Mahesh Binzer-Panchal

Mahesh Binzer-Panchal NBIS expert

genome assembly, transcriptome assembly, metagenomic assembly, variant calling, amplicon analysis, Nextflow, shell scripting, perl, groovy, java, R

emailmahesh.panchal@nbis.se

I have a background in Computer Science and Mathematics from Imperial College London. I then went on do to my PhD on the Automation of Nested Clade Phylogeographic Analysis at Reading University. I then pursued postdoctoral research at the Max Planck Institute in Plön, Germany, working on Bioinformatics related to lake-river adaptation and host-parasite coevolution in three-spined stickleback. My research included working with various NGS data, doing de novo assembly, resequencing studies, transcriptomic studies, and metagenomic studies.

I currently specialise in de novo genome assembly in the NBIS genomic assembly group, from quality control to filtering and assembly, and then assembly validation. I also specialise in writing and supporting Nextflow workflows, and teaching both these subject areas.

Selected publications

Del Angel, V. D., Hjerde, E., Sterck, L., Capella-Gutierrez, S., Notredame, C., Pettersson, O. V., Amselem, J., Bouri, L., Bocs, S., Klopp, C., and others (2018) Ten steps to get started in Genome Assembly and Annotation. F1000Research, 7.

Panchal, M. and Beaumont, M. A. (2007) The automation and evaluation of nested clade phylogeographic analysis. Evolution, 61, 1466–1480.

Panchal, M. (2007) The automation of nested clade phylogeographic analysis. Bioinformatics, 23, 509–510.

Beaumont, M. A., Nielsen, R., Robert, C., Hey, J., Gaggiotti, O., Knowles, L., Estoup, A., Panchal, M., Corander, J., Hickerson, M., and others (2010) In defence of model-based inference in phylogeography. Molecular Ecology, 19, 436–446.

Panchal, M. and Beaumont, M. A. (2010) Evaluating nested clade phylogeographic analysis under models of restricted gene flow. Systematic Biology, syq022.

Beaumont, M. A. and Panchal, M. (2008) On the validity of nested clade phylogeographical analysis. Molecular Ecology, 17, 2563–2565.

Feulner, P. G. D., Chain, F. J. J., Panchal, M., Eizaguirre, C., Kalbe, M., Lenz, T. L., Mundry, M., Samonte, I. E., Stoll, M., Milinski, M., and others (2013) Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks. Molecular ecology, 22, 635–649.

Chain, F. J. J., Feulner, P. G. D., Panchal, M., Eizaguirre, C., Samonte, I. E., Kalbe, M., Lenz, T. L., Stoll, M., Bornberg-Bauer, E., Milinski, M., and others (2014) Extensive copy-number variation of young genes across stickleback populations. PLoS genetics, 10, e1004830.

Feulner, P. G. D., Chain, F. J. J., Panchal, M., Huang, Y., Eizaguirre, C., Kalbe, M., Lenz, T. L., Samonte, I. E., Stoll, M., Bornberg-Bauer, E., and others (2015) Genomics of divergence along a continuum of parapatric population differentiation. PLoS Genet, 11, e1004966.