Genetics & Heredity

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Article Genetics & Heredity

The UGT2A1/UGT2A2 locus is associated with COVID-19-related loss of smell or taste

Janie F. Shelton, Anjali J. Shastri, Kipper Fletez-Brant, Stella Aslibekyan, Adam Auton

Summary: Multi-ancestry genome-wide analyses have identified variants near UGT2A1 and UGT2A2 genes that are associated with COVID-19-related loss of smell or taste. These genes are expressed in the olfactory epithelium and play a role in metabolizing odorants.

NATURE GENETICS (2022)

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Article Biotechnology & Applied Microbiology

circ-EIF6 encodes EIF6-224aa to promote TNBC progression via stabilizing MYH9 and activating the Wnt/beta-catenin pathway

Yaming Li, Zekun Wang, Peng Su, Yiran Liang, Zheng Li, Hanwen Zhang, Xiaojin Song, Dianwen Han, Xiaolong Wang, Ying Liu, Jingwen Yang, Bing Chen, Lijuan Wang, Wenjing Zhao, Qifeng Yang

Summary: The protein-coding ability of circRNAs in TNBC has not been well understood. This study identified a circRNA called circ-EIF6, which was associated with poorer prognosis and clinicopathological characteristics in TNBC patients. Functional experiments showed that circ-EIF6 promoted proliferation and metastasis of TNBC cells, mediated by encoding a novel peptide called EIF6-224aa that interacted with MYH9, leading to activation of the Wnt/β-catenin pathway.

MOLECULAR THERAPY (2022)

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Review Ecology

Freshwater salinisation: a research agenda for a saltier world

David Cunillera-Montcusi, Meryem Beklioglu, Miguel Canedo-Arguelles, Erik Jeppesen, Robert Ptacnik, Cihelio A. Amorim, Shelley E. Arnott, Stella A. Berger, Sandra Brucet, Hilary A. Dugan, Miriam Gerhard, Zsofia Horvath, Silke Langenheder, Jens C. Nejstgaard, Marko Reinikainen, Maren Striebel, Pablo Urrutia-Cordero, Csaba F. Vad, Egor Zadereev, Miguel Matias

Summary: The salinisation of freshwater ecosystems is a significant threat, affecting biodiversity and human societies. Understanding its ecological and evolutionary consequences is still a challenge, with various research gaps identified. Focusing on global- and landscape-scale processes, functional approaches, genetic and molecular levels, and ecoevolutionary dynamics can help predict the impacts of freshwater salinisation.

TRENDS IN ECOLOGY & EVOLUTION (2022)

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Article Cell Biology

The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer-promoter communication

Jonathan P. Karr, John J. Ferrie, Robert Tjian, Xavier Darzacq

Summary: This Perspective presents a new model for understanding how distal cis-regulatory elements communicate with promoters, diverging from the traditional enhancer-promoter looping paradigm. The model focuses on the coactivator p300 and offers a synthesis of the current literature to support its plausibility.

GENES & DEVELOPMENT (2022)

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Review Genetics & Heredity

Diagnostic yield of exome sequencing for prenatal diagnosis of fetal structural anomalies: A systematic review and meta-analysis

Rhiannon Mellis, Kathryn Oprych, Elizabeth Scotchman, Melissa Hill, Lyn S. Chitty

Summary: Prenatal exome sequencing provides an additional diagnostic yield of 31% for structurally abnormal fetuses. Case selection and fetal phenotype significantly affect the diagnostic yield.

PRENATAL DIAGNOSIS (2022)

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Article Biotechnology & Applied Microbiology

lncRNA ITGB8-AS1 functions as a ceRNA to promote colorectal cancer growth and migration through integrin-mediated focal adhesion signaling

Xiaoting Lin, Shiwen Zhuang, Xue Chen, Jun Du, Longhua Zhong, Jiancheng Ding, Lei Wang, Jia Yi, Guosheng Hu, Guohui Tang, Xi Luo, Wen Liu, Feng Ye

Summary: The long non-coding RNA ITGB8-AS1 is highly expressed in colorectal cancer (CRC) and plays an oncogenic role in promoting tumor growth. ITGB8-AS1 regulates cell proliferation and tumor growth in CRC by controlling focal adhesion signaling and interacting with miR-33b-5p and let-7c-5p/let-7d-5p. Additionally, ITGB8-AS1 can be detected in the plasma of CRC patients and is associated with differentiation, TNM stage, and plasma levels of ITGA3 and ITGB3.

