@article{MTMT:34789427,
	title = {Shared evolutionary processes shape landscapes of genomic variation in the great apes},
	url = {https://m2.mtmt.hu/api/publication/34789427},
	author = {Rodrigues, Murillo F. and Kern, Andrew D. and Ralph, Peter L.},
	doi = {10.1093/genetics/iyae006},
	journal-iso = {GENETICS},
	journal = {GENETICS},
	unique-id = {34789427},
	issn = {0016-6731},
	abstract = {For at least the past 5 decades, population genetics, as a field, has worked to describe the precise balance of forces that shape patterns of variation in genomes. The problem is challenging because modeling the interactions between evolutionary processes is difficult, and different processes can impact genetic variation in similar ways. In this paper, we describe how diversity and divergence between closely related species change with time, using correlations between landscapes of genetic variation as a tool to understand the interplay between evolutionary processes. We find strong correlations between landscapes of diversity and divergence in a well-sampled set of great ape genomes, and explore how various processes such as incomplete lineage sorting, mutation rate variation, GC-biased gene conversion and selection contribute to these correlations. Through highly realistic, chromosome-scale, forward-in-time simulations, we show that the landscapes of diversity and divergence in the great apes are too well correlated to be explained via strictly neutral processes alone. Our best fitting simulation includes both deleterious and beneficial mutations in functional portions of the genome, in which 9% of fixations within those regions is driven by positive selection. This study provides a framework for modeling genetic variation in closely related species, an approach which can shed light on the complex balance of forces that have shaped genetic variation.},
	keywords = {DIFFERENTIATION; Genetic Diversity; POSITIVE SELECTION; adaptive protein evolution; Selective sweep; GC-biased gene conversion; Selective sweeps; ULTRACONSERVED ELEMENTS; linked selection; linked selection; BACKGROUND SELECTION; BACKGROUND SELECTION; MUTATION-RATE; mutation rate variation},
	year = {2024},
	eissn = {1943-2631},
	orcid-numbers = {Ralph, Peter L./0000-0002-9459-6866}
}

@article{MTMT:34760932,
	title = {What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species},
	url = {https://m2.mtmt.hu/api/publication/34760932},
	author = {Basenko, Evelina Y and Shanmugasundram, Achchuthan and Böhme, Ulrike and Starns, David and Wilkinson, Paul A and Davison, Helen R and Crouch, Kathryn and Maslen, Gareth and Harb, Omar S and Amos, Beatrice and McDowell, Mary Ann and Kissinger, Jessica C and Roos, David S and Jones, Andrew},
	doi = {10.1093/genetics/iyae035},
	journal-iso = {GENETICS},
	journal = {GENETICS},
	volume = {&},
	unique-id = {34760932},
	issn = {0016-6731},
	abstract = {FungiDB (https://fungidb.org) serves as a valuable online resource that seamlessly integrates genomic and related large-scale data for a wide range of fungal and oomycete species. As an integral part of the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org), FungiDB continually integrates both published and unpublished data addressing various aspects of fungal biology. Established in early 2011, the database has evolved to support 674 datasets. The datasets include over 300 genomes spanning various taxa (e.g. Ascomycota, Basidiomycota, Blastocladiomycota, Chytridiomycota, Mucoromycota, as well as Albuginales, Peronosporales, Pythiales, and Saprolegniales). In addition to genomic assemblies and annotation, over 300 extra datasets encompassing diverse information, such as expression and variation data, are also available. The resource also provides an intuitive web-based interface, facilitating comprehensive approaches to data mining and visualization. Users can test their hypotheses and navigate through omics-scale datasets using a built-in search strategy system. Moreover, FungiDB offers capabilities for private data analysis via the integrated VEuPathDB Galaxy platform. FungiDB also permits genome improvements by capturing expert knowledge through the User Comments system and the Apollo genome annotation editor for structural and functional gene curation. FungiDB facilitates data exploration and analysis and contributes to advancing research efforts by capturing expert knowledge for fungal and oomycete species.},
	year = {2024},
	eissn = {1943-2631},
	orcid-numbers = {Basenko, Evelina Y/0000-0001-8611-5447; Shanmugasundram, Achchuthan/0000-0003-2349-6929; Böhme, Ulrike/0000-0002-0248-5924; Starns, David/0000-0001-6583-9067; Wilkinson, Paul A/0000-0002-8836-5439; Davison, Helen R/0000-0002-4302-5756; Crouch, Kathryn/0000-0001-9310-4762; Maslen, Gareth/0000-0001-7318-3678; Harb, Omar S/0000-0003-4446-6200; McDowell, Mary Ann/0000-0003-4115-8464; Kissinger, Jessica C/0000-0002-6413-1101; Roos, David S/0000-0001-6725-4089; Jones, Andrew/0000-0001-6118-9327}
}

