User:Abhishek Kumar

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Abhishek Kumar (Abhishek Kumar)
  • Dr. Abhishek Kumar
  • Abteilung für Botanische Genetik und Molekularbiologie
  • Botanisches Institut und Botanischer Garten
  • Christian-Albrechts-Universität zu Kiel
  • Kiel, SH, Germany.
  • Email me through OpenWetWare

I work in the AG Kempken at University of Kiel (Christian-Albrechts-Universität zu Kiel) at Kiel, Germany. I learned about OpenWetWare from on web search!!!, and I've joined because Sharing information.

Profile

  • Research Associate in Next generation genome and transcriptome sequencing University of Kiel, Kiel, Germany (webpage: www.uni-kiel.de)
  • Postdoc in insect transcriptome sequencing University of Padova, Padova, Italy (webpage: www.unipd.it)
  • PhD in Bioinformatics University of Bielefeld, Bielefeld, Germany (webpage: www.uni-bielefeld.de)
  • MS, School of Biotechnology, Madurai Kamaraj University, Madurai, India (webpage: www.biotechmku.org)
  • BS, Ewing Christian College, Allahabad University, Allahabad, India (webpage: http://www.ecc.ac.in/)

Research interests

  1. Bioactive compounds from fungi
  2. Next generation sequencing (NGS)
  3. Application of NGS
  4. Molecualr evolution of superfamilies of proteins
  5. Evolution of introns
  6. Gene/Genome Duplications