MOLECULAR THERAPY (2022)

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Article Genetics & Heredity

Leveraging fine-mapping and multipopulation training data to improve cross-population polygenic risk scores

Omer Weissbrod, Masahiro Kanai, Huwenbo Shi, Steven Gazal, Wouter J. Peyrot, Amit Khera, Yukinori Okada, Alicia R. Martin, Hilary K. Finucane, Alkes L. Price

Summary: PolyPred and PolyPred(+) methods greatly improve cross-population polygenic prediction accuracy, particularly when applied to diseases and complex traits in UK Biobank populations. This is crucial for reducing health disparities in non-European populations.

NATURE GENETICS (2022)

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Article Genetics & Heredity

KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences

Zhang Zhang

Summary: KaKs_Calculator 3.0 is an updated toolkit for calculating selective pressure on coding and non-coding sequences, with great potential for genome-wide studies on natural selection.

GENOMICS PROTEOMICS & BIOINFORMATICS (2022)

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Review Genetics & Heredity

Obtaining genetics insights from deep learning via explainable artificial intelligence

Gherman Novakovsky, Nick Dexter, Maxwell W. Libbrecht, Wyeth W. Wasserman, Sara Mostafavi

Summary: This Review describes the advances in explainable artificial intelligence (xAI) in genomics, where researchers are using deep learning approaches to gain biological insights behind the models, moving beyond the traditional 'black box' nature.

NATURE REVIEWS GENETICS (2023)

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Article Genetics & Heredity

Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities

Abrar Choudhury, Stephen T. Magill, Charlotte D. Eaton, Briana C. Prager, William C. Chen, Martha A. Cady, Kyounghee Seo, Calixto-Hope G. Lucas, Tim J. Casey-Clyde, Harish N. Vasudevan, S. John Liu, Javier E. Villanueva-Meyer, Tai-Chung Lam, Jenny Kan-Suen Pu, Lai-Fung Li, Gilberto Ka-Kit Leung, Danielle L. Swaney, Michael Y. Zhang, Jason W. Chan, Zhixin Qiu, Michael V. Martin, Matthew S. Susko, Steve E. Braunstein, Nancy Ann Oberheim Bush, Jessica D. Schulte, Nicholas Butowski, Penny K. Sneed, Mitchel S. Berger, Nevan J. Krogan, Arie Perry, Joanna J. Phillips, David A. Solomon, Joseph F. Costello, Michael W. McDermott, Jeremy N. Rich, David R. Raleigh

Summary: DNA methylation profiling identified three groups of meningiomas with distinct clinical outcomes, biological drivers, and therapeutic vulnerabilities. Cytostatic cell cycle inhibitors showed efficacy in attenuating meningioma growth.

NATURE GENETICS (2022)

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Article Genetics & Heredity

High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads

Bo Wang, Xiaofei Yang, Yanyan Jia, Yu Xu, Peng Jia, Ningxin Dang, Songbo Wang, Tun Xu, Xixi Zhao, Shenghan Gao, Quanbin Dong, Kai Ye

Summary: This study successfully assembled a high-quality and almost complete genome of Arabidopsis thaliana using multiple advanced sequencing technologies. The new genome assembly contains more information compared to the previous reference genome, providing valuable insights into the global pattern of centromeric polymorphisms and the genetic and epigenetic features in plants.

GENOMICS PROTEOMICS & BIOINFORMATICS (2022)

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Review Genetics & Heredity

Navigating the pitfalls of applying machine learning in genomics

Sean Whalen, Jacob Schreiber, William S. Noble, Katherine S. Pollard

Summary: This review discusses common pitfalls encountered when applying supervised machine learning in genomics, emphasizing how the structure of genomics data can bias performance evaluations and predictions. It also presents solutions and appropriate use cases to address the challenges associated with applying cutting-edge ML methods to genomics.

