We have investigated microsatellite evolution in the framework of a life-cycle hypothesis, according to which microsatellites are born and expand into adulthood, until their degradation and death (Kelkar et al. 2011). Studies of microsatellite mutagenesis have significant utility, as microsatellites are implicated in numerous diseases and are popular markers in population genetics and forensics. To commence this project, we had to determine the minimal number of repeats constituting a microsatellite (Kelkar et al. 2010). Next, using sequenced primate genomes, we dissected the intricacies of the mutational processes leading to microsatellite birth and death (Kelkar et al. 2011). We also evaluated the contribution of transposable elements to microsatellite births and deaths, and described the mechanisms of births for many disease-causing microsatellites (Kelkar et al. 2011). We investigated how interruptions affect microsatellite mutability (Ananda et al. 2014) and developed a computational pipeline, STR-FM, to genotype microsatellites from next-generation sequencing data (Fungtammasan, Ananda, et al. 2015). (Figure: Kelkar et al. 2011). Collaborators: Kristin Eckert, Paul Medvedev, Francesca Chiaromonte.
Microsatellite variation and evolution
N Stoler, B Arbeithuber, G Povysil, M Heinzl, R Salazar, KD Makova, I Tiemann-Boege, A Nekrutenko. Family reunion via error correction: an efficient analysis of duplex sequencing data. BMC BIOINFORMATICS, 2020.
MA Cremona, A Pini, F Cumbo, KD Makova, F Chiaromonte, S Vantini. IWTomics: testing high-resolution sequence-based `Omics' data at multiple locations and scales. BIOINFORMATICS, 2018.
A Fungtammasan, M Tomaszkiewicz, R Campos-Sánchez, KA Eckert, M DeGiorgio, KD Makova. Reverse Transcription Errors and RNA–DNA Differences at Short Tandem Repeats. MOL BIOL EVOL, 2016.
A Fungtammasan, G Ananda, SE Hile, MS-W Su, C Sun, RS Harris, P Medvedev, KA Eckert, KD Makova. Accurate typing of short tandem repeats from genome-wide sequencing data and its applications. GENOME RES, 2015.
G Ananda, SE Hile, A Breski, Y Wang, YD Kelkar, KD Makova, KA Eckert. Microsatellite Interruptions Stabilize Primate Genomes and Exist as Population-Specific Single Nucleotide Polymorphisms within Individual Human Genomes. PLOS GENET, 2014.
BA Baptiste, G Ananda, N Strubczewski, A Lutzkanin, SJ Khoo, A Srikanth, N Kim, KD Makova, MM Krasilnikova, KA Eckert. Mature Microsatellites: Mechanisms Underlying Dinucleotide Microsatellite Mutational Biases in Human Cells. G3-GENES GENOM GENET, 2013.
G Ananda, E Walsh, KD Jacob, MM Krasilnikova, KA Eckert, F Chiaromonte, KD Makova. Distinct Mutational Behaviors Differentiate Short Tandem Repeats from Microsatellites in the Human Genome. GENOME BIOL EVOL, 2013.
SB Montgomery, DL Goode, EM Kvikstad, CA Albers, ZD Zhang, XJ Mu, G Ananda, B Howie, KJ Karczewski, KS Smith, V Anaya, R Richardson, J Davis, The 1000 Genomes Project Consortium, DG MacArthur, A Sidow, L Duret, M Gerstein, KD Makova, J Marchini, G McVean, G Lunter. The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes. GENOME RES, 2013.
A Fungtammasan, E Walsh, F Chiaromonte, KA Eckert, KD Makova. A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?. GENOME RES, 2012.
YD Kelkar, KA Eckert, F Chiaromonte, KD Makova. A matter of life or death: How microsatellites emerge in and vanish from the human genome. GENOME RES, 2011.
YD Kelkar, N Strubczewski, SE Hile, F Chiaromonte, KA Eckert, KD Makova. What Is a Microsatellite: A Computational and Experimental Definition Based upon Repeat Mutational Behavior at A/T and GT/AC Repeats. GENOME BIOL EVOL, 2010.
YD Kelkar, S Tyekucheva, F Chiaromonte, KD Makova. The genome-wide determinants of human and chimpanzee microsatellite evolution. GENOME RES, 2008.
JL Longmire, JL Roach, M Maltbie, PS White, OL Tatum, KD Makova, DC Hahn. Tetranucleotide microsatellite markers for the Brown-headed Cowbird Molothrus ater. J AVIAN BIOL, 2003.
KD Makova, A Nekrutenko, RJ Baker. Evolution of Microsatellite Alleles in Four Species of Mice (Genus Apodemus). J MOL EVOL, 2000.
A Nekrutenko, KD Makova, RJ Baker. Isolation of binary species-specific PCR-based markers and their value for diagnostic applications. GENE, 2000.
A Nekrutenko, KD Makova, RK Chesser, RJ Baker. Representational difference analysis to distinguish cryptic species. MOL ECOL, 1999.
RJ Baker, KD Makova, RK Chesser. Microsatellites indicate a high frequency of multiple paternity in Apodemus (Rodentia). MOL ECOL, 1999.
. Microsattelite markers in wood mouse and striped field mouse (genus Apodemus). MOL ECOL, 1998.
KD Makova, JC Patton. Increased Yield of Tri- and Tetranucleotide Heterospecific Microsatellites from Unenriched Small-Insert Libraries. BIOTECHNIQUES, 1998.