DataPhiles is a community for those who love data. Email to request to be added to the mailing list:
Fall Semesters: Reading Group Format
DataPhiles is an opportunity to get together in a casual setting to discuss recent papers. To qualify, a paper just needs to use data in an interesting way to learn about the natural world. Send paper suggestions to:
Spring Semesters: Lunch Discussion Format
DataPhiles is an opportunity to discuss practical issues surrounding analyzing data in an informal, low pressure forum. Each week, a volunteer will bring a data set, give a short presentation (8-12 minutes) outlining the basic biology/natural history of their system, giving a general description of their questions (why/what they want out of the data), perhaps presenting a few preliminary and/or graphical results on the data (graphical presentations of the data are strongly encouraged), and a description of the statistical techniques they've used or are thinking of using, or particular problems they're having with the analysis. The floor is then open for general question & answer/discussion. Email a one- or two-sentence blurb about your topic to volunteer to present:
January 2019

January 24

December 2018

December 21 & December 28

December 14
Dunn et al. 2018 Pairwise comparisons across species are problematic when analyzing functional genomic data

December 7
Fay et al. 2018 A polyploid admixed origin of beer yeasts derived from European and Asian wine populations

November 2018

November 30
Gerard et al. 2018 Genotyping Polyploids from Messy Sequencing Data

November 23
NO DATAPHILES (Thanksgiving week)
Bonus Turkey Paper:
Stover et al. 2018 Patterns of musculoskeletal growth and dimensional changes associated with selection and developmental plasticity in domestic and wild strain turkeys

November 16
NO DATAPHILES (conflict with DBS happy hour)

November 9
Ilska et al. 2018 Genetic Characterization of Dog Personality Traits

November 2
Martincorena et al. 2018 Somatic mutant clones colonize the human esophagus with age

October 2018

October 26
Bernstein et al. 2018 Tightly-linked antagonistic-effect loci underlie polygenic demographic variation in C. elegans

October 19
Slon et al. 2018 The genome of the offspring of a Neanderthal mother and a Denisovan father

October 12
Zan et al. 2018 On the Relationship Between High-Order Linkage Disequilibrium and Epistasis

October 5
Castel et al. 2018 Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk

September 2018

September 28
Setter et al. 2018 Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima

September 21
Timpson et al. 2017 Genetic architecture: the shape of the genetic contribution to human traits and disease

September 14
Technow et al. 2015 Integrating Crop Growth Models with Whole Genome Prediction through Approximate Bayesian Computation

September 7
NO DATAPHILES - Go to Data Blitz! Location: Lefevre 112

August 2018

August 31
Cheng et al. 2018 Novel Resampling Improves Statistical Power for Multiple-Trait QTL Mapping

August 24

Simon et al. 2018 Coadapted genomes and selection on hybrids: Fisher's geometric model explains a variety of empirical patterns

August 17
Rosen et al. 2018 Geometry of the Sample Frequency Spectrum and the Perils of Demographic Inference

August 10
End of Summer Hiatus: Analyze some data instead!

August 3
End of Summer Hiatus: Analyze some data instead!

July 2018

July 27
Kruschke 2018 Rejecting or accepting parameter values in Bayesian estimation

July 20
Norouzzadeh et al. 2018 Automatically identifying, counting, and describing wild animals in camera-trap images with deep learning

July 13
Berg et al. 2018 Reduced signal for polygenic adaptation of height in UK Biobank
Also see: Sohail et al. 2018 Signals of polygenic adaptation on height have been overestimated due to uncorrected population structure in genome-wide association studies

July 6
Miller et al. 2014 Modular Skeletal Evolution in Sticklebacks Is Controlled by Additive and Clustered Quantitative Trait Loci

Optional additional reading:
Hart et al. 2018 Convergent evolution of gene expression in two high-toothed stickleback populations
Cleves et al. 2018 An intronic enhancer of Bmp6 underlies evolved tooth gain in sticklebacks

June 2018

June 29
Kern and Hahn 2018 The Neutral Theory in Light of Natural Selection

June 22
Fountain et al. 2017 Inferring dispersal across a fragmented landscape using reconstructed families in the Glanville fritillary butterfly

June 15
Peter et al. 2017 Genetic landscapes reveal how human genetic diversity aligns with geography

June 8
2 great papers this week:
Boyle et al. 2017 An Expanded View of Complex Traits: From Polygenic to Omnigenic
Rockman 2012 The QTN program and the alleles that matter for evolution: all that's gold does not glitter

June 1
No DataPhiles - IPG symposium conflict
Start reading for June 8th!

May 2018

May 25
Xue et al. 2017 Parallel evolution of influenza across multiple spatiotemporal scales

May 18
PEQG Debriefing (No paper to read this week)

May 11
No DataPhiles (get ready for

May 4
Lemoine et al. 2018 Renewing Felsenstein’s phylogenetic bootstrap in the era of big data
Original phylogenetic bootstrap paper: Confidence Limits on Phylogenies: An Approach Using the Bootstrap

April 2018

April 27
Koren et al. 2018 Complete assembly of parental haplotypes with trio binning

April 20
O'Reilly et al. 2012 MultiPhen: Joint Model of Multiple Phenotypes Can Increase Discovery in GWAS
Bonus extra paper for Bayesians: Stephens 2013 A Unified Framework for Association Analysis with Multiple Related Phenotypes

April 13
Palamara et al. 2018 High-throughput inference of pairwise coalescence times identifies signals of selection and enriched disease heritability

April 6
Behrman et al. 2018 Natural variation in couch potato mediates rapid evolution of learning and reproduction in natural populations of Drosophila melanogaster

March 2018

March 31
No DataPhiles (work on analyzing data!)

March 23
*** Special Location - DBS Happy Hour in Tucker 111 *****
Lasisi and Shriver 2017 Focus on African diversity confirms complexity of skin pigmentation genetics

March 16
Lee and Coop 2017 Distinguishing Among Modes of Convergent Adaptation Using Population Genomic Data

March 8 #TBT!
Gould and Lewontin 1979 The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme

March 1
Collins and Didelot 2018 A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination