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Dr. B. R. AmbedkarCenter for Biomedical Research, University of Delhi (North Campus), Delhi 110007


About the Bioinformatics Centre
 

Bioinformatics Facility was created at ACBR in the year 2003 with purchase of Molecular Modeling software Insight II, GCG, TSAR from Accelrys. Later on, since 2006 the facility is being funded and supported by Department of Biotechnology (DBT), Govt. of India. The primary objective of this facility is to promote biology teaching and understand its different aspects computationally through bioinformatics. It provides services to the host faculty and other neighbouring institutions of higher education in terms of Internet connectivity, retrieval of online and offline biological databases, bioinformatics software and tools for facilitating biological research particularly in the area of sequence and phylogenetic analysis, database development, molecular modeling and drug design, etc. We also periodically organize hands-on trainings on various aspects of application of bioinformatics tools and molecular techniques in biological research. ACBR since 2008 has consecutively organised workshops for the better understanding of different modules of drug design tools. These workshops trained number approximately 150 participants from different universities over the period of time in the field of bioinformatics and its applications in computer aided drug design.
 
BIF Centre
 
Objectives
The primary objective of this facility is to promote biology teaching and understand its different aspects computationally through bioinformatics. It provides services to the host faculty and other neighbouring institutions of higher education in terms of retrieval of online and offline biological databases, bioinformatics software and tools for facilitating biological research particularly in the area of mining genomes and functional analysis, database development, molecular modeling and drug design and other fields of Bioinformatics.
 
Academic Programme at ACBR
The Masterís & Ph.D. program of ACBR provides an unparalleled opportunity for highly self-motivated independent minded young scholars to acquire superb academic training, while participating as colleagues in research of fundamental importance. Prospective students should develop a commitment to a career in scientific research. Admissions to this program are granted on the basis of test conducted on all India basis, followed by interview and group discussion. Students are selected, given an opportunity to explore the research interest before selecting their field of research in specific laboratory. Under the M.Sc.-Ph.D. Combined Program in Biomedical Sciences students usually spend the first two years in both course work and the laboratory, and the remaining years predominantly pursuing their thesis research.
  • M.Sc.-Ph.D. Combined Degree and M.Sc. Degree Program in Biomedical Sciences.
  • Ph.D. Programme
 
Current area of research
 

ACBR has core faculty in the field of Chemistry and Biology, thus facilitating research and teaching in interdisciplinary areas in Biomedical Sciences. The areas of research pursued by the faculty encompasses molecular pathology of infectious diseases, Molecular Oncology, Gene Regulation, Molecular Genetics, Epigenetics, Medicinal Chemistry and Natural Product Chemistry, Drug Discovery and Drug Designing, Bioinformatics and Molecular Microbiology and Immunology.

Inter Institutional collaboration

The faculty of ACBR and other departments of University of Delhi, IGIB, INMAS, DIPAS and VPCI, ICPO, AIIMS collaborate in offering a M.Sc.-Ph.D. program of advanced study and research in advanced Biology, Chemistry and Biomedical Sciences. In addition to the didactic teaching, the ACBR arranges many research colloquia, seminars, lectures by visiting scientists under SURP (Summer Undergraduate Research Program) and other special scientific programs.

Infrastructure facilities
Computer & Communication facility
We have state of art computer and communication facility at the center with a number of workstations and computers. All the research labs have computers for Ph.D. students and M.Sc. Students and a well maintained computerized library and networking through Delhi University Computer Center.ACBR is equipped with two HPZ210, eight HP 4300 and 4600 workstations, one SGI silicon graphics workstation. Besides this a good number of latest computers are available in central computer room, Library and laboratories and students get hands on training on these computers which are placed in very spacious air conditioned Computer labs.
Scientific Software packages
ACBR BIF facility is equipped with Molecular Modelling Software from Acclerys, Sybyl X, HIPERCHEM, AMBER, discovery series (Quantity 1) for gel documentation, Cn3D, Rasmol for Molecular visualization. The centre has Omega (GCG for sequence analysis of DNA & Proteins) and. We have number of workstations with LINUX as well as windows platform for study of Protein-protein Interaction, Ligand-protein and Ligand-DNA Interaction studies. This program can also be used to design primers from a given sequence & various sites for restriction enzymes can also be mapped on a given sequence.
Recent publications

Prashant K Mishra, Subash C Sonkar, SreeRohit Raj, Uma Chaudhry and Daman Saluja, 2013.Functional Analysis of Hypothetical Proteins of Chlamydia Trachomatis: A Bioinformatics Based Approach for Prioritizing the Targets J ComputSciSystBiol, 7:1

PrijaPonnan, Shikhar Gupta, Madhu Chopra, RashmiTandon, Anil S. Baghel, Garima Gupta, Ashok K. Prasad, Ramesh C. Rastogi, Mridula Bose, and Hanumantharao G. Raj., 2013. 2D-QSAR, Docking Studies, and In SilicoADMET Prediction of Polyphenolic Acetates as Substrates for Protein Acetyltransferase Function of Glutamine Synthetase of Mycobacterium tuberculosis, ISRN Structural Biology, Volume  2013, Article ID 373516, http://dx.doi.org/10.1155/2013/373516 (Hindawi).

