2/21 : We are excited to be recruiting for postdocs and/or staff computational scientists. Please contact John with a CV and cover letter if interested.
1/21 : Our ‘GeoVar’ paper came out in eLife over the holidays!
12/20 : Postdoc Dan Rice moves to the NCBI to take a position as a Data Scientist Outreach Coordinator. In this position, Dan will pursue his passion for outreach and education by designing and leading hackathons to bring together researchers and focus them on interesting problems.
12/20 : Arjun Biddanda finished his PhD and joins Palamara Lab (Oxford)
9/20 : Joe Marcus completed his Phd and moves to join Grail Biosciences
7/20 : Xinyi Li and Chi-Chun Liu join the lab
: John enjoyed giving talks in the Iowa City Darwin Day celebration and as a plenary speaker at the Advances in Genome Biology and Technology Meeting.
11/19 : We’re very excited to welcome new postdoctoral fellow Mashaal Sohail to Chicago!
10/19 : John, Joe, Arjun,and Chris all attended the American Society of Human Genetics Meeting in Houston, TX. It was exciting seeing many former alumni of the lab including Charleston Chiang and Evan Koch.
8/19 : We helped to host the Midwest Population Genetics Conference at UChicago.
6/19 : Our paper on de novo mutation rate estimation in wolves has been accepted at MBE.
4/19 : Our NIH grant proposal on ‘Extending Tools for Visualization of Geographic Structure in Population Genomic Data’ has been awarded.
3/19 : John is back from his sabbatical!
12/18 : We’re very happy that Jeremy Berg and Manaasa Raghavan have both arrived and settled in nicely on the fourth floor of Cummings!
11/18 : The lab’s long-term project on the analysis of modern genome data from Sardinia to learn about population history is published in Nature Genetics!
9/18 : John has gone on sabbatical! He’s now on an ‘academic walkabout’ through Central America, Europe, and the US.
8/18 : Midwest PopGen V was a great time in Minneapolis. Thanks Yaniv Brandvain for organizing
7/18 : Hussein defended his dissertation on methods for phyologenetic analyses of selection, spatial genetics and ancient DNA quality control. He’s taking a position at Adaptive biotech and will be greatly missed!
6/18 : Evan defended his dissertation on demographic effects on deleterious variation and quantitative traits (as well as mutation rates in wolves)! We wish him well as he heads onward to a postdoc with Shamil Sunyaev in the fall!
5/18 : The lab had a great time at the GSA - PEQG18 meeting!
4/18 : John and colleague Darrell Wagonner spoke at the Baderbauer brewery in Chicago as part of the Taste of Science festival for public outreach in the sciences.
4/18 : Joel defended his dissertation on haploytpe methods for studying selected alleles and on models for ancestry tracts in hybrid zones. He’s been a joy to work with and will be sorely missed!
4/18 : John published with Nick Barton a perspective piece in Genetics on the challenges to interpreting the results of polygenic tests of selection
2/18 : A subset of the lab took part in our second ice fishing trip, this time heading to Green Bay, Wisconsin and with much better success catching some delicious whitefish.
9/17 : Wonderful to welcome new faculty Matthias Steinrucken and Yang Li to campus.
8/17 : The tradition continues! Midwest PopGen took place at Michigan State University and lab members Evan Koch and Ben Peter had great presentations there.
7/17 : Novembre Lab represented at SMBE and the ULCA CGSI workshop!
5/17 : The SardiNIA project’s discovery of the BAFF gene’s role in multiple sclerosis is published in New England Journal of Medicine. This interesting risk allele appears to have been favored in Sardinia.
4/17 : The Human Genetics department had a great showing at the Chicago March for Science!
4/17 : Quanta magazine did an profile piece on John
3/17 : Joe and John attended the Gordon Conference on Quantitative Genetics
2/17 : Joel, Hussein, and John took a fishing trip that resulted in John’s first midwestern steelhead catch!
2/17 : Our paper, led by PhD student Joel Smith, on inferring coalsecent times for selected alleles came out in Molecular Biology and Evolution.
1/17 : Dan Rice helped put together a fun 2-day lab retreat/workshop on presentation skills (the “Talkathon”).
11/17 : The lab enjoyed a visit from Constanza de la Fuente, a PhD student with Eske Willerslev at the GeoGenetics Institute in Copenhagen. Constanza brought a wealth of information about ancient DNA and population genetic analysis of Siberian populations.
