Welcome to the homepage for the Veeramah Lab at Stony Brook University. Our primary focus is Evolutionary Genomics and Paleogenomics. We work on various species, ranging from humans and other non-human primates, through to Three-spined stickleback. We are particularly interested in analyzing genomic data from multiple time points to study evolution. Here you can find out about our latest research, who is working on what, access resources such as software and data and find out how you might join the lab.
Our lab can be found in the Life Sciences Building towards the south of the main Stony Brook University campus. The main campus is located in the historic north shore hamlet of Stony Brook near the geographic midpoint of Long Island. Penn Station on the island of Manhattan is a 90 minute train ride for those wanting to experience the bright lights of New York City. Long Island itself is home to 20 state parks for those interested in hiking, biking, skating, camping and picnicking, while fine white sand beaches are a feature of the island and are popular destinations for fishing, kayaking, surfing and scuba diving.
Our paper characterizing the genomes of 63 individuals from two 6th century cemeteries associated with the Lombards is out in Nature Communications.
Krishna Veeramah's opinion piece on integrating paleogenomics and archaeology is now out in Current Opinion in Genetics & Development.
Krishna Veeramah's review of Primate Paleogenomics is now out as part of the Population Genomics Paleogenomics book series.
Our paper on levels of neutrality in the human genome (or lack of it), led by August Woerner from the Hammer Lab, is now out in MBE.
Our paper on dog Y chromosomes, led by Matthew Oetjens from the Kidd Lab, is now out in BMC Genomics.
Our paper on natural selection in dogs during domestication and the role the neural crest, led by Amanda Pendelton from the Kidd Lab, is now out in BMC Biology.
Our paper on ancient Bavarians with elongated skulls is out in PNAS.
Deven Vyas has joined us as a new postdoc from the University of Florida.
Our paper on ancient dog genomes is now out in Nature Communications
The Veeramah Lab, along with co-PIs Mike Bell (Stony Brook) and Kat Milligan-Myhre (Alaska) have recieved a $1.5 million NIH R01 award for looking at the contemporary evolutionary genomics of the Three-spined stickleback.
The software ATLAS for processing ancient DNA is now available from the following Bitbucket link. The accompanying preprint can be found on biorxiv.
Shruti Iyer joins the lab as a rotation student as part of the Genetics program.
A review on Medieval Paleogenomics co-authored by Patrick Geary and Krishna Veeramah is now out in Medieval Worlds
Taylor Medwig joins the lab as a rotation student as part of the Genetics program.
It has been a while since the website was last updated but there a number of developments.
We recieved a Leakey Grant entitled Validating novel mutations in a whole genome sequenced gibbon quartet.
Our paper on ancient genomes from the first Iranian farmers, led by Farnaz Broushaki, is now out in Science.
Our paper on ancient genomes from the first Anatolian farmers, led by Zuzana Hofmanová, is now out in PNAS.
Our paper on recombination rates, led by Laurie Stevison is now out in MBE.
Our paper on selection in Central African Pygmies, led by PingHsun Hsieh is now out in Genome Research.
Our paper on X/A evolution in apes, led by Kiwoong Nam is now out in PNAS.
A pre-print on our analysis of ancient dogs, led by Laura Botigue, Shiya Song and Amelie Scheu is available on bioRxiv.
The software lcMLkin for inferring biological relatedness between pairs of individuals from low coverage 2nd generation sequencing data is now available from the following GitHub link. The accompanying preprint can be found on biorxiv.
Our companion paper on the gibbon phylogeny is now out in Genetics as an Early Online article.
Also our paper on whole Y chromosome sequencing, led by Monika Karmin and Toomas Kivisild, is now out in Genome Research.
Patrick Geary and I have been awarded an NSF Archaeology grant entitled Inferring Biological Relatedness And Genomic Ancestry Using 2nd Generation Sequencing.
On a related note, our first Lombard themed paper looking at mtDNA, led by Stefania Vai and Silvia Ghirotto, is now out in PLOS One.
Our paper on Dagestan inbreeding, led by Tanya Karafet, is now out in the European Journal of Human Genetics in Advanced Access form.
Our paper on gorilla demographic history, led by Kimberley McManus, Joanna Kelley and Shiya Song, is now out in MBE in Advanced Access form.
Our reply to the criticism of Elhaik et al. to our A00 paper is now out in EJHG. Their "reply to our reply" is also available.
Misha Lipatov has joined the lab as a postdoctoral scholar. Misha previously worked with Brenna Henn on human mutation rates.
Giulia Bagarolo will spend the first half of 2015 in Veeramah lab. Giulia comes as an exchange student from the University of Ferrara, Italy, where she previously worked in Guido Barbujani's lab.
The Veeramah lab is officially accepting applications for a postdoctoral position in Primate Genomics. See Opportunities.
The gibbon genome paper is finally out in Nature. If your looking for the companion paper mentioned in the main text, a pre-review version is available on bioRxiv.
Krishna Veeramah and John Novembre have a review on genetics and European history out in Cold Spring Harbour Perspectives in Biology.
Krishna Veeramah will be at ASHG San Diego to give an invited talk on selection on the X vs autosomes amongst apes. This is part of the session "The X-Factor of Complex Disease: From Evolution to Association Studies of the X Chromosome" taking place on Saturday, October 19, 10am-12pm. The session will be chaired by Alon Keinan and Melissa Wilson Sayres.
Undergraduate Sheilly Banerjee has joined the lab to look at primate life history traits.
Our paper examining positive and negative selection on the X chromosome and autosomes in humans is now out on MBE's Advanced Access.
Joshua Rest, Xuefeng Wang and Krishna Veeramah have started a Genomics/NGS journal club for all Stony Brook faculty, graduate students and research staff. Visit our website for more details, including how to be added to the mailing list.
The lab is now part of the Interdepartmental Doctorate Program in Anthropological Sciences.
Our review on using next generation sequencing data to infer population history was published in the March issue of Nature Reviews Genetics.
The Veeramah lab officially opened on the 9th January 2014.