Dr. Malabika Sarker

KEY ACCOMPLISHMENTS

Awarded a phase 1 STTR grant in 2013 from the National Institutes of Health (NIH) to develop a computational approach for predicting drug targets and small molecules for Chagas disease.
Awarded a STTR grant (phase I in 2010 and phase II in 2012) from NIH and identified novel therapeutics for tuberculosis.
Helped developing TB Mobile: Appifying Data on Anti-tuberculosis Molecule Targets (Link).
Curated the largest biosynthesis pathway for Biocyc for the design of anti-tubercular drugs (Link1, Link2).
Curated the pathways and enzymes of EcoCyc version 14.5 (Link).
Identified key metabolites as potential drug targets for tuberculosis as part of GATES project.
Implemented Pathway Logic, a formal modeling technique, to develop metabolic pathways of bacterial metabolism for understanding bacterial pathogenesis (Link).
Co-PI for Plasma Proteome Database (Link).
One of the key Reviewers of Human Protein Reference Database (Link).
One of the lead players in Human Interactome Analysis (Link).

1. Combining Metabolite-Based Pharmacophores with Bayesian Machine Learning Models for

Mycobacterium tuberculosis Drug Discovery, PLOS ONE 2015 (PMID: 26517557)

2. Machine Learning Models and Pathway Genome Data Base for Trypanosoma cruzi Drug Discovery,

PLOS NTD 2015 (PMID: 26114876)

3. New target prediction and visualization tools incorporating open source molecular fingerprints for TB

Mobile 2.0, Journal of Cheminformatics 2014 (PMID: 25302078)

4. Computational Models for Neglected Diseases: Gaps and Opportunities, Pharmaceutical Research 2013

5. TB mobile: a mobile app for anti-tuberculosis molecules with known targets, Journal of Cheminformatics

6. Combining Cheminformatics Methods and Pathway Analysis to Identify Molecules with Whole-Cell

Activity Against Mycobacterium Tuberculosis, Pharmaceutical Research 2012 (PMID: 22477069)

7. In Silico Pathway Analysis Predicts Metabolites That Are Potential Antimicrobial Targets, J Comput Sci

Syst Biol 2011 (ResearchGate)

8. Computational databases, pathway and cheminformatics tools for tuberculosis drug discovery, Trends

Microbiol. 2011 (PMID: 21129975)

9. EcoCyc: a comprehensive database of Escherichia coli biology, Nucleic Acids Res. 2011 (PMID:

10. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction

datasets, Nat Genet. 2006 (PMID: 16501559)

11. Human protein reference database--2006 update, Nucleic Acids Res 2006 (PMID: 16381900)

12. Plasma Proteome Database as a resource for proteomics research, Proteomics 2005 (PMID: 16041672)

13. SPOTS: signaling protein oligomeric transduction structures are early mediators of death receptor-induced

apoptosis at the plasma membrane, J Cell Biol. 2004 (PMID: 15557123)

14. Stimulation of the mitogen-activated protein kinase pathway antagonizes TRAIL-induced apoptosis

downstream of BID cleavage in human breast cancer MCF-7 cells, Oncogene 2002 (PMID: 12082620)

15. PARP-1 modifies the effectiveness of p53-mediated DNA damage response, Oncogene 2002 (PMID:

16. Activation of protein kinase C inhibits TRAIL-induced caspases activation, mitochondrial events and

apoptosis in a human leukemic T cell line, Cell Death Differ. 2001 (PMID: 11313719)

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1. In Silico Systems Biology Approaches for the Identification of Antimicrobial Targets, Springer, Methods

in Molecular Biology Volume 993, 2013, pp 13-30 2013 (PMID: 23568461)

2. Plasma Proteome Database, Proteomics of human body fluids Thongboonkerd, V. Editor (Humana Press,