Project-wise Reports of Sectoral Monitoring Committee

1. Project Title: Genomics and Informatics Solutions for Integrating Biology (GENESIS)

2. Project Details:

Nodal lab CSIR-Institute of Microbial Technology (CSIR-IMT)

Participating Labs CSIR-CCMB, CSIR-IGIB, CSIR-IICB, CSIR-IHBT, CSIR-IICT, CSIR-IITR, CSIR-CDRI, CSIR-CIMAP, CSIR-NBRI, CSIR-NCL, CSIR-CLRI, CSIR-NIIST, CSIR-CMMACS, CSIR Hqr

Nodal Officer Dr G. P. S. Raghava

Taskforce Director, CSIR-IMT Chairman

Total Man Days 47265

Approved Cost 49861akhs

Fund received 3467 lakhs

Fund utilized 3200 lakhs (Approx.), 26811akhs (up to March 2016)

3. Periodic Key Recommendations of Task Force/RC/Monitoring Committee

S.No Key Recommendations of Task Action taken on Key Proposed Revised

Force/RC/ Monitoring Committee Recommendations Deliverables Deliverable

1. Nil (22nd November 2013, RC Yes N.A. N.A. meeting)

2. Due to cut in budget, difficult to Yes N.A. N.A. achieve all objectives (First Taskforce on17 Feb 2014)

3. Nil (20th December 2014, RC Yes N.A. N.A. meeting)

4. Training/workshop should be Yes N.A. N.A. organized for HRD (Second Taskforce on 24th March 2015)

5. Nil (16th January 2016, RC Yes N.A. N.A. meeting)

6. Emphasis should be on Yes N.A. N.A. translational research

7. Completion of project with more Yes N.A. N.A. emphasis on translational & packing (Fourth Taskforce on 26th and 27th Dec., 2016)

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4. Project Achievements:

S. No. Deliverables promised at start Deliverables Achieved If not achieved, reasons thereof

1 122 research publications -424 publications

2 50 Software & web services > 100 software/webservers

3 195 genome sequencing of human, -96 genomes Cut in funding and microbes and pathogen sequencing of exomes

sufficient

4 170 Sequencing of Exomes 574 sequenced

5 Training of 35 PhD students - 126 PhD students trained

6 2 Disease forecasting systems 8 Disease forecasting systems

7 65 Patents/copyrights/books 65 Patents/copyrights

8 Validation of 1100 inhibitors 1634 inhibitors validated

5. Outcomes and outputs from the projects:

a. Outcomes

1. Lead(s) identified:'10 a) Discovery of cell penetrating peptide for topical delivery of drugs, TRL7 b) Repository of biological databases for computer-aided research, TRL4 c) Genome-based platform for managing viral diseases, TRL4 d) In silico models for screening and designing inhibitors, TRL3 e) Fingerprinting of genomic variations for precision/personalize medicine, TRL2 f) Disease forecasting systems for wide range of diseases, TRL3 g) Highly efficient pipelines for annotating genomic & proteomic data, TRL4 h) World-class techniques for structural annotation of peptides & proteins, TRL5 i) Genomic repositories of Indian specific organisms, TRL3 j) lmmonomodulatory potential of biomolecules, TRL4

2. Technology/Product developed: >100 (All in TRL9) List of Major Web Servers (Heavily used by community) • IFNepitope: Designing of interferon-gamma inducing MHC class-11 binders. • CancerDR: cancer drug resistance database • CeiiPPD: In silico approaches for designing highly effective cell penetrating peptides. J

Transl Med 11: 1-12. • HIVcoPred: Hybrid Approach for Predicting Coreceptor Used by HIV-1 from Its V3 Loop

Amino Acid Sequence. PLOS One 8: e61437. • TumorHPD: Computational approach for designing tumor homing peptides. • Lbtope: lmproved method for linear B-cell epitope prediction using Antigen's primary

sequence. PLOS One 8: e6221 6. • VitaPred: Prediction of vitamin interacting residues in a vitamin binding protein using

evolutionary information. BMC bioinformatics 14: 44.

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• GlycoEP:In silica platform for prediction of N-, 0-and C-glycosites in eukaryotic protein sequences. PLOS One 8: e67008.

• ToxinPred:ln Silica Approach for Predicting Toxicity of Peptides and Proteins. PLOS One 8: e73957.

• PHDcleav: a SVM based method for predicting human Dicer cleavage sites using sequence and secondary structure of miRNA precursors. BMC bioinformatics 14: S9.

• AntiCP:In Silico Models for Designing and Discovering Novel Anticancer Peptides. Scientific reports 3.