Publications

  1. Kumar, A*., & Bhandari, A.(2014). A. Urochordate serpins are classified into six groups encoded by exon-intron structures, microsynteny and Bayesian phylogenetic analyses. J. Genomics, 2:131-140. doi:10.7150/jgen.9437, (New Journal)
  2. Kumar, A*., Bhandari, A., Sarde, S. J., & Goswami, C.(2014). Molecular phylogeny of C1 inhibitor depicts two immunoglobulin-like domains fusion in fishes and ray-finned fishes specific intron insertion after separation from zebrafish. Biochemical and Biophysical Research Communications (In press).
  3. Kumar, A*., Bhandari, A., Sarde, S. J., & Goswami, C. Genetic variants and evolutionary analyses of heparin cofactor II. Immunobiology, 219 (2014) 713–728. doi:10.1016/j.imbio.2014.05.003
  4. Kumar, A. …. Grapputo, A. (2014) Sequencing, De Novo Assembly and Annotation of the Colorado Potato Beetle, Leptinotarsa decemlineata, Transcriptome . PloS ONE 9(1): e86012.doi:10.1371/journal.pone.0086012.
  5. Kumar, A*., Bhandari, A., Sarde, S. J., & Goswami, C. (2013). Sequence, phylogenetic and variant analyses of antithrombin III. BBRC, 440(4), 714–724. doi:10.1016/j.bbrc.2013.09.134
  6. Kumar, A., Kollath-Leiß, K., & Kempken, F. (2013). Characterization of bud emergence 46 (BEM46) protein: sequence, structural, phylogenetic and subcellular localization analyses. BBRC, 438(3), 526–532. doi:10.1016/j.bbrc.2013.07.103
  7. Traeger, S., Altegoer, F., Freitag, M., Gabaldon, T., Kempken, F., Kumar, A., … Nowrousian, M. (2013). The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution. PLoS Genetics, 9(9), e1003820.
  8. Majhi, R. K., ….Kumar, A., Goswami, C. (2013). Thermosensitive ion channel TRPV1 is endogenously expressed in the sperm of a fresh water teleost fish (Labeo rohita) and regulates sperm motility. Channels (Austin, Tex.), 7(6), 1–10.
  9. Vidotto, M., Grapputo, A., Boscari, E., … Kumar, A., Congiu, L. (2013). Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon. BMC genomics, 14(1), 407. doi:10.1186/1471-2164-14-407 Highly accessed.
  10. Gruettner S., Hopf, C., Kumar, A., & Kempken, F. (2013). Deletions in cox2 mRNA result in loss of splicing and RNA editing and gain of novel RNA editing sites. PLoS ONE, 8(12): e82067. doi:10.1371/journal.pone.0082067.
  11. Kumar A*, Bhandari A, Sinha R, Sardar P, Sushma M, et al. (2012) Molecular Phylogeny of OVOL Genes Illustrates a Conserved C2H2 Zinc Finger Domain Coupled by Hypervariable Unstructured Regions. PLoS ONE 7(6): e39399. doi:10.1371/journal.pone.0039399.
  12. Sardar P., Kumar A., Bhandari A., Goswami C. (2012) Conservation of Tubulin-Binding Sequences in TRPV1 throughout Evolution. PLoS ONE 7(4): e31448. doi:10.1371/journal.pone.0031448
  13. Kumar, A.* Bhandari, A. Sinha, R. Goyal, P. Grapputo, A. (2011) Spliceosomal Intron Insertions in Genome Compacted Ray-Finned Fishes as Evident from Phylogeny of MC Receptors, Also Supported by a Few Other GPCRs. PLoS ONE 6(8): e22046.
  14. Goyal, P. Behring, A. Kumar, A. Siess, W. (2011) STK35L1 Associates with Nuclear Actin and Regulates Cell Cycle and Migration of Endothelial Cells. PLoS ONE 6(1): e16249.
  15. Ragg, H. Kumar, A. ………..(2009). Multiple gains of spliceosomal introns in a superfamily of vertebrate protease inhibitor genes. BMC Evolutionary Biology,9:208.
  16. Goyal, P. Behring, A. Kumar, A. Siess, W. (2009). Characterization of a novel protein kinase STK35L1 and deciphering its orthologs and close-homologs in vertebrates. PLoS ONE 4(9): e6981.
  17. Kumar, A. & Ragg, H. (2008). Ancestry and evolution of a secretory pathway serpin. BMC Evolutionary Biology, 8:250. Highly accessed.
  18. Kumar, A. & Krishnaswamy, S (2008). Temperature factor analysis of outer membrane beta-stranded porin crystal structures suggests the pore is not uniformly rigid. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2008.2495.1>
  19. Kumar, A*. (2005). Delving into vertebrate serpins for understanding their evolution, BREW 2005, Berlin. Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3050.1> (2009).
  20. Tripathi, S. Sonkar, S.K. Kumar, A. Khan, M.Y. & Sarkar, S. (2009). Water soluble carbon nanotubes affect growth of the common gram (Cicer arietinum). Nature Precedings <http://hdl.handle.net/10101/npre.2009.4056.1>.

Books

  1. Kumar, A. (2013). Phylogenomics of vertebrate serpins: Molecular evolution of vertebrate Serine protease inhibitors. Publisher: LAMBERT Academic Publishing, ISBN: 9783659336454. Available from Amazon.
  2. Kumar, A. (2010). Bioinformatic Analysis of Beta Barrel Porins. Publisher: VDM Verlag, ISBN: 9783639244502. Available from Amazon.

