Top 10 Biorxiv Papers Today in Genomics


2.262 Mikeys
#1. Genomic architecture of artificially and sexually selected traits in a wild cervid
Spencer J Anderson, Steeve D Côté, Julien H Richard, Aaron BA Shafer
Characterization of the complex genomic architecture underlying quantitative traits can provide valuable insights into the study, conservation, and management of natural populations. This is particularly true for fitness-related traits such as body size and male ornamentation in mammals because as indicators of quality and health, these traits are often subject to sexual and artificial selective pressures. Here we performed high-depth whole genome re-sequencing on pools of individuals representing the phenotypic extremes in our study system for antler and body size in white-tailed deer (Odocoileus virginianus). Samples were selected from a database containing phenotypic data for 4,466 male white-tailed deer from Anticosti Island, Quebec, with four pools representing the extreme phenotypes for antler and body size in the population. Our results revealed a largely panmictic population ( F ST ~ 0.01), but also detected diverged regions ( F ST > 0.11) between pools for both traits. These regions revealed genomic islands with...
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biorxivpreprint: Genomic architecture of artificially and sexually selected traits in a wild cervid https://t.co/kbqoERkrIe #bioRxiv
biorxiv_genomic: Genomic architecture of artificially and sexually selected traits in a wild cervid https://t.co/fY9Bof91Q2 #biorxiv_genomic
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Authors: 4
Total Words: 0
Unqiue Words: 0

2.041 Mikeys
#2. The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptions to host-switching
Tobias Mourier, Denise Anete Madureira de Alvarenga, Abhinav Kaushik, Anielle de Pina-Costa, Francisco J Guzman-Vega, Olga Douvropoulou, Qingtian Guan, Sarah Forrester, Filipe Vieira Santos de Abreu, Cesare Bianco Junior, Julio Cesar de Souza Junior, Zelinda Maria Braga Hirano, Alcides Pissinatti, Silvia Bahadian Moreira, Maria de Fatima Ferreira-da-Cruz, Ricardo Laurenco de Oliveira, Stefan T Arold, Daniel C Jeffares, Patricia Brasil, Cristiana Ferreira Alves de Brito, Richard Culleton, Claudio Tadeu Daniel-Ribeiro, Arnab Pain
Plasmodium simium, a malaria parasite of non-human primates in the Atlantic forest region of Brazil was recently shown to cause zoonotic infection in humans in the region. Phylogenetic analyses based on the whole genome sequences of six P. simium isolates infecting humans and two isolates from brown howler monkeys revealed that P. simium is monophyletic within the broader diversity of South American Plasmodium vivax, consistent with the hypothesis that P. simium first infected non-human primates as a result of a host-switch from humans carrying P. vivax. We provide molecular evidence that the current zoonotic infections of people have likely resulted from multiple independent host switches, each seeded from a different monkey infection. Very low levels of genetic diversity within P. simium genomes and the absence of P. simium-P. vivax hybrids suggest that the P. simium population emerged recently and has subsequently experienced a period of independent evolution in Platyrrhini monkeys. We further find that Plasmodium Interspersed...
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biorxivpreprint: The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptions to host-switching https://t.co/dJjiZlOEPH #bioRxiv
biorxiv_genomic: The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptions to host-switching https://t.co/cLZAqvozB0 #biorxiv_genomic
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Authors: 23
Total Words: 14653
Unqiue Words: 4815

2.019 Mikeys
#3. Whole Genome Sequencing and Assembly of the Asian Honey Bee Apis dorsata
Sara Oppenheim, Xiaolong Cao, Olav Rueppel, Panuwan Chantawannakul, Sasiprapa Krongdang, Patcharin Phokasem, Rob DeSalle, Sara Goodwin, Jinchuan Xing, Jeffrey A Rosenfeld
The Asian honey bee (Apis dorsata) is distinct from its more widely distributed cousin A. mellifera by a few key characteristics. Most prominently, A. dorsata, nest in the open by forming a colony clustered around the honeycomb, while A. mellifera nest in concealed cavities. Additionally, the worker and reproductive castes are all of the same size in A. dorsata. In order to investigate these differences, we performed whole genome sequencing of A. dorsata using a hybrid Oxford Nanopore and Illumina approach. The 223MB genome has an N50 of 35kb with the largest scaffold of 302kb. We have found that there are many genes in the dorsata genome that are distinct from other hymenoptera and also large amounts of transposable elements, and we suggest some candidate genes for A. dorsata's exceptional level of defensive aggression.
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biorxivpreprint: Whole Genome Sequencing and Assembly of the Asian Honey Bee Apis dorsata https://t.co/IRAawKEQna #bioRxiv
biorxiv_genomic: Whole Genome Sequencing and Assembly of the Asian Honey Bee Apis dorsata https://t.co/SEhOl5hWDu #biorxiv_genomic
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Authors: 10
Total Words: 0
Unqiue Words: 0

2.008 Mikeys
#4. Deep profiling reveals substantial heterogeneity of integration outcomes in CRISPR knock-in experiments
Hera Canaj, Jeffrey A Hussmann, Han Li, Kyle A Beckman, Leeanne Goodrich, Nathan H Cho, Yucheng J Li, Daniel A Santos, Aaron McGeever, Edna M Stewart, Veronica Pessino, Mohammad A Mandegar, Cindy Huang, Li Gan, Barbara Panning, Bo Huang, Jonathan S Weissman, Manuel D Leonetti
CRISPR/Cas technologies have transformed our ability to add functionality to the genome by knock-in of payload via homology-directed repair (HDR). However, a systematic and quantitative profiling of the knock-in integration landscape is still lacking. Here, we present a framework based on long-read sequencing and an integrated computational pipeline (knock-knock) to analyze knock-in repair outcomes across a wide range of experimental parameters. Our data uncover complex repair profiles, with perfect HDR often accounting for a minority of payload integration events, and reveal markedly distinct mis-integration patterns between cell-types or forms of HDR templates used. Our analysis demonstrates that the two sides of a given double-strand break can be repaired by separate pathways and identifies a major role for sequence micro-homology in driving donor mis-integration. Altogether, our comprehensive framework paves the way for investigating repair mechanisms, monitoring accuracy, and optimizing the precision of genome engineering.
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UrnovFyodor: Caveat editor!!! If your life depends on a pristine insert (mis-edited cow, anyone?) - make a clone and either Southern or pacbio it. Btw the albumin strategy is fine because insert goes into intron. Beautiful job @LeonettiManuel @jeff_hussmann @czbiohub https://t.co/H1AlUmsVZs
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Authors: 18
Total Words: 0
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2.0 Mikeys
#5. Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen
Hao Fei Wang, Tushar Warrier, Chadi El Farran, Zihao Zheng, Qiaorui Xing, Melissa Jane Fullwood, Li-Feng Zhang, Hu Li, Jian Xu, Tit-Meng Lim, Yuin-Han Loh
Cis Regulatory Elements (CREs) regulate the expression of the genes in their genomic neighborhoods and influence cellular processes such as cell-fate maintenance and differentiation. To date, there remain major gaps in the functional characterization of CREs and the identification of its target genes in the cellular native environment. In this study, we performed a Features Oriented CRISPR Utilized Systematic (FOCUS) screen of OCT4-bound CREs using CRISPR/Cas9 to identify functional enhancers important for pluripotency maintenance in mouse ES cells. From the initial 235 candidates tested, 16 CREs were identified to be essential stem cell enhancers. Using RNA-seq and genomic 4C-seq, we further uncovered a complex network of candidate CREs and their downstream target genes, which supports the growth and self-renewal of mESCs. Notably, an essential enhancer, CRE111, and its target, Lrrc31, form the important switch to modulate the LIF-JAK1-STAT3 signaling pathway.
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biorxivpreprint: Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen https://t.co/fwgxqGR7ht #bioRxiv
biorxiv_genomic: Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen https://t.co/PeB19E0d61 #biorxiv_genomic
NewcotianaP: Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen https://t.co/DBrf9qjQ0h
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Authors: 11
Total Words: 0
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1.997 Mikeys
#6. Aire-dependent genes undergo Clp1-mediated 3'UTR shortening associated with higher transcript stability in the thymus
Clotilde Guyon, Nada Jmari, Francine Padonou, Li Yen-Chin, Olga Ucar, Noriyuki Fujikado, Fanny Coulpier, Christophe Blanchet, David E Root, Matthieu Giraud
The ability of the immune system to avoid autoimmune disease relies on tolerization of thymocytes to self-antigens whose expression and presentation by thymic medullary epithelial cells (mTECs) is controlled predominantly by Aire at the transcriptional level and possibly regulated at other unrecognized levels. Aire-sensitive gene expression is influenced by several molecular factors, some of which belong to the 3'end processing complex, suggesting they might impact transcript stability and levels through an effect on 3'UTR shortening. We discovered that Aire-sensitive genes display a pronounced preference for short-3'UTR transcript isoforms in mTECs, a feature preceding Aire's expression and correlated with the preferential selection of proximal polyA sites by the 3'end processing complex. Through an RNAi screen and generation of a lentigenic mouse, we found that one factor, Clp1, promotes 3'UTR shortening associated with higher transcript stability and expression of Aire-sensitive genes, revealing a post-transcriptional level of...
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Authors: 10
Total Words: 16393
Unqiue Words: 4193

