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Genome-based Biomarkers

One of the major challenges in the field oh health sciences is to design genome based biomarkers, as these biomarkers are more sensitive and accurate than traditional tests. Here, aim is to develop computational tools to predict wide range of biomrakers from genomic information. These resources can be classified in following categories; i) disease identification, ii) disease progression, iii) drug biomarkers.

Webservers for Genome based biomakers  (Raghava's Group)

  1. CancerCSP: Gene expression-based biomarkers for discriminating early and late stage of clear cell renal cancer.
  2. CancerDP: Prioritization of anticancer drugs against a cancer using genomic features of cancer cells.
  3. CancerDR: Cancer drug resistance database.
  4. CancerLivER: Repository of liver cancer-specific biomarkers
  5. CancerLSP: Identification of early stage liver hepatocellular carcinoma patients
  6. CancerPDF: Database of cancer-associated peptides of human bodyfluids.
  7. Cancertope: A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer.
  8. CancerTSP: Discrimination of early and late-stage samples of thyroid carcinoma
  9. CancerUBM: Web bench for analysis of proteomics data and prediction of cancer status of a urine samples.
  10. CCDB: Database of genes involved in Cervix Cancer.
  11. CMcrpred: Estimate survival risk in cutaneous melanoma patients
  12. CRCRpred: Prediction of risk scores of colorectal cancer patients
  13. HerceptinR: Information about assays performend to test sensitivity/resistance of Herceptin Antibodies.
  14. HIVcoPRED: Predicting coreceptor used by HIV-1 from Its V3 loop amino acid sequence.
  15. MtbVeb: A webportal for designing vaccine against drug resistant and emerging strains of M. tuberculosis.
  16. RNAcon: A web-server for the prediction and classification of non-coding RNAs.
  17. SKCMhrp: Classification of high-risk cutaneous melanoma patients

External Links to web servers developed/maintained by other groups

This section provides URL/links to important websites developed and maintained by other researchers. It exclude servers by Raghava's group, which is given in above section. 

  1. 16S classifier: a tool for fast and accurate taxonomic classification of 16S rRNA hypervariable regions in metagenomic datasets.
  2. Bisgoat: Locus minimization in breed prediction using artificial neural network approach.
  3. CBD : Biomarker database for colorectal cancer
  4. CRC-EBD: Database for epigenetic biomarkers on colorectal cancer
  5. FBIS: A regional DNA barcode archival & analysis system for Indian fishes.
  6. FmMDb: a versatile database of foxtail millet markers for millets and bioenergy grasses research.
  7. Haemophilus influenzae Genome Database (HIGDB): a single point web resource for Haemophilus influenzae.
  8. IGVBrowser: a genomic variation resource from diverse Indian populations.
  9. IRESPred: Web Server for Prediction of Cellular and Viral Internal Ribosome Entry Site (IRES)
  10. MarkerDB: Database of molecular biomarkers
  11. MGEx-Tdb: A novel tissue specific meta:analysis approach for gene expression predictions initiated with a mammalian gene expression testis database.
  12. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data.
  13. OncoMX : A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data
  14. OSblca: Webserver to investigate prognostic biomarkers of bladder cancer patients
  15. OSluca: Webserver to evaluate prognostic biomarkers for lung cancer
  16. PlantRGS: a web server for the identification of most suitable candidate reference genes for quantitative gene expression studies in plants.
  17. QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice.
  18. RCDB: Renal Cancer Gene Database.
  19. SMBMDb: First whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications.
  20. Streptococcus pneumoniae Genome Database (SPGDB): a database for strain specific comparative analysis of Streptococcus pneumoniae genes and proteins.
  21. SurvExpres: Tool and database for cancer gene expression data using survival analysis
  22. TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes.
  23. WebGeSTer DB: a transcription terminator database.
  24. WNV Typer: a server for genotyping of West Nile viruses using an alignment:free method based on a return time distribution.