I am mainly responsible for genomics analysis and cooking curries. Additionally, I am also responsible for developing bioinfomatics analysis workflows for our group.
- Hossain, A. S. M. M., Blackburne, B. P., Shah, A. & Whelan, S. Evidence of statistical inconsistency of phylogenetic methods in the presence of multiple sequence alignment uncertainty. Genome Biol Evol evv127 (2015). doi:10.1093/gbe/evv127
- Huber, B., Whibley, A., Poul, Y. L., Navarro, N., Martin, A., Baxter, S., Shah, A., Gilles, B., Wirth, T., McMillan, W. O., and Joron, M. “Conservatism and novelty in the genetic architecture of adaptation in Heliconius butterflies”. Heredity 114.5 (2015): 515–524.
- Vendrami, D., Shah, A., Telesca, L., and Hoffman, J. “Mining the transcriptomes of four commercially important shellfish species for single nucleotide polymorphisms within biomineralization genes”. Mar. Genomics Special Issue “Cells to Shells”,27:17:23. DOI: 10.1016/j.margen.2015.12.009
- Shah, A. B., Schielzeth, H., Albersmeier, A., Kalinowski, J. and Hoffman, J. I. (2016), High-throughput sequencing and graph-based cluster analysis facilitate microsatellite development from a highly complex genome. Ecol Evol. doi:10.1002/ece3.2305
- Wollenberg Valero, K. C. Garcia-Porta. J., Rodríquez, A., Arias, M., Shah, A., Randrianiaina R. D., Brown J. L., Glaw, F., Amat, F., Künzel, S., Metzler, D., Isokpehi, R. D. and Vences, M. (2017), Transcriptomic and macroevolutionary evidence for phenotypic uncoupling between frog life history phases. Nat. Commun. 8, 15213 doi: 10.1038/ncomms15213 (2017)
Previous Research and Other Interests
Previously, I have extensively worked with next generation sequencing data, especially with gene expression analysis (RNA-seq). At the Muséum National D’Histoire Naturelle, Paris, France, I was involved in the analysis of differentially expressed genes and isoforms of Heliconius butterfly wing tissue at different developmental stages and morphs using RNA-seq methods in the lab of Dr Mathieu Joron.
During my Masters degree, at the Metzler Lab, Ludwig-Maximilians-Universität, Munich, Germany, I investigated the bias in estimating multiple sequence alignments (MSAs) that is carried forward downstream into estimating phylogenetical branch lengths, genetic diversity and, allele frequencies using a simulation framework.
Dr. Joe Hoffman
Prof. Dr. Holger Schielzeth (Institute of Ecology, Friedrich Schiller University Jena)
Public Code Repositories
RADseqR : The R package for designing, managing, filtering and running the Stacks pipeline for building loci from short-read sequences.
- October 2012: Master of Science, Ludwig-Maximilians-Universität, Munich Graduate School for Evolution, Ecology and Systematics, Munich, Germany
- August 2009: Bachelor of Science, Iowa State University of Science and Technology, Ames, Iowa, USA. Major: Genetics Minor: Applied Statistics
- April 2014–Present: Research Assistant: Bioinformatic analysis of high-throughput sequence data from natural vertebrate populations
- July 2013–December 2013: Short-Term Scientist: Institute of Biotechnology, University of Helsinki, Helsinki, Helsinki, Finland. P.I.: Dr. Ari Löytynoja Title: Method development of RNA-seq analysis leveraging phylogenetical information.
- Feburary 2013–June 2013: Short-Term Scientist: Department of Systematics and Evolution, National Natural History Museum, Paris, France. P.I.: Dr. Mathieu Joron Title: Differential gene and transcript expression analysis of RNA-seq experiments of Heliconious butterflies.
- November–December 2012: Short-Term Visiting Scientist: Computational and Evolutionary Biology Group, University of Manchester, Manchester, United Kingdom. P.I.: Dr. Simon Whelan Title: The downstream impact of multiple sequence alignment on inferring phylogenies for a star-tree topology.
- April 2011–October 2012: Masters Thesis Project: Statistical Genetics Group, Ludwig-Maximilians-Universität, Munich, Germany. P.I.: Prof. Dr. Dirk Metzler Title: Effect of multiple sequence alignment over- optimization bias in inferring phylogenies, genetic diversity, and allele frequencies .
- September 2006–June 2009: Meta!Blast: a real-time 3D game designed for high school and college level students, Virtual Reality Applications Center, Iowa State University, Ames, Iowa, USA. P.I.: Prof. Dr. Eve Wurtele. Position: Cell Biology Writer
- January 2004–December 2005: Powell-Coffman Lab, Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA. P.I.: Prof. Dr. Jo-Anne Powell-Coffman Position: Undergraduate Research Assistant
Department of Animal Behaviour
email: abhijeet [ dot ] shah [at the rate of] gmail [dot] com