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Currently indexing 161,164 papers from 673,080 authors.

Most tweeted biology preprints, last 24 hours

Results 1 through 20 out of 112


1: The impact of SARS-CoV-2 vaccination on Alpha and Delta variant transmission

David W Eyre, Donald Taylor et al.

30 tweets (posted 29 Sep 2021) infectious diseases

Background Pre-Delta, vaccination reduced SARS-CoV-2 transmission from individuals infected despite vaccination, potentially via reducing viral loads. While vaccination still lowers the risk of infection, similar viral loads in vaccinated and unvaccinated individuals infected with Delta question how much vaccination prevents transmission. Methods We performed a retrospective observational cohort study of adult contacts of SARS-CoV-2-infected adult index cases using English contact testing data. We used multivariable Poisson regression to investigate associations between transmission and index case and contact vaccination, and how these vary with Alpha and Delta variants (classified using S-gene detection/calendar trends) and time since second vaccination. Results 54,667/146,243(37.4%) PCR-tested contacts of 108,498 index cases were PCR-positive. Two doses of BNT162b2 or ChAdOx1 vaccines in Alpha index cases were independently associated with reduced PCR-positivity in contacts (aRR, adjusted rate ratio vs. unvaccinated=0.32[95%CI 0.21-0.48] and 0.48[0.30-0.78] respectively). The Delta variant attenuated vaccine-associated reductions in transmission: two BNT162b2 doses reduced Delta transmission (aRR=0.50[0.39-0.65]), more than ChAdOx1 (aRR=0.76[0.70-0.82]). Variation in Ct values (indicative of viral load) explained 7-23% of vaccine-associated transmission reductions. Transmission reductions declined over time post-second vaccination, for Delta reaching similar levels to unvaccinated individuals by 12 weeks for ChAdOx1 and attenuating substantially for BNT162b2. Protection in contacts also declined in the 3 months post-second vaccination. Conclusions Vaccination reduces transmission of Delta, but by less than the Alpha variant. The impact of vaccination decreased over time. Factors other than PCR Ct values at diagnosis are important in understanding vaccine-associated transmission reductions. Booster vaccinations may help control transmission together with preventing infections.


2: Alveolar type II cells harbouring SARS-CoV-2 show senescence with a proinflammatory phenotype

Konstantinos Evangelou, Dimitris Veroutis et al.

27 tweets (posted 02 Jan 2021) cell biology

SARS-CoV-2 infection of the respiratory system can evolve to a multi-system disease. Excessive levels of proinflammatory cytokines, known as a cytokine storm are associated with high mortality rates especially in the elderly and in patients with age-related morbidities. Senescent cells, characterized by secretion of such cytokines (Senescence Associated Secretory Phenotype - SASP), are known to occur in this context as well as upon a variety of stressogenic insults. Applying both: i) a novel "in house" antibody against...


3: LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants

Jyun-Hong Lin, Liang-Chi Chen et al.

24 tweets (posted 11 Sep 2021) bioinformatics

Long-read phasing has been used for reconstructing diploid genomes, improving variant calling, and resolving microbial strains in metagenomics. However, the phasing blocks of existing methods are broken by large Structural Variations (SVs), and the efficiency is unsatisfactory for population-scale phasing. This paper presents an ultra-fast algorithm, LongPhase, which can simultaneously phase single nucleotide polymorphisms (SNPs) and SVs of a human genome in ~10-20 minutes, 10x faster than the state-of-the-art WhatsHap ...


4: Comparison of read mapping and variant calling tools for the analysis of plant NGS data

Hanna Marie Schilbert, Andreas Rempel et al.

24 tweets (posted 11 Mar 2020) bioinformatics

High-throughput sequencing technologies have rapidly developed during the past years and became an essential tool in plant sciences. However, the analysis of genomic data remains challenging and relies mostly on the performance of automatic pipelines. Frequently applied pipelines involve the alignment of sequence reads against a reference sequence and the identification of sequence variants. Since most benchmarking studies of bioinformatics tools for this purpose have been conducted on human datasets, there is a lack of...


5: No Significant Difference in Viral Load Between Vaccinated and Unvaccinated, Asymptomatic and Symptomatic Groups Infected with SARS-CoV-2 Delta Variant

Charlotte B. Acharya, John Schrom et al.

20 tweets (posted 29 Sep 2021) infectious diseases

We found no significant difference in cycle threshold values between vaccinated and unvaccinated, asymptomatic and symptomatic groups infected with SARS-CoV-2 Delta. Given the substantial proportion of asymptomatic vaccine breakthrough cases with high viral levels, interventions, including masking and testing, should be considered for all in settings with elevated COVID-19 transmission.