11/17 : We welcomed a new scientific programmer, Chi-Chun Liu! Chi-Chun just finished his masters in Statistics working with Dan Nicolae on admixture models and local ancestry inference.
10/17 : Members of the lab attended and presented at the ASHG meeting in Orlando, Florida.
10/17 : Dan Rice and Hussein attended the Probabilistic Modeling in Genomics (ProbGen) meeting in Aarhus, where Dan gave a talk on his work on multiple merger coalescents and Hussein presented a poster on his work on migration maps.
9/17 : We said goodbye to Ben Peter, who is now a group leader at the Max Planck Institute in Leipzig, Germany!
8/17 : The lab attended the fourth Midwest PopGen Meeting at Michigan State University. Visiting Rich Lenski’s lab to see the home of his famous artificial evolution experiment was a great highlight.
6/17 : We bid farewell to Mark Reppell, who is now a senior scientist at AbbVie Pharmaceuticals!
5/17 : PhD student Arjun Biddanda successfully defended his PhD proposal.
5/17-7/17 : PhD student Evan Koch is participating in the NSF GROW program by spending a few months in Uppsala, Sweden where he is working in the lab of Hans Ellegren.
5/17 : John gave a keynote at the Great Lakes Bioinformatics Meeting here in Chicago.
5/17 : John served as an external examiner for the PhD of Jose Victor Moreno Mayar, a student of Eske Willerslev and Anna Sapfo Malaspinas in the GeoGenetics Institute in Copenhagen.
5/17 : The SardiNIA/Progenia project had a paper led by Mauro Pala and Stephen Montgomery’s team published in Nature Genetics and the long awaited BAFF paper led by Maristella Steri and Francesco Cucca’s team was published in the New England Journal of Medicine!
5/17 : The search for a population geneticist in the Ecology and Evolution department is complete and we’re excited that Matthias Steinrucken will be coming this September to join our faculty!
4/17 : A long interview article published by Quanta magazine featured John.
4/17 : The lab enjoyed a visit from Erik Lundgren, a PhD student with Peter Ralph, working on non-stationary isolation-by-distance problems.
3/17 : We welcomed a new postdoctoral fellow Daniel Rice, who is part of the prestigious Chicago Fellows program!
3/17 : Evan and John’s paper on the impact of demography and selection on deleterious variation is out in G3.
2/17 : Joe Marcus and John traveled to the Gordon Conference for Quantitative Genetics where John gave plenary on their collaborative work.
12/16 : The lab enjoyed a week-long hackathon on the geographic distribution of genetic variants.
12/16 : A new version of our “Geography of Genetics Variants” server has been posted that allow simple url-based query of a variant.
12/16 : Our pre-print on demographic history and population structure of Sardinia is now on the bioRxiv.
11/16 : Ben and John contributed to a large collaborative paper led by Tomas Marques on chimpanzee and bonobo genetics that is now published in Science.
11/16 : John spoke at the NAS/Kavli Frontiers of Science Symposium in Irvine.
10/16 : The whole lab travelled to Vancouver to attend and present at the annual ASHG convention.
10/16 : Hussein attended and presented at the Probabilistic Genomes meeting at Oxford.
9/16 : Ben and John’s review on fine-scale population structure in humans goes online at Current Opinions Genetics and Development as part of an excellent special issue edited by Anna Di Rienzo and Josh Akey.
9/16 : Arjun Biddanda and Joe Marcus officially joined the lab as our newest PhD students!
8/16 : We hosted the 3rd annual Midwest PopGen meeting here at UChicago - it was once again a great amount of fun.
6/16-8/16 : Summer travel: Arjun, Joe, and John travelled to Sardinia to teach in the summer school short course on Complex Disease Mapping and had some excellent side adventuring. Arjun, Joe, Hussein, and John all attended the Computational Genomics Summer Institute at UCLA. Evan attended SSE in Austin and presented a poster. Joel did an internship on science policy in Brasilia, Brazil.
6/16 : PhD student Diego Ortega del Vecchyo crossed the threshold and defended his PhD - he’ll be greatly missed and is now onto a postdoctoral fellowship at UC-Berkeley.
5/16 : Charleston’s paper on the challenges of interpreting IBD tract lengths is published in G3.
4/16 : John, David Witonsky and Anna Di Rienzo submitted their report to the Army Corps of Engineers reanalyzing the aDNA data with regards to the origins of the Kennewick Man Sample
3/16 : Adam’s paper on the inferring regions of selection in early dog domestication is published in PLoS Genetics.
