Grants
- NIH grant on transcriptional analysis of the guinea pig model of tuberculosis
- DBT grant on biomarker discovery and validation of blood immune response following HIV -TB co-infection
Completed Projects
- Development of chickpea gene expression microarray
- Completed Next Generation Sequencing and de novo transcriptome analysis of Costus pictus D. Don, a non-model plant with potent anti-diabetic
properties
- Completed de novo Transcriptome Assembly (NGS) of Curcuma longa L. Rhizome Reveals Novel Transcripts Related to Anticancer and Antimalarial
Terpenoids
- Cancer profiling for clinical intervention and biomarker discovery
- Genomics approach to identify diseases related to chromosomal aberrations in humans
- Development of gene panel for mitochondrial genome
- Development of SNP markers in plants
Publications from Genotypic
Publications Co-authored by Genotypic
- Sanjeev Kumar Shukla, Shubhra Shukla, Rehan Khan, Anuj Ahuja, Lakshya Veer Singh, Nitin M. Kamble, Anupam Dhasmana, Naveen Sharma, Bipin Chand, Ajay Vir Singh, Pathway analysis of differentially expressed genes in Mycobacterium bovis challenged bovine macrophages, Microbial Pathogenesis, Volume 115, 2018, Pages 343-352, ISSN 0882-4010, https://doi.org/10.1016/j.micpath.2017.11.065.
- Crystal A. Shanley, Marcela I. Henao-Tamayo, Chand Bipin, Raja Mugasimangalam, Deepshika Verma, Diane J. Ordway, Elizabeth M. Streicher, Ian M. Orme, Biology of clinical strains of Mycobacterium tuberculosis with varying levels of transmission,Tuberculosis, Volume 109,2018,Pages 123-133,ISSN 1472-9792,https://doi.org/10.1016/j.tube.2018.02.003
- Nizar Jamal Haddad, Noureddine Adjlane, Deepti Saini, Athul Menon, Venkatesh Krishnamurthy, Devan Jonklaas J., Paul Tomkins, Wahida Loucif‐Ayad, Lisa Horth. Whole‐genome sequencing of north African honey bee Apis mellifera intermissa to assess its beneficial traits. Entomological Research (2018). https://doi.org/10.1111/1748-5967.12272
- Ramasamy Yasodha, Ramesh Vasudeva, Swathi Balakrishnan, Ambothi Rathnasamy Sakthi, Nicodemus Abel, Nagarajan Binai, Balaji Rajashekar, Vijay Kumar Waman Bachpai, Chandrasekhara Pillai, Suma Arun Dev, Draft genome of a high value tropical timber tree, Teak (Tectona grandis L. f): insights into SSR diversity, phylogeny and conservation, DNA Research, Volume 25, Issue 4, August 2018, Pages 409–419, https://doi.org/10.1093/dnares/dsy013
- Pandey I, Kaur R, Subudhi AK et al. A tiling array-based comparative genomic hybridization approach to predict copy number variations between Plasmodium falciparum field isolates from the Indian Sub-continent [version 1; peer review: 1 approved, 1 approved with reservations]. F1000Research 2018, 7:1033 (https://doi.org/10.12688/f1000research.14599.1)
- Deepika Pandey Tiwari, Poonam Mishra Chatterjee, Harish Rotti, Bipin Chand, Ritu Raval, Ashok Kumar Dubey, Expression dynamics of the poly-γ-glutamic acid biosynthesis genes of Bacillus subtilis in response to glucose and glutamic acid—a pilot study, FEMS Microbiology Letters, Volume 365, Issue 22, November 2018, fny248, https://doi.org/10.1093/femsle/fny248
- Tandon D, Haque MM, R. S, Shaikh S, P. S, Dubey AK, et al. (2018) A snapshot of gut microbiota of an adult urban population from Western region of India. PLoS ONE 13(4): e0195643. https://doi.org/10.1371/journal.pone.0195643
- Usha R. Dutta, Sudha N. Rao, Vijaya Kumar Pidugu, Vineeth V.S., Amrita Bhattacherjee, Aneek Das Bhowmik, Sathish K. Ramaswamy, Kumar Gautam Singh, Ashwin Dalal, Breakpoint mapping of a novel de novo translocation t(X;20)(q11.1;p13) by positional cloning and long read sequencing, Genomics(2018)
- Nizar Haddad , Noureddine Adjlane, Wahida Loucif-Ayad, Abhinandita Dash, Naganeeswaran S., Balaji Rajashekar, Kosai Al-Nakeeb & Thomas SicheritzPonten (2017) Mitochondrial genome of the North African Sahara Honeybee, Apis mellifera sahariensis (Hymenoptera: Apidae), Mitochondrial DNA Part B, 2:2, 548-549, DOI: 10.1080/23802359.2017.1365647
