The Pritchard Lab

Departments of Genetics and Biology, Stanford University

Welcome to the Pritchard Lab Website. Our group uses statistical and computational methods to study questions in genomics and evolutionary biology.

Much of our work focuses on questions relating to genetic variation and evolution. What can we learn from DNA sequence data about population structure, population histories and natural selection?

How does genetic variation impact phenotypic traits, both at the organismal and cellular level (including an emphasis on gene regulation)? What are the molecular pathways from genetic variation to cellular and organismal phenotypes? Why does so much of the genome contribute to the genetic basis of complex traits?

Our lab includes people trained in a variety of different fields using computational and experimental approaches to tackle these problems. We often work on problems where there are no off-the-shelf statistical methods. Thus, an important part of our work is in developing appropriate statistical and computational approaches that can yield new insights into biological data.

Useful links

Jonathan's new online textbook in human genetics

Jonathan Pritchard homepage and CV
Stanford Genetics
Stanford Biology and Eco-Evo group
Center for Computational and Evolutionary Genomics
Stanford Bio-X and Clark Center

The STRUCTURE software page

Lab News

January 2023: This past year was a big one for us as we wrapped up most of the backlog of papers that had accumulated from the pandemic, and preprinted or published about 15 papers. That's definitely a record for us. I'm very proud of the work our team has done in the last three years. You can read all about their great work on our publications page.

And we had the bittersweet pleasure of wishing bon voyage to five wonderful lab members: Jake (to Genentech), Nasa (Asst Prof, Fred Hutch), Shaila (Asst Prof, Cornell), Satu (back to FIMM, Helsinki), and Margaret (Grail). We will miss all of you, but we're excited to see what you will achieve in your new positions!

Of course, that's balanced by some wonderful newcomers: postdocs Mineto (from Tokyo), Ron (Caltech), and Wilder (Oxford/Broad, now doing an MD); as well as new graduate students Jon, Alvina, and Tony. This quarter we also have three rotation students, Tami, Julie and Kate. Welcome all!

November 2021: There is loads to catch up on, now that things are somewhat more normal (thank you, vaccinations). We have all been back in the lab since the summer, and Stanford classes are in person again this quarter. It's been wonderful to be back to near-normal, with lab events and daily lunch (and a very popular new espresso machine--thanks Margaret and Clemens for organizing!).

Comings and Goings: There's lots to update here since our last news, back before most of us knew what a coronavirus was. First, it was bittersweet to wish farewell to Ziyue (assistant professor at Penn), Harold (assistant professor at UCLA) and Hannah (postdoc at U Chicago)... though we are excited to see what wonderful things they will achieve in their new positions!

However, as always, we are also fortunate to have wonderful new people in the lab. They are all making great contributions: from 2020, Daphna who is a joint postdoc with Maria Barna and us, working on ribosomal DNA variation; Courtney who is a Genetics student, working on the genetics of metabolites; and Matt who is a BMI student working on theoretical models of gene regulatory networks.

And new this year: Josh who is working jointly with Alexis Battle and us on inference methods for gene regulatory networks; and Romain who is working jointly with Aviv Regev's lab on inference methods for single cell and perturbation data. Welcome to all!

November 2019: We have a new paper out on ancient DNA of Romans. We sequenced genomes for 127 ancient samples spanning 12,000 years to create a transect of how the Roman population changed over time. This was led by Margaret, Ziyue and Hannah, in collaboration with the Coppa lab (Rome) and Pinhasi lab (Vienna). Links: [PDF]; [Twitter Thread]; [Short Video Summary] produced by Nathan Collins and Farrin Abbott, Stanford News Service; [Science news article] by Lizzie Wade. Congratulations to Margaret, Hannah and Ziyue!

September: Lots to catch up on! First, congratulations to our newest PhD graduates: Jessica, Diego, and Evan! We will miss you, but excited to follow your ongoing successes in your new positions!

And welcome to our new PhD students Alyssa Fortier and Roshni Patel and new postdocs: Sahin Naqvi, Jeff Spence, Hakhamanesh Mostafavi and Clemens Weiss!

May: New papers include our latest work on understanding genetic architecture of complex traits (the "Omnigenic 2" paper) with Xuanyao Liu and Yang Li: [Link] and our paper with the Criswell, Marson and Greenleaf labs on the chromatin structure of immune cells (led by Diego in our lab, with Michelle Nguyen and Anja Mezger): [Link] Congratulations to Diego, Xuanyao, Yang and the rest of the teams!

