Genetic variants associated with motion sickness point to roles for inner ear development, neurological processes, and glucose homeostasis

B. S. Hromatka, J. Y. Tung, A. K. Kiefer, C. B. Do, D. A. Hinds, N. Eriksson

Submitted, 2014.

Summary: The first 35 variants associated with motion sickness.


Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease

M. A. Nalls, N. Pankratz, C. M. Lill, C. B. Do, D. G. Hernandez, M. Saad, A. L. DeStefano, E. Kara, J. Bras, M. Sharma, C. Schulte, M. F. Keller, S. Arepalli, C. Letson, C. Edsall, H. Stefansson, X. Liu, H. Pliner, J. H. Lee, R. Cheng, International Parkinson's Disease Genomics Consortium (IPDGC), Parkinson's Study Group (PSG) Parkinson's Research: The Organized GENetics Initiative (PROGENI), 23andMe, GenePD, NeuroGenetics Research Consortium (NGRC), Hussman Institute of Human Genomics (HIHG), The Ashkenazi Jewish Dataset Investigator, Cohorts for Health and Aging Research in Genetic Epidemiology (CHARGE), North American Brain Expression Consortium (NABEC), United Kingdom Brain Expression Consortium (UKBEC), Greek Parkinson's Disease Consortium, Alzheimer Genetic Analysis Group, M. A. Ikram, J. P. A. Ioannidis, G. M Hadjigeorgiou, J. C. Bis, M. Martinez, J. S. Perlmutter, A. Goate, K. Marder, B. Fiske, M. Sutherland, G. Xiromerisiou, R. H. Myers, L. N. Clark, K. Stefansson, J. A. Hardy, P. Heutink, H. Chen, N. W. Wood, H. Houlden, H. Payami, A. Brice, W. K. Scott, T. Gasser, L. Bertram, N. Eriksson, T. Foroud, A. B. Singleton

Nature Genetics (2014) doi:10.1038/ng.3043

Summary: Six new loci for Parkinson's disease in the largest meta-analysis to date


Reducing pervasive false positive identical-by-descent segments detected by large-scale pedigree analysis

E. Y. Durand, N. Eriksson, C. Y. McLean

Mol Biol Evol, 30 April 2014.

Summary: Improving the accuracy of germline on short IBD segments


Genome-wide association analysis identifies 11 risk variants associated with the asthma with hay fever phenotype

M. A. R. Ferreira, M. C. Matheson, C. S. Tang, R. Granell, W. Ang, J. Hui, A. K. Kiefer, D. L. Duffy, S. Baltic, P. Danoy, M. Bui, L. Price, P. D. Sly, N. Eriksson, P. A. Madden, M. J. Abramson, P. G. Holt, A. C. Heath, M. Hunter, B. Musk, C. F. Robertson, P. Le Souef, W. Montgomery, A.J. Henderson, J. Y. Tung, S. C. Dharmage, M. A. Brown, A. James, P. J. Thompson, C. Pennell, N. G. Martin, D. M. Evans, D. A. Hinds, J. L. Hopper

Journal of Allergy and Clinical Immunology, 31 December 2013

Summary: Meta-analysis of hay fever with asthma


Gradiant Boosting as a SNP filter: an evaluation using simulated and hair morphology data

G. H. Lubke, C. Laurin, R. Walters, N. Eriksson, P. Hysi, T. D. Spector, G. W. Montgomery, D. I. Boomsma, N. G. Martin, and S. E. Medland

Journal of Data Mining in Genomics & Proteomics, 2013, 4:4

Summary: Gradiant boosting applied to GWAS data


A genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci

D. A. Hinds, G. McMahon, A. K. Kiefer, C. B. Do, N. Eriksson, D. M. Evans, B. St Pourcain, S. M. Ring, J. L. Mountain, U. Francke, G. Davey-Smith, N. J. Timpson, and J. Y. Tung

Nat Genet, 2013 June 30.

Summary: Sixteen associations with allergies, eight of them shared with asthma


Serum iron levels and the risk of Parkinson's disease: a Mendelian randomization study

I. Pichler, F. Del Greco M., M. Gogele, C. M. Lill, L. Bertram, C. B. Do, N. Eriksson, T. Foroud, R. H. Myers, M. Nalls, M. F. Keller, B. Benyamin, J. B. Whitfield, P. P. Pramstaller, A. A. Hicks, J. Thompson, and C. Minelli

PLOS Med. 10(6): e1001462.