ChandraBhushan Mishra, Dimpy Sharma, AmreshPrakash, NamrataKumari, Nitin Kumar, Pratibha Mehta Luthra, 2013. Design and synthesis of (4E)-4-(4-substitutedbenzylideneamino)-3-substituted-2,3-dihydro-2-thioxothiazole-5-carbonitrile as novel A2A receptor antagonists, Bioorg. Med. Chem., 21, 6077.

HemantBengani, ShwetaMendiratta , JayantMaini, DasariVasanthi  , Hina Sultana , Mohsen Ghasemi, JasmineAhluwalia, SowmyaRamachandran,  Rakesh K Mishra and VaniBrahmachari, 2013. Identification and validation of a putative polycomb responsive element in the human genome. PLoS One. Jun 21; 8(6):e67217.

SarojKumari, JoyitaChaudhury, SudhirChandana, Daman Saluja, Anil K. Mishra, Madhu Chopra*, 2012. Synthesis and evaluation of a fluorescent non-peptidic Cholecystokinin-B/Gastrin receptor specific antagonist for cancer cell imaging. ChemBioChem. 13, 282-292.

Bargaje R, Alam P, Patowary A, Sarkar M, Ali T, Gupta S, Garg M, Singh M, Purkanti R, Scaria V, Sivasubbu S, Brahmachari V, Pillai B,  2012. Proximity of H2A.Z containing nucleosome to the transcription start site influences gene expression levels in the mammalian liver and brain. Nucleic Acids Res. doi: 10.1093/nar/gks665.

Ahluwalia JK, Soni K, Sivasubbu S, Brahmachari V. 2012. Modeling SNP mediated differential targeting of homologous 3'UTR by MicroRNA, RNABiol. Mar 1; 9(3).

Mahesh C Patra, M. Krishan C Kumar, Santosh Pasha, Madhu Chopra, 2012. Comparative modeling of human kappa opioid receptor and docking analysis with the peptide YFa. Journal of Molecular Graphics and Modelling, 33,  44–51

Prakash A, Pratibha Mehta Luthra, 2012 In silico Study of the A2AR-D2R Kinetics and Interfacial Contact Surface for Heteromeriza- tion. Amino Acids. DOI 10.1007/s00726-012-1218-x. 25

Contacts

Name of the Coordinator

Dr.Madhu Chopra

Postal Address

Dr. B. R. AmbedkarCenter for Biomedical Research,
University of Delhi, Delhi 110007

Phone Number

011-27666272

Fax No.

011-27666248

Email

acbrdu.btisnet@nic.in, mchopradu@gmail.com,

Website

www.acbrdu.edu


About the Institution
 

institute

Dr. B.R. AmbedkarCenter for Biomedical Research (ACBR) came into existence in March, 1991. The mandate of the Centre is high quality postgraduate education and research in Biomedical Sciences. The institute also has provision for doctoral and postdoctoral training to young scientists at the start of their research career to gain the skills and insights in frontier areas of biomedical sciences. During the last two decades the Center has grown to have strength of 220 comprising faculties, students, Ph.D scholars and supporting staff. ACBR presents a unique amalgamation of basic and applied research in the field of human health and disease, which is first of its kind in the Indian University System. The Centerpossesses a unique structure having an interdisciplinary, goal oriented approach with an objective to meet the high standards of research and teaching in Biomedical Sciences. Specialised laboratories, rather than conventional departments, are the fundamental units of the ACBR. Typically headed by a senior faculty, the lab may include several other faculty and scientists from neighbouring institutes such as IGIB, INMAS, DIPAS, VPCI, ICPO, AIIMS etc. in addition to postdoctoral fellows and Ph.D. students, who share common scientific interest and teaching at the Center. This structure provides flexibility and enhances the opportunity for wide intellectual interaction and collaboration and minimizes the administrative traffic that may impede university life. The post graduate teaching program is dedicated to educating a carefully selected group of students considered as potential leaders in their area of specialization. Students associate with a faculty/scientist-scholars, all actively engaged in research, and learn primarily through a combination of courses, discussion groups, tutorial guidance, and apprenticeship in research laboratories.
 
Achievements at a glance
Achievements of the ACBR students
M.Sc-Ph.D Combined Degree Program in Biomedical Sciences being an interdisciplinary course we have surveyed the background of students who qualify the admission criteria of the Centre as a reflection of the effectiveness of the selection procedures practiced at the Centre. It is observed that students with various backgrounds at the undergraduate level satisfy the selection criteria. The students of ACBR have consistently performed extremely well at the level of University and National level examinations. The ACBR offers a unique research program in the multidisciplinary area of Biomedical Sciences. More than 126 students have completed their Ph.D from ACBR since 1998. The Ph.D students have done exceptionally well so far. More than 210 publications (Last five years) have ensued as a result of the research work being carried out. This work has been published in several prestigious journals such as Blood, Cancer Research, Molecular Pharmacology, Journal of Bacteriology, Journal of Biological Chemistry, New England Journal of Medicine Biochemistry, Journal of Medicinal chemistry, Nucleic Acids Research, Biochemical and Biophysical Research Communications, Phytomedicine, Journal of Chemical Information and Molecular Modeling, Sexually Transmitted Infections, Molecular and Cellular Biology, Tetrahedron, Bioorganic and Medicinal Chemistry. Almost all the students who complete their Ph.D. at ACBR pursue post-doctoral research in India or abroad. Several students have joined teaching positions at various universities and some have chosen to join pharmaceutical companies as research scientists. ACBR has successfully fulfilled its mandate of human resource development so far and continues to aim higher each passing year.
 