January: Welcome to Shaila Musharoff who is joining us this month!

December: Farewell to David and Emily! They will both be greatly missed. David will be starting his own lab at NY Genome Center, and Emily is taking her genomics expertise into the consulting world.

9/18/2018. News roundup:

Comings and goings:
August: Welcome to our new postdocs Jake Freimer and Yuval Simons!

Eilon took a job as one of the first scientists at the new firm Insitro, founded by Daphne Koller. Bon Voyage to Eilon!

Emily defended her thesis! Congratulations Emily! She will stay in the lab through the end of the year to finish papers.

Congratulations to Natalie and Ben, both lab alumni, on their lovely wedding.

July: Lab alumna Alexis Battle was awarded early tenure in Biomedical Engineering at Johns Hopkins. Wonderful news!

June: Hannah M received the Robert Baynard Textor award from the Department of Anthropology, for 'creativity in anthropology'. Well done, and well-deserved, Hannah!

May: Arbel graduated and moved to a postdoc position in Molly Przeworski's lab at Columbia. In August he and his wife Maya welcomed twin baby boys! Congratulations! This is the third twin pair in the lab in the last 7 years. Is this a significant enrichment?

Jonathan's plenary talk from PEQG on the Omnigenic model (with Evan, Yang and Xuanyao) is online here.

March: Natalie graduated and moved to a position as a staff scientist at Ancestry. Congratulations Natalie! We miss you!

January: Kelley has moved to start her own lab in the Department of Genome Sciences at University of Washington. We are excited to follow her progress in Washington!

10/25/2017. News roundup:

October: ASHG: Natalie gave a well-received plenary talk to 7000 people on her side-project on conference gender dynamics and Nasa, Yang, Emily and David also gave very nice platform presentations. Well done everyone!

Update: Nasa won ASHG's best student talk (for work with Melina Claussnitzer). Well done!!

We have several papers out or about to come out in journals: Eilon on using cfDNA to measure transplant rejection; Yang and David on LeafCutter (splicing); Diego on estimating cell types driving complex traits; Arbel on NAGC in gene duplicates; Jessica on triclosan and microbiomes (working with Ami's lab).

Congratulations to Ziyue on her wedding!

September: Yang and Xun moved on to start their own labs. Bon voyage!!

Congratulations to Harold who has been awarded a prestigious Hannah Gray postdoc-faculty fellowship from HHMI.

June: Welcome Nasa, Hannah and Margaret to the lab!

6/22/2017. News roundup for the last few months:

June: release of our perspective piece on the 'omnigenic' model of complex traits, with lead authors Evan Boyle and Yang Li [PDF Link]. Our paper stimulated a lot of discussion on social media and elsewhere, including Ed Yong's article in the Atlantic and in Stanford news.

May: Congratulations to 3 of our postdocs who have accepted assistant professor faculty positions for the coming academic year: Kelley Harris (U Washington, Genome Sciences), Yang Li (U Chicago, Genetic Medicine), and Xun Lan (Tsinghua U, Basic Medical Sciences).

And Kelley also received a prestigious faculty transition award through the CASI program at Burroughs Wellcome Fund.

Natalie and Arbel received graduate fellowships from CEHG. Well done! And Jonathan will become co-director of CEHG starting in June.

Diego's paper on inferring cell types that drive disease is up on bioRxiv.

April: Kelley had a very nice paper building on striking results from her PhD work: Rapid evolution of the human mutation spectrum, out this month in eLife [Link].

Harold, Evan and David each have new papers out about their work with other labs: Sleuth [Harold] and Cas9 Binding [Evan] and ASE for detecting GxE [David].

March: Anand has moved to a data scientist position at Facebook. We'll miss his amazing technical expertise and informal contributions to many projects in the lab! Bon Voyage, Anand!

December 2016. Arbel and Anand's work on how recurrent mutation alters the site frequency spectrum in large samples is now out in PLOS Genetics: [Link]. Congratulations!

Natalie had a fun article in which she applied computational methods to study the history of the journal Genetics since 1917 [Link]. [Timelapse plot of author locations]

November. Yair, Evan, and Natalie's paper on SDS and polygenic adaptation: Detection of human adaptation during the past 2000 years is out now in Science [Link]. Congratulations!