@article{MTMT:34536872,
	title = {Dissection of the role of a Src homology 3 domain in the evolution of binding preference of paralogous proteins},
	url = {https://m2.mtmt.hu/api/publication/34536872},
	author = {Lemieux, P. and Bradley, D. and Dubé, A.K. and Dionne, U. and Landry, C.R.},
	doi = {10.1093/genetics/iyad175},
	journal-iso = {GENETICS},
	journal = {GENETICS},
	volume = {226},
	unique-id = {34536872},
	issn = {0016-6731},
	year = {2024},
	eissn = {1943-2631}
}

@article{MTMT:34511760,
	title = {Catalytic activity of the Bin3/MePCE methyltransferase domain is dispensable for 7SK snRNP function in Drosophila melanogaster},
	url = {https://m2.mtmt.hu/api/publication/34511760},
	author = {Palumbo, R.J. and Yang, Y. and Feigon, J. and Hanes, S.D.},
	doi = {10.1093/genetics/iyad203},
	journal-iso = {GENETICS},
	journal = {GENETICS},
	volume = {226},
	unique-id = {34511760},
	issn = {0016-6731},
	year = {2024},
	eissn = {1943-2631}
}

@article{MTMT:34666712,
	title = {Copy number variations and their effect on the plasma proteome},
	url = {https://m2.mtmt.hu/api/publication/34666712},
	author = {Schmitz, Daniel and Li, Zhiwei and Lo Faro, Valeria and Rask-Andersen, Mathias and Ameur, Adam and Rafati, Nima and Johansson, Asa},
	doi = {10.1093/genetics/iyad179},
	journal-iso = {GENETICS},
	journal = {GENETICS},
	unique-id = {34666712},
	issn = {0016-6731},
	keywords = {Copy number variation; Long-read sequencing; Whole-genome sequencing; Plasma proteome},
	year = {2023},
	eissn = {1943-2631},
	orcid-numbers = {Ameur, Adam/0000-0001-6085-6749}
}

@article{MTMT:34657271,
	title = {Bradysia (Sciara) coprophila larvae up-regulate DNA repair pathways and down-regulate developmental regulators in response to ionizing radiation},
	url = {https://m2.mtmt.hu/api/publication/34657271},
	author = {Urban, John M. and Bateman, Jack R. and Garza, Kodie R. and Borden, Julia and Jain, Jaison and Brown, Alexia and Thach, Bethany J. and Bliss, Jacob E. and Gerbi, Susan A.},
	doi = {10.1093/genetics/iyad208},
	journal-iso = {GENETICS},
	journal = {GENETICS},
	unique-id = {34657271},
	issn = {0016-6731},
	keywords = {Bradysia (Sciara) coprophila; gamma-radiation resistance level; gene expression changes to ionizing radiation; radiation-induced developmental delay},
	year = {2023},
	eissn = {1943-2631}
}

@article{MTMT:34638774,
	title = {A cosmopolitan inversion facilitates seasonal adaptation in overwintering Drosophila},
	url = {https://m2.mtmt.hu/api/publication/34638774},
	author = {Nunez, Joaquin C. B. and Lenhart, Benedict A. and Bangerter, Alyssa and Murray, Connor S. and Mazzeo, Giovanni R. and Yu, Yang and Nystrom, Taylor L. and Tern, Courtney and Erickson, Priscilla A. and Bergland, Alan O.},
	doi = {10.1093/genetics/iyad207},
	journal-iso = {GENETICS},
	journal = {GENETICS},
	unique-id = {34638774},
	issn = {0016-6731},
	keywords = {Drosophila melanogaster; seasonality; balancing selection; inversions; Adaptive tracking},
	year = {2023},
	eissn = {1943-2631},
	orcid-numbers = {Nunez, Joaquin C. B./0000-0002-3171-8918}
}

@article{MTMT:34637039,
	title = {Mutations in yeast Pcf11, a conserved protein essential for mRNA 3′ end processing and transcription termination, elicit the Environmental Stress Response},
	url = {https://m2.mtmt.hu/api/publication/34637039},
	author = {Graber, Joel H. and Hoskinson, Derick and Liu, Huiyun and Kaczmarek Michaels, Katarzyna and Benson, Peter S. and Maki, Nathaniel J. and Wilson, Christian L. and McGrath, Caleb and Puleo, Franco and Pearson, Erika and Kuehner, Jason N. and Moore, Claire},
	doi = {10.1093/genetics/iyad199},
	journal-iso = {GENETICS},
	journal = {GENETICS},
	unique-id = {34637039},
	issn = {0016-6731},
	keywords = {ATTENUATION; transcription termination; mRNA 3 ' end processing; Environmental stress response; Pcf11},
	year = {2023},
	eissn = {1943-2631}
}

