Hawkesbury Institute for the Environment

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Dr Khachane joined HIE as a Career Development Fellow in October 2012. He is a Bioinformatics scientist and has extensive experience in the computational analysis of large-scale and diverse biological data sets. His research work has involved development and application of bioinformatics algorithms and tools to gain novel biological insights. At HIE, his work involves developing bioinformatics methods for the analysis of NGS metagenomic/metatranscriptomic data, surveying for (universal) genomic patterns in microbes associated with adaptation to environmental physicochemical parameters, investigating the influence of soil microbiome on soil health and crop productivity, studying co-evolution of symbiont and host genomes, and discovering novel biotechnologically relevant microorganisms/genes/enzymes from metagenomic data.

He began his career in Bioinformatics working at the ‘Indian Institute of Science, India’ where he developed algorithms/tools to study the influence of post-translational modification (PTMs) on the physico-chemical properties of a protein. PTMs play a critical regulatory role in several cellular processes. He then carried out his doctoral research at ‘Helmholtz Center for Infection Research (Technical University Braunschweig, Germany)’, where he developed an interest in the evolution of biological sequences. Using comparative genomics approaches his work answered some interesting biological questions such as: how the genome of obligate intracellular microbes evolves over long evolutionary time-scales, how microorganisms adapt to their environmental stresses, and why some enzymes derived from organisms that thrive in harsh habitats possess enhanced functional activities. He has studied microbial adaptation in a wide range of habitats such as geo-thermally heated and cold environments, intracellular compartments, marine habitat, soil, deep-sea hypersaline anoxic basins (>3000m below sea level), and rumen of dairy cows. He has played an active role in the bioinformatics analysis of data arising from several genome and meta-genome sequencing projects that were published in Nature Biotechnology and other high impact journals. Several of these investigations have focused on establishing genotype-phenotype relationship and interpreting its relevance.

His post-doctoral tenures at 'McGill University, Canada’, and at ‘Center for Biomarker Research and Personalized Medicine, USA’, focused on the analysis of mammalian genomes. He performed computational analyses of large-scale mammalian transcriptome (expression), genetic, and epigenetic data for discovery of novel functional non-protein-coding genomic elements and disease biomarkers. He played a critical role in the bioinformatics analysis of complex and voluminous genome-wide association and methylome data (in the terabyte range) arising from next-generation sequencing projects for researching a cohort of 1500 individuals to understand mechanisms underlying neurological disorders and drug response.

He is an expert in the analysis of next-generation sequencing (NGS) data. The various NGS platforms and workflows he has worked with include:

• NGS Workflows: whole genome re-sequencing and variant calling (DNA-Seq), de novo transcriptome assembly, differential expression analysis (RNA-Seq), targeted sequencing (Exome-Seq), epigenetic regulation (Methylome-Seq) and protein-DNA interactions (ChiP-Seq)
• NGS Platforms: Illumina GA/HiSeq, ABI SOLiD 3+/4, Roche 454
• Reference Genomes: Microbes, Plants and Mammal

Areas of research/expertise

Bioinformatics, Evolutionary biology, Genomics, Microbial adaptation, Microbial pathogenicity, Metagenomics, Next-generation sequencing data analysis, Systems Biology

Awards and recognition

• 1995 Ranked among the top 0.25% students in state medical entrance exam in India
• 2001 Ranked among top 3% students in national level Bioinformatics entrance exam
• 2003 Ph.D. fellowship from German National Research Center for Biotechnology, Germany (funded by BMBF)
• 2007 ‘Ausgezeichnet’ - excellent (for PhD dissertation work in Bioinformatics)

Selected publications

a) Related to evolutionary biology and microbial genomics

Harrison PM, Khachane A, Kumar M, (2010) 'Genomic assessment of the evolution of the prion protein gene family in vertebrates', Genomics, vol.95, no.5, pp 268-77

Khachane AN, Harrison PM, (2009) 'Strong association between pseudogenization mechanisms and gene sequence length', Biology Direct, vol.4, p 38

Khachane AN, Timmis KN, Martins Dos Santos VAP, (2007) 'Dynamics of reductive genome evolution in mitochondria and obligate intracellular microbes', Mol Biol Evol, vol.24, no.2, pp 449-56