NATURE REVIEWS GENETICS (2022)

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Article Genetics & Heredity

Genetic architecture of 11 major psychiatric disorders at biobehavioral, functional genomic and molecular genetic levels of analysis

Andrew D. Grotzinger, Travis T. Mallard, Wonuola A. Akingbuwa, Hill F. Ip, Mark J. Adams, Cathryn M. Lewis, Andrew M. McIntosh, Jakob Grove, Soren Dalsgaard, Klaus-Peter Lesch, Nora Strom, Sandra M. Meier, Manuel Mattheisen, Anders D. Borglum, Ole Mors, Gerome Breen, Phil H. Lee, Kenneth S. Kendler, Jordan W. Smoller, Elliot M. Tucker-Drob, Michel G. Nivard

Summary: A joint analysis of 11 major psychiatric disorders identified four broad factors underlying the genetic correlations among the disorders, along with multiple loci acting on these factors. These findings suggest the presence of genetic overlap among different psychiatric disorders, but also highlight the heterogeneity within each factor. However, a single dimension of genetic risk does not appear to be useful in explaining the biobehavioral correlates or individual variants of psychiatric disorders.

NATURE GENETICS (2022)

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Article Genetics & Heredity

Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

Hequan Sun, Wen-Biao Jiao, Jose A. Campoy, Kristin Krause, Manish Goel, Kat Folz-Donahue, Christian Kukat, Bruno Huettel, Korbinian Schneeberger

Summary: This study reports the reconstruction of the autotetraploid genome of potato based on high-quality long reads, single-cell sequencing, and Hi-C data, revealing the characteristics of genome similarity and structural rearrangements caused by recent inbreeding. Only a portion of the genes were present in all four haplotypes, and some genes may be regulated through allele-specific DNA methylation.

NATURE GENETICS (2022)

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Review Genetics & Heredity

The potential of mitochondrial genome engineering

Pedro Silva-Pinheiro, Michal Minczuk

Summary: Mitochondria are controlled by both nuclear DNA and their own genome, mtDNA, with mutations in mtDNA potentially leading to devastating hereditary diseases. Recent advancements in genetic modification of mammalian mtDNA show promise in using genome editing technologies for treating mitochondrial diseases.

NATURE REVIEWS GENETICS (2022)

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Review Biochemistry & Molecular Biology

Critical roles of FTO-mediated mRNA m6A demethylation in regulating adipogenesis and lipid metabolism: Implications in lipid metabolic disorders

Zhou Yang, Guang-li Yu, Xiao Zhu, Tian-hong Peng, Yun-cheng Lv

Summary: FTO mediates m(6)A demethylation to modulate lipid metabolism by affecting gene expression, leading to alterations in lipid synthesis, storage, and utilization.

GENES & DISEASES (2022)

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Article Genetics & Heredity

Deep learning enables genetic analysis of the human thoracic aorta

James P. Pirruccello, Mark D. Chaffin, Elizabeth L. Chou, Stephen J. Fleming, Honghuang Lin, Mahan Nekoui, Shaan Khurshid, Samuel F. Friedman, Alexander G. Bick, Alessandro Arduini, Lu-Chen Weng, Seung Hoan Choi, Amer-Denis Akkad, Puneet Batra, Nathan R. Tucker, Amelia W. Hall, Carolina Roselli, Emelia J. Benjamin, Shamsudheen K. Vellarikkal, Rajat M. Gupta, Christian M. Stegmann, Dejan Juric, James R. Stone, Ramachandran S. Vasan, Jennifer E. Ho, Udo Hoffmann, Steven A. Lubitz, Anthony A. Philippakis, Mark E. Lindsay, Patrick T. Ellinor

Summary: Genome-wide association analyses identified variants associated with thoracic aortic diameter and polygenic score for ascending aortic diameter was correlated with a diagnosis of thoracic aortic aneurysm. Enlargement or aneurysm of the aorta predisposes to dissection, and a deep learning model along with genome-wide association studies successfully identified loci associated with ascending and descending thoracic aortic diameter, highlighting the potential for rapidly defining quantitative traits with deep learning in biomedical images.