6: GABOLA: A Reliable Gap-Filling Strategy for de novo Chromosome-Level Assembly

Wei-Hsuan Chuang, Hsueh-Chien Cheng et al.

20 tweets (posted 08 Sep 2021) genomics

We propose a novel method, GABOLA, which utilizes long-range genomic information provided by accurate linked short reads jointly with long reads to improve the integrity and resolution of whole genome assemblies especially in complex genetic regions. We validated GABOLA on human and Japanese eel genomes. On the two human samples, we filled in more bases spanning 23.3 Mbp and 46.2 Mbp than Supernova assembler, covering over 3,200 functional genes which includes 8,500 exons and 15,000 transcripts. Among them, multiple gen...


7: A Chromosome-level Sequence Assembly Reveals the Structure of the Arabidopsis thaliana Nd-1 Genome and its Gene Set

Boas Pucker, Daniela Holtgräwe et al.

20 tweets (posted 06 Sep 2018) genomics

Background In addition to the BAC-based reference sequence of the accession Columbia-0 from the year 2000, several short read assemblies of THE plant model organism Arabidopsis thaliana were published during the last years. Also, a SMRT-based assembly of Landsberg erecta has been generated that identified translocation and inversion polymorphisms between two genotypes of the species. Results Here we provide a chromosome-arm level assembly of the A. thaliana accession Niederzenz-1 (AthNd-1\_v2c) based on SMRT sequencing...


8: Comparing SARS-CoV-2 natural immunity to vaccine-induced immunity: reinfections versus breakthrough infections

Sivan Gazit, Roei Shlezinger et al.

17 tweets (posted 25 Aug 2021) infectious diseases

Background: Reports of waning vaccine-induced immunity against COVID-19 have begun to surface. With that, the comparable long-term protection conferred by previous infection with SARS-CoV-2 remains unclear. Methods: We conducted a retrospective observational study comparing three groups: (1)SARS-CoV-2-naive individuals who received a two-dose regimen of the BioNTech/Pfizer mRNA BNT162b2 vaccine, (2)previously infected individuals who have not been vaccinated, and (3)previously infected and single dose vaccinated individ...


9: ELeFHAnt: A supervised machine learning approach for label harmonization and annotation of single cell RNA-seq data

Praneet Chatuverdi, Aaron Zorn et al.

16 tweets (posted 08 Sep 2021) bioinformatics

Annotation of single cells has become an important step in the single cell analysis framework. With advances in sequencing technology thousands to millions of cells can be processed to understand the intricacies of the biological system in question. Annotation through manual curation of markers based on a priori knowledge is cumbersome given this exponential growth. There are currently ~200 computational tools available to help researchers automatically annotate single cells using supervised/unsupervised machine learnin...


10: Animal, fungi, and plant genome sequences harbour different non-canonical splice sites

Katharina Sielemann, Boas Pucker

16 tweets (posted 23 Apr 2019) genomics

Most protein encoding genes in eukaryotes contain introns which are interwoven with exons. After transcription, introns need to be removed in order to generate the final mRNA which can be translated into an amino acid sequence. Precise excision of introns by the spliceosome requires conserved dinucleotides which mark the splice sites. However, there are variations of the highly conserved combination of GT at the 5’ end and AG at the 3’ end of an intron in the genome. GC-AG and AT-AC are two major non-canonical splice si...


11: MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs

Vijini Mallawaarachchi, Yu Lin

16 tweets (posted 11 Sep 2021) bioinformatics

Metagenomics binning has allowed us to study and characterize various genetic material of different species and gain insights into microbial communities. While existing binning tools bin metagenomics de novo assemblies, they do not make use of the assembly graphs that produce such assemblies. Here we propose MetaCoAG, a tool that utilizes assembly graphs with the composition and coverage information to bin metagenomic contigs. MetaCoAG uses single-copy marker genes to estimate the number of initial bins, assigns contigs...


12: Mapping-based genome size estimation

Boas Pucker

16 tweets (posted 13 Apr 2019) genomics

While the size of chromosomes can be measured under a microscope, the size of genomes cannot be measured precisely. Biochemical methods and k-mer distribution-based approaches allow only estimations. An alternative approach to predict the genome size based on high contiguity assemblies and short read mappings is presented here and optimized on Arabidopsis thaliana and Beta vulgaris. Brachypodium distachyon, Solanum lycopersicum, Vitis vinifera, and Zea mays were also analyzed to demonstrate the broad applicability of th...


13: The R2R3-MYB gene family in banana (Musa acuminata): genome-wide identification, classification and expression patterns

Boas Pucker, Ashutosh Pandey et al.

15 tweets (posted 03 Feb 2020) plant biology

The R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, defense responses and metabolite accumulation. To date MYB family genes have not yet been comprehensively identified in the major staple fruit crop banana. In this study, we present a comprehensive, genome-wide analysis of the MYB genes from Musa acuminata DH-Pahang (A genome). A total of 285 R2R3-MYB genes as well as genes encoding three other classes of MYB pr...