@article{MTMT:34602561,
	title = {rvTWAS: identifying gene-trait association using sequences by utilizing transcriptome-directed feature selection},
	url = {https://m2.mtmt.hu/api/publication/34602561},
	author = {He, Jingni and Li, Qing and Zhang, Qingrun},
	doi = {10.1093/genetics/iyad204},
	journal-iso = {GENETICS},
	journal = {GENETICS},
	unique-id = {34602561},
	issn = {0016-6731},
	abstract = {Toward the identification of genetic basis of complex traits, transcriptome-wide association study (TWAS) is successful in integrating transcriptome data. However, TWAS is only applicable for common variants, excluding rare variants in exome or whole-genome sequences. This is partly because of the inherent limitation of TWAS protocols that rely on predicting gene expressions. Our previous research has revealed the insight into TWAS: the 2 steps in TWAS, building and applying the expression prediction models, are essentially genetic feature selection and aggregations that do not have to involve predictions. Based on this insight disentangling TWAS, rare variants' inability of predicting expression traits is no longer an obstacle. Herein, we developed "rare variant TWAS," or rvTWAS, that first uses a Bayesian model to conduct expression-directed feature selection and then uses a kernel machine to carry out feature aggregation, forming a model leveraging expressions for association mapping including rare variants. We demonstrated the performance of rvTWAS by thorough simulations and real data analysis in 3 psychiatric disorders, namely schizophrenia, bipolar disorder, and autism spectrum disorder. We confirmed that rvTWAS outperforms existing TWAS protocols and revealed additional genes underlying psychiatric disorders. Particularly, we formed a hypothetical mechanism in which zinc finger genes impact all 3 disorders through transcriptional regulations. rvTWAS will open a door for sequence-based association mappings integrating gene expressions.},
	keywords = {Rare genetic variants; transcriptome-wide association study; gene-trait association mapping; Bayesian feature selection; kernel-based feature aggregation},
	year = {2023},
	eissn = {1943-2631},
	orcid-numbers = {Li, Qing/0009-0005-1327-4347}
}

@article{MTMT:34597993,
	title = {rec-1 loss of function increases recombination in the central gene clusters at the expense of autosomal pairing centers},
	url = {https://m2.mtmt.hu/api/publication/34597993},
	author = {Paree, Tom and Noble, Luke and Ferreira Goncalves, Joao and Teotonio, Henrique},
	doi = {10.1093/genetics/iyad205},
	journal-iso = {GENETICS},
	journal = {GENETICS},
	unique-id = {34597993},
	issn = {0016-6731},
	abstract = {Meiotic control of crossover (CO) number and position is critical for homologous chromosome segregation and organismal fertility, recombination of parental genotypes, and the generation of novel genetic combinations. We here characterize the recombination rate landscape of a rec-1 loss of function modifier of CO position in Caenorhabditis elegans, one of the first ever modifiers discovered. By averaging CO position across hermaphrodite and male meioses and by genotyping 203 single-nucleotide variants covering about 95% of the genome, we find that the characteristic chromosomal arm-center recombination rate domain structure is lost in the loss of function rec-1 mutant. The rec-1 loss of function mutant smooths the recombination rate landscape but is insufficient to eliminate the nonuniform position of CO. Lower recombination rates in the rec-1 mutant are particularly found in the autosomal arm domains containing the pairing centers. We further find that the rec-1 mutant is of little consequence for organismal fertility and egg viability and thus for rates of autosomal nondisjunction. It nonetheless increases X chromosome nondisjunction rates and thus male appearance. Our findings question the maintenance of recombination rate heritability and genetic diversity among C. elegans natural populations, and they further suggest that manipulating genetic modifiers of CO position will help find quantitative trait loci located in low-recombining genomic regions normally refractory to discovery.},
	keywords = {RECOMBINATION; genetic linkage; meiosis; C. ELEGANS; crossover: RIAIL; rec-1},
	year = {2023},
	eissn = {1943-2631},
	orcid-numbers = {Noble, Luke/0000-0002-5161-4059; Teotonio, Henrique/0000-0003-1057-6882}
}