BIO INFORMATICS FACILITY

  • Sanctioned on 22nd September 2006


Details about the staff members working in the centre :

Dr. MB Nagaveni              : Co-ordinator
Ms. Usha T.                       : Research Associate
 
Awards:
 
 DBT-Incentive Award                Lab


Dr. Sushil Kumar Middha

DBT-CTEP and UGCTravel grant for presenting a research paper titled"In      silicoexploration of  cyclooxygenaseinhibitory activity of natural compounds    found in Myrica nagi usingGC-MS" in International conference at Montpellier,          France  Aug25-26th, 2015.

Mukta Poojary, Raj Kamal, Asma Amtul Hai, Sushil Kumar Middha “In silico  studies of Anti-Cancerous Compounds for HumanCyclin-dependentKinase 2associated Protein 1” Presented in BangaloreBio2015, Bangalore, India held on10th -11th Feb, 2015.

Usha T

Vijay, Pallabi Misra, Sushil Kumar Middha, Usha T. “Cyperus rotundus withanti-cancerous compounds: A dry-wet lab interaction study,” Presented in BangaloreBio2015, Bangalore,India held on 10th -11th Feb, 2015.(Awarded Ist Best Poster)

Area of specialization of the center:  Database creation and Drug   Discovery

Facilities

Computerand communication facility:  25computers, A     dedicated BSNL line forinternet access, High end Server
Scientificsoftware packages: CLC BIO, Accelrys GCG     package, Quantum software, Discoverystudio 3.5 (all are       commercialpackages and free ware Hex, RasMol etc.)
Databasesand other information resources:  PFam (Proteindatabase)

Publications
  • Usha T, Raj Kamal, Poojary M, Goyal AK,Singh MK, Pande V,Sharma N, Hai AA, Bhardwaj A, Babu D, Middha SK*. Synergeticevaluation of Anti-Cancerous Herbal Compounds for Human Cyclin-dependentKinase 2associated Protein 1- An In silico Approach APJCP 2016 (Ist Review Completed) (IF :2.5)

  • Pradhan S, Goyal AK, Basistha BC, Neelam, Pradhan P,Kumar S, Usha T, MiddhaSK* In Silico basedCombinatorial Modelling andAntioxidant activities of Zingiberaceae familyrhizomes found at higher latitude from North-East India Phcog Mag2016   (in press) (IF : 1.25)

  •  MiddhaSK, Goyal AK, Bhardwaj A, Rajkamal, Lokesh P, Prashanth HP, Wadwa G, Usha T* In silicoexploration of cyclooxygenaseinhibitory activity of natural compounds found in Myrica nagi using GC-MS Symbiosis (Accepted) (IF : 1.45)


 

Bioinformatics Infrastructure Facility (BIF) was established at MLACW duringNovember 2006. This facility has been regularly used by students and faculty members of the Department of Biotechnology of MLACW (40 PG students, and 5 faculty members) and neighboring institutions. The computational facilityprovided by the BIF since its creation paved the way for (i) publication of 15 research papers in SCI journals with an averageimpact factor of 1.5 in the area of bioinformatics and Biotechnology and 40+ oral/poster presentations by the Faculty, Research Scholars and PG students in many national/international fora. A database called PhytoMellitus has been developed which includes the compounds, plants related to diabetes. In collaboration,  Bamboo Database with NBU, Siliguri, WB as well as EctomychorizalDB with Kumaun university were initiated and developed.

Coordinator of the Facility : Dr. MB Nagaveni

            Faculty In-charge: Dr. Sushil Kumar Middha     

        

Department of Biotechnology withinitiation of undergraduate program was later upgraded with theintroduction  of post graduate courses with Biotechnology and Biochemistry.  Add-on courses introducedare:

  1. Diploma and certificate courses in Bioinformatics
  2. PG Diploma course under Karnataka Govenment called BT-Finishing School

 

Researchprojects of the Department:UGC sponsored major research projects (2) on sericulture and neuroscience,minor research projects (8), research projects sponsored by VGST, Dept. ofIT-BT, Govt. of Karnataka (2) Student research projects:  15

 

Ouroutreach program and collaborations:

Institution fundedresearch in collaboration with premier research institutes/ industries. Ourcollege has signed MoU with:

