Check out my Google Scholar for the list of all publications.
Identifying the favored mutation in a positive selective sweep
Methods that scan population genomics data to identify signatures of selective sweep have been actively developed, but mostly do not identify the specific favored mutation. The selective sweep signal can extend to large, linked regions, as far as 1Mbp on either side of the favored allele. These ‘soft-shoulders’ of sweeps are helpful in identifying the region under selection, but make it harder to pinpoint the favored mutation. We present a method, iSAFE (integrated Selection of Allele Favored by Evolution), that uses coalescent-based signals and a boosting approach to pinpoint the favored mutation within a 5Mbp around the region under selection. The iSAFE technique is motivated by boosting weak classifiers and exploits the soft shoulders.
Ali Akbari, Joseph J Vitti, Arya Iranmehr, Mehrdad Bakhtiari, Pardis C Sabeti, Siavash Mirarab, and Vineet Bafna. Identifying the favored mutation in a positive selective sweep. Nature methods, 2018.
Favored haplotype in human adaptation to high altitude
Human high-altitude (HA) adaptation is explored to understand the physiology, pathophysiology, and molecular mechanisms that underlie long-term exposure to hypoxia. Here, we report the results of an analysis of the largest whole-genome-sequencing of Chronic Mountain Sickness (CMS) and nonCMS individuals, identified candidate genes and functionally validated these candidates in a genetic model system (Drosophila). We used PreCIOSS algorithm that uses Haplotype Allele Frequency score to separate haplotypes carrying the favored allele from the noncarriers and accordingly, prioritize genes associated with the CMS or nonCMS phenotype. Closer examination of individual genes in these regions revealed the involvement of previously identified candidates (e.g., SENP1) and also unreported ones SGK3, COPS5, PRDM1, and IFT122 in CMS.
Tsering Stobdan*, Ali Akbari*, Priti Azad, Dan Zhou, Orit Poulsen, Otto Appenzeller, Gustavo F Gonzales, Amalio Telenti, Emily HM Wong, Shubham Saini, and others. New insights into the genetic basis of monges disease and adaptation to high-altitude. Molecular biology and evolution, 2017. (Cover issue)
Roy Ronen*, Glenn Tesler*, Ali Akbari*, Shay Zakov, Noah A Rosenberg, and Vineet Bafna. Predicting carriers of ongoing selective sweeps without knowledge of the favored allele. PLoS genetics, 2015.
* denotes equal contributions