Centre for Bioinformatics

About Department

The Centre for Bioinformatics in Pondicherry University was started as Sub Distributed Information Centre of the Department of Biotechnology, Govt. of India (DBT) in 1991. The mandate of the Centre is to train manpower and conduct research in various areas of Bioinformatics and Computational Biology. Recognizing the progress made by the Centre, DBT upgraded the Centre to a full Centre level in 2002 and several new positions were sanctioned and additional funding was allocated.

The Centre is identified as a Centre of Excellence for Research and Training in the field of Bioinformatics by the Department of Information Technology, Govt. of India, New Delhi from 2007 to 2013 and awarded a special grant of ` 3.69 crores. The Centre has taken up several research projects and has offered modular courses in Bioinformatics under this Grant.

The Centre started a M.Sc., program in Bioinformatics in 2007 supported by the University Grants Commission (UGC) under the scheme of “Innovative Programme - Teaching & Research in Interdisciplinary and Emerging Areas”. For advanced research in Bioinformatics and Computational Biology, the Centre started Ph.D. Programme in 2009. The Centre also received UGC Special Assistance Program (SAP) at the DRS-I level in 2012.The Centre for Bioinformatics has received a grant of ` 1 crore under DST-FIST program for procuring sophisticated equipment.

The Centre started an innovative M.Sc. program in Computational Biology fully funded by DBT in a network mode with Madurai Kamaraj University, Madurai and Anna University, Chennai in 2010. This programme is first of its kind in the country and upgraded to M.Tech program in Computational Biology from 2014 in collaboration with Anna University, Chennai. The Centre has also signed an MoU with Institute of Bioinformatics (IoB), Bangalore for collaborative research and Ph.D. guidance. The Ph.D. students can visit these labs for collaborative research and the details are available at www.bicpu.edu.in.

All students, research scholars and faculty are provided round-the-clock computing facility. The Centre has established a separate wet lab facility with sophisticated equipments. Most of the past students have been placed in various leading research institutions and industries.

Over the past few years, the Centre has taken up research activities in the areas of molecular evolution, systems biology, molecular modeling, structural biology, database development etc., and several papers have been published in highly reputed International and National Journals. The faculty and students have received projects/fellowships from various funding agencies like Department of Biotechnology, Department of Information Technology, University Grants Commission, Council of Scientific and Industrial Research-JRF/SRF, Department of Science and Technology, Bioinformatics National Certificate (BINC), DST-Innovation in Science pursuit for Inspired Research (INSPIRE) and Rajiv Gandhi Fellowship.

The University has provided a new state-of-the art building for our Centre.

Entrance Examination

Ph.D.
Selection is based on an entrance examination conducted at various Centres by Pondicherry University. The test consists of multiple choice questions in Bioinformatics, Computational Biology, Biochemistry, Molecular Biology, Biotechnology, Chemistry, Biophysics, Computer Science, Statistics and Mathematics at PG level. Candidates who have qualified for JRF (UGC / CSIR-NET / DBT-BINC) are exempted from entrance exam. They can apply directly.

M.Sc. Bioinformatics
Selection is based on an entrance examination conducted at various Centres by Pondicherry University. The test consists of multiple choice questions in Biology, Biochemistry, Molecular Biology, Biotechnology, Chemistry, Biophysics, Computer Science, Statistics and Mathematics.

M.Tech. Computational Biology
Selection will be based on a common entrance examination to be conducted at various Centres by Pondicherry University. The details will be advertised in newspapers and will be available at www.pondiuni.edu.in, www.bicpu.edu.in and www.annauniv.edu. The test consists of multiple choice questions in Biology, Biochemistry, Molecular Biology, Biotechnology, Chemistry, Biophysics, Computer Science, Statistics and Mathematics.
A stipend of ` 8,000/- p.m. will be provided by the Department of Biotechnology, Government of India, New Delhi for all the students admitted.

