Inspired by R.E.H.A.B., as well as its fellow journal clubs including EvolFri, C.A.M.P., E.H.R.A.B., Detox, etc., we assemble an informal journal club at UNL to share ideas regarding recent papers or preprints of interest. We focus on, but not limited to, QUantitative genetics and genomics, bio-Informatics and breeding Technologies in all aspects.
Anyone is welcome to suggest a paper (by sending an email to jinliang.yang at unl.edu) and come to talk with us. Nobody will present or defend the papers. We directly jump right into discussion with the assumption that you have read the paper. There is no email list; articles are posted below along with the date.
Notice: Changing time and Location
We meet every Thursday at 3:00 pm, at UNL East Campus (ask to find the location).
May (Field Season! No Q.U.I.T.!)
- Working on seed preparation, planting and crossing …
- 04-26-2018: The genomic impacts of drift and selection for hybrid performance in maize. By Gerke et al.,
selection, maize, hyrbid
- 04-19-2018: Identification and validation of genomic regions influencing kernel zinc and iron in maize. By Hindu et al., 2018.
GWAS, biofortification, mineral
04-12-2018: Field Prep. Skip once.
- 04-05-2018: A population genetic interpretation of GWAS findings for human quantitative traits. By Simons et al., 2018. And a primer by Gibson about Population genetics and GWAS
- 03-29-2018: The effect of artificial selection on phenotypic plasticity in maize. By Gage et al., 2017
GWAS, GxE, maize
- 03-22-2018: Dysregulation of expression correlates with rare-allele burden and fitness loss in maize. By Kremling et al., 2018
RNA-seq, fitness, maize
- 03-15-2018: Microbial genome-enabled insights into plant–microorganism interactions. By Guttman et al., 2014
- 03-08-2018: Dissecting the genetic architecture controlling highly polygenic traits via simulations in crop species. Contact Jinliang.yang at unl.edu to get the paper.
- 03-02-2018: Quantitative Genetic Analysis of the Maize Leaf Microbiome. by Wallace et al., 2018
- 02-23-2018: Enhancing resolution of natural methylome reprogramming behavior in plants. by Sanchez et al., 2017
- 02-16-2018: No Q.U.I.T. Celebrating Lunar New Year! Read below ones:
Genetic architecture: the shape of the genetic contribution to human traits and disease. by Timpson et al., 2018
Using partitioned heritability methods to explore genetic architecture. by Evans and Keller
- 02-09-2018: No Q.U.I.T. because of the weather. Stay warm and read this at home.
A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination. by Collins and Didelot, 2018
- 02-02-2018: Dynamic DNA methylation reconfiguration during seed development and germination. by Kawakatsu et al., 2017
- 01-26-2018: Genomic features shaping the landscape of meiotic double-strand-break hotspots in maize. by He et al., 2017
- 01-19-2018: Pairwise comparisons across species are problematic when analyzing functional genomic data. by Dunn et al., 2017
functional genomics, comparative
- 12-08-2017: Genetics of trans-regulatory variation in gene expression. by Albert et al., 2017
- 12-01-2017: Information Theory Broadens the Spectrum of Molecular Ecology and Evolution. by Sherwin et al., 2017. Jinliang is out of town. Zhian Kamvar will lead the discussion.
Information Theory, Ecology, Evolution
11-24-2017: It is Black Friday. Go shopping! No QUIT.
- 11-17-2017: Widespread natural variation of DNA methylation within angiosperms. by Niederhuth et al., 2017
- 11-08-2017: The dynamics of molecular evolution over 60,000 generations. by Good et al., 2017.
Note that Dr. Jeff Ross-Ibarra, the founder of R.E.H.A.B., will join us for this special Q.U.I.T. (a REHAB-like event at UNL). (It is on Wednesday at The Oven Haymarket from 5:15-6:00pm for this Q.U.I.T. only!)
evolution, E. coli
- 11-03-2017: Machine Learning for Population Genetics: A New Paradigm. by Scheider and Kern. 2017
Machine learning, popgen
10-27-2017: No Q.U.I.T. CASNR New Faculty Social.
- 10-20-2017: Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana. by Exposito-Alonso et al., 2017
- 10-13-2017: Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America. by Swarts et al., 2017
maize, ancient DNA, adaptation
- 10-06-2017: An Expanded View of Complex Traits: From Polygenic to Omnigenic. by Boyle, Li, and Pritchard, 2017
complex trait, polygenic, review
- 09-29-2017: Gene expression drives the evolution of dominance. by Huber et al., 2017
RNA-seq, dominance, evolution
- 09-22-2017: Discovering genetic interactions bridging pathways in genome-wide association studies. by Fang et al., 2017
GWAS, pathway, method
- 09-15-2017: Patterns of gene body methylation predict coral fitness in new environments. by Dixon et al., 2017
gene body methylation, fitness
09-08-2017: no Q.U.I.T.
- 09-01-2017: Genomic prediction reveals significant non-additive effects for growth in hybrid Eucalyptus. by Tan et al., 2017
Genomic Prediction, non-additive
August 25, 2017
- Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells. by Maria Angels de Luis Balaguer et al., 2017
Prediction, gene network
August 18, 2017
- Detecting Gene Subnetworks Under Selection In Biological Pathways. by Gouy et al., 2017
gene network, selection
July 28, 2017
- Negative selection in humans and fruit flies involves synergistic epistasis. by Sohail et al., 2017
Epistasis, negative selection
July 28, 2017
- Narrow-sense heritability estimation of complex traits using identity-by-descent information. by Evans et al., 2017
Missing heritability, simulated phenotype
June 16, 2017
- Widespread signatures of negative selection in the genetic architecture of human complex traits. by Zeng et al., 2017
Deleterious alleles, MAF, purifying selection, genomic selection, and polygenicity.
April 21, 2017
- Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data. by Huang et al., 2017
Deleterous annotation, machine learning
January 6, 2017
- Methylome evolution in plants? by Vidalis et al., 2016
A review paper on using methylation site frequency spectrum (mSFS) of natural populations to study methylome evolution.
December 16, 2016
- How does epistasis influence the response to selection? by Barton 2016
December 9, 2016
- Genomic Rearrangements Considered as Quantitative Traits by Imprialou et al. 2016