Top 10 Biorxiv Papers Today in Genetics


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#1. Bayesian copy number detection and association in large-scale studies
Stephen Cristiano, David McKean, Jacob Carey, Paige Bracci, Paul Brennan, Michael Chou, Mengmeng Du, Steven Gallinger, Michael G. Goggins, Manal Hassan, Rayjean Hung, Robert Kurtz, Donghui Li, Lingeng Lu, Rachel Neale, Sara Olson, Gloria Petersen, Kari Rabe, Jack Fu, Harvey Risch, Gary Rosner, Ingo Ruczinski, Alison P. Klein, Robert B. Scharpf
Germline copy number variants (CNVs) increase risk for many diseases, yet detection of CNVs and quantifying their contribution to disease risk in large-scale studies is challenging. We developed an approach called CNPBayes to identify latent batch effects, to provide probabilistic estimates of integer copy number across the estimated batches, and to fully integrate the copy number uncertainty in the association model for disease. We demonstrate this approach in a Pancreatic Cancer Case Control study of 7,598 participants where the major sources of technical variation were not captured by study site and varied across the genome. Candidate associations aided by this approach include deletions of 8q24 near regulatory elements of the tumor oncogene MYC and of Tumor Supressor Candidate 3 (TUSC3). This study provides a robust Bayesian inferential framework for estimating copy number and evaluating the role of copy number in heritable diseases.
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Authors: 24
Total Words: 0
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#2. A paleogenetic perspective of the Sabana de Bogota (Northern South America) population history over the Holocene (9000 – 550 cal BP)
Miguel Eduardo Delgado, Freddy Rodriguez, Kalina Kassadjikova, Lars Fehren Schmitz
On the basis of distinct lines of evidence, detailed reconstructions of the Holocene population history of the Sabana de Bogota (SB) region, Northern South America, have been performed. Currently, there exist two competing models that support temporal continuity or, alternatively, divergence. Despite recent research that lends support to the population discontinuity model, several discrepancies remain, calling for other kinds of evidences to be explored for a more detailed picture of Holocene biocultural evolution. In this study, we analyze the mitochondrial genetic diversity of 30 individuals (including 15 newly reported complete mitochondrial genomes) recovered from several archaeological sites spanning from the late Pleistocene (12,164 cal BP) until the final late Holocene (2,751 cal BP) along with published data from the region dating ~9,000-550 cal BP in order to investigate diachronic genetic change. Genetic diversity and distance indices were calculated, and demographic models tested in an approximate Bayesian computation...
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biorxivpreprint: A paleogenetic perspective of the Sabana de Bogota (Northern South America) population history over the Holocene (9000 - 550 cal BP) https://t.co/6ONPcxw2xo #bioRxiv
biorxiv_genetic: A paleogenetic perspective of the Sabana de Bogota (Northern South America) population history over the Holocene (9000 - 550 cal BP) https://t.co/8PPX7x5JuK #biorxiv_genetic
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Authors: 4
Total Words: 0
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#3. Evaluation of Genetic Diversity in Cultivated and Exotic Germplasm Sources of Faba Bean Using Important Morphological Traits
Praveen Kumar, Prashant Kaushik
Here we determined the diversity in the 65 genotypes of faba bean of different agro-ecological origins. Plants were grown in randomized block design in three replications. Further, the genotypes were characterized based on the ten morphological traits. Highly significant differences were determined for all of the studied traits. Whereas, the number of cluster per plant was positively correlated with the pods per plants. Moreover, the trait number of cluster per plant determined the most substantial positive effect on seed yield. Overall, our results indicate a wide range of variability for further selection and improvement of faba bean ideotype.
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biorxivpreprint: Evaluation of Genetic Diversity in Cultivated and Exotic Germplasm Sources of Faba Bean Using Important Morphological Traits https://t.co/CAhCN4ua3S #bioRxiv
biorxiv_genetic: Evaluation of Genetic Diversity in Cultivated and Exotic Germplasm Sources of Faba Bean Using Important Morphological Traits https://t.co/A7kRF71f0P #biorxiv_genetic
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Sample Sizes : [126]
Authors: 2
Total Words: 3253
Unqiue Words: 1286

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#4. Pesticides and transgenerational inheritance of pathologies: Designing, analysing and reporting rodent studies.
Ian Plewis
The evidence for transgenerational transmission of pathologies in rodents exposed to pesticides is largely based on studies with weaknesses in design and analysis and a lack of transparency in reporting the results. This paper examines these methodological and statistical issues in detail. Its particular focus is on the estimation of ‘litter effects’: the tendency for rodents within a litter to be more alike than rodents in different litters. Appropriate statistical models were fitted to published data from a series of widely reported studies carried out at Washington State University. These studies were amalgamated into a single dataset in order to estimate these litter effects and the associated treatment effects. Litter effects varied by outcome and were often substantial. Consequently, the effective sample size was often substantially less than the number of observations with implications for the power of the studies. Moreover, the reported precision of the estimates of treatment effects was too low. These problems are...
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Authors: 1
Total Words: 5346
Unqiue Words: 1709

