Naveen Kumar

Introduction

I am working as a Senior Technical Scientist in the Laboratory for Integrated Bioinformatics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.

I completed my Bachelor of Science (Information Technology) and Master of Computer Applications from Punjab Technical University, India and Advance Diploma in Bioinformatics from DOEACC Center, India. My role within the team is to design and develop application software and administrate Linux servers.

Contact Information

RIKEN Center for Integrative Medical Sciences
1-7-22 Suehiro-cho, Tsurumi-ku
Yokohama, Kanagawa 230-0045 Japan
Tel: +81 (0)45 503-9280
Fax: +81 (0)45 503-9694
E-mail: naveen dot kumar at riken dot jp

Bioinformatics Software and Databases

  • iCLiKVAL Chrome Extensions : An offline-first browser extensions to accumulate annotation information for scientific literature and media found online [1]
  • iCLiKVAL : An open-access tool for adding value to scientific media one annotation at a time [2]
  • MetaBin : Comprehensive Taxonomic Assignments of Metagenomic Sequences [3]
  • ConjoinG : Database of Conjoined Genes [4]
  • MetaBioME : Comprehensive Metagenomic Biomining Engine [5]
  • Malarial Adhesins and Adhesin-like proteins Predictor [6]
  • Automated Resource Classifier [7]
  • Expression Linked Polymorphism Database [8]

RIKEN Publications

  • "Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin." Sharma VK, Kumar N, Prakash T, Taylor TD. PLoS ONE 7(3):e34030. (April 4, 2012) PMID 22496776
  • "Complete genome sequences of rat and mouse segmented filamentous bacteria, a potent inducer of Th17 cell differentiation." Prakash T, Oshima K, Morita H, Fukuda S, Imaoka A, Kumar N, Sharma VK, Takahashi M, Saitou N, Taylor TD, Ohno H, Umesaki Y, Hattori M. Cell Host & Microbe 10(3):273-284. (September 15, 2011) PMID 21925114
  • "Expression of conjoined genes: another mechanism for gene regulation in eukaryotes." Prakash T, Sharma VK, Adati N, Ozawa R, Kumar N, Nishida Y, Fujikake T, Takeda T, Taylor TD. PLoS ONE 5(10):1-9 e13284. (October 12, 2010) PMID 20967262
  • "MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets." Sharma VK, Kumar N, Prakash T, Taylor TD. Nucleic Acids Research 38(Database):D468-D472. (November 11, 2009) PMID 19906710

Recent Presentations

  • "Semantic annotation and knowledge extraction using iCLiKVAL." Genome Informatics. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York. November 1-4, 2017. (Poster)
  • "Semantic annotation and knowledge discovery using iCLiKVAL." ISMB/ECCB 2017. Prague, Czech Republic. July 21-25, 2017. (Poster)
  • "An offline-first iCLiKVAL browser extension for scientific media annotation." 10th International Biocuration Conference. Stanford University, California, USA. March 26-29, 2017. (Poster)
  • "Scientific media annotation using the iCLiKVAL offline-first browser extension." Genome Informatics. Wellcome Genome Campus, Hinxton, Cambridge, UK. September 19-22, 2016. (Poster)
  • "Scientific literature and media annotation using the iCLiKVAL browser extension." 9th International Biocuration Conference. Campus Biotech Geneva, Geneva, Switzerland. April 12, 2016. (Poster)
  • "Multimedia annotation using the iCLiKVAL browser extension." Genome Informatics. Cold Spring Harbor Laboratory, New York, USA. October 30, 2015. (Poster)
  • "iCLiKVAL API: a RESTful Hypermedia API for literature annotation and discovery." 8th International Biocuration Conference. Beijing, China. April 24, 2015. (Poster)
  • "iCLiKVAL API: a RESTful web service for semantic literature mining." Genome Informatics. Churchill College, Cambridge, UK. September 22, 2014. (Poster)
  • "iMetaSys: An integrated Metagenomic and Microbial Systems Analysis Workbench." International Human Microbiome Congress. Vancouver, Canada. March 10, 2011. (Poster)
  • "Meeting the computational challenges of Metagenomics." 18th Annual international conference on Intelligent Systems for Molecular Biology (ISMB 2010). John B. Hynes Convention Center, Boston, MA, USA. July 11, 2010. (Poster)

Pre-RIKEN Publications

  • "Genetic landscape of the people of India: a canvas for disease gene exploration." Indian Genome Variation Consortium. Journal of genetics 87(1):3-20. (April, 2008) PMID 18560169
  • "MAAP: Malarial adhesins and adhesin-like proteins predictor." Ansari FA, Kumar N, Bala Subramanyam M, Gnanamani M, Ramachandran S.. Proteins 70(3):659-666. (Feb, 2008) PMID 17879344
  • "Abundance of dinucleotide repeats and gene expression are inversely correlated: a role for gene function in addition to intron length." Sharma VK, Kumar N, Brahmachari SK, Ramachandran S. Physiological Genomics 31(1):96-103. (September, 2007) PMID 17550993
  • "ARC: automated resource classifier for agglomerative functional classification of prokaryotic proteins using annotation texts." Gnanamani M, Kumar N, Ramachandran S.. Journal of Biosciences 32(5):937-945. (August, 2007) PMID 17914236
  • "Expoldb: EXpression linked POLymorphism DataBase with inbuilt tools for analysis of expression and simple repeats." Sharma VK, Sharma A, Kumar N, Khandelwal M, Mandapati KK, Horn-Saban S, Strichman-Almashanu L, Lancet D, Brahmachari SK, Ramachandran S. BMC Genomics 7:258-265. (October, 2006) PMID 17038195