Year of Course Commencement

:

1998 (M.Sc.-Ph.D. Combined Programme in Biomedical Sciences)

Research Publications (Total in Last 5 years)

:

212

Publications involving Bioinformatics work Patents & Technologies Transferred

:

26  (BIF) Patents Granted = 2, Technology transferred = 1, Patents Filed = 14

Details of funding (Ongoing projects) Number of Projects ongoing

:

Govt.  Agencies:  60
Total Grant = Rs. 13.49 Cr.

Research projects completed
(2009-2013)

:

Govt.Agencies : 20
Total Grant =  Rs. 3.76 cr.

Ph. D. Students                 (last 5 yrs)

:

Completed : 51, Ongoing : 48

M.Sc. Students                 (last 5 yrs)

:

Govt.Agencies : 20
Total Grant =  Rs. 3.76 cr.

Manpower trained in Bioinformatics (In silico analysis carried out as a part of Ph.D. thesis work)
Ph.D. Completed

Divya,  2014: Development of diagnostic assay for co-detection of Neisseria gonorhoeaeand Chlamydia trachomatis and elucidating the molecular mechanism of  antimicrobial resistance in Neisseria gonorrhoeae, Supervisor Prof. Daman Saluja

PriyankaVerma, 2013: Estimation of the level of cartilage oligomeric matrix protein (COMP) in osteoarthritis and Designing of an inhibitor to control progression of osteoarthritis, Joint Supervisor Dr.Madhu Chopra (ACBR), Supervisor Dr. Krishna Dalal (AIIMS)

Jyoti Zack 2013:   To study the mechanism of Runx 1 and its mutants in DNA binding and altered gene   expression, Supervisor Prof. Daman Saluja

DivyaSachdeva 2013:   Studies on molecular mechanism of antibiotic resistance in Neisseria and to develop easy diagnostic methods. Supervisor Prof. Daman Saluja

Ruby Gupta, 2012: “PharmacophoreModeling, Virtual Screening and Development of novel COX-2 Selective Inhibitors.  Supervisor Dr.Madhu Chopra

AmreshPrakash, 2012:“In silico Approaches to Study the Role of adenosine A2A receptor (A2AR) in Parkinson’s Disease for Development of Novel Therapeutics” Supervisor Dr. P. M. Luthra.

 
Ph. D under progress (In silico analysis carried out as a part of Ph.D., thesis work)

Monika Sharma, Computational Design and Development of HDAC inhibitors.

LubnaWasim, Epigenetic regulation of cancer through HDAC inhibitors understanding the mechanism through networks.

PriyankaVerma, Joint Registration at AIIMS with Dr.KrishanaDalal, “Estimation of the level of Cartilage Oligomeric Matrix protein (COMP) in Osteoarthritis and Computational Designing of an Inhibitor to control the progression of Osteoarthritis”

NaliniYadav: Rational design and Development of anticancer compound taking lead from natural sources.

ShwetaMehndirata “Analysis of INO80 binding motif in the 5’ and 3’ flanking sequences of protein and regulatory RNA coding genes in the human genome”

Shruti Jain “Analysis of dINO80 binding motif in the 5’ flanking sequences of protein and coding genes in the Drosophila genome”.

JayantMaini: Characterization and functional analysis of cis-element involved in developmental memory in human Genome

Kausik Bhattacharya: Comparative analysis of Genome Sequence variation in Clinical Isolates of M. tuberculosis : In silico analysis and validation of their functional implication

Vishal Nimeysh: Structure Prediction of Platelet Derived Epidermal Growth Factor Receptor (PDEGFR) to design novel PDEGFR antagonists for targeting tumor of brain. Supervisor Dr. P. M. Luthra.

Prashant Kumar:  Identification of Chlamydial proteins as potential  vaccine candidates

 
Faculty members

Name

Designation

VaniBrahmachar

Professor
Epigenetics lab
Email: vbrahmachari@acbr.du.ac.in,vani.brahmachari@gmail.com

Daman Saluja

Professor
Medical Biotechnology
E-mail: dsalujach59@gmail.com

Pratibha M. Luthra

Associate Professor
Medicinal Chemistry Lab
E-mail: luthra_pm@delhiuniversity.com

Madhu Chopra

Assistant Professor
Molecular Modelling and Anticancer Drug Development
E-mail : mchopradu@gmail.com,mchopra@acbr.du.ac.in

 

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