Special Grants

DBT - Centre for Bioinformatics (Continuing Scheme)
DIT - CoE in Bioinformatics (2007 - 2013)
DBT – M.Sc./M.Tech. Computational Biology (Continuing Scheme)
UGC - Innovative Programme-Teaching and research in Interdisciplinary (Continuing Scheme)
DBT - Advanced P.G. Diploma in Bioinformatics (2001 - 2008)
UGC – Special Assistance Program (Continuing Scheme)
DST-FIST program (Continuing Scheme)

Placements

Some of the Institutions/ Industries who have recruited our students are as follows:

Industry Placements: HCL Info Systems; Tata Consultancy Services; Molecular Connections, Bangalore; Institute of Bioinformatics, Bangalore; Protein Lounge, Bhubaneswar; Genemines, Chennai; BIOBASE Databases Indian Pvt. Ltd., Bangalore; Computational Research Lab, Pune; Jubilant Biosys, Bangalore; Wipro Technologies, Chennai; Schrödinger, Hyderabad; EnZene Biosciences Pvt. Ltd., Bangalore; ABLE C Drive, Bangalore; Persistent Systems Limited, Pune
Teaching/ Research Placements: Pusan National University, South Korea; Stony Brook University, New York; Sungkyunkwan University, South Korea; University of Madras, Chennai; Central Sericulture Research & Training Institute, Mysore; Institute of Microbial Technology Institute, Chandigarh; Centre for Cellular and Molecular Biology, Hyderabad; Alagappa University, Karaikudi; Indian Institute of Technology, Chennai; Jawaharlal Nehru University, New Delhi; National Institute of Immunology, New Delhi; Kumaun University, Nainital; Maulana Azad National Institute of Technology, Bhopal; Amity University; Yeungnam University, South Korea; Maharshi Dayanand University, Haryana; Technical University of Munich, Germany; La Trobe University, Australia; Swinburne University of Technology, Australia; Louisiana State University, USA; University of Illinois; University of Lisbon, Portugal

Publication

Basant K. Tiwary
The coordinated expression, interaction and evolution of the neuroendocrine genes. Integrative Biology, 2012, 4, 1377-1385 (Published by Royal Society of Chemistry, Cambridge)
IF: 4.509

Basant K. Tiwary
The severity of mental disorders is linked to interaction among candidate genes. Integrative Biology, 2012, 4, 1096-1101 (Published by Royal Society of Chemistry, Cambridge)
IF: 4.509

Vaishnavi V, Manikandan M, Tiwary BK, Munirajan AK
Insights on the Functional Impact of MicroRNAs Present in Autism-Associated Copy Number Variants. PLoS ONE 8(2): e56781. (2013) DOI:10.1371/journal.pone.0056781
IF: 4.092

Basant K. Tiwary
Correlated Evolution of Gonadotropin-Releasing Hormone and Gonadotropin-Inhibitory Hormone and Their Receptors in Mammals. Neuroendocrinology (Published by S.Karger AG, Basel) DOI:10.1159/000342694. (2012)
IF: 2.376

Annamalai A, Christina V.L.P, Sudha D, Kalpana M, and Lakshmi P.T.V.
Green synthesis, characterization and antimicrobial activity of Au NPs using Euphorbia hirta L. leaf extract. Colloids and Surfaces B: Biointerfaces.
IF: 3.456

Vijayakumar Saravanan and Lakshmi P.T.V.
SCLAP: An Adaptive Boosting Method for Predicting Subchloroplast Localization of Plant Proteins. Omics A Journal of Integrative Biology, Volume 17, Number 2, 2013, (DOI: 10.1089/omi.2012.0070)
IF: 2.441

Manivel Panneerselvam, Kannan Muthu, Muthukumaran Jayaraman, Upasana Sridharan, Pranitha Jenardhanan and Krishna Ramadas
Molecular dynamic simulations of the tubulin–human gamma synuclein complex: structural insight into the regulatory mechanism involved in inducing resistance against Taxol. DOI:10.1039/C3MB25427E (Paper) Molecular BioSystem, 2013, Advance Article
IF: 3.859

Om Prakash Sharma, Yellamandayya vadlamudi, Qinghua Liao, Birgit strodel and M. Suresh Kumar.
Molecular modeling, Dynamics, and an insight into the structural inhibition of cofactor independent phosphoglycerate mutase isoform 1 from Wuchereria bancrofti using cheminformatics and mutational studies. J Biomol Struct Dyn. 2012 Aug 22. [Epub ahead of print][PMID:22908983] (2012)
IF: 4.986

Ismail AM, Om Prakash Sharma, M. Suresh Kumar, Eapen CE, Kannangai R, Abraham P.
Virological response and antiviral resistance mutations in chronic hepatitis B subjects experiencing entecavir therapy: An Indian subcontinent perspective. Antiviral Res. 2013 Feb 26. pii: S0166-3542(13)00049-1. doi: 10.1016/j.antiviral.2013.02.012. [Epub ahead of print] (2013)
IF: 4.301

