Md. Shamim Ahasan,PhD

• Expertise in molecular laboratory techniques

  • Nucleic acid (DNA/RNA) extraction, purification and quantification from pure culture, blood, tissue, stool and environmental samples

  • Operating QIAcube and QIAgility robots used for samples processing

  • Skilled in conventional PCR, Real-time PCR and Quantitative PCR

  • Primer and probe design and validation

  • Cloning, gel electrophoresis and spectrophotometry

  • Illumina sequencing library preparation

  • 16S amplicon and whole genome sequencing

  • Familiar with LIMS (Laboratory Information Management System)

  • Illumina MiSeq run and maintenance of MiSeq machine

  • Antimicrobial susceptibility determination using disc diffusion and broth microdilution

  • Competent in RNAscope in Situ Hybridization assay

  • Proficient in direct, indirect and competitive ELISA, Immunofluorescence and other serological, and biochemical assays.

 

• Expertise in bioinformatics

  • 16S amplicon sequencing and whole genome sequencing

  • Quality control of sequence data

  • Processing of sequence data includes host sequence removal, genome assembly, alignments, annotation, mapping, BLAST etc.

  • Phylogenetic analysis and sequence similarity/genetic analysis of sequence data

  • Submission of raw data/Bioproject and genome sequence in web server.

  • Experienced in different bioinformatics tools such as Quantitative Insights Into Microbial Ecology (QIIME), CLC work bench 11, Geneious, Galaxy, Calypso, MEGA 5, BioEdit, IQ-TREE, Bowtie 2, GeneMarkS, ExPASy, UGENE, Tablet, NCBI blast, Blast2GO 5 PRO, SPAdes, Sequence Demarcation Tool (SDT) v1.2 etc.

 

• Expertise in virological, bacteriological, mycological, histopathological and other laboratory techniques

  • Proficient in preparation of virological tissue culture, growth and maintenance, virus isolation, purification, CPE and TCID50 determination

  • Skilled in bacteriophage screening, isolation, purification and identification

  • Skilled in bacteriological media preparation, sample inoculation, propagation, pure bacterial colony isolation, purification and molecular characterization

  • Bacterial identification using bioMerieux API system.

  • Competent in fungal media preparation, culture, phenotypic and molecular characterization of fungal species

  • Competent in histopathology and histopathological slide preparation, and staining techniques such as Haematoxylin and Eosin (H&E), Gram-Twort, Ziehl-Neelsen (ZN) and Periodic acid Schiff (PAS)

 

• Expertise in statistical analysis

  • Competent in different data analytic software like STATA 12, Python, R software, Epi-info, PRIMER 6, SPSS etc.

  • Competent in Bayesian modelling using WinBUGS and R software

 

• Skilled in geographical information system (GIS) software such as Manifold system 8.

 

Professional membership:

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• Member, International Association for Aquatic Animal Medicine (IAAAM), USA

• Member, Sea Turtle Organization, USA

• Member, Wildlife Disease Association (WDA), Australia

• Member, Centre for Biosecurity and Tropical Infectious Diseases (CBTID), Australia

• Member, Centre for sustainable Tropical Fisheries and Aquaculture (CSTFA), Australia

• Member, Tropical Water and Aquatic Ecosystem Research (TropWater), Australia

• Life member, Bangladesh Society for Veterinary Research and Education (BSVER)

• Life member, Bangladesh Journal of Veterinary Medicine, Bangladesh

• Associate Member, Belgian Platform on Tropical Animal Health & Production (be.troplive)

• Member, World’s Poultry Science Association (WPSA)

• Member, International Society of Zoological Sciences (ISZS)

• Member, International Veterinary Information Service (IVIS)

• Member, European Federation of Biotechnology (EFB)

• Member, Global Network of Bangladeshi Biotechnologists

• Member, Bangladesh Veterinary Council (Registration no. 2679)

• Member, Krishibid Institution of Bangladesh (KIB)

• As a faculty member of a Public University directly involved with the Departmental affairs

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Social skills and competences

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• Working for developing awareness on wildlife and biodiversity conservation

• Voluntary veterinary services to rural poor livestock farmers

• Veterinary clinical service at Veterinary Teaching Hospital and public-good activities

• Involved in social and cultural activities within and outside the University

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Computer skills and competences

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• Efficient user of Mac OX and Windows operating system.

• Microsoft office (MS Word, MS Excel, Power Point)

• Competent in Unix, Python, Latex, ICT, Web page design, Internet browsing etc.

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Training, workshops and short courses

 

1. Training on RNAscope in Situ Hybridization assay organized by ACDBio in the Aquatic Pathobiology Laboratory, University of Florida. USA, October 18, 2018

2. Compliance: A collaboration for success. UF training and organizational development. University of Florida. USA, September 19, 2018

3. An introduction to the linux command line. UF training and organizational development. University of Florida. USA, May 10th, 2018

4. Effort fundamentals. Research administration and compliance.Pay roll Management. UF training and organizational development. University of Florida. USA, March 15th, 2018.

5. Cost principles. Research administration and compliance. UF training and organizational development. University of Florida. USA, March 8th, 2018.

6. Introduction to research computing and HiPerGator, UF training and organizational development. University of Florida. USA, January 11th, 2018.

7. Molecular biology, Illumina library preparation and sequencing, Department of Infectious Diseases and Pathology, University of Florida, 20 Oct-15 Nov 2016.

8. Advanced Statistics (SPSS), Graduate Research School, James Cook University, 6 June 2016.

9. Transcriptomics and small genome assembly, James Cook University, 8-9 December 2014.

10. Metagenomics and metagenome assembly, James Cook University, 10- 11 December 2014.

11. Training on SKIP (Skills for International Postgraduates), Graduate Research School, James Cook University, 18 March to 26 June 2014.

12. Thesis & Oral Examinations (PhD & master’s by Research), Graduate Research School, James Cook University, 20 May 2014.

13. Training on Contextualising the research & research integrity, Graduate Research School, James Cook University, 19 May 2014.

14. Training on PELA (Post-Entry Language Assessment), James Cook University, 29 April 2014.

15. Attended workshop on Academic and Thesis Writing Workshop, Graduate Research School, James Cook University, 16 April 2014.

16. Laboratory Bio-safety Training (online module), James Cook University, 4 April 2014.Training on Data storage and management, Graduate Research School, James Cook University, 21 March 2014.

17. Training on Professional Writing and Editing, Graduate Research School, James Cook University, 18 March 2014.

18. Training on Plagiarism and Safe Assign, Graduate Research School, James Cook University, 18 March 2014.

19. Training on ePortfolio and eGRS, Graduate Research School, James Cook University, 19 March 2014.

20. Training on Intellectual Property and Copyright, Graduate Research School, James Cook University, 20 March 2014.

21. Training on Overview of Workplace Safety Management, Graduate Research School, James Cook University, 20 March 2014.

22. Workshop on Endnote Workshop, Graduate Research School, James Cook University, 26 March 2014.