Invited Talks

  1. Application of next-generation genome and transcriptome based methods for the exploration of secondary metabolites from marine fungi for the treatment of cancer, CAMDA, ISMB/ECCB, July 2013, Berlin, Germany.
  2. Genome and RNA sequencing, assembly and annotation of three marine fungal isolates using different next generation DNA sequencing methods for pharmaceutically important secondary metabolites. Eurofung Meeting, 15.10.2012, Berlin, Germany.
  3. Marine fungal isolates: genome sequence analysis using different next generation DNA sequencing methods to find potential cancer drugs. 60 Jahre Deutsch - Indische Zusammenarbeit, 14.09.2012, Berlin, Germany.
  4. Genome sequencing of three marine fungi:genome characterisation for secondary metabolite catalogues, kinomes and transposons using next-generation genome sequencing, GZMB-Kolloquium Mikrobiologie ,Goettingen, Germany
  5. Genome sequencing, assembly and annotation of a marine isolate of Scopulariopsis brevicaulis using three different next generation sequencing technologies. Biobased World, June 2012, Frankfurt.
  6. Next-generation genome and transcriptome sequencing, assembly and annotation of biologically significant organisms, 8-9 Dec, 2011, Microbiology Dept. Delhi University, New Delhi.
  7. Understanding the bud emergence 46 (BEM46) protein from functional and evolutionary perspectives. The XXXV All India Cell Biology conference and symposium on Membrane dynamics and disease, Dec, 16 - 18, 2011, Bhubaneswar.
  8. Sequence, Structure and Evolution of Metazoan Ovo-like genes. National Symposium on Modern Approaches and Innovations in Biotechnology, Nov 2010, Meerut, India. Full article in conference proceeding.
  9. Comparative genomics gets a boost with next generation sequencing. Nov 2010, Biologisches Kolloquium im Biologiezentrum der Christian-Albrechts-Universität zu Kiel, Kiel.
  10. Evolutionary genomics of multigene superfamilies. Dec 2009, Max Plank Institute for Chemical Ecology, Jena.
  11. Evolutionary genomics of multigene superfamilies. Oct 2009, Department of Biological and Environmental Sciences, University of Helsinki, Finland.
  12. Delving into vertebrate serpins for understanding their evolution, BREW 2005, Berlin.