1/16 : Our paper with Desi Petkova and Matthew Stephens on visualizing migration surfaces the EEMS method) was published in Nature Genetics.
11/15 : November issue of Nature Genetics highlights Sardinia genetics and includes two papers we contributed to!
11/15 : Ask-Me-Anything series on Reddit put John to the test.
10/15 : John was awarded a MacArthur fellowship! Check out the video biography they did, with background cameos from various members of the lab.
7/15, 8/15 : Summer conference travel: Much of the lab attended SMBE in Austria where talks were given by Diego Ortega, Ben Peter, and myself and a poster was presented by Evan Koch. Many of us also attended the second edition of the Midwest Population Genetics meeting, this time held at the University of Michigan. Joel Smith attended SSE in Brazil where he gave a talk, and Ben Peter gave a talk at the ESEB meeting in Laussane
6/15 : Lab programmer Joe Marcus spent three months of the summer in the lab of our collaborator Francesco Cucca in Cagliari, Sardinia as part of our work in the SardiNIA/Progenia project
6/15 : The lab was awarded one of a new BD2K targeted software development awards based on our research proposal “Tools for Visualization of Geographic Structure in Population Genomic Data”
6/15 : John authored a News and Views article “Human evolution: ancient DNA steps into the language debate”
6/15 : The lab enjoyed a great 1-day retreat at the University’s Warren Woods research station.
6/15 : Former postdoctoral fellow Charleston Chiang did a tour in China and Taiwan giving talks, finished his fellowship, and transitioned to a new position at UCLA with Nelson Freimer
5/15 : Anna di Rienzo and John organized and hosted the Department of Human Genetics Mitchell Symposium with a focus this year on ancient DNA. We enjoyed great talks from David Reich, Matthias Meyer, Tina Warriner, and Alan Cooper. The event brought together a diverse audience on campus and was held in the University of Chicago’s home for archaeology, the Oriental Institute.
5/15 : Johannes Krause visited for a Human Genetics seminar, and with Johannes we took a joy trip to see the Cahokia Mounds outside of “Mound City” (a.k.a. St. Louis).
3/15 : Eunjung’s manuscript “Fast and accurate site frequency spectrum estimation from low coverage sequence data” was published in Bioinformatics. She’s now working as a computational biologist for Ancestry.com.
2/15 : Darren Kessner’s manuscript “ Power analysis of artificial selection experiments using efficient whole genome simulation of quantitative traits” was published in February in Genetics. Darren is now teaching math and expanding the computer science program at the Marlborough School in Los Angeles.
7/14 : We hosted the first Midwest Popgen Group meeting with the help of the great staff and students/postdocs here at U of C and organizing committee with Sebastian Zollner (U Michigan), Don Conrad (Wash-U), and Bret Payseur (U Wisc-Madison). We had approximately 80 attendees, from 20 different off-campus labs and 17 on-campus labs. Attendees drove in from Illinois, Michigan, Indiana, Missouri, Wisconsin, and Minnesota. There were 11 talks total, with 7 by grad-students/postdocs and 4 by assistant professors, and 15 posters. We had a great set of talks and then a fun BBQ at the Point. Mo Siddiq is preparing a website with photos from the event.
7/15 : We have released a new teaching/research tool. The Geography of Genetic Variants browser. This is the hard work of our “programmer-at-large” Joe Marcus. It’s also a pilot project for a grant we submitted earlier this summer to work on challenges that arise visualizing population structure in genomic-scale variation data.
7/14 : A Huffington Post article quotes me raising doubts about a recent PNAS paper on how genetics influence friend pairings
7/14 : Joel Smith and Hussein Al-asadi successfully defended their thesis proposals!
7/14 : Genetics recently published an invited short perspective piece on the new fastSTRUCTURE paper in which I give an overview of work on the model behind STRUCTURE and its subsequent variants.
7/14 : We have enjoyed some great summer conferences including the SMBE meeting in Puerto Rico back in June and a meeting with our SardiNIA project collaborators in Ann Arbor, Michigan earlier in July.
5/14 : Darren Kessner and Eunjung Han submitted their final chapters for publication and successfully defended their PhDs! Darren is off to a fantastic job at the elite Marlborough School in Los Angeles where he will be teaching math and expanding the computer science curriculum. Eunjung (a.k.a. Christine) is now joining the excellent team at AncestryDNA developing tools for interfacing genealogical and genetic data. We had a big party in LA to celebrate their achievement and are wishing them the best as they move onwards in their new adventures!