  1. Institute of Computational Biology for Bioinformatics (use of tools, software and technology related to data base management and development, drug designing, molecular modeling etc.)
  2. Jubliant Biosys for Drug Discovery project
  3. Connexios life Sciences for rational drug designing  
  4. IGNOU for developing curriculum for molecular medicine
  5. Institute of Veterinary Research & Animal Husbandry for Leptospiral RT-PCR work.
  6. Institute of Wood Science and Technology for plant tissue culture
  7. Chan-Re research institute for research on cytokines pathway and developing low cost diagnostic equipment for malaria
  8. NIVEDI for networking approaches

Major Activities of theCentre (in bullet form)

Ø  Data mining, Data annotation and Database creation such as

a)       Apetite regulating compounddatabase (under construction)

b)       Phototoxic compound database(under construction)

c)       Phytohelmentics:A phytochemicaldatabase of antihelmentic plants(under construction)

Ø  Networking studies of Diabetes and colon cancer.

Ø  Faculty members andstudents use BIF for carrying out their various research activities. 

Ø  Facility is being usedto conduct interactive classes for school children of neighbourhood to promotethe objective of popularizing biology.

Ø  Diploma andcertificate course students of Bioinformatics comprising both UG and PGstudents utilize this facility.

 

Quantifiable  major achievements (in bullet form)

Databases created:

a)                           Phytomellitus: A photochemical database

b)                           Bambooinfoline: A database for NorthBengal Bamboo speicies (in collaboration with North Bengaluniversity)

Publications:


Biplab Bhattacharjee,Jayadeepa.R.M, Talambedu Usha,Jayadev Joshi, Sushil Kumar Middha : Mapping of the Natural Cancer Chemo Preventive Compounds on PotentialDrug Target Network Relevant to different types Cancer: A Network PharmacologyApproach – Current  Bioinformatics2011, 6: 54-63.

Arvind Kumar Goyal, Sushil Kumar Middha, Talambedu Usha, Subhojyoti Chatterjee, Asim Kumar Bothra, Madhugiri Bhujangrao Nagaveni, Arnab Sen : BAMBOO-INFOLINE: A plant database for north bengal bamboo species. Bioinformation 2010, 5(4):184-185.

Biplab Bhattacharjee, Jayadeepa.R.M, Sanghita Banerjee,Vijay Mathen George, Ajoe.P.Chako and Sushil Kumar Middha “Mapping of natural MMP inhibitor targets on lung cancer network using systems biology approach ” Int J. Curr. Res. 2010; 73-79.   
Mittal Yashoda,Kumar Dharmendra, Middha, Sushil Kumar : Influenza Virus: Mutational Variants in H5N1 and H1N1 J Comp Intelligence in Bioinformatics. 2010, 3(1):91-99.

Biplab Bhattacharjee,Jayadeepa R.M,Anantharamanan R, Samuel Sunil Pillay, Nirmala Kumari, Sushil Kumar Middha “Screening of novel inhibitors for Five natural compounds namely Caffeic Acid,Luteolin, Curcumin, Genistein, and Quercetin: An Insilico Approach” EMBLnet Journal 2009; 16 (A),25-26

Paperpresentations:

 