9/20/2016. Welcome to Harold Pimentel who joined the lab last month!

Also, Eilon has a paper out in Nature Genetics showing trans-interactions (i.e., trans-eQTLs) between MHC protein alleles and the expression of T cell receptor genes. With help from Leah Sibener and Chris Garcia we were able to interpret these in terms of physical interactions in the protein structure [Link]

6/1/2016. Lots of exciting news to report from April and May:

Anil's paper on using ribosome profiling data to detect novel open reading frames is now online at eLife [Link].

Xun's paper on the evolution of gene duplicates was published in Science [Link]. This received some nice attention, including in a blog post by Francis Collins.

Yair, Evan and Natalie's paper on very recent polygenic adapation is now out on bioRxiv [Link]. This got lots of attention, including news pieces in Nature and Science.

Yair and Yang both gave talks at Cold Spring's Biology of Genomes Meeting. It was also great to see talks from lab alumni Alexis Battle, Joe Pickrell and Dan Gaffney, and to get to hang out with many other colleagues, friends, and other lab alumni.

Here you can see a pair of great sketches of Yang and Yair, drawn by Alex Cagan.

4/28/2016. Well done Yang, whose paper RNA splicing is a primary link between genetic variation and disease is out today [Link]. This paper uses data from 7 years of joint projects between our lab and Yoav's lab to provide a detailed accounting of the links between genetic variation, variation in gene regulation and disease.

3/29/2016. Congrats to Evan (NSF predoc!). Also to Yang and David K on their Leafcutter paper on quantification of RNA splicing, out now on bioRxiv.

1/4/2016. Farewell and best wishes to Bryce (postdoc, Alkes Price lab, Harvard); and to Graham and Kyle, starting their own labs at the Salk Institute and UCSD, respectively.

11/20/2015. Congratulations to Bryce for his masterful PhD defense in Chicago. It was a bittersweet occasion, marking the end of the U Chicago era.

9/14/2015. Bryce and Graham's WASP paper (QTL mapping with allele-specific reads) is out today in Nature Methods.

8/18/2015. We enjoyed a farewell dinner at the Counter on Friday for Audrey and Towfique (starting their own labs at U of Idaho and Mt Sinai, respectively). Bon voyage!

A big welcome to Kelley Harris and Ziyue Gao who are joining us as new postdocs from Rasmus Nielsen and Molly Przeworski's labs!

Welcome to short term visitor Dan Lawson and also Alexis Battle who is back to visit us briefly this month.

Congrats to Eilon and Michal on birth of their son Yuval!

In the grants department, well done to Kelley (NRSA), David G (EMBO/LLHF), Yang (CEHG), Jessica (NSF predoc)! And Natalie and Evan got a pair of internal research grants, one from Genetics and one from Systems Biology. Kudos.

5/22/2015. JKP nearly done teaching... Catching up on news: Congratulations to Graham who is taking a faculty job at the Salk Institute!!

And congratulations to Towfique who is taking a faculty job at Mt Sinai!!.

And more congrats to Yang who has been awarded a CEHG postdoc fellowship for next year!

And Xun's paper on evolution of gene duplications is out on bioRxiv.

4/2/2015. Congratulations to David G. who has won a Dan David Prize scholarship!

3/31/2015. Congratulations to former lab member Melissa Hubisz, now at Cornell, for winning an NSF predoc award! Also well done to Jessica, Emily and Evan for honorable mentions.

12/18/2014. Alexis, Zia and Sidney's paper on the relationship between genetic variation and phenotypic variation in RNA, ribosomes, and proteins is out today. Congrats!

12/16/2014. Congratulations to Cristina who completed her Ph.D defense in CS yesterday!!

12/04/2014. Anil and Heejung's paper on using multi-scale approaches to model DNase data at TF binding sites is out on bioRxiv.

11/11/2014. Our new website SciReader for scientific recommendations is out in beta release. You can check it out here: Well done Priya, Natalie, Yonggan!

11/11/2014. Bryce and Graham's paper and software on unbiased allele-specific read mapping and powerful QTL mapping is out on bioRxiv and the corresponding WASP software is on GitHub.

9/22/2014. Lots of new arrivals this month: David, Yang, Anand and Emily; visiting scholars: Audrey, Towfique and Kyle. Welcome!