Conference Posters

  1. Kumar, A. and Kempken, F. (2014) NGS genome and transcriptome based methods for the exploration of secondary metabolites from marine fungi for the treatment of cancer. ELRIG - Research and Innovation Impact into Cancer, 11th March 2014, Telford, UK.
  2. Kumar, A. and Kempken, F. (2014) Genome sequencing, assembly and annotation of a marine isolate of Scopulariopsis brevicaulis using three different next generation sequencing technologies. ELRIG - Research and Innovation Impact into Cancer, 11th March 2014, Telford, UK.
  3. Kramer, A. Beck, H.C. and Kumar, A. (2014) Quantitative proteomics of the regulation patterns in scopularide A and B production by a marine Scopulariopsis brevicaulis strain LF580. ELRIG - Research and Innovation Impact into Cancer, 11th March 2014, Telford, UK.
  4. Kumar, A. and Kempken, F. (2013) Next-generation genome and transcriptome based methods for the exploration of secondary metabolites from marine fungi for the treatment of cancer. International Conference of Fungal Biology, 29.09.-02.10.2013, Karlsruhe, Germany.
  5. Kumar, A. and Kempken, F. (2013) Genome sequencing, assembly and annotation of three marine fungal isolates using different next generation DNA sequencing methods for pharmaceutically important secondary metabolites. 27. Fungal Genetics Conference, 12.-17.03.2013, Pacific Grove, California, USA.
  6. Kumar, A., Kollath-Leiß, K., & Kempken, F. (2013). Structural, functional and molecular evolution of eukaryotic BEM46, 3DSIG, ISMB/ECCB, July 2013, Berlin, Germany.
  7. Kumar, A. and Kempken, F. (2013) Genome sequencing, assembly and annotation of a marine fungal isolate of Scopulariopsis brevicaulis using three different next generation sequencing technologies. 27. Fungal Genetics Conference, 12.-17.03.2013, Pacific Grove, California, USA.
  8. Shbat Y, Kumar, A. and Kempken, F. (2013) Comparative analysis of fungal kinomes. 27. Fungal Genetics Conference, 12.-17.03.2013, Pacific Grove, California, USA.
  9. Kumar, A. Kollath-Leiss, K. and Kempken, F. (2013) Known unknown genes: evolution of eukaryotic BEM46, 27. Fungal Genetics Conference, 12.-17.03.2013, Pacific Grove, California, USA.
  10. Kumar, A.and Kempken, F. (2013) Genome sequencing, assembly and annotation of a marine fungal isolate of Calcarisporium using different next generation sequencing technologies. 27. Fungal Genetics Conference, 12.-17.03.2013, Pacific Grove, California, USA.
  11. Kumar, A.and Kempken, F. (2013) Genome sequencing, assembly and annotation of a marine fungal isolate of Pestalotiopsis using next generation sequencing technologies. 27. Fungal Genetics Conference, 12.-17.03.2013, Pacific Grove, California, USA.
  12. Kumar, A.and Kempken, F. (2012) Genome sequence analysis of three marine fungal isolates using different next generation DNA sequencing methods, German conference on Bioinformatics (GCB) 2012, Jena, Germany, pp.38
  13. Kumar, A.Kollath-Leiss, K. and Kempken, F. (2012) Sequence, structure, function and evolution of BEM46 proteins, German conference on Bioinformatics (GCB) 2012, Jena, Germany pp.40
  14. Shbat, Y., #Kumar, A. and Kempken, F. (2012) Establishment and analysis of fungal kinomes, German conference on Bioinformatics (GCB) 2012, Jena, Germany pp.42
  15. Kumar, A.and Grapputo, A. (2012) Transcriptomic analysis of the adult life stage of the invasive Colorado potato beetle (Leptinotarsa decemlineata) using Roche 454, German conference on Bioinformatics (GCB) 2012, Jena, Germany pp.71
  16. Vidotto, M., Coppe, A., Kumar, A. Grapputo, A., Grandi, G. & Congiu, L. (2012) Trancriptomic analysis of the polyplod adriatic sturgeon, Acipenser nacarii, German conference on Bioinformatics (GCB) 2012, Jena, Germany, pp.125
  17. Kumar, A. and Kempken, F. (2012) Next-generation genome sequencing, assembly, annotation and analysis of a marine isolate of Scopulariopsis brevicaulis, VAAM Conference, Tuebingen, Germany, pp. 79
  18. Kumar, A. & Kempken, F. (2012) The draft genome of marine isolate of Scopulariopsis brevicaulis using three different next generation sequencing methods. SUBMARINER Blue Biotechnology Cooperation Event: New Strategies and Future Perspectives, Kiel, Germany, pp. 21.
  19. Kumar, A. Kollath-Leiss, K. & Kempken, F. (2011) Molecular Phylogeny of bud emergence 46 (BEM46). VAAM Symposium - Molecular biology of fungi, Sept 2011, Marburg, Germany.
  20. Grapputo, A. & Kumar, A. (2011) Transcriptomic analysis of the invasive Colorado potato beetle (Leptinotarsa decemlineata). Evolution2011, June 2011 ~ Norman, Oklahoma, USA
  21. Kumar, A. & Ragg, H. (2008). Deciphering the phylogenetic history of neuroserpin orthologs across metazoans by analysis of synteny and rare genomic characters. German Conference on Bioinformatics (GCB2008), Dresden, Germany. Nature Precedings <http://dx.doi.org/10.1038/npre.2008.2496.1>.
  22. Kumar, A. Behring, A. Siess, W. Goyal, P. (2008). Serine threonine kinases STK35 homologs: characterization of a novel protein sub-family and orthology assignment across vertebrates using computational genomics. German Conference on Bioinformatics (GCB2008), Dresden, Germany.
  23. Kumar, A. & Krishnaswamy, S. (2003). Structural analysis of outer membrane beta stranded porins using B-factor. 2nd International Conference on Structure, Dynamics, and Function of Proteins in Biological Membranes, Ascona, Switzerland. Nature Precedings <http://dx.doi.org/10.1038/npre.2009.2803.1> (2009).
  24. Kumar, A. & Krishnaswamy S. (2001). Structural analysis of outer membrane beta stranded porins using temperature factor. International Symposium on Crystallography and Bioinformatics (CBSB'01), Indian Institute of Science Bangalore. India.
  25. Kumar, A. & Bhat, R.(2001). The Thermal Effects on Biomolecular Systems: Molecular Modeling and Simulational Studies. 5th ADNAT Symposium on genomics perspectives at Centre for Cellular & Molecular Biology (CCMB), Hyderabad, India.

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