  • Sushil Kumar Middha, Biplab Bhattacharjee, Jayadeepa.R.M,  Nagaveni M.B and  Usha T. paper entitled “Mapping of natural Signal Transduction modulators in drug target network of Prostrate Cancer– A Network Biology”- oral presentation in  "International Conference on Frontiers in Biological Sciences-InCoFIBS- 2010” held from 01 to 03 October, 2010 at National Institute of Technology, Rourkela, Orissa
  • Biplab Bhattacharjee, Sushil Kumar Middha, , Jayadeepa.R.M Nagaveni M.B and  Usha T paper entitled “Mapping of the potential drug targets on the global cancer network with the aid of network biology approach”- oral presentation in  "International Conference on Frontiers in Biological Sciences- InCoFIBS- 2010”  held from 01 to 03 October, 2010 at National Institute of Technology, Rourkela, Orissa
  • Sushil Kumar Middha,Akshaya, Radika.Nair  Nagaveni M.B and  Usha T. paper entitled “Phtyomellitus-A phytochemical database for Diabetes”- oral presentation in  "National Conference on Frontiers in Biological Sciences and Advances in biotechnology 2010” held from 23rd  to 25th Jan, 2010 at Bannari Amman Institute of Technology, Coimbatore,Tamil Nadu.
  • Anantha ramanan , Biplab Bhattacharjee, Sushil Kumar Middha, Amit Kumar, Anirudh research  paper on "Use of Antioxidants as chemopreventive agents an insilico approach " selected in International Satellite Symposium for Society for Free Radical Research-India on 17 -18 March 2009.
  • Biplab Bhattacharjee, Jayadeepa R.M, Anantharamanan R, Samuel Sunil Pillay, Nirmala Kumari, Sushil Kumar Middha research paper entitled “Screening of novel inhibitors for MEK1 induced Breast Cancer-An Insilico Approach" in International EMBnet-RIBio Conference 2009, jointly organized by the European Molecular Biology(EMBL) network (EMBnet) and the Red Iberoamericana de Bioinformatica (RIBio) at the Paradisus Riviera Cancun Resort, located at the Mayan Riviera, Quintana Roo, Mexico, from the 26th to the 29th of October, 2009.
  • Subhojyoti Chatterjee , Deepak Choubey, Biplab Bhattacharjee ,Anantharamanan.R, Jayadeepa RM, Anirudh Chowdhary , Sushil K Middha  and Usha Talambedu research paper entitled “Screening for anti-angiogenic natural inhibitors for vascular endothelial growth factor receptor-An Insilco approach” selected for presentation in BIOT -2009, The 6th Annual Biotechnology and Bioinformatics Symposium  held at Lincoln, Nebraska, hosted by  Center for Plant Science Innovation,  the University of Nebraska-Lincoln,USA .
  • Biplab Bhattacharjee, Anantharamanan R, Sushil Kumar Middha, Jayadeepa R.M, Indhuja. R, Seema Vaidya, Shoba.G, Prema G, Sreedevi S, Usha T, Anirudh Chowdhary, Animesh Acharjee research paper entitled "Appetite Regulating Compound Database" InCOB 2009 Singapore, An Official Conference of Asia Pacific Bioinformatics Network 7 -11 September 2009.
  • Anantharamanan.R, Biplab Bhattacharjee,Indhuja, Jayadeepa, Shafna Asmy, Naveen Prem, Sushil Kumar Middha, Amit Kumar research paper entitled "Selective Estrogen Receptor Modulator effect of Malvidin on Estrogen Dependent Breast Cancer" selected for Oral Presentation in 4th International Symposium on Health Informatics and Bioinformatics, Turkey 09 April 16-17, 2009, METU Informatics Institute, Ankara, Turkey
  • Anantharamanan.R, Biplab Bhattacharjee, Sushil Kumar Middha, Amit Kumar, Krashi Shetty, Neerajana Dutta, Sharon Misquith, Shiva Kumar  research paper entitled “STUDY OF CHEMOPREVENTIVE EFFECT OF NATURAL MOLECULES ON VARIOUS BIOLOGICAL TARGETS OF BREAST CANCER” selected for Oral Presentation  in International Conference on Open Source for Computer Aided Drug Discovery on 22-26th March 2009. 
  • Biplab Bhattacharjee, Jayadeepa R.M., Anantharamanan.R, Shibhin Babu, Anamika Prasad, Shalika Srivastava, Dharmendra Kumar,  Sushil Kumar Middha, T.Usha, Animesh Acharjee  research paper entitled “Screening of natural inhibitors of Neuraminidase Type 1 in H1N1 for Treatment of Swine Flu-An Insilico Approach”   selected for presentation  in APBC2010 -The Eighth Asia Pacific Bioinformatics Conference, 18-21 January 2010.