• Hemolytik: a database of experimentally determined hemolytic and non-hemolytic peptides • lgPred: Identification of B-cell epitopes in an antigen for inducing specific class of

antibodies. Biology direct 8: 27. • DrugMint: a webserverfor predicting and designing of drug-like molecules. Biology direct

8: 1-12. • IL4Pred:Prediction of IL4 inducing peptides. Clin Dev lmmunol: 263952. • ToxiPred: A Server for Prediction of Aqueous Toxicity of Small Chemical Molecules in T.

Pyriformis • ParaPep: a web resource for experimentally validated antiparasitic peptide sequences and

their structures. Database 2014: bau051. • RNAcon: Prediction and classification of ncRNAs using structural information • PCMdb: Pancreatic Cancer Methylation Database. Scientific reports 4. • HerceptinR: Herceptin Resistance Database for Understanding Mechanism of Resistance

in Breast Cancer Patients • DipCell: Designing of promiscuous inhibitors against pancreatic cancer cell lines. Scientific

reports 4. • EGFRpred: QSAR based model for discriminating EGFR inhibitors and non-inhibitors

using Random forest • CancerPPD: a database of anticancer peptides and proteins • EGFRindb: Epidermal Growth Factor Receptor Inhibitor Database • HLP:A web server for predicting intestinal half-life of peptides and to design mutant

peptides with better half-life and physicochemical properties. • tRNAmod: Prediction of uridine modifications in tRNA sequences. BMC Bioinformatics. • AHTPDB :Database of Antihypertensive Peptides. • EGFRpred: QSAR based model for discriminating EGFR inhibitors and non-inhibitors

using Random forest • RNApin: Identification of protein-interacting nucleotides in a RNA sequence using

composition profile of tri-nucleotides. Genomics. • Betapred3:1n silica platform for predicting and initiating ~-turns in a protein at desired

locations. • AHTpin:An in silico platform for predicting, screening and designing of antihypertensive

peptides • XIAPin: In Silica Designing and Screening of Antagonists against Cancer Drug Target

X lAP • PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified

residues • dbEM: A database of epigenetic modifiers curated from cancerous and normal genomes • SA TPdb: a database of structurally annotated therapeutic peptides. • CPPsite 2.0: a repository of experimentally validated cell-penetrating peptides. • CancerlN: Prediction of anticancer molecules using hybrid model developed on molecules

screened against NCI-60 cancer cell lines. • ApoCanD: Database of human apoptotic proteins in the context of cancer. • lmRNA: Prediction of lmmunomodulatory potential of an RNA sequence for designing non­

toxic siRNAs and RNA-based vaccine adjuvants • HemoPI: A Web Server and Mobile App for Computing Hemolytic Potency of Peptides

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• LPicom: A web server for analysis, oomparison and prediction of protein ligand binding sites

• cancerDP: Prioritization of anticancer drugs against a cancer using genomic features of cancer cells: A step towards personalized medicine

• MtbVeb: A Web-Based Platform for Designing Vaccines against Existing and Emerging Strains of Mycobacterium tuberculosis

• EbolaVCR: A web-based resource for designing therapeutics against Ebola Virus • ProCarDB: a database of bacterial carotenoids • PEPiife: A Repository of the Half-life of Peptides • StarPdb: BLAST-based structural annotation of protein residues using Protein Data Bank • VaccineDA: Prediction, design and genome-wide screening of oligodeoxynucleotide­

based vaccine adjuvants • ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and

Therapeutic Analysis • SMEpred workbench: a web server for predicting efficacy of chemically modified siRNAs • AVCpred: An integrated web server for prediction and design of antiviral compounds • ge-CRISPR-An integrated pipeline for the prediction and analysis of sgRNAs genome

editing efficiency for CRISPR/Cas system • MSLVP: prediction of multiple subcellular localization of viral proteins using a support

vector machine • siRNAmod: A database of experimentally validated chemically modified siRNAs • ViraiEpi v1 . 0: a high-throughput spectrum of viral epigenomic methylation profiles from

diverse diseases • SigMol: repertoire of quorum sensing signaling molecules in prokaryotes • HPVbase-a knowledge base of viral integrations, methylation patterns and microRNAs

aberrant expression: As potential biomarkers for Human papillomaviruses mediated carcinomas

• AVP-IC50Pred: Multiple machine learning techniques based prediction of peptide antiviral activity in terms of half maximal inhibitory concentration (IC50)

• QSPpred: Prediction and Analysis of Quorum Sensing Peptides Based on Sequence Features

• CrisprGE: a central hub of CRISPR/Cas-based genome editing • VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their

targets • AVPdb: a database of experimentally validated antiviral peptides targeting medically

important viruses • VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human

viruses • HIPdb: A Database of Experimentally Validated HIV Inhibiting Peptides • AVPpred: collection and prediction of highly effective antiviral peptides • MitoLSDB : Comprehensive Resource to Study Genotype to Phenotype Correlations in