Khachane AN, Timmis KN, dos Santos VAPM, (2005) 'Uracil content of 16S rRNA of thermophilic and psychrophilic prokaryotes correlates inversely with their optimal growth temperatures', Nucleic Acids Res, vol.33, no.13, pp 4016-22

b) Related to microbial genome and metagenome sequencing

Gross R, Guzman CA, Sebaihia M, dos Santos VA, Pieper DH, Koebnik R, Lechner M, Bartels D, Buhrmester J, Choudhuri JV, Ebensen T, Gaigalat L, Herrmann S, Khachane AN, Larisch C, Link S, Linke B, Meyer F, Mormann S, Nakunst D, Rückert C, Schneiker-Bekel S, Schulze K, Vorhölter FJ, Yevsa T, Engle JT, Goldman WE, Pühler A, Göbel UB, Goesmann A, Blöcker H, Kaiser O, Martinez-Arias R, (2008) 'The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic bordetellae', BMC Genomics, vol.9

Schneiker S, Martins dos Santos VA, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova TN, Denaro R, Ferrer M, Gertler C, Goesmann A, Golyshina OV, Kaminski F, Khachane AN, Lang S, Linke B, McHardy AC, Meyer F, Nechitaylo T, Pühler A, Regenhardt D, Rupp O, Sabirova JS, Selbitschka W, Yakimov MM, Timmis KN, Vorhölter FJ, Weidner S, Kaiser O, Golyshin PN, (2006) 'Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium alcanivorax borkumensis', Nat Biotechnol, vol.24, no.8, pp 997-1004

Ferrer M, Golyshina OV, Chernikova TN, Khachane AN, Martins Dos Santos VA, Yakimov MM, Timmis KN, Golyshin PN, (2005) 'Microbial enzymes mined from the urania deep-sea hypersaline anoxic basin', Chemistry and Biology, vol.12, no.8, pp 895-904

Ferrer M, Golyshina OV, Chernikova TN, Khachane AN, Reyes-Duarte D, Santos VA, Strompl C, Elborough K, Jarvis G, Neef A, Yakimov MM, Timmis KN, Golyshin PN, (2005) 'Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora', Environ Microbiol, vol.7, no.12, pp 1996-2010

c) Related to transcriptomics

Khachane AN, Harrison PM, (2010) 'Mining mammalian transcript data for functional long non-coding RNAs', PLoS ONE, vol.5, no.4

Khachane AN, Harrison PM, (2009) 'Assessing the genomic evidence for conserved transcribed pseudogenes under selection', BMC Genomics, vol.10, p 435

d) Related to proteomics

Khachane A, Kumar R, Jain S, Jain S, Banumathy G, Singh V, Nagpal S, Tatu U, (2005), '"Plasmo2D": An ancillary proteomic tool to aid identification of proteins from plasmodium falciparum', Journal of Proteome Research, vol.4, no.6, pp 2369-74

Kumar Y, Khachane A*, Belwal M, Das S, Somsundaram K, Tatu U, (2004) 'ProteoMod: A new tool to quantitate protein post-translational modifications', Proteomics, vol.4, no.6, pp 1672-83 * Equal contribution

e) Related to epigenetics

Aberg K, Khachane AN, McClay JL, Aberg K, Bukszár J, Sullivan PF, van den Oord EJ, (2012) 'Methylome-wide comparison of human genomic DNA extracted from whole blood and from EBV transformed lymphocyte cell lines', Eur J Hum Genet, doi: 10.1038/ejhg.2012.33

Selected posters/conferences/meetings/workshops

• Bukszar J, Khachane A, (4 authors), van den Oord E (2011) Mathematically Based General Framework for Integrating Multiple Heterogeneous Existing Data Sets Into a Novel Data Collection. Joint statistical meeting (JSM), Florida
• Khachane AN (2010) Advanced Genetic Epidemiology and Statistical Molecular Genetics Workshop. Virginia Institute for Psychiatric and Behavioral Genetics. Virginia Commonwealth University, Richmond VA.
• Khachane AN, Harrison PM. (2008) Robert Cedegren colloquium, Montreal, Canada.
• Khachane AN, Puchalka J, Timmis KN and Martins dos Santos VA. (2006) An Evolutionary Systems Biology approach for analysing the dynamics of reductive genome evolution. (Poster). 7th International Conference on Systems Biology, Yokohama, Japan.
• Khachane AN, Timmis KN and Martins dos Santos VA. (2005) Sequence-based prediction of optimum growth temperatures of uncultured prokaryotes. (Poster). 4th European Conference on Computational Biology, Madrid, Spain.
• Khachane A, Banumathy G, Singh V, Pavithra S, Padma Priya P, and Tatu U. (2003) Genome Wide Analysis of the Heat Shock Response Machinery in the Malarial Parasite Plasmodium falciparum.  Poster presented at HUPO 2nd Annual & IUBMB XIX World Congress, Montreal, Canada.

Specialized Training

• Next-Generation Sequencing Data Analysis for Applied BioSystems SOLiD 3+/4 Platform Using BioScope Package - Conducted by Life Technologies, 2011