Summary: Mendelian randomization study shows that higher iron levels are protective for Parkinson's disease


Variants near elastic microfibril genes are associated with non-syndromic striae distensae

J. Y. Tung, A.K. Kiefer, M. Mullins, U. Francke, and N. Eriksson

J Invest Dermatol, 2013 Apr 30

Summary: Variants near the elastin gene influence stretch marks


Genome-wide analysis points to roles for extracellular matrix remodeling, the visual cycle, and neuronal development in myopia

A. K. Kiefer, J. Y. Tung, C. B. Do, D. A. Hinds, J. L. Mountain, U. Francke, and N. Eriksson

PLoS Genet., 9(2): e1003299.

Summary: Twenty-two associations for myopia age of onset, many of which are near genes with interesting roles in vision development.


Dealing with the unexpected: Consumer responses to direct-access BRCA mutation testing

U. Francke, C. Dijamco, A. K. Kiefer, N. Eriksson, B. R. Moiseff, J. Y. Tung, and J. L. Mountain

PeerJ, 1:e8.

Summary: How do people respond to learning their BRCA status via 23andMe?


Androgenetic alopecia: identification of four new genetic risk loci and evidence for the contribution of WNT-signaling to its etiology

S. Heilmann, A. K. Kiefer, N. Fricker, D. Drichel, A. M. Hillmer, C. Herold, J. Y. Tung, N. Eriksson, S. Redler, R. C. Betz, R. Li, A. Karason, D. R. Nyholt, K. Song, S. H. Vermeulen, S. Kanoni, G. Dedoussis, N. G. Martin, L. A. Kiemeney, V. Mooser, K. Stefansson, J. B. Richards, T. Becker, F. F. Brockschmidt, D. A. Hinds, and M. M. Nothen

J Invest Dermatol, 2013 Jan 28.

Summary: Four new loci for male-pattern baldness.


A genetic variant near olfactory receptor genes influences cilantro preference

N. Eriksson, S. Wu, C. B. Do, A. K. Kiefer, J. Y. Tung, J. L. Mountain, D. A. Hinds, and U. Francke

Flavour, 1:22, Dec 2012.

Summary: We uncover a cluster of olfactory receptor genes that play a role in cilantro dislike.

Press: Nature NPR Gizmodo BoingBoing MetaFilter Business Insider Huffington Post

Blogs: The Spittoon Haldane's Sieve


Comparison of Family History and SNPs for Predicting Risk of Complex Disease

C. B. Do, D. A. Hinds, U. Francke, and N. Eriksson

PLoS Genet., 8(10): e1002973, October 2012.

Summary: We develop models based on quantitative genetic theory to analyze and compare family history and SNP-based risk prediction models.

Press: SF Chronicle

Blogs: The turning of the key The Spitoon


Genetic variants associated with breast size also influence breast cancer risk

N. Eriksson, G. M. Benton, C. B. Do, A. K. Kiefer, J. L. Mountain, D. A. Hinds, U. Francke, and J. Y. Tung

BMC Med Genet, 13(1):53, Jun 2012

Summary: We discover a number of SNPs associated with breast size. Surprisingly, several are also involved in breast cancer.

Press: Jezebel Huffington Post The Telegraph

Blogs: The Spitoon


Six novel susceptibility Loci for early-onset androgenetic alopecia and their unexpected association with common diseases

R. Li, F. F. Brockschmidt, A. K. Kiefer, H. Stefansson, D. R. Nyholt, K. Song, S. H. Vermeulen, S. Kanoni, D. Glass, S. E. Medland, M. Dimitriou, D. Waterworth, J. Y. Tung, F. Geller, S. Heilmann, A. M. Hillmer, V. Bataille, S. Eigelshoven, S. Hanneken, S. Moebus, C. Herold, M. den Heijer, G. W. Montgomery, P. Deloukas, N. Eriksson, A. C. Heath, T. Becker, P. Sulem, M. Mangino, P. Vollenweider, T. D. Spector, G. Dedoussis, N. G. Martin, L. A. Kiemeney, V. Mooser, K. Stefansson, D. A. Hinds, M. M. Nothen, and J. B. Richards

PLoS Genet., 8(5):e1002746, May 2012.