1.997 Mikeys
#7. Sex identification of ancient pinnipeds using the dog genome
Maiken Hemme Bro-Joergensen, Xenia Keighley, Hans Ahlgren, Camilla Hjorth Scharff-Olsen, Aqqalu Rosing-Asvid, Rune Dietz, Steven H. Ferguson, Anne Birgitte Gotfredsen, Peter Jordan, Aikaterini Glykou, Kerstin Liden, Morten Tange Olsen
Determining the male and female representation in zooarchaeological material from hunted animal species is essential, to fully investigate the effects and means of prehistoric hunting practices, and may further provide valuable biological information on past animal life-history, behaviour and demography. However, the fragmented nature of the zooarchaeological record and a lack of clear diagnostic skeletal markers, often prevents such inference. Here, we test the usability of the dog nuclear genome (CanFam3.1) for sex identification of pinnipeds. First, a contemporary sample set (n=72) of ringed seals (Pusa hispida), with known sex was used to test the genetic sex identification method. By quantifying the proportion of X chromosome reads, as the chrX/chr1 ratio, the ratios clustered in two clearly distinguishable sex groups. Of the 72 individuals, 69 were identified to the accurate sex, which proves a high reliability of the genetic method. Second, random down sampling of a subset of the ringed seal samples to different read...
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biorxivpreprint: Sex identification of ancient pinnipeds using the dog genome https://t.co/SbbcDrmsig #bioRxiv
biorxiv_genomic: Sex identification of ancient pinnipeds using the dog genome https://t.co/rM4OB04efQ #biorxiv_genomic
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Sample Sizes : [72]
Authors: 12
Total Words: 6942
Unqiue Words: 2362

1.997 Mikeys
#8. A/T/N polygenic risk score for cognitive decline in old age
Annah M. Moore, Teresa J. Filshtein, Logan Dumitrescu, Amal Harrati, Fanny Elahi, Elizabeth C. Mormino, Yuetiva Deming, Brian W. Kunkle, Dan M. Mungas, Trey Hedden, Liana G. Apostolova, Andrew J Saykin, Danai Chasioti, Qiongshi Lu, Jessica Dennis, Julia Sealock, Lea K. Davis, David W. Fardo, Rachel Buckley, Timothy J. Hohman
We developed a novel polygenic risk score (PRS) based on the A/T/N (amyloid plaques (A), phosphorylated tau tangles (T), and neurodegeneration (N)) framework and compared a PRS based on clinical AD diagnosis to assess which was a better predictor of cognitive decline. We used summary statistics from genome wide association studies of cerebrospinal fluid amyloid β (A β 42) and phosphorylated tau (ptau181), left hippocampal volume (LHIPV), and late-onset AD dementia to calculate PRS for 1181 participants in the Alzheimers Disease Neuroimaging Initiative (ADNI). Individual PRS were averaged to generate a composite A/T/N PRS. We assessed the association of PRS with baseline and longitudinal cognitive composites of executive function and memory. The A/T/N PRS showed superior predictive performance on AD biomarkers and executive function decline compared to the clinical AD PRS. Results suggest that integration of genetic risk across AD biomarkers may improve prediction of disease progression.
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Sample Sizes : [390, 336, 640, 205, 1182, 1182, 1182, 1182, 1182]
Authors: 20
Total Words: 6939
Unqiue Words: 2291

1.997 Mikeys
#9. Transcriptional analysis of sodium valproate in a serotonergic cell line reveals gene regulation through both HDAC inhibition-dependent and independent mechanisms
Priyanka Sinha, Simone Cree, Allison L Miller, John F Pearson, Martin A Kennedy
Sodium valproate (VPA) is a histone deacetylase (HDAC) inhibitor, widely prescribed in the treatment of bipolar disorder, and yet the precise modes of therapeutic action for this drug are not fully understood. After exposure of the rat serotonergic cell line RN46A to VPA, RNA-sequencing (RNA-Seq) analysis showed widespread changes in gene expression. Analysis by multiple pipelines revealed as many as 230 genes were significantly upregulated and 72 genes were significantly downregulated. A subset of 23 differentially expressed genes was selected for validation using the nCounter platform, and of these we obtained robust validation for ADAM23, LSP1, MAOB, MMP13, PAK3, SERPINB2, SNAP91, WNT6, and ZCCHC12. We investigated the effect of lithium on this subset and found four genes, CDKN1C, LSP1, SERPINB2 and WNT6 co-regulated by lithium and VPA. We also explored the effects of other HDAC inhibitors and the VPA analogue valpromide on the subset of 23 selected genes. Expression of eight of these genes, CDKN1C, MAOB, MMP13, NGFR, SHANK3,...
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Authors: 5
Total Words: 10854
Unqiue Words: 3737

1.997 Mikeys
#10. Decoding the genomic basis of osteoarthritis
Julia Steinberg, Lorraine Southam, Natalie C Butterfield, Theodoros I. Roumeliotis, Andreas Fontalis, Matthew J Clark, Raveen L Jayasuriya, Diane Swift, Karan M Shah, Katherine F Curry, Roger A Brooks, Andrew W McCaskie, Christopher J Lelliott, Jyoti S Choudhary, JH Duncan Bassett, Graham R Williams, Jeremy Mark Wilkinson, Eleftheria Zeggini
Osteoarthritis is a serious joint disease that causes pain and functional disability for a quarter of a billion people worldwide, with no disease-stratifying tools nor modifying therapy. Here, we use primary chondrocytes, synoviocytes and peripheral blood from patients with osteoarthritis to construct a molecular quantitative trait locus map of gene expression and protein abundance in disease. By integrating data across omics levels, we identify likely effector genes for osteoarthritis-associated genetic signals. We detect stark molecular differences between macroscopically intact (low-grade) and highly degenerated (high-grade) cartilage, reflecting activation of the extracellular matrix-receptor interaction pathway. Using unsupervised consensus clustering on transcriptome-wide sequencing, we identify molecularly-defined patient subgroups that correlate with clinical characteristics. Between-cluster differences are driven by inflammation, presenting the opportunity to stratify patients on the basis of their molecular profile for...
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Authors: 18
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