John Novembre, PhD

The Novembre research group uses computational tools to study genetic diversity in natural populations. Our goal is to develop widely used statistical methods for intelligently extracting information from large-scale genomic data with the aim to improve understanding of: (1) basic genomic biology, (2) the biology of heritable disease traits, (3) the genetic basis of evolutionary processes, and (4) the history and evolution of various species, especially humans. From a disciplinary perspective, most of the ideas we use are from theoretical population genetics, statistical genetics, and computational statistics. Much of our work is invigorated by addressing data from emerging genotyping and sequencing technologies applied to large or particularly interesting population samples.

Genetic Landscapes Reveal How Human Genetic Diversity Aligns with Geography.
Peter BM, Petkova D, Novembre J. Genetic Landscapes Reveal How Human Genetic Diversity Aligns with Geography. Mol Biol Evol. 2020 04 01; 37(4):943-951.
PMID: 31778174

Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia.
Marcus JH, Posth C, Ringbauer H, Lai L, Skeates R, Sidore C, Beckett J, Furtwängler A, Olivieri A, Chiang CWK, Al-Asadi H, Dey K, Joseph TA, Liu CC, Der Sarkissian C, Radzeviciute R, Michel M, Gradoli MG, Marongiu P, Rubino S, Mazzarello V, Rovina D, La Fragola A, Serra RM, Bandiera P, Bianucci R, Pompianu E, Murgia C, Guirguis M, Orquin RP, Tuross N, van Dommelen P, Haak W, Reich D, Schlessinger D, Cucca F, Krause J, Novembre J. Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia. Nat Commun. 2020 02 24; 11(1):939.
PMID: 32094358

Exploring Population Structure with Admixture Models and Principal Component Analysis.
Liu CC, Shringarpure S, Lange K, Novembre J. Exploring Population Structure with Admixture Models and Principal Component Analysis. Methods Mol Biol. 2020; 2090:67-86.
PMID: 31975164

Genetic landscapes reveal how human genetic diversity aligns with geography.
Peter BM, Petkova D, Novembre J. Genetic landscapes reveal how human genetic diversity aligns with geography. Mol Biol Evol. 2019 Nov 28.
PMID: 31778174

De novo mutation rate estimation in wolves of known pedigree.
Koch E, Schweizer RM, Schweizer TM, Stahler DR, Smith DW, Wayne RK, Novembre J. De novo mutation rate estimation in wolves of known pedigree. Mol Biol Evol. 2019 Jul 12.
PMID: 31297530

Inference and visualization of DNA damage patterns using a grade of membership model.
Al-Asadi H, Dey KK, Novembre J, Stephens M. Inference and visualization of DNA damage patterns using a grade of membership model. Bioinformatics. 2019 04 15; 35(8):1292-1298.
PMID: 30192911

Estimating recent migration and population-size surfaces.
Al-Asadi H, Petkova D, Stephens M, Novembre J. Estimating recent migration and population-size surfaces. PLoS Genet. 2019 01; 15(1):e1007908.
PMID: 30640906

Circuit-theory applications to connectivity science and conservation.
Dickson BG, Albano CM, Anantharaman R, Beier P, Fargione J, Graves TA, Gray ME, Hall KR, Lawler JJ, Leonard PB, Littlefield CE, McClure ML, Novembre J, Schloss CA, Schumaker NH, Shah VB, Theobald DM. Circuit-theory applications to connectivity science and conservation. Conserv Biol. 2019 04; 33(2):239-249.
PMID: 30311266

A tribute to a true conservation innovator, Brad McRae, 1966-2017.
Lawler J, Beier P, Dickson B, Fargione J, Novembre J, Theobald D. A tribute to a true conservation innovator, Brad McRae, 1966-2017. Conserv Biol. 2019 Apr; 33(2):480-482.
PMID: 30480336

The genetic prehistory of the Andean highlands 7000 years BP though European contact.
Lindo J, Haas R, Hofman C, Apata M, Moraga M, Verdugo RA, Watson JT, Viviano Llave C, Witonsky D, Beall C, Warinner C, Novembre J, Aldenderfer M, Di Rienzo A. The genetic prehistory of the Andean highlands 7000 years BP though European contact. Sci Adv. 2018 11; 4(11):eaau4921.
PMID: 30417096

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