PERFORM Publications

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Title		Authors	PubMed ID
1	Neural topic modeling on hyperspheres: Spherical representation learning with von Mises-Fisher mixtures	Guo D; Luo Z; Bouguila N; Fan W;	41791177 ENCS
2	Spatio-temporal distribution of AOD and its response to regional energy consumption and air pollution factors in China	Su Y; Chen X; Guo J; Yang A;	41308902 ENCS
3	Disentangled representation learning for multi-view clustering via von Mises-Fisher hyperspherical embedding	Li Z; Luo Z; Bouguila N; Su W; Fan W;	40664160 ENCS
4	No species left behind: borrowing strength to map data-deficient species	Sharma S; Winner K; Pollock LJ; Thorson JT; Mäkinen J; Merow C; Pedersen EJ; Chefira KF; Portmann JM; Iannarilli F; Beery S; de Lutio R; Jetz W;	40571432 BIOLOGY
5	Strategies to Reduce Uncertainties from the Best Available Physicochemical Parameters Used for Modeling Novel Organophosphate Esters across Multimedia Environments	Xing C; Ge J; Chen R; Li S; Wang C; Zhang X; Geng Y; Jones KC; Zhu Y;	40105294 CHEMBIOCHEM
6	Exon junction complexes regulate osteoclast-induced bone resorption by influencing the NFATc1 m6A distribution through the "shield effect"	Sun B; Yang JG; Wang Z; Wang Z; Feng W; Li X; Liu SN; Li J; Zhu YQ; Zhang P; Wang W;	40051055 ENCS
7	Spatial Variations of Atmospheric Alkylated Polycyclic Aromatic Hydrocarbons across the Western Pacific to the Southern Ocean: Unexpected Increasing Deposition	Zhu FJ; Lu XM; Jia JW; Zhang X; Xing DF; Cai MH; Kallenborn R; Li YF; Muir DCG; Zhang ZF; Zhang X;	40025703 CHEMBIOCHEM
8	In Shift and In Variance: Assessing the Robustness of HAR Deep Learning Models Against Variability	Khaked AA; Oishi N; Roggen D; Lago P;	39860799 ENCS
9	Asymmetric autocatalytic reactions and their stationary distribution	Gallinger C; Popovic L;	39679357 MATHSTATS
10	Brain tumor detection based on a novel and high-quality prediction of the tumor pixel distributions	Sun Y; Wang C;	38493601 ENCS
11	The infimum values of two probability functions for the Gamma distribution	Sun P; Hu ZC; Sun W;	38261930 MATHSTATS
12	Unsupervised Mixture Models on the Edge for Smart Energy Consumption Segmentation with Feature Saliency	Al-Bazzaz H; Azam M; Amayri M; Bouguila N;	37837127 ENCS
13	The evolution of plasticity at geographic range edges	Usui T; Lerner D; Eckert I; Angert AL; Garroway CJ; Hargreaves A; Lancaster LT; Lessard JP; Riva F; Schmidt C; van der Burg K; Marshall KE;	37183152 BIOLOGY
14	Tide-induced infiltration and resuspension of microplastics in shorelines: Insights from tidal tank experiments	Feng Q; Chen Z; An C; Yang X; Wang Z;	37084574 ENCS
15	Identifying climate change refugia for South American biodiversity	Sales LP; Pires MM;	36919472 BIOLOGY
16	Human Activity Recognition with an HMM-Based Generative Model	Manouchehri N; Bouguila N;	36772428 ENCS
17	Species compositions mediate biomass conservation: the case of lake fish communities	Arranz I; Fournier B; Lester NP; Shuter BJ; Peres-Neto PR;	34905222 BIOLOGY
18	Bayesian Learning of Shifted-Scaled Dirichlet Mixture Models and Its Application to Early COVID-19 Detection in Chest X-ray Images	Bourouis S; Alharbi A; Bouguila N;	34460578 ENCS
19	Formation of oil-particle aggregates: Impacts of mixing energy and duration	Ji W; Boufadel M; Zhao L; Robinson B; King T; An C; Zhang BH; Lee K;	34252767 ENCS
20	Grape seed extract supplementation along with a restricted-calorie diet improves cardiovascular risk factors in obese or overweight adult individuals: A randomized, placebo-controlled trial.	Yousefi R, Parandoosh M, Khorsandi H, Hosseinzadeh N, Madani Tonekaboni M, Saidpour A, Babaei H, Ghorbani A	33044768 HKAP
21	The Odonata of Quebec: Specimen data from seven collections.	Favret C, Moisan-De Serres J, Larrivée M, Lessard JP	32174757 CONCORDIA
22	Diversity, evolution, and classification of virophages uncovered through global metagenomics.	Paez-Espino D, Zhou J, Roux S, Nayfach S, Pavlopoulos GA, Schulz F, McMahon KD, Walsh D, Woyke T, Ivanova NN, Eloe-Fadrosh EA, Tringe SG, Kyrpides NC	31823797 BIOLOGY
23	Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLs.	Xu J, Dai X, Ramasamy RK, Wang L, Zhu T, McGuire PE, Jorgensen CM, Dehghani H, Gulick PJ, Luo MC, Müller HG, Dvorak J	30670607 BIOLOGY

Title:	Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLs.
Authors:	Xu J, Dai X, Ramasamy RK, Wang L, Zhu T, McGuire PE, Jorgensen CM, Dehghani H, Gulick PJ, Luo MC, Müller HG, Dvorak J
Link:	https://www.ncbi.nlm.nih.gov/pubmed/30670607?dopt=Abstract
DOI:	10.1534/g3.118.200921
Publication:	G3 (Bethesda, Md.)
Keywords:	QTL database; QTL distribution; Web portal; fusarium head blight; meta-QTL; probability; recombination rate;
PMID:	30670607	Category:	G3 (Bethesda)	Date Added:	2019-06-07
Dept Affiliation:	BIOLOGY 1 Department of Plant Sciences, University of California, Davis, California. 2 Department of Statistics, Iowa State University, Iowa. 3 Department of Plant Breeding, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran, and. 4 Department of Biology, Concordia University, Montreal, Quebec, Canada. 5 Department of Statistics, University of California, Davis, California. 6 Department of Plant Sciences, University of California, Davis, California, jdvorak@ucdavis.edu.

Description:

Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLs.

G3 (Bethesda). 2019 03 07;9(3):841-853

Authors: Xu J, Dai X, Ramasamy RK, Wang L, Zhu T, McGuire PE, Jorgensen CM, Dehghani H, Gulick PJ, Luo MC, Müller HG, Dvorak J

Abstract

Numerous quantitative trait loci (QTL) have been mapped in tetraploid and hexaploid wheat and wheat relatives, mostly with simple sequence repeat (SSR) or single nucleotide polymorphism (SNP) markers. To conduct meta-analysis of QTL requires projecting them onto a common genomic framework, either a consensus genetic map or genomic sequence. The latter strategy is pursued here. Of 774 QTL mapped in wheat and wheat relatives found in the literature, 585 (75.6%) were successfully projected onto the Aegilops tauschii pseudomolecules. QTL mapped with SNP markers were more successfully projected (92.2%) than those mapped with SSR markers (66.2%). The QTL were not distributed homogeneously along chromosome arms. Their frequencies increased in the proximal-to-distal direction but declined in the most distal regions and were weakly correlated with recombination rates along the chromosome arms. Databases for projected SSR markers and QTL were constructed and incorporated into the Ae. tauschii JBrowse. To facilitate meta-QTL analysis, eight clusters of QTL were used to estimate standard deviations ([Formula: see text]) of independently mapped QTL projected onto the Ae. tauschii genome sequence. The standard deviations [Formula: see text] were modeled as an exponential decay function of recombination rates along the Ae. tauschii chromosomes. We implemented four hypothesis tests for determining the membership of query QTL. The hypothesis tests and estimation procedure for [Formula: see text] were implemented in a web portal for meta-analysis of projected QTL. Twenty-one QTL for Fusarium head blight resistance mapped on wheat chromosomes 3A, 3B, and 3D were analyzed to illustrate the use of the portal for meta-QTL analyses.

PMID: 30670607 [PubMed - in process]

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