Sunitha K, Suresh P, Santhosh MS, Hemshekhar M, Thushara RM, Marathe GK, Thirunavukkarasu C, Kemparaju K, Kumar MS, Girish KS.
Inhibition of Hyaluronidase by N-acetyl cysteine and Glutathione: Role of Thiol group in Hyaluronan protection. Int J Biol Macromol. 2013 Apr;55:39-46. doi: 10.1016/j.ijbiomac.2012.12.047. Epub 2013 Jan 8. (2013)
IF: 2.453

Buvaneswari S., Archana Pan
Identification and Characterization of Potential Therapeutic Candidates in Emerging Human Pathogen Mycobacterium abscessus: A Novel Hierarchical in silico Approach. PLoS One (2013), Vol.8 (Issue 3), e59126
IF: 4.092

Aditya Sharma and Archana Pan
Identification of potential drug targets in Yersinia pestis using metabolic pathway analysis: MurE ligase as a case study. European Journal of Medicinal Chemistry (2012), Vol. 57, 185-195.
IF: 3.346

Jiann-Yih Yeh, Mohane Selvaraj Coumar, Hui-Yi Shiao, Ta-Jen Lin, Yen-Chun Lee, Hui-Chen Hung, Shengkai Ko, Fu-Ming Kuo, Ming-Yu Fang, Yu-Lin Huang, John T. A. Hsu, Teng-Kuang Yeh, Shin-Ru Shih, Yu-Sheng Chao, Jim-Tong Horng, and Hsing-Pang Hsieh.
Anti-influenza Drug Discovery: Identification of an Orally Bioavailable Quinoline Derivative through Activity and Property Guided Lead Optimization. ChemMedChem 2012,7,1546-1550
IF: 3.151

Yi-Yu Ke, Hui-Yi Shiao, Yung Chang Hsu, Chang-Ying Chu, Wen-Chieh Wang, Yen-Chun Lee, Wen-Hsing Lin, Chun-Hwa Chen, John T. A. Hsu, Chun-Wei Chang, Chen g-Wei Lin, Teng-Kuang Yeh, Yu-Sheng Chao, Mohane Selvaraj Coumar,* and Hsing-Pang Hsieh.*
3D-QSAR Assisted Drug Design: Identification of a Potent Quinazoline Based Aurora Kinase Inhibitor. ChemMedChem. 2013, 8, 136-148
IF: 3.151

Mohane Selvaraj Coumar, Fang-Ying Tsai, Jagat Rakesh Kanwar, Sailu Sarvagalla, Chun Hei Antonio Cheung.
Treat cancers by targeting survivin: Just a dream or future reality? Cancer Treatment Reviews. 2013. doi:10.1016/j.ctrv.2013.02.002
IF: 6.054

Gallery

Infrastructure Facilities

Infrastructure Facilities – Computers, Networks & Accessories

Servers

Tesla Software Server(4TF) - 1No.: One Super Micro Tesla Server with 2 x Intel Xeon Quad-Core processor @2.4GHz/12MB L3 Cache, 896 GPU based cores (2 x NVIDIA Tesla C2050), 64 GB of DDR3 memory, 6 TB of storage controlled by 128MB cache SAS RAID, 24” wide LED Display and loaded with CentOS.
Web Server, File Server, DB Server, DBT Web Server - 4Nos.: Super Micro HCL Server with 2 x Intel Xeon Quad-Core processor @1.6GHz, 4 GB of DDR2 memory, 6 x 146 GB of storage controlled by SAS RAID, 19”wide LCD Display, Integrated KVM 15” LCD switch and loaded with RHEL 5.
Cluster Server - 3Nos.: HCL Servers with 2 x Intel Xeon @3.2GHz, 4 GB of DDR2 memory, 6 x 146GB of storage controlled by SAS RAID, 17” LCD Display, KVM switch and loaded with RHL Advanced Sever 4.
Mail Server - 1Nos. HCL Server with 2 x Itanium 2@1.7GHz, 4 GB of DDR2 memory, 6 x 146GB of storage controlled by SAS RAID, 17” LCD Display with KVM switch and loaded with RHL Advanced Sever 4.
Domain Name Server - 1Nos.: Wipro Server with Intel Xeon @3.0GHz, 1 GB of memory, 120GB of storage, 17” LCD Display and loaded with RHL Advanced Sever 4.
Domain Controller Server - 1Nos.: HCL AMD Server with AMD 8131/8111 Motherboard, 1 GB of memory, 100GB of storage, 12/24GB-DAT drive, 17” LCD Display and loaded with Windows 2003 Server R2.