Summary: A large meta-analysis of male-pattern baldness uncovers unexpected connections with Parkinson's disease

Blogs: The Spitoon


Cryptic distant relatives are common in both isolated and cosmopolitan genetic samples

B. M. Henn, L. Hon, J. M. Macpherson, N. Eriksson, S. Saxonov, I. Pe'er, and J. L. Mountain

PLoS ONE, 7(4):e34267, 2012.

Summary: An analysis of the number of cryptic distant relatives among various populations.


Novel associations for hypothyroidism include known autoimmune risk loci

N. Eriksson, J. Y. Tung, A. K. Kiefer, D. A. Hinds, U. Francke, J. L. Mountain, and C. B. Do

PLoS ONE, 7(4):e34442, 2012.

Summary: A GWAS for hypothyroidism implicates genes involved in both autoimmune disorders and thyroid function.


Comprehensive research synopsis and systematic meta-analyses in Parkinson's disease genetics: The PDGene database

C. M. Lill, J. T. Roehr, M. B. McQueen, F. K. Kavvoura, S. Bagade, B. M. Schjeide, L. M. Schjeide, E. Meissner, U. Zauft, N. C. Allen, T. Liu, M. Schilling, K. J. Anderson, G. Beecham, D. Berg, J. M. Biernacka, A. Brice, A. L. DeStefano, C. B. Do, N. Eriksson, S. A. Factor, M. J. Farrer, T. Foroud, T. Gasser, T. Hamza, J. A. Hardy, P. Heutink, E. M. Hill-Burns, C. Klein, J. C. Latourelle, D. M. Maraganore, E. R. Martin, M. Martinez, R. H. Myers, M. A. Nalls, N. Pankratz, H. Payami, W. Satake, W. K. Scott, M. Sharma, A. B. Singleton, K. Stefansson, T. Toda, J. Y. Tung, J. Vance, N. W. Wood, C. P. Zabetian, P. Young, R. E. Tanzi, M. J. Khoury, F. Zipp, H. Lehrach, J. P. Ioannidis, and L. Bertram

PLoS Genet., 8(3):e1002548, 2012.

Summary: A comprehensive collection and meta-analysis of all genetic research in Parkinson's disease.

Blogs: The Spitoon


The temporal order of genetic and pathway alterations in tumorigenesis

M. Gerstung, N. Eriksson, J. Lin, B. Vogelstein, and N. Beerenwinkel

PLoS ONE, 6(11):e27136, 2011.

Summary: Analysis of mutation accumulation in cancer using next-generation sequence data and conjunctive Bayesian networks.


Efficient replication of over 180 genetic associations with self-reported medical data

J. Y. Tung, C. B. Do, D. A. Hinds, A. K. Kiefer, J. M. Macpherson, A. B. Chowdry, U. Francke, B. T. Naughton, J. L. Mountain, A. Wojcicki, and N. Eriksson

PLoS ONE, 6(8):e23473, 2011.

Summary: Replication of many associations using the 23andMe database.

Blogs: The Spitoon


Web-based genome-wide association study identifies two novel loci and a substantial genetic component for Parkinson's disease

C. B. Do, J. Y. Tung, E. Dorfman, A. K. Kiefer, E. M. Drabant, U. Francke, J. L. Mountain, S. M. Goldman, C. M. Tanner, J. W. Langston, A. Wojcicki, and N. Eriksson

PLoS Genet., 7(6):e1002141, Jun 2011.

Press: Wired FastCompany WebMD Nature Bloomberg


ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data

O. Zagordi, A. Bhattacharya, N. Eriksson, and N. Beerenwinkel

BMC Bioinformatics, 12:119, Apr 2011.


Parametric analysis of alignment and phylogenetic uncertainty

A. S. Malaspinas, N. Eriksson, and P. Huggins

Bull. Math. Biol., 73:795--810, Apr 2011.

Summary: We show how to analyze the robustness of phylogenies to perturbations in alignment parameters.


Web-based, participant-driven studies yield novel genetic associations for common traits

N. Eriksson, J. M. Macpherson, J. Y. Tung, L. S. Hon, B. Naughton, S. Saxonov, L. Avey, A. Wojcicki, I. Pe'er, and J. Mountain

PLoS Genet., 6:e1000993, Jun 2010.