NATURE GENETICS (2022)

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Review Genetics & Heredity

Functions and consequences of AID/APOBEC-mediated DNA and RNA deamination

Riccardo Pecori, Salvatore Di Giorgio, J. Paulo Lorenzo, F. Nina Papavasiliou

Summary: The AID/APOBEC polynucleotide cytidine deaminases have diverse functions as both DNA mutators and RNA editors, and their strict functional classification needs to be reconsidered. Understanding the structural differences and similarities between these enzymes will contribute to improving the design of programmable base editors for therapeutic purposes.

NATURE REVIEWS GENETICS (2022)

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Article Genetics & Heredity

WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans

Paul Davis, Magdalena Zarowiecki, Valerio Arnaboldi, Andres Becerra, Scott Cain, Juancarlos Chan, Wen J. Chen, Jaehyoung Cho, Eduardo da Veiga Beltrame, Stavros Diamantakis, Sibyl Gao, Dionysis Grigoriadis, Christian A. Grove, Todd W. Harris, Ranjana Kishore, Tuan Le, Raymond Y. N. Lee, Manuel Luypaert, Hans-Michael Muller, Cecilia Nakamura, Paulo Nuin, Michael Paulini, Mark Quinton-Tulloch, Daniela Raciti, Faye H. Rodgers, Matthew Russell, Gary Schindelman, Archana Singh, Tim Stickland, Kimberly Van Auken, Qinghua Wang, Gary Williams, Adam J. Wright, Karen Yook, Matt Berriman, Kevin L. Howe, Tim Schedl, Lincoln Stein, Paul W. Sternberg

Summary: WormBase is a central repository for genetics and genomics research on Caenorhabditis elegans, providing data and tools to facilitate the study of this organism and related nematodes. They continually evolve to incorporate new data types and services, aiming to integrate and utilize knowledge from published nematode genetics literature. Additionally, they collaborate with the Alliance of Genome Resources to harmonize infrastructure, processes, and tools.

GENETICS (2022)

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Article Genetics & Heredity

Rare coding variation provides insight into the genetic architecture and phenotypic context of autism

Jack M. Fu, F. Kyle Satterstrom, Minshi Peng, Harrison Brand, Ryan L. Collins, Shan Dong, Brie Wamsley, Lambertus Klei, Lily Wang, Stephanie P. Hao, Christine R. Stevens, Caroline Cusick, Mehrtash Babadi, Eric Banks, Brett Collins, Sheila Dodge, Stacey B. Gabriel, Laura Gauthier, Samuel K. Lee, Lindsay Liang, Alicia Ljungdahl, Behrang Mahjani, Laura Sloofman, Andrey N. Smirnov, Mafalda Barbosa, Catalina Betancur, Alfredo Brusco, Brian H. Y. Chung, Edwin H. Cook, Michael L. Cuccaro, Enrico Domenici, Giovanni Battista Ferrero, J. Jay Gargus, Gail E. Herman, Irva Hertz-Picciotto, Patricia Maciel, Dara S. Manoach, Maria Rita Passos-Bueno, Antonio M. Persico, Alessandra Renieri, James S. Sutcliffe, Flora Tassone, Elisabetta Trabetti, Gabriele Campos, Simona Cardaropoli, Diana Carli, Marcus C. Y. Chan, Chiara Fallerini, Elisa Giorgio, Ana Cristina Girardi, Emily Hansen-Kiss, So Lun Lee, Carla Lintas, Yunin Ludena, Rachel Nguyen, Lisa Pavinato, Margaret Pericak-Vance, Isaac N. Pessah, Rebecca J. Schmidt, Moyra Smith, Claudia I. S. Costa, Slavica Trajkova, Jaqueline Y. T. Wang, Mullin H. C. Yu, David J. Cutler, Silvia De Rubeis, Joseph D. Buxbaum, Mark J. Daly, Bernie Devlin, Kathryn Roeder, Stephan J. Sanders, Michael E. Talkowski

Summary: This study investigated genes associated with functional mutations in individuals with autism spectrum disorder (ASD) and found that some of these genes are also associated with developmental delay (DD). The findings suggest that ASD and DD may share common pathological pathways.

NATURE GENETICS (2022)

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