Publications

• • Intragenic Enhancers Attenuate Host Gene Expression

    • • Cinghu S, Yang P, Kosak JP, Conway AE, Kumar D, Oldfield AJ, Adelman K, Jothi R.

      • Mol Cell. 2017 Oct 5

• GLIS3 is indispensable for TSH/TSHR-dependent thyroid hormone biosynthesis and follicular cell proliferation

  • • Kang HS, Kumar D, Liao G, Lichti-Kaiser K, Gerrish K, Liao XH, Refetoff S, Jothi R, Jetten AM.

    • J Clin Invest. 2017 Oct 30

• • Kumar D, Yadav AK, Dash D.

  • Methods in Molecular Biology 2016 Dec 15 (Book Chapter)

  • Kumar D, Dash D.

• Adv Exp Med Biol. 2016 Sep 30 (Book Chapter)

• Integrating transcriptome and proteome profiling: Strategies and applications

• • Kumar D*, Bansal G, Narang A, Basak T, Abbas T, Dash D.

  • Proteomics. 2016 Jun 25

• Polyketide Quinones Are Alternate Intermediate Electron Carriers during Mycobacterial Respiration in Oxygen-Deficient Niches

• • Anand A, Verma P, Singh AK, Kaushik S, Pandey R, Shi C, Kaur H, Chawla M, Elechalawar CK, Kumar D, Yang Y, Bhavesh NS, Banerjee R, Dash D, Singh A,Natarajan VT, Ojha AK, Aldrich CC, Gokhale RS

  • Mol Cell. 2015 Nov 19;60(4):637-50

• Integrated transcriptomic-proteomic analysis using a proteogenomic workflow refines rat genome annotation.

• • Kumar D, Yadav AK, Jia X, Mulvenna J, Dash D.

  • Mol Cell Proteomics. 2015 Nov 11.

• Proteogenomics of rare taxonomic phyla: a prospective treasure trove of protein coding genes

• • Kumar D*, Mondal AK, Kutum R and Dash D

  • Proteomics 2015. (Accepted)

• Probing the missing human proteome: A computational perspective

• • Kumar D, Jain A and Dash D

  • J. Proteome Res. 2015. (Accepted)

• Expression profiling of lymph nodes in tuberculosis patients reveal inflammatory milieu at site of infection

Maji A, Misra R, Kumar Mondal A, Kumar D, Bajaj D, Singhal A, Arora G, Bhaduri A, Sajid A, Bhatia S, Singh S, Singh H, Rao V, Dash D, Baby Shalini E,Sarojini Michael J, Chaudhary A, Gokhale RS, Singh Y.

Sci. Rep. 2015. (Accepted)

• • Transcriptome and venom proteome of the box jellyfish Chironex fleckeri.

• Brinkman DL, Jia X, Potriquet J, Kumar D, Dash D, Kvaskoff D, Mulvenna J.

  • BMC Genomics. 2015 May 27

• Extensive copy number variations in admixed Indian population of african ancestry: potential involvement in adaptation.

Narang A, Jha P, Kumar D, Kutum R, Mondal AK; Indian Genome Variation Consortium, Dash D, Mukerji M.

Genome Biol Evol. 2014 Nov 13

• Discovery of rare protein coding genes in model methylotroph Methylobacterium extorquens AM1

Kumar D, Mondal AK, Yadav AK , Dash D.

Proteomics. 2014 Aug 24

• • Gene rich large deletions are overrepresented in POAG patients of Indian and Caucasian origins

• Kaurani L, Vishal M, Kumar D, Sharma A, Mehani B, Sharma C, Chakraborty S, Jha P, Ray J, Sen A, Dash D, Ray K, Mukhopadhyay A.

  • Invest Ophthalmol Vis Sci. 2014 Apr 24

• ProteoStats - a library for estimating false discovery rates in proteomics pipelines

Yadav AK, Kadimi PK, Kumar D and Dash D

Bioinformatics. 2013 Aug 20

• Integration Host Factor of Mycobacterium tuberculosis, mIHF, Compacts DNA by a Bending Mechanism.

Mishra A, Vij M, Kumar D, Taneja V, Mondal AK, Bothra A, Rao V, Ganguli M, Taneja B.

PLoS One. 2013 Jul 26;

• Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using Genosuite, an automated multi-algorithmic pipeline. Mol Cell Proteomics.

Kumar D, Yadav AK, Kadimi PK, Nagaraj SH, Grimmond SM, Dash D.

Mol Cell Proteomics. 2013 Jul 23.

• Learning from Decoys to Improve the Sensitivity and Specificity of Proteomics Database Search Results.

Yadav AK, Kumar D, Dash D

PLoS one. 2012 Nov 26. 2012;7(11):e50651.

• • Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry.

    • • Kelkar DS, Kumar D, Kumar P, Balakrishnan L, Muthusamy B, Yadav AK, Shrivastava P, Marimuthu A, Anand S, Sundaram H, Kingsbury R, Harsha HC, Nair B, Keshava Prasad TS, Chauhan DS, Katoch K, Katoch VM, Kumar P, Chaerkady R, Ramachandran S, Dash D, Pandey A.

Mol Cell Proteomics. 2011 Oct 3. [Epub ahead of print]

• • A systematic analysis of eluted fraction of plasma post immunoaffinity depletion: implications in biomarker discovery.

    • Yadav AK, Bhardwaj G, Basak T, Kumar D, Ahmad S, Priyadarshini R, Singh AK, Dash D, Sengupta S.

    • PLoS One. 2011;6(9):e24442. Epub 2011 Sep 7.

  • Spectrum of large copy number variations in 26 diverse Indian populations: potential involvement in phenotypic diversity.

    • Gautam P, Jha P, Kumar D, Tyagi S, Varma B, Dash D, Mukhopadhyay A; Indian Genome Variation Consortium, Mukerji M.

    • Hum Genet. 2011 Jul 9. [Epub ahead of print]

  • MassWiz: a novel scoring algorithm with target-decoy based analysis pipeline for tandem mass spectrometry.

    • Yadav AK, Kumar D, Dash D.

    • J Proteome Res. 2011 May 6;10(5):2154-60.