2021.

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View recording >>

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OUR UPCOMING EVENTS
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Galaxy Pre-Conference workshop InBix’21

Introducing Galaxy workshop as part of InBix Conference. The pre-conference workshop will highlight how the Galaxy ecosystem is endowing the podium to data intensive science research. The main focus will be on Drug discovery supplementing the theme of InBix’21 by demonstrating keynotes and workflows relating to Structural Bioinformatics, Cheminformatics, Molecular dynamics with analysis of techniques related to computational chemistry, protein-ligand docking. The workshop will further enumerate topics related to NGS, Epigenetics, Microbial Genomics, Proteomics and the molecular property diagnostic suite. The sessions will be engaged by a great mix of Bharat and Global speakers. During the workshop, you will have the opportunity to perform hands-on analysis along with the presenters which would be a welcoming opportunity for the young scientists and researchers. The Pre-Conference will be held on 9-10 Nov 2021 virtually. For more information, follow the Pre-Conference workshop page of CSIR-NEIST
Tentative registration fee

  • Faculty & Researchers - 1000 INR
  • Students - 500 INR

Registration Link: https://easychair.org/cfp/inBix2021

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Introducing IN-KIND Life Memberships
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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 loves 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 to express your interest sugu...@bioclues.org

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Check out the Benefits enjoyed by a Life Member!

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FEATURED LIFE MEMBER OF THE QUARTER
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Dr. Sudhir Navathe

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Scientist (Wheat Pathology)
Genetics and Plant Breeding Group
Agharkar Research Institute, Pune
Maharashtra, India

Google Scholar | Research Gate | Publons |
Orcid | Twitter

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I am pleased to be part of the lively youth and experienced group, and I hope tol contribute significantly to Bioclues. I envisage Bioclues supporting the academics, in particular young academics, especially in the fusion area of Bioinformatics, who want to make a difference in life sciences. I want Dr. Sakshi Singh to be mentioned in special and thank her for bringing me into the group. Currently, I am working as a wheat pathologist at the Genetics and Plant breeding group at Agharkar Research Institute, Pune. My research is focused on developing new wheat varieties resistant to leaf and stem rust diseases, fungal biology, host-pathogen interaction, diversity of fungal plant pathogens, effectors of plant pathogens, and phytopathology.

 

I started my career in plant pathology at an agricultural university Dr. Balasaheb Sawant Konkan Krishi Vidyapeeth, Dapoli, Maharashtra India. My topic of research was based on the identification and reporting of mushroom biodiversity in the Konkan part of the Western Ghat Region, a biodiversity hotspot and world heritage site of India, and recycling agricultural waste for mushroom cultivation. I was awarded the University Hexamer Gold Medal in Plant Pathology.

Further, I developed my research interest in molecular plant pathology during my doctoral studies at the Institute of Agricultural Sciences, Banaras Hindu University, Varanasi India. There served as an INSPIRE Fellow Department of Science and Technology, Govt. of India. My focus area of research was the molecular and biochemical basis of spot blotch disease resistance in spring wheat. The research at Banaras Hindu University was mainly emphasized to histochemical and pathological analysis for localization of reactive oxygen species and infection process of Bipolaris sorokiniana-wheat interaction, studies on antioxidant enzymes and different reactive oxygen species and their role in response to different stress conditions, marker-based assessment of the population for the QTL mapping/ fine mapping for spot disease resistance in wheat.

Currently, I am working on the projects Mapping of disease resistance in wheat and mungbean, Stress biology and mechanism of biotic and abiotic stress tolerance in crop plants, Surveillance for the black stem rust and brown leaf rust of wheat in Peninsular India, Germplasm Characterization and Trait Discovery in Wheat using Genomics Approaches and its Integration for Improving Climate Resilience, Productivity, and Nutritional quality. Sub Project-3: Evaluation of wheat germplasm for abiotic stresses funded by SERB, DBT, ICAR India, and CIMMYT Mexico.

 

I am looking forward to working with the Bioclues team to enrich myself and also contribute to the area befitting my specialization.

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WELCOME TO NEW LIFE MEMBERS
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Bioclues team welcomes new members of this quarter. 
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Welcome to 

  1. Aruna Vigneshwari 
  2. Zaved Hazarika
  3. Dr. Partha Pratim Baruah
  4. S. Uday Kanth 
  5. Subhomoi Borkotoky
  6. Achanta kavya 
  7. Dr. Altaf Ali 
  8. Ghazala Sultan 
  9. Dr. Sneha Rai 
  10. Dr. Aishwarya 
  11. Dr. Suresh Velpula
  12. Sonali mishra
  13. Dr. Sagar Barage
  14. Dr. Sandeep Kumar
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Become a Life Member!

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Benefits enjoyed by a Life Member

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BIFS PROGRAM UPDATES
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Bioinformatics for School (BIFS) is a six-month bioinformatics program for school children. The first two batches passed out successfully in December 2020 and June 2021. The third batch kicked off on July 17, 2021 with an orientation.

Brief curriculum weeks ( Two lectures a month during saturdays) :
Introduction to Bioinformatics
Molecules
Microbiology
Big data
Basics of Linux programming
Systems biology and Protein Interactions
Statistics
Genetics
9-12 orientation followed by 16-24 weeks of projects

 

The wonderful third cohort includes 13 young minds:

  1. Master. Mohammed Fahad
  2. Master. Achuthan
  3. Miss. Vijaya Niharika Sanapala
  4. Master. Karthik Duppala
  5. Miss. Jyotsna
  6. Miss. Valliyammai Kadappan
  7. Miss. Rachita Kotwal
  8. Miss. Suhani
  9. Master. Gaurav
  10. Miss. Tanesha
  11. Miss. Shristi Kothari
  12. Miss. Bhoomi
  13. Master. Zain Sheezausman
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OUR INDUSTRY PARTNERS

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NanoTemper

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Enabling everyone to do science that matters by always pushing the limits

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WOULD YOU LIKE TO CONTRIBUTE?

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

Write to us at mo...@bioclues.org or sak...@bioclues.org.

Newsletter Editors: Sakshi Singh, Mohankumar Megha and Rashmi Sukumaran

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