- Laha, R.C., De Mandal, S., Ralte, L. et al. Meta-barcoding in combination with palynological inference is a potent diagnostic marker for honey floral composition. AMB Expr 7, 132 (2017). https://doi.org/10.1186/s13568-017-0429-7
- Tarique Anwar, Bijoya Sen, Savera Aggarwal, Rhisita Nath, Ajay Katoch, Mohamed Aiyaz, Nirupma Trehanpati, Sanjeev Khosla, Gayatri Ramakrishnan. Differentially regulated gene expression in quiescence vs. senescence and identification of ARID5A as a quiescence associated marker. Journal of Cellular physiology (2017). https://doi.org/10.1002/jcp.26227
- Shukla A, Singh VK, Bharadwaj DR, et al. De Novo Assembly of Bitter Gourd Transcriptomes:Gene Expression and Sequence Variations in Gynoecious and Monoecious Lines. PLoS ONE. 2015;10(6):e0128331
- Rastogi S, Kalra A, Gupta V, et al. Unravelling the genome of Holy basil: an “incomparable” “elixir of life” of traditional Indian medicine. BMC Genomics. 2015;16:413
- B. Kesavan, K.V. Srividhya, S. Krishnaswamy, Mugasimangalam Raja, N. Vidya, A.V.S.K. Krishna Mohan. Understanding the virulence of the entero-aggregative E. coli O104:H4.Int. J. of Bioinformatics Research and Applications. 2015
- Bose D, Shetty M, Kutty A.V.M, et al. Molecular Delineation of Partial Trisomy 14q and Partial Trisomy 12p in a Patient with Dysmorphic Features, Heart Defect and Developmental Delay. Cytogenet Genome Res. 2015
- Chendamarai E, Ganesan S, Alex AA, et al. Comparison of newly diagnosed and relapsed patients with acute promyelocytic leukemia treated with arsenic trioxide: insight into mechanisms of resistance. PLoS ONE. 2015;10(3):e0121912
- Haddada NJ, AlShagoora B, Batainh AM, et al. Draft genome sequence of the Algerian bee Apis mellifera intermissa. Genomics Data. 2015
- Haddad NJ, Batainh AM, Migdadi OS, et al. Next generation sequencing of Apis mellifera syriaca identifies genes for Varroa resistance and beneficial bee keeping traits. Insect Sci. 2015
- Dasgupta MG, Dharanishanthi V, Agarwal I, Krutovsky KV. Development of genetic markers in eucalyptus species by target enrichment and exome sequencing. PLoS ONE. 2015;10(1):e0116528
- Boopathi PA, Subudhi AK, Garg S, et al. An in vivo Transcriptome Dataset of Natural Antisense Transcripts from Plasmodium falciparum Clinical Isolates.J Genomics Data.2014
- Aiyaz M, Bipin C, Pantulwar V, Mugasimangalam R, Shanley CA, Ordway DJ, Orme IA. Whole genome response in guinea pigs infected with the high virulence strain Mycobacterium tuberculosis TT372. Tuberculosis J. 2014
- Boopathi PA, Subudhi AK, Garg S, et al. Dataset of Natural Antisense Transcripts in P. vivax clinical isolates derived using custom designed strand- specific microarray. J Genomics Data. 2014
- Nagaraj S, Raghavan AV, Rao SN, Manjappara UV. Obestatin and Nt8U influence glycerolipid metabolism and PPAR gamma signaling in mice. Int J Biochem Cell Biol. 2014;53:414-22
- Janbon G, Ormerod KL, Paulet D, et al. Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation. PLoS Genet. 2014
- Subudhi AK, Boopathi PA, Garg S, et al. Natural antisense transcripts in Plasmodium falciparum isolates from patients with complicated malaria. Exp Parasitol. 2014;141:39-54
- Boopathi PA, Subudhi AK, Garg S, et al. Revealing natural antisense transcripts from Plasmodium vivax isolates: evidence of genome regulation in complicated malaria. Infect Genet Evol. 2013;20:428-43
- Rao PP, Reddy YN, Ganesh K, Nair SG, Niranjan V, Hegde NR. Deep sequencing as a method of typing bluetongue virus isolates. J Virol Methods. 2013;193(2):314-9
- Chakraborty U, Mohamed A, Kakade P, Mugasimangalam RC, Sadhale PP, Sanyal K. A stable hybrid containing haploid genomes of two obligate diploid Candida species. Eukaryotic Cell. 2013;12(8):1061-71
- Biswal DK, Ghatani S, Shylla JA, et al. An integrated pipeline for next generation sequencing and annotation of the complete mitochondrial genome of the giant intestinal fluke, Fasciolopsis buski (Lankester, 1857) Looss, 1899. PeerJ. 2013;1:e207
A Novel Cuckoo Search Algorithm for Genome Sequence Assembly