14: Metabolic pathway analysis in the presence of biological constraints

Philippe Dague

14 tweets (posted 02 Jul 2020) bioinformatics

Metabolic pathway analysis is a key method to study a metabolism in its steady state and the concept of elementary fluxes (ELFs) plays a major role in the analysis of a network in terms of non-decomposable pathways. The supports of the ELFs contain in particular those of the elementary flux modes (EFMs), which are the support-minimal pathways, and ELFs coincide with EFMs when the only flux constraints are given by the irreversibility of certain reactions. Practical use of both EFMs and ELFs has been hampered by the comb...


15: Automatic identification of players in the flavonoid biosynthesis with application on the biomedicinal plant Croton tiglium

Boas Pucker, Franziska Reiher et al.

14 tweets (posted 29 Jun 2020) plant biology

The flavonoid biosynthesis is a well characterised model system for specialised metabolism and transcriptional regulation in plants. Flavonoids have numerous biological functions like UV protection and pollinator attraction, but also biotechnological potential. Here, we present Knowledge-based Identification of Pathway Enzymes (KIPEs) as an automatic approach for the identification of players in the flavonoid biosynthesis. KIPEs combines comprehensive sequence similarity analyses with the inspection of functionally rele...


16: High contiguity de novo genome sequence assembly of Trifoliate yam (Dioscorea dumetorum) using long read sequencing

Christian Siadjeu, Boas Pucker et al.

13 tweets (posted 02 Feb 2020) genomics

Trifoliate yam ( Dioscorea dumetorum ) is one example of an orphan crop, not traded internationally. Post-harvest hardening of the tubers of this species starts within 24 hours after harvesting and renders the tubers inedible. Genomic resources are required for D. dumetorum to improve breeding for non-hardening varieties as well as for other traits. We sequenced the D. dumetorum genome and generated the corresponding annotation. The two haplophases of this highly heterozygous genome were separated to a large extent. The...


17: Covid-19 genomic analysis reveals clusters of emerging sublineages within the delta variant

Evans Kiplangat Rono

12 tweets (posted 12 Oct 2021) genomics

The emerging SARS-CoV-2 variants may potentially have enhanced transmissibility and virulence of the virus, and impacts on performance of diagnostic tools and efficacy of vaccines. Genomic surveillance provides an opportunity to detect and characterize new mutations early enough for effective deployment of control strategies. Here, genomic data from Germany and United Kingdom were examined for genetic diversity by assessing gene mutations and inferring phylogeny. Delta variant sublineages were grouped into seven distinc...


18: The BNT162b2 mRNA vaccine against SARS-CoV-2 reprograms both adaptive and innate immune responses

F. Konstantin Föhse, Büsranur Geckin et al.

11 tweets (posted 06 May 2021) infectious diseases

The mRNA-based BNT162b2 vaccine from Pfizer/BioNTech was the first registered COVID-19 vaccine and has been shown to be up to 95% effective in preventing SARS-CoV-2 infections. Little is known about the broad effects of the new class of mRNA vaccines, especially whether they have combined effects on innate and adaptive immune responses. Here we confirmed that BNT162b2 vaccination of healthy individuals induced effective humoral and cellular immunity against several SARS-CoV-2 variants. Interestingly, however, the BNT162...


19: mRNA Vaccination Induces Durable Immune Memory to SARS-CoV-2 with Continued Evolution to Variants of Concern

Rishi R Goel, Mark M Painter et al.

11 tweets (posted 23 Aug 2021) immunology

SARS-CoV-2 mRNA vaccines have shown remarkable efficacy, especially in preventing severe illness and hospitalization. However, the emergence of several variants of concern and reports of declining antibody levels have raised uncertainty about the durability of immune memory following vaccination. In this study, we longitudinally profiled both antibody and cellular immune responses in SARS-CoV-2 naive and recovered individuals from pre-vaccine baseline to 6 months post-mRNA vaccination. Antibody and neutralizing titers d...


20: Domain adaptive neural networks improvecross-species prediction of transcription factor binding

Kelly Cochran, Divyanshi Srivastava et al.

9 tweets (posted 14 Feb 2021) bioinformatics

The intrinsic DNA sequence preferences and cell-type specific cooperative partners of transcription factors (TFs) are typically highly conserved. Hence, despite the rapid evolutionary turnover of individual TF binding sites, predictive sequence models of cell-type specific genomic occupancy of a TF in one species should generalize to closely matched cell types in a related species. To assess the viability of cross-species TF binding prediction, we train neural networks to discriminate ChIP-seq peak locations from genomi...