8/07/2014. This week we are moving into our long-term lab space in the Clark Center! We are very happy to be in the new space. In other news, Anand has been awarded a CEHG fellowship for next year. Well done, Anand!

6/24/2014. Alexis will be starting her own lab next month at Johns Hopkins in the departments of CS and Biostats [Link]. We wish her all the very best in her new position!!

6/24/2014. Well done to Eilon on winning the prestigious EMBO fellowship! David Golan, who will be joining in September has been awarded the Rothschild and Fulbright fellowships. Congrats to both!!

6/24/2014. Xun and Nick's paper on genetic influences on DNA methylation is out on bioRxiv [Link].

4/29/2014. Anil's fastSTRUCTURE paper is now out in Genetics: Link.

Alexis will be speaking next week at Biology of Genomes about her work with Zia and Sydney on understanding the effects of genetic variation on mRNA, translation and proteins.

4/2/2014. Darren Cusanovich's paper on knockdown of TFs in LCLs (with Yoav's lab) is out now in PLOS Genetics: Link. Choongwon Jeong's paper on adaptive introgression of high altitude adaptations from Sherpa into Tibetans (collaboration with Anna Di Rienzo's lab), is out now in Nature Communications: Link.

4/1/2014. Bon voyage to Heejung Kim; she spent the winter term visiting us from Matthew's lab in Chicago.

3/1/2014. Welcome to Yair who has now arrived from Chicago with his family!

2/10/2014. Our paper on genetic load in human populations, joint with Guy Sella's lab, is out now in Nature Genetics. Well done to Yuval Simons (in Guy's lab) and Michael Turchin (now in Matthew Stephens' lab)! Link.

2/10/2014. Welcome to our new postdoc Eilon Sharon, who has moved here from Eran Segal's lab. Eilon will be joint with Hunter Fraser's lab. Welcome also to this term's rotation students: Peyton Greenside, Natalie Telis, Diego Calderon, Arbel Harpak and Emily Glassberg!

12/6/2013. Joe Davis has written a great blog post about Graham and Bryce's recent paper on genetic variation and histone modification.

12/4/2013. fastSTRUCTURE is out! Links to Anil's manuscript and beta-release software are here.

12/4/2013. Thanks to Christine Vogel for her perspective on Zia's evolution of mRNA/protein paper.

11/12/2013. Welcome to Yonggan and Priya who are joining the lab this month!

11/12/2013. Congrats to Jack/Athma/Roger whose paper on DNase QTLs was chosen as one of the top papers of 2012 in Regulatory and Systems Genomics at the RECOMB/ISCB meeting.

11/1/2013. There's a nice perspective in NRG by Hannah Storey on 4 recent papers--including one by Graham and Bryce--that studied the effects of genetic variation on histone mods.

10/30/2013. Kudos to Shyam for winning the prestigious Charles Epstein Trainee Research Award (postdoc division) for his talk at ASHG on historical inference for African populations. Graham Coop is a previous winner from our lab (in 2007).

10/22/2013. Congratulations to lab alum Joe Pickrell who has just accepted a position as one of the first faculty at the New York Genome Center. In addition, Zia Khan is now in transit to his first faculty position--in CS at U. Maryland. Good luck to both!

10/22/2013. Darren's paper on knockdown experiments targeting 59 TFs is out on ArXiv.

10/17/2013. Zia and Graham/Bryce have a pair of papers out in Science today: evolution of protein expression in primates and effects of genetic variation on histone modifications. Congrats to Zia, Graham and Bryce!

10/17/2013. Ben Voight's 2006 paper on selection was highlighted in a nice blog article by Emma Ganley as part of the 10th anniversary celebrations at PLOS Biology.

10/11/2013. Welcome to our first two Stanford rotation students: Ilana Arbisser from the Biology department and Michael Sikora from Genetics!

8/1/2013. We are delighted to be moving to Stanford University. This will be a fantastic academic environment and a great place to live. That said, we will miss our many friends at the University of Chicago, where the lab was based for 12 years.

8/1/2013. Welcome to our newest postdoc Alexis Battle! It's great to have her onboard.

8/1/2013. Welcome to Anil, Stoyan and Xun, who are arriving at Stanford this month. The rest of the lab will follow soon or work from Chicago during the transitional period.

Hello World. The lab moves to Stanford on 8/1/2013, after 12 years at the University of Chicago.