Human Mitochondrial DNA Variations • Investigating the role of site specific synonymous variation in disease association studies • FROG: Fingerprinting Variations: Ontology Revisited • dPABBs: A Novel in silico Approach for Predicting and Designing Anti-biofilm Peptides • Mitolink : Integrated web-based platfform for evaluating genotype-phenotype correlation

for human mtDNA • Specy: An affordable hand-help Spectrophotometer • EpiDBase: a manually curated database for small molecule modulators of epigenetic

landscape. • ONRLDB-manually curated database of experimentally validated ligands for orphan

nuclear receptors • PROMOP-a pipeline is design to deliver single platform for modeling of proteins

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• LeukmiR: database for miRNA and their targets in Acute lymphoblastic leukemia (ALL) • PTP1 BiPred : Multiple machine learning based descriptive and predictive workflow for the

identification of potential PTP1B inhibitors • GKAPredR: A web server for the prediction of glucokinase (GK) activator. • SVMDLF: application is an OpenCPU server app which is a novel single pageR web

application for the DPP4 inhibitors prediction. • Q-Lead online software/tool: An online tool for bioactivity (anticancer, anti-inflammatory,

immunomodulatory) prediction of phytomolecules & their derivatives/analogues or lead identification & optimization through integrated in-house developed QSAR models is expected

• AROMA online database: An aroma molecules database based on aromatic & medicinal plants is expected at the end of network project. Database will cover plants essential oils, aroma/fragrance molecules detail information, 2D & 3D structures for downloads & structure-activity relationship, activity data, plants details, trade data (export/import) and different search applications

• MassWiz: A Novel Scoring Algorithm with Target-Decoy Based Analysis Pipeline for Tandem Mass Spectrometry

• Flexi-FDR-Learning from Decoys to Improve the Sensitivity and Specificity of Proteomics Database Search Results

• ProteoStats-a library for estimating false discovery rates in proteomics pipelines. • GenoSuite - Proteogenomic analysis of Bradyrhizobium japonicum USDA 110 using

GenoSuite, an automated multi-algorithmic pipeline • EuGenosuite-lntegrated Transcriptomic-Proteomic Analysis Using a Proteogenomic

Workflow Refines Rat Genome Annotation. • ITP-Integrated Transcriptome Proteome Pipeline-Integrating transcriptome and proteome

profiling: Strategies and applications • mycobacrvR - Integrative immunoinformatics for Mycobacterial diseases in R platform • Mythology of micro-RNA: A legion of potential regulatory sRNAs exists beyond the typical

microRNAs microcosm • Plant Regulomics Portal • MauPir: Global De Novo Protein-Protein lnteractome Elucidates Interactions of Drought­

Responsive Proteins in Horse Gram (Macrotyloma uniflorum) • IPFIP: The first ever molecular information database on deadly incurable disease

Idiopathic Pulmonary Fibrosis. Will also help in diagnosing the disease on the given database server

• AVA (Assembly validator)- A tool to detect misassembly in de novo assembled contigs • miReader: Discovering Novel miRNAs in Species without Sequenced Genome • RBPSighter: A software to detect RBP-RNA interactions from next generation sequencing

data • miR-BAG: bagging based identification of microRNA precursors • Indian Genetic Disease Database (IGDD) • BPGA (Bacterial Pan Genome Analysis) - an ultra-fast pan-genome analysis pipeline • PALM-IST: Pathway Assembly from Literature Mining-an Information Search Tool • Malarial Important Interacting proteins Database • PresRAT: Predicting smaii-RNAs and their target • DBETH: a Database of Bacterial Exotoxins for Human • Leishmania exclusive protein database • SPEER-SERVER: a web server for prediction of protein specificity determining sites • Interactive web based portal for hosting genome data • SubSite allows the user to identify subfamily determining sites (SDS) within a protein

family • MMpl: A Wide-Range of Available Compounds of Matrix Metalloproteinase Inhibitors • AntiAngioPred: A server for prediction of anti-angiogenic peptides

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S.No

1

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• OncomiR: A database for Breast cancer

3. Technology/Product transferred: NIL 4. Facility created: >100 (All products used as facility by public) 5. Sponsored projects obtained (with details): NIL 6. External Cash Flow (ECF) generated: NIL 7. Societal impact created (quantified data): 47707 Lakhs (Total)

i. Web Servers/Software: Rs 33320 Lakhs ii. Human Resource Development: Rs 14387 Lakhs

b. Outputs:

1. Periodic Reports Submitted: 8 2. Publications

i. Total number: 366 ii. Cumulative IF (as per 2015 figures): 1581.77 (IF in year of published) iii. Average IF: 4.32 (1581 .77/366) iv. Average IF/scientist: 71.89