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#5. Hmx3a does not require its homeodomain for its essential functions in spinal cord, ear and lateral line development.
Samantha J. England, Gustavo A. Cerda, Angelica M Kowalchuk, Taylor Sorice, Ginny M Grieb, Katharine E. Lewis
Homeodomain-containing transcription factors have crucial functions in most aspects of cellular function and embryonic development in both animals and plants. Hmx proteins are a sub-family of NK homeodomain proteins and previous research has shown that they have crucial functions in the development of sensory structures such as the eye and the ear. However, the functions of Hmx proteins in spinal cord development have not been analyzed. Here we show that zebrafish hmx2 and hmx3a are co-expressed in spinal dI2 and V1 neurons, whereas hmx3b, hmx1 and hmx4 are not expressed in the spinal cord. Using mutational analyses, we demonstrate that, in addition to its previously demonstrated role in ear development, Hmx3a is required for survival to adulthood, lateral line progression and correct specification of spinal interneuron neurotransmitter fates. However, despite the fact that hxm2 is also expressed in the developing ear, lateral line and spinal cord, we have not detected any requirement for Hmx2 in the development of these...
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biorxivpreprint: Hmx3a does not require its homeodomain for its essential functions in spinal cord, ear and lateral line development. https://t.co/2QbJh1m8nk #bioRxiv
biorxiv_genetic: Hmx3a does not require its homeodomain for its essential functions in spinal cord, ear and lateral line development. https://t.co/eM1frUIIin #biorxiv_genetic
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Authors: 6
Total Words: 20785
Unqiue Words: 4167

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#6. MISTR: A conserved MItochondrial STress Response network revealed by signatures of evolutionary conflict
Mahsa Sorouri, Tyron Chang, Palmy Jesudhasan, Chelsea Pinkham, Nels C. Elde, Dustin Hancks
Host-pathogen conflicts leave genetic signatures of variation in homologous host genes. Using these molecular scars as a guide, we discovered a vertebrate-specific MItochondrial STress Response circuit (MISTR). MISTR proteins are associated with electron transport chain factors and activated by stress signals such as interferon-gamma and hypoxia. Upon stress, ultraconserved miRNAs downregulate MISTR1 followed by replacement with paralogs MISTR AntiViral (MISTRAV) or MISTR Hypoxia (MISTRH), depending on the insult. While cells lacking MISTR1 are more sensitive to apoptotic triggers, cells lacking MISTRAV or expressing the poxvirus-encoded vMISTRAV exhibit resistance to the same insults. Rapid evolution signatures across primate genomes for MISTR1 and MISTRAV indicate ancient and ongoing conflicts with pathogens. MISTR proteins are also found in plants, yeasts, and an algal virus indicating ancient origins and suggesting diverse means of altering mitochondrial function under stress. The discovery of MISTR circuitry highlights the...
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Authors: 6
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#7. Conservation genomics of an Australian orchid complex with implications for the taxonomic and conservation status of Corybas dowlingii
Natascha D. Wagner, Mark A Clements, Lalita Simpson, Katharina Nargar
This study assessed genomic diversity in an Australian species complex in the helmet orchids to clarify taxonomic delimitation and conservation status of the threatened species Corybas dowlingii, a narrow endemic from southeast Australia. Taxonomic delimitation between the three closely related species C. aconitiflorus, C. barbarae, and C. dowlingii has been mainly based on floral traits which exhibit varying degrees of overlap, rendering species delimitation in the complex difficult. Genomic data for the species complex was generated using double-digest restriction-site associated DNA (ddRAD) sequencing. Maximum likelihood, NeighborNet, and Bayesian structure analyses showed genetic differentiation within the species complex and retrieved genomic signatures consistent with hybridisation and introgression between C. aconitiflorus and C. barbarae, and an intermediate genetic position of C. dowlingii indicating a hybrid origin of the species. The genetic structure analysis showed varying levels of genetic admixture for several C....
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biorxivpreprint: Conservation genomics of an Australian orchid complex with implications for the taxonomic and conservation status of Corybas dowlingii https://t.co/5uxyreCmUn #bioRxiv
biorxiv_genetic: Conservation genomics of an Australian orchid complex with implications for the taxonomic and conservation status of Corybas dowlingii https://t.co/IRkSMGzrik #biorxiv_genetic
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Authors: 4
Total Words: 0
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#8. Summary-data-based mendelian randomisation reveals druggable targets for multiple sclerosis
Benjamin Meir Jacobs, Thomas Taylor, Amine Awad, Gavin Giovannoni, David Baker, Alastair J Noyce, Ruth Dobson
Background: Multiple Sclerosis (MS) is a complex autoimmune disease caused by a combination of genetic and environmental factors. Translation of Genome-Wide Association Study (GWAS) findings in MS into therapeutics and effective preventive strategies has been limited to date. Methods: We used Summary Data-Based Mendelian Randomisation (SMR) to synthesise findings from public expression quantitative trait locus (eQTL; eQTLgen and CAGE), methylation quantitative trait locus (mQTL; Lothian Birth Cohort and Brisbane Systems Genetics Study), and MS GWAS datasets (International Multiple Sclerosis Genomics Consortium). By correlating the effects of methylation on MS (M-2-MS), methylation on expression (M-2-E), and expression on MS susceptibility (E-2-MS), we prioritise genetic loci with strong evidence of causally influencing MS susceptibility. We overlay these findings onto a list of druggable genes, i.e. genes which are currently, or could theoretically, be targeted by therapeutic compounds. We use GeNets and STRING to identify...
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Sample Sizes : [503, 503]
Authors: 7
Total Words: 8126
Unqiue Words: 2472