Bestposters

·        Sushilkumar Middha, Usha Talambedu Mapping of the NaturalCancer Chemo Preventive Compounds on Potential Drug Target Network Relevant toColon Cancer: A Network Pharmacology Approach held at Pondicherry university in21st DBT BIF meet inPondicherry.(1st  prize)

  • Sushil kumar Middha, Usha Talambedu, Akshaya, Radika N. “Phytomellitus:A phytochemical database for Diabetes” at National conference on Bioinformatics, Bangalore, 22nd-24th Feb 2010.( II Prize for Poster Presentation)
  • Dharmendra Kumar, Sushil Kumar Middha, Shweta Gupta, Biplab Bhattacharjee, Kavitha Iyer and Pushpa Agrawal, Sushant Bhushan, “Sequence Analysis of H5N1 & H1N1 for Ascertaining Test System”, at Intl. Symposium on Computational Biology & Bioinformatics (ISBB 06), Bhubaneshwar,15-17 Dec. 2006. (Best Poster award)
  • Sushil kumar Middha, Jai Kamat, Akashatha Shanbhag “Sequence analysis in CFTR  in ascerting test system” ,  Presented in National Symposium on Bioinformatics (Motif’ 06),  (II Prize for Poster Presentation )
  • Schonidger Award for Best Poster/Paper Award : Anantha, Monisha, Biplab and Sushil Kumar Middha New Lead molecule prediction for Uterine Cancer”, at Intl. Symposium on Computational Biology & Microarray (2007), at Hyderabad Univ., 15-22 Dec. 2007
  • Sushil kumar Middha, Reshma Anjum, Amitha, Sherry Jann  “Sequence analysis of H1N1 and H2N2”-  National Symposium on Bioinformatics (2007), at Acharya College, Nov. 2007 (II Prize)

 

NationalConference/symposium:

·      National Conference onComputational Biology, Bioinformatics and Life Sciences, May 2-3, 2007 

·      Featuresand Future of Clinical Research  at  J.N. Tataauditorium, Indian Institute of Science, Bangalore  on April 22, 2008.

 

      Nationalworkshops:

·     In silico drugdesigning and molecular modeling July 25- Aug 10, 2007

·      Microarray,Microarray data analysis and Systems biology Sept. 18 – 21, 2008 incollaboration with Institution of computa-tional Biology (IOCB).

·     Role of system biologyand algorithms in drug discovery process 26- 28, December 2008 (IOCB  and DBT-BIF centre, MLACW jointly organizedthis workshop)

·     Molecular Detection ofa gene (Wet lab) and post genomic studies with the help of bioinformatics tools(Dry lab studies)from April 10-12, 2009

·      cDNA analysis with the help of RT-PCR (Wet Lab) and post Genomic studieswith the help of bioinformatics tools (Dry lab studies)  from 31March-April 3, 2010

·     Gene Expression analysis and post genomicstudies with the help of Bioinformatics tools’  17-19 September, 2010

 

    Collegiatelevel workshops:

·     3-days  hands on session on “Molecular Detection of agene (Wet lab) and post genomic studies with the help of bioinformatics tools(Dry lab studies)”  June 2009

·     3-days  hands on session on “Teach syllabus” forBangalore University Bioinformatics syllabus (PG course), June 2009

·     Summertraining program on laboratory techniques in pre clinical drug developmentprocess, July 1-15, 2009

 

Hands-onworkshop for faculty members:

·     GCG wiscon package incollaboration with Accelrys on May 15, 2007

·     Genious Pro  software by Orsby Engineering Pvt. Ltd.BIOWARE Div.(April 11, 2007)

 

Placements

Ø  Students who haveundergone training in bioinformatics diploma course are placed in companieslike  Jubilant Biosys, Accenture,Molecular Connections, Quintiles, Empower, Clinigene (Biocon group),  Biowares, Apsara Innovation center etc.  as bioinformatics professionals and researchassistants at Raman Research Institute.  Oneof the students has joined IISc as Ph.D. student                                            

Bioinformaticsdivision of our college got strengthened further after the establishment ofDBT-BIF centre.  Since then several majoractivities like national/collegiate level symposia/conferences/workshops havebeen conducted for the benefit of biology enthusiasts. Creation and publicationof databases which are available for public domain, publications of severalresearch papers in journals of repute where research work was carried out by integratingwet lab work  with bioinformatics tools ,paper presentations at international and national symposia and conferences werepossible through using the facilities which were made available throughgenerous financial assistance from DBT.  Thushaving DBT-BIF has realized the institution’s dream of catering to societalneeds through our contributions in the form of learning and sharing theknowledge.

Creationof databases which have been already initiated and also those which arementioned below require continuous support from DBT for  Bioinformatics facility at our college.