Specialized Workstations

Docking & Modeling studies - 2Nos: HP workstation with Intel Core 2 Duo @3.00GHz, 4 GB of DDR2 memory, 320 GB of SATA storage, 21” LCD wide Display and loaded with Windows Vista Business Edition.
3D and 2D Graphical Analyze - 2Nos: Apple iMac workstation with Intel Core 2 Duo @3.00GHz, 1 GB of DDR2 SD memory, 250 GB of SATA storage, 20” LCD Display loaded with Mac OS.
Onyx3 Infinite Performance Fuel - 1Nos: SGI workstations of 800Mhz. MIPS R16000 (IP35) with MIPS R16000 FPU with 1 GB of memory, 176 GB of storage with V10 graphics along with 20” CRT Display loaded with IRIX64 Release 6.5 OS.

Desktop Computers

Around 105 Nos. of desktop computers with Intel core 2 duo processor @1.8Ghz to 2.8GHz, 1 GB to 4 GB of DRR2 memory, 160GB to 320GB of SATA storage, 17” wide and normal LCD display and loaded with dual OS Windows XP and RHEL5.
Around 30 Nos. of desktop computers with Intel Pentium D processor @2.8Ghz to 3.0GHz with 1 GB to 3 GB of DRR2 memory, 160GB of SATA storage with 15” LCD display and loaded with dual OS Windows XP and RHEL5.

Network Hardware

Cisco 1800 with 2 Fast Ethernet ports, 1 AUX port, 1 Console port to manage LAN Connectivity along with 12 manageable 24 port Switches including 5 Giga byte manageable switches.
5 CCTV cam with wide-angle, IR facility technology to monitor function of Students’ Lab since it has been allowed 24x7 for access.

Other Facilities

Printers: Samsung Color Laser Network Printer -2, HP Color Laser Printer, Samsung Laser Black Network Printer, Samsung Laser Black Printer -5, HP LaserJet Black Network Printer -2, Mono Printer -1, DeskJet Printer -1, Infocus Projectors -4, HP ScanJet -2
Photocopier: Toshiba Multi functionality Digital Photocopiers cum Network Printer -1, Toshiba Digital Photocopiers cum Network Printer -2.
Scanner: HP Scan Jet -2.
Projectors: Hitachi Multimedia projectors -2 one with wall mount facility for M.Sc. Bioinformatics teaching program, Infocus projectors -2 for M.Sc. Computational Biology teaching program, Toshiba TDP LCD wall mount projector for seminar hall

UPS Backup

Numeric 75KVA (in total) UPS to provide 4 hours to 12 hours power backup. 15 KVA - 3 Nos. 10 KVA – 3Nos. 0.5 KVA – 5 Nos.

Infrastructure Facilities – Scientific Software

Molecular Modeling:
Modeler (DISCOVERY STUDIO 2.5), Protein Families (DISCOVERY STUDIO 2.5), Protein Health (DISCOVERY STUDIO 2.5), Protein Refine (DISCOVERY STUDIO 2.5)

Molecular Docking:
Flexible Docking (DISCOVERY STUDIO 2.5), LibDock (DISCOVERY STUDIO 2.5), Ludi (DISCOVERY STUDIO 2.5), LigPrep (DISCOVERY STUDIO 1.5), LigandFIT (DISCOVERY STUDIO 1.5), LigandScore (DISCOVERY STUDIO 1.5), GOLD, AUTODOCK, Database of 1.5million Compound Library (DISCOVERY STUDIO 1.5)

Toxicity Prediction:
ADMET (DISCOVERY STUDIO 2.5), TOPKAT (DISCOVERY STUDIO 2.5)

QSAR:
QSARPlus (VLife)
Rapid calculation of 1000+ descriptors including 2D, 3D alignment independent, atom type count etc.,

GQSAR (VLife)
Intelligent QSAR using molecular fragments of interest and their features, evaluation of descriptors from template scaffold to form relationship with the activity.

Molecular Dynamics:
AMBER 11, GROMOS96

Infrastructure Facilities – Wetlab
Our wet lab is equipped with state of the Art facility, highly sophisticated Akta Purifier for protein purification with various columns (size exclusion, Ion exchange, Affinity). Each and every student is equipped with both Page and slab gel electrophoresis system, which is also equipped with centrifuges, Spectrophotometer and Elisa Reader. We are also having facilities for Protein cloning, expression and purification. We are in the process of furnishing cell culture facilities.

Equipments used for Research:

Invert Fluorescence Microscope -(Model Ti-s)
Specification: Inverted fluorescence microscope with fast research grade high resolution CCD with 5 Mega Pixel Camera and image analysis system.

Galaxy Co2 Incubator-(Model CO170S)
Specification: Direct Heat Co2 incubator with fan less design and High Temp Decontamination wit 170 liter capacity, 6.0 cu. Ft on a minimal footprint.

Bio safety Cabinet - HITECH (Type B2-350 Lts)
Specification : HEPA-filtered unidirectional (laminar) flow (ISO 5/Class 100) with removable screen for cleaning purpose with UV light for Sterilization and fluorescent light above work space.

Liquid Nitrogen Container (3L and 25 L)
Specifiacation: Evaporation :<0.143 Litter Per day is present in this instrument

Bench Top Freeze Dryer
Specification: ILSHIN- TFD5505 Table top model
Used for lyophilization and to stabilize the product, minimizing effects of oxidation and other degradation processes.

Cold cabinet
Specification: UNICHROMAT 1500 – PRO
Equipped with temperature control sensor which helps to maintain temperature constantly at 4ºC.

Sonicator
Specification: Sonics
To speed up dissolution, disrupt or deactivate a biological material.

HPLC System
Specification: AKTA PURIFIER 10
To identify, quantify and purify individual components from a mixture of biological sample.

ELISA Reader
Specification: Versamax Model 2020
For assays such as ELISA, protein and nucleic acid quantification and for enzyme activity assays (viz. in the MTT assay for cell viability).

Deep Freezer-80ºC
Specification: Premium Upright Model (U4100)
It is used for quick-freezing and long-term storage of biological samples.

Equipment used for Teaching:

UV-Visible Spectrophotometer
Specification: Shimadzu Model - Uv-1800
Used in quantitative determination of solutions of transition metal ions and highly conjugated organic compounds.

Thermo Cycler
Specification: Bangalore Genei
To amplify a single or a few copies of a piece of DNA across several orders of magnitude.

Electrophoresis unit
Specification: Bangalore Genei
Used for separation of DNA, RNA or protein molecules using an electric field applied to a gel matrix.

Refrigerated Centrifuge
Specification: 5 415 Eppendorf
Used for isolating and separating suspensions.

Infrastructure Facilities – Other Resourses

Resources & Services

A separate website available at www.bicpu.edu.in is being maintained by the Centre. All the activities of the centre are updated regularly
Web server for sequence analysis, Blast, Predict Protein, Sequence Manipulation suite are available at http://www.bicpu.edu.in
Web server for offline blast for sequence homology search is available at http://www.bicpu.edu.in/blast
Web based database administration tool phpmyadmin is available at http://www.bicpu.edu.in
Free Biosoftware Artemis, Bioedit, Clustal W, Glimmer, Munner, Philip etc. are available at http://www.bicpu.edu.in
A minor site of all publicly available protein structure co-ordinate in the form of the Protein Data Bank available at http:// www.bicpu.edu.in.pdb
A full mirror of the SCOP database linked to PDB available at http://www.bicpu.edu.in/ scop
Micro Array Animation will be available http://www.bicpu.edu.in/Microarray.php

Databases Developed

Humet database will be at http://hmdb.bicpu.edu.in
DrugMetZDB database will be at http://dmdb.bicpu.edu.in
Immune Epitope Prediction database will be at http://iep.bicpu.edu.in
Membrane Protein database will be at http://memprot.bicpu.edu.in
E-Learning Module in Bioinformatics will be available at http://dbtel.bicpu.edu.in
Peptide Binding Protein database will be at http://pepbind.bicpu.edu.in
FiloBase:A Comprehensive database for filaria will be available at http://filobase.bicpu.edu.in

Books
550 books (In addition to the books available in the Central Library)

Journals
Scientific American, Cell, Current Science.

Faculty

Research Activities

Molecular Evolution, Systems Biology, DNA-Protein Interactions, Comparative Genomics, Protein Structure Modeling, Molecular modeling, X-ray Crystallography, Drug Design, Cell Signaling, Single particle analysis, Medicinal Chemistry, Computational Biology, Molecular Biology.

Dr. M. Suresh Kumar Assistant Professor	Dr. Archana Pan Assistant Professor	Dr. R. Amutha Assistant Professor	Dr. B. Syed Ibrahim Assistant Professor
Dr. A. Murali Assistant Professor	Dr. Mohane Coumar Assistant Professor	Ms. V. Amouda Assistant Professor

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