3. Patents (or other forms of IP generated such as Copyrights, Designs etc.) i. Filed: 65 ii. Granted: 51 iii. Licensed: NIL

4. Human Resource generated i. PhD fellows: 62 Completed, 64 continue ii. Project fellows: 178 iii. Skills imparted: - 250

- Including skill set developed for technical services/ consultancy/ training purposes

c. External collaborations established: NIL

Lead/Technology/Pro Salient TRL of the IP Status of Status of duct (listed above in Features of the Lead/ Lead!T echnology/Pro DPR/Commercial outcomes) Lead/T echnolog Technology duct Technical Report of

y/ Product /Product Lead/ Technology/ Product

Cell penetrating Highly efficient TRL7 1 Patent granted, 1 peptide cell penetrating patent applied

peptide, suitable for topical drug delivery. Effective in handling drug resistance

Repository of Number of TRL4 Copyrights of biological databases biological components for computer-aided databases of research international

standard has been developed

6

3

4

5

6

7

8

9

Number of tools TRL4 Genome-based platform managing diseases

for for designing viral

In silico models for screening and designing inhibitors

Fingerprinting of genomic variations for precision/personalize medicine

Disease forecasting systems for wide range of diseases

Highly efficient pipelines for annotating genomic & proteomic data

World-class techniques for structural annotation of peptides & proteins

Genomic repositories of Indian specific organisms

antiviral inhibitors, disease biomarkers have been developed Numerous inhibitors predicted and experimentally validated using in vitro assays. Fingerprinting techniques have been developed for identification of variation in genomes. As well tools have been developed foe personalized medicine

TRL3

TRL2

Number disease forecasting

of TRL3

systems have been developed. Highly efficient pipelines have been developed for annotation of genomes and proteomes. Highly accurate techniques have been developed for protein & peptide structure prediction. Number of India-specific organisms have been sequenced, it includes human genome and pathogenic strains.

TRL4

TRL5

TRL3

Copyrights of components

Copyrights/Patent of components

No protection

No protection

No protection

Copyrights of components

No protection

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10. lmmonomodulatory Number of tools TRL4 Copyrights of potential of developed for components biomolecules predicting

epitopes and vaccine adjuvants

6. Sectoral Monitoring Committee Recommendations on LeadfTechnology/Product (listed above):

For each Lead!Technology/Product provide details separately:

Criteria SMC Recommendations

Name of LeadfTechnology /Product • Cell penetrating peptide .

• Software and database development for biological applications

Is the Lead/ Technology/Product Yes worth taking up further?

What is the further R&D efforts that Further R&D efforts on different leads of project wrt to need to be put by CSIR/CSIR infrastructure and recurring costs should be identified. CSIR-IMT laboratories? to be the nodal lab for all the web-resources developed which

should be centralized and made available to all researchers alike. The laboratory may license a few to generate revenue.

Global benchmarking of the Software and database are being used globally and are well cited. LeadfT echnology/Product specifically wrt specifications and cost

Is the Lead/Technology/Product Yes worthy of c·ommissioning a DPR at this stage?

What are the likely resources and Financial support for three years. time duration required for taking forward the identified Lead/ Technology/Product to the desired TRL?

Potential stake holders who may be Researchers from academic institutions and industries. appropriate to partner technically as well as financially

Suggestion for plausible road map towards further development of lead/technology/product for achieving desired TRL

GO/NO GO further development GO

Other suggestions, if any, related to benefits/usage/ commercialization

8

7. Identified "lessons to be learnt", especially from shortcomings/failures.

NA

8. Comments on financial progress on the project • fund availability and utilization of fund in the project:

The financial progress is satisfactory and the investment is jus1ified.

9. Sectoral Monitoring Committee Recommendations on Facility creation or other outcomes:

Database and web resources developed should be continued to be maintained and supported.

10. Grading of Project Execution: Outstanding/ExcellenWery Good/Good/Satisfactory/Unsatisfactory

Excellent

11. Additional comments, if any:

The use of web resources developed should be expanded.

~- ~ Prot'r.P. Sin'i.( (Member)

~L. Prof. D. Narasimha R~

(Member) Dr. S. Srikanth

(Member)

~:e!ann:.:-(Member)

Dr. K. Sumathy (Member)

Dr. Ramesh Hariharan (Member)

~~ ~-~ Director, CSIR-CCMB

CtL-Director, C~I~IGIB­(TF Chairman • Member)

•

~ Director, CSIR-IMTECH (TF Chairman • Member)

(Member) (TF Chairman • Member)

J~d.~~~;;~ Director, CSIR-IICB

(TF Chairman • Member)

(TF Chairman · Member)

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Prof. Seyed E. Hasnain (Member)

?/ ~~ Padmanaban

(Chairman)

10