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#9. C. elegans reads bacterial non-coding RNAs to learn pathogenic avoidance
Rachel Kaletsky, Rebecca S. Moore, Geoffrey D. Vrla, Lance L. Parsons, Zemer Gitai, Coleen T. Murphy
C. elegans is exposed to many different bacteria in its environment, and must distinguish pathogenic from nutritious bacterial food sources. Here, we show that a single exposure to purified small RNAs isolated from pathogenic Pseudomonas aeruginosa (PA14) is sufficient to induce pathogen avoidance, both in the treated animals and in four subsequent generations of progeny. The RNA interference and piRNA pathways, the germline, and the ASI neuron are required for bacterial small RNA-induced avoidance behavior and transgenerational inheritance. A single non-coding RNA, P11, is both necessary and sufficient to convey learned avoidance of PA14, and its C. elegans target, maco-1, is required for avoidance. A natural microbiome Pseudomonas isolate, GRb0427, can induce avoidance via its small RNAs, and the wild C. elegans strain JU1580 responds similarly to bacterial sRNA. Our results suggest that this ncRNA-dependent mechanism evolved to survey the microbial environment, use this information to make appropriate behavioral decisions, and...
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biorxivpreprint: C. elegans reads bacterial non-coding RNAs to learn pathogenic avoidance https://t.co/oetkg3EEQR #bioRxiv
biorxiv_genetic: C. elegans reads bacterial non-coding RNAs to learn pathogenic avoidance https://t.co/aMv4PsyhJz #biorxiv_genetic
zamanian_: RT @biorxivpreprint: C. elegans reads bacterial non-coding RNAs to learn pathogenic avoidance https://t.co/oetkg3EEQR #bioRxiv
khats97: RT @biorxivpreprint: C. elegans reads bacterial non-coding RNAs to learn pathogenic avoidance https://t.co/oetkg3EEQR #bioRxiv
schraderlab: RT @biorxivpreprint: C. elegans reads bacterial non-coding RNAs to learn pathogenic avoidance https://t.co/oetkg3EEQR #bioRxiv
KztZoo: RT @biorxiv_genetic: C. elegans reads bacterial non-coding RNAs to learn pathogenic avoidance https://t.co/aMv4PsyhJz #biorxiv_genetic
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Authors: 6
Total Words: 0
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#10. USP15 deubiquitinase safeguards hematopoiesis and genome integrity in hematopoietic stem cells and leukemia cells
Paul van den Berk, Cesare Lancini, Carlos Company, Michela Serresi, Danielle Hulsman, Colin Pritchard, Ji-Ying Song, Matthias Jurgen Schmitt, Ellen Tanger, Ivo J. Huijbers, Heinz Jacobs, Maarten van Lohuizen, Gaetano Gargiulo, Elisabetta Citterio
Altering ubiquitination by disruption of individual deubiquitinating enzymes (DUBs) has proven to affect hematopoietic stem cell (HSC) maintenance. However, comprehensive knowledge of DUB function during hematopoiesis in vivo is lacking. To accomplish this goal, we systematically inactivated DUBs in mouse hematopoietic progenitors using in vivo small hairpin RNAs (shRNAs) screens. We found that multiple DUBs may be individually required for hematopoiesis and that the ubiquitin-specific protease 15 (USP15) is particularly important for the maintenance of murine hematopoietic stem and progenitor cells in vitro and in vivo. Consistently, Usp15 knockout mice exhibited a reduced HSC pool. The defect was intrinsic to HSCs, as demonstrated by competitive repopulation assays. Importantly, USP15 is highly expressed in normal human hematopoietic cells and leukemias, and USP15 depletion in murine early progenitors and myeloid leukemia cells impaired in vitro expansion and increased genotoxic stress. Our study underscores the importance of...
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Sample Sizes : [3, 4, 9, 5, 13, 7, 6, 4, 5, 2, 3, 2, 5, 3, 3, 2]
Authors: 14
Total Words: 19781
Unqiue Words: 5436

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