Summary: We discover novel genetic associations for hair curl, photic sneeze reflex, freckling, and asparagus metabolite detection.

Press: F1000 Nature ABC


Using invariants for phylogenetic tree construction

N. Eriksson

In Emerging Applications of Algebraic Geometry, pages 89--108. Springer, New York, 2009.

Summary: A survey of how to use algebraic techniques to solve practical problems in phylogenetics.


Viral population estimation using pyrosequencing

N. Eriksson, L. Pachter, Y. Mitsuya, S. Y. Rhee, C. Wang, B. Gharizadeh, M. Ronaghi, R. W. Shafer, and N. Beerenwinkel

PLoS Comput. Biol., 4:e1000074, Apr 2008.

Summary: We show how to reconstruct an entire viral population from next-generation sequencing data.


Metric learning for phylogenetic invariants

N. Eriksson and Y. Yao

ArXiv preprint, 2007.

Summary: A novel use of machine learning to optimize the use of algebraic techniques in phylogenetics.


Conjuctive Bayesian networks

N. Beerenwinkel, N. Eriksson, and B. Sturmfels

Bernoulli, 13(4):893--909, 2007.

Summary: A new statistical model for describing the accumulation of events that are constrained in the order of their occurrence, applied to HIV drug resistance.


Apollonian Circle Packings: Number Theory II. Spherical and Hyperbolic Packings

N. Eriksson and J. C. Lagarias

Ramanujan Journal, 14(3):437--469, 2007.

Summary: A study of Apollonian circule packings in spherical and hyperbolic geometries


Algebraic combinatorics for computational biology

N. Eriksson

PhD thesis, University of California, Berkeley, 2006.

Summary: My PhD thesis.


Polyhedral conditions for the nonexistence of the MLE for hierarchical log-linear models

N. Eriksson, S. E. Fienberg, A. Rinaldo, and S. Sullivant

J. Symbolic Comput., 41(2):222--233, 2006.

Summary: We give geometric conditions for the existence of the maximum likelihood estimate (MLE) for a hierarchical log-linear model.


Markov bases for noncommutative Fourier analysis of ranked data

P. Diaconis and N. Eriksson

J. Symbolic Comput., 41(2):182--195, 2006.

Summary: A combination of statistics, commutative algebra, and the representation theory of the symmetric group.


Evolution on distributive lattices

N. Beerenwinkel, N. Eriksson, and B. Sturmfels

J Theor Biol, 242(2):409--420, Sep 2006.

Summary: We develop a new mathematical model in order to study the development of HIV drug resistance.


Ultra-Conserved Elements in Vertebrate and Fly Genomes

M. Drton, N. Eriksson, and G. Leung

In L. Pachter and B. Sturmfels, editors, Algebraic Statistics for Computational Biology, chapter 22, pages 387--402. Cambridge University Press, Cambridge, UK, 2005.

Summary: An analysis of some of the most conserved DNA sequences


Tree Construction using Singular Value Decompsition

N. Eriksson

In L. Pachter and B. Sturmfels, editors, Algebraic Statistics for Computational Biology, chapter 19, pages 347--358. Cambridge University Press, Cambridge, UK, 2005.

Summary: A novel technique for constructing phylogenies using linear algebra.


Phylogenetic algebraic geometry

N. Eriksson, K. Ranestad, B. Sturmfels, and S. Sullivant

In C. Ciliberto, A. Geramita, B. Harbourne, R-M. Roig, and K. Ranestad, editors, Projective varieties with unexpected properties, pages 237--255. Walter de Gruyter GmbH & Co. KG, Berlin, 2005.

Summary: An introduction to phylogenetics for algebraic geometers.


Toric ideals of homogeneous phylogenetic models

N. Eriksson

In the proceedings of ISSAC 2004, pages 149--154. ACM, New York, 2004.

Summary: An application of some algebraic techniques to a simple problem in phylogenetics.


$q$-series, elliptic curves, and odd values of the partition function

N. Eriksson

International Journal of Mathematics and Mathematical Sciences, 22(1):55--66, 1999

Summary: A number theory paper that uses a bit of technical machinery to find odd values of the partition function. A high-school project that won third place in the Westinghouse Science